Download Prokaryotic genome-size evolution Range of C values in prokaryotes

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