{ "componentChunkName": "component---src-templates-article-page-js", "path": "/journals/biology/micropub-biology-002436", "result": {"data":{"article":{"manuscript":{"id":"d9bc3df2-581b-42c5-aa22-578a1945bf92","submissionTypes":["new finding"],"citations":[],"doi":"10.17912/micropub.biology.002436","dbReferenceId":null,"pmcId":null,"pmId":null,"proteopedia":null,"reviewPanel":null,"species":["bacteriophage"],"integrations":[],"corrections":null,"history":{"received":"2026-09-23T15:16:51.728Z","revisionReceived":"2026-10-22T21:25:43.734Z","accepted":"2026-10-31T01:55:57.930Z","published":"2026-11-04T23:02:58.909Z","indexed":"2026-11-18T23:02:58.909Z"},"versions":[{"id":"a8d2f944-4bf1-4523-bee3-08f6ec84fa01","decision":"revise","abstract":"

MamaT was isolated from a soil sample collected adjacent to an irrigation canal in Pocatello, Idaho, USA. The bacteriophage has a podovirus morphology, infects Microbacterium foliorum NRRL B-24224, and has been grouped with bacteriophages in cluster GI based on sequence similarity. The genome size is 16,854 bp with 53.8% GC content. The annotation of the genome provides evidence for 23 putative protein-coding genes, of which 12 have predicted functions based on sequence and structure analysis. While MamaT has no tRNA genes, it appears to have a unique prohead packaging RNA (pRNA) system that includes a putative noncoding pRNA component.

","acknowledgements":"

MamaT was isolated by Douglas B. Madlock and Idaho State University’s SEA-PHAGES class in fall semester 2024. We thank Billy Biederman, Graham Hatfull, Deborah Jacobs-Sera, Daniel Russell, and Vic Sivanathan for training and resources, and Rebecca Garlena & Daniel Russell for phage DNA sequencing and assembly. A special thanks to Jason Werth and Lisa McDougall from ISU’s Molecular Research Core Facility (MRCF) for their assistance with TEM imaging, troubleshooting DNA extraction, and helping with the assembly of genome sequences.

","authors":[{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["investigation","writing_originalDraft"],"email":"bellasuseno@isu.edu","firstName":"Isabella","lastName":"Edwin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0006-1090-5171"},{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["validation"],"email":"treytonharris@isu.edu","firstName":"Treyton","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0005-7981-4342"},{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["investigation","validation","writing_reviewEditing"],"email":"mthomas@isu.edu","firstName":"Michael","lastName":"Thomas","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-2982-0291"}],"awards":[{"awardId":"R25AI179573","funderName":"National Institute of Allergy and Infectious Diseases (United States)","awardRecipient":"Michael A. Thomas"}],"conflictsOfInterest":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[],"funding":"

This project was made possible by the ISU Bridges to Research Careers Program under NIH grant #R25AI179573, the ISU Department of Biological Sciences, the ISU Office for Research, and the Howard Hughes Medical Institute’s Science Education Alliance – Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES) program.

","image":{"url":"https://portal.micropublication.org/uploads/5fa60e87005132429e9615e8e20d7fb3.jpg"},"imageCaption":"

A) Podovirus morphology of MamaT with a mean capsid diameter of 35nm +/- 0 nm (n=5 phage particles examined). Image produced by a Zeiss EM900 TEM with an accelerating voltage of 80 kV and 1% uranyl acetate negative staining. B) The minimum free energy (MFE) structure of the putative pRNA fold (located between the stop codon of gp6 and the start codon of gp7), predicted by RNAfold. Colors reflect base-pair probabilities calculated from the partition function (red reflects high confidence).

","imageTitle":"

Characterization of MamaT

","methods":"

Sequence data was deposited in sequence read archive SRR33718591 and GenBank accession number PZ362296. For collection information, see PhagesDB/phages/MamaT.

","reagents":"

","patternDescription":"

Bacteriophages are exceedingly diverse but largely under-sampled (Dion et al., 2020). Because of this, great advances in bioengineering and biotherapy are anticipated from the continued discovery of novel phages with unique properties (Mu & Lawley, 2023). Here, we describe the isolation and genetic composition of MamaT, a bacteriophage that infects Microbacterium foliorum.

MamaT was isolated from a soil sample consisting of clay and decaying plant material, collected near the Portneuf River at the Price Road wetlands near McCammon, ID (42.622464 N, 112.169022 W) on August 27, 2024, using the following established procedures  (Adams et al., 2022; Zorawik et al., 2024). The soil sample was washed with PYCa liquid medium and the supernatant filtered with a 0.22-μm filter. The filtrate was inoculated with M. foliorum NRRL B-24224. After incubation with shaking at 30°C for 48 h, the culture was filtered (0.22-mm pore size), and the filtrate was plated using M. foliorum PYCa top agar overlays, resulting in plaques after incubation at 30°C for 48 h. Plaques were purified through three additional rounds of plating. A high-titer lysate (>1010 pfu/mL) was prepared for DNA sequencing and transmission electron microscopy (TEM). Negative-stain TEM revealed phages with podovirus morphology (Figure 1A). The lack of an identifiable tape measure protein in the genome supports the classification of this phage as a podovirus.

Promega Wizard DNA clean up kit was used to extract genomic DNA from a high-titer lysate. A sequencing library was then prepared using a NEB Ultra II library kit and sequenced on an Illumina NextSeq 1000 (XLEAP-PI kit), resulting in 922,020 single-end 100-bp reads with 1,825-fold coverage. Raw reads were trimmed with cutadapt 4.7 (using the option: –nXextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, yielding a single contig. Consed v29 was used to check for completeness and accuracy and determine phage termini, using default settings (Chung et al., 2017). MamaT’s genome length is 16,854 bp with a GC content of 53.8% (notably lower than the host, at 68.7%; Russell et al., 2019); the genome ends are characterized by having covalently bound terminal proteins.

