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DUAL TARGETING OF GLUTATHIONE REDUCTASE TO
MITOCHONDRIA AND CHLOROPLASTS
by Charlotta Rudhe
Department of Biochemistry and Biophysics
The Arrhenius Laboratories for Natural Science
Stockholm University
S-106 91 Stockholm
Sweden
Stockholm, 2005
Doctoral thesis
© 2005 Charlotta Rudhe
ISBN 91-7155-019-4, pp. 1-55
Intellecta Docusys, Stockholm 2005
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TABLE OF CONTENTS
Abstract...................................................................................................................................... 4 List of Publications for the thesis............................................................................................. 5 Abbreviations ............................................................................................................................ 7
THE STRUCTURE OF MITOCHONDRIA AND CHLOROPLASTS........................... 8 Cellular structure...................................................................................................................... 8 The mitochondrion.................................................................................................................... 8 The plant mitochondrial proteome.......................................................................................... 9 The chloroplast ........................................................................................................................ 10 The chloroplastic proteome.................................................................................................... 10
EVOLUTION OF THE PLANT CELL .......................................................................... 11 Origin of the plant cell ............................................................................................................ 11 Reduction of the organellar genomes .................................................................................... 12
TARGETING SIGNAL SEQUENCES........................................................................... 14 Evolution of targeting signal sequences ................................................................................ 14 Features of targeting signal sequences .................................................................................. 14
PROTEIN IMPORT INTO MITOCHONDRIA............................................................. 16 Interaction of mitochondrial proteins with cytosolic factors .............................................. 17 Translocase of the outer membrane (TOM)......................................................................... 19 Import receptors ..................................................................................................................... 19 The sorting and assembly machinery (SAM) ....................................................................... 20 The general import pore (GIP) .............................................................................................. 21 Translocase of the inner membrane (TIM) .......................................................................... 22 The TIM23 complex................................................................................................................ 23 The TIM22 complex................................................................................................................ 24 The mitochondrial processing peptidase (MPP) .................................................................. 25
PROTEIN IMPORT INTO CHLOROPLASTS ............................................................. 26 Interaction of chloroplastic proteins with cytosolic factors ................................................ 27 Translocase of the outer envelope membrane (TOC) .......................................................... 28 Translocase of the inner envelope membrane (TIC)............................................................ 30 The stromal processing peptidase (SPP) ............................................................................... 31
DUAL TARGETING........................................................................................................ 31 Specificity of import and mis-targeting of proteins ............................................................. 32
Dual targeting to mitochondria and chloroplasts................................................................. 33 The Dual import system ......................................................................................................... 35 The glutathione reductase targeting signal........................................................................... 37 Domain structure of glutathione reductase targeting signal ............................................... 38 Import of glutathione reductase ............................................................................................ 40 Processing of glutathione reductase ...................................................................................... 43
CONCLUDING REMARKS........................................................................................... 46
ACKNOWLEDGEMENTS.............................................................................................. 48
REFERENCES ................................................................................................................ 49
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Abstract
As a consequence of the presence of both mitochondria and chloroplasts in plant cells
there is a higher sorting requirement in a plant cell than in a non-plant cell. Reflecting
this, protein import to mitochondria and chloroplasts has been shown to be highly
specific. However, there is a group of proteins which are encoded by a single gene in the
nucleus, translated in the cytosol and targeted to both mitochondria and chloroplasts.
These proteins are referred to as dual targeted proteins. The first protein shown to be dual
targeted was pea glutathione reductase (GR). The focus of this thesis is the targeting
properties of the dual targeted protein glutathione reductase.
In order to overcome the limitations with traditional in vitro import systems we have
developed an import system for simultaneous import of precursor proteins into
mitochondria and chloroplasts (dual import system). The chloroplastic precursor of the
small subunit of ribulose bisphosphate carboxylase/oxygenase (SSU) was mis-targeted to
pea mitochondria in a single import system, but was imported only into chloroplasts in
the dual system. The dual GR reductase precursor was targeted to both mitochondria and
chloroplasts in both the single and dual import system.
We have investigated the targeting and processing properties of the GR targeting signal.
Using N-terminal truncations we have demonstrated that the GR targeting signal has a
domain organisation. Our results show that the C-terminal is sufficient for chloroplast
import, the internal part required for mitochondrial import and the N-terminal part
contain a “fine-tuning” function. Furthermore, we have constructed a range of point
mutations on the GR signal sequence, changing positive amino acid residues and
stretches of hydrophobic amino acid residues. Overall single mutations had a greater
effect on mitochondrial import than on import into chloroplasts. We have also shown that
the recognition of the GR processing site differs between MPP and SPP. Single amino
acid substitutions in the vicinity of the processing site clearly affected processing by MPP
while processing by SPP showed low sensitivity to single mutations.
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List of Publications for the thesis
I. Rudhe, C., Chew, O., Whelan, J., Glaser, E. (2002) A novel in vitro system for
simultaneous import of precursor proteins into mitochondria and chloroplasts. Plant
J. 30, 213-220.
II. Rudhe, C., Clifton, R., Whelan, J., Glaser, E. (2002) N-terminal domain of the
dual-targeted pea glutathione reductase signal peptide controls organellar targeting
efficiency. J. Mol. Biol. 324, 577-585.
III. Chew, O., Rudhe, C., Glaser, E., Whelan, J. (2003) Characterization of the
targeting signal of dual-targeted pea glutathione reductase. Plant Mol. Biol. 53,
341-356.
IV. Rudhe, C., Clifton, R., Chew, O., Zemam, K., Richter, S., Lamppa, G., Whelan, J.,
Glaser, G. (2004) Processing of the dual targeted precursor protein of glutathione
reductase in mitochondria and chloroplasts. J. Mol. Biol. 22, 639-647
Additional Publications
1. Dessi, P., Rudhe., C., Glaser, E. (2000) Studies on the topology of the protein import
channel in relation to the plant mitochondrial processing peptidase integrated into the
cytochome bc1 complex. Plant J. 24, 637-644.
2. Lister, R., Chew, O., Rudhe, C., Lee, MN., Whelan, J. (2001) Arabidopsis thaliana
ferrochelatase-I and –II are not imported into Arabidopsis mitochondria. FEBS Lett.
506, 291-295
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3. Dessi, P., Pavlov, PF., Wallberg, F., Rudhe, C., Brack, S., Whelan, J., Glaser, E.
(2003) Investigation on the in vitro import ability of mitochondrial precursor proteins
synthesized in wheat germ transcription-translation extract. Plant Mol. Biol. 52, 259-
271.
4. Taylor, NL., Rudhe, C., Hulett, JM., Lithgow, T., Glaser, E., Day, DA., Millar, AH.,
Whelan, J. (2003) Environmental stresses inhibit and stimulate different protein
import pathways in plant mitochondria. FEBS Lett. 547, 125-130.
5. Moore, CS., Cook-Johnson, RJ., Rudhe, C., Whelan, J., Day, DA., Wiskich, JT.,
Soole, KL. (2003) Identification of AtNDI1, and internal non-phosphorylating
NAD(P)H dehydrogenase in Arabidopsis mitochondria. Plant Physiol. 133, 1968-
1978.
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Abbreviations
AIP Arylhydrocarbon receptor-interacting protein AKAP protein kinase A anchor protein AOX Alternative oxidase At Arabidopsis thaliana CAT chloramphenicol acetyltransferase EM Electron microscopy GFP Green fluorescent protein GIP General import pore GR Glutathione reductase Hsp70 Heat shock protein 70 Hsp90 Heat shock protein 90 IM Inner membrane IMS Intermembrane space MPP Mitochondrial processing peptidase MSF Mitochondrial import stimulating factor mtHsp70 Mitochondrial Hsp70 NMR Nuclear magnetic resonance OM Outer membrane PAM Presequence translocase-associated motor PBF Presequence binding factor PreP Presequence protease SAM Sorting and assembly machinery SDS-PAGE Sodium dodecyl sulfate polyacrylamide gel electrophoresis SET Serial endosymbiotic theory SPP Stromal processing peptidase SSU Small subunit of riboluse bisphosphate carboxylase/oxygenase TF Targeting factor TIC Translocase of the inner envelope membrane of the chloroplast TIM Translocase of the inner membrane of the mitochondrion TM Transmembrane TOC Translocase of the outer envelope membrane of the chloroplast TOM Translocase of the outer membrane of the mitochondrion TPR Tetratricopeptide repeat
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THE STRUCTURE OF MITOCHONDRIA AND CHLOROPLASTS Cellular structure
A plant cell as we know it today shares many features with other eukaryotic organisms
such as mammals and fungi. It contains a nucleus harbouring most of the genetic material
as well as a range of membrane bound organelles. Despite many similarities, the plant
cell has some unique characteristics, maybe the most prominent being that they are able
to manufacture their own food by using sunlight to convert water and carbon dioxide to
carbohydrates.
A plant cell is approximately 10 to 100 µm in diameter and if has a spherical shape if
grown in isolation, but when surrounded by other cells they are pressed in to a
polyhedron and adjacent cells are often connected via the plasmosedsmata. Each cell is
enclosed by a rigid cell wall, which contains about 90 % carbohydrates and 10 %
proteins. Inside the cell wall there is a plasma membrane (plasmalemma) which contains
proteinaceous receptors and various transporters. Besides the nucleus, the plant cell
contains the two energy converting organelles; plastids and mitochondria. Plant cells do
not have lysosomes but their vacuole carries out virtually the same functions. Young
plants usually contain numerous small vacuoles which merge to form a lager vacuole in
the mature plant. The vacuole occupies a large part of the cell volume and plays an
important role in maintaining cell turgor.
The mitochondrion
Virtually all eukaryotic cells contain mitochondria, and an average plant cell contains
several hundred with an approximate diameter of about 1 µm. The shape can be oval,
spherical or an elongated worm like structure. Most work concerning mitochondrial
structure and morphology has been done in non-plant organisms. The mitochondrion
contains two major compartments, the inter membrane space (IMS) and the matrix,
bound by two membranes, the outer membrane (OM) and the inner membrane (IM). The
OM contains large amounts of the pore forming protein porin, which renders it permeable
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to low molecular mass proteins (less than 10 kDa) and ions. The IM on the other hand is
highly impermeable and molecules and ions have to pass through specific translocators.
