Genome Sequences of Cluster K Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley

Gaballa, Joseph M.; Dabrian, Keeyon; Desai, Rachel; Ngo, Ryan; Park, Diane; Sakaji, Erin; Sun, Yiwei; Tan, Boon Xin; Brinck, Marcia; Brobst, Olivia; Fernando, R Gomes; Kim, Hannah; McCarthy, Siobhán; Murphy, M. Dianne; Sarkis, Alexandra; Sevier, Parker; Singh, Amitoj; Wu, Darwin; Wu, Min-Ying; Ennis, Hayley A.; Luhar, Rohan; Miller, Justin E.; Orchanian, Stephanie B.; Salbato, A.; Alam, Sai; Brenner, Lauren; Kailani, Zilla; Laskow, Joel; Ma, Xinyu; Miikeda, Aika; Nol-Bernardino, Paola; Sukhina, Alisa; Walas, Nikolina; Wei, W.; Do, Nam Phuong; Fournier, Christina T.; Kim, Christy J.; Mosier, Samantha F.; Pierson, Carly; Romero, Ivonne G.; Sánchez, M Leonardo; Sawyerr, Oyinlola; Wang, Joyce; Watanabe, Rina; Wu, Samuel S.; Chen, Annie; Kazane, Katelynn R.; Kettoola, Yousif; Goodwin, Emma; Lund, Andrew J.; Villella, William; Williams, D.; Freise, Amanda C.; Parker, Jordan Moberg

doi:10.1128/mra.01481-18

Cited by 3 publications

(4 citation statements)

References 15 publications

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“… Phamerator map of the whole genomes of Stinson and two closely related Mycobacterium bacteriophages, LaterM ( Gaballa et al 2019 ) and Murucutumbu ( Pope et al 2015 ). In this Phamerator map, protein-coding genes with their putative functional assignments (if available) are displayed above or below a ruler, signifying genes on forward or reverse strands, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…This classification is supported by both the dot plot analysis ( Figure 3 and Supplementary Figures S2–S8 ) as well as the pairwise ANI ( Figure 4 ), which also highlights the strong relatedness between Stinson and other cluster K1 mycobacteriophages on the sequence level. Among the 67 subcluster K1 mycobacteriophages, Stinson is most closely related to LaterM ( Gaballa et al 2019 ) and Murucutumbu ( Pope et al 2015 ), with a nucleotide percent identity of 98.34% and 97.73%, respectively.…”

Section: Resultsmentioning

confidence: 99%

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Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages

Crane

Versoza

Hua

et al. 2021

G3 Genes|Genomes|Genetics

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Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections, but also offering novel insights into pathogen genetics and evolution. A prominent example are cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative non-pathogenic relatives, such as M. smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate sub-cluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host-ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with M. leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, sub-cluster K1 mycobacteriophages are able to integrate into the genomes of M. abscessus and M. marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages

Crane

Versoza

Hua

et al. 2021

G3 Genes|Genomes|Genetics

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“…Over the past decade, the SEA-PHAGES curriculum has been widely implemented at many different institutions worldwide, with varying course structures [ 34 , 35 ]. This network curriculum has resulted in many publications, both in education research [e.g., 36 , 37 ] and basic science [e.g., 38 , 39 ].…”

Section: Methodsmentioning

confidence: 99%

Not the same CURE: Student experiences in course-based undergraduate research experiences vary by graduate teaching assistant

2022

Self Cite

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To expose all undergraduate science students to the benefits of participating in research, many universities are integrating course-based undergraduate research experiences (CUREs) into their introductory biology laboratory curriculum. At large institutions, the bulk of introductory labs are instructed by graduate teaching assistants (GTAs). Graduate students, who are often teachers and researchers in training, may vary in their capacity to effectively teach undergraduates via the CURE model. To explore variation in GTA teaching and the subsequent outcomes for students, we used a case study research design at one institution where introductory biology students participate in GTA-taught CURE lab sections. We used multiple data sources, including in-class focus groups, worksheets, and surveys to explore student perceptions of the GTA-led CURE. Students perceived variation both in the ability of their GTAs to create a supportive and comfortable learning environment, and in the instructional priorities of their GTAs. We also compared student and GTA perspectives of student engagement with research elements in the CURE. While GTAs were divided in their perceptions of whether the CURE provided students with the opportunity to experience the element of relevant discovery, most students—regardless of their GTA—did not perceive that relevant discovery was emphasized in the CURE. Finally, individual GTAs seemed to influence how students perceived why they were participating in the CURE. These data imply that students in CUREs may have vastly different and potentially inequitable research experiences depending on their instructor.