The MamaT genome was auto-annotated by DNAmaster v5.23.6 (http://cobamide2.bio.pitt.edu) using Genemark v2.5 (Besemer and Borodovsky 2005) and Glimmer v3.0 (Delcher et al., 2008) and subsequently manually inspected and refined using PECAAN (http://discover.kbrinsgd.org), Phamerator v454 (Cresawn et al., 2011) for synteny analysis and Starterator (http://phages.wustl.edu/starterator/) to identify start sites by manually comparing to genes within the same protein family (pham) (Horton et al., 2024). To predict putative gene functions, the following tools were deployed: HHPred v2.0 (Soding et al., 2005), using the PDB_mmCIF70, Pfam v.36, and NCBI Conserved Domains databases; BLAST v2.13.0 (Altschul et al. 1990), using the Actinobacteriophage and NCBI non-redundant databases; and Phamerator, using Actino_draft database v578 (cutoff values were 10-7 for BLAST and probability >90% over >50% coverage for HHPred). AlphaFold 3 (Jumper et al. 2021) was used to identify putative function of minor tail proteins. No tRNAs were identified using Aragorn v1.2.41 (Laslett 2004) and tRNAscan-SE v2.0 (Lowe and Eddy 1997). Using default parameters, the annotation process resulted in the identification of 23 putative protein-coding genes, 12 of which could be assigned gene functions. MamaT was assigned to cluster GI based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, PhagesDB (https://phageDB.org) (Pope et al., 2017; Russell and Hatfull 2017).

MamaT is the fifth annotated bacteriophage within cluster GI, to date, which includes phages Curie (Horton et al., 2024) and PineapplePizza (LaBianca et al., 2023), and with substantial similarity to Bacillus phage φ29 (Xu et al., 2019). Interestingly, phage φ29 has a prohead packaging RNA (pRNA) system that includes a noncoding pRNA component along with genes associated with packaging DNA into the prohead. In MamaT, homologs to these genes include gp15 (terminase) and gp10 (portal protein), and a putative pRNA appears to reside between the stop codon of gp6 and the start codon of gp7 (nucleotide position 4,625 to 4,801). Folded with RNAfold (Gruber et al., 2008), the 177 nt putative pRNA segment is highly consistent with φ29 pRNA in both length (the full-length φ29 pRNA is ~174 nt) and secondary structure: a characteristic 5-way junction with a central hub, a stable closing stem at the 5′/3′ ends, an apical hairpin, and flexible loop regions at appropriate positions within a well-folded, thermodynamically stable RNA (Figure 1B). No conventional upstream promoter was identified in the intergenic space, consistent with the known internal promoter architecture of φ29-family pRNA genes. Sequence-level similarity to φ29 pRNA was not detected by BLAST, which is unsurprising given that pRNAs from different φ29-family phages (φ29, B103, GA-1, SF5) share very little sequence identity while maintaining the same overall fold.

","references":[{"reference":"

Adams BM, Adams JB, Brewster RL, Cutler MS, Davis AE, Gallegos AH, et al., Thomas MA. 2022. Annotation of the Complete Genome Sequences of Bacteriophages Sara and Birdfeeder. Microbiol Resour Announc 11(10): e0078022.

","pubmedId":"36121218","doi":""},{"reference":"

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.

","pubmedId":"2231712","doi":""},{"reference":"

Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33(Web Server issue): W451-4.

","pubmedId":"15980510","doi":""},{"reference":"

Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics 18(1): 350.

","pubmedId":"28472946","doi":""},{"reference":"

Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 395.

","pubmedId":"21991981","doi":""},{"reference":"

Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6): 673-9.

","pubmedId":"17237039","doi":""},{"reference":"

Dion MrB, Oechslin F, Moineau S. 2020. Phage diversity, genomics and phylogeny. Nature Reviews Microbiology 18: 125-138.

","pubmedId":"","doi":"10.1038/s41579-019-0311-5"},{"reference":"

Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Research 36: W70-W74.

","pubmedId":"","doi":"10.1093/nar/gkn188 "},{"reference":"

Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.

","pubmedId":"","doi":"doi.org/10.1101/2022.04.08.487609"},{"reference":"

Hardies SC, Thomas JA, Black L, Weintraub ST, Hwang CY, Cho BC. 2016. Identification of structural and morphogenesis genes of Pseudoalteromonas phage φRIO-1 and placement within the evolutionary history of Podoviridae. Virology 489: 116-27.

","pubmedId":"26748333","doi":""},{"reference":"

Horton EN, Beach EK, Cook KT, Cronin KG, Haag AT, Salter SM, et al., Anders. 2024. Complete genome sequence of\n Microbacterium foliorum\n phage Curie, a podovirus isolated from soil in Spokane, Washington. Microbiology Resource Announcements 13: 10.1128/mra.00408-24.

","pubmedId":"","doi":"doi.org/10.1128/mra.00408-24"},{"reference":"

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al., Hassabis D. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596(7873): 583-589.

","pubmedId":"34265844","doi":""},{"reference":"

LaBianca K, Butura J, McKnight A, Pan K, Whelan S, Punska E, et al., Rocheleau. 2023. Complete genome sequence of phi29-like\n Microbacterium foliorum\n podovirus phage PineapplePizza. Microbiology Resource Announcements 12: 10.1128/mra.00478-23.

","pubmedId":"","doi":"doi.org/10.1128/MRA.00478-23"},{"reference":"

Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32(1): 11-6.

","pubmedId":"14704338","doi":""},{"reference":"

Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5): 955-64.

","pubmedId":"9023104","doi":""},{"reference":"

Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.

","pubmedId":"28811342","doi":""},{"reference":"

Pyra A, Urbańska N, Filik K, Tyrlik K, Brzozowska E. 2020. Biochemical features of the novel Tail Tubular Protein A of Yersinia phage phiYeO3-12. Sci Rep 10(1): 4196.

","pubmedId":"32144374","doi":""},{"reference":"

Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics 33(5): 784-786.

","pubmedId":"28365761","doi":""},{"reference":"

Russell DA, Garlena RA, Hatfull GF. 2019. Complete Genome Sequence of Microbacterium foliorum NRRL B-24224, a Host for Bacteriophage Discovery. Microbiol Resour Announc 8(5): 10.1128/MRA.01467-18.

","pubmedId":"30714032","doi":""},{"reference":"

Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue): W244-8.

","pubmedId":"15980461","doi":""},{"reference":"

Xu J, Wang D, Gui M, Xiang Y. 2019. Structural assembly of the tailed bacteriophage ϕ29. Nature Communications 10: 10.1038/s41467-019-10272-3.

