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 mc(2)155 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.
  
  
  OBJECTIVE
  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.
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
authors.forename: Welkin H
authors.initials: WH
authors.lastname: Pope
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
authors.forename: Deborah
authors.initials: D
authors.lastname: Jacobs-Sera
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Russell
authors.affiliation: Harvard College, Cambridge, Massachusetts, USA.
authors.forename: Daniel H F
authors.initials: DH
authors.lastname: Rubin
authors.affiliation: University of KwaZulu-Natal, School of Laboratory Medicine, College of Health Sciences, Inkosi Albert Luthuli Hospital, Durban, South Africa.
authors.forename: Afsana
authors.initials: A
authors.lastname: Kajee
authors.affiliation: Department of Infection Prevention and Control, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Zama N P
authors.initials: ZN
authors.lastname: Msibi
authors.affiliation: Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: Michelle H
authors.initials: MH
authors.lastname: Larsen
authors.affiliation: Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
authors.forename: William R
authors.initials: WR
authors.lastname: Jacobs
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Lawrence
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
authors.forename: Roger W
authors.initials: RW
authors.lastname: Hendrix
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA gfh@pitt.edu.
authors.forename: Graham F
authors.initials: GF
authors.lastname: Hatfull
mesh_terms: D001482:Base Composition; D003062:Codon; D016679:Genome, Viral; D013058:Mass Spectrometry; D009160:Mycobacteriophages / Q000737:chemistry* / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D020102:Mycobacterium smegmatis / Q000821:virology*; D020543:Proteome / Q000032:analysis*; D014764:Viral Proteins / Q000032:analysis* / Q000235:genetics*; D014779:Virus Replication
chemical_list: D003062:Codon; D020543:Proteome; D014764:Viral Proteins