Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> 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 inf...

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Autores principales:	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
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Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7866087a909b421888f6ab374fdbed2b
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spelling	oai:doaj.org-article:7866087a909b421888f6ab374fdbed2b2021-11-15T15:47:03ZGenomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood10.1128/mBio.02145-142150-7511https://doaj.org/article/7866087a909b421888f6ab374fdbed2b2014-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02145-14https://doaj.org/toc/2150-7511ABSTRACT 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.Welkin H. PopeDeborah Jacobs-SeraDaniel A. RussellDaniel H. F. RubinAfsana KajeeZama N. P. MsibiMichelle H. LarsenWilliam R. JacobsJeffrey G. LawrenceRoger W. HendrixGraham F. HatfullAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 6 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 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 Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood
description	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.
format	article
author	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
author_facet	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
author_sort	Welkin H. Pope
title	Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood
title_short	Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood
title_full	Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood
title_fullStr	Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood
title_full_unstemmed	Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood
title_sort	genomics and proteomics of mycobacteriophage patience, an accidental tourist in the <italic toggle="yes">mycobacterium</italic> neighborhood
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/7866087a909b421888f6ab374fdbed2b
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Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the <italic toggle="yes">Mycobacterium</italic> Neighborhood

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