UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 1

1

UNITY and DIVERSITY

in MICROBIAL GENOMES

Kishore Sakharkar

National University of Singapore

ksakharkar@gmail.com

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Microbes everywhere

Amazing but true

More bacteria in our bodies

than human cells!

More different types

of bacterial genes

in our body

than there are human genes!

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Different shapes of bacteriaCopy right © The M c Graw-Hi l l Com panies , Inc . Perm is s ion requi red for reproduc tion or d is p lay .

Coccus Rod, or bacillus Curved forms: Spirillum/Spirochete

Vibrios (curved rods)Coccobacilli

Mycobacteria Spirilla

Spirochetes

Streptococci

(cocci in chains)

Filamentous

Spirochete

Sta lkHy pha

Coc c us RodSpi ri l lum

Budding and

appendaged

bacteria

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 2

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Different sizes

• Size affects rate of nutrient and waste transport across the cell membrane

• Small size � more efficient exchange, support of higher metabolic rate

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There are now ~200

complete genomes!

Where are we?

Diversity is Good

Parasites vs. free-living organisms

Large genomes vs. small genomes

Archaea vs. Bacteria vs. Eukaryotes

Eucarya

Bacteria

Archaea

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BacteriaEukaryotesArchea

Genomes sequenced

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UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 3

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Microbial evolutionary genomics

• Broad questions that are now being addressed:

� How do genomes acquire their contents,

as lineages evolve over long time scales?

� What are the forces that enable complex biological

processes to be maintained?

� How do genes (and their associated functions)

originate in genomes and how are they lost?

� How do biological capabilities move from one organism

to another and how do they persist over space and time?

For each question, answers are likely to depend on the particular niche

and may differ among microbial communities associated with different processes or sites

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Bacterial lifestyles

• Commensalism

• Mutualism

• Parasitism

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Topics

• Diversity in genome size

• Unity and diversity in gene order

• Unity and diversity in protein length profi les

• Genome reduction in obligatory intracellular parasites

• Overlapping genes in obligatory intracellular parasites

(common patterns in genome architecture)

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 4

10

Compared 115 bacterial genomes

Size varies between bacterial genomes

Smaller genomes have lesser number of genes (ORFs)

Konstantinidis et al., 2004, PNAS

Genome size and number of genes

Genome size

R = 0.98

Tot

al num

ber

of ORFs

in the ge

nome

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• Minimum number of genes to maintain free-living organism

• Mycoplasma genitalium contains only 468 identified

protein-coding genes – Is it the minimal gene set?

• M. genitalium vs. H. influenzae

• Two ancient bacterial lineages, i.e. , Gram-positive

and Gram-negative bacteria, respectively

• 240 genes are orthologous

• Some genes in intermediate steps in essential pathways

are missing? - Nonorthologous gene displacement

• 256 genes are close to the minimal gene set

Minimal genome

Mushegian AR, Koonin EV. (1996) A minimal gene set for cellular life derived by comparison

of complete bacterial genomes. Proc Natl Acad Sci U S A. , 93, 10268-10273

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Gene order comparison

Sakharkar KR, Chow VT (2004). Exploring genome architecture through GOV

a WWW-based gene order visualizer, Bioinformatics , 20, 984-985

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 5

13

Gene order as a common theme

in microbial genomes

• Parallel analysis of multiple genomes can contribute

to understanding of their functional subsystems

e.g., operons

• Gene order:

�Genome architecture

�Functions and interactions of the proteins

�Genome and organism evolution

�Genome annotation

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Conservation of gene order in bacterial

species of the same genus

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M. genitaliumvs.

M. pneumoniae

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Mycoplasma species and gene orderGene order in genomes

Functional description

Multiple genomes

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 6

16

Conservation of gene order in closely related

reduced bacterial genera

C. trachomatisvs.

C. pneumoniae

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Lack of gene order conservation - even in “closely related” bacteria of the same Proteobacterial subdivision

P. aeruginosavs.

E. coli

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Protein length profile

Sakharkar KR, Chow VTK (2004). PPD - Proteome Profile Database, In Silico Biol, 4, 0019

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

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PPD – Proteome Profile Database

Sakharkar KR, Chow VT (2004) PPD - Proteome Profile Database, In Silico Biol, 4, 0019

E.Coli K12Chlamydia trachornatis

Chlamydophila pneumoniae CWL029

Ricketts ia prowazekiiRicketts ia conorii

Comparative length distribution profile: Protein length X (steps) vs. % distribution

