The document discusses genome evolution in bacterial pathogens. It describes two main ways that phenotypic similarities can evolve between species: parallel evolution where similar mutations arise independently, and collateral evolution where alleles are shared between populations. It provides examples of how pathogenic strains like Shigella arose from E. coli through plasmid acquisition and phenotypic convergence. The document also summarizes key points from a workshop on bacterial pathogen origin and evolution, including the four main forms of genome evolution and the role of horizontal gene transfer in transmitting virulence genes.

1. PRESENTED BY: SUMEENA
KARKI
ROLL NO: 5
FIRST SEMESTER,CDBT
KIRTIPUR,KATHMANDU
SUBMITTED TO: SHISHIR SIR
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DATE:26TH JULY 2015

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The process by which the content and organization of genetic information o
species changes over time is called genome evolution

3. : Evolution of phenotypic similarities
between species.
o Two ways: the evolution of similar or identical mutations in
independent lineages, which is termed parallel evolution; and the
evolution in independent lineages of alleles that are shared among
populations called collateral evolution
o Dysentry-causing Shigella strains
have arisen several times from
Escherichia coli via plasmid
acquisition and phenotypic
convergence.
:
o Divergence from a common
ancestral structure
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4.  Workshop on the ‘Origin and Evolution of Human Pathogens’ organized
by Eduardo A. Groisman (Washington University, USA) in 20-23 October
2004 in Baez a (Spain)
 Focusing on pathogenicity islands , bacteriophages (virulence
properties), cell surface modification and also addressing the properties
of ORFan genes
 Genome evolution takes place mainly in four forms:
1. Point mutation and gene conversion
2. Rearrangement(e.g. inversion or translocation)
3. Deletion and insertion of foreign DNA
( e.g. plasmid integration ,transposition)
4. Horizontal gene flux(conjugative plasmids, bacteriophages,
transposons, insertion elements and genomic islands, mechanism of
recombination of foreign DNA into host DNA)
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5. Horizontal gene transfer
 Pathogens often harbor chromosomal gene clusters
encoding virulence functions – termed pathogenicity
islands – that are absent from related non-pathogenic
species
 E.g. different strains of E. coli shares only <40% gene
 Pseudomonas aurigunosa (95%): PAO1 and PA14 strain
differs in G-C content of non –conserved genes but
located on 15 position of genome . Also can kill
fungi- phospholipase C, type IV pili and phenazines
produced during virulence in mouse
 ORFans (Daubin and Ochman, 2004)- class of genes
that encode putative proteins
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6.  May be derived from DNA bacteriophages and have
no homologues in the sequence databases
 Varies within a closely related group of organisms
 Shorter than ancestral genes
 Have a distinct nucleotide composition(low GC even
in organisms with an overall low GC)
 Encode proteins
 Some ORFans are highly conserved
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7.  Some bacteria have fast generation time
 New mutations and gene combinations
 Adapt to our defenses, evolving right out from under
our attempts to rid ourselves of them
 E.g. ratio of beneficial to deleterious mutations is
1:40 000 in the lac system(Roth et al., 2003).
 Stresses are temporary hence mutagenesis is pointless
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8.  Groisman and Ochman ,1994
 Phenotypic difference between E. coli and Salmonella:
i. Presence of pathogen-specific virulence genes
ii. Absence of virulence ‘suppressor’ gene
iii. The existence of allelic differences between
homologous genes
iv. Differential regulation of homologous sequences
 Difference in Trans and/or cis regulatory sites may
cause change in phenotypic traits
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9.  DNA adenine(Dam) methylase regulates
chromosome replication and chromosome
partition(Marinus, 1996; Low et al., 2001).
 E. coli and Salmonella pathogenesis
 lack of Dam methylation causes pleiotropic virulence
defects
Genome size
 Percentage of genes devoted to regulatory functions
increases with genome size (Stover et al.,2000)
 Gene loss and deterioration extends to structural
genes involved in biosynthetic and catabolic
pathways leads to complete dependent on host
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10.  Richard Moxon (University of Oxford, UK)
 Harbour homo- or heteropolymeric repeats in either
the coding or promoter regions of genes
 Slippage at these homopolymeric tracts during DNA
replication
 Often encode surface molecules or enzymes
involved in the production of surface molecules
 H. influenzae :phosphorylcholine(+)- nasopharynx ,
phosphorylcholine(-) –middle ear
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11.  2 types- Divergence and Creation of new strain
 Contribution of recombination to clonal
diversification in various bacterial species ( Enright
and Spratt, 1999; Feil and Spratt,2001)
 High ratios of recombination to mutation yielded
non-clonal species whereas low ratio yielded clonal
species
 Another estimation method-Differences in prophage
assortment
 phages often carry genes that contribute to bacterial
virulence. e.g. S. enterica serovar Typhimurium
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12. • CONVENTIONAL WISDOM
i. May and Anderson ,1983
ii. Evolution of symbiosis or mutation
iii. Vast no. of species of bacteria that colonize cause disease
• EPIDEMIOLOGICAL SELECTION
i. Levin et al ,1982
ii. Interaction between bacteria and individual host they colonize(
e.g. Plaque)
• COINCIDENTAL EVOLUTION
