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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References
1.
HaqIU, ChaudhryWN, AkhtarMN, et al.Bacteriophages and their implications on future biotechnology: A review. Virol J, 2012; 9:9; doi: 10.1186/1743-422X-9-9
2.
VarandaC, FélixMDR, CamposMD, et al.An overview of the application of viruses to biotechnology. Viruses, 2021; 13(10):2073; doi: 10.3390/v13102073
3.
HatfullGF, Jacobs-SeraD, LawrenceJG, et al.Comparative genomic analysis of 60 Mycobacteriophage genomes: Genome clustering, gene acquisition, and gene size. J Mol Biol, 2010; 397(1):119–143; doi: 10.1016/j.jmb.2010.01.011
4.
PopeWH, Jacobs-SeraD, RussellDA, et al.Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution. PLoS One, 2011; 6(1):e16329; doi: 10.1371/journal.pone.0016329
5.
JordanTC, BurnettSH, CarsonS, et al.A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. mBio, 2014; 5(1):e01051-13–e01013; doi: 10.1128/mBio.01051-13
6.
HanauerD, GrahamM, BetancurL, et al.An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning. Proc Natl Acad Sci U S A, 2017; 114(51):13531–13536; doi: 10.1073/pnas.1718188115
7.
NguyenL. Antibiotic resistance mechanisms in M. tuberculosis: An update. Arch Toxicol, 2016; 90(7):1585–1604; doi: 10.1007/s00204-016-1727-6
8.
GriffithDE. Mycobacterium abscessus and antibiotic resistance: Same as it ever was. Clin Infect Dis, 2019; 69(10):1687–1689; doi: 10.1093/cid/ciz071
9.
HatfullGF. Mycobacteriophages: Windows into tuberculosis. PLoS Pathog, 2014; 10(3):e1003953; doi: 10.1371/journal.ppat.1003953
10.
HatfullGF. Wildy prize lecture, 2020-2021: Who wouldn't want to discover a new virus? Microbiology (Reading), 2021; 167(9):001094; doi: 10.1099/mic.0.001094
11.
Jacobs-SeraD, MarinelliLJ, BowmanC, et al.On the nature of mycobacteriophage diversity and host preference. Virology, 2012; 434(2):187–201; doi: 10.1016/j.virol.2012.09.026Epub 2012 Oct 22
DelcherAL, BratkeKA, PowersEC, et al.Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 2007; 23(6):673–679; doi: 10.1093/bioinformatics/btm009
17.
BesemerJ, BorodovskyM. GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res, 2005; 33(Web Server issue):W451–W454; doi: 10.1093/nar/gki487
18.
BoratynGM, SchäfferAA, AgarwalaR, et al.Domain enhanced lookup time accelerated BLAST. Biol Direct, 2012; 7:12; doi: 10.1186/1745-6150-7-12
19.
GablerF, NamSZ, TillS, et al.Protein sequence analysis using the MPI bioinformatics toolkit. Curr Protoc Bioinformatics, 2020; 72(1):e108; doi: 10.1002/cpbi.108
20.
LaslettD, CanbackB. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res, 2004; 32(1):11–16; doi: 10.1093/nar/gkh152
21.
CresawnSG, BogelM, DayN, et al.Phamerator: A bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics, 2011; 12:395; doi: 10.1186/1471-2105-12-395
22.
GauthierCH, CresawnSG, HatfullGF. PhaMMseqs: A new pipeline for constructing phage gene phamilies using MMseqs2. G3 (Bethesda), 2022; 12(11):jkac233; doi: 10.1093/g3journal/jkac233
23.
PopeWH, BowmanCA, RussellDA, et al.Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife, 2015; 4:e06416; doi: 10.7554/eLife.06416
24.
