Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood

Welkin H. Pope, Deborah Jacobs-Sera, Daniel A. Russell, Daniel H F Rubin, Afsana Kajee, Zama N P Msibi, Michelle H. Larsen, William R. Jacobs, Jeffrey G. Lawrence, Roger W. Hendrix, Graham F. Hatfull

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Newly emerging human viruses such as Ebola virus, severe acute respiratory syndrome (SARS) virus, and HIV likely originate within an extant population of viruses in nonhuman hosts and acquire the ability to infect and cause disease in humans. Although several mechanisms preventing viral infection of particular hosts have been described, the mechanisms and constraints on viral host expansion are ill defined. We describe here mycobacteriophage Patience, a newly isolated phage recovered using Mycobacterium smegmatis mc2155 as a host. Patience has genomic features distinct from its M. smegmatis host, including a much lower GC content (50.3% versus 67.4%) and an abundance of codons that are rarely used in M. smegmatis. Nonetheless, it propagates well in M. smegmatis, and we demonstrate the use of mass spectrometry to show expression of over 75% of the predicted proteins, to identify new genes, to refine the genome annotation, and to estimate protein abundance. We propose that Patience evolved primarily among lower-GC hosts and that the disparities between its genomic profile and that of M. smegmatis presented only a minimal barrier to host expansion. Rapid adaptions to its new host include recent acquisition of higher-GC genes, expression of out-of-frame proteins within predicted genes, and codon selection among highly expressed genes toward the translational apparatus of its new host.

IMPORTANCE The mycobacteriophage Patience genome has a notably lower GC content (50.3%) than its Mycobacterium smegmatis host (67.4%) and has markedly different codon usage biases. The viral genome has an abundance of codons that are rare in the host and are decoded by wobble tRNA pairing, although the phage grows well and expression of most of the genes is detected by mass spectrometry. Patience thus has the genomic profile of a virus that evolved primarily in one type of host genetic landscape (moderate-GC bacteria) but has found its way into a distinctly different high-GC environment. Although Patience genes are ill matched to the host expression apparatus, this is of little functional consequence and has not evidently imposed a barrier to migration across the microbial landscape. Interestingly, comparison of expression levels and codon usage profiles reveals evidence of codon selection as the genome evolves and adapts to its new environment.

Original languageEnglish (US)
Article numbere02145-14
JournalmBio
Volume5
Issue number6
DOIs
StatePublished - Oct 14 2014

Fingerprint

Mycobacteriophages
Mycobacterium smegmatis
Mycobacterium
Genomics
Codon
Proteomics
Base Composition
Genome
Viruses
Bacteriophages
Genes
Mass Spectrometry
Ebolavirus
SARS Virus
Gene Expression
Proteins
Viral Genome
Virus Diseases
Transfer RNA
HIV

ASJC Scopus subject areas

  • Microbiology
  • Virology

Cite this

Pope, W. H., Jacobs-Sera, D., Russell, D. A., Rubin, D. H. F., Kajee, A., Msibi, Z. N. P., ... Hatfull, G. F. (2014). Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood. mBio, 5(6), [e02145-14]. https://doi.org/10.1128/mBio.02145-14

Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood. / Pope, Welkin H.; Jacobs-Sera, Deborah; Russell, Daniel A.; Rubin, Daniel H F; Kajee, Afsana; Msibi, Zama N P; Larsen, Michelle H.; Jacobs, William R.; Lawrence, Jeffrey G.; Hendrix, Roger W.; Hatfull, Graham F.

In: mBio, Vol. 5, No. 6, e02145-14, 14.10.2014.

