1
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Badiola MLP, Befano KD, Berger ML, Blanco CR, Ghunney N, Lee JG, Myat LP, Nguyen JK, Ober EM, Press-Porter KM, She BT, Watkins JS, Caruso SM. Genome sequence of bacteriophage GiJojo, isolated using Streptomyces mirabilis in Catonsville, Maryland. Microbiol Resour Announc 2024:e0058424. [PMID: 39177367 DOI: 10.1128/mra.00584-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/12/2024] [Indexed: 08/24/2024] Open
Abstract
Bacteriophage GiJojo is a myovirus isolated from soil that infects Streptomyces mirabilis NRRL B-2400, with a genome length of 115,161 bp containing 180 genes and 29 tRNAs. Of those genes, 59 have been assigned functions. GiJojo is a member of the BS cluster of actinobacteriophages.
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Affiliation(s)
- Marie Louise P Badiola
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Kaela D Befano
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - McKayla L Berger
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Claudine R Blanco
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Nhyira Ghunney
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Jaehyun G Lee
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Lin P Myat
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - James K Nguyen
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Ellison M Ober
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Karla M Press-Porter
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Brendan T She
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Justin S Watkins
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Steven M Caruso
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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2
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Mathew B, Lee AS, Chen K, Kaczmarski M, Oommen N, Mehaboob A, Patel V, Patel Y, Saji H, Shamsi MA, Gibb B. Complete genome sequences of Arthrobacter globiformis phages Uzumaki and Argan of cluster AU6. Microbiol Resour Announc 2024; 13:e0029324. [PMID: 38990022 PMCID: PMC11320949 DOI: 10.1128/mra.00293-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/05/2024] [Indexed: 07/12/2024] Open
Abstract
Bacteriophages Uzumaki and Argan infect Arthrobacter globiformis B-2880 isolated from soil samples in Long Island, New York. These bacteriophages have lambda-like morphology with prolate capsid and share 97% gene content similarity. These traits place them in cluster AU6 with other related Arthrobacter phages.
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Affiliation(s)
- Brandon Mathew
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Andrew Sean Lee
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Katie Chen
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Michael Kaczmarski
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Nigel Oommen
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Asweel Mehaboob
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Vrushali Patel
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado, USA
| | - Yamini Patel
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Hannah Saji
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Muhammad Ayaan Shamsi
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Bryan Gibb
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
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3
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Horton EN, Beach EK, Cook KT, Cronin KG, Haag AT, Salter SM, Stojanovic NA, Fry ZE, Connolly BM, Hare RF, Ettinger ASH, Poxleitner MK, Anders KR. Complete genome sequence of Microbacterium foliorum phage Curie, a podovirus isolated from soil in Spokane, Washington. Microbiol Resour Announc 2024; 13:e0040824. [PMID: 39037314 PMCID: PMC11320940 DOI: 10.1128/mra.00408-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/22/2024] [Indexed: 07/23/2024] Open
Abstract
Bacteriophage Curie is a podovirus that infects Microbacterium foliorum. The Curie genome spans 16,810 bp, has 90 bp terminal inverted repeats, and includes 23 protein-coding genes. Its genome architecture resembles phage PineapplePizza and other phi29-like phages. Together, Curie and PineapplePizza form a new actinobacteriophage Cluster GI.
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Affiliation(s)
- Emma N. Horton
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | - Erika K. Beach
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | - Kathryn T. Cook
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | - Kyra G. Cronin
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | - Avery T. Haag
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | - Sierra M. Salter
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | | | - Zoe E. Fry
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | | | - Rebekah F. Hare
- Department of Biology, Gonzaga University, Spokane, Washington, USA
| | | | | | - Kirk R. Anders
- Department of Biology, Gonzaga University, Spokane, Washington, USA
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4
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Berry NE, Cassford MS, Agostino CJ, Dionne EN, Schmitt OJ, Butela KA, Jacobs-Sera D, DeGiorgis JA, Cornely K. Genomic sequences of Mycobacterium smegmatis A cluster phages LBerry, Pembroke, and Zolita. Microbiol Resour Announc 2024; 13:e0050424. [PMID: 38980043 PMCID: PMC11320968 DOI: 10.1128/mra.00504-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
LBerry, Pembroke, and Zolita are newly isolated bacteriophages that infect Mycobacterium smegmatis mc²155. Based on gene content similarity, LBerry and Pembroke are assigned to cluster A3, and Zolita is assigned to cluster A5. LBerry and Pembroke are 99% identical to Anaysia and Caviar, and Zolita is 99% identical to SydNat.
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Affiliation(s)
- Nathan E. Berry
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Marly S. Cassford
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Colby J. Agostino
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Ethan N. Dionne
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Olivia J. Schmitt
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
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5
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Pelagalli C, Sera DJ, DeGiorgis JA, Cornely K. Mycobacteriophage maravista: a cluster F1 phage discovered on Cape Cod, Massachusetts. Microbiol Resour Announc 2024; 13:e0050224. [PMID: 38860805 PMCID: PMC11256854 DOI: 10.1128/mra.00502-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Mycobacterium virus Maravista, a member of the family Gracegardnervirianae and species Cheoctovirus, is an F1 cluster phage that infects Mycobacterium smegmatis mc²155. The Maravista genome has 61.3% GC content, is 60,140 bp in length, and encodes 104 putative genes. Maravista encodes two putative glycosyltransferases, suggesting glycosylation of its capsid protein.
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Affiliation(s)
- Charles Pelagalli
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Debbie-Jacobs Sera
- Department of Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
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6
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Patel Y, Patel VP, Syeda A, Saji H, Gibb BP. Genome sequence of bacteriophage Janeemi isolated on Arthrobacter globiformis from soil collected in New York. Microbiol Resour Announc 2024; 13:e0017724. [PMID: 38860811 PMCID: PMC11256828 DOI: 10.1128/mra.00177-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
Janeemi is a bacteriophage that infects Arthrobacter globiformis B-2880, which was isolated from soil collected in New York City. The genome has a length of 43,877 bp and contains 69 predicted genes. Based on gene content similarity to phages in the actinobacteriophage database, Janeemi is assigned to phage cluster AZ1.
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Affiliation(s)
- Yamini Patel
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Vrushali P. Patel
- Department of Psychology and Neuroscience, University of Colorado, Boulder, Colorado, USA
| | - Amna Syeda
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Hannah Saji
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Bryan P. Gibb
- Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, New York, USA
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7
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Chong Qui E, Habtehyimer F, Germroth A, Grant J, Kosanovic L, Singh I, Hancock SP. Mycobacteriophage Alexphander Gene 94 Encodes an Essential dsDNA-Binding Protein during Lytic Infection. Int J Mol Sci 2024; 25:7466. [PMID: 39000573 PMCID: PMC11242194 DOI: 10.3390/ijms25137466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Mycobacteriophages are viruses that specifically infect bacterial species within the genera Mycobacterium and Mycolicibacterium. Over 2400 mycobacteriophages have been isolated on the host Mycolicibacterium smegmatis and sequenced. This wealth of genomic data indicates that mycobacteriophage genomes are diverse, mosaic, and contain numerous (35-60%) genes for which there is no predicted function based on sequence similarity to characterized orthologs, many of which are essential to lytic growth. To fully understand the molecular aspects of mycobacteriophage-host interactions, it is paramount to investigate the function of these genes and gene products. Here we show that the temperate mycobacteriophage, Alexphander, makes stable lysogens with a frequency of 2.8%. Alexphander gene 94 is essential for lytic infection and encodes a protein predicted to contain a C-terminal MerR family helix-turn-helix DNA-binding motif (HTH) and an N-terminal DinB/YfiT motif, a putative metal-binding motif found in stress-inducible gene products. Full-length and C-terminal gp94 constructs form high-order nucleoprotein complexes on 100-500 base pair double-stranded DNA fragments and full-length phage genomic DNA with little sequence discrimination for the DNA fragments tested. Maximum gene 94 mRNA levels are observed late in the lytic growth cycle, and gene 94 is transcribed in a message with neighboring genes 92 through 96. We hypothesize that gp94 is an essential DNA-binding protein for Alexphander during lytic growth. We proposed that gp94 forms multiprotein complexes on DNA through cooperative interactions involving its HTH DNA-binding motif at sites throughout the phage chromosome, facilitating essential DNA transactions required for lytic propagation.