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“…Chancellor/Siphoviridae [126] Virion structure and assembly genes, lytic activity, Lysin A, Lysin B, holin genes, ability to infect M. tuberculosis [126] K/K4 [126] Soil [126] 68 [126] M. smegmatis mc 2 155 [126], predicted to infect M. tuberculosis [126] Temperate [126] Yes [126] Mitti/Siphoviridae [126] Virion structure and assembly genes, lytic activity, Lysin A, Lysin B, holin genes, ability to infect M. tuberculosis [126] K/K4 [126] Soil [126] 68 [126] M. smegmatis mc 2 155 [126], predicted to infect M. tuberculosis [126] Temperate [126] Yes [126] Wintermute/Siphoviridae [126] Virion structure and assembly genes, lytic activity, Lysin A, Lysin B, holin genes, ability to infect M. tuberculosis [126] K/K4 [126] Soil [126] 68 [126] M. smegmatis mc 2 155 [126], predicted to infect M. tuberculosis [126] Temperate [126] Yes [126] ShedlockHolmes /Siphoviridae [127] Ability to infect M. tuberculosis, having tRNA [127] K/K3 [127] Soil [127] 67.3 [127] M. smegmatis MC 2 155 [127], predicted to infect M. tuberculosis [127] Temperate [127] Yes [127] Deby/Siphoviridae [128] Ability to infect M. tuberculosis, structural and assembly genes, having tRNA [128] K/K1 [1...…”

Section: An Explanation Of Discovered Mycobacteriophages Infective To...mentioning

confidence: 99%

A Review on Mycobacteriophages: From Classification to Applications

Hosseiniporgham

Sechi

2022

Pathogens

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Mycobacterial infections are a group of life-threatening conditions triggered by fast- or slow-growing mycobacteria. Some mycobacteria, such as Mycobacterium tuberculosis, promote the deaths of millions of lives throughout the world annually. The control of mycobacterial infections is influenced by the challenges faced in the diagnosis of these bacteria and the capability of these pathogens to develop resistance against common antibiotics. Detection of mycobacterial infections is always demanding due to the intracellular nature of these pathogens that, along with the lipid-enriched structure of the cell wall, complicates the access to the internal contents of mycobacterial cells. Moreover, recent studies depicted that more than 20% of M. tuberculosis (Mtb) infections are multi-drug resistant (MDR), and only 50% of positive MDR-Mtb cases are responsive to standard treatments. Similarly, the susceptibility of nontuberculosis mycobacteria (NTM) to first-line tuberculosis antibiotics has also declined in recent years. Exploiting mycobacteriophages as viruses that infect mycobacteria has significantly accelerated the diagnosis and treatment of mycobacterial infections. This is because mycobacteriophages, regardless of their cycle type (temperate/lytic), can tackle barriers in the mycobacterial cell wall and make the infected bacteria replicate phage DNA along with their DNA. Although the infectivity of the majority of discovered mycobacteriophages has been evaluated in non-pathogenic M. smegmatis, more research is still ongoing to find mycobacteriophages specific to pathogenic mycobacteria, such as phage DS6A, which has been shown to be able to infect members of the M. tuberculosis complex. Accordingly, this review aimed to introduce some potential mycobacteriophages in the research, specifically those that are infective to the three troublesome mycobacteria, M. tuberculosis, M. avium subsp. paratuberculosis (MAP), and M. abscessus, highlighting their theranostic applications in medicine.

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Genome Sequences of Cluster K Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley

Abstract: Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley were isolated from soil using Mycobacterium smegmatis mc2155. Genomic analysis indicated that they belong to subclusters K1 and K5.

Cited by 3 publications

References 15 publications

Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages

Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages

Not the same CURE: Student experiences in course-based undergraduate research experiences vary by graduate teaching assistant

A Review on Mycobacteriophages: From Classification to Applications

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