Research output: Contribution to journalArticle

Pope, WH, Jacobs-Sera, D, Russell, DA, Rubin, DHF, Kajee, A, Msibi, ZNP, Larsen, MH, Jacobs, WR, Lawrence, JG, Hendrix, RW & Hatfull, GF 2014, 'Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood', mBio, vol. 5, no. 6, e02145-14. https://doi.org/10.1128/mBio.02145-14
Pope WH, Jacobs-Sera D, Russell DA, Rubin DHF, Kajee A, Msibi ZNP et al. Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood. mBio. 2014 Oct 14;5(6). e02145-14. https://doi.org/10.1128/mBio.02145-14
Pope, Welkin H. ; Jacobs-Sera, Deborah ; Russell, Daniel A. ; Rubin, Daniel H F ; Kajee, Afsana ; Msibi, Zama N P ; Larsen, Michelle H. ; Jacobs, William R. ; Lawrence, Jeffrey G. ; Hendrix, Roger W. ; Hatfull, Graham F. / Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood. In: mBio. 2014 ; Vol. 5, No. 6.
@article{0d42ff76b9bf4542845b7142dba05f93,
title = "Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood",
abstract = "Newly emerging human viruses such as Ebola virus, severe acute respiratory syndrome (SARS) virus, and HIV likely originate within an extant population of viruses in nonhuman hosts and acquire the ability to infect and cause disease in humans. Although several mechanisms preventing viral infection of particular hosts have been described, the mechanisms and constraints on viral host expansion are ill defined. We describe here mycobacteriophage Patience, a newly isolated phage recovered using Mycobacterium smegmatis mc2155 as a host. Patience has genomic features distinct from its M. smegmatis host, including a much lower GC content (50.3{\%} versus 67.4{\%}) and an abundance of codons that are rarely used in M. smegmatis. Nonetheless, it propagates well in M. smegmatis, and we demonstrate the use of mass spectrometry to show expression of over 75{\%} of the predicted proteins, to identify new genes, to refine the genome annotation, and to estimate protein abundance. We propose that Patience evolved primarily among lower-GC hosts and that the disparities between its genomic profile and that of M. smegmatis presented only a minimal barrier to host expansion. Rapid adaptions to its new host include recent acquisition of higher-GC genes, expression of out-of-frame proteins within predicted genes, and codon selection among highly expressed genes toward the translational apparatus of its new host.IMPORTANCE The mycobacteriophage Patience genome has a notably lower GC content (50.3{\%}) than its Mycobacterium smegmatis host (67.4{\%}) and has markedly different codon usage biases. The viral genome has an abundance of codons that are rare in the host and are decoded by wobble tRNA pairing, although the phage grows well and expression of most of the genes is detected by mass spectrometry. Patience thus has the genomic profile of a virus that evolved primarily in one type of host genetic landscape (moderate-GC bacteria) but has found its way into a distinctly different high-GC environment. Although Patience genes are ill matched to the host expression apparatus, this is of little functional consequence and has not evidently imposed a barrier to migration across the microbial landscape. Interestingly, comparison of expression levels and codon usage profiles reveals evidence of codon selection as the genome evolves and adapts to its new environment.",
author = "Pope, {Welkin H.} and Deborah Jacobs-Sera and Russell, {Daniel A.} and Rubin, {Daniel H F} and Afsana Kajee and Msibi, {Zama N P} and Larsen, {Michelle H.} and Jacobs, {William R.} and Lawrence, {Jeffrey G.} and Hendrix, {Roger W.} and Hatfull, {Graham F.}",
year = "2014",
month = "10",
day = "14",
doi = "10.1128/mBio.02145-14",
language = "English (US)",
volume = "5",
journal = "mBio",
issn = "2161-2129",
publisher = "American Society for Microbiology",
number = "6",

}

TY - JOUR

T1 - Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood

AU - Pope, Welkin H.

AU - Jacobs-Sera, Deborah

AU - Russell, Daniel A.

AU - Rubin, Daniel H F

AU - Kajee, Afsana

AU - Msibi, Zama N P

AU - Larsen, Michelle H.

AU - Jacobs, William R.

AU - Lawrence, Jeffrey G.

AU - Hendrix, Roger W.

AU - Hatfull, Graham F.

