rna processing and rnps. rna processing very few rna molecules are transcribed directly into the...
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RNA ProcessingRNA Processing Very few RNA molecules are transcribed Very few RNA molecules are transcribed
directly into the final directly into the final mature RNA.mature RNA. Most newly transcribed RNA molecules Most newly transcribed RNA molecules
((primary transcriptsprimary transcripts) undergo various ) undergo various alterations to yield the mature productalterations to yield the mature product
RNA processingRNA processing is the collective is the collective term used to describe the molecular term used to describe the molecular events allowing the events allowing the primary primary transcriptstranscripts to become the to become the mature mature RNARNA..
primary transcriptprimary transcript
mature RNAmature RNA..
Nucleus or Nucleolus
Cytoplasm
RN
A
pro
cessin
g
Romoval of nucleotides
addition of nucleotides to the 5’- or 3’- ends
modification of certain nucleotides
(1) Removal of nucleotides by both endonucleases and exonucleases
endonucleasesendonucleases to cut at specific to cut at specific sites sites within within a precursor RNAa precursor RNA
exonucleasesexonucleases to trim the to trim the endsends of a of a precursor RNAprecursor RNA
This general process is seen in This general process is seen in prokaryotes and eukaryotes for all prokaryotes and eukaryotes for all types of RNAtypes of RNA
(2) Addition of nucleotides to 5’-or 3’-ends of the primary transcripts or
their cleavage products.
Add a cap and a Add a cap and a poly(A)poly(A) tail to pre-mRNA tail to pre-mRNA
(3) Modification of certain nucleotides on either the base or
the sugar moiety.
–Add a methyl group to 2’-OH of ribose in mRNA (A) and rRNA
–Extensive changes of bases in tRNA
RNPs
Ribonucleoproteins = RNA protein complexs
The RNA molecules in cells usually The RNA molecules in cells usually exist complexed with proteinsexist complexed with proteins
specific proteins attach to specific specific proteins attach to specific RNAsRNAs
RibosomesRibosomes are the largest and most are the largest and most complex RNPscomplex RNPs
Ribosomes Protein biosynthetic
machinery Made of 2 subunits
(bacterial 30S and 50S, Eukaryotes 40S and 60S)
Intact ribosome referred to as 70S ribosome in Prokaryotes and 80S ribosome in Eukaryotes
In bacteria, 20,000 ribosomes per cell, 25% of cell's mass.
Mass of ribosomes is roughly 2/3 RNA
Eukaryotic Ribosome Structure larger and more complex than
prokaryotic ribosomes, but with similar structural and functional properties
tRNA PROCESSING, RNASE P AND RIBOZYMES
tRNA processing in prokaryotes
tRNA processing in eukaryotes
RNase P
Ribozymes
tRNA processing in prokaryotes
Mature tRNAs are generated by processing longer pre-tRNA transcripts, which involves
1. specific exo- and endonucleolytic cleavage by RNases D, E, F and P (general) followed by
2. base modifications which are unique to each particular tRNA type.
tRNA processing in prokaryotes
Primary transcripts
RNase D,E,F and P
tRNA with mature ends
Base modifications
mature tRNAs
tRNA processing in eukaryotes
The pre-tRNA is synthesized with a
1. 16 nt 5’-leader, 2. a 14 nt intron and 3. two extra 3’-nucleotides.
tRNA processing in eukaryotes
1. Primary transcripts forms secondary structures recognized by endonucleases
2. 5’ leader and 3’ extra nucleotide removal
3. tRNA nucleotidyl transferase adds 5’-CCA-3’ to the 3’-end to generate the mature 3’-end
4. Intron removal
RNase P
Ribonuclease P (RNase P) is an enzyme involved in tRNA processing that removes the 5' leader sequences from tRNA precursors
RNase P
RNase P enzymes are found in both prokaryotes and eukaryotes, being located in the nucleus of the latter where they are therefore small nuclear RNPs (snRNPs)
RNase P
RNA component can catalyze pre-tRNA in vitro in the absence of protein. Thus RNase P RNA is a catalytic RNA, or ribozyme.
Ribozyme
Ribozymes are RNAs with catalytic activity that can catalyze particular biochemical reactions depending on their capacity to assume particular structures
RNase P RNA is a ribozyme. Ribozymes function during protein synthesis, in RNA processing reactions, and in the regulation of gene expression
Ribozyme
Self-splicing introns: the intervening RNA that catalyze the splicing of themselves from their precursor RNA, and the joining of the exon sequences
Ribozyme
Self-cleaving RNA encoded by viral genome to resolve the concatameric molecules of the viral genomic RNA produced. These molecules are able to fold up in such a way as to selfcleave themselves into monomeric.
Ribozyme
Ribozymes can be used as therapeutic agents in
1. correcting mutant mRNA in human cells
2. inhibiting unwanted gene expression
Kill cancer cells Prevent virus replication
The Power of RNA interference
LOSS OF FUNCTION Easy in yeast
Difficult in mammals
RNA Interference (RNAi) isable to block selective mRNA
RNAi Pathway
RNAi = RNA interference
siRNA = small interfering RNA
siRNP = small interfering Ribonucleoprotein
RISC = RNA Induced Silencing Complex
Dicer
mRNA PROCESSING, hnRNPs AND snRNPs
Processing of mRNA hnRNP snRNP particles 5’Capping 3’Cleavage and polyadenylation Splicing Pre-mRNA methylation
Processing of mRNA
There is essentially no processing of prokaryotic mRNA, it can start to be translated before it has finished being transcribed.