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Affiliation(s)
| | | | | | | | | | | | - Stephen P. Hancock
- Department of Chemistry, Towson University, Towson, MD 21252, USA; (E.C.Q.); (F.H.); (A.G.); (J.G.); (L.K.); (I.S.)
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8
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Das R, Arora R, Nadar K, Saroj S, Singh AK, Patil SA, Raman SK, Misra A, Bajpai U. Insights into the genomic features and lifestyle of B1 subcluster mycobacteriophages. J Basic Microbiol 2024; 64:e2400027. [PMID: 38548701 DOI: 10.1002/jobm.202400027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/24/2024] [Indexed: 06/06/2024]
Abstract
Bacteriophages infecting Mycobacterium smegmatis mc2155 are numerous and, hence, are classified into clusters based on nucleotide sequence similarity. Analyzing phages belonging to clusters/subclusters can help gain deeper insights into their biological features and potential therapeutic applications. In this study, for genomic characterization of B1 subcluster mycobacteriophages, a framework of online tools was developed, which enabled functional annotation of about 55% of the previously deemed hypothetical proteins in B1 phages. We also studied the phenotype, lysogeny status, and antimycobacterial activity of 10 B1 phages against biofilm and an antibiotic-resistant M. smegmatis strain (4XR1). All 10 phages belonged to the Siphoviridae family, appeared temperate based on their spontaneous release from the putative lysogens and showed antibiofilm activity. The highest inhibitory and disruptive effects on biofilm were 64% and 46%, respectively. This systematic characterization using a combination of genomic and experimental tools is a promising approach to furthering our understanding of viral dark matter.
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Affiliation(s)
- Ritam Das
- Department of Life Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Ritu Arora
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
| | - Kanika Nadar
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
| | - Saroj Saroj
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
| | - Amit K Singh
- Experimental Animal Facility, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Shripad A Patil
- Experimental Animal Facility, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Sunil K Raman
- Pharmaceutics and Pharmacokinetic Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Amit Misra
- Pharmaceutics and Pharmacokinetic Division, CSIR-Central Drug Research Institute, Lucknow, India
- Pharmaceutics and Pharmacokinetic Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India
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9
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Delesalle VA, Ankeriasniemi RE, Lewis CM, Mody JM, Roy AM, Sarvis WA, Vo DD, Walsh AE, Zappia RJ. Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:84-90. [PMID: 39119203 PMCID: PMC11304909 DOI: 10.1089/phage.2024.0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Background As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc2155 continue to be discovered. Materials and Methods Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared. Results Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence. Conclusions Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.
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Affiliation(s)
| | | | - Colin M. Lewis
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jehan M. Mody
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Abigail M. Roy
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Ward A. Sarvis
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Duy D. Vo
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Allison E. Walsh
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Rose J. Zappia
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
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10
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Pollenz RS, Barnhill K, Biggs A, Bland J, Carter V, Chase M, Clark H, Coleman C, Daffner M, Deam C, Finocchiaro A, Franco V, Fuller T, Pinera JG, Horne M, Howard Z, Kanahan O, Miklaszewski C, Miller S, Morgan R, Onalaja O, Otero L, Padhye S, Rainey E, Rasul F, Robichaux K, Rodier A, Schlosser S, Sciacchitano A, Stewart E, Thakkar R, Heller DM. A genome-wide cytotoxicity screen of cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth. G3 (BETHESDA, MD.) 2024; 14:jkae049. [PMID: 38456318 PMCID: PMC11075535 DOI: 10.1093/g3journal/jkae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes (~28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic no known functions proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.
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Affiliation(s)
- Richard S Pollenz
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Kaylee Barnhill
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Abbigail Biggs
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Jackson Bland
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Victoria Carter
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Michael Chase
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Hayley Clark
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Caitlyn Coleman
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Marshall Daffner
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Caitlyn Deam
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Alyssa Finocchiaro
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Vanessa Franco
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Thomas Fuller
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Juan Gallardo Pinera
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Mae Horne
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Zoe Howard
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Olivia Kanahan
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | | | - Sydney Miller
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Ryan Morgan
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Oluwatobi Onalaja
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Louis Otero
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Shivani Padhye
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emily Rainey
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Fareed Rasul
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Kobe Robichaux
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Alexandra Rodier
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Sydni Schlosser
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Ava Sciacchitano
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emma Stewart
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Rajvi Thakkar
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Danielle M Heller
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
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11
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Bearhart JM, Bethke JL, Christian CS, Cour FN, Creasey KR, Crowe EJ, Dahl JG, Hanson LA, Jaecks AL, Lamantia VA, Madison M, Roskowiak AL, Scheberl JD, VanEperen BM, Wurst ME, Klyczek KK. Complete genome sequence of Microbacterium paraoxydans phage Damascus. Microbiol Resour Announc 2024; 13:e0128723. [PMID: 38624212 PMCID: PMC11080557 DOI: 10.1128/mra.01287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Phage Damascus was isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The Damascus genome is 56,477 bp with 3' single-stranded overhangs and 56.5% G+C content. Damascus was assigned to cluster EL and shares 42.6%-91.7% gene content with the three other phages in this cluster.
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Affiliation(s)
- Julisa M. Bearhart
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Jenna L. Bethke
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Cassie S. Christian
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Faith N. Cour
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Karleigh R. Creasey
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Emily J. Crowe
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Julia G. Dahl
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Lindsey A. Hanson
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Abby L. Jaecks
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Vincent A. Lamantia
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Mercedes Madison
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Autumn L. Roskowiak
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Justin D. Scheberl
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Bekkah M. VanEperen
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Morgan E. Wurst
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Karen K. Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
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12
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Valentin Caban K, Kalesnik E, Green KA, Negro CJ, Nunez Rodriguez U, Peele MC, Nguyen CT, Cahill S, Dougherty K, Logue M, Hargraves S, Radziak H, Willette L, Ogunyinka E, Campbell DC, Adebamiro O, Schmeltzer C, Onimus J, Asaka HA, Bangura W, Shimp CM, Alade A, Sequira DM, Jimenez T, Swerdlow SJ, Harrison MK, Fallest-Strobl PC, Mastropaolo MD. Complete genome sequences of seven Microbacterium foliorum phages Albedo, Kenzers, Swervy, Cranjis, JaimeB, Fullmetal, and Stormbreaker. Microbiol Resour Announc 2024; 13:e0125123. [PMID: 38451225 PMCID: PMC11008123 DOI: 10.1128/mra.01251-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Seven bacteriophages were isolated from soil in Pennsylvania and Wisconsin using the host Microbacterium foliorum. These bacteriophages range in the number of predicted genes encoded, from 25 to 91, and are distributed across actinobacteriophage clusters EB, EC, EE, and EK.