","pubmedId":"","doi":"doi.org/10.1038/s41467-019-10272-3 "},{"reference":"

Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.

","pubmedId":"38526736","doi":""}],"title":"

Isolation and Genome Annotation of MamaT, a Cluster GI Bacteriophage with Podovirus Morphology

","reviews":[{"reviewer":{"displayName":"Rodney King"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"375b1904-6d23-407d-bd08-06205b1f3f30","decision":"accept","abstract":"

MamaT was isolated from a soil sample collected adjacent to an irrigation canal in Pocatello, Idaho, USA. The bacteriophage has a podovirus morphology, infects Microbacterium foliorum NRRL B-24224, and has been grouped with bacteriophages in cluster GI based on sequence similarity. The genome size is 16,854 bp with 53.8% GC content. The annotation of the genome provides evidence for 23 putative protein-coding genes, of which 12 have predicted functions based on sequence and structure analysis. While MamaT has no tRNA genes, it appears to have a unique prohead packaging RNA (pRNA) system that includes a putative noncoding pRNA component.

","acknowledgements":"

MamaT was isolated by Douglas B. Madlock and Idaho State University’s SEA-PHAGES class in fall semester 2024. We thank Billy Biederman, Graham Hatfull, Deborah Jacobs-Sera, Daniel Russell, and Vic Sivanathan for training and resources, and Rebecca Garlena & Daniel Russell for phage DNA sequencing and assembly. A special thanks to Jason Werth and Lisa McDougall from ISU’s Molecular Research Core Facility (MRCF) for their assistance with TEM imaging, troubleshooting DNA extraction, and helping with the assembly of genome sequences.

","authors":[{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["investigation","writing_originalDraft"],"email":"bellasuseno@isu.edu","firstName":"Isabella","lastName":"Edwin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0006-1090-5171"},{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["validation"],"email":"treytonharris@isu.edu","firstName":"Treyton","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0005-7981-4342"},{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["investigation","validation","writing_reviewEditing"],"email":"mthomas@isu.edu","firstName":"Michael","lastName":"Thomas","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-2982-0291"}],"awards":[{"awardId":"R25AI179573","funderName":"National Institute of Allergy and Infectious Diseases (United States)","awardRecipient":"Michael A. Thomas"}],"conflictsOfInterest":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[],"funding":"

This project was made possible by the ISU Bridges to Research Careers Program under NIH grant #R25AI179573, the ISU Department of Biological Sciences, the ISU Office for Research, and the Howard Hughes Medical Institute’s Science Education Alliance – Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES) program.

","image":{"url":"https://portal.micropublication.org/uploads/5fa60e87005132429e9615e8e20d7fb3.jpg"},"imageCaption":"

A) Podovirus morphology of MamaT with a mean capsid diameter of 35nm +/- 0 nm (n=5 phage particles examined). Image produced by a Zeiss EM900 TEM with an accelerating voltage of 80 kV and 1% uranyl acetate negative staining. B) The minimum free energy (MFE) structure of the putative pRNA fold (located between the stop codon of gp6 and the start codon of gp7), predicted by RNAfold. Colors reflect base-pair probabilities calculated from the partition function (red reflects high confidence).

","imageTitle":"

Characterization of MamaT

","methods":"

Sequence data was deposited in sequence read archive SRR33718591 and GenBank accession number PZ362296. For collection information, see PhagesDB/phages/MamaT.

","reagents":"

","patternDescription":"

Bacteriophages are exceedingly diverse but largely under-sampled (Dion et al., 2020). Because of this, great advances in bioengineering and biotherapy are anticipated from the continued discovery of novel phages with unique properties (Mu & Lawley, 2023). Here, we describe the isolation and genetic composition of MamaT, a bacteriophage that infects Microbacterium foliorum.

MamaT was isolated from a soil sample consisting of clay and decaying plant material, collected near the Portneuf River at the Price Road wetlands near McCammon, ID (42.622464 N, 112.169022 W) on August 27, 2024, using the following established procedures  (Adams et al., 2022; Zorawik et al., 2024). The soil sample was washed with PYCa liquid medium and the supernatant filtered with a 0.22-μm filter. The filtrate was inoculated with M. foliorum NRRL B-24224. After incubation with shaking at 30°C for 48 h, the culture was filtered (0.22-mm pore size), and the filtrate was plated using M. foliorum PYCa top agar overlays, resulting in plaques after incubation at 30°C for 48 h. Plaques were purified through three additional rounds of plating. A high-titer lysate (>1010 pfu/mL) was prepared for DNA sequencing and transmission electron microscopy (TEM). Negative-stain TEM revealed phages with podovirus morphology (Figure 1A). The lack of an identifiable tape measure protein in the genome supports the classification of this phage as a podovirus.

Promega Wizard DNA clean up kit was used to extract genomic DNA from a high-titer lysate. A sequencing library was then prepared using a NEB Ultra II library kit and sequenced on an Illumina NextSeq 1000 (XLEAP-PI kit), resulting in 922,020 single-end 100-bp reads with 1,825-fold coverage. Raw reads were trimmed with cutadapt 4.7 (using the option: –nXextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, yielding a single contig. Consed v29 was used to check for completeness and accuracy and determine phage termini, using default settings (Chung et al., 2017). MamaT’s genome length is 16,854 bp with a GC content of 53.8% (notably lower than the host, at 68.7%; Russell et al., 2019). Based on genomic synteny, sequence homology to known protein-priming phages, and an abrupt drop-off in raw sequencing read coverage at the genome boundaries, MamaT is predicted to possess a linear genome capped by covalently bound terminal proteins.