Prokaryotic mRNA is degraded rapidly from the 5’ end
Processing of mRNA in eukaryotes
In eukaryotes, mRNA is synthesized by RNA Pol II as longer precursors (pre-mRNA), the population of different RNA Pol II transcripts are called heterogeneous nuclear RNA (hnRNA).
Among hnRNA, those processed to give mature mRNAs are called pre-mRNAs
Pre-mRNA molecules are processed to mature mRNAs by 5’-capping, 3’-cleavage and polyadenylation, splicing and methylation.
Processing of mRNA in eukaryotes
hnRNP: hnRNA + proteins
The hnRNA synthesized by RNA Pol II is mainly pre-mRNA and rapidly becomes covered in proteins to form heterogeneous nuclear ribonucleoprotein(hnRNP)
The hnRNP proteins are though to help keep the hnRNA in a single-stranded form and to assist in the various RNA processing reactions
snRNP particles: snRNA + proteins
1. snRNAs are rich in the base uracil, which complex with specific proteins to form snRNPs.
2. The most abundant snRNP are involved in pre-mRNA splicing, U1,U2,U4,U5 and U6.
3. A large number of snRNP define methylation sites in pre-rRNA.
snRNP particles
They are synthesized in the nucleus by RNA Pol II and have a normal 5’-cap.
They are exported to the cytoplasm where they associate with the common core proteins and with other specific proteins.
Their 5’-cap gains two methyl groups and they are then imported back into the nucleus where they function in splicing.
Splicing
Introns: non-coding sequences Exons: coding sequences RNA splicing: removal of introns and joining of exons Splicing mechanism must be precise to maintain open reading frame Catalyzed by spliceosome (RNA + protein)
5’ Capping
Very soon after RNA Pol II starts making a transcript, and before the RNA chain is more than 20 -30 nt long, the 5’-end is chemically modified.
7-methylguanosine is covalently to the 5´ end of pre-mRNA.
Linked 5´ 5´ Occurs shortly after initiation
Function of 5´ cap
Protection from degradation Increasing translational efficiency Transport to cytoplasm Splicing of first exon
3’ Cleavage and polyadenylation
In most pre-mRNAs, the mature 3’-end of the molecule is generated by cleavage followed by the addition of a run, or tail, of A residues which is called the poly(A) tail.
3’ Cleavage and polyadenylation
RNA polymerase II does not usually terminate at distinct site
Pre-mRNA is cleaved ~20 nucleotides downstream of polyadenylation signal (AAUAAA)
~250 AMPs are then added to the 3´ end
Almost all mRNAs have poly(A) tail
Function of poly(A) tail
Increasing mRNA stability Increasing translational efficiency Splicing of last intron
Splicing
the process of cutting the pre-mRNA to remove the introns and joining together of the exons is called splicing.
it takes place in the nucleus before the mature mRNA can be exported to the cytoplasm.
Splicing
Splicing requires a set of specific sequences to be present. The 5’-end of almost all introns has the sequence 5’-GU-3’ and the 3’-end is usually 5’-AG-3’. The AG at the 3’-end is preceded by a pyrimidine-rich sequence called the polypyrimidine tract
Spliceosome
Catalyzes pre-mRNA splicing in nucleus
Composed of five small nuclear RNAs (snRNAs) and associated proteins (snRNPs) assembled on the pre-mRNA
Splicing reaction is catalyzed by RNA
Splicing
Introns: non-coding sequences Exons: coding sequences RNA splicing: removal of introns and joining of exons Splicing mechanism must be precise to maintain open
reading frame Catalyzed by spliceosome (RNA + protein)
Pre-mRNA methylation
The final modification or processing event that many pre-mRNAs undergo is specific methylation of certain bases.
The methylations seem to be largely conserved in the mature mRNA.
ALTERNATIVE mRNA PROCESSING
Alternative processing
Alternative poly(A) sites
Alternative splicing
RNA editing
Alternative processing
Alternative mRNA processing is the conversion of pre-mRNA species into more than one type of mature mRNA.
Types of alternative RNA processing include alternative (or differential) splicing and alternative (or differential) poly(A) processing.
Alternative poly(A) sites
Some pre-mRNAs contain more than one poly(A) site and these may be used under different circumstances to generate different mature mRNAs.
In one cell the stronger poly(A) site is used by default, but in other cell a factor may prevent stronger site from being used.
Alternative splicing The generation of different mature
mRNAs from a particular type of gene transcript can occur by varying the use of 5’- and 3’- splice sites in four ways:
(i) By using different promoters(ii) By using different poly(A) sites(iii) By retaining certain introns(iv) By retaining or removing certain
exons
Alternative splicing
1. By using different promoters.2. By using different poly(A) sites.3 By retaining certain introns.4. By retaining or removing certain exons
Alternative splicing
• the potential for an increase in phenotypic diversity without increasing the overall number of genes. Is achieved by altering the pattern of exons that are spliced together,
• different proteins can arise from the processed mRNA from a single gene.
Alternative splicing
• Alternative splicing can occur either at specific developmental stages or in different cell types.
• the calcitonin gene yields an mRNA that synthesizes calcitonin (thyroid) or calcitonin gene– related peptide (CGRP, brain): 2 proteins with distinctly different functions.
• the α-tropomyosin mRNA have at least 8 different alternatively spliced α-tropomyosin mRNAs.
Alternative splicing
Many defects in the β-globin genes are known to exist leading to β-thalassemias. Some of these defects are caused by mutations in the sequences of the mRNA required for intron recognition and, therefore, result in abnormal processing of the β-globin primary transcript.
RNA editing
AN unusual form of RNA processing in which the sequence of the primary transcript is altered is called RNA editing.
Changing RNA sequence (after transcription)
Two types Base modification (A or C deamination) Base (U) insertion and deletion