Prokaryotic genome-size

evolution

Range of C values in prokaryotes______________________________________________________________________Taxon Size range Ratio

(kb) (highest/lowest)______________________________________________________________________

Bacteria 159-13,200 8383 Mollicutes 580-2,200 4 Gram negativesa 159-9,500 60 Gram positives 1,600-11,600 7 Cyanobacteria 3,100-13,200 4Archaea 491-5,750 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 Prokaryotes do notdo not contain contain large quantities of nongenic large quantities of nongenic DNA. DNA.

In most bacteria, protein-In most bacteria, protein-coding regions take about coding regions take about ~~90%90% of the genome. of the genome.

Exceptions: Intracellular Exceptions: Intracellular parasites parasites

Rickettsia prowazekiiRickettsia prowazekii (typhus)(typhus)(24% noncoding DNA)(24% noncoding DNA)

Mycobacterium lepraeMycobacterium leprae(Hansen's disease, a.k.a. leprosy)(Hansen's disease, a.k.a. leprosy)(51% noncoding DNA)(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 bp182 ORFs (97% coding density)3 rRNA-specifying genes28 tRNA-specifying genes

Bacterial symbiont on psyliid on hackberry

There is no relationship There is no relationship between genome size and between genome size and bacterial phylogeny.bacterial phylogeny.

Increases and decreases in Increases and decreases in genome size must have have genome size must have have occurred frequently during occurred frequently during bacterial evolution.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.

*

Is this the minimal size?Is this the minimal size?

182

The analytical approach

Nonorthologous gene displacement

Example of nonorthologous Example of nonorthologous gene displacement gene displacement

The phosphoglycerate mutase The phosphoglycerate mutase function is performed in function is performed in different bacteria by different bacteria by twotwo unrelated proteins. unrelated proteins.

The minimal gene set for life = 256 genesThe minimal gene set for life = 256 genes

The minimal gene set contains: The minimal gene set contains: (1) a nearly complete translation system(1) a nearly complete translation system(2) a nearly complete DNA-replication set(2) a nearly complete DNA-replication set(3) a small set of recombination genes(3) a small set of recombination genes(4) a small set of DNA-repair genes(4) a small set of DNA-repair genes(5) a four RNA-polymerase-transcription (5) a four RNA-polymerase-transcription

apparatusapparatus(6) a large set of chaperones(6) a large set of chaperones(7) a few proteins for anaerobic metabolism(7) a few proteins for anaerobic metabolism(8) several enzymes for lipid and cofactor (8) several enzymes for lipid and cofactor

biosynthesisbiosynthesis(9) several transmembrane proteins(9) several transmembrane proteins

(10) 18 proteins of unknown function(10) 18 proteins of unknown function

The experimental approach.

Bacillus subtilis

79 random genes were knocked out6 (7.5%) knockouts were lethalThe genome contains 4112 genesErgo 308 genes are indispensible

Bacillus subtilis

C.A. Hutchison, S.N. Peterson, S.R. Gill, R.T. C.A. Hutchison, S.N. Peterson, S.R. Gill, R.T. Cline, O. White, C.M. Fraser, H.O. Smith, J.C. Cline, O. White, C.M. Fraser, H.O. Smith, J.C. Venter . 1999. Global transposon mutagenesis Venter . 1999. Global transposon mutagenesis and a minimal and a minimal MycoplasmaMycoplasma genome. genome. ScienceScience 286: 2165-2169. 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) (1) gene transfergene transfer(2) (2) gene lossgene loss

Genome-size reduction following endosymbiosis

The yeast nuclear genome contains about 300 protein-coding genes300 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-28 protein-coding genescoding genes.

Lynn Margulis Lynn Margulis proposed that proposed that flaflaggellaeellae and and ciliacilia were derived from were derived from spirochetes through spirochetes through endosymbiosisendosymbiosis

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

Treponema pallidum

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

Parasitism involves an intimate association between two organisms: a hosthost that provides many metabolic and physiological requirements for the other, the parasiteparasite.

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 4242 genes.

In comparison, the chloroplast of the photosynthetic Nicotiana tabacum (155,939 bp) contains 102102 genes.

gene addition due to cellular parasitism:

(1) adhesins(1) adhesins(2) attachment organelles(2) attachment organelles(3) membrane antigens directed (3) membrane antigens directed towards evading the immune towards evading the immune system.system.