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Prokaryotic genome-size evolution

Prokaryotic genome-size evolution. Range of C values in prokaryotes ______________________________________________________________________ Taxon Size range Ratio (kb) (highest/lowest) ______________________________________________________________________

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Prokaryotic genome-size evolution

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  1. Prokaryotic genome-size evolution

  2. Range of C values in prokaryotes ______________________________________________________________________ Taxon Size range Ratio (kb) (highest/lowest) ______________________________________________________________________ Bacteria 159-13,200 83 Mollicutes 580-2,200 4 Gram negativesa 159-9,500 60 Gram positives 1,600-11,600 7 Cyanobacteria 3,100-13,200 4 Archaea 491-5,750 12 ______________________________________________________________________ a Most probably a paraphyletic group.

  3. Relationship between gene number and genome size in Bacteria. circular genome linear genome

  4. Pelagibacter ubique are possibly the most numerous bacteria in the world (perhaps 1028 individual cells).

  5. Prokaryotes do not contain large quantities of nongenic DNA. In most bacteria, protein-coding regions take about ~90% of the genome.

  6. Exceptions: Intracellular parasites Rickettsia prowazekii (typhus) (24% noncoding DNA) Mycobacterium leprae (Hansen's disease, a.k.a. leprosy) (51% noncoding DNA)

  7. Relationship between gene number and genome size in Bacteria. circular genome linear genome

  8. Carsonella ruddii is an endosymbiotic gamma-proteobacterium with the smallest genome of any characterized bacteria. Genome size = 159,662 bp 182 ORFs (97% coding density) 3 rRNA-specifying genes 28 tRNA-specifying genes Bacterial symbiont on psyliid on hackberry

  9. There is no relationship between genome size and bacterial phylogeny. Increases and decreases in genome size must have have occurred frequently during bacterial evolution.

  10. * *The Oxygen Catastrophe was a massive environmental change during the Siderian period about 2.4 billion years ago. It is also called the Oxygen Revolution or The Great Oxidation.

  11. 182 Is this the minimal size?

  12. The analytical approach

  13. Nonorthologous gene displacement

  14. Example of nonorthologous gene displacement The phosphoglycerate mutase function is performed in different bacteria by two unrelated proteins.

  15. The minimal gene set for life = 256 genes

  16. The minimal gene set contains: (1) a nearly complete translation system (2) a nearly complete DNA-replication set (3) a small set of recombination genes (4) a small set of DNA-repair genes (5) a four RNA-polymerase-transcription apparatus (6) a large set of chaperones (7) a few proteins for anaerobic metabolism (8) several enzymes for lipid and cofactor biosynthesis (9) several transmembrane proteins (10) 18 proteins of unknown function

  17. The experimental approach. Bacillus subtilis

  18. Bacillus subtilis 79 random genes were knocked out 6 (7.5%) knockouts were lethal The genome contains 4112 genes Ergo 308 genes are indispensible

  19. C.A. Hutchison, S.N. Peterson, S.R. Gill, R.T. Cline, O. White, C.M. Fraser, H.O. Smith, J.C. Venter . 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286: 2165-2169. “… 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including about 100 genes of unknown function.”

  20. “One day a scientist will drop gene number 297 into a test tube, then number 298, then 299... and presto: what was not alive a moment ago will be alive now.” Hayden 1999

  21. “The parsimony approach suggests that the last universal common ancestor (LUCA) of all extant life forms might have had as few as 500−600 genes. The gene set of LUCA that is derived in this fashion mightresemble the minimal gene-set for a free-living prokaryote. However, arguments have also been made for a morecomplex LUCA.” E. V. Koonin. 2003. Comparative genomics, minimal gene-sets and the last universal ancestor. Nature Rev. Microbiol. 1:127-136

  22. GENOME MINIATURIZATION: “use and disuse” in evolution (1) gene transfer (2) gene loss

  23. Genome-size reduction following endosymbiosis The yeast nuclear genome contains about 300 protein-coding genes that function exclusively in the mitochondria. Presumably, some of these genes were once part of the mitochondrial genome which currently contains 28 protein-coding genes.

  24. Lynn Margulis proposed that flagellae and cilia were derived from spirochetes through endosymbiosis

  25. If this hypothesis is true, then these organelles must have undergone maximal genome miniaturization, i.e., they have lost their entire genome. Treponema pallidum

  26. Cryptomonad = Guillardia theta Nucleomorph genome size = 551,000 bp Chromosomes = 3 Protein-coding genes = 464 Introns = 17 Overlapping genes = 44 Gene density = 1 gene / 977 bp

  27. Parasitism involves an intimate association between two organisms: a host that provides many metabolic and physiological requirements for the other, the parasite. Parasitism invariably entails loss of genetic functions in the parasite and a consequent reduction in genome size.

  28. Beechdrop (Epiphagus virginiana), a nonphotosynthetic parasite relative of lavender, basil and catnip.

  29. The chloroplast of the nonphotosyntheticEpiphagus virginiana (70,028 bp) contains 42 genes. In comparison, the chloroplast of the photosynthetic Nicotiana tabacum (155,939 bp) contains 102 genes.

  30. gene addition due to cellular parasitism: (1) adhesins (2) attachment organelles (3) membrane antigens directed towards evading the immune system.

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