PY - 2014/10/14

Y1 - 2014/10/14

N2 - Newly emerging human viruses such as Ebola virus, severe acute respiratory syndrome (SARS) virus, and HIV likely originate within an extant population of viruses in nonhuman hosts and acquire the ability to infect and cause disease in humans. Although several mechanisms preventing viral infection of particular hosts have been described, the mechanisms and constraints on viral host expansion are ill defined. We describe here mycobacteriophage Patience, a newly isolated phage recovered using Mycobacterium smegmatis mc2155 as a host. Patience has genomic features distinct from its M. smegmatis host, including a much lower GC content (50.3% versus 67.4%) and an abundance of codons that are rarely used in M. smegmatis. Nonetheless, it propagates well in M. smegmatis, and we demonstrate the use of mass spectrometry to show expression of over 75% of the predicted proteins, to identify new genes, to refine the genome annotation, and to estimate protein abundance. We propose that Patience evolved primarily among lower-GC hosts and that the disparities between its genomic profile and that of M. smegmatis presented only a minimal barrier to host expansion. Rapid adaptions to its new host include recent acquisition of higher-GC genes, expression of out-of-frame proteins within predicted genes, and codon selection among highly expressed genes toward the translational apparatus of its new host.IMPORTANCE The mycobacteriophage Patience genome has a notably lower GC content (50.3%) than its Mycobacterium smegmatis host (67.4%) and has markedly different codon usage biases. The viral genome has an abundance of codons that are rare in the host and are decoded by wobble tRNA pairing, although the phage grows well and expression of most of the genes is detected by mass spectrometry. Patience thus has the genomic profile of a virus that evolved primarily in one type of host genetic landscape (moderate-GC bacteria) but has found its way into a distinctly different high-GC environment. Although Patience genes are ill matched to the host expression apparatus, this is of little functional consequence and has not evidently imposed a barrier to migration across the microbial landscape. Interestingly, comparison of expression levels and codon usage profiles reveals evidence of codon selection as the genome evolves and adapts to its new environment.

AB - Newly emerging human viruses such as Ebola virus, severe acute respiratory syndrome (SARS) virus, and HIV likely originate within an extant population of viruses in nonhuman hosts and acquire the ability to infect and cause disease in humans. Although several mechanisms preventing viral infection of particular hosts have been described, the mechanisms and constraints on viral host expansion are ill defined. We describe here mycobacteriophage Patience, a newly isolated phage recovered using Mycobacterium smegmatis mc2155 as a host. Patience has genomic features distinct from its M. smegmatis host, including a much lower GC content (50.3% versus 67.4%) and an abundance of codons that are rarely used in M. smegmatis. Nonetheless, it propagates well in M. smegmatis, and we demonstrate the use of mass spectrometry to show expression of over 75% of the predicted proteins, to identify new genes, to refine the genome annotation, and to estimate protein abundance. We propose that Patience evolved primarily among lower-GC hosts and that the disparities between its genomic profile and that of M. smegmatis presented only a minimal barrier to host expansion. Rapid adaptions to its new host include recent acquisition of higher-GC genes, expression of out-of-frame proteins within predicted genes, and codon selection among highly expressed genes toward the translational apparatus of its new host.IMPORTANCE The mycobacteriophage Patience genome has a notably lower GC content (50.3%) than its Mycobacterium smegmatis host (67.4%) and has markedly different codon usage biases. The viral genome has an abundance of codons that are rare in the host and are decoded by wobble tRNA pairing, although the phage grows well and expression of most of the genes is detected by mass spectrometry. Patience thus has the genomic profile of a virus that evolved primarily in one type of host genetic landscape (moderate-GC bacteria) but has found its way into a distinctly different high-GC environment. Although Patience genes are ill matched to the host expression apparatus, this is of little functional consequence and has not evidently imposed a barrier to migration across the microbial landscape. Interestingly, comparison of expression levels and codon usage profiles reveals evidence of codon selection as the genome evolves and adapts to its new environment.

UR - http://www.scopus.com/inward/record.url?scp=84920896638&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84920896638&partnerID=8YFLogxK

U2 - 10.1128/mBio.02145-14

DO - 10.1128/mBio.02145-14

M3 - Article

C2 - 25467442

AN - SCOPUS:84920896638

VL - 5

JO - mBio

JF - mBio

SN - 2161-2129

IS - 6

M1 - e02145-14

ER -