Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Host Strain and Culture Conditions
2.2. Isolation of Prophage
2.3. Morphological Observation
2.4. Host Range
2.5. Extraction and Identification of Phage DNA
2.6. Phage Genome Sequencing and Analysis
2.7. Data Analysis
3. Results
3.1. Isolation and Biological Characteristics of Prophage vB_G30_01
3.2. Analysis of the Genome of vB_G30_01
3.3. Comparative Genomic Analysis
3.4. Phylogenetic Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Feiner, R.; Argov, T.; Rabinovich, L.; Sigal, N.; Borovok, I.; Herskovits, A.A. A new perspective on lysogeny: Prophages as active regulatory switches of bacteria. Nat. Rev. Microbiol. 2015, 13, 641–650. [Google Scholar] [CrossRef] [PubMed]
- Touchon, M.; De Sousa, J.A.M.; Rocha, E.P. Embracing the enemy: The diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Curr. Opin. Microbiol. 2017, 38, 66–73. [Google Scholar] [CrossRef] [PubMed]
- Gabashvili, E.; Osepashvili, M.; Koulouris, S.; Ujmajuridze, L.; Tskhitishvili, Z.; Kotetishvili, M. Phage transduction is involved in the intergeneric spread of antibiotic resistance-associated blaCTX-M, mel, and tetM loci in natural populations of some human and animal bacterial pathogens. Curr. Microbiol. 2020, 77, 185–193. [Google Scholar] [CrossRef] [PubMed]
- Wagner, P.L.; Waldor, M.K. Bacteriophage control of bacterial virulence. Infect. Immun. 2002, 70, 3985–3993. [Google Scholar] [CrossRef] [PubMed]
- Yendo, T.M.; Valente, N.S.; Nico, M. Botryomycosis caused by Staphylococcus warneri: The first case reported. Int. J. Dermatol. 2021, 60, 509–511. [Google Scholar] [CrossRef]
- Bonar, E.; Międzobrodzki, J.; Władyka, B. The Staphylococcal Coagulases; Elsevier: Amsterdam, The Netherlands, 2018; pp. 95–102. [Google Scholar]
- Lianou, D.T.; Petinaki, E.; Cripps, P.J.; Gougoulis, D.A.; Michael, C.K.; Tsilipounidaki, K.; Skoulakis, A.; Katsafadou, A.I.; Vasileiou, N.G.C.; Giannoulis, T.; et al. Prevalence, patterns, association with biofilm formation, effects on milk quality and risk factors for antibiotic resistance of staphylococci from bulk-tank milk of goat herds. Antibiotics 2021, 10, 1225. [Google Scholar] [CrossRef]
- Ohara-Nemoto, Y.; Haraga, H.; Kimura, S.; Nemoto, T.K. Occurrence of staphylococci in the oral cavities of healthy adults and nasal–oral trafficking of the bacteria. J. Med. Microbiol. 2008, 57, 95–99. [Google Scholar] [CrossRef]
- Arslan, F.; Saltoglu, N.; Mete, B.; Mert, A. Recurrent Staphylococcus warnerii prosthetic valve endocarditis: A case report and review. Ann. Clin. Microb. Anti. 2011, 10, 14. [Google Scholar] [CrossRef]
- Kamath, U.; Singer, C.; Isenberg, H.D. Clinical significance of Staphylococcus warneri bacteremia. J. Clin. Microbiol. 1992, 30, 261–264. [Google Scholar] [CrossRef]
- Campoccia, D.; Montanaro, L.; Visai, L.; Corazzari, T.; Poggio, C.; Pegreffi, F.; Maso, A.; Pirini, V.; Ravaioli, S.; Cangini, I.; et al. Characterization of 26 Staphylococcus warneri isolates from orthopedic infections. Int. J. Artif. Organs 2010, 33, 575–581. [Google Scholar] [CrossRef]
- Karthigasu, K.T.; Bowman, R.A.; Grove, D.I. Vertebral osteomyelitis due to Staphylococcus warneri. Ann. Rheum. Dis. 1986, 45, 1029–1030. [Google Scholar] [CrossRef] [PubMed]
- Cimiotti, J.P.; Haas, J.P.; Della-Latta, P.; Wu, F.; Saiman, L.; Larson, E.L. Prevalence and clinical relevance of Staphylococcus warneri in the neonatal intensive care unit. Infect. Control Hosp. Epidemiol. 2007, 28, 326–330. [Google Scholar] [CrossRef]
- Hira, V.; Kornelisse, R.F.; Sluijter, M.; Kamerbeek, A.; Goessens, W.H.F.; de Groot, R.; Hermans, P.W.M. colonization dynamics of antibiotic-resistant coagulase-negative staphylococci in neonates. J. Clin. Microbiol. 2013, 51, 595–597. [Google Scholar] [CrossRef]
