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Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform.

Hatfull, GF and Pedulla, ML and Jacobs-Sera, D and Cichon, PM and Foley, A and Ford, ME and Gonda, RM and Houtz, JM and Hryckowian, AJ and Kelchner, VA and Namburi, S and Pajcini, KV and Popovich, MG and Schleicher, DT and Simanek, BZ and Smith, AL and Zdanowicz, GM and Kumar, V and Peebles, CL and Jacobs, WR and Lawrence, JG and Hendrix, RW (2006) Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS genetics, 2 (6).

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Abstract

Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 "phamilies" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three-encoding tape-measure proteins, lysins, and minor tail proteins-are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Hatfull, GFgfh@pitt.eduGFH
Pedulla, ML
Jacobs-Sera, Ddjs@pitt.eduDJS0000-0001-7838-3257
Cichon, PM
Foley, A
Ford, ME
Gonda, RM
Houtz, JM
Hryckowian, AJ
Kelchner, VA
Namburi, S
Pajcini, KV
Popovich, MG
Schleicher, DT
Simanek, BZ
Smith, AL
Zdanowicz, GM
Kumar, V
Peebles, CLcpeebles@pitt.eduCPEEBLES0000-0001-7938-3312
Jacobs, WR
Lawrence, JGjlawrenc@pitt.eduJLAWRENC
Hendrix, RWrhx@pitt.eduRHX
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorFraser-Liggett, ClaireUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 1 June 2006
Date Type: Publication
Journal or Publication Title: PLoS genetics
Volume: 2
Number: 6
DOI or Unique Handle: 10.1371/journal.pgen.0020092
Schools and Programs: Dietrich School of Arts and Sciences > Biological Sciences
Refereed: Yes
PubMed ID: 16789831
Date Deposited: 11 Jul 2012 17:32
Last Modified: 07 May 2018 17:55
URI: http://d-scholarship.pitt.edu/id/eprint/12850

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