i. Levin and Svanborg Eden , 1990
ii. Bacteria being in the wrong host or in the wrong site in the right
place
iii. e.g. H . pylori (commensal but causes gastric and peptic ulcers)
• WITHIN HOST EVOLUTION
i. Levin and Bull , 1994
ii. Product of selection of favoring more pathogenic no. of a
population colonizing an individual host
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14.  Jorg Hacker and colleagues in Werner Geobel’s group at University of
Wurzburg, Germany in 1980s
 “ Pathogenicity DNA islands”
 Found deletion of PAI led to non pathogenic phenotype of E. coli
 One or more virulence gene ( lacking virulence gene called genomic or
metabolic islands)
 Large genomic regions(10-200 kb) and different base composition i.e.
G+C is between 40%-60%
 Located adjacent to tRNA genes( anchor points for integration of
foreign DNA acquired by horizontal gene transfer)
 Associated with mobile genetic elements( transposons like ) flanked by
Direct Repeats(DR)
 Are unstable or have intrinsic genetic instability
 Are mosaic like structure
 Fitness island if colonizes a host organism together with virulence
genes clusters than this locus becomes PAI
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15.  Export of virulence factors
 Gram positive- extracellular and surface proteins by general secretion pathway
 Gram negative- different types of secretory systems due to presence of outer envelop
 5 types
1) Type I secretion system(T1SS)
• ATP binding cassette(ABC) transport protein , periplasmic protein and outer membrane
protein –forms secretion pore
• Substrates of TISS are delivered to extracellular medium
• Mostly hemolysin ( α- hemolysin of UPEC)
2)Type II (T2SS)
• Main terminal branch
• Mostly encoded by genes within PAI and have 12 subunits(inner periplasmic and outer –
outer membrane pore k/a secretin)
• In Gm +ve-substrate protein (preproteins) with typical N-terminal signal sequence is
transported across cytoplasm membrane and signal sequence is cleaved by proteases.
• In Gm –ve – T2SS are employed to transport the periplasmic derivatives of substrate protein
across outer membrane
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16. 3)Type III (T3SS)
• similarity with flagellum system
• Translocation of effecter proteins across third
membrane(eukaryotic cell)
• Results Cell invasion, inactivation of phagocytic cells,
apoptosis and interference with intracellular transport process
• Genes present in virulence plasmid as well as in PAI
• Extracellular pathogens- cytoplasmic membrane and
intracellular pathogens- phagosomal membrane
4) Type IV (T4SS)
• Similar to conjugation system for transfer of DNA
• Genes encoded in PAI
• e.g. Agrobacterium tumefaciens
• Also in Bordetella pertusis, Legionella,Brucella, H. pylori
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17. 5)Type V(T5SS) or Auto transporters
• The entire transport systems and the substrate protein
are synthesized in the form of a single preprotein
• E.g. LPA and EspC PAI of E .coli
• Extends spectrum of habitat
• Diagnostic marker –identification of pathogens
• Differentiation from non pathogenic relatives
• Therapeutic inventions
• Protein secretion system-deliver heterogenous antigens
for vaccination
• Identification of virulence traits
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18.  Respiratory infections disease are 3rd
cause of world wide death
 Neisseria meningitisdis and Moraxella
catarrhalis – observed same
evolutionary trait
 Studied
 Differences in cell wall structures
 Modification of peptidoglycan
composition(increased proportion of
pentapeptides) and cell shape change
from rod to coccus
 Deletion of gene yacF leads to cocci
shape formation
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19.  Cell shape is governed by two mechanism : cell
elongation and division
 Mainly by yacF (zapD) and Cell Elongation
Machinery(CEM)
 CEM comprises:
 Penicillin Binding Proteins(PBPs)-
Transglycosylation( polymerization of
disaccharide pentapepeptide precursor) and
Transpeptidation (cross linking of peptide
residues)
 MreB ( actin structural homology)
 FtsZ- tublin like protein that helps in cell division
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20.  yacF was present only in bacilli, but not in cocci
 Deleted the gene : N. elongata and N. bacilliformis
 Observed strong morphological defects
 Increase of muropeptides composed of
pentapeptides (GM5) and a decreased of tetra-
peptides (GM4) compared to wild-type bacteria
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21.  Allow permissive interaction with immune
system
 Adhesions to target cells
 Reduction of cellular surface area exposed to
immune attacks without reducing intracellular
storage capacity
 Redistribute surface
 appendages such as pili
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22.  Gram negative diplococcci , 13 serogroups
 Pathogenic strains: N.meningitidis and N. gonorrhoea
 (G+C) is 43%, hmbR-iron uptake
 ORF- cold shock protein homologue( cspA),ORF exp1 and
exp2
 Sac4-serum resistance( dessiminated disease)
 atlA gene (horizontal gene transfer)
 N. gonorrhoea – release of lipooligosaccharide (endotoxin) and
PG fragments ( cytotoxin)
 N. meningitidis – 8 genetic islands
 Naturally transformable and high frequency recombination
and DNA uptake
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23. Mostly PAI are responsible for emergence of
pathogens
BACTERIAL PATHOGENS WITHOUT PAI
 Absent in Mycobacterium spp., Chlamydia spp.,
the spirochetes, most streptococcal species
 Shows extreme adaptation to specific host
environment(reduction of genomic size and
ability to replicate),less flexibility
 Resistance/chromosomal islands
,chromosomal insertions that encodes one or
several antibiotic resistances e.g. MRSA , MDR
strains of S. enterica and Shigella spp.
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