The MamaT genome was auto-annotated by DNAmaster v5.23.6 (http://cobamide2.bio.pitt.edu) using Genemark v2.5 (Besemer and Borodovsky 2005) and Glimmer v3.0 (Delcher et al., 2008) and subsequently manually inspected and refined using PECAAN (http://discover.kbrinsgd.org), Phamerator v454 (Cresawn et al., 2011) for synteny analysis and Starterator (http://phages.wustl.edu/starterator/) to identify start sites by manually comparing to genes within the same protein family (pham) (Horton et al., 2024). To predict putative gene functions, the following tools were deployed: HHpred v2.0 (Soding et al., 2005), using the PDB_mmCIF70, Pfam v.36, and NCBI Conserved Domains databases; BLAST v2.13.0 (Altschul et al. 1990), using the Actinobacteriophage and NCBI non-redundant databases; and Phamerator, using Actino_draft database v578 (cutoff values were 10-7 for BLAST and probability >90% over >50% coverage for HHpred). AlphaFold 3 (Jumper et al. 2021) was used to identify putative function of minor tail proteins. No tRNAs were identified using Aragorn v1.2.41 (Laslett 2004) and tRNAscan-SE v2.0 (Lowe and Eddy 1997). Using default parameters, the annotation process resulted in the identification of 23 putative protein-coding genes, 12 of which could be assigned gene functions. MamaT was assigned to cluster GI based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, PhagesDB (https://phageDB.org) (Pope et al., 2017; Russell and Hatfull 2017).

MamaT is the fifth annotated bacteriophage within cluster GI, to date, which includes phages Curie (Horton et al., 2024) and PineapplePizza (LaBianca et al., 2023), and with substantial similarity to Bacillus phage φ29 (Xu et al., 2019). Interestingly, phage φ29 has a prohead packaging RNA (pRNA) system that includes a noncoding pRNA component along with genes associated with packaging DNA into the prohead. In MamaT, homologs to these genes include gp15 (terminase) and gp10 (portal protein), and a putative pRNA appears to reside between the stop codon of gp6 and the start codon of gp7 (nucleotide position 4,625 to 4,801). Folded with RNAfold (Gruber et al., 2008), the 177 nt putative pRNA segment is highly consistent with φ29 pRNA in both length (the full-length φ29 pRNA is ~174 nt) and secondary structure: a characteristic 5-way junction with a central hub, a stable closing stem at the 5′/3′ ends, an apical hairpin, and flexible loop regions at appropriate positions within a well-folded, thermodynamically stable RNA (Figure 1B). No conventional upstream promoter was identified in the intergenic space, consistent with the known internal promoter architecture of φ29-family pRNA genes. Sequence-level similarity to φ29 pRNA was not detected by BLAST, which is unsurprising given that pRNAs from different φ29-family phages (φ29, B103, GA-1, SF5) share very little sequence identity while maintaining the same overall fold.

","references":[{"reference":"

Adams BM, Adams JB, Brewster RL, Cutler MS, Davis AE, Gallegos AH, et al., Thomas MA. 2022. Annotation of the Complete Genome Sequences of Bacteriophages Sara and Birdfeeder. Microbiol Resour Announc 11(10): e0078022.

","pubmedId":"36121218","doi":""},{"reference":"

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.

","pubmedId":"2231712","doi":""},{"reference":"

Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33(Web Server issue): W451-4.

","pubmedId":"15980510","doi":""},{"reference":"

Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics 18(1): 350.

","pubmedId":"28472946","doi":""},{"reference":"

Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 395.

","pubmedId":"21991981","doi":""},{"reference":"

Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6): 673-9.

","pubmedId":"17237039","doi":""},{"reference":"

Dion MrB, Oechslin F, Moineau S. 2020. Phage diversity, genomics and phylogeny. Nature Reviews Microbiology 18: 125-138.

","pubmedId":"","doi":"10.1038/s41579-019-0311-5"},{"reference":"

Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Research 36: W70-W74.

","pubmedId":"","doi":"10.1093/nar/gkn188 "},{"reference":"

Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.

","pubmedId":"","doi":"doi.org/10.1101/2022.04.08.487609"},{"reference":"

Hardies SC, Thomas JA, Black L, Weintraub ST, Hwang CY, Cho BC. 2016. Identification of structural and morphogenesis genes of Pseudoalteromonas phage φRIO-1 and placement within the evolutionary history of Podoviridae. Virology 489: 116-27.

","pubmedId":"26748333","doi":""},{"reference":"

Horton EN, Beach EK, Cook KT, Cronin KG, Haag AT, Salter SM, et al., Anders. 2024. Complete genome sequence of\n Microbacterium foliorum\n phage Curie, a podovirus isolated from soil in Spokane, Washington. Microbiology Resource Announcements 13: 10.1128/mra.00408-24.

","pubmedId":"","doi":"doi.org/10.1128/mra.00408-24"},{"reference":"

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al., Hassabis D. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596(7873): 583-589.

","pubmedId":"34265844","doi":""},{"reference":"

LaBianca K, Butura J, McKnight A, Pan K, Whelan S, Punska E, et al., Rocheleau. 2023. Complete genome sequence of phi29-like\n Microbacterium foliorum\n podovirus phage PineapplePizza. Microbiology Resource Announcements 12: 10.1128/mra.00478-23.

","pubmedId":"","doi":"doi.org/10.1128/MRA.00478-23"},{"reference":"

Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32(1): 11-6.

","pubmedId":"14704338","doi":""},{"reference":"

Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5): 955-64.

","pubmedId":"9023104","doi":""},{"reference":"

Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.

","pubmedId":"28811342","doi":""},{"reference":"

Pyra A, Urbańska N, Filik K, Tyrlik K, Brzozowska E. 2020. Biochemical features of the novel Tail Tubular Protein A of Yersinia phage phiYeO3-12. Sci Rep 10(1): 4196.

","pubmedId":"32144374","doi":""},{"reference":"

Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics 33(5): 784-786.

","pubmedId":"28365761","doi":""},{"reference":"

Russell DA, Garlena RA, Hatfull GF. 2019. Complete Genome Sequence of Microbacterium foliorum NRRL B-24224, a Host for Bacteriophage Discovery. Microbiol Resour Announc 8(5): 10.1128/MRA.01467-18.

","pubmedId":"30714032","doi":""},{"reference":"

Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue): W244-8.

","pubmedId":"15980461","doi":""},{"reference":"

Xu J, Wang D, Gui M, Xiang Y. 2019. Structural assembly of the tailed bacteriophage ϕ29. Nature Communications 10: 10.1038/s41467-019-10272-3.

","pubmedId":"","doi":"doi.org/10.1038/s41467-019-10272-3 "},{"reference":"

Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.