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Affiliation(s)
| | | | | | | | | | | | | | - Sydney Cahill
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | - Melissa Logue
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | | | - Luke Willette
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | | | | | | | | | | | | | | | - Ameera Alade
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | | | - Tommy Jimenez
- Sciences, Neumann University, Aston, Pennsylvania, USA
| | - Neumann University Phage Discovery Group
- Sciences, Neumann University, Aston, Pennsylvania, USA
- Biological Sciences, University of Pittsburgh Greensburg, Greensburg, Pennsylvania, USA
- Sciences, Cabrini University, Radnor, Pennsylvania, USA
| | - Sarah J. Swerdlow
- Biological Sciences, University of Pittsburgh Greensburg, Greensburg, Pennsylvania, USA
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13
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Baumgartner BM, Bono KA, McIntosh DR, Vu AM, Adams CF, Benik BC, Chavez J, Gresky SJ, Sotelo A, Ray JI, Peister A, Kimberley KW, McKenna CC, Theoret JR, Yoon EJ, Windsor EJ. Genome sequences of actinobacteriophages JorRay, Blocker23, Nibbles, and OlgasClover. Microbiol Resour Announc 2024; 13:e0125623. [PMID: 38445868 PMCID: PMC11008117 DOI: 10.1128/mra.01256-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
JorRay, Blocker23, Nibbles, and OlgasClover are actinobacteriophages belonging to clusters G1, B2, CT, and DJ, respectively. JorRay and Blocker23 were identified in host bacterium Mycobacterium smegmatis mc2155. Nibbles and OlgasClover were identified in host bacterium Gordonia rubripertincta NRRL B-16540.
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Affiliation(s)
| | - Kayla A. Bono
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Dawn R. McIntosh
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Anna M. Vu
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Chanel F. Adams
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Brooklyn C. Benik
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Jessica Chavez
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Samantha J. Gresky
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Andres Sotelo
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Jordan I. Ray
- Department of Biology, Morehouse College, Atlanta, Georgia, USA
| | | | - Kendra W. Kimberley
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Chelsey C. McKenna
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - James R. Theoret
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Earl J. Yoon
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Erin J. Windsor
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
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14
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Tatum B, Murray P, Bicknell C, Webb SA, Kanak A. Genome sequence and annotation of Arthrobacter globiformis phage Ruchi (AS1) isolated from soil in Lumpkin County, Georgia. Microbiol Resour Announc 2024; 13:e0122423. [PMID: 38466103 PMCID: PMC11008183 DOI: 10.1128/mra.01224-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
Ruchi, a temperate, AS1 subcluster bacteriophage isolated in Lumpkin County, Georgia using host Arthrobacter globiformis, possesses a genome of 38,571 bp and 67.7% GC. Annotation of this virus revealed 64 predicted reading frames, no predicted tRNA genes, and a close evolutionary relationship to AS1 phage Basilisk.
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Affiliation(s)
- Brooke Tatum
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Payton Murray
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Claire Bicknell
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Shane A. Webb
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Alison Kanak
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
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15
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Kumar SV, Schaffer N, Bharmal Z, Mood Q, Erill I, Caruso SM. Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using Streptomyces mirabilis NRRL B-2400 in Columbia, MD. Microbiol Resour Announc 2024; 13:e0006824. [PMID: 38394246 PMCID: PMC11008112 DOI: 10.1128/mra.00068-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Here, we present bacteriophage SoJo, a siphovirus infecting Streptomyces mirabilis, with a circularly permuted genome of 39 kbp and GC content of 71.5%. Its genome length and content are similar to that of other phages in the Actinobacteriophage Database BC cluster. SoJo was isolated from soil in Columbia, MD, USA.
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Affiliation(s)
- Soven Verma Kumar
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Nicholas Schaffer
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Zainab Bharmal
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Quinn Mood
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | | | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Departament d’Enginyeria de la Informació i de les Comunicacions, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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16
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Bailey DS, Dotson DR, Berkes C, Agbede O, Augustin M, Blackman-Murray I, Chambers T, Felber N, Fleming D, Frazier L, Gray N, Harrison A, Hernandez G, Iwuchukwu N, Iwuji C, Jackson T, Jefferson A, Jordan D, Jordan M, Nicolas B, Person M, Richardson G, Roman A, Stevens C, Suggs M, Thompson N, Timmons-Smith S, Wilfong S, Wilson-Wheatley M. Complete genome sequence of Mycobacterium smegmatis phage Rummer, a subcluster A3 actinophage. Microbiol Resour Announc 2024; 13:e0126823. [PMID: 38466105 PMCID: PMC11008113 DOI: 10.1128/mra.01268-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Bacteriophage Rummer is a siphovirus morphology actinophage isolated from Mycobacterium smegmatis. Rummer has a 50,908 base pair genome encoding 89 predicted protein-coding genes and three tRNAs. Based on gene content similarity to sequenced actinobacteriophages, Rummer is assigned to phage subcluster A3.
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Affiliation(s)
- Dondra S. Bailey
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Dominique R. Dotson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Charlotte Berkes
- Department of Biology, Merrimack College, North Andover, Massachusetts, USA
| | - Oluwanifemi Agbede
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Marcelaine Augustin
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | | | - Talaeya Chambers
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nicolas Felber
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Dy'Mon Fleming
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Loretta Frazier
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Natalie Gray
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ayanna Harrison
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Genesis Hernandez
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nina Iwuchukwu
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Chika Iwuji
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Taysha Jackson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Angelic Jefferson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Daya Jordan
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Miracle Jordan
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Brian Nicolas
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Monae Person
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ga'Nayah Richardson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ashley Roman
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Christian Stevens
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - My'Sean Suggs
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nahshon Thompson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Summer Timmons-Smith
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Shiaishea Wilfong
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
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17
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Adams RM, Britton HA, Bruce ED, De La Paz Y, Kratz EN, Pfeifer EJ, Priddy DE, Schotter BI, Stuffle WA, Wagner J, Weiss MR, Watt DK, Connerly PL, Rueschhoff EE. Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta . Microbiol Resour Announc 2024; 13:e0120423. [PMID: 38526095 PMCID: PMC11008160 DOI: 10.1128/mra.01204-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/03/2024] [Indexed: 03/26/2024] Open
Abstract
Novel actinobacteriophage Soos was isolated and purified from Southern Indiana soil using host Gordonia rubripertincta NRRL B-16540. Sequencing revealed a 57,509 bp circularly permuted genome encoding 87 predicted protein-coding genes. Soos is only the third phage in cluster CP, along with phages Clawz and Sting.
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Affiliation(s)
- Reese M. Adams
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Holly A. Britton
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emily D. Bruce
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Yucita De La Paz
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emily N. Kratz
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emma J. Pfeifer
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Daisy E. Priddy
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Brooklyn I. Schotter
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Wyatt A. Stuffle
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Jordyn Wagner
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Meredith R. Weiss
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Danielle K. Watt
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Pamela L. Connerly
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
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18
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Easterwood JC, Katsanos JM, Lloyd J. The genomic characterization of three Microbacterium foliorum-specific bacteriophages, "Nucci," "MCubed," and "QMacho". Microbiol Resour Announc 2024; 13:e0020324. [PMID: 38597796 PMCID: PMC11080523 DOI: 10.1128/mra.00203-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Nucci, MCubed, and QMacho are microbacteriophages that were isolated from soil samples in Charlotte, NC. They were classified into EA10, EA2, and EB clusters, respectively. Nucci and MCubed each had 63 predicted genes, while QMacho had 73 predicted genes.
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Affiliation(s)
| | | | - Jenna Lloyd
- Department of Biology, Queens University of Charlotte, Charlotte, North Carolina, USA
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19
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Willner DL, Paudel S, Halleran AD, Solini GE, Gray V, Saha MS. Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1. BMC Microbiol 2024; 24:107. [PMID: 38561651 PMCID: PMC10986025 DOI: 10.1186/s12866-024-03241-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process. RESULTS By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host's regulatory mechanisms to create an environment conducive for virion production. CONCLUSIONS The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.
