Genome

1. 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

2. 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. • Replicative form of viral genomes • all ssRNA viruses produce dsRNA molecules • many linear DNA molecules become circular • Molecular weight and contour length: • duplex length per nucleotide = 3.4 Å • Mol. Weight per base pair = ~ 660

3. 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 • Homologues: • H. influenzae (1130 of 1703) • Synechocystis (675 of 3168) • M. jannaschii (231 of 1738) • S. cerevisiae (254 of 5885)

4. Procaryotic genomes • Generally 1 circular chromosome (dsDNA) • Usually without introns • Relatively high gene density (~2500 genes per mm of E. coli DNA) • Contour length of E.coli genome: 1.7 mm • Often indigenous plasmids are present

5. Easy problemBacterial Gene-finding • Dense Genomes • Short intergenic regions • Uninterrupted ORFs • Conserved signals • Abundant comparative information • Complete Genomes

6. GenomesGene Content E. coli 4000 genes X 1 kbp/gene=4 Mbp Genome=4 Mbp! Gene-rich

7. Plasmids -lactamase ori Extra chromosomal circular DNAs • 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 • Multipcopy plasmids (~ up to 400 plasmids/per cell) • Low copy plasmids (1 –2 copies per cell) • Plasmids may be incompatible with each other • Are used as vectors that could carry a foreign gene of interest (e.g. insulin) foreign gene

8. Agrobacterium tumefaciens • Characteristics • Plant parasite that causes Crown Gall Disease • Encodes a large (~250kbp) plasmid called Tumor-inducing (Ti) plasmid • Portion of the Ti plasmid is transferred between bacterial cells and plant cells  T-DNA (Tumor DNA)

9. Agrobacterium tumefaciens • 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

10. Agrobacterium tumefaciens • Tumor formation = hyperplasia • Hormone imbalance • Caused by A. tumefaciens • Lives in intercellular spaces of the plant • Plasmid contains genes responsible for the disease • Part of plasmid is inserted into plant DNA • Wound = entry point  10-14 days later, tumor forms

11. Agrobacterium tumefaciens • What is naturally encoded in T-DNA? • Enzymes for auxin and cytokinin synthesis • Causing hormone imbalance  tumor formation/undifferentiated callus • Mutants in enzymes have been characterized • Opine synthesis genes (e.g. octopine or nopaline) • Carbon and nitrogen source for A. tumefaciens growth • Insertion genes • Virulence (vir) genes • Allow excision and integration into plant genome

12. Ti plasmid of A. tumefaciens

14. Auxin, cytokinin, opine synthetic genes transferred to plant Plant makes all 3 compounds Auxins and cytokines cause gall formation Opines provide unique carbon/nitrogen source only A. tumefaciens can use!

15. 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

16. Eucaryotic genomes • Located on several chromosomes • Relatively low gene density (50 genes per mm of DNA in humans) • Contour length of DNA • Carry organellar genome as well

17. Human Genomes Human 50,000 genes X 2 kbp=100 Mbp • Introns=300 Mbp? • Regulatory regions=300 Mbp? • Only 5-10% of human genome codes for genes • - function of other DNA (mostly repetitive sequences) unknown • but it might serve structural or regulatory roles 2300 Mbp=???

18. Plant genomes • It contains three genomes • The size of genomes is given in base pairs (bp) • 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 • Genetic information is divided in the chromosome • The DNA in the genome is replicated during the interphase of mitosis

19. Size of the genome in plants and in human

20. 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 • A model plant for the investigation of plant function • 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

21. Plant genomes: Arabidopsis thaliana • Cross-phylum matches: • Vertebrates 12% • Bacteria / Archaea 10% • Fungi 8% • 60% have no match in non-plant databases • Evolution involved whole genome duplication followed by subsequent gene loss and extensive local gene duplications

22. Complex Genome DNA • ~10% highly repetitive (300 Mbp) • NOT GENES • ~25% moderate repetitive (750 Mbp) • Some genes • ~25% exons and introns (800 Mbp) • 40%=? • Regulatory regions • Intergenic regions

23. Genome organization

24. “Nonfunctional” DNA • Higher eukaryotes have a lot of noncoding DNA • Some has no known structural or regulatory function (no genes) 80 kb