","pubmedId":"38526736","doi":""}],"title":"

Isolation and Genome Annotation of MamaT, a Cluster GI Bacteriophage with Podovirus Morphology

","reviews":[{"reviewer":{"displayName":"Rodney King"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"96e00e60-955e-493e-9b66-ce1091418507","decision":"edit","abstract":"

MamaT was isolated from a soil sample collected adjacent to an irrigation canal in Pocatello, Idaho, USA. The bacteriophage has a podovirus morphology, infects Microbacterium foliorum NRRL B-24224, and has been grouped with bacteriophages in cluster GI based on sequence similarity. The genome size is 16,854 bp with 53.8% GC content. The annotation of the genome provides evidence for 23 putative protein-coding genes, of which 12 have predicted functions based on sequence and structure analysis. While MamaT has no tRNA genes, it appears to have a unique prohead packaging RNA (pRNA) system that includes a putative noncoding pRNA component.

","acknowledgements":"

MamaT was isolated by Douglas B. Madlock and Idaho State University’s SEA-PHAGES class in fall semester 2024. We thank Billy Biederman, Graham Hatfull, Deborah Jacobs-Sera, Daniel Russell, and Vic Sivanathan for training and resources, and Rebecca Garlena & Daniel Russell for phage DNA sequencing and assembly. A special thanks to Jason Werth and Lisa McDougall from ISU’s Molecular Research Core Facility (MRCF) for their assistance with TEM imaging, troubleshooting DNA extraction, and helping with the assembly of genome sequences.

","authors":[{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["investigation","writing_originalDraft"],"email":"bellasuseno@isu.edu","firstName":"Isabella","lastName":"Edwin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0006-1090-5171"},{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["validation"],"email":"treytonharris@isu.edu","firstName":"Treyton","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0005-7981-4342"},{"affiliations":["Idaho State University"],"departments":["Biology"],"credit":["investigation","validation","writing_reviewEditing"],"email":"mthomas@isu.edu","firstName":"Michael","lastName":"Thomas","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-2982-0291"}],"awards":[{"awardId":"R25AI179573","funderName":"National Institute of Allergy and Infectious Diseases (United States)","awardRecipient":"Michael A. Thomas"}],"conflictsOfInterest":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[],"funding":"

This project was made possible by the ISU Bridges to Research Careers Program under NIH grant #R25AI179573, the ISU Department of Biological Sciences, the ISU Office for Research, and the Howard Hughes Medical Institute’s Science Education Alliance – Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES) program.

","image":{"url":"https://portal.micropublication.org/uploads/5fa60e87005132429e9615e8e20d7fb3.jpg"},"imageCaption":"

A) Podovirus morphology of MamaT with a mean capsid diameter of 35nm +/- 0 nm (n=5 phage particles examined). Image produced by a Zeiss EM900 TEM with an accelerating voltage of 80 kV and 1% uranyl acetate negative staining. B) The minimum free energy (MFE) structure of the putative pRNA fold (located between the stop codon of gp6 and the start codon of gp7), predicted by RNAfold. Colors reflect base-pair probabilities calculated from the partition function (red reflects high confidence).

","imageTitle":"

Characterization of MamaT

","methods":"

Sequence data was deposited in sequence read archive SRR33718591 and GenBank accession number PZ362296. For collection information, see PhagesDB/phages/MamaT.

","reagents":"

","patternDescription":"

Bacteriophages are exceedingly diverse but largely under-sampled (Dion et al., 2020). Because of this, great advances in bioengineering and biotherapy are anticipated from the continued discovery of novel phages with unique properties (Mu & Lawley, 2023). Here, we describe the isolation and genetic composition of MamaT, a bacteriophage that infects Microbacterium foliorum.

MamaT was isolated from a soil sample consisting of clay and decaying plant material, collected near the Portneuf River at the Price Road wetlands near McCammon, ID (42.622464 N, 112.169022 W) on August 27, 2024, using the following established procedures  (Adams et al., 2022; Zorawik et al., 2024). The soil sample was washed with PYCa liquid medium and the supernatant filtered with a 0.22-μm filter. The filtrate was inoculated with M. foliorum NRRL B-24224. After incubation with shaking at 30°C for 48 h, the culture was filtered (0.22-mm pore size), and the filtrate was plated using M. foliorum PYCa top agar overlays, resulting in plaques after incubation at 30°C for 48 h. Plaques were purified through three additional rounds of plating. A high-titer lysate (>1010 pfu/mL) was prepared for DNA sequencing and transmission electron microscopy (TEM). Negative-stain TEM revealed phages with podovirus morphology (Figure 1A). The lack of an identifiable tape measure protein in the genome supports the classification of this phage as a podovirus.

Promega Wizard DNA clean up kit was used to extract genomic DNA from a high-titer lysate. A sequencing library was then prepared using a NEB Ultra II library kit and sequenced on an Illumina NextSeq 1000 (XLEAP-PI kit), resulting in 922,020 single-end 100-bp reads with 1,825-fold coverage. Raw reads were trimmed with cutadapt 4.7 (using the option: –nXextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, yielding a single contig. Consed v29 was used to check for completeness and accuracy and determine phage termini, using default settings (Chung et al., 2017). MamaT's genome length is 16,854 bp with a GC content of 53.8% (notably lower than the host, at 68.7%; Russell et al., 2019). Based on genomic synteny, sequence homology to known protein-priming phages, and an abrupt drop-off in raw sequencing read coverage at the genome boundaries, MamaT is predicted to possess a linear genome capped by covalently bound terminal proteins.