The IM comprises a much larger surface than the OM and is invaginated to fold the
cristae which enclose the highly concentrated soluble matrix. Electron microscopic (EM)
tomography has revealed that the cristae are connected to the inner boundary membrane
via tubular structures termed crista junctions, which have an approximate diameter of 28
nm (Frey and Mannella 2000)
The plant mitochondrial proteome
The accumulation of nucleic acid data and recent advances in protein identification
technology have enabled us to gain information about the mitochondrial proteome. Two-
dimensional electrophoresis studies indicate that about 500-1500 protein spots can be
resolved from plant mitochondrial samples (Bardel et al. 2002; Kruft et al. 2001; Millar et
al. 2001), although the non-redundant set of proteins is probably lower. This is in
agreement with proteomic studies from mammalian (Taylor et al. 2003a) and yeast
mitochondria (Kumar et al. 2002). Taylor et al. were able to identify 615 mitochondrial
proteins from human heart tissue using mass spectrometry (Taylor et al. 2003b). They
were able to assign a function to 81% of the identified proteins with a significant
proportion involved in respiration, signaling, RNA, DNA and protein synthesis, ion
transport and lipid metabolism.
In another study Sickmann et al. were able to identify 750 mitochondrial proteins from
the yeast, Saccharomyces cerevisiae, and based on mitochondrial proteins described in
the literature they calculated this set to compromise about 90 % of the total mitochondrial
proteome (Sickmann et al. 2003).
Although plant mitochondria are thought to resemble mammalian and yeast mitochondria
they have some additional functions such as uncoupled bypasses of the electron transport
chain and the synthesis of lipids and vitamins (Bartoli et al. 2000; Gueguen et al. 2000;
Rebeille et al. 1997). There have been several attempts to identify the protein content of
mitochondria from Arabidopsis (Kruft et al. 2001; Millar et al. 2001) and pea (Bardel et
al. 2002) using two-dimensional electrophoreses coupled to mass spectrometric methods.
These reports each identified 40-90 proteins. However, the use of gel based technologies
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has several limitations, the most prominent being the difficulty to separate hydrophobic
proteins and to detect low abundant proteins. To overcome this Heazlewood et al.
undertook a systematic LC-MS/MS study of Arabidopsis mitochondria which allowed
direct analysis of trypsin digested proteins with out any prior gel separation. Combining
the LC-MS/MS data with the gel based data generated a non-redundant set of 416
proteins where 407 were nuclear encoded and the remaining 9 were encoded in the
mitochondrial genome. The identified proteins were assigned to different functional
groups where most proteins were related to energy (24%), metabolism (19%) or protein
fate (13%) (Heazlewood et al. 2004).
The chloroplast
Plant cells contain plastids which all originate from protoplastids found in meristematic
cells. During plant development the protoplastids will differentiate to form three major
groups of plastids, the green chloroplasts, the colored chromoplasts and the colorless
leucoplasts. The most important and abundant plastids are the chloroplasts, which are
mainly found in the mesophyll of green leaves. Chloroplasts are the second largest
compartment in the plant cell and take up about 16% of the total cell volume.
Chloroplasts are usually lens-shaped and are about 5-8 µm in diameter and 1 µm in
length.
Chloroplasts are surrounded by two membranes, the outer envelope membrane which is
permeable to molecules up to 10 kDa, but not to macromolecules such as bigger proteins
and nucleic acids. The inner envelope membrane is a permeability barrier and molecules
can only be transported across the membrane through specific translocaters. Chloroplasts
also contain an internal system of membranes made up of thylakoids vesicles. Thylakoids
are often stacked together and form flattered sacs called grana, which are connected by
the non-stacked stroma lamellae. The membranes enclose three distinctive compartments,
the inner membrane space, the stroma space and the thylakoid lumen.
The chloroplastic proteome
The chloroplast proteome has been estimated in silico using software tools
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like TargetP and ChloroP (Emanuelsson et al. 2000; Emanuelsson et al. 1999). More than
3600 proteins are predicted to be targeted to the chloroplast (Baginsky and Gruissem
2004). However, the prediction programs can be erroneous since they are based on transit
peptide prediction and transit peptides are not very well conserved (Bruce 2001).
Furthermore there are examples of choroplastic proteins without canonical transit
peptides (Miras et al. 2002) which therefore can not be detected by prediction programs.
A big challenge in proteomic studies is to identify both high and low abundant proteins.
This is particularly difficult in compartments like the thylakoid membranes, in which the
photosynthetic apparatus and its hydrophobic chromophores dominate. Friso et al. used a
combination of different fractionation methods in an attempt to identify as many proteins
as possible associated with the thylakoid membanes in Arabidopsis (Friso et al. 2004). In
combination with the results from a previous study (Peltier et al. 2002) they were able to
identify 198 proteins of which 76 (39%) were integral membrane proteins. Theoretical
predictions of the luminal proteome from Arabidopsis chloroplasts estimated it to contain
approximately 80 proteins. 2-D gels followed by both MALDI-TOF mass spectrometry
and amino-terminal microsequencing identified 36 proteins in the lumen of Arabidopsis
which is in agreement with studies from Spinach (Schubert et al. 2002). LC-MS/MS
studies have identified at least 100 proteins in the envelope membranes many of which
are ion and metabolite transporters, proteins involved in fatty acid, glycerolipid, vitamin
and pigment metabolism, components of the protein import machinery and proteases
(Ferro et al. 2003).
EVOLUTION OF THE PLANT CELL
Origin of the plant cell
Both chloroplasts and mitochondria were once free-living bacteria and the modern
eukaryotic cell is a descendant from an endosymbiotic event. The enodsymbiotic
hypothesis was proposed by Margulis et al. 1970 and a few years later named the serial
endosymbiotic theory (SET). The SET states that mitochondria and chloroplasts are
direct descendants of eubacterial ancestors that were engulfed by a host cell, probably
already containing a nucleus (Lang 1999).
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Phylogenetic data suggest that an ancient α-protobacterium is the ancestor of
mitochondria and was taken up by a host cell more than 2 billion years ago (Dyall et al.
2004). The α-protobacterium Rickettsia prowazekii, an obligate intracellular parasite and
the causative agent of epidemic typhus is more closely related to the mitochondrial
genome than any other microbe studied so far and is thought to be the closest living
relative of the proto-mitochondria (Andersson et al. 1998). R. prowazekii has a small
genome of 1.1 million base pairs (bp) encoding 834 proteins, which is less than a fourth
of the gene content in the well studied γ-protobacterium Escherichia coli (4288 protein-
coding genes) (Blattner et al. 1997). Gene structure is frequently conserved between
bacterial and mitochondrial genomes, for example the genes rplKAJL and rpoBC are
organized in an identical manner in R. prowazekii and in the mitochondrial genome of
Reclinomonas americana, a freshwater protozoan. Sequence data from several other α-
protobacteria further support the idea of a protobacterial ancestor of mitochondria
(Adams and Palmer 2003). Although genetic data points towards a monophylogenetic
origin of mitochondria the progenitor is probably not R. prowazekii, although it might be
another free-living bacteria prone to a parasitic life style.
Both phylogenetic and fossil data indicate that the chloroplast was taken up in an
endosymbiotic event after the mitochondrion. In a first primary endosymbiosis about 1.5
billion years ago an ancient cyanobacterium was engulfed by a mitochondria-containing
eukaryote. The plastids that have arisen from this primary endosymbiosis are surrounded
by two membranes and are found in land plants, glaucoscystophytes and in red and green
algae (Gray 1999). Plastids were further distributed throughout the plant kingdom via a
secondary endosymbiotic event where a heterotrophic eukaryote was fused with a
primary algae already containing a primary plastid. Secondary plastids are found in
lineages such as apicomplexa, dinoflagellates and ciliates and are characterized by the
presence of three or four surrounding membranes (Archibald and Keeling 2002).
Reduction of the organellar genomes
As a remnant of once being free-living prokaryotes both mitochondria and chloroplasts
still maintain their own genomes. Today organellar genomes are heavily reduced,
encoding less than 5 % of the protein content of the respective organelle. During the
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course of evolution a massive gene reduction of the organellar genome has occurred
whereby the majority of the genes have been lost or transferred to the nucleus.
As a consequence of becoming an intracellular organelle, many genes were expendable
and therefore lost from the organellar genome, while the function of other genes was
replaced by nuclear genes. Additionaly, a considerable number of genes have been
transferred to the nucleus. Functional gene transfer ceased approximately 600 million
years ago in animals and the majority of sequenced animal mitochondrial genomes
contain the same 13 protein coding genes (Boore 1999). However, in plants and
particular in angiosperms, gene transfer is a frequent and ongoing event (Adams et al.
2002).
A frequently asked question is what drives gene transfer. One popular hypothesis is
Mullers’s ratchet which states that the asexual reproduction of mitochondria and
chloroplasts can lead to a faster accumulation of deleterious mutations (Berg and Kurland
2000; Kurland 1992). Chloroplasts and mitochondria have a higher volume-based redox
activity, hence the production of oxygen free radicals is higher (Allen and Raven 1996;
Martin and Palumbi 1993). An increase in oxygen free radicals has been shown to lead to
an increase in mutation rate and therefore it would be advantageous to relocate genetic
material from the organelles to the nucleus. However, this might not be true for plant
mitochondria where the substitution rate is lower than for nuclear DNA (Wolfe et al.
1987). As photosynthetic plants have three genomes and hence the need for three sets of
gene expression apparatus, it has also been argued that having all genes in one location
would be more economical and favourable to the organism (Berg and Kurland 2000).
Why then have organelles retained some genes when the majority have been transferred?
There are two major explanations, one being the ‘hydrophobicity hypothesis’, which
states that many hydrophobic, membrane embedded proteins are difficult to transfer (von
Heijne 1986). Indeed many of the proteins still encoded in organellar genome are
hydrophobic, membrane spanning proteins, and it has been shown that reduction in
hydrophobicity was crucial for gene transfer in some cases (Daley et al. 2002). However,
many genes encoding for hydrophobic proteins have been transferred and the expressed
protiens are successfully imported back to the organelle. The second explanation, the
CORR theory (Co-location for Redox Regulation) was proposed in 1992 (Allen 1992;
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Allen 1993). This theory proposes that there is a direct correlation between coding
location and gene expression, and that organellar control over certain genes would give a
fitness advantage for the organism.
TARGETING SIGNAL SEQUENCES
Evolution of targeting signal sequences
To become activated the transferred gene has to acquire several regulatory elements for
proper expression and in most cases this includes the gain of a targeting signal sequence
to direct the precursor protein back to the correct compartment. There are several ways
by which the acquisition of a targeting signal sequence can occur. One way is by
associating with pre-existing organellar genes and examples of this are the rps genes
from various plant species. For some transferred genes the flanking regions give no clue
to where the targeting signal sequence came from although strategically located introns
indicate that some exon shuffling has occurred (Daley et al. 2002; Nugent and Palmer
1991; Wischmann and Schuster 1995). One case of exon shuffling is glyeraldehyde-3
phosphate dehydrogenase from which three N-terminal exons were moved to
cyctochrome c1 and those three exons evolved to become the mitochondrial targeting
signal sequence of cytochrome c1 (Long et al. 1996). Given the diversity in targeting
signal sequences, it is also possible that some have formed de novo. It has also been
suggested that some proteobacterial and cyanobacterial proteins carry rudimentary
features of mitochondrial and chloroplastic targeting signals respectively, such as basic
and amphipathic extensions at their amino terminal end and that those sequences might
have functioned as targeting signal sequences for the first transferred genes (Lucattini et
al. 2004).
