Download CONFOUNDING PHYLOGENETIC TREES

CONFOUNDING PHYLOGENETIC TREES
-according to rRNA based phylogenies, there are 3
kingdoms of life – bacteria, archaea and eukarya with
eukarya derived from archaea
-the sequencing of hundreds of genomes has called into
question this tree because many proteins in any one
organism can be archaeal or bacterial in origin
-gene swapping is rampant in prokaryotes
-original cells may have used different genetic codes, but
the most successful cells were able to take up foreign DNA
from neighbours allowing quick adaptations – this
advantage would have selected for organisms with the same
genetic code
-gene swapping appears to have occurred in eukaryotes as
well
-in fact, yeast have twice as many bacterial derived
nuclear genes as archaeal derived genes
-the bacterial genes may have replaced archaeal
derived genes as bacteria were eaten
-even though the uptake of foreign DNA is rare in
eukaryotes, these events had hundreds of millions of years
to occur and once the endogenous gene is lost, it’s lost
forever
- gene swapping in prokaryotes allows for rapid acquisition
of genes for antibiotic resistance, pathogenicity, alternate
metabolic pathways, symbiosis
Pathogenic E. coli O157:H7
-strain O157:H7 has 1,387 genes not found in E. coli K-12,
K-12 has 582 genes not present (lost) in O157:H7
-carry virulence genes for:
host invasion – adhesion, endocytosis, extracellular
matrix breakdown
immune evasion - capsules, antigenic variation,
invasion of macrophages
-pathogenic bacteria often also carry genes for antibiotic
resistance
-these genes can be carried on transposons, phages,
plasmids or on the chromosome
-these genes often occur in clusters called pathogenicity
islands (PAIs)
-PAIs include mobility genes such as integrases
-have repeats or IS elements at end
-usually occur next to tRNAs
-are unstable, often deleted or added in closely related
species or strains
-Despite instability in clones of E. coli, some PAIs have
been part of genome for millions of years
-these features suggest that PAIs are derived from
transposons that have become fixed in the genome leading
to speciation
-because the transfer of islands are often relatively recent
events in evolution, the DNA these islands can often be
seen from the difference in DNA structure compared to rest
of chromosome
-differences in codon bias, nucleotide composition,
intrinsic curvature, etc. because the replication and repair
machinery hasn’t had a chance to alter the base
composition to that normally present in the chromosome
(-different species often differ in mutations present in the
replication and repair machinery, especially pathogenic
species)
-non-pathogenic bacteria also have islands that confer
antibiotic resistance, metabolic functions, etc.
-transfer of islands often occur via conjugation (if islands
on plasmids), transformation or transduction by phages
-gene transfer leads to formation of new strains and
(along with other forms of genetic change such as DNA
rearrangements and mutations) can lead to speciation
-some pathogenic bacteria show little evidence of gene
transfer
-these are usually obligate intracellular parasites and
probably have little opportunity to pick up stray DNA
from other bacteria
Changing codon usage
-genetic isolation and speciation can also occur by changes
in codon usage The genetic code isn’t universal
-How do changes occur without killing organism
-codon capture
-changes in base composition lead to loss of a
particular codon
-codon then reappears but tRNA encodes different a.a.
-ambiguous intermediate
-two tRNAs can bind to same codon (one does so
wrongly by base pairing but structure of tRNA allows
binding)
-evntually the “wrong” tRNA takes over and the
correct one is lost
eg. Ser-tRNACAG translates leucine CUG in
Candida albicans
ORIGINS OF REPLICATION
The E. coli chromosome has a single replication origin
termed oriC (origin of Chromosome)
*
The functional origin is about 245-bp in length and
contains four 9-bp repeats that are bound by a cluster of
DnaA polypeptides
*
The DNA wraps in a left handed coil around the DnaA
cluster, which facilitates the melting of a nearby set of three
13-basepair AT-rich repeats
*
The melted region serves as an entry point for DnaB
protein (helicase), which requires ATP and DnaC to load
onto DNA
*
DnaG (primase) and SSB (single strand binding
protein) then add & leading strand synthesis can begin
CHROMOSOME PARTITIONING
-in different bacteria (B. subtilis, C. crescentus, and E. coli)
origin of replication is segregated and tethered and
terminus is pulled behind by DNA condensation
-sop/par proteins bind to cis elements (called pars) near
origins and are required for portioning
-smc-like proteins are also required
-replisome is often stationary and might provide the force
for partitioning by spooling the DNA