The MamaT genome was auto-annotated by DNAmaster v5.23.6 (http://cobamide2.bio.pitt.edu) using Genemark v2.5 (Besemer and Borodovsky 2005) and Glimmer v3.0 (Delcher et al., 2008) and subsequently manually inspected and refined using PECAAN (http://discover.kbrinsgd.org), Phamerator v454 (Cresawn et al., 2011) for synteny analysis and Starterator (http://phages.wustl.edu/starterator/) to identify start sites by manually comparing to genes within the same protein family (pham) (Horton et al., 2024). To predict putative gene functions, the following tools were deployed: HHpred v2.0 (Soding et al., 2005), using the PDB_mmCIF70, Pfam v.36, and NCBI Conserved Domains databases; BLAST v2.13.0 (Altschul et al. 1990), using the Actinobacteriophage and NCBI non-redundant databases; and Phamerator, using Actino_draft database v578 (cutoff values were 10-7 for BLAST and probability >90% over >50% coverage for HHpred). AlphaFold 3 (Jumper et al. 2021) was used to identify putative function of minor tail proteins. No tRNAs were identified using Aragorn v1.2.41 (Laslett 2004) and tRNAscan-SE v2.0 (Lowe and Eddy 1997). Using default parameters, the annotation process resulted in the identification of 23 putative protein-coding genes, 12 of which could be assigned gene functions. MamaT was assigned to cluster GI based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, PhagesDB (https://phagesdb.org/) (Pope et al., 2017; Russell and Hatfull 2017).

MamaT is the fifth annotated bacteriophage within cluster GI, to date, which includes phages Curie (Horton et al., 2024) and PineapplePizza (LaBianca et al., 2023), and with substantial similarity to Bacillus phage φ29 (Xu et al., 2019). Interestingly, phage φ29 has a prohead packaging RNA (pRNA) system that includes a noncoding pRNA component along with genes associated with packaging DNA into the prohead. In MamaT, homologs to these genes include gp15 (terminase) and gp10 (portal protein), and a putative pRNA appears to reside between the stop codon of gp6 and the start codon of gp7 (nucleotide position 4,625 to 4,801). Folded with RNAfold (Gruber et al., 2008), the 177 nt putative pRNA segment is highly consistent with φ29 pRNA in both length (the full-length φ29 pRNA is ~174 nt) and secondary structure: a characteristic 5-way junction with a central hub, a stable closing stem at the 5′/3′ ends, an apical hairpin, and flexible loop regions at appropriate positions within a well-folded, thermodynamically stable RNA (Figure 1B). No conventional upstream promoter was identified in the intergenic space, consistent with the known internal promoter architecture of φ29-family pRNA genes. Sequence-level similarity to φ29 pRNA was not detected by BLAST, which is unsurprising given that pRNAs from different φ29-family phages (φ29, B103, GA-1, SF5) share very little sequence identity while maintaining the same overall fold.

","references":[{"reference":"

Adams BM, Adams JB, Brewster RL, Cutler MS, Davis AE, Gallegos AH, et al., Thomas MA. 2022. Annotation of the Complete Genome Sequences of Bacteriophages Sara and Birdfeeder. Microbiol Resour Announc 11(10): e0078022.

","pubmedId":"36121218","doi":""},{"reference":"

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.

","pubmedId":"2231712","doi":""},{"reference":"

Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33(Web Server issue): W451-4.

","pubmedId":"15980510","doi":""},{"reference":"

Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics 18(1): 350.

","pubmedId":"28472946","doi":""},{"reference":"

Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 395.

","pubmedId":"21991981","doi":""},{"reference":"

Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6): 673-9.

","pubmedId":"17237039","doi":""},{"reference":"

Dion MrB, Oechslin F, Moineau S. 2020. Phage diversity, genomics and phylogeny. Nature Reviews Microbiology 18: 125-138.

","pubmedId":"","doi":"10.1038/s41579-019-0311-5"},{"reference":"

Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Research 36: W70-W74.

","pubmedId":"","doi":"10.1093/nar/gkn188 "},{"reference":"

Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.

","pubmedId":"","doi":"doi.org/10.1101/2022.04.08.487609"},{"reference":"

Hardies SC, Thomas JA, Black L, Weintraub ST, Hwang CY, Cho BC. 2016. Identification of structural and morphogenesis genes of Pseudoalteromonas phage φRIO-1 and placement within the evolutionary history of Podoviridae. Virology 489: 116-27.

","pubmedId":"26748333","doi":""},{"reference":"

Horton EN, Beach EK, Cook KT, Cronin KG, Haag AT, Salter SM, et al., Anders. 2024. Complete genome sequence of\n Microbacterium foliorum\n phage Curie, a podovirus isolated from soil in Spokane, Washington. Microbiology Resource Announcements 13: 10.1128/mra.00408-24.

","pubmedId":"","doi":"doi.org/10.1128/mra.00408-24"},{"reference":"

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al., Hassabis D. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596(7873): 583-589.

","pubmedId":"34265844","doi":""},{"reference":"

LaBianca K, Butura J, McKnight A, Pan K, Whelan S, Punska E, et al., Rocheleau. 2023. Complete genome sequence of phi29-like\n Microbacterium foliorum\n podovirus phage PineapplePizza. Microbiology Resource Announcements 12: 10.1128/mra.00478-23.

","pubmedId":"","doi":"doi.org/10.1128/MRA.00478-23"},{"reference":"

Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32(1): 11-6.

","pubmedId":"14704338","doi":""},{"reference":"

Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5): 955-64.

","pubmedId":"9023104","doi":""},{"reference":"

Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.

","pubmedId":"28811342","doi":""},{"reference":"

Pyra A, Urbańska N, Filik K, Tyrlik K, Brzozowska E. 2020. Biochemical features of the novel Tail Tubular Protein A of Yersinia phage phiYeO3-12. Sci Rep 10(1): 4196.

","pubmedId":"32144374","doi":""},{"reference":"

Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics 33(5): 784-786.

","pubmedId":"28365761","doi":""},{"reference":"

Russell DA, Garlena RA, Hatfull GF. 2019. Complete Genome Sequence of Microbacterium foliorum NRRL B-24224, a Host for Bacteriophage Discovery. Microbiol Resour Announc 8(5): 10.1128/MRA.01467-18.

","pubmedId":"30714032","doi":""},{"reference":"

Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue): W244-8.

","pubmedId":"15980461","doi":""},{"reference":"

Xu J, Wang D, Gui M, Xiang Y. 2019. Structural assembly of the tailed bacteriophage ϕ29. Nature Communications 10: 10.1038/s41467-019-10272-3.

","pubmedId":"","doi":"doi.org/10.1038/s41467-019-10272-3 "},{"reference":"

Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.