25. Duplicated genes • Encode closely related (homologous) proteins • Clustered together in genome • Formed by duplication of an ancestral gene followed by mutation Five functional genes and two pseudogenes

26. Pseudogenes • Nonfunctional copies of genes • Formed by duplication of ancestral gene, or reverse transcription (and integration) • Not expressed due to mutations that produce a stop codon (nonsense or frameshift) or prevent mRNA processing, or due to lack of regulatory sequences

27. Repetitive DNA • Moderately repeated DNA • Tandemly repeated rRNA, tRNA and histone genes (gene products needed in high amounts) • Large duplicated gene families • Mobile DNA • Simple-sequence DNA • Tandemly repeated short sequences • Found in centromeres and telomeres (and others) • Used in DNA fingerprinting to identify individuals

28. Mobile DNA • Move within genomes • Most of moderately repeated DNA sequences found throughout higher eukaryotic genomes • L1 LINE is ~5% of human DNA (~50,000 copies) • Alu is ~5% of human DNA (>500,000 copies) • Some encode enzymes that catalyze movement

29. Transposition • Movement of mobile DNA • Involves copying of mobile DNA element and insertion into new site in genome

30. Why? • Molecular parasite: “selfish DNA” • Probably have significant effect on evolution by facilitating gene duplication, which provides the fuel for evolution, and exon shuffling

31. 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

32. 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)

33. “Cellular” Genomes Viruses Procaryotes Eucaryotes Nucleus Capsid Plasmids Viral genome Bacterial chromosome Chromosomes (Nuclear genome) Mitochondrial genome Chloroplast genome Genome: all of an organism’s genes plus intergenicDNA Intergenic DNA = DNA between genes

34. Estimated genome sizes mammals plants fungi bacteria (>100) mitochondria (~ 100) viruses (1024) 1e1 1e2 1e3 1e4 1e5 1e6 1e7 1e8 1e9 1e10 1e11 1e12 Size in nucleotides. Number in ( ) = completely sequenced genomes

35. What Did These Individuals Contribute to Molecular Genetics? • Anton van Leeuwenhoek • Discovered cells • Bacteria • Protists • Red blood

36. What Did These Individuals Contribute to Molecular Genetics? • Gregor Johan Mendel • Discovered genetics

37. What Did These Individuals Contribute to Molecular Genetics? • Walter Sutton • Discovered Chromosomes

38. What Did These Individuals Contribute to Molecular Genetics? • Thomas Hunt Morgan • Discovered how genes are transmitted through chromosomes

39. What Did These Individuals Contribute to Molecular Genetics? • Rosalind Elsie Franklin • Research led to the discovery of the double helix structure of DNA

40. What Did These Individuals Contribute to Molecular Genetics? • James Watson and Francis Crick • Discovered DNA

41. DNA’s History

42. Chromosome parts • Chromatid • sister strands after replication • still joined at centromere • Centromere • ~ “middle” of Chromosomes • spindle attachment sites • Telomeres • ends of chrm • important for the stability of chromosomestips.

43. Chromosomal Regions • Heterochromatin • compact; • few genes; • largely structural role • Euchromatin • contains most of the genes.

44. Chromosome

47. Gene • The hereditary determinant of a specified difference between individual • The unit of heredity • The unit which passed from generation to generation following simple Mendelian inheritance • A segment of DNA which encodes protein synthesis • Any of the units occurring at specific points on the chromosomes, by which hereditary characters are transmitted and determined, and each is regarded as a particular state of organization of the chromatin in the chromosome, consisting primarily DNA and protein

48. Gene classification intergenic region non-coding genes coding genes Chromosome (simplified) Messenger RNA Structural RNA Proteins transfer RNA ribosomal RNA other RNA Structural proteins Enzymes

49. Gene Molecular definition: DNA sequence encoding protein What are the problems with this definition?

50. Gene • Some genomes are RNA instead of DNA • Some gene products are RNA (tRNA, rRNA, and others) instead of protein • Some nucleic acid sequences that do not encode gene products (noncoding regions) are necessary for production of the gene product (RNA or protein)