PopeWH, MavrichTN, GarlenaRA, et al.Bacteriophages of Gordonia spp. display a spectrum of diversity and genetic relationships. mBio, 2017; 8(4):e01069-17; doi: 10.1128/mBio.01069-17
Rodriguez-RLM, KonstantinidisKT. The Enveomics Collection: A Toolbox for Specialized Analyses of Microbial Genomes and Metagenomes. preprint. PeerJ Preprints; 2016.; doi: 10.7287/peerj.preprints.1900v1
PollenzRS, BlandJ, PopeWH. Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta. PLoS One, 2022; 17(11):e0276603; doi: 10.1371/journal.pone.0276603
31.
RussellDA, HatfullGF. Actinobacteriophage database at PhagesDB.org. Available from: https://phagesdb.org [Last accessed: December15, 2023].
32.
CresawnSG. Phamerator database. Available from: https://phamerator.org [Last accessed: December15, 2023].
33.
PayneK, SunQ, SacchettiniJ, et al.Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase. Mol Microbiol, 2009; 73(3):367–381; doi: 10.1111/j.1365-2958.2009.06775.x
34.
PayneKM, HatfullGF. Mycobacteriophage endolysins: Diverse and modular enzymes with multiple catalytic activities. PLoS One, 2012; 7(3):e34052; doi: 10.1371/journal.pone.0034052
VillAC, DelesalleVA, TomkoBE, et al.Comparative genomics of Six Lytic Bacillus subtilisPhages from the Southwest United States. Phage (New Rochelle), 2022; 3(3):171–178; doi: 10.1089/phage.2022.0030
37.
JohnsonEP, MincerT, SchwabH, et al.Plasmid RK2 ParB protein: Purification and nuclease properties. J Bacteriol, 1999; 181(19):6010–6018; doi: 10.1128/JB.181.19.6010-6018.1999
38.
DedrickRM, MavrichTN, NgWL, et al.Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. Mol Microbiol, 2016; 101(4):625–644; doi: 10.1111/mmi.13414
39.
WillenbücherK, WibbergD, HuangL, et al.Phage genome diversity in a biogas-producing microbiome analyzed by Illumina and Nanopore GridION sequencing. Microorganisms, 2022; 10(2):368; doi: 10.3390/microorganisms10020368
40.
PedullaML, FordME, HoutzJM, et al.Origins of highly mosaic mycobacteriophage genomes. Cell, 2003; 113(2):171–182; doi: 10.1016/s0092-8674(03)00233-2
41.
NovikovaO, JayachandranP, KelleyDS, et al.Intein clustering suggests functional importance in different domains of life. Mol Biol Evol, 2016; 33(3):783–799; doi: 10.1093/molbev/msv271Epub 2015 Nov 25
42.
KelleyDS, LennonCW, BelfortM, et al.Mycobacteriophages as Incubators for Intein dissemination and evolution. mBio, 2016; 7(5):e01537-16; doi: 10.1128/mBio.01537-16
43.
KalaS, CumbyN, SadowskiPD, et al.HNH proteins are a widespread component of phage DNA packaging machines. Proc Natl Acad Sci U S A, 2014; 111(16):6022–6027; doi: 10.1073/pnas.1320952111
44.
MakarovaKS, GrishinNV, KooninEV. The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics, 2006; 22(21):2581–2584; doi: 10.1093/bioinformatics/btl418Epub 2006 Aug 8
45.
LiG, ShenM, LuS, et al.Identification and Characterization of the HicAB Toxin-Antitoxin System in the Opportunistic Pathogen Pseudomonas aeruginosa. Toxins (Basel), 2016; 8(4):113; doi: 10.3390/toxins8040113
46.
JørgensenMG, PandeyDP, JaskolskaM, et al.HicA of escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea. J Bacteriol, 2009; 191(4):1191–1199; doi: 10.1128/JB.01013-08
47.
StamereilersC, LeBlancL, YostD, et al.Comparative genomics of 9 novel Paenibacillus larvae bacteriophages. Bacteriophage, 2016; 6(3):e1220349; doi: 10.1080/21597081.2016.1220349
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