Features of targeting signal sequences
The great majority targeting signal sequences from plant mitochondrial are between 20-
60 amino acids long (Zhang and Glaser 2002) which is longer than targeting signals from
animals and fungi. However, they can vary substantially in length, from 13 amino acids
to 136 amino acids. Chloroplastic targeting signal sequences are considerably longer than
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mitochondrial ones and can vary between 13 to 146 amino acids with an average of 58
residues (Zhang and Glaser 2002).
The amino acid composition of plant mitochondrial and chloroplastic targeting signal
sequences is remarkably similar in that it is rich in hydrophobic, hydroxylated and
positively charged amino acid residues, and low in acidic residues. Serine residues are
clearly over represented (16.2 % for mitochondrial and 19.5 % for chloroplastic) which is
in contrast to the serine content of mitochondrial presequences in yeast (7 %), mammals
(3 %) and Neurospora crassa (10 %) (Glaser and Dessi 1999; Peeters and Small 2001).
Both NMR experiments and in silico analysis have shown that mitochondrial
presequences have a propensity to form amphiphilic α-helices in the N-terminal portion
of the presequence (Chupin et al. 1995; Karslake et al. 1990; von Heijne 1986), and
substitution of amino acids in the predicted amphiphilic α-helix has shown that this
structure is important for targeting to mitochondria (Roise et al. 1988). Structural data are
available mainly for presequences from non-plant species of which most are less than 26
amino acid residues long. Mitochondrial presequences have been shown to adopt a
helical conformation in the presence of membrane model systems such as micelles or
organic solvents while being unstructured in aqueous environments. Recently, the first
NMR structure of a mitochondrial presequence from higher plants, the Nicotiana
plumbaginifolia F1β, was reported (Moberg et al. 2004). In bicelles, the F1β presequence
adopted three α-helices, an N-terminal amphiphatic helix, a small helix in the middle
region and a C-terminal helix, separated by unstructured internal domains (Moberg et al.
2004).
Although different mitochondrial presequences do not share any sequence similarity there
are some amino acids that are more abundant around the cleavage site and hence might
be needed for processing. Mitochondrial presequences can be divided into three groups
based on there cleavage site. Two major groups representing 38% and 42% of
presequences contain an arginine either at position –2 or –3 relative to the cleavage site,
and have a loosely conserved motif around the cleavage site, Arg-X ↓ Ser-Thr/Ser-Thr
and Arg-X-Phe/Thr ↓ Ala/Ser-Thr/Ser/Ala, respectively. A third group includes
presequences lacking a conserved arginine in the vicinity of the cleavage site (Zhang et
al. 2001).
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Initial studies indicated that chloroplastic targeting peptides contained three major
homolgous blocks of amino acids (Karlin-Neumann and Tobin 1986; Schmidt and
Mishkind 1986; von Heijne et al. 1989), but this was later shown not to be valid for
targeting peptides as a group. However, in general they contain three distinct regions, an
uncharged N-terminal domain, a central domain lacking acidic residues and a C-terminal
domain with the potential to form an amphiphilic β-strand (Claros and Vincens 1996; von
Heijne et al. 1989). The secondary structure of targeting peptides is predicted to be
mainly random coil (Pilon et al. 1992; Theg and Geske 1992), although later data suggest
that chloroplastic targeting peptides in a hydrophobic solution or inserted into micelles
have the ability to form an α-helical structure (Bruce 2000). Most data concerning the
structure of chloroplastic targeting peptides come from proteins in Chlamydomonas
reinhardtii, a lower photosynthetic eukaryote, which has much shorter targeting peptides
than higher plants. The only NMR structure available of a higher plant targeting peptide
is Silenes ferredoxin, which is mainly unstructured with the ability to form two helical
domains when introduced into micelles (Wienk et al. 1999).
It has been suggested that chloroplastic targeting peptides contain a loosely conserved
motif around the processing site, Val/Ile-X-Ala/Cys ↓ Ala, and that most signal
sequences contain a basic residue within the 7 most C-terminal amino acids of the
targeting peptide (Gavel and von Heijne 1990). Extensive logos of 277 chloroplast
targeting peptides with an experimentally mapped cleavage site confirmed the high
abundance of Val in position –3 and Ala in position –1 (Zhang and Glaser 2002).
PROTEIN IMPORT INTO MITOCHONDRIA
The vast majority of mitochondrial proteins are encoded in the nucleus and synthesized
in the cytosol and hence have to be imported into the organelle. This is facilitated by a
cooperation between the newly synthesized precursor protein, cytosolic chaperones and
proteinaceous components located in the outer and inner mitochondrial membrane.
The protein import machinery of mitochondria has been studied extensively for decades
and the majority of the work has been done in S. cerevisiae and N. crassa using
biochemical and genetic approaches (for review see Truscott et al. 2003a). The plant
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mitochondrial import machinery has been characterized in S. tuberosum and A. thaliana
(Jansch et al. 1998; Lister et al. 2002; Murcha et al. 2003; Werhahn et al. 2001).
Although sharing several features, the plant mitochondrial import machinery differs in
some respects from the import machinery in yeast.
Figure 1. The plant mitochondrial import machinery. Model of the import of precursor proteins into mitochondria and components of the translocation apparatus. Interaction of mitochondrial proteins with cytosolic factors
Generally mitochondrial proteins are more hydrophobic than cytoplasmic proteins and
nascent polypeptides have to be protected against aggregation and misfolding on their
route to the mitochondrial surface (Claros et al. 1995). There are two mechanisms
working to minimize this; interaction of polypeptides and cytosolic chaperones or
coupling of protein translation and translocation (Beddoe and Lithgow 2002).
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It has traditionally been assumed that the majority of mitochondrial proteins are
translated on ribosomes distant from the mitochondrial surface and then imported in a
post-translational manner (Honlinger et al. 1995; Reid and Schatz 1982; Wienhues et al.
1991). This is mainly based on the observation that in vitro synthesized precursor
proteins can be imported into mitochondria. To prevent misfolding or aggregation and to
keep the newly synthesized precursor protein in an import-competent conformation, they
interact with a range of cytosolic chaperones. Using two-hybrid screening Yano et al.
were able to identify an arylhydrocarbon receptor-interacting protein (AIP) interacting
with Tom20. Using an in vitro import assay they were also able to show that AIP binds
specifically to mitochondrial preproteins. Furthermore, in cultured cells the
overexpression of AIP stimulated import of preornithine transcarbamylse and depletion
of AIP with RNA interference impaired import. They concluded that AIP forms a ternary
complex together with Tom20 and the preprotein, and functions as a cytosolic chaperone
to prevent mitochondrial precursor proteins from aggregation (Yano et al. 2003).
There is a range of other cytosolic chaperones described in the literature such as the
presequence binding factor (PBF), the targeting factor (TF), the mitochondrial import
stimulating factor (MSF). Since first being reported more than a decade ago not much
attention has been paid to these proteins.
Already in the 1970’s it was demonstrated that translationally active ribosomes
containing mRNA for mitochondrial proteins were accumulating on the surface of yeast
mitochondria (Kellems et al. 1974). Several more recent reports support the idea that a
co-translational process is involved in the import of some mitochondrial proteins (for
review see (Lithgow 2000). One example is fumarase, which in yeast is found both in the
cytosol and in mitochondria, and could only be co-translationally translocated into the
mitochondrial matrix using in vitro assays (Knox et al. 1998).
Marc et al. preformed a genome-wide analysis to characterize the mRNA encoding
mitochondrial proteins and showed that almost half of the studied mRNA’s were
translated in the vicinity of the mitochondrial surface. Interestingly, it seems like proteins
of prokayotic origin are mainly translated in a co-translational manner while proteins of
eukaryotic origin are post-translationally imported (Marc et al. 2002).
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Translocase of the outer membrane (TOM)
Initial recognition and translocation of precursor proteins earmarked for mitochondria are
accomplished by the TOM complex. The TOM complex has a dual function in protein
import. Firstly, via the action of import receptors TOM recognizes mitochondrial
precursor proteins that have been translated in the cytosol (Brix et al. 1999). Secondly, it
forms the import channel through which the precursor proteins are translocated across the
outer membrane. Isolation of the TOM complex from yeast, mammals and plants
indicates that the overall structure is rather well conserved between different organisms.
However, it appears that the plant complex differs from its counterparts in yeast and
mammals with respect to some of the receptor components.
Import receptors
In yeast the main receptors for protein recognition are Tom70, Tom20 and Tom22 (Abe
et al. 2000; Brix et al. 1999; Kunkele et al. 1998), and are named according to their
apparent molecular mass as determined by SDS-PAGE.
Tom70 is attached to the outer mitochondrial membrane via an N-terminal hydrophobic
membrane anchor and has a large hydrophilic domain exposed to the cytosol (Hines et al.
1990). It is the major receptor for precursor proteins that contain internal targeting
signals, such as members of the metabolite carrier family. Tom70 does not only serve as
an import receptor but can also function as docking point for cytosolic chaperones
(Young et al. 2003). Despite several biochemical characterizations Tom70 has not been
found as a component of the mitochondrial outer membrane in plants (Werhahn and
Braun 2002). Furthermore, no homologue with significant sequence similarity could be
identified in the Arabidopsis genome (Lister et al. 2003). Although some of the carrier
proteins in plants contain an N-terminal targeting signal, 50-70 % of the carrier family in
the Arabidopsis genome are predicted to contain internal signals (Millar and Heazlewood
2003). The absence of Tom70 in plants is therefore intriguing since a carrier import
pathway has been demonstrated (Lister et al. 2002). Recently, Chew et al. identified an
N-terminally anchored protein on the plant mitochondrial outer membrane, mtOM64,
showing sequence similarity to the choroplastic receptor protein Toc64. It is possible that
19
mtOM64 could substitute for the missing Tom70 in plant mitochondria (Chew et al.
2004).
Tom20 is the main receptor used by proteins containing an N-terminal cleavable
presequence and thus utilizing the general import pathway. The structure of the cytosolic
domain of rat Tom20 in complex with a peptide derived from the rat mitochondrial
aldehyde dehydrogenase transit peptide has been solved and shows that the transit peptide
binds in an apolar groove in Tom20 (Abe et al. 2000). Although sharing some sequence
similarity, the plant Tom20 differs from Tom20 in mammals and fungi in its topology.
