* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Prokaryotic genome-size evolution Range of C values in prokaryotes
Extrachromosomal DNA wikipedia , lookup
Gene nomenclature wikipedia , lookup
Short interspersed nuclear elements (SINEs) wikipedia , lookup
Gene therapy wikipedia , lookup
Mitochondrial DNA wikipedia , lookup
Metagenomics wikipedia , lookup
Quantitative trait locus wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Polycomb Group Proteins and Cancer wikipedia , lookup
Essential gene wikipedia , lookup
Copy-number variation wikipedia , lookup
Nutriepigenomics wikipedia , lookup
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing wikipedia , lookup
Oncogenomics wikipedia , lookup
Whole genome sequencing wikipedia , lookup
Gene desert wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Genetic engineering wikipedia , lookup
Transposable element wikipedia , lookup
Gene expression programming wikipedia , lookup
Biology and consumer behaviour wikipedia , lookup
Genomic imprinting wikipedia , lookup
Epigenetics of human development wikipedia , lookup
Ridge (biology) wikipedia , lookup
Non-coding DNA wikipedia , lookup
Public health genomics wikipedia , lookup
Helitron (biology) wikipedia , lookup
Microevolution wikipedia , lookup
Human genome wikipedia , lookup
Pathogenomics wikipedia , lookup
Genomic library wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Gene expression profiling wikipedia , lookup
Human Genome Project wikipedia , lookup
Genome (book) wikipedia , lookup
Designer baby wikipedia , lookup
History of genetic engineering wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Genome editing wikipedia , lookup
Prokaryotic genome-size evolution Range of C values in prokaryotes ______________________________________________________________________ Taxon Size range (kb) Ratio (highest/lowest) ______________________________________________________________________ Bacteria 159-13,200 Mollicutes 580-2,200 Gram negativesa 159-9,500 Gram positives 1,600-11,600 Cyanobacteria 3,100-13,200 Archaea 491-5,750 83 4 60 7 4 12 ______________________________________________________________________ a Most probably a paraphyletic group. Relationship between gene number and genome size in Bacteria. circular genome linear genome Pelagibacter ubique are possibly the most numerous bacteria in the world (perhaps 1028 individual cells). Prokaryotes do not contain large quantities of nongenic DNA. In most bacteria, proteincoding regions take about ~90% of the genome. Exceptions: Intracellular parasites Rickettsia prowazekii (typhus) (24% noncoding DNA) Mycobacterium leprae (Hansen's disease, a.k.a. leprosy) (51% noncoding DNA) Relationship between gene number and genome size in Bacteria. circular genome linear genome 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 There is no relationship between genome size and bacterial phylogeny. Increases and decreases in genome size must have have occurred frequently during bacterial evolution. * *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. 182 Is this the minimal size? The analytical approach Nonorthologous gene displacement Example of nonorthologous gene displacement The phosphoglycerate mutase function is performed in different bacteria by two unrelated proteins. The minimal gene set for life = 256 genes 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 The experimental approach. Bacillus subtilis Bacillus subtilis 79 random genes were knocked out 6 (7.5%) knockouts were lethal The genome contains 4112 genes Ergo 308 genes are indispensible 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.” “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 “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 might resemble the minimal gene-set for a free-living prokaryote. However, arguments have also been made for a more complex LUCA.” E. V. Koonin. 2003. Comparative genomics, minimal gene-sets and the last universal ancestor. Nature Rev. Microbiol. 1:127-136 GENOME MINIATURIZATION: “use and disuse” in evolution (1) gene transfer (2) gene loss 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 proteincoding genes. Lynn Margulis proposed that flagellae and cilia were derived from spirochetes through endosymbiosis If this hypothesis is true, then these organelles must have undergone maximal genome miniaturization, i.e., they have lost their entire genome. Treponema pallidum 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 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. Beechdrop (Epiphagus virginiana), a nonphotosynthetic parasite relative of lavender, basil and catnip. The chloroplast of the nonphotosynthetic Epiphagus virginiana (70,028 bp) contains 42 genes. In comparison, the chloroplast of the photosynthetic Nicotiana tabacum (155,939 bp) contains 102 genes. gene addition due to cellular parasitism: (1) adhesins (2) attachment organelles (3) membrane antigens directed towards evading the immune system.