* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download No Slide Title
Essential gene wikipedia , lookup
RNA interference wikipedia , lookup
Cancer epigenetics wikipedia , lookup
Quantitative trait locus wikipedia , lookup
Whole genome sequencing wikipedia , lookup
Long non-coding RNA wikipedia , lookup
Gene desert wikipedia , lookup
X-inactivation wikipedia , lookup
Short interspersed nuclear elements (SINEs) wikipedia , lookup
Primary transcript wikipedia , lookup
Metagenomics wikipedia , lookup
Point mutation wikipedia , lookup
Nutriepigenomics wikipedia , lookup
Mitochondrial DNA wikipedia , lookup
Oncogenomics wikipedia , lookup
Public health genomics wikipedia , lookup
Genetic engineering wikipedia , lookup
Transposable element wikipedia , lookup
Gene expression programming wikipedia , lookup
Biology and consumer behaviour wikipedia , lookup
Polycomb Group Proteins and Cancer wikipedia , lookup
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing wikipedia , lookup
Ridge (biology) wikipedia , lookup
Extrachromosomal DNA wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Genomic imprinting wikipedia , lookup
Human Genome Project wikipedia , lookup
Pathogenomics wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Non-coding DNA wikipedia , lookup
Human genome wikipedia , lookup
Gene expression profiling wikipedia , lookup
Epigenetics of human development wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Genomic library wikipedia , lookup
Genome (book) wikipedia , lookup
Designer baby wikipedia , lookup
Microevolution wikipedia , lookup
Genome editing wikipedia , lookup
History of genetic engineering wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Helitron (biology) wikipedia , lookup
Genome Gene expression signal transduction Plant microbial interaction Genome Organization Genome Complete set of instructions for making an organism (master blueprints for all enzymes, cellular structures & activities) an organism‘s complete set of DNA The total genetic information carried by a single set of chromosomes in a haploid nucleus Located in every nucleus of trillions of cells Consists of tightly coiled threads of DNA organized into chromosomes Typical viral genome DNA or RNA 4-200 genes Viral genomes Viral genomes: ssRNA, dsRNA, ssDNA, dsDNA, linear or circular Viruses with RNA genomes • Almost all plant viruses and some bacterial and animal viruses • Genomes are rather small (a few thousand nucleotides) Viruses with DNA genomes (e.g. lambda = 48,502 bp): • Often a circular genome. Replication of viral genomes all ssRNA viruses produce dsRNA molecules many linear DNA molecules become circular Procaryotic genomes one circular doublestranded DNA chromosome often plasmid(s) Generally 1 circular chromosome (dsDNA) Usually without introns Relatively high gene density (~2500 genes per mm of E. coli DNA) Often indigenous plasmids are present 1. Eschericia coli 2. Agrobacterium tumefaciens Bacterial genomes: E. coli 4288 protein coding genes: • Average ORF: 317 amino acids • Very compact: average distance between genes 118bp Numerous paralogous gene families: 38 – 45% of genes arisen through duplication Short intergenic regions Uninterrupted ORFs Conserved signals Abundant comparative information Plasmids Extra chromosomal circular DNAs ori Found in bacteria, yeast and other fungi Size varies form ~ 3,000 bp to 100,000 bp. Replicate autonomously (origin of replication) May contain resistance genes May be transferred from one bacterium to another May be transferred across kingdoms Low - Multicopy plasmids (1 to 400 plasmids/per cell) Plasmids may be incompatible with each other Agrobacterium tumefaciens Plant parasite that causes Crown Gall Disease Lives in intercellular spaces of the plant Encodes a large (~250kbp) plasmid called Tumor-inducing (Ti) plasmid) Plasmid contains genes responsible for the disease Wound = entry point 10-14 days later, tumor forms Portion of the Ti plasmid is transferred between bacterial cells and plant cells T-DNA (Transfer DNA) T-DNA integrates stably into plant genome Single stranded T-DNA fragment is converted to dsDNA fragment by plant cell Then integrated into plant genome 2 x 23bp direct repeats play an important role in the excision and integration process Ti plasmid of A. tumefaciens 1. Auxin, cytokinin, opine synthetic genes transferred to plant 2. Plant makes all 3 compounds 3. Auxins