While yeast Tom20 is anchored via its N-terminal region the plant protein seems to be
attached via the C-terminal domain. A common feature that seems to emerge for plant
genes is that they exist in gene families and there are at least four isoforms of Tom20 in
Arabidopsis (Lister et al. 2003; Werhahn et al. 2001). The third receptor of the outer
membrane is Tom22, and as well as Tom20 it is involved in the recognition of precursor
proteins containing N-terminal targeting peptides. Tom22 probably interacts with the
targeting peptide via ionic forces where the positively charged surface of the targeting
peptide binds to the negatively charged Tom22 (Brix et al. 1997). Tom22 is a
multifunctional protein, which is required for the high level organization of the TOM
complex and is stably associated with import channel protein Tom40. It binds preproteins
through both its cytosolic domain and its intermembrane space domain (van Wilpe et al.
1999). Although Tom22 is highly conserved between fungi and metazoan the plant
protein differs substantially in size. The plant Tom22 homologue has a transmembrane
segment and a trans domain equivalent to Tom22 but lacks the cytosolic acidic cis
domain and is about 9 kDa in size. It has been suggested that the difference is due to the
unique environment in plants where both mitochondria and chloroplasts are present and it
is possible that this protein is involved in the targeting specificity (Macasev et al. 2000;
Macasev et al. 2004).
The sorting and assembly machinery (SAM)
Three proteins of the SAM complex in yeast mitochondria are known, Sam50 and Sam35
which are essential proteins, and Sam37. The SAM-complex plays an important role in
20
the assembly of outer membrane β-barrel proteins such as Tom40 and porin. Sam50
contains a β-barrel domain, which is conserved from bacteria to man (Kozjak et al.
2003). The bacterial homologue Omp85 is involved in transport of either proteins or
lipids to the outer membrane of gram-negative bacteria (Genevrois et al. 2003; Voulhoux
et al. 2003), and it is possible that mitochondria have retained this conserved domain for
import and assembly of β-barrel proteins. Sam35 is a peripheral membrane protein that is
exposed on the mitochondrial surface (Milenkovic et al. 2004). When the SAM-complex
was purified a fourth subunit Mdm10, a β-barrel protein, was found (Meisinger et al.
2004). Mdm10 has been previously identified by its role in maintaining mitochondrial
distribution and morphology (Sogo and Yaffe 1994). Whereas the three subunits of the
SAM core complex, Sam35, Sam37 and Sam50, are generally required for the biogenesis
of β-barrel proteins of the outer membrane, Mdm10 plays a specific role in the assembly
of the TOM-complex (Pfanner et al. 2004).
The general import pore (GIP)
Subsequent to interaction with receptors the precursor proteins are transferred to the
general import pore (GIP), which consists of the channel forming protein Tom40 and
three small proteins, Tom5, Tom6 and Tom7 (Hill et al. 1998; Kunkele et al. 1998).
Tom5 functions as a link between the receptor proteins and the general import pore.
Directly after interaction with Tom22 the precursor proteins are transferred to Tom5,
which mediates their insertion into Tom40. Despite its small size Tom5 is an integral
membrane protein with its negatively charged N-terminal portion exposed to the cytosol
(Dietmeier et al. 1997). Tom40 is a pore-forming integral membrane protein which
consists mainly of β-sheet structures and forms a cation-selective high conductance
channel (Ahting et al. 2001). All mitochondrial proteins, which cross the outer membrane
are imported via the Tom40 pore (Ahting et al. 2001). Each Tom40 molecule contains
two to three channels where each channel has an approximate diameter of 22 Å, which is
sufficient for the passage of a single α-helical segment or a loop (Kunkele et al. 1998).
Tom40 is the only Tom protein that is essential for cell viability under all growth
conditions (Baker et al. 1990).
21
The small subunits Tom6 and Tom7 do not interact with precursor proteins during
protein import, rather they modulate the stability of the Tom components (Alconada et al.
1995; Honlinger et al. 1996). Tom6 has been proposed to support the cooperation
between the receptors, in particular Tom22 and the general import pore (Alconada et al.
1995; Dekker et al. 1998; van Wilpe et al. 1999). Lack of Tom7 stabilizes the GIP
complex and hence it was suggested that Tom7 plays a role opposite to that of Tom6 by
exerting a destabilizing affect on the association of Tom components (Honlinger et al.
1996).
Translocation across the outer mitochondrial membrane is unidirectional and the
movement across the membrane is thought to be promoted by electrostatic interactions,
the so-called “acid chain hypothesis” (Komiya et al. 1998). A presequence containing
protein successively interacts with at least five different binding sites on its way across
the membrane – Tom20, the cytosolic domain of Tom22, Tom5, Tom40 and the
intermembrane space domain of Tom22. Several of these receptor proteins contain
negatively charged patches, and it has been suggested that the positively charged
presequence is recognised by increasing affinity along the import pathway (Dietmeier et
al. 1997; Komiya et al. 1998). However, Muto et al. reported that the presequence
interacts with Tom20 via hydrophobic patches showing that forces other than ionic are
crucial for interactions of the presequence with Tom proteins (Muto et al. 2001). This led
to the re-naming of the “acid-chain hypothesis” to the “binding-chain hypothesis”.
Translocase of the inner membrane (TIM)
After guidance across the outer membrane by the chain of TOM proteins, preproteins
interact with one of two TIM complexes in the inner membrane – the TIM23 complex
and the TIM22 complex. The TIM23 complex mediates the translocation of proteins into
the matrix, whereas the TIM22 complex is required for the insertion of some polytopic
proteins into the inner membrane (Jensen and Dunn 2002).
22
The TIM23 complex
The majority of presequence-containing proteins destined for the matrix use the
TIM17:23 channel to pass the inner membrane. After release from the TOM complex the
protein first interacts with the membrane spanning protein Tim50, which exposes a large
domain to the IMS. After interaction with Tim50 the precursor protein is transferred to
Tim23 and Tim17, two essential integral membrane proteins that form a core complex of
90 kDa (Dekker et al. 1997) Jensen and Dunn 2002). Electrophysiological studies using
mitochondrial IM fractions have shown that Tim23 and Tim17 form the pore through
which proteins are translocated into the matrix (Lohret et al. 1997). In addition to the
membrane domain Tim23 has an extension protruding across the IMS to the OM which is
thought to link the outer and inner mitochondrial membrane (Donzeau et al. 2000). The
role of Tim17 in yeast is not clear but based on its sequence similarity to Tim23 it is
likely to function in channel formation as well (Jensen and Dunn 2002). The TIM17:23
translocase seems to be highly conservered among all eukaryotes (Rassow et al. 1999). In
A. thaliana there are three genes present for each of TIM23 and TIM17. Although being
homologous to their yeast counterparts AtTim23 and AtTim17 differ in their topology. In
plants it seems like Tim17 rather than Tim23 contains a C-terminal extension that
protrudes into the IMS and it has been suggested that this extension links the outer and
inner mitochondrial membrane (Murcha et al. 2003).
The majority of presequence carrying proteins are imported into the matrix by the
combined action of the TIM23 translocase and the presequence translocase-associated
motor PAM. For decades it has been thought that the ATP dependent import motor
consists of three essential proteins; the peripheral inner membrane protein Tim44, the
chaperone mtHsp70, and the nucleotide exchange factor Mge1. Tim44 recruits mtHsp70
in its ATP-bound form, which has an open peptide-binding site (Schneider et al. 1994)
(Schneider et al. 1996). After binding to the emerging precursor chain, ATP is
hydrolysed, the peptide binding site closes and mtHsp70 is released from Tim44. As the
precursor chain moves into the matrix mtHsp70 is released and this requires the
nucleotide exchange factor Mge1 (Schneider et al. 1996). Mge1 removes the bound
nucleotide and allows regeneration of the ATP-bound form and hence opening of the
23
peptide-binding site (Bolliger et al. 1994; Ikeda et al. 1994; Nakai et al. 1994). Recently
two new essential co-chaperones have been identified, Pam18 (Tim14) and Pam16
(Tim16). Pam18 belongs to the J-protein family and stimulates the ATPase activity of
mtHsp70 (D'Silva et al. 2003; Mokranjac et al. 2003; Truscott et al. 2003b). Pam16 is
involved in the recruitment of Pam18 to the TIM23 complex (Frazier et al. 2004; Kozany
et al. 2004).
Two models for the action of the import motor have been proposed and most likely both
mechanisms co-operate to translocate precursor proteins across the membrane. In the
Brownian ratchet (trapping) model Hsp70 acts as an arresting component of a ratchet
which allows only forward movement of the polypeptide chain (Neupert and Brunner
2002). In this way retrograde movement of the polypeptide chain is prevented and
spontaneous forward movement can be transduced into vectorial transport by cycles of
successive mtHsp70 binding (Neupert and Brunner 2002). In the other model, the power
stroke model, mtHsp70 has a more active role in which, in concert with Tim44 and Mge1
it pulls the precursor protein inwards to the matrix. After binding to the incoming
presequence mtHsp70 undergoes a conformational change. By this repeated cycle of
ATP-dependent binding mtHsp70 will function as a motor pulling the precursor into the
matrix (Matouschek et al. 1997).
The TIM22 complex
A second translocon exists in the mitochondrial inner membrane, called the TIM22
complex. The TIM22 complex is responsible for the import of polytopic IM proteins such
as the carrier proteins and the membrane imbedded members of the TIM23 complex.
Tim22 was first found as a protein homologue to Tim23 and Tim17 in the yeast genomic
DNA sequence (Sirrenberg et al. 1996). Like Tim23 and Tim17, Tim22 has four TM
segments and is positioned with its C- and N- terminus facing the IMS. Tim22 forms a
large aqueous pore 11 to 18 Å wide (Kovermann et al. 2002). Import via the TIM22
complex requires a membrane potential but does not appear to use ATP (Jensen and
Dunn 2002). The TIM22 complex consists of two additional integral membrane proteins,
Tim54 and Tim18 (Kerscher et al. 1997). Neither Tim54 nor Tim18 appear to play an
essential role in protein import since gene disruption of TIM18 is not lethal (Kerscher et
24
al. 2000; Koehler et al. 2000). Although the exact role for Tim54 and Tim18 are
unknown, both proteins are required for formation or stability of the TIM22 complex
(Jensen and Dunn 2002).