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Affiliation(s)
- Dana L Willner
- Data Science Program, William & Mary, Williamsburg, VA, USA
| | - Sudip Paudel
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Wyss Institute, Harvard University, Cambridge, MA, USA
| | - Andrew D Halleran
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Atalaya Capital Management, New York, NY, USA
| | - Grace E Solini
- Department of Biology, William & Mary, Williamsburg, VA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - Veronica Gray
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Georgetown University School of Medicine, Washington, DC, USA
| | - Margaret S Saha
- Department of Biology, William & Mary, Williamsburg, VA, USA.
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20
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Chuhran L, Whitlow C, Teems C, Kanak A, Webb SA. Genome sequence and annotation of Arthrobacter globiformis phage Vulpecula (AS1) isolated from soil in Dahlonega, Georgia. Microbiol Resour Announc 2024; 13:e0009024. [PMID: 38385671 DOI: 10.1128/mra.00090-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
Vulpecula, a temperate bacteriophage collected from soil in Dahlonega, Georgia using host Arthrobacter globiformis, is an AS1 subcluster virus of 37,766 bp (67.7% GC). Genome annotation suggests 64 open reading frames, no predicted tRNA genes, and ~98% sequence similarity to AS1 phages Ruchi (from GA) and Jamun (New Hampshire).
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Affiliation(s)
- Lily Chuhran
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Chase Whitlow
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Carson Teems
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Alison Kanak
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Shane A Webb
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
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21
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Diggins AE, Gubitose MG, Hinrichsen EG, Jones PT, Kearns BS, Lord CE, Parsons MT, Pitt RA, Woods IA, Zarakotas TR, Wilkes BM. Genome sequence of Arthrobacter globiformis phage MaGuCo. Microbiol Resour Announc 2024; 13:e0117923. [PMID: 38376341 DOI: 10.1128/mra.01179-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
MaGuCo is a temperate phage isolated from soil collected in Alton, NH, USA, using Arthrobacter globiformis. Its genome is 43,924 base pairs long and contains 63 protein-encoding genes, 44 of which were assigned putative functions. MaCuGo is assigned to cluster AZ2 based on gene content similarity to actinobacteriophages.
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Affiliation(s)
- Amanda E Diggins
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Mary G Gubitose
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Elijah G Hinrichsen
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Patrick T Jones
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Brian S Kearns
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Caitlynn E Lord
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Mary T Parsons
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Rachel A Pitt
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Isabella A Woods
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Teagan R Zarakotas
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Beth M Wilkes
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
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22
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Migueletti MR, García Rey J, Micheloni J, Lomanto C, Martelli E, Sánchez G, Colombo JM, Vallecillo LM, Lamagni F, Giusti T, Acosta F, Villagrán F, Gvozdenovich M, Pricco Frakich A, Pianesi T, Tulin G, Mascali FC, Petitti TD, Torres Manno MA, Fusari CM, Buttigliero L, Giordana MF, Gramajo H, Diacovich L, Espariz M, Mussi MA. Complete genome sequence of the Microbacterium foliorum bacteriophage Garey24. Microbiol Resour Announc 2024; 13:e0121523. [PMID: 38315107 DOI: 10.1128/mra.01215-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in Funes, Argentina. Its 41,522 bp circularly permuted genome contains 63 putative protein-coding genes. Based on gene content similarity, Garey24 was assigned to subcluster EA1.
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Affiliation(s)
- Matías R Migueletti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julieta García Rey
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Josefina Micheloni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Camila Lomanto
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Elisa Martelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gastón Sánchez
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julián M Colombo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano M Vallecillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Francisco Lamagni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Giusti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Fabrina Acosta
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Franco Villagrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Gvozdenovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Abril Pricco Frakich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tulio Pianesi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gonzalo Tulin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia C Mascali
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás D Petitti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariano A Torres Manno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Corina M Fusari
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | | | - Hugo Gramajo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Espariz
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Alejandra Mussi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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23
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Oliveros AM, McDougall SA, Snyder MA, Snowden SK, Richard JD, Rao CM, Ponce M, Pitonza CJ, Ozcelik M, Mannina SS, Magna JR, Lopez AS, Gustafson LC, Glackin BK, Dolge AE, DeLancy ND, Davis ABC, Davis TP, Blagodar M, Natale SN, Dennis MK, Godin EA. Genome sequence of bacteriophage Djungelskog isolated from an Arthrobacter globiformis culture. Microbiol Resour Announc 2024; 13:e0129423. [PMID: 38376224 DOI: 10.1128/mra.01294-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Actinobacteriophage Djungelskog was isolated from a sample of degraded organic material in Poughkeepsie, NY, using Arthrobacter globiformis B-2979. Its genome is 54,512 bp and encodes 86 putative protein-coding genes. Djungelskog has a siphovirus morphology and is assigned to cluster AW based on gene content similarity to actinobacteriophages.
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Affiliation(s)
| | | | - Miles A Snyder
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sara K Snowden
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Joseph D Richard
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Marybeth Ponce
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Mira Ozcelik
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sofia S Mannina
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Juliana R Magna
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Andrew S Lopez
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Brynn K Glackin
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Abigail E Dolge
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Nate D DeLancy
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Andrew B C Davis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Thomas P Davis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Max Blagodar
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sydney N Natale
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Megan K Dennis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
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24
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Bass S, Coates D, Frasketi N, James S, Marella V, Pulla R, Stoecker K, Tupurani S, Johnson AA. Complete genome sequences of mycobacteriophages Ageofdapage, Aubs, BABullseye, CheetoDust, ShaboiShabazz, and TomBrady. Microbiol Resour Announc 2024; 13:e0125323. [PMID: 38334400 DOI: 10.1128/mra.01253-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
We report genome sequences of six mycobacteriophages. Each virus was isolated from a soil sample and belongs to the siphovirus morphology. Genomes are 41,901-60,613 bp in length, contain between 62 and 103 protein-coding genes, with up to 40% of those genes having a predicted function.
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Affiliation(s)
- Shelbie Bass
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Danielle Coates
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Nina Frasketi
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Smeetha James
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Vishnu Marella
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Riya Pulla
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Kyle Stoecker
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Srichandra Tupurani
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Allison A Johnson
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, Virginia, USA
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25
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Ngove Z, Matthews R, Goedken J, Huntington S, Kirkle L, Coleman ST. Complete genome sequences of bacteriophages Guetzie and SirVictor, isolated from Microbacterium foliorum. Microbiol Resour Announc 2024; 13:e0107423. [PMID: 38294214 DOI: 10.1128/mra.01074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/21/2024] [Indexed: 02/01/2024] Open
Abstract
Cluster EA4 Guetzie and SirVictor are lytic siphoviral bacteriophages that were isolated from soil in Waverly, Iowa, using Microbacterium foliorum NRRL B-24224 as the host. The Guetzie and SirVictor genomes are both 39,758 bp each, and both contain 58 predicted protein-coding genes with one tRNA gene each.
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Affiliation(s)
- Zefanias Ngove
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | | | - Jack Goedken
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | | | - Lauren Kirkle
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | - Sean T Coleman
- Biology Department, Wartburg College, Waverly, Iowa, USA
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26
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Westover KM, Atkinson AR, Bowers AG, Brown AL, Ferebee JC, Keisler CA, Lee KL, Payton AO, Peralta LA, Phu JV, Pollock KA, Scott MG, Vaughan BE, Wilczak KM, Frost VJ. Complete genome sequences of Mycobacterium smegmatis phages Ashballer and Bombitas. Microbiol Resour Announc 2024; 13:e0099023. [PMID: 38231182 PMCID: PMC10868224 DOI: 10.1128/mra.00990-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
We report the discovery of two mycobacteriophages isolated from soil in Rock Hill, South Carolina. Ashballer has a genome sequence length of 52,231 bp, while Bombitas is relatively larger at 110,129 bp. Both have siphovirus morphologies and have temperate lifecycles.