- De Oliveira, R.P.; Da Silva, J.G.; Aragão, B.B.; de Carvalho, R.G.; Juliano, M.A.; Frazzon, J.; Farias, M.P.O.; Mota, R.A. Diversity and emergence of multi-resistant Staphylococcus spp. isolated from subclinical mastitis in cows in of the state of Piauí, Brazil. Braz. J. Microbiol. 2022, 53, 2215–2222. [Google Scholar] [CrossRef]
- Dolder, C.; van den Borne, B.H.P.; Traversari, J.; Thomann, A.; Perreten, V.; Bodmer, M. Quarter- and cow-level risk factors for intramammary infection with coagulase-negative staphylococci species in Swiss dairy cows. J. Dairy Sci. 2017, 100, 5653–5663. [Google Scholar] [CrossRef] [PubMed]
- Leinweber, H.; Sieber, R.N.; Larsen, J.; Stegger, M.; Ingmer, H. Staphylococcal phages adapt to new hosts by extensive attachment site variability. Mbio 2021, 12, e225921. [Google Scholar] [CrossRef]
- Kürekci, C. Short communication: Prevalence, antimicrobial resistance, and resistant traits of coagulase-negative staphylococci isolated from cheese samples in Turkey. J. Dairy Sci. 2016, 99, 2675–2679. [Google Scholar] [CrossRef] [PubMed]
- Nunes, A.; Teixeira, L.; Iorio, N.; Bastos, C.; Fonseca, L.; Soutopadron, T.; Dossantos, K. Heterogeneous resistance to vancomycin in Staphylococcus epidermidis, Staphylococcus haemolyticus and Staphylococcus warneri clinical strains: Characterisation of glycopeptide susceptibility profiles and cell wall thickening. Int. J. Antimicrob. Agents 2006, 27, 307–315. [Google Scholar] [CrossRef]
- Regecová, I.; Výrostková, J.; Zigo, F.; Gregová, G.; Pipová, M.; Jevinová, P.; Becová, J. Detection of resistant and enterotoxigenic strains of Staphylococcus warneri Isolated from food of animal Origin. Foods 2022, 11, 1496. [Google Scholar] [CrossRef]
- Azam, A.H.; Tanji, Y. Peculiarities of Staphylococcus aureus phages and their possible application in phage therapy. Appl. Microbiol. Biot. 2019, 103, 4279–4289. [Google Scholar] [CrossRef]
- Monteiro, R.; Pires, D.P.; Costa, A.R.; Azeredo, J. Phage therapy: Going temperate? Trends Microbiol. 2019, 27, 368–378. [Google Scholar] [CrossRef] [PubMed]
- Al-Anany, A.M.; Fatima, R.; Hynes, A.P. Temperate phage-antibiotic synergy eradicates bacteria through depletion of lysogens. Cell. Rep. 2021, 35, 109172. [Google Scholar] [CrossRef]
- Melo, L.D.R.; Sillankorva, S.; Ackermann, H.; Kropinski, A.M.; Azeredo, J.; Cerca, N. Characterization of Staphylococcus epidermidis phage vB_SepS_SEP9—A unique member of the Siphoviridae family. Res. Microbiol. 2014, 165, 679–685. [Google Scholar] [CrossRef] [PubMed]
- Fisarova, L.; Botka, T.; Du, X.; Maslanova, I.; Bardy, P.; Pantucek, R.; Benesik, M.; Roudnicky, P.; Winstel, V.; Larsen, J.; et al. Staphylococcus epidermidis phages transduce antimicrobial resistance plasmids and mobilize chromosomal islands. Msphere 2021, 6, e00223-21. [Google Scholar] [CrossRef] [PubMed]
- Gutierrez, D.; Martinez, B.; Rodriguez, A.; Garcia, P. Genomic characterization of two Staphylococcus epidermidis bacteriophages with anti-biofilm potential. BMC Genom. 2012, 13, 228. [Google Scholar] [CrossRef]
- Melo, L.D.R.; Sillankorva, S.; Ackermann, H.; Kropinski, A.M.; Azeredo, J.; Cerca, N. Isolation and characterization of a new Staphylococcus epidermidis broad-spectrum bacteriophage. J. Gen. Virol. 2014, 95, 506–515. [Google Scholar] [CrossRef]
- Freeman, M.E.; Kenny, S.E.; Lanier, A.; Cater, K.; Wilhite, M.C.; Gamble, P.; O’Leary, C.J.; Hatoum-Aslan, A.; Young, R.R.; Liu, M. Complete genome sequences of Staphylococcus epidermidis phages Quidividi, Terranova, and Twillingate. Microbiol. Resour. Ann. 2019, 8, e00598-19. [Google Scholar] [CrossRef]