For its function the TIM22 complex also requires the action of a family of small proteins
called the small Tims (Adam et al. 1999; Koehler et al. 1998a; Koehler et al. 1998b;
Sirrenberg et al. 1998). Tim12 is associated with the TIM22 complex while Tim9 and
Tim10 are found both as a part of the TIM22 complex and as a soluble 70 kDa complex
in the IMS. Tim8 and Tim13 form a complex similar in size to the Tim9-Tim10 complex
in the IMS (Koehler et al. 1999). The small Tim proteins are thought to shuttle imported
proteins from the TOM complex in the OM to the TIM22 complex in the IM. When the
precursor protein emerges from the Tom40 pore it binds to the Tim9-Tim10 complex
which functions in a chaperone-like manner, and binds to hydrophobic regions of the
precursor (Paschen et al. 2000). In contrast to the Tim9-Tim10 complex the Tim8-Tim13
complex is not essential and only a few substrates require this complex, one of which is
Tim23 (Paschen et al. 2000).
The mitochondrial processing peptidase (MPP)
After translocation of the precursor protein the matrix-targeting signal is no longer
necessary and is protolytically removed by the mitochondrial processing peptidase MPP
(Arretz et al. 1994; Braun et al. 1992; Eriksson 1992; Hawlitschek et al. 1988). MPP
removes presequences in one proteolytical step from precursor proteins that are fully
translocated as well as precursors in transit. MPP was originally purified from the
mitochondria of N. crassa (Hawlitschek et al. 1988), S. cerevisiae (Yang 1988) and rat
(Kleiber et al. 1990; Ou et al. 1989), and later from the potato (Braun et al. 1992),
spinach (Eriksson 1992) and wheat (Braun et al. 1995). In yeast and mammals MPP has
been shown to consist of two structurally related subunits, α-MPP and β-MPP. The α
subunit is responsible for peptide binding and the β subunit for catalysis (Luciano and
Geli 1996). The enzyme exists as a soluble hetrodimer of about 100-110 kDa (Glaser and
Dessi 1999). In contrast to the situation in yeast and mammals the plant enzyme is
intergrated as core subunits in the membrane bound cytochrome bc1 complex facing the
25
mitochondrial matrix (Braun and Schmitz 1995; Glaser and Dessi 1999). It has been
shown that the translocation channel and the MPP/ bc1 are located separately in the inner
membrane of plant mitochondria. Using chimeric constructs consisting of a
mitochondrial presequence and dihydrofolic reductase (DHFR) it has been shown that the
presequence is not processed directly upon exposure to the matrix, rather the precursor
must be translocated some distance beyond the cleavage site. This result implicates the
lack of a direct link between precursor translocation and processing (Additional
publication 1).
The removed presequences are potentially harmful to the structure and function of
mitochondria as they can penetrate and disrupt biological membranes and must therefore
be rapidly degraded. This is carried out by a matrix located metallopeptidase, the
Presequence Protease, PreP (Stahl et al. 2002).
PROTEIN IMPORT INTO CHLOROPLASTS
As for mitochondria, more than 95 % of chloroplastic proteins are encoded by genes
located in the nucleus and have to be transported to, and imported into the chloroplast.
This transport is aided by cytosolic factors and proteinaceous components located in the
outer and inner chloroplastic envelope. As chloroplasts are the most recent organelle in
the modern eukaryotic cell and several post-translational import systems were already in
operation, such as those of mitochondria, peroxisomes and the plasma membrane (Kunau
2001; Neuhaus and Rogers 1998; Pfanner and Geissler 2001), the chloroplastic import
machinery therefore, had to develop unique features to ensure organelle specificity. Over
the past decade, a variety of biochemical techniques, using pea chloroplasts as a model
system, have been used to identify and characterize the protein components of the
chloroplastic import apparatus (Perry and Keegstra 1994; Schnell et al. 1994). The
availability of Arabidopsis genomic sequence data has led to the use of more molecular-
genetic strategies and has enabled the functional study of the import apparatus in vivo
(Jarvis and Soll 2001).
26
Figure 2. The chloroplastic import machinery. Model of the import of precursor proteins into chloroplasts and components of the translocation apparatus.
Interaction of chloroplastic proteins with cytosolic factors
As for mitochondrial proteins, newly synthesized chloroplastic proteins are prone to
aggregation and non-productive interactions, and hence need to be protected in the
cytosol. Several, but not all chloroplastic transit peptides contain a motif, which can be
phosphorylated on a serine or threonine residue (May and Soll 2000). The consensus for
the phosphorylation motif, (P/G)Xn(K/R)Xn(S/T)Xn(S*/T*) (where * indicates the
phosphorylated residues), resembles the motif for binding of 14-3-3 proteins. 14-3-3
proteins belong to a ubiquitous eukaryotic protein family of regulatory proteins, which
serve as molecular chaperones mediating protein-protein interactions (Aitken et al. 1992).
27
The precursor proteins are phophorylated subsequently to synthesis by a protein kinase.
The phosphorylated precursor interacts with the 14-3-3 protein together with Hsp70 to
form a hetero-oligomeric cytosolic guidance complex. The guidance complex is then
targeted to the appropriate receptor of the outer envelope membrane. Although not being
necessary for import into chloroplasts the formation of a guidance complex will result in
a 4-fold higher import efficiency for some proteins than for free precursor proteins.
Before the precursor protein can be translocated it has to be dephosphorylated by a
phosphatase. The model of a guidance complex is supported by the notion that a 14-3-3
protein in the wheat germ translation system can co-immunoprecipitate two different
chloroplast proteins in a transit peptide dependent manner. Furthermore, interaction
between the 14-3-3 protein and the precursor could only be detected when the transit
peptide was phosphorylated on a serine residue within the predicted 14-3-3 binding motif
(May and Soll 2000). Besides forming a guidance complex with 14-3-3 proteins,
phophorylated precursor proteins bind to receptors at the outer envelope membrane with
a higher affinity than non-phosphorylated (May and Soll 2000). Therefore it has been
proposed that a cycle of phophorylation/dephosphorylation could be used as a regulatory
mechanism, which converts the protein from low import competent to a highly import
competent form. A recent study, however, found that point mutations within the 14-3-3
binding site of several proteins did not affect protein targeting efficiency or specificity
(Nakrieko et al. 2004).
Translocase of the outer envelope membrane (TOC)
As for the TOM complex of mitochondria the TOC translocon is involved in both
recognition of precursor proteins and translocation of precursor proteins across the outer
envelope membrane. Once a precursor protein arrives to the surface of the chloroplast a
highly specific recognition process is initiated in which both lipid and protein
components of the outer envelope membrane are involved (Jarvis and Soll 2001).
Following recognition, the precursor protein is translocated through the TOC complex in
an energy-dependent process (Jarvis and Soll 2001).
Four TOC components have been described to date, namely Toc159, Toc34, Toc75 and
Toc64 which are named according to their predicted molecular masses (Jarvis and Soll
28
2001). Toc159 has been regarded as the major point of contact for precursor proteins
arriving to the import apparatus and has therefore been thought to be the main chloroplast
import receptor (Hirsch et al. 1994; Kessler et al. 1994; Perry and Keegstra 1994). The
Toc159 protein has a three domain structure: an N-terminal acidic domain (A-domain), a
central GTP-binding domain (G-domain) and a C-terminal membrane anchor domain (M-
domain) (Chen et al. 2000). Toc159 belongs to a class of GTP-binding proteins and
possesses characteristic GTP-binding site motifs within its central domain. In
Arabidopsis four homologues to pea Toc159 have been identified (Hiltbrunner et al.
2001).
Toc34 belongs to same class of GTP-binding proteins as Toc159, and shares homology
with Toc159 even outside of the conserved GTP-binding site motifs (Kessler et al. 1994).
Toc34 is anchored to the outer envelope membrane by its carboxy-terminal tail, and most
of the protein is exposed to the cytosol (Seedorf et al. 1995). Recently it has been
suggested that Toc34 acts as an initial receptor (Becker et al. 2004b). Two different
Toc34 homologues exist in Arabidopsis and are referred to as atToc33 and atToc34
(Gutensohn et al. 2000; Jackson-Constan and Keegstra 2001; Jarvis et al. 1998).
Toc75 forms the pore through which precursor proteins are translocated across the outer
membrane and is the most abundant protein of the chloroplast outer envelope membrane
(Joyard et al. 1983; Keegstra et al. 1984). Toc75 is predicted to be a β-barrel protein with
16 transmembrane β-sheets (Sveshnikova et al. 2000). It forms a cation-selective high-
conductance ion channel (Hinnah et al. 1997), which is approximately 25 Å wide at the
entrance and 15-17 Å wide inside the channel. This is wide enough to accommodate a
polypeptide stretch that still retains some secondary structure (Hinnah et al. 2002). Four
different Toc75 homologues exist in Arabidopsis, and as for Toc159 and Toc34 one
isoform is dominantly expressed (Jackson-Constan and Keegstra 2001).
The role of the fourth TOC component, Toc64, is less well-defined. Toc64 contains three
tetratricopeptide motifs in the cytosolic part of the protein (Sohrt and Soll 2000), which
are involved in protein-protein interactions. Similar motifs have been found in the
mitochondrial receptor Tom70 and it has been suggested that Toc64 has a similar role to
that of Tom70 in recognition of hydrophobic precursor proteins (Soll and Schleiff 2004).
29
Recently a new Toc component was identified, Toc12. Toc12 is an outer envelope
protein exposing a soluble domain into the intermembrane space. Toc12 contains a J-
domain and stimulates the ATPase activity of DnaK (Becker et al. 2004a).
Translocase of the inner envelope membrane (TIC)
After translocation across the outer envelope membrane via the TOC complex the
precursor protein is transferred to the TIC complex of the inner envelope membrane. The
translocation across the inner envelope membrane requires ATP hydrolysis (Flugge and
Hinz 1986), which is probably needed for the action of molecular chaperones in the
stroma (Kessler and Blobel 1996; Nielsen et al. 1997). The TIC tranlocase is a multi-
subunit complex which consists of Tic110, Tic62, Tic55, Tic40, Tic22 and Tic20 (Soll
and Schleiff 2004). Relatively little is known about the role of these proteins and there
are some disagreements in the literature. It has been suggested that the discrepancies are
due to the existence of two or more TIC complexes as in the case of the TIM translocase
in mitochondria (Soll and Schleiff 2004). Tic110 is the most abundant of the TIC
components and has one or two transmembrane segments in its amino-terminal region
(Kessler and Blobel 1996; Lubeck et al. 1996). Tic110 is thought to constitute the pore
through the inner envelope membrane and can form a cation-selective channel in lipid
bilayers (Heins et al. 2002). Besides Tic110 the two most abundant subunits are Tic62
and Tic55, which both have the potential to catalyse electron transfer reactions (Caliebe
et al. 1997; Kuchler et al. 2002). Tic55 contains an iron-sulphur centre and a
mononuclear iron binding site. Tic62 has a conserved NAD(P) binding site and its
carboxy terminal, exposed to the stroma, can interact with ferredoxin NAD(P) reductase.