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Affiliation(s)
- Kristi M. Westover
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Alexis R. Atkinson
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Abby G. Bowers
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Amaya L. Brown
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - James C. Ferebee
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Chase A. Keisler
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Kaylyn L. Lee
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Amaya O. Payton
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Lidia A. Peralta
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Julianne V. Phu
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Khamryn A. Pollock
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Maya G. Scott
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Bryson E. Vaughan
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Karissa M. Wilczak
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
| | - Victoria J. Frost
- Department of Biology, Winthrop University, Rock Hill, South Carolina, USA
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27
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Prout AE, Swerdlow SJ. Genome sequences of Microbacterium foliorum phages, BabyYoda and Lynlen. Microbiol Resour Announc 2024; 13:e0100623. [PMID: 38132671 PMCID: PMC10871031 DOI: 10.1128/mra.01006-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BabyYoda and Lynlen are two cluster EB phages that were discovered at Thiel College using Microbacterium foliorum NRRL B-24224. Both BabyYoda and Lynlen are predicted to be lytic, with siphovirus morphologies, with genome sizes of 41,557 and 41,448 base pairs, respectively.
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Affiliation(s)
- Ashley E. Prout
- Biology Department, Thiel College, Greenville, Pennsylvania, USA
| | - Sarah J. Swerdlow
- Department of Natural Sciences-Biological Sciences, University of Pittsburgh-Greensburg, Greensburg, Pennsylvania, USA
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28
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Makhoul JC, Valentine M, Campbell C, McLaughlin EG, Vereline FH, Collins JM, Crandall SIG, Rabideau EL, Tender WJ, Fairweather SL, Miller CJ, Mcleish KQY, Izquierdo JD, Gallagher LN, Tyrrell LP, Gleichsner AM. Genome sequence of Microbacterium foliorum phage CandC. Microbiol Resour Announc 2024; 13:e0111723. [PMID: 38231186 PMCID: PMC10868228 DOI: 10.1128/mra.01117-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024] Open
Abstract
We report the discovery and genome sequence of CandC, a lytic bacteriophage with siphovirus morphology. CandC was isolated from a soil sample from Plattsburgh, NY, USA (Fall 2021). It has a genome size of 62,344 bp with 106 predicted protein-encoding genes, 30 of which are assigned putative functions.
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Affiliation(s)
- Joëlle C. Makhoul
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Megan Valentine
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Caila Campbell
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Emma G. McLaughlin
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Frank H. Vereline
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Jenna M. Collins
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Sophia I. G. Crandall
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Emma L. Rabideau
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Wesley J. Tender
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Shaniah L. Fairweather
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Carson J. Miller
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Kori Q. Y. Mcleish
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Justin D. Izquierdo
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Leah N. Gallagher
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Luke P. Tyrrell
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Alyssa M. Gleichsner
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
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29
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Andro MN, Cansler AJJ, Conley OS, Cruz NO, Dionne JA, Edwards JI, Furtuna D, Green CJ, Huber M, Hudson GJ, Humphries IR, Karazin AA, Mombille PI, Pell MM, Shickle G, Shipp ZJ, Timmons CA, Trembush JI, Turnmire CD, Yemofio NY, Burleson MD, Gainey MD. From Cullowhee Creek to Conley: genome sequence and annotation of a cluster DJ Gordonia phage. Microbiol Resour Announc 2024; 13:e0117623. [PMID: 38133170 PMCID: PMC10868162 DOI: 10.1128/mra.01176-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
We report the discovery of Gordonia phage Conley, a siphovirus isolated from Cullowhee Creek in the Fall of 2022. The 60,078bp genome contains 90 predicted protein-coding genes all transcribed in the same direction and has been assigned to genetic cluster DJ based on gene content similarity.
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Affiliation(s)
- Mindy N. Andro
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - AJ J. Cansler
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Olivia S. Conley
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Naidelyn O. Cruz
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Joshua A. Dionne
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Jordan I. Edwards
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Daniel Furtuna
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Carlee J. Green
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Miriam Huber
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Gunnar J. Hudson
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Isabella R. Humphries
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Amanda A. Karazin
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Patrizia I. Mombille
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Montana M. Pell
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Gabriela Shickle
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Zahria J. Shipp
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Chloe A. Timmons
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Jasmine I. Trembush
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Cameron D. Turnmire
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Naa Yemoley Yemofio
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Mathew D. Burleson
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Maria D. Gainey
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
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30
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Alexander WK, Allen RR, Anderson JD, Brumfield AN, Cook TM, Dana GM, Ethridge GJ, Gailey EC, Netzley RA, Nguyen JV, Souza PJ, Yoder BM, Wallen JR, Gainey MD, Bates TC, Wisner EM. From compost to culver: genome sequence and annotation of a cluster CQ1 Gordonia phage. Microbiol Resour Announc 2024; 13:e0106623. [PMID: 38132830 PMCID: PMC10868165 DOI: 10.1128/mra.01066-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Phage Culver, with a siphovirus morphology, was isolated using Gordonia terrae CAG3. Culver is assigned to phage cluster CQ1 based on gene content similarity to actinobacteriophages. Notably, Culver is predicted to encode eight tRNAs, lysin A by two adjacent genes, and, unlike other CQ1 phages, two putative integrase genes.
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Affiliation(s)
- William K. Alexander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Rianna R. Allen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Jaden D. Anderson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Amber N. Brumfield
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Tiffany M. Cook
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Giana M. Dana
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Gregory J. Ethridge
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Emily C. Gailey
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Rebekah A. Netzley
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Joshua V. Nguyen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Phillip J. Souza
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Briggs M. Yoder
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Jamie R. Wallen
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Maria D. Gainey
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Tonya C. Bates
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Ellen M. Wisner
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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31
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Radersma MD, Lathrop G, Moleakunnel KC, Harlow LA, Baker AE, Chen AJ, Churu JG, Dole CA, Doorn SL, Hill EM, Howland A, Janvier A, Kramer CM, Minasian MJ, Nieze JR, Perezrios IK, Ramsey FJ, Seinen KL, Swierenga SK, Veenstra MM, Weaver GE, White AC, Yoon E, Wertz JT, DeJong RJ. Complete genome sequences of nine Rhodococcus equi phages. Microbiol Resour Announc 2024; 13:e0108823. [PMID: 38179906 PMCID: PMC10868187 DOI: 10.1128/mra.01088-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
We report genomes of nine phages isolated from Actinobacteria Rhodococcus equi NRRL B-16538. Six of these phages belong to actinobacteriophage cluster CR, which otherwise contains Gordonia phages; two form the CF cluster; and one is a singleton. Genome lengths are 62,017-80,980 bp with 63.9%-67.3% GC content.