","pubmedId":"38526736","doi":""}],"title":"

Isolation and Genome Annotation of MamaT, a Cluster GI Bacteriophage with Podovirus Morphology

","reviews":[],"curatorReviews":[]},{"id":"0ad0a53a-260e-42dd-8e27-3a4221b51d35","decision":"publish","abstract":"

MamaT was isolated from a soil sample collected adjacent to an irrigation canal in Pocatello, Idaho, USA. The bacteriophage has a podovirus morphology, infects Microbacterium foliorum NRRL B-24224, and has been grouped with bacteriophages in cluster GI based on sequence similarity. The genome size is 16,854 bp with 53.8% GC content. The annotation of the genome provides evidence for 23 putative protein-coding genes, of which 12 have predicted functions based on sequence and structure analysis. While MamaT has no tRNA genes, it appears to have a unique prohead packaging RNA (pRNA) system that includes a putative noncoding pRNA component.

","acknowledgements":"

MamaT was isolated by Douglas B. Madlock and Idaho State University’s SEA-PHAGES class in fall semester 2024. We thank Billy Biederman, Graham Hatfull, Deborah Jacobs-Sera, Daniel Russell, and Vic Sivanathan for training and resources, and Rebecca Garlena & Daniel Russell for phage DNA sequencing and assembly. A special thanks to Jason Werth and Lisa McDougall from ISU’s Molecular Research Core Facility (MRCF) for their assistance with TEM imaging, troubleshooting DNA extraction, and helping with the assembly of genome sequences.

","authors":[{"affiliations":["Idaho State University, Pocatello, ID, United States"],"departments":["Biology"],"credit":["investigation","writing_originalDraft"],"email":"bellasuseno@isu.edu","firstName":"Isabella","lastName":"Edwin","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0006-1090-5171"},{"affiliations":["Idaho State University, Pocatello, ID, United States"],"departments":["Biology"],"credit":["validation"],"email":"treytonharris@isu.edu","firstName":"Treyton","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0005-7981-4342"},{"affiliations":["Idaho State University, Pocatello, ID, United States"],"departments":["Biology"],"credit":["investigation","validation","writing_reviewEditing"],"email":"mthomas@isu.edu","firstName":"Michael","lastName":"Thomas","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-2982-0291"}],"awards":[{"awardId":"R25AI179573","funderName":"National Institute of Allergy and Infectious Diseases (United States)","awardRecipient":"Michael A. Thomas"}],"conflictsOfInterest":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[],"funding":"

This project was made possible by the ISU Bridges to Research Careers Program under NIH grant #R25AI179573, the ISU Department of Biological Sciences, the ISU Office for Research, and the Howard Hughes Medical Institute’s Science Education Alliance – Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES) program.

","image":{"url":"https://portal.micropublication.org/uploads/5fa60e87005132429e9615e8e20d7fb3.jpg"},"imageCaption":"

A) Podovirus morphology of MamaT with a mean capsid diameter of 35nm +/- 0 nm (n=5 phage particles examined). Image produced by a Zeiss EM900 TEM with an accelerating voltage of 80 kV and 1% uranyl acetate negative staining. B) The minimum free energy (MFE) structure of the putative pRNA fold (located between the stop codon of gp6 and the start codon of gp7), predicted by RNAfold. Colors reflect base-pair probabilities calculated from the partition function (red reflects high confidence).

","imageTitle":"

Characterization of MamaT

","methods":"

Sequence data was deposited in sequence read archive SRR33718591 and GenBank accession number PZ362296. For collection information, see PhagesDB/phages/MamaT.

","reagents":"

","patternDescription":"

Bacteriophages are exceedingly diverse but largely under-sampled (Dion et al., 2020). Because of this, great advances in bioengineering and biotherapy are anticipated from the continued discovery of novel phages with unique properties (Mu & Lawley, 2023). Here, we describe the isolation and genetic composition of MamaT, a bacteriophage that infects Microbacterium foliorum.

MamaT was isolated from a soil sample consisting of clay and decaying plant material, collected near the Portneuf River at the Price Road wetlands near McCammon, ID (42.622464 N, 112.169022 W) on August 27, 2024, using the following established procedures  (Adams et al., 2022; Zorawik et al., 2024). The soil sample was washed with PYCa liquid medium and the supernatant filtered with a 0.22-μm filter. The filtrate was inoculated with M. foliorum NRRL B-24224. After incubation with shaking at 30°C for 48 h, the culture was filtered (0.22-mm pore size), and the filtrate was plated using M. foliorum PYCa top agar overlays, resulting in plaques after incubation at 30°C for 48 h. Plaques were purified through three additional rounds of plating. A high-titer lysate (>1010 pfu/mL) was prepared for DNA sequencing and transmission electron microscopy (TEM). Negative-stain TEM revealed phages with podovirus morphology (Figure 1A). The lack of an identifiable tape measure protein in the genome supports the classification of this phage as a podovirus.

Promega Wizard DNA clean up kit was used to extract genomic DNA from a high-titer lysate. A sequencing library was then prepared using a NEB Ultra II library kit and sequenced on an Illumina NextSeq 1000 (XLEAP-PI kit), resulting in 922,020 single-end 100-bp reads with 1,825-fold coverage. Raw reads were trimmed with cutadapt 4.7 (using the option: –nXextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, yielding a single contig. Consed v29 was used to check for completeness and accuracy and determine phage termini, using default settings (Chung et al., 2017). MamaT's genome length is 16,854 bp with a GC content of 53.8% (notably lower than the host, at 68.7%; Russell et al., 2019). Based on genomic synteny, sequence homology to known protein-priming phages, and an abrupt drop-off in raw sequencing read coverage at the genome boundaries, MamaT is predicted to possess a linear genome capped by covalently bound terminal proteins.