Gene product between 700 and 800 amino acids

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Chlamydophila pneumoniae - causes pharyngitis , bronchitis

and pneumonit is

Chlamydia trachomatis - causes pharyngitis, bronchitis

and pneumonit is

Rickettsia conorii - causes Rocky Mountain spotted fever

Rickettsia prowazekii - causes louse-borne typhus

and Mediterranean spotted fever

Mycobacterium leprae - causative agent of human leprosy

Obligatory genomes and associated diseases

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Obligatory intracellular parasites possess

small genomes and display a tendency

towards further genome reduction

# of genes decrease with decrease

reduction in genome size

• Reduction targets are potentially

dispensable genes

• Reduction, while adapting

to selective pressure of the niche

Sakharkar KR, Dhar PK and Chow VT (2004). Genome reduction in prokaryotic obligatory intracellular parasites

of humans: a comparative analysis. Int J Syst Evol Microbiol, 54, 1937-1941

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No. of genes

Genome size (kb)

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 8

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Genome compaction by differential

gene loss in obligatory intracellular parasites

Sakharkar KR, Dhar PK and Chow VT (2004). Genome reduction in prokaryotic obligatory

intracellular parasites of humans: a comparative analysis. Int J Syst Evol Microbiol, 54, 1937-1941

Critical questions:

• The size

• The processes

• The content of deletions

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Their problems

• How to get in host cell

• Inside, how to avoid being killed

• How to multiply

• How to get out � infect new cells

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1 00 2 00 3 00 4 00 500 600 70 0 80 0 90 0 1 000 1 10 0 1 20 0 1 30 0 1 40 0 150 0 >1 50 0

R. prowazeki i

R. cono ri i

C. tra chomatis

C. pneumoniae

M. leprae

E. coli

Protein length

distribution

% genome/length

% change

Max. reduction230-600 AA

Metabolic enzymes

Housekeeping genesNot lost

RNA polymerase,Gyrase, adhesion -10

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R. prowazekiiR. conoriiC. trachomat isC. pneumon iaeM. lep raeE.coli

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 9

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E. coliC. trachomatisC. pneunoniaeR. prowazekiiM. lepraeR. conorii

“Backbone genome” and gene loss

M. leprae – genome in reduction

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More genomes and “backbone genome”

Sakharkar KR. , Sakharkar MK., Chow VT (2005). Footprints of genome reduction in obligatory

intracellular parasites (under review)

Genomes in reductionM. Lepraeand C.burnetti

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UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 10

28

COG category distribution

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J A K L B D Y V T M N Z W U O C G E F H I P Q R S

COG category

% g

en

om

e

R.prowaze kii R.co nor ii

C.trac homatis C.pn eumon iae

M.le pra e E.Coli

Translation

IncreaseJ – TranslationH,I,U - Transports / Metabolism

Life StyleQ – Sec metabolites

& biosynthesis

N - MotilityV - Defense

DecreaseT – TransductionG – Carbo. metabolism

P – InOrg transport

UnknownB - Chromatin structure and dynamics Y - Nuclear structure Z - Cytoskeleton

W - Extracellular structures

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Common themes/unity

• Genome of size <2Mb

� Intracellular (depend on host)

• Increased, pseudogenes

(more number of genes in decay)

• Increased, transport proteins

(uptake from the host)

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Overlapping genes

Sakharkar KR, Chandra Verma, and Vincent TK Chow (2004). Comparative study of overlapping genes

in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii.Int J Syst Evol Microbiol, 55, 1205-1209

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 11

31

Overlapping genes

• Overlapping genes have been proposed as a means

of achieving genome reduction by compressing

the maximum amount of information in limited

sequence space

• Detai led analyses of two reduced genomes

with obligatory lifestyle revealed that

mutations at the ends of coding regions

and elimination of intergenic DNA are the main

forces that determine overlapping of genes

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Directions of overlap

Unidirectional (++)

Unidirectional (--)

Convergent (+-)

Divergent (-+)

>90%

Operons or clusters of gene transcribed together

5’ 3’

Divergent < ConvergentIn divergent 5’ overlap

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Proportion of genomes represented

by overlapping genes in nine genomes

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Chlamydia

trachomatis

Chlamydia

pneumoniae

Mycobacterium

leprae

Rickettsia

prowazekii

Rickettsia conorii

Mycoplasma

genitalium

Mycoplasma

pneumoniae

Clostridium

perfringens

Buchnera

aphidicola

% G

en

om

e

Obligatory ReducedFreeliving

All genes (incl. unknown and hypothetical

Genuine genes

Endosymbiont

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 12

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Which genes overlap

• Essential genes

• Genes in operons

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Conclusion

Common themes

• Genome size

• Protein length profiles

• Niche dependent gene loss

• Backbone genome

• Overlapping genes

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Thank you!

UNITY and DIVERSITY in

MICROBIAL GENOMES

Dr. Kishore Sakharkar

The screen versions of these slides have full details of copyright and acknowledgements 13

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