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Affiliation(s)
- Myles D. Radersma
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Gabrielle Lathrop
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Luke A. Harlow
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Aerin E. Baker
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Alison J. Chen
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Jason G. Churu
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Carly A. Dole
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Sophia L. Doorn
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Ethan M. Hill
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Anna Howland
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Amanda Janvier
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Catie M. Kramer
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Matt J. Minasian
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Jocelyn R. Nieze
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Fiona J. Ramsey
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Katie L. Seinen
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | | | - Grace E. Weaver
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Esther Yoon
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - John T. Wertz
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Randall J. DeJong
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
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32
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Guerrero-Bustamante CA, Hatfull GF. Bacteriophage tRNA-dependent lysogeny: requirement of phage-encoded tRNA genes for establishment of lysogeny. mBio 2024; 15:e0326023. [PMID: 38236026 PMCID: PMC10865867 DOI: 10.1128/mbio.03260-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Bacteriophages are large and diverse components of the biosphere, and many phages are temperate. Upon infection, temperate phages can establish lysogeny in which a prophage is typically integrated into the bacterial chromosome. Here, we describe the phenomenon of tRNA-dependent lysogeny, a previously unrecognized behavior of some temperate phages. tRNA-dependent lysogeny is characterized by two unusual features. First, a phage-encoded tyrosine family integrase mediates site-specific recombination between a phage attP site and a bacterial attB site overlapping a host tRNA gene. However, attP and attB share only a short (~10 bp) common core such that a functional tRNA is not reconstructed upon integration. Second, the phage encodes a tRNA of the same isotype as the disrupted but essential host tRNA, complementing its loss, and consequently is required for the survival of lysogenic progeny. As expected, an integrase-defective phage mutant forms turbid plaques, and bacterial progeny are immune to superinfection, but they lack stability, and the prophage is rapidly lost. In contrast, a tRNA-defective phage mutant forms clear plaques and more closely resembles a repressor mutant, and lysogens are recovered only at very low frequency through the use of secondary attachment sites elsewhere in the host genome. Integration-proficient plasmids derived from these phages must also carry a cognate phage tRNA gene for efficient integration, and these may be useful tools for mycobacterial genetics. We show that tRNA-dependent lysogeny is used by phages within multiple different groups of related viruses and may be prevalent elsewhere in the broader phage community.IMPORTANCEBacteriophages are the most numerous biological entities in the biosphere, and a substantial proportion of phages are temperate, forming stable lysogens in which a prophage copy of the genome integrates into the bacterial chromosome. Many phages encode a variety of tRNA genes whose roles are poorly understood, although it has been proposed that they enhance translational efficiencies in lytic growth or that they counteract host defenses that degrade host tRNAs. Here, we show that phage-encoded tRNAs play key roles in the establishment of lysogeny of some temperate phages. They do so by compensating for the loss of tRNA function when phages integrate at an attB site overlapping a tRNA gene but fail to reconstruct the tRNA at the attachment junction. In this system of tRNA-dependent lysogeny, the phage-encoded tRNA is required for lysogeny, and deletion of the phage tRNA gives rise to a clear plaque phenotype and obligate lytic growth.
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Affiliation(s)
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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33
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Cao Yao JC, Garcia Cehic D, Quer J, Méndez JN, Gorrín AD, Hevia LG, Fernández MTT. Complete Genome Sequences of Four Mycobacteriophages Involved in Directed Evolution against Undisputed Mycobacterium abscessus Clinical Strains. Microorganisms 2024; 12:374. [PMID: 38399778 PMCID: PMC10893344 DOI: 10.3390/microorganisms12020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Phage therapy is still in its infancy, but it is increasingly promising as a future alternative for treating antibiotic-resistant bacteria. To investigate the effect of phages on Mycobacterium abscessus complex (MABC), we isolated 113 environmental phages, grown them to high titres, and assayed them on MABC clinical strains through the spot test. Of all the phages, only 16 showed killing activity. Their activity was so temperate to MABC that they could not generate any plaque-forming units (PFUs). The Appelmans method of directed evolution was carried out to evolve these 16 phages into more lytic ones. After only 11 of 30 rounds of evolution, every single clinical strain in our collection, including those that were unsusceptible up to this point, could be lysed by at least one phage. The evolved phages were able to form PFUs on the clinical strains tested. Still, they are temperate at best and require further training. The genomes of one random parental phage and three random evolved phages from Round 13 were sequenced, revealing a diversity of clusters and genes of a variety of evolutionary origins, mostly of unknown function. These complete annotated genomes will be key for future molecular characterisations.
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Affiliation(s)
- Juan Carlos Cao Yao
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
| | - Damir Garcia Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Hospital Universitari Vall d’Hebron, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (D.G.C.); (J.Q.)
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Hospital Universitari Vall d’Hebron, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (D.G.C.); (J.Q.)
- CIBER de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jesús Navas Méndez
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Alexis Dorta Gorrín
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Lorena García Hevia
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| | - María Teresa Tórtola Fernández
- Mycobacteria Unit, Clinical Laboratories, Microbiology Service, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
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34
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Stamm J, Merkle JA, Abernathy A, Ackerman E, Brown J, Harris A, Hoffman K, Hoskins A, Jahn A, Jones N, Kitch A, Mathavan N, Rose N, Taylor J. Complete genome sequences of Streptomyces griseus phages Spelly and Phredrick. Microbiol Resour Announc 2024; 13:e0104923. [PMID: 38112473 PMCID: PMC10793280 DOI: 10.1128/mra.01049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
We present the complete genome sequences of two viruses with siphovirus morphology, isolated from soils collected in Southwestern Indiana using the host Streptomyces griseus. Spelly is a BE2 cluster phage with a 131,347-bp genome. Phredrick is a BK1 cluster phage with a 128,873-bp genome.
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Affiliation(s)
- Joyce Stamm
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Julie A. Merkle
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ava Abernathy
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Elizabeth Ackerman
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - John Brown
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Abbey Harris
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Kayli Hoffman
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ashleigh Hoskins
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Abbie Jahn
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nathan Jones
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ashley Kitch
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nandini Mathavan
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nat Rose
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Joey Taylor
- Department of Biology, University of Evansville, Evansville, Indiana, USA
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35
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Anders KR, Abeyta A, Andrade CC, Bonilla CY, Braley AB, Bratt AG, Duncan KA, Hayes SG, Robinson CJ, Smith-Flores H, Ettinger ASH, Ettinger WF, Fay MM, Haydock J, McKenzie SK, Garlena RA, Russell DA, Poxleitner MK. Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc 2155 at room temperature. Microbiol Resour Announc 2024; 13:e0108623. [PMID: 38099681 DOI: 10.1128/mra.01086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024] Open
Abstract
We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-coding genes that have no close relatives among the actinobacteriophages.
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Affiliation(s)
- Kirk R Anders
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Antonio Abeyta
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Christy C Andrade
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Carla Y Bonilla
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Amanda B Braley
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Alexandra G Bratt
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Kaya A Duncan
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Stephen G Hayes
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Ciara J Robinson
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | | | | | | | - Marta M Fay
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Joseph Haydock
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Sean K McKenzie
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania, USA
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36
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Kim J, Herrera C, Aung WY, Gonzales Boyles GP, Chavez C, Cibulka M, Foley E, Guerra J, Kumar DBM, Levrant W, Lim L, Llanes J, O'Brien ZK, Pagaduan A, Richardson JA, Rosales K, Schrecengost J, Shin T, Strong-Lundquist G, Tat W, Vanderford F, Vrinceanu I, Wang V, Yang S, Strong C, Tsourkas PK, Regner K. Complete genome sequences of cluster F1 and cluster B1 Mycobacterium smegmatis phages Karhdo and Basato. Microbiol Resour Announc 2024; 13:e0093823. [PMID: 38051075 DOI: 10.1128/mra.00938-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023] Open
Abstract
We present the complete genome sequences of Mycobacterium smegmatis phages Karhdo and Basato, isolated in Clark County, Nevada. The phages were isolated and annotated by students enrolled in undergraduate research courses over two semesters at the University of Nevada, Las Vegas.
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Affiliation(s)
- Jireh Kim
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Carlos Herrera
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Wai Yan Aung
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Carmina Chavez
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Mona Cibulka
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Emma Foley
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Jose Guerra
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Willow Levrant
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Lewis Lim
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Jose Llanes
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Art Pagaduan
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Khristian Rosales
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Tommy Shin
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Winnie Tat
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Fritz Vanderford
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Vicky Wang
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Stephanie Yang
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Christy Strong
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Philippos K Tsourkas
- School of Medicine and Public Health, University of Wisconsin , Madison, Wisconsin, USA
| | - Kurt Regner
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
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37
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Carline KBR, Fleeharty MS, Fang L, Shijo M, Doherty MK, Riddick ZA, Royster MO, Stukes AR, Tchadi BV, Thomas AN, Williamson KE, Saha MS. Sequence analysis of Discoknowium, an A5 mycobacteriophage. Microbiol Resour Announc 2024; 13:e0092023. [PMID: 38047653 PMCID: PMC10793274 DOI: 10.1128/mra.00920-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Discoknowium is a temperate A5 bacteriophage that infects the bacterial host Mycobacterium smegmatis. Isolated from a rat fecal sample, Discoknowium's genome is 50,222 bp in length, contains 84 genes and 1 tRNA, and shares 82%-98% nucleotide identity with other A5 subcluster phages.
