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Diah Rachmawati

Faculty of Biology UGM

Genetic Factor of Plant DevelopmentGenetic Factor of Plant DevelopmentGenetic Factor of Plant DevelopmentGenetic Factor of Plant Development

• The differences between cells in a multicellular organism come almost entirely from differences in gene expression, not differences in the cell’s genomes.

• These differences arise during development, as regulatory mechanisms turn specific genes off and on.

• Much evidence supports the conclusion that nearly all the cells of an organism have genomic equivalence - that is, they all have the same genes.

Introduction

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

• During embryonic development, cells become obviously different in structure and function as they

differentiate.

• The earliest changes that set a cell on a path to

specialization show up only at the molecular level.

• Molecular changes in the embryo drive the process, termed determination, that leads up to observable

differentiation of a cell.

Different cell types make different proteins, usually as a result of transcriptional regulation

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Nuclear genomesCytoplasmic (non-nuclear) genomes

- mitochondria- chloroplast

Nuclear genome• The size of the nuclear genome varies among organisms• Haploid genome size (C-value). Plants have C values ranging from 107

to 1011 base pairs (bp) coding for 15 thousand to 60 thousand genes. • The genome size is roughly correlated with organism complexity. • Inherited in a Mendelian fashion

Genome Size, Organization and Complexity

• Genome size is measured in two ways: by weight, in picograms, and by base pairs

• Haploid genome size (C-value) is correlated positively with cell size and negatively with cell division rate.

• Genome size and developmental rate are related to one another both within and among similar species.

• The lack of a direct relationship between genome size and organism complexity is called the C-value paradox.

• The c-value paradox is due to repetitive DNA and polyploidy

Why does the Genome Size Differ in Different Organisms?

Structure of nuclear genes

Plant gene structure : discontinuous

Structural genesControlling seguences

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Structure of nuclear genes

• Promoter – Proximal elements are involved general control of transcription and

consist two motif CAAT or AGGA box and TATA box. Site for initial RNA polimerase binding

– Distal elements are involved in specific pattern of gene expression.Enhancer → stimulate gene expression

• Intervening sequences (intron)Intron excised from the primary transcript by a process known as splicing

• Protein – coding genes (exon)

• Poly(A) signals

Flowering plants

Birds

Mammals

Reptiles

Amphibians

Bony fish

Echinoderms

Crustaceans

Insects

Molluscs

Worms

Fungi

Algae

Bacteria

Mycoplasmas

Viruses

103 105 10 7 109 1011

DNA content (bp)

Haploid Genome Size of Various Phyla

100

83

17

70

30

6436

5446

30

70

Gen

om

e s

ize (

bp

)

109

108

107

106

105

Nonrepetitive and Repetitive DNA in various Species

Nonrepetitive

DNA

Repetitive

DNAThe size of nuclear genome

Species Genome size (Mbp)

Arabidopsis thaliana 145

Oryza sativa ssp. Indica 419-463

Sorghum bicolor 748-772

Lycopersicon esculentum 907-100

Nicotiana plumbaginifolia 2287

Zea mays 2292-2716

Homo sapiens 3500

Caenorhabditis elegans 100

Drosophila melanogaster 165

Saccharomyces cereviseae 4

Escherichia coli 4

The nuclear genomes of higher plants differ in size and complexity

Why do plants have larger genomes?

In prokaryotes: - nearly all of the DNA consists of unique sequences encodingfunctional RNA/proteins

In eukaryotes: - unique sequences + noncoding DNA (for chromosome organization and structure)

- most of noncoding DNA exists as multicopy sequences of →→→→ repetitive DNA

- rest of noncoding DNA is single-copy sequences →→→→ spacer DNA

In plants with large genomes: most of the DNA is repetitive.

The Mitochondrial genome - chondriome• The content of the mitochondrial genome is conserved among

plants, but the physical arrangement of the DNA is highly variable.