and cytokines cause gall formation 4. Opines provide unique carbon/nitrogen source that only A. tumefaciens can use! Typical eukaryotic genome Located on several chromosomes Relatively low gene density (50 genes per mm of DNA in humans) 5,000 - 125,000 genes Carry organellar genome Fungal genomes: S. cerevisiae First completely sequenced eukaryote genome Very compact genome: • Short intergenic regions • Scarcity of introns • Lack of repetitive sequences Strong evidence of duplication: • Chromosome segments • Single genes Redundancy: non-essential genes provide selective advantage Plant genomes Plant contains three genomes Genetic information is divided in the chromosome. The size of genomes is species dependent The difference in the size of genome is mainly due to a different number of identical sequence of various size arranged in sequence The gene for ribosomal RNAs occur as repetitive sequence and together with the genes for some transfer RNAs in several thousand of copies Structural genes are present in only a few copies, sometimes just single copy. Structural genes encoding for structurally and functionally related proteins often form a gene family The DNA in the genome is replicated during the interphase of mitosis Plant genomes: Arabidopsis thaliana A weed growing at the roadside of central Europe It has only 2 x 5 chromosomes It is just 70 Mbp It has a life cycle of only 6 weeks It contains 25,498 structural genes from 11,000 families The structural genes are present in only few copies sometimes just one protein Structural genes encoding for structurally and functionally related proteins often form a gene family Peculiarities of plant genomes Huge genomes reaching tens of billions of base pairs Numerous polyploid forms Abundant (up to 99%) non coding DNA which seriously hinders sequencing, gene mapping Poor morphological, genetics, and physical mapping of chromosomes A large number of “small-chromosome” in which the chromosome length does not exceed 3 μm The difficulty of chromosomal mapping of individual genes using in situ hybridization The number of chromosomes and DNA content in many species is still unknown Size of the genome in plants and in human Genome Arabidopsis thaliana Zea mays Vicia faba Human Nucleus 70 Millions 3900 Millions 14500 Millions 2800 Millions Plastid 0.156 Millions 0.136 Millions 0.120 Millions Mitochondrion 0.370 Millions .570 Millions .290 Millions .017 Millions What we learned from plant genome project? The number of genes in plants is similar to other higher eukaryots, including humans Most differences between plant species are due to different expression level and different timing of expression of a common or core set of genes, not due to different genes Plant evolution has in large part proceeded through changes in transcriptional and other regularly control (arabidopsis has > 1500 transcription factors) Global Increase in Genome Size Polyploidization (whole genome duplication): Allopolyploidy: combination of genetically distinct chromosome sets. Autopolyploidy: multiplication of one basic set of chromosomes Regional duplication Repetitive Structure of Eukaryotic Genome Eukaryotic genomes contain various degrees of repetitive structure: satellites, micro/mini-satellites, retrotransposons, retrovirus Repetitive sequence size correlates with genome size Heterochromatin (*109bp) Gorrila gorilla Symphalangus syndactylus Pan troglodites Homo sapiens Hylobates muelleri Genome size (*109bp) Mechanisms for Regional Increase in Genome Size Duplicative transposition Unequal crossing-over Replication slippage Gene amplification (rolling circle replication) Gene Duplication duplication of a part of the gene: domain/internal sequence duplication enhance function, novel function by new combination duplication of a complete gene (gene family) invariant duplication: dose repetitions, variant duplication: new functions. duplication of a cluster of genes Internal Gene Duplication 5’ 1 2 3 4 5 3’ 6 Ancestral trypsinogen gene Deletion 6’ 1 5’ 3’ Thr Ala Ala Gly 4 fold duplication + addition of spacer sequence 6’ 1 5’ Internal duplications + addition of intron sequence 5’ 1 1 2 3 4 5 6 3’ Spacer: Gly 7 … 37 38 Antifreeze glycoprotein gene 39 40 41 6’ 3’ Complete Gene Duplication Invariant duplication: RNA specifying genes: Number of tRNA and rRNA correlates with genome size. Variant duplication: X-linked autosomal