Tic62 and Tic55 are implicated in redox regulation of protein import through the TIC
complex (Soll and Schleiff 2004). Tic40 is an integral membrane protein which is tightly
associated with Tic110 (Stahl et al. 1999). The exact function of Tic40 is not known but
it shares some sequence similarity with the Hsp70-interacting protein (Hip) in its C-
terminal domain (Chou et al. 2003). Hip is a mammalian co-chaperone that regulates
nucleotide exchange by Hsp70 (Frydman and Hohfeld 1997; Hohfeld et al. 1995) and it is
possible that Tic40 has a similar role in regulating the chaperones involved in driving
chloroplast protein import. Tic22 is localized to the inter-envelope space and has been
30
suggested to have a role in the coordination of TOC and TIC functions or in transport of
proteins across the inter-envelope space (Kouranov et al. 1998; Soll and Schleiff 2004).
After interaction with Tic22 the precursor protein is transferred to Tic20, which is an
integral membrane protein with four putative transmembrane segments (Kouranov et al.
1998). Tic20 shares some sequence similarity with the mitochondrial import component
Tim17 (Rassow et al. 1999) and has been proposed to participate in channel formation.
The stromal processing peptidase (SPP)
Immediately upon arrival in the stroma, precursor proteins are proteolytically processed
in order to remove their transit peptide by the stromal processing peptidase (SPP). It has
been shown that SPP removes transit peptides from an array of chloroplastic precursor
proteins (Richter and Lamppa 1998). The enzyme was first purified from pea chloroplast
extract using the chloroplastic protein LHCP as an affinity ligand (Oblong and Lamppa
1992). SPP is a soluble, monomeric enzyme of about 100 kDa and dependent on metal
ions for its activity (Oblong and Lamppa 1992). The enzyme contains an inverted zinc-
binding motif, which is characteristic of members of the metallopeptidase family M16,
such as pitrilysin, insulin-degrading enzymes, PreP and the β-subunit of the
mitochondrial processing peptidase (Rawlings and Barrett 1995; VanderVere et al. 1995).
SPP initially recognizes a precursor by binding to the transit peptide and then removes it
in a single endoproteolytic step. The mature part is then released while the transit peptide
remains bound to SPP. After initial processing by SPP a second cleavage is performed
and the transit peptide is converted to a subfragment form (Richter and Lamppa 2003).
The trimmed transit peptide is further degraded by the same metallopeptidase, PreP, as
for presequences in mitochondria (Bhushan et al. 2003; Moberg et al. 2003; Stahl et al.
2002).
DUAL TARGETING
As a consequence of the presence of both mitochondria and chloroplasts in a plant cell
there is a higher sorting requirement than in non-plant cells. Reflecting this, protein
import to mitochondria and chloroplasts has been shown to be highly specific in vivo
31
(Boutry et al. 1987; Schmitz and Lonsdale 1989; Silva-Filho et al. 1997). The vast
majority of proteins that are involved in similar biological functions in more than one
organelle are encoded by distinct genes for each organelle. However, an increasing
number of studies have shown that some proteins are targeted to more than one
compartment (Peeters and Small 2001). Proteins that are encoded by a single gene in the
nucleus and targeted to both mitochondria and chloroplasts are referred to as dual
targeted proteins (Peeters and Small 2001). The first protein to be reported as dual
targeted was glutathione reductase (GR) from pea in 1995 (Creissen et al. 1995). Since
then, more than 20 dual targeted proteins have been identified and it is expected that there
will be many more.
Specificity of import and mis-targeting of proteins
Mitochondria originated much earlier than chloroplasts and thus the chloroplasts arose in
cells that already contained an efficient system for targeting to mitochondria. To maintain
specificity of import, chloroplastic import systems and import signals had to evolve
unique features to avoid unnecessary or lethal mis-targeting between organelles.
Interestingly, plant mitochondrial presequences differ from other eukaryotic
mitochondrial presequences, since they are longer and richer in serine residues (Glaser et
al. 1998). Furthermore, the outer mitochondrial proteins Tom20 and Tom22 in plants
have greatly diverged from their eukaryotic counterparts (Macasev et al. 2000). The
sequence of Arabidopsis Tom22 is different from Tom22 in non-plant species and this
could possibly have been a response to the arrival of chloroplasts, so that the two import
systems would not interfere with each other (Macasev et al. 2000).
Although being specific there are reports of mis-targeting of proteins. Hurt et al. have
shown that the targeting signal of ribulose 1,5-bisphosphate carboxylase/oxygenase from
C. reinhardtii supported import of yeast cytochrome oxidase subunit IV into yeast
mitochondria (Hurt 1986). Furthermore, the mitochondrial presequence of the yeast
cytochrome oxidase subunit Va can function both as a mitochondrial and chloroplastic
targeting peptide in transgenic tobacco plants (Huang et al. 1990). The chloroplastic PsaF
protein from C. reinhardtii was shown to be imported in vitro into both spinach and C.
reinhardtii mitochondria (Hugosson et al. 1995). The transit peptide of the chloroplast
32
inner envelope protein, triose-3-phosphoglycerate phosphate translocator (TPT) coupled
to reporter CAT was imported into plant mitochondria in vitro but not in vivo (Brink et al.
1994) (Silva-Filho et al. 1997). More recent studies have reported mis-targeting of
chloroplastic proteins into pea mitochondria in vitro such as the small subunit of Rubisco
(SSU) and ferrochelatase-I (Fc-I). Notably, the mis-targeting of SSU and Fc-I seems to
be a property of pea mitochondria as soybean and Arabidopsis mitochondria did not
display this activity (Lister et al. 2001). Furthermore, it has been demonstrated that a
range of chloroplastic proteins could be imported into pea mitochondria with the same
efficiency as into chloroplasts, including plastocyanin, the 33-kDa photosystem II
protein, Hcf136 and coproporphyrinogen III oxidase (Cleary et al. 2002). In contrast to
the situation for mitochondria no cases of mis-targeting of mitochondrial proteins to
chloroplasts have been reported. (Cleary et al. 2002).
Dual targeting to mitochondria and chloroplasts
The majority of proteins that are targeted to more than one compartment are localized in
mitochondria and chloroplasts. There are two ways in which a single gene can provide a
product that is targeted to both mitochondria and chloroplasts; either through an
ambiguous targeting signal or via a twin targeting signal (Peeters and Small 2001). The
ambiguous targeting signal arises from genes encoding single precursor proteins carrying
a targeting signal that is recognized by the import apparatus of both organelles (Small et
al. 1998). Twin-targeting signals may arise from alternative forms of transcription
initiation, translation initiation, splicing or post-translational modifications all resulting in
the production of multiple precursor proteins, each possessing different targeting
information (Danpure 1995). As a result each precursor protein has a different targeting
signal located at its N-terminus. It has been shown that when two targeting signals are put
in tandem the most N-terminal will dictate the destination of the protein (de Castro Silva
Filho et al. 1996). One protein utilizing a twin targeting signal is protoporphyrinogen
oxidase II (protox-II), an enzyme necessary for the biosynthesis of chlorophyll in the
chloroplasts and for heam in chloroplasts and mitochondria. Protox-II has two in-frame
initiation codons, hence two different proteins are made by the means of alternative
translation in which the longer form is imported into chloroplasts and the shorter into
33
mitochondria (Watanabe et al. 2001). Dual targeting of the THI1 protein, an enzyme of
the thiamine biosynthesis pathway, also uses two alternative translation sites, and as for
protox-II the longer form directs the protein to chloroplasts and the shorter to
mitochondria (Chabregas et al. 2001). Monodehydroascorbate reductase (MDAR) is dual
targeted to both mitochondria and chloroplasts by the use of multiple transcription
initiation sites. Obara et al. showed that two MDAR mRNAs are produced from a single
gene and give rise to two different proteins in which the longer is transported to
mitochondria and the shorter to chloroplasts (Obara et al. 2002).
The vast majority of proteins dual targeted to mitochondria and chloroplasts have an
ambiguous targeting signal (Peeters and Small 2001). Many of these proteins are
involved in gene expression in the organelles such as several aminoacyl-tRNA
synthetases, RNA polymerase, methionine aminopeptidase and a peptidyl deformylase
(Peeters and Small 2001). Other dual targeted proteins are involved in the protection
against oxidative stress such as pea GR (Creissen et al. 1995) and several other enzymes
from the ascorbate-glutathione cycle. Ascorbate peroxidase (APX),
monodehydroascorbate reductase (MDHAR) and glutathione reductase (GR) from A.
thaliana have been shown to be dual targeted to both organelles in vivo and in vitro
(Chew et al. 2003). Recently, a targeting peptide degrading zinc metallopeptidase (PreP)
from A. thaliana was shown to be dual targeted to both mitochondria and chloroplasts
(Bhushan et al. 2003; Moberg et al. 2003). An ambiguous targeting signal possesses
features of both mitochondrial and chloroplastic targeting signals and evidence from in
vitro work suggests that the import pathway used by dual targeted proteins is the same as
for other imported precursor proteins (Peeters and Small 2001). Peeters and Small
compiled 19 ambiguous targeting signals and compared their features with a large set of
mitochondrial and chloroplastic targeting signals. They concluded that dual targeted
peptides contain classical features of both mitochondrial and chloroplastic targeting
signals but they contain fewer alanine residues and a greater abundance of phenylalanine
and leucine, suggesting that they are more hydrophobic (Peeters and Small 2001). Some
dual targeted proteins seem to have a domain structure in which different domains
regulate the import to the organelles. The pea GR targeting signal has a triple domain
structure in which two domains are responsible for the targeting to the respective
34
organelles and the third, most N-terminal domain harbours a fine-tuning function which
controls the distribution between the organelles (Paper II). RNA polymerase RpoT2 also
has a domain structure in which the N-terminal region is responsible for chloroplastic
targeting and the C-terminal portion for mitochondrial targeting (Hedtke et al. 2000).
Furthermore, the dual targeted zinc metallopeptidase PreP has a reversed domain
structure in which the N-terminal domain is necessary for mitochondrial import and the
C-terminal domain mediates chloroplastic targeting (Bhushan et al. 2003).
The Dual import system
Targeting of proteins to mitochondria and chloroplasts can be studied using both in vitro
and in vivo approaches. In vivo approaches use an intact cellular system and reflect the in
vivo targeting capacity of a signal. However, in vivo approaches have limitations: (i)
chimeric constructs usually contain passenger proteins and therefore the role of the
mature protein is ignored; (ii) the investigated proteins are usually over-expressed at very
high levels with great variations in expression, which can affect targeting; (iii) no kinetics
or efficiency of targeting can be assessed; and (iv) dissection of the mechanism involved
in protein recognition and import is not possible. In vitro approaches can overcome these
limitations but they have other disadvantages instead; (i) a lack of an intact cellular
system: (ii) it is possible to get incorrect targeting which is not seen in vivo; and (iii)
competition between organelles is absent.
