Are essential genes conserved? Fatemeh Ashari Ghomi University of - - PowerPoint PPT Presentation

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Are essential genes conserved?

Fatemeh Ashari Ghomi

University of Canterbury fatemeh.asharighomi@pg.canterbury.ac.nz

October 20, 2016

Fatemeh Ashari Ghomi Are essential genes conserved?

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Essentiality and conservation

Are essential genes conserved? Essential genes are the set of genes required for the growth of an organism. Conserved genes have emerged long time ago and are not lost yet.

Fatemeh Ashari Ghomi Are essential genes conserved?

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Transposon insertion

Fatemeh Ashari Ghomi Are essential genes conserved?

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How is transposon insertion related to essentiality?

Fatemeh Ashari Ghomi Are essential genes conserved?

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Bacteria used in this study

Salmonella Typhimurium D23580 Klebsiella pneumoniae RH201207 Salmonella Typhimurium A130 Salmonella Typhi Ty2 Escherichia coli UPEC ST131 Enterobacter cloacae NCTC 9394 Citrobacter rodentium ICC168 Salmonella Typhimurium SL3261 Salmonella Enteritidis P125109 Salmonella Typhimurium SL1344 Escherichia coli ETEC CS17 Escherichia coli ETEC H10407 Escherichia coli K-12 MG1655 Klebsiella pneumoniae Ecl8

Fatemeh Ashari Ghomi Are essential genes conserved?

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Are there biases in transposon insertion data?

• 1. Is there any origin of replication bias?
• 2. Is there any preferred insertion motif bias?
• 3. Is there any GC bias?
• 4. Is there any positional bias within genes?

Fatemeh Ashari Ghomi Are essential genes conserved?

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There is a replication bias

• rigin

terminus 1 2 3 4 5 Distance bias Gene position insertion index

Origin Terminus Origin Terminus

Fatemeh Ashari Ghomi Are essential genes conserved?

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There is almost no preferred insertion motif bias

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Fatemeh Ashari Ghomi Are essential genes conserved?

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There is a GC bias

0.2 0.3 0.4 0.5 0.6 0.7 1 2 3 4 5 GC bias GC content insertion index

AT AAT GAT T AT T ACT A DNA- Binding Protein Transposon

• S. Kimura, T. P. Hubbard, B. M. Davis, and M. K. Waldor. The nucleoid

binding protein h-NS biases genome-wide transposon insertion landscapes.

Fatemeh Ashari Ghomi Are essential genes conserved?

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Essential genes have more insertions at the ends while beneficial losses have less insertions at the ends

Essential Position Mean Insertion Index 0.2 0.4 5' 3'

First 5% internal Last 20%

Beneficial loss Position

Mean Insertion Index

1 2 5' 3'

First 5% internal Last 20%

Stop Start Functional part Stop Functional part Start Start

Fatemeh Ashari Ghomi Are essential genes conserved?

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Most of the essential genes are single copy genes and most

• f the beneficial losses are genus specific

Single copy Multi-copy Genus specific

All clusters Insertion Index Frequency

1 2 3 4 200

n = 7280 Essential Ambiguous Non−essential Beneficial loss

1 2 3 4 200

n = 3367

Single copy

1 2 3 4

n = 2984

Multi−copy

1 2 3 4

n = 929

Genus specific

Fatemeh Ashari Ghomi Are essential genes conserved?

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Essential genes are mostly related to replication, transcription, and translation

methionyl−trna cyclohydrolase thymidylate carboxyl cytidylyltransferase preprotein translation acyl−carrier−protein initiation dna−directed topoisomerase carboxylase riboflavin shape−determining ligase cell division polymerase synthetase ribosomal 50 100 150

−log10(P−value) Word

Essential genes

Fatemeh Ashari Ghomi Are essential genes conserved?

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Non-essential genes are mostly membrane associated

sensor glutathione hydrogenase formate lyase efflux hydrolase periplasmic repair atpase abc−type anaerobic nitrate reductase

• xidoreductase

transport flagellar dehydrogenase permease transporter 20 40 60

−log10(P−value) Word

Non−essential genes

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Beneficial losses are mostly putative and hypothetical proteins or related to mobile genetic elements

• uter

insb universal exported insa membrane invasion virulence secreted prophage effector is200 insertion fimbrial hypothetical island pathogenicity iscro1 putative transposase 50 100

−log10(P−value) Word

Beneficial losses

Fatemeh Ashari Ghomi Are essential genes conserved?

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Summary

• 1. Biases should be considered before evaluating essentiality.
• 2. Essential genes are more likely to be conserved.
• 3. Multi-copy genes are mostly non-essential.
• 4. Beneficial losses are mostly genus specific.
• 5. Essential genes are mostly related to replication, transcription,

and translation.

• 6. Non-essential genes are mostly membrane associated.
• 7. Beneficial losses are mostly putative and hypothetical proteins or

related to mobile genetic elements.

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Acknowledgement

Paul Gardner Anthony Poole Lars Barquist UC bioinformatcs group

Fatemeh Ashari Ghomi Are essential genes conserved?