• The mitochondrial genome also contains smaller DNA molecules known as Mitochondrial plasmids.

The mitochondrial genome encodes only a small proportion of the mitochondrial proteins; less than 40 as compared to up to thousands of nuclear-encoded mitochondrial proteins (Emanuelsson et al. 2000).

Cytoplasmic (non-nuclear) genomes

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Mitochondrial genome organization

� Plant mitochondrial genomes are larger than the mitochondrial genome of mammals and yeast

� Plant mitochondrial genome is diverse in size and organization. No relationship between mitochondrial genome size and genetic complexity.

� Mitochondrial genome encodes many membrane proteins involved in electron transport and ATP synthesis

� Mitochondrial genome organization and transcription and translation machinery is similar to that of prokaryotes.

� Chondriome’s coding capacity is not sufficient to code for all the known mitochondrial protein and RNAs. Mitochondria like a plasmids are genetically semi-autonomous.

� Maternally inherited

The chloroplast genome – plastome

• All plastids within a plant contain exactly the same genome.

• Plastome includes genes coding for ribosomal RNA, transfer RNA and several proteins which in turn control photosynthesis as well as other traits.

• Plastid genomes have a highly conserved structural organization.Gene content and organization of genes within the genome is highly conserved.

• Most of size variations in the plastid genomes of higher plants are due to variations in the size of the inverted repeats.

• Maternal inheritance

Plastid differentiation Interaction between chloroplast and nucleus

• Chloroplast genome is not large enough to encode all of the protein present inside the cell.

• Plastids are semi-autonomous organelles

• The expression of the plastid genes is strictly regulated by the nuclear genes.

• The L subunit mRNA is transcribed from a chloroplast genes and light control of mRNA stability. Nuclear genome encodes S subunit

Most plastid protein are encoded in the nucleus and have to be transported into the plastid after they have been translated in the cytosol

Interaction between different genetic compartment

� Nuclear genes control the expression of plastid genes, but so

can plastid affect nuclear gene expression

� Nuclear genes control the expression of plastid genes : photosystem II biogenesis

Pengendalian genetik perkembangan

� Gen → DNA dengan urutan nukleotida tertentu dan dapat

diekspresikan menjadi protein

� Sintesis protein spesifik yang dikode oleh gen spesifik.

� Tidak semua gen terekspresikan (aktif) selama siklus hidup suatu

individu atau di seluruh bagian tubuh tumbuhan

� Sifat totipotensi → cell do not lose genes

� Aktif atau inaktif tergantung kebutuhan dan respon gen terhadap

perubahan lingkungan.

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Gene and gene expression

- Housekeeping genes : responsible for the enzyme involved in basic cellular metabolism → necessary for normal development of plants

- Regulatory genes: responsible for the enzyme involved in gene expression

- Developmental genes : associated for development process

Plant genome contains many genes → each affect development

Genes consist of specific sequence of nucleotides in the DNA molecule.

Constitutive vs. inducible vs. repressible gene regulation

Constitutive: genes expressed at constant level all the time

(e.g. housekeeping genes regulating basic cellular processes)

Inducible: genes turned on in certain circumstances

(at low level present in non-induced conditions = basal level)

Repressible: genes turned off in certain circumstances

All involved in regulation of transcription initiation….

Gene Expression

Regulation of gene expression

� the cellular control of the amount and timing of appearance of the functional product of a gene

� Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation and morphogenesis

Gene Regulatory Network – Signal Transduction

Signal Transduction Pathway

(An environmental signal, such as a hormone)

Feedback pathways regulate

Pendekatan untuk mempelajari perkembangan tumbuhan

� analisis mekanisme genetik-molekuler yang mendasari proses perkembangan

� karakterisasi reaksi-reaksi biokimia yang menyebabkan terjadinya perkembangan (misal: sintesis klorofil, antosianin, dll)

� investigasi struktur sel dan perannya dalam proses perkembangan

� investigasi struktur serta fungsi jaringan dan sistem organ