In order to overcome the limitations of the in vitro import system and to elucidate the
mechanisms involved in dual targeting we have developed a novel in vitro dual import
system for simultaneous targeting of precursor proteins into mitochondria and
chloroplasts (Paper I). We used purified organelles that were mixed, incubated with
precursor protein and re-purified after import. This allowed the determination of the
targeting specificity of import when both mitochondria and chloroplasts are present. The
in vitro dual import system also allowed the use of authentic precursors so that the role of
the mature part could be assessed.
In order to examine the fidelity of protein import we carried out in vitro import
experiments using both single and dual import systems. We investigated import into pea
leaf mitochondria and chloroplasts and soybean mitochondria with precursor proteins of
35
the soybean mitochondrial alternative oxidase (AOX), the pea chloroplast small subunit
of RUBISCO (SSU) and the pea dual targeted glutathione reductase (GR). In the single
import system SSU was imported into isolated chloroplasts while AOX was only
imported into isolated mitochondria. The dual targeted protein GR was imported into
both mitochondria and chloroplasts. Additionally, SSU was mis-targeted into isolated pea
mitochondria and cleaved to the same apparent molecular mass product as in
chloroplasts. This import was transit peptide dependent as the mature protein of SSU
alone could not be imported. In contrast, in the dual import system SSU was imported
only into chloroplasts. This shows that the dual import system can overcome the
limitation with single import systems as it abolishes mis-targeting of chloroplast
precursor observed in pea leaf mitochondria. It should be emphasised that under the same
experimental conditions the dual targeted protein GR was imported into both
mitochondria and chloroplasts.
In order to investigate the targeting capability of the dual targeting signal of GR we have
constructed chimeric constructs between the GR targeting signal and the mature proteins
of AOX, FAd and SSU and investigated import of these constructs in the single and dual
import system. In both import systems, the GR targeting signal supported import of
mature FAd into mitochondria and chloroplasts whereas the mature AOX could be
imported only into mitochondria. There was efficient targeting of the mature SSU under
the control of the GR targeting signal into chloroplasts in both of the systems, however
this construct was only imported into mitochondria using the single system whereas the
dual system did not support import of GR(p)-SSU(m). From these results we conclude
that the GR targeting signal has the ability to direct proteins to both mitochondria and
chloroplasts. However, this ability seems to be selective and dependent of the nature of
the passenger protein.
36
plantcDNA
Figure 3. Overview of the procedure of the dual import assay.
The glutathione reductase targeting signal
The precursor protein of pea GR is dual targeted to mitochondria and chloroplasts by
means of an N-terminal targeting signal of 60 amino acid residues, which has been
described as an ambiguous targeting signal (Creissen et al. 1995) Peeters and Small
2001). It has been shown that the dual targeting capability of pea GR to both
mitochondria and chloroplasts is dependant on the targeting peptide by, in vivo targeting
of a fusion protein between pGR and phospinothricin acetyl transferase (Creissen et al.
1995) and in vitro studies with chimeric constructs containing the GR signal coupled to a
reporter protein or different mitochondrial or chloroplastic proteins (Paper I) (Cleary et
al. 2002). The GR targeting signal possesses features of both mitochondrial and
chloroplastic targeting signals. It has a high serine content (17 %), an abundance of
aliphatic amino acid residues, an overall positive charge and an uncharged N-terminus. In
the GR targeting signal the most positively charged N-terminal residue, arginine, occurs
first at position 20, which is unusual for mitochondrial presequences but common for
chloroplastic transit peptides. When compared with chloroplastic transit peptides,
mitochondrial presequences are shorter and contain a higher content of positively charged
transcription & tranlationcell-free lysate
mitochondria chloroplast precursor protein Mixture
+ Thermolysin - Thermolysin
Re-purify organelles
chloroplasts mitochondriamitochondria chloroplast
37
residues in the N-terminal portion (Zhang and Glaser 2002). The GR targeting signal is
successfully identified as a mitochondrial targeting signal by MitoProt (Claros and
Vincens 1996) and as a chloroplastic targeting signal by ChloroP (Emanuelsson et al.
1999), programs that are single location predictors. However, TargetP (Emanuelsson et
al. 2000) and Predotar, designed to predict intracellular targeting ability, predict the GR
targeting peptide as a solely chloroplastic targeting signal. In line with this observation,
in silico removal of the uncharged N-terminal portion of the GR targeting signal
increased the probability for the peptide to function as a mitochondrial presequence and
accordingly decreased the probability to function as chloroplastic transit peptide.
However, removal of 30 N-terminal amino acids, halfing the targeting signal, decreased
the predicted targeting ability to the extent that none of the available prediction programs
gave a confident prediction for either destination.
Domain structure of glutathione reductase targeting signal
In silico predictions using programs, such as TargetP and Predotar suggest that the GR
targeting signal has a domain structure in which different regions of the targeting signal
are important for targeting to mitochondria or chloroplasts. In order to determine
whether the predictions reflect the situation in situ, we created deletion constructs and
performed in vitro import assays into isolated mitochondria and chloroplasts (Paper II).
When the different deletion constructs; GR∆2-16 and GR∆2-30, were incubated with
mitochondria and chloroplasts, the same 55 kDa mature form as for wild type GR was
produced. However, the import efficiency of the constructs varied depending on the
number of N-terminal amino acid residues removed. GR∆2-16 import was stimulated into
mitochondria to 160 % compared to wild type, whereas the removal of 16 N-terminal
amino acids did not significantly affect import into chloroplasts. As predicted, import of
GR∆2-30 was decreased into both mitochondria and chloroplasts. Mitochondrial import
was completely inhibited while chloroplastic import was reduced by 65 %. These results
are in line with the domain model of targeting signal organization for mitochondrial
protein import proposing that the information for targeting to mitochondria is housed in
the N-terminal domain. However, our findings show that substantial import into
chloroplasts can be achieved with the C-terminal part of the targeting signal.
38
Furthermore, the results show that the 16 amino acid portion of the targeting signal has an
inhibitory effect on mitochondrial targeting and that the region between Tyr17 and Pro30
in the GR targeting signal allowed mitochondrial import. This data indicates that the GR
targeting signal has evolved a dual targeting signal with the C-terminal part being
sufficient for chloroplast import, the internal part required for mitochondrial import and
the most N-terminal part housing a “fine tuning” function. Removal of N-terminal
residues seems to have an inhibitory effect on translocation into chloroplasts, but not for
targeting or binding, since the amount of bound but not imported precursor increased 2-3-
fold for the shorter construct in comparison to wild-type GR. In contrast, binding to
mitochondria was not affected for the GR∆2-16 mutant and decreased by approximately
35 % for the GR∆2-30 mutant. Measurements of the valinomycin sensitivity of GR
import into mitochondria revealed that import of GR wild-type was partially membrane
potential insensitive. However, the two deletion constructs, GR∆2-16 and GR∆2-30, were
imported in an almost complete membrane potential dependent manner. This might imply
that the shorter constructs were completely passed through the membranes and imported
into the matrix while some of the longer GR wild-type was accumulating in the
intermembrane space. It may also reflect different requirements for membrane potential
for the longer and shorter constructs as observed with pb2-barnase constructs (Huang et
al. 2002). Precursors with short presequences required membrane potential, whereas
those that were long enough to reach the matrix and mitochondrial Hsp70 were imported
in the absence of membrane potential.
The presence of a second methionine residue in the GR targeting signal at position 5
raised the possibility that the import of GR into mitochondria and chloroplasts was a
result of two different translation products, one starting from the first methionine and a
shorter starting from the second methionine. Four N-terminal amino acid residues were
removed in order to investigate the role of the second methionine residue in the targeting
signal. Removal of the four first amino acids did not affect import into pea mitochondria
or chloroplasts. This negated the possibility of an essential role of the second methionine
residue in the targeting capacity.
GR is important in scavenging of reactive oxygen species in both the chloroplast and the
mitochondria where ROS are produced. In pea leaves 77 % of the total activity of GR has
39
been localised to the chloroplast and 3 % to the mitochondria (Edwards 1990). There is
no detailed information regarding GR protein distribution in chloroplasts and
mitochondria but a great excess of the chloroplast GR protein is expected as there is
about ten fold excess of chloroplast protein over mitochondrial protein in leaf cells. A
mechanism regulating the distribution of GR precursor between mitochondria and
chloroplasts is required. This study suggests that the mechanism for controlling targeting,
hence import of GR, into the two organelles may be located within the targeting signal
itself. We propose that the 16 residue N-terminal region functions to dampen the rate of
import into mitochondria.
Figure 4. Domain structure of GR targeting signal. The C-terminal part is sufficient for chloroplast import, the internal part required for mitochondrial import and the N-terminal part housing a “fine-tuning” function.
Import of glutathione reductase
To characterize the signal responsible for dual targeting we further examined the
targeting signal of pea GR. We investigated if the determinants for dual targeting of GR
into mitochondria and chloroplasts and if changes of amino acid residues affect targeting
only to one, or to both organelles (Paper III). In this and earlier studies we noticed that
GR is imported into mitochondria in a partially membrane independent manner. This
suggests that at least some of the precursor protein has not crossed the inner membrane.
In order to assess the intraorganellar location of imported GR we ruptured the outer
membrane after import to allow access of added protease to intermembrane space
components. Some imported GR was still protease protected under these conditions
40
indicating that some protein had been imported across the inner membrane. We
calculated that 30-50 % of GR was imported to the intermebrane space. This dual
intraorganellar location is consistent with studies in Phaseolus which suggested that up to
50 % of the activity could be located in the intermembrane space (Iturbe-Ormaetxe et al.