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Affiliation(s)
| | | | - Lin Fang
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | - Mahima Shijo
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | - Zoe A. Riddick
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | - Amiyah R. Stukes
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | - Alana N. Thomas
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | - Margaret S. Saha
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
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38
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Baliraine FW, Mathews KE, Livingston EG, Martinez CA, Donnelly OL, Pledger TM, Feroz T, Harbison ZJ, Schlimme SG, Andrade C, Salazar KN, Berryhill EC, DeLosSantos MM, Foree HL, Gicheru W, Jett AM, Mendez SN, Odebiyi TM, Pitman JI, Tan MJ, McLoud JD, Baliraine FN. Complete genome sequences and characteristics of mycobacteriophages Diminimus, Dulcita, Glaske16, and Koreni. Microbiol Resour Announc 2024; 13:e0101023. [PMID: 38063427 DOI: 10.1128/mra.01010-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
Complete genome sequences of four novel mycobacteriophages, Diminimus, Dulcita, Glaske16, and Koreni, isolated from soil are presented. All these bacteriophages belong to subcluster M1, except Koreni that belongs to subcluster A4. Moreover, all have siphovirus morphologies, with genome sizes ranging from 51,055 to 81,156 bp.
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Affiliation(s)
- Faith W Baliraine
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Kaitlyn E Mathews
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Emma G Livingston
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Clarissa A Martinez
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Olivia L Donnelly
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Taryn M Pledger
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Tadeen Feroz
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Zoe J Harbison
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Sarah G Schlimme
- Department of Electrical, Computer, and Biomedical Engineering, LeTourneau University , Longview, Texas, USA
| | - Camila Andrade
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Keren N Salazar
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Elise C Berryhill
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | | | - Hannah L Foree
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Wanjiru Gicheru
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Adrienne M Jett
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Sofia N Mendez
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Toluwalope M Odebiyi
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Jacob I Pitman
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Michael J Tan
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Josh D McLoud
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
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39
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Dojs M, Fleischacker C, Ackerman S, Boyle B, Feiring S, Fleischacker T, Frank J, Jackson S, Schaefbauer A, Vigness C, Webb R. Genome sequences of bacteriophage Shambre1 and Renna12, isolated from Arthrobacter globiformis. Microbiol Resour Announc 2024; 13:e0085823. [PMID: 38088575 DOI: 10.1128/mra.00858-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/18/2023] [Indexed: 01/18/2024] Open
Abstract
Bacteriophages Shambre1 and Renna12 were isolated from soil in Bismarck, ND, using Arthrobacter globiformis. Genomic characterization and analyses allowed Renna12 to be assigned to phage cluster AS3, while Shambre1, which is not closely related to any phage, is a singleton.
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Affiliation(s)
- Madeline Dojs
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | | | - Skylar Ackerman
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Blaise Boyle
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Shambre Feiring
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | | | - Jaycee Frank
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Sarah Jackson
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | | | - Corinna Vigness
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Rylie Webb
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
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40
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Cousins SR, Dufour GR, Law K, Nichols RM, Sladek BJ, Aniapam CR, Tarbox BP, Savage EF. Genome sequence of the lytic bacteriophage Alucard, a cluster EE actinophage. Microbiol Resour Announc 2024; 13:e0101723. [PMID: 38051077 DOI: 10.1128/mra.01017-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023] Open
Abstract
Bacteriophage Alucard is a lytic phage isolated from the soil collected in southern Maine on Microbacterium foliorum NRRL B-24224. Alucard has siphovirus morphology with a 17,363-bp genome encoding 25 putative genes. Based on gene content similarity to actinobacteriophages, Alucard is assigned to cluster EE.
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Affiliation(s)
- Samuel R Cousins
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Gemma R Dufour
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Kendra Law
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Robert M Nichols
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Bradi J Sladek
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | | | - Brian P Tarbox
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Emily F Savage
- Biology, Southern Maine Community College , South Portland, Maine, USA
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41
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Hyde JR, Armond T, Herring JA, Hope S, Grose JH, Breakwell DP, Pickett BE. Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria. Microbiol Spectr 2024; 12:e0282723. [PMID: 37991376 PMCID: PMC10783043 DOI: 10.1128/spectrum.02827-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.
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Affiliation(s)
- Jonathan R. Hyde
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Thomas Armond
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jacob A. Herring
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P. Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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42
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Turner D, Adriaenssens EM, Lehman SM, Moraru C, Kropinski AM. Bacteriophage Taxonomy: A Continually Evolving Discipline. Methods Mol Biol 2024; 2734:27-45. [PMID: 38066361 DOI: 10.1007/978-1-0716-3523-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with the National Center for Biotechnology Information (NCBI) and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.
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Affiliation(s)
- Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, UK
| | | | - Susan M Lehman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Cristina Moraru
- Department of The Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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43
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Bazinet N, Biro E, Geydoshek A, Hodgkin G, Jestel E, Klute E, MacDonald C, Russano M, Thatcher J, Neely MN, Molloy S. Characterization of the genomes of cluster CT Gordonia terrae phages, Horseradish and Yummy. Microbiol Resour Announc 2023; 12:e0074723. [PMID: 37982651 PMCID: PMC10720472 DOI: 10.1128/mra.00747-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023] Open
Abstract
The genomes of lytic, cluster CT Gordonia terrae phages, Horseradish and Yummy, are 45,764 and 45,878 bp in length, respectively, and each encodes 71 protein-coding genes. The genomes are identical in sequence with the exception of a 38-bp insertion/deletion in the minor tail protein, gp26.
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Affiliation(s)
- Nicole Bazinet
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Esther Biro
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Ashley Geydoshek
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Grace Hodgkin
- The Honors College, University of Maine, Orono, Maine, USA
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Eric Jestel
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Emily Klute
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Clare MacDonald
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Marcus Russano
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Jayson Thatcher
- The Honors College, University of Maine, Orono, Maine, USA
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Melody N. Neely
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Sally Molloy
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
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44
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Bansal D, Fazilat AZ, Genchev MV, Han S, Ho DY, Kumar A, Lam BJ, Le NQ, Lin RP, Lopez AJ, Lu NY, Marroquin M, Neemuchwala ZH, Seng WJ, Shah PT, Toliao JM, Bancroft CT. Genome sequences of Arthrobacter globiformis B-2979 phages MidnightRain and Gusanita. Microbiol Resour Announc 2023; 12:e0093623. [PMID: 37991359 PMCID: PMC10871062 DOI: 10.1128/mra.00936-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
Phages MidnightRain and Gusanita, with siphovirus morphology, were isolated on Arthrobacter globiformis B-2979. MidnightRain's genome consists of 53,674 bp, encoding 101 putative genes and 1 tRNA, whereas Gusanita's genome is 42,742 bp, encoding 68 putative genes and 2 tRNAs.
