Prokaryotic genomesize evolution

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 491-5,75
0 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
(No Transcript)
11
(No Transcript)
12
Many independent genome duplications
13

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.
14
182
Is this the minimal size?
15
The analytical approach
16
Nonorthologous gene displacement
17
Example of nonorthologous gene displacement The
phosphoglycerate mutase function is performed in
different bacteria by two unrelated proteins.
18
The minimal gene set for life 256 genes
19
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-transc
ription 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
20
The experimental approach.
Bacillus subtilis
21
Bacillus subtilis
79 random genes were knocked out 6 (7.5)
knockouts were lethal The genome contains 4112
genes Ergo 308 genes are indispensible
22
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.
23
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
24
(No Transcript)
25
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. 1127-136
26
(No Transcript)
27
GENOME MINIATURIZATION use and disuse in
evolution
(1) gene transfer (2) gene loss
28
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.
29
Lynn Margulis proposed that flagellae and cilia
were derived from spirochetes through
endosymbiosis
30
If this hypothesis is true, then these organelles
must have undergone maximal genome
miniaturization, i.e., they have lost their
entire genome.
Treponema pallidum
31
(No Transcript)
32
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
33
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.
34
Beechdrop (Epiphagus virginiana), a
nonphotosynthetic parasite relative of lavender,
basil and catnip.
35
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.
36
gene addition due to cellular parasitism (1)
adhesins (2) attachment organelles (3) membrane
antigens directed towards evading the immune
system.