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1. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages

   https://doi.org/10.1093/g3journal/jkac244  

   Howell, Abigail A; Versoza, Cyril J; Cerna, Gabriella; Johnston, Tyler; Kakde, Shriya; Karuku, Keith; Kowal, Maria; Monahan, Jasmine; Murray, Jillian; Nguyen, Teresa; et al (September 2022, G3 Genes|Genomes|Genetics)

   Reyes-Lamothe, R (Ed.)

   Abstract Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages—and thus one of the selective pressures acting on complex microbial systems in nature—remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from 6 subclusters (P1–P6). A series of comparative genomic analyses revealed that mycobacteriophages of subcluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of subclusters P2–P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles—a temperate characteristic that impedes their usage in antibacterial applications. 

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2. Genome Sequence of Mycobacteriophage Bassalto

   https://doi.org/10.1128/mra.01351-22  

   Barekzi, Nazir; Wilkins, Meagan N.; Williams, Aumon L.; Moore, Afiya J.; Duckett, Zachary R.; Tindall, Danielle M.; Eaddy, Donnetta R.; Johnson, Mary B.; Bass, Malcolm; Mageeney, Catherine M. (April 2023, Microbiology Resource Announcements)

   Dennehy, John J. (Ed.)

   ABSTRACT Bassalto is a newly isolated phage of Mycobacterium smegmatis mc 2 155 from the campus grounds of Norfolk State University in Norfolk, VA. Bassalto belongs to the cluster B and subcluster B3 mycobacteriophages, based on the nucleotide composition and comparison to known mycobacteriophages. 

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3. Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions

   https://doi.org/10.3390/microorganisms11010170  

   Milhaven, Mark; Versoza, Cyril J.; Garg, Aman; Cai, Lindsey; Cherian, Sanjana; Johnson, Kamalei; Salas Perez, Kevin; Blanco, Madison; Lobatos, Jackelyn; Mitra, Corinne; et al (January 2023, Microorganisms)

   Bacteriophages are being widely harnessed as an alternative to antibiotics due to the global emergence of drug-resistant pathogens. To guide the usage of these bactericidal agents, characterization of their host specificity is vital—however, host range information remains limited for many bacteriophages. This is particularly the case for bacteriophages infecting the Microbacterium genus, despite their importance in agriculture, biomedicine, and biotechnology. Here, we elucidate the phylogenomic relationships between 125 Microbacterium cluster EA bacteriophages—including members from 11 sub-clusters (EA1 to EA11)—and infer their putative host ranges using insights from codon usage bias patterns as well as predictions from both exploratory and confirmatory computational methods. Our computational analyses suggest that cluster EA bacteriophages have a shared infection history across the Microbacterium clade. Interestingly, bacteriophages of all sub-clusters exhibit codon usage preference patterns that resemble those of bacterial strains different from ones used for isolation, suggesting that they might be able to infect additional hosts. Furthermore, host range predictions indicate that certain sub-clusters may be better suited in prospective biotechnological and medical applications such as phage therapy. 

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4. Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages

   https://doi.org/10.3390/v14081647  

   Versoza, Cyril J.; Howell, Abigail A.; Aftab, Tanya; Blanco, Madison; Brar, Akarshi; Chaffee, Elaine; Howell, Nicholas; Leach, Willow; Lobatos, Jackelyn; Luca, Michael; et al (August 2022, Viruses)

   Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera—from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies. 

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5. The Impact of Leadered and Leaderless Gene Structures on Translation Efficiency, Transcript Stability, and Predicted Transcription Rates in Mycobacterium smegmatis

   https://doi.org/10.1128/JB.00746-19  

   Nguyen, Tien G.; Vargas-Blanco, Diego A.; Roberts, Louis A.; Shell, Scarlet S. (April 2020, Journal of Bacteriology)

   Henkin, Tina M. (Ed.)

   ABSTRACT Regulation of gene expression is critical for Mycobacterium tuberculosis to tolerate stressors encountered during infection and for nonpathogenic mycobacteria such as Mycobacterium smegmatis to survive environmental stressors. Unlike better-studied models, mycobacteria express ∼14% of their genes as leaderless transcripts. However, the impacts of leaderless transcript structures on mRNA half-life and translation efficiency in mycobacteria have not been directly tested. For leadered transcripts, the contributions of 5′ untranslated regions (UTRs) to mRNA half-life and translation efficiency are similarly unknown. In M. tuberculosis and M. smegmatis , the essential sigma factor, SigA, is encoded by a transcript with a relatively short half-life. We hypothesized that the long 5′ UTR of sigA causes this instability. To test this, we constructed fluorescence reporters and measured protein abundance, mRNA abundance, and mRNA half-life and calculated relative transcript production rates. The sigA 5′ UTR conferred an increased transcript production rate, shorter mRNA half-life, and decreased apparent translation rate compared to a synthetic 5′ UTR commonly used in mycobacterial expression plasmids. Leaderless transcripts appeared to be translated with similar efficiency as those with the sigA 5′ UTR but had lower predicted transcript production rates. A global comparison of M. tuberculosis mRNA and protein abundances failed to reveal systematic differences in protein/mRNA ratios for leadered and leaderless transcripts, suggesting that variability in translation efficiency is largely driven by factors other than leader status. Our data are also discussed in light of an alternative model that leads to different conclusions and suggests leaderless transcripts may indeed be translated less efficiently. IMPORTANCE Tuberculosis, caused by Mycobacterium tuberculosis , is a major public health problem killing 1.5 million people globally each year. During infection, M. tuberculosis must alter its gene expression patterns to adapt to the stress conditions it encounters. Understanding how M. tuberculosis regulates gene expression may provide clues for ways to interfere with the bacterium’s survival. Gene expression encompasses transcription, mRNA degradation, and translation. Here, we used Mycobacterium smegmatis as a model organism to study how 5′ untranslated regions affect these three facets of gene expression in multiple ways. We furthermore provide insight into the expression of leaderless mRNAs, which lack 5′ untranslated regions and are unusually prevalent in mycobacteria. 

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