Trichromatic Human female Trichromatic Human male Human male (color blind) New world monkey female or or Dichromatic Trichromatic New world monkey female New world monkey male Dichromatic or Dichromatic What do the genes encode? Microbes highly specialized Basic functions + Yeast – simplest eukaryote Fly – complex development Genes for basic cellular functions such as translation, transcription, replication and repair share similarity among all organisms Worm – programmed development Arabidopsis – plant life cycle Gene families expand to meet biological needs. Gene classification coding genes Chromosome (simplified) intergenic non-coding region genes Messenger RNA Structural RNA Proteins transfer RNA Structural proteins Enzymes ribosomal RNA other RNA Prokaryotic genes Most do not have introns Many are organized in operons: contiguous genes, transcribed as a single polycistronic mRNA, that encode proteins with related functions Polycistronic mRNA encodes several proteins Bacterial operon Eukaryotic coding genes Most have introns Produce monocistronic mRNA: only one encoded protein Large Protein Coding Genes Segment of DNA which can be transcribed and translated to amino acid Protein Coding Genes Plant contains about 10 000 – 30 000 structural genes They are present in only a few copies, sometimes just one (single copy gene) They often form a gene family The transcription of most structural genes is subject to very complex and specific regulation The gene for enzymes of metabolism or protein biosynthesis which proceed in all cells are transcribed more often Most of the genes are switched off and are activated only in certain organ and then often only in certain cells Many genes are only switched on at specific times House keeping gene: The genes which every cell needs for such basic functions independent of its specialization Mitochondrial genome (mtDNA) Number of mitochondria in plants can be between 50-2000 One mitochondria consists of 1 – 100 genomes (multiple identical circular chromosomes). They are one large and several smaller Size ~15 Kb in animals Size ~ 200 kb to 2,500 kb in plants Mt DNA is replicated before or during mitosis Transcription of mtDNA yielded an mRNA which did not contain the correct information for the protein to be synthesized. RNA editing is existed in plant mitochondria Over 95% of mitochondrial proteins are encoded in the nuclear genome. Often A+T rich genomes Chloroplast genome (ctDNA) Multiple circular molecules, similar to procaryotic cyanobacteria, although much smaller (0.001-0.1%of the size of nuclear genomes) Cells contain many copies of plastids and each plastid contains many genome copies Size ranges from 120 kb to 160 kb Plastid genome has changed very little during evolution. Though two plants are very distantly related, their genomes are rather similar in gene composition and arrangement Some of plastid genomes contain introns Many chloroplast proteins are encoded in the nucleus (separate signal sequence) The family of plastids Buchannan et al. Fig. 1.44 Endosymbiosis Well accepted that chloroplasts and mitochondria were once free living bacteria Their metabolism is bacterial (e.g. photosynthesis) Retain some DNA (circular chromosome) • Protein synthesis sensitive to chloramphenicol • Cytosolic P synthesis sensitive to cycloheximide Most genes transferred from symbiont to nucleus • Requires protein targeting DNA for chloroplast proteins can be come from the nucleus or chloroplast genome Buchannan et al. Fig. 4.4 Import of proteins into chloroplasts Buchannan et al. Fig. 4.6 Biochemistry inside plastids Photosynthesis – reduction of C, N, and S Amino acids, essential amino acid synthesis restricted to plastids • Phenylpropanoid amino acids and secondary compounds start in the plastids (shikimic acid pathway) • Site of action of several herbicides, including glyphosate • Branched-chain amino acids • Sulfur amino acids Fatty acids – all fatty acids in plants made in plastids Exploring metabolism by genetic methods Antisense – what happens when the amount of an enzyme is reduced • not clear how antisense works Knockouts • Often more clear-cut since all of the enzyme is gone • Use of t-DNA, Salk lines Overexpression • Use an unregulated version of the protein or express on a strong promoter • Sometimes leads to cosuppression RNA interference • 21 to 26 mers seem very effective in regulating translation