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 Hawai‘i · December 2009
Intr Introduction to Phages Definition Phages are viruses tha that infect prokaryotes (bacteria). Composition All contain nucleic acid acid and protein. Structure Typical structure conta ontains a Head and a Tail. Nucleic acid is id is in the head. Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Phylo ylogeny Study of Phages Traditional Approach Categorize pages by th y their physical characteristics, such as as host range, capsid shape, genome size, an and genome type. Authority Phage taxonomic syste tem is approved and updated by ICTV. CTV. Problems Visualization of phage hage particles is not always possible. le. Information about phage lifestyle is not a ot always available. Resources/Opportunities Large GenBank databa tabase of complete sequenced phages is s is accessible. Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Obstacle for Phage age Genome Based Taxonomica mical Study Genomic Marker (rDNA, rRNA) Ribosomal DNA, RNA NA are highly conservative and serve as e as evolutionary clocks. A speculatively rooted tree for rRNA genes Phages do not contain ribosomal al sequences. Phage biodiversity stu study based on genetic markers or stru structural proteins has achieved limited succe uccess. Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Approach Propos posed: Predicted Proteome An Analysis “Proteome” Proteome is the entire tire complement of proteins expressed b sed by a genome. “Predicted” Open Reading Frame es (ORF) were used, not the actual prot proteome of phages. Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘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 Hawai‘i · December 2009
Pha Phage Proteomic Tree Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Conclusion 1 on 1: No Single Genomic Marke arker Genomic Marker (rDNA, rRNA) Ribosomal DNA, RNA NA are highly conservative and serve as e as evolutionary clocks. Phage Genomic Marker Researchers continuou uously search for a single phage genomi omic marker. Conclusion from the image No single protein was as found in all 105 genomes; in fact no none were even close. Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Conclusion 2: C : Compatible with ICTV standa andards Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Conclusion 2 Examples Con Example One ssDNA phage Pf3 is only distantly related ted to M13, f1, and fd Y Y Y Y Y Y Y Example Two Podoviruses SIO1, T7, YeO3-12 are related lated Y Y Y Y Y Y Y Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Proposals Phage Taxonomy Scheme The proteomic tree sh should be used as the genomic-based sed taxonomy system of phages. Phage Naming Scheme then � (indicating it is Phage genotypes shou hould be named using the first host, the the first reference; e.g. E. coli � X174. a phage), and then the The current ICTV phage naming scheme Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
Discussion Does this phage proteomic tree re ee reflect an evolutionary history? � According to the pap paper, the answer is yes (of course). � Its reasoning is weak eak. � It states subtle impr mprovements in the algorithm should pr d provide a better tree. Opposing Voices Some people suggest est it might be impossible to have a s a strictly hierarchical taxonomic system of of phages. Jade Cheng · ICS-675 Paper Review · University of Hawa awai‘i · December 2009
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