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Jade Cheng · ICS-675 Paper Review · University of Hawai‘i · December 2009

The Phage Proteomic Tree: A Genome-Based Taxonomy for Phage

Student: Jade Cheng Course: ICS 675 Assignment: Final Paper Review Date: December 3, 2009

Jade Cheng · ICS-675 Paper Review · University of Hawa

Intr

Definition Phages are viruses tha Composition All contain nucleic acid Structure Typical structure conta

awai‘i · December 2009

Introduction to Phages

that infect prokaryotes (bacteria). acid and protein.

• ntains a Head and a Tail. Nucleic acid is

id is in the head.

Jade Cheng · ICS-675 Paper Review · University of Hawa

Phylo

Traditional Approach Categorize pages by th shape, genome size, an Authority Phage taxonomic syste Problems Visualization of phage phage lifestyle is not a Resources/Opportunities Large GenBank databa

awai‘i · December 2009

ylogeny Study of Phages

y their physical characteristics, such as and genome type. tem is approved and updated by ICTV. hage particles is not always possible.

• t always available.

tabase of complete sequenced phages is as host range, capsid CTV.

• le. Information about

s is accessible.

Jade Cheng · ICS-675 Paper Review · University of Hawa

Obstacle for Phage

Genomic Marker (rDNA, rRNA) Ribosomal DNA, RNA Phages do not contain ribosomal Phage biodiversity stu achieved limited succe

awai‘i · December 2009

age Genome Based Taxonomica

NA are highly conservative and serve as e

A speculatively rooted tree for rRNA genes

al sequences. study based on genetic markers or stru uccess.

mical Study

as evolutionary clocks. structural proteins has

Jade Cheng · ICS-675 Paper Review · University of Hawa

Approach Propos

“Proteome” Proteome is the entire “Predicted” Open Reading Frame

awai‘i · December 2009

posed: Predicted Proteome An

tire complement of proteins expressed b es (ORF) were used, not the actual prot

Analysis

sed by a genome. proteome of phages.

Jade Cheng · ICS-675 Paper Review · University of Hawai‘i · December 2009

Tools

BLASTP Distances BLASTP generates a Distance Matrix based on user-supplied protein

• sequences. The distance score () between pair-wise genomes is:

1 # #

Proteomic Distances CLUSTALW and PROTDIST generate a Distance Matrix based on user-supplied protein sequences. Plotting the Tree Tree generation methods, such as neighbor-joining, were used to draw the phylogeny tree based on the Distance Matrix.

Jade Cheng · ICS-675 Paper Review · University of Hawa

Pha

awai‘i · December 2009

Phage Proteomic Tree

Jade Cheng · ICS-675 Paper Review · University of Hawa

Conclusion 1

Genomic Marker (rDNA, rRNA) Ribosomal DNA, RNA Phage Genomic Marker Researchers continuou Conclusion from the image No single protein was

awai‘i · December 2009

• n 1: No Single Genomic Marke

NA are highly conservative and serve as e uously search for a single phage genomi as found in all 105 genomes; in fact no

arker

as evolutionary clocks.

• mic marker.

none were even close.

Jade Cheng · ICS-675 Paper Review · University of Hawa

Conclusion 2: C

awai‘i · December 2009

: Compatible with ICTV standa andards

Jade Cheng · ICS-675 Paper Review · University of Hawa

Con

Example One

ssDNA phage Pf3 is only distantly related

Example Two

Podoviruses SIO1, T7, YeO3-12 are related

awai‘i · December 2009

Conclusion 2 Examples

ted to M13, f1, and fd Y Y Y lated Y Y Y Y Y Y Y Y Y Y Y

Jade Cheng · ICS-675 Paper Review · University of Hawa

Phage Taxonomy Scheme The proteomic tree sh

• f phages.

Phage Naming Scheme Phage genotypes shou a phage), and then the

awai‘i · December 2009

Proposals

should be used as the genomic-based hould be named using the first host, the the first reference; e.g. E. coli X174.

The current ICTV phage naming scheme

sed taxonomy system then (indicating it is

Jade Cheng · ICS-675 Paper Review · University of Hawa

Does this phage proteomic tree re According to the pap Its reasoning is weak It states subtle impr Opposing Voices Some people suggest taxonomic system of

awai‘i · December 2009

Discussion

ee reflect an evolutionary history? paper, the answer is yes (of course). eak. mprovements in the algorithm should pr est it might be impossible to have a s

• f phages.

d provide a better tree. a strictly hierarchical