Exploring the Mycobacteriophage Metaproteome: Phage Genomics as an Educational Platform

Graham F Hatfull ,Vanaja Kumar,Pauline M Cichon,Swathi Namburi,Mark G Popovich,Deborah Jacobs-Sera,Donald T Schleicher,Amy Foley,Brian Z Simanek,Vanessa Kelchner ,Andrew J Hryckowian ,Rebecca L Gonda ,Jennifer M Houtz ,Craig L Peebles ,Marisa L Pedulla ,Kostandin V Pajcini ,Jeffrey G Lawrence ,William R Jacobs ,Alexis L Smith ,Gina Zdanowicz ,Michael E Ford ,Roger W Hendrix

doi:10.1371/journal.pgen.0020092

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.

Highlights

1031 tailed bacteriophages are estimated to be on planet Earth, representing the majority of all biological entities in the biosphere [1,2]
Isolation and Characterization of Mycobacteriophages We previously reported the genome sequences of mycobacteriophages L5 [28], D29 [30], TM4 [31], and Bxb1 [29], along with a comparative genomic analysis of these and ten additional mycobacteriophages: Barnyard, Bxz1, Bxz2, Che8, Che9c, Che9d, Cjw1, Corndog, Omega, and Rosebush [6]
Since the primary focus of this paper is to report on the diversity of mycobacteriophage gene phamilies and the use of phage genomics as a discovery-based educational platform, further details of the individual phages and their genomes will be reported elsewhere

Summary

Introduction

1031 tailed bacteriophages are estimated to be on planet Earth, representing the majority of all biological entities in the biosphere [1,2]. We found that a curve with PhamMax 1⁄4 3,064 and K_Phage 1⁄4 29 fit the data well (Figure 6) That is, this sample of 30 phages contains representatives of only half of the predicted total number of 3,064 phams to be found among mycobacteriophages, and sequencing a further 100 mycobacteriophage genomes would probably uncover members of an additional approximately 1,000 phams, assuming that phages that are closely related to known phages are not excluded from the sample. The prospect of naming their new phage generates considerable interest among these novice scientists while offering opportunities to learn about the justification of a nonsystematic nomenclature for viruses that contain genomes with highly individualized mosaic architectures This educational platform is clearly not restricted to mycobacteriophages and can be readily extended to the isolation and characterization of environmental phages for other nonpathogenic hosts; comparative genomic analyses of dairy,.

Concluding Remarks

Findings

Materials and Methods