The MamaT genome was auto-annotated by DNAmaster v5.23.6 (http://cobamide2.bio.pitt.edu) using Genemark v2.5 (Besemer and Borodovsky 2005) and Glimmer v3.0 (Delcher et al., 2008) and subsequently manually inspected and refined using PECAAN (http://discover.kbrinsgd.org), Phamerator v454 (Cresawn et al., 2011) for synteny analysis and Starterator (http://phages.wustl.edu/starterator/) to identify start sites by manually comparing to genes within the same protein family (pham) (Horton et al., 2024). To predict putative gene functions, the following tools were deployed: HHpred v2.0 (Soding et al., 2005), using the PDB_mmCIF70, Pfam v.36, and NCBI Conserved Domains databases; BLAST v2.13.0 (Altschul et al. 1990), using the Actinobacteriophage and NCBI non-redundant databases; and Phamerator, using Actino_draft database v578 (cutoff values were 10-7 for BLAST and probability >90% over >50% coverage for HHpred). AlphaFold 3 (Jumper et al. 2021) was used to identify putative function of minor tail proteins. No tRNAs were identified using Aragorn v1.2.41 (Laslett 2004) and tRNAscan-SE v2.0 (Lowe and Eddy 1997). Using default parameters, the annotation process resulted in the identification of 23 putative protein-coding genes, 12 of which could be assigned gene functions. MamaT was assigned to cluster GI based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, PhagesDB (https://phagesdb.org/) (Pope et al., 2017; Russell and Hatfull 2017).

MamaT is the fifth annotated bacteriophage within cluster GI, to date, which includes phages Curie (Horton et al., 2024) and PineapplePizza (LaBianca et al., 2023), and with substantial similarity to Bacillus phage φ29 (Xu et al., 2019). Interestingly, phage φ29 has a prohead packaging RNA (pRNA) system that includes a noncoding pRNA component along with genes associated with packaging DNA into the prohead. In MamaT, homologs to these genes include gp15 (terminase) and gp10 (portal protein), and a putative pRNA appears to reside between the stop codon of gp6 and the start codon of gp7 (nucleotide position 4,625 to 4,801). Folded with RNAfold (Gruber et al., 2008), the 177 nt putative pRNA segment is highly consistent with φ29 pRNA in both length (the full-length φ29 pRNA is ~174 nt) and secondary structure: a characteristic 5-way junction with a central hub, a stable closing stem at the 5′/3′ ends, an apical hairpin, and flexible loop regions at appropriate positions within a well-folded, thermodynamically stable RNA (Figure 1B). No conventional upstream promoter was identified in the intergenic space, consistent with the known internal promoter architecture of φ29-family pRNA genes. Sequence-level similarity to φ29 pRNA was not detected by BLAST, which is unsurprising given that pRNAs from different φ29-family phages (φ29, B103, GA-1, SF5) share very little sequence identity while maintaining the same overall fold.

","references":[{"reference":"

Adams BM, Adams JB, Brewster RL, Cutler MS, Davis AE, Gallegos AH, et al., Thomas MA. 2022. Annotation of the Complete Genome Sequences of Bacteriophages Sara and Birdfeeder. Microbiol Resour Announc 11(10): e0078022.

","pubmedId":"36121218","doi":""},{"reference":"

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.

","pubmedId":"2231712","doi":""},{"reference":"

Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33(Web Server issue): W451-4.

","pubmedId":"15980510","doi":""},{"reference":"

Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics 18(1): 350.

","pubmedId":"28472946","doi":""},{"reference":"

Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 395.

","pubmedId":"21991981","doi":""},{"reference":"

Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6): 673-9.

","pubmedId":"17237039","doi":""},{"reference":"

Dion MrB, Oechslin F, Moineau S. 2020. Phage diversity, genomics and phylogeny. Nature Reviews Microbiology 18: 125-138.

","pubmedId":"","doi":"10.1038/s41579-019-0311-5"},{"reference":"

Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Research 36: W70-W74.

","pubmedId":"","doi":"10.1093/nar/gkn188 "},{"reference":"

Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.

","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"

Hardies SC, Thomas JA, Black L, Weintraub ST, Hwang CY, Cho BC. 2016. Identification of structural and morphogenesis genes of Pseudoalteromonas phage φRIO-1 and placement within the evolutionary history of Podoviridae. Virology 489: 116-27.

","pubmedId":"26748333","doi":""},{"reference":"

Horton EN, Beach EK, Cook KT, Cronin KG, Haag AT, Salter SM, et al., Anders. 2024. Complete genome sequence of\n Microbacterium foliorum\n phage Curie, a podovirus isolated from soil in Spokane, Washington. Microbiology Resource Announcements 13: 10.1128/mra.00408-24.

","pubmedId":"","doi":"10.1128/mra.00408-24"},{"reference":"

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al., Hassabis D. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596(7873): 583-589.

","pubmedId":"34265844","doi":""},{"reference":"

LaBianca K, Butura J, McKnight A, Pan K, Whelan S, Punska E, et al., Rocheleau. 2023. Complete genome sequence of phi29-like\n Microbacterium foliorum\n podovirus phage PineapplePizza. Microbiology Resource Announcements 12: 10.1128/mra.00478-23.

","pubmedId":"","doi":"10.1128/MRA.00478-23"},{"reference":"

Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32(1): 11-6.

","pubmedId":"14704338","doi":""},{"reference":"

Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5): 955-64.

","pubmedId":"9023104","doi":""},{"reference":"

Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8(4): 10.1128/mBio.01069-17.

","pubmedId":"28811342","doi":""},{"reference":"

Pyra A, Urbańska N, Filik K, Tyrlik K, Brzozowska E. 2020. Biochemical features of the novel Tail Tubular Protein A of Yersinia phage phiYeO3-12. Sci Rep 10(1): 4196.

","pubmedId":"32144374","doi":""},{"reference":"

Russell DA, Garlena RA, Hatfull GF. 2019. Complete Genome Sequence of Microbacterium foliorum NRRL B-24224, a Host for Bacteriophage Discovery. Microbiol Resour Announc 8(5): 10.1128/MRA.01467-18.

","pubmedId":"30714032","doi":""},{"reference":"

Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics 33(5): 784-786.

","pubmedId":"28365761","doi":""},{"reference":"

Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue): W244-8.

","pubmedId":"15980461","doi":""},{"reference":"

Xu J, Wang D, Gui M, Xiang Y. 2019. Structural assembly of the tailed bacteriophage ϕ29. Nature Communications 10: 10.1038/s41467-019-10272-3.

","pubmedId":"","doi":"10.1038/s41467-019-10272-3 "},{"reference":"

Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.

","pubmedId":"38526736","doi":""}],"title":"

Isolation and Genome Annotation of MamaT, a Cluster GI Bacteriophage with Podovirus Morphology

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