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Affiliation(s)
- Devansh Bansal
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Alexander Z. Fazilat
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Matthew V. Genchev
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Sanguk Han
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - David Y. Ho
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Amisha Kumar
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Brian J. Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Noah Q. Le
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Ryan P. Lin
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Amanda J. Lopez
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Nicole Y. Lu
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Marco Marroquin
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Zainab H. Neemuchwala
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - William J. Seng
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Priya T. Shah
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jason M. Toliao
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Christa T. Bancroft
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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45
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Haines I, Blakely J, Branson A, Estrada D, Fernandez Robles R, Fitzgerald K, Jeffers S, Leung T, Munoz J, Olivos A, Ramirez A, Smith C, Spere J, Tavarez I, Wood I, Zavala E, Arrighi M, Coronel-Galindo A, Dennis MK, Goppert M, Edwards D. Complete genome sequence of bacteriophage MrAaronian isolated from an Arthrobacter globiformis culture. Microbiol Resour Announc 2023; 12:e0077823. [PMID: 37933970 PMCID: PMC10720457 DOI: 10.1128/mra.00778-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023] Open
Abstract
Arthrobacteriophage MrAaronian contains a 54,509 bp DNA genome with 87 predicted protein-coding genes. MrAaronian has siphovirus morphology and was collected from a flowerbed soil sample in Poughkeepsie, NY, and isolated on an Arthrobacter globiformis B-2979 culture. MrAaronian has > 99% nucleotide identity with cluster AW arthrobacteriophages Michelle, Stayer, Sloopyjoe, and StarLord.
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Affiliation(s)
- Ian Haines
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Jessica Blakely
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Ashley Branson
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Diana Estrada
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | | | - Katelyn Fitzgerald
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Shelby Jeffers
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Timyee Leung
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Jasmine Munoz
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Ashley Olivos
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Anayeli Ramirez
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Caressa Smith
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Justin Spere
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Idaleth Tavarez
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Isabella Wood
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Ethan Zavala
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Madison Arrighi
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Megan K. Dennis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Marlee Goppert
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
| | - Dustin Edwards
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
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46
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Guerrero JA, Maldonado N, Mbajiofor EO, Ramirez L, Valencia MJ, Healy CD, Garza AA, Mizell SA, Jackson BN, Vargas Ayala M. Characterization and genome sequence of Microbacterium foliorum phage Morrigan, of cluster EA6 with siphovirus morphology. Microbiol Resour Announc 2023; 12:e0071923. [PMID: 37975671 PMCID: PMC10720499 DOI: 10.1128/mra.00719-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
Bacteriophage Morrigan, which was isolated from soil using Microbacterium foliorum NRRL B-24224, is lytic with siphovirus morphology. Morrigan's 40,509-bp genome has a GC content of 62.8% and 66 putative protein-coding genes, of which 31 could be assigned putative functions. Based on gene content similarity to actinobacteriophages, Morrigan is assigned to subcluster EA6.
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Affiliation(s)
- Jennifer A. Guerrero
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Nery Maldonado
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Emmanuella O. Mbajiofor
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Lisette Ramirez
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Mary Jo Valencia
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Creehan D. Healy
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Alejandro A. Garza
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Samantha A. Mizell
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Brianna N. Jackson
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Mayra Vargas Ayala
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
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47
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Bishop E, Earley W, Greco A, Hofseth E, Kinerson E, Lafayette B, Llanot-Arocho N, Mazen B, Cevasco M, Williams DC. Genome sequence and annotation of the B3 mycobacteriophage Phayeta. Microbiol Resour Announc 2023; 12:e0091523. [PMID: 38014973 PMCID: PMC10720561 DOI: 10.1128/mra.00915-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/29/2023] Open
Abstract
Mycobacteriophage Phayeta was extracted from soil near Myrtle Beach, South Carolina using Mycobacterium smegmatis as a host. Annotation of the 68,700 base-pair circularly permuted genome identified 104 predicted protein-encoding genes, 34 of which have functional assignments.
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Affiliation(s)
- Emily Bishop
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | - Warren Earley
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | - Alexandra Greco
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | - Emma Hofseth
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | - Emma Kinerson
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | - Brandon Lafayette
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | | | - Brittney Mazen
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | - Megan Cevasco
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
| | - Daniel C. Williams
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
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48
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McLean N, Jackson T, Govardhan Y, Dharanendiran A, Bost C, Brown F, Cowen B, Deselem J, Parkhurst N, Stewart J, Leonard J, Collins DP. Genome sequences of cluster GA phages Phonegingi and Dropshot. Microbiol Resour Announc 2023; 12:e0091823. [PMID: 38014965 PMCID: PMC10720569 DOI: 10.1128/mra.00918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Bacteriophages Phonegingi and Dropshot were isolated from soil in North Carolina using the host Microbacterium foliorum. Both phages have siphovirus morphologies. Based on gene content similarity to one another and to other actinobacteriophages, both phages are assigned to phage cluster GA.
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Affiliation(s)
- Natalie McLean
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Tabitha Jackson
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Yajat Govardhan
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Aditi Dharanendiran
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Caden Bost
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Frederick Brown
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Benjamin Cowen
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Jenna Deselem
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Nico Parkhurst
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Jacob Stewart
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Justin Leonard
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - D. Parks Collins
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
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49
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Wood PR, Sullivan EA, Mathison RT, Hepworth SM, Graves RS, Danklefsen B, Almahie O, Serna C, Hunt DJ, Brewster R, Bartholomew S, Shurley JF, Grinath AS, Thomas MA. Isolation and genome sequence annotation of SallyK, a newly discovered cluster EG bacteriophage infecting Microbacterium. Microbiol Resour Announc 2023; 12:e0094323. [PMID: 37991360 PMCID: PMC10720488 DOI: 10.1128/mra.00943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/15/2023] [Indexed: 11/23/2023] Open
Abstract
Discovered from soil in a flower planter in Pocatello, Idaho and using Microbacterium foliorum, SallyK is a lytic bacteriophage with a siphovirus morphology. It has a 62,883 bp-long genome with 103 putative genes. Based on gene content similarity to actinobacteriophages, SallyK is assigned to cluster EG.
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Affiliation(s)
- Paige R. Wood
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Emily A. Sullivan
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Rylee T. Mathison
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Sariah M. Hepworth
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - R. Scott Graves
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Breanna Danklefsen
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Omer Almahie
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Carlos Serna
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Dylan J. Hunt
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Reganne Brewster
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Skylar Bartholomew
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Jack F. Shurley
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Anna S. Grinath
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Michael A. Thomas
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
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50
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Amaya I, Edwards K, Wise BM, Bhattacharyya A, Pablo CHD, Mushrush E, Coats AN, Dao S, Dittmar G, Gore T, Jarva TM, Kenkebashvili G, Rathan-Kumar S, Reyes GM, Watts GL, Watts VK, Dubrow D, Lewis G, Stone BH, Xue B, Cresawn SG, Mavrodi D, Sivanathan V, Heller D. A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy. G3 (BETHESDA, MD.) 2023; 13:jkad240. [PMID: 37934806 PMCID: PMC10700055 DOI: 10.1093/g3journal/jkad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023]
Abstract
During infection, bacteriophages produce diverse gene products to overcome bacterial antiphage defenses, to outcompete other phages, and to take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing ∼25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known antimycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.
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Affiliation(s)
- Isabel Amaya
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Kaylia Edwards
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Bethany M Wise
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Ankita Bhattacharyya
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Clint H D Pablo
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Ember Mushrush
- Department of Biology, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Amber N Coats
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Sara Dao
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Grace Dittmar
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Taylor Gore
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Taiya M Jarva
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Giorgi Kenkebashvili
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Sudiksha Rathan-Kumar
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Gabriella M Reyes
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Garrett L Watts
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Victoria Kalene Watts
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Deena Dubrow
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Gabrielle Lewis
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Benjamin H Stone
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Bingjie Xue
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Steven G Cresawn
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Dmitri Mavrodi
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Viknesh Sivanathan
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Danielle Heller
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
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