2001). Using site-directed mutagenesis we changed positive residues and groups of
hydrophobic residues in the targeting signal. Arginine residues were changed to negative
residues or glycine whereas lysine residues were changed simply to abolish the positive
charge. Any group of 3 hydrophobic residues was changed to non-hydrophobic residues
to disrupt an amphiphilic structure that might be present. All changes were analysed with
TargetP and notably the targeting prediction remained largely unchanged. Since the
import kinetics into chloroplasts are different from mitochondria we checked the import
kinetics for several of the mutated proteins. It was clear that all mutations showed typical
chloroplastic kinetics with import saturated after 5-10 min. However, it was apparent that
the amount of import after 30 min was similar to that of 10 min. We used import assays
of 25 min in order to standardize with mitochondrial import. Using single in vitro import
systems it was evident that changing individual amino acid residues had a greater
inhibitory effect on mitochondrial import compared to chloroplastic import. Substitution
of arginine residues in the C-terminal (R-2) and middle region (R-28) had the greatest
inhibitory effect on mitochondrial import, in which R-2 inhibited mitochondrial import
by more than 50 % and R-28 by as much as 80 %. In contrast, changing lysine residues
(K-17, K-34) had a more similar inhibitory effect on mitochondrial and chloroplastic
import. Furthermore, mutation of the N-terminal hydrophobic region of the targeting
signal (AMA-57) almost completely abolished mitochondrial import whereas
chloroplastic import was still 60 % compared to wild-type GR. Chloroplastic import was
most powerfully inhibited by changing hydrophobic residues in the N-terminus, as PL-
53QC almost completely abolished chloroplastic import, and LFF-38QYY and FPF-
32SQC reduced chloroplastic import to below 40 %. R-41G and LFF-38QYY also
substantially reduced both mitochondrial and chloroplastic import. In summary,
mutations of positive or hydrophobic residues in the N-terminal or middle portion of the
targeting signal inhibited both the mitochondrial and chloroplastic import but mutations
in the most C-terminal region had the strongest effect on mitochondrial import. A
41
construct, in which the N-terminal and C-terminal region were removed (GR∆2-16,∆30-
52) could only be imported into mitochondria if 8 C-terminal residues were left. This is in
agreement with the notion that the R-2 mutation inhibited mitochondrial import. In order
to investigate if the in vitro situation reflects the in vivo situation we created constructs in
which GFP was linked to either the targeting signal of GR or the full length protein. We
used soybean suspensions and tobacco leaves to investigate the targeting of GR in vivo.
The targeting signal of GR, as well as the full length protein, only produced a typical
chloroplastic pattern when it was used to direct GFP. Therefore we conclude that
although pea GR has been convincingly shown to target phosphinothricin acetyl
transferase to both organelles (Creissen et al. 1995) it does not appear to be able to
achieve this with GFP as a passenger protein. The lack of mitochondrial import could be
due to a number of reasons. Firstly, the GR targeting signal may not be sufficient to
support import of GFP to mitochondria. In a study of the targeting properties of three
different dual targeting signals it has been shown that they vary in their ability to target
different passenger proteins to mitochondria, despite the fact that under the same
conditions they all supported import of their native passenger into both organelles (Chew
2003). A similar case was observed with aminoimidazole ribonucleotide synthetase from
cowpea, which despite being dual localised in mitochondria and plastids was not capable
of targeting GFP to mitochondria or plastids (Goggin et al. 2003). Alternatively, targeting
of GR-GFP to mitochondria may be below the limit of detection. We further investigated
the effect of various mutations on chloroplastic import in vivo. We chose constructs
mutated at hydrophobic regions since these mutations had the greatest effect on
chloroplastic targeting in vitro. All mutated versions examined had disrupted targeting to
plastids as determined by the pattern of GFP targeting. The distinctive of plastidic pattern
was lost when compared with the chloroplastic control, Toc64. Clearly, mutations that
affect chloroplastic import in vitro have a similar effect in vivo. Furthermore, we
preformed import into two organelles simultaneously using a dual import system. Using
the dual import system we could study the effect of mutations on both mitochondria and
chloroplast under the same conditions. Although a few differences were noted the overall
results from dual import was in agreement with the results from single organelle import
in that single mutants had a greater effect on mitochondrial import. In this study we used
42
several different approaches to study organellar import. We found that although no
approach gives the complete picture by itself, all are in a general agreement.
Processing of glutathione reductase
Dual targeting peptides not only have to be recognised by the import apparatus of two
different organelles, they also have to be properly cleaved inside the organelle. The
majority of mitochondrial presequences are cleaved by MPP (Eriksson 1992) and most
chloroplastic transit peptides by SPP (Richter and Lamppa 1998). The recognition
elements for processing by MPP or SPP are not fully understood. However, it has been
shown that an arginine is frequently located in position -2 or -3 upstream of the cleavage
site in mitochondrial presequences (Zhang et al. 2001). For processing with SPP, an
alanine in position -1 and a valine in position -3 are often found. In order to establish the
recognition determinants for processing of GR we performed processing experiments
with the different deletions as well as single amino acid residues mutations (Paper IV).
GR∆2-16 did not affect stromal processing while processing by the MPP/bc1 complex
was increased three fold compared to wild-type. In contrast to the import results, for
GR∆2-30 processing by both the MPP/bc1 complex and stromal extract were significantly
increased. Processing with the MPP/bc1 complex was increased as much as six fold,
whereas stromal processing was increased by a moderate 50%. Processing efficiency is a
reflection of the ability of the precursor to access the binding cleft of the processing
peptidase. Furthermore, bend promoting residues are frequent in order to improve access
to the processing site. The access may be limited by peptide length, i.e. a shorter targeting
signal will access the catalytic site more easily and thus be processed more efficiently.
Mukhopadhyay et al. showed that the efficiency of cleavage decreased dramatically as
the number of residues on the N-terminal side increased (Mukhopadhyay et al. 2002).
Our findings are in line with these results as reducing precursor length resulted in a more
significant increase in processing efficiency with both MPP and with SPP.
Amino acid residues in the vicinity of the processing site, as well as positive residues
throughout the targeting signal have been shown to play a role in processing. Therefore, a
series of point mutations were created. The mutated proteins can be divided into two
groups: i) those with changes in the vicinity of the processing site and ii) those with
43
changes of positive residues throughout the targeting signal. In the first group, three
amino acid residues on each side of the processing site were mutated to amino acids with
different properties. Both isolated stroma and recombinant SPP processed all mutated
constructs with efficiency similar to the wild-type construct, regardless of position or
property of the amino acid introduced. However, when the same mutated constructs were
incubated with the isolated MPP/bc1 complex, mutations at position -1 had the greatest
effect, reducing processing activity by more than 90 %. Mutations at position -2 and +1
reduced processing by almost 60 %. Furthermore, mutations in position +2 reduced
processing by about 50 %. Mutations at position -3 and +3 had no significant effect on
processing. From these results we concluded that amino acid residues in the proximity of
the processing site, in the range of -2 to +2 are involved in the recognition of the cleavage
site by MPP. As no effect was observed with single mutations on the SPP processing
activity, we made double and triple mutations upstream of the cleavage site. The bulky
phenylalanine was introduced in position -3 and -1 instead of valine and alanine,
respectively, and a negatively charged aspartate was introduced in position -2 instead of
arginine. Stroma and the recombinant SPP catalysed processing were inhibited by 33 %
and 52 % with the double mutant and by 70 % and 67 % with the triple mutant,
respectively. These results show that great changes around the cleavage site are required
to affect SPP catalysed processing activity and indicate preference for small uncharged
and positively charged residues upstream of the cleavage site. In the second group, in
which positive amino acid residues were changed throughout the targeting signal, none of
the mutations had any significant effect on processing by stroma. When processed by the
MPP/bc1 complex no significant change was seen for N-terminal mutants. Changing R-28
to an uncharged residue, R-28G, did not effect processing by MPP/bc1 complex whereas
changing to a negative residue, R-28D, inhibited processing with about 50 %. When L-17
was changed to asparagine (L-17N) no difference was seen, however, changing to a
threonine (L-17T), another uncharged amino acid, inhibited processing by 45 %. Besides
R-2, there are two additional positive charged amino acid residues, H-8 and R-7, within
the eight most C-terminal residues. When both of these residues were changed to
uncharged amino acid residues and incubated with MPP/bc1 complex processing
efficiency was reduced by almost 70 %. These results show that positive charges
44
throughout the GR targeting signal have significance for recognition by MPP, but not by
SPP. Positively charged amino acid residues might be required for binding of the
presequence to the negatively charged cleft of the MPP/bc1 complex.
45
CONCLUDING REMARKS
To date approximately 25 different proteins have been reported as dual targeted (Peeters
and Small 2001) Silva-Filho 2003). This might just be the tip of the ice berg and there
might be a significant proportion of proteins, which utilize this solution. It should also be
noted that a large number of the studies were carried out using A. thaliana. A wider, more
representative analysis of gene products from different plant species would provide a
better understanding. We know that glutathione reductase is dual targeted in both pea and
Arabidopsis and it would be of interest to broaden this study to a range of different plant
species.
Confirming that similar proteins in different compartments are encoded by the same gene
is not always a trivial exercise. The most common ways to study dual targeted proteins
are by preforming in vitro or in vivo imports. However, both these methods have their
limitations and one must be careful with interpretation of results. We have developed a
dual import system that will overcome some of the disadvantages with traditional import
assays. In our system we preform in vitro import with both mitochondria and chloroplasts
present simultaneously. This allows us to study targeting of native precursor proteins
with competition between organelles. Furthermore, this system abolishes mis-targeting of
chloroplastic precursor proteins to mitochondria which occurs in single in vitro assays.
We have shown that the targeting signal of the dual targeted protein glutathione reductase
has a domain structure in which the most N-terminal part regulates the amount of protein
imported to each of the organelles. A range of constructs could be made to further
investigate this issue. We have initiated this work by creating deletion mutations that only
contain the central domain of the glutathione reductase targeting signal. If this portion by
itself can support import into mitochondria it would further strengthen the domain
structure hypothesis. It would also be of great interest to take a more global approach. Is
the domain structure a general feature for dual targeting proteins or is it unique to
glutathione reductase and a few more proteins?
An interesting experiment would be to solve the structure of the GR targeting signal. So
far no structure of a dual targeted signal has been solved. Most likely there is not a
separate pathway for import of dual targeted proteins but they use the general import
46
pathways to the respective organelles. A structure of GR in complex with import
receptors from mitochondria and chloroplasts would help in elucidating the mechanisms
for recognition. Surprisingly, using secondary structure prediction programs no α-helix in
the N-terminal part is predicted for GR. Since it is known that an amphiphilic α-helix is
of importance for at least mitochondrial targeting it would be of great interest to see what
kind of secondary structure is present in the GR targeting signal.
47
ACKNOWLEDGEMENTS
There are so many people I would like to thank, I will mention but a few. For those not
mentioned: I have not forgot.
Elzbieta, my excellent supervisor, thanks for all your support and for letting me spend so
much time away from “home”.
Jim, for letting me spend so much time in your lab, it has been a pleasure. For always
supporting and encouraging me.
Stefan Nordlund, for being there when I needed it most.
Orinda for being my “parhäst”, working with you has been great!!
Past and present members of the PMBG at the University of Western Australia; Monika,
Kate, Rachel, Dan, Dave, May-Nee, Ryan and all the rest of you.
Harvey Millar and David Day.
Members of the EG-group, and especially Annelie.
Patrick Dessi for introducing me to science.
All my friends at DBB.
I also want to thank my family, my mum Wera and dad Carl-Axel, my brother Petter and
sister Maja.
48
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