- Culbertson, E.K.; Bari, S.M.N.; Dandu, V.S.; Kriznik, J.M.; Scopel, S.E.; Stanley, S.P.; Lackey, K.; Hernandez, A.C.; Hatoum-Aslan, A.; Dennehy, J.J. Draft Genome sequences of Staphylococcus podophages JBug18, Pike, Pontiff, and Pabna. Microbiol. Resour. Ann. 2019, 8, e00054-19. [Google Scholar] [CrossRef]
- Xie, X.; Sun, Q.; Liao, X.; Tong, Y.; Peng, S. Complete genomes of two novel active prophages discovered by bioinformatics methods from high-throughput sequencing data. IOP Conf. Ser. Mater. Sci. Eng. 2018, 466, 12032. [Google Scholar] [CrossRef]
- Yokoi, K.; Kawahigashi, N.; Uchida, M.; Sugahara, K.; Shinohara, M.; Kawasaki, K.; Nakamura, S.; Taketo, A.; Kodaira, K. The two-component cell lysis genes holWMY and lysWMY of the Staphylococcus warneri M phage ϕWMY: Cloning, sequencing, expression, and mutational analysis in Escherichia coli. Gene 2005, 351, 97–108. [Google Scholar] [CrossRef]
- Zheng, H.; Liu, B.; Xu, Y.; Zhang, Z.; Man, H.; Liu, J.; Chen, F. An inducible Microbacterium prophage vB_MoxS-R1 represents a novel lineage of Siphovirus. Viruses 2022, 14, 731. [Google Scholar] [CrossRef] [PubMed]
- Schubert, M.; Lindgreen, S.; Orlando, L. AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Res. Notes 2016, 9, 88. [Google Scholar] [CrossRef] [PubMed]
- Luo, R.; Liu, B.; Xie, Y.; Li, Z.; Huang, W.; Yuan, J.; He, G.; Chen, Y.; Pan, Q.; Liu, Y. SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. Gigascience 2012, 1, 2047–2217. [Google Scholar] [CrossRef]
- Coil, D.; Jospin, G.; Darling, A.E. A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015, 31, 587–589. [Google Scholar] [CrossRef] [PubMed]
- Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef]
- Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403–410. [Google Scholar] [CrossRef]
- Kurtz, S.; Phillippy, A.; Delcher, A.L.; Smoot, M.; Shumway, M.; Antonescu, C.; Salzberg, S.L. Versatile and open software for comparing large genomes. Genome Biol. 2004, 5, 1–9. [Google Scholar] [CrossRef]
- Walker, B.J.; Abeel, T.; Shea, T.; Priest, M.; Abouelliel, A.; Sakthikumar, S.; Cuomo, C.A.; Zeng, Q.; Wortman, J.; Young, S.K. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 2014, 9, e112963. [Google Scholar] [CrossRef]
- Arndt, D.; Grant, J.R.; Marcu, A.; Sajed, T.; Pon, A.; Liang, Y.; Wishart, D.S. PHASTER: A better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016, 44, W16–W21. [Google Scholar] [CrossRef]
- Besemer, J.; Lomsadze, A.; Borodovsky, M. GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001, 29, 2607–2618. [Google Scholar] [CrossRef]
- Buchfink, B.; Xie, C.; Huson, D.H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 2015, 12, 59–60. [Google Scholar] [CrossRef] [PubMed]
- Hildebrand, A.; Remmert, A.; Biegert, A.; Söding, J. Fast and accurate automatic structure prediction with HHpred. Proteins 2009, 77, 128–132. [Google Scholar] [CrossRef]
- Alcock, B.P.; Raphenya, A.R.; Lau, T.T.; Tsang, K.K.; Bouchard, M.; Edalatmand, A.; Huynh, W.; Nguyen, A.V.; Cheng, A.A.; Liu, S. CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020, 48, D517–D525. [Google Scholar] [CrossRef]
- Liu, B.; Zheng, D.; Jin, Q.; Chen, L.; Yang, J. VFDB 2019: A comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res. 2019, 47, D687–D692. [Google Scholar] [CrossRef]
- Moraru, C.; Varsani, A.; Kropinski, A.M. VIRIDIC—A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 2020, 12, 1268. [Google Scholar] [CrossRef] [PubMed]
- Sullivan, M.J.; Petty, N.K.; Beatson, S.A. Easyfig: A genome comparison visualizer. Bioinformatics 2011, 27, 1009–1010. [Google Scholar] [CrossRef]
- Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef]
- Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; Von Haeseler, A.; Lanfear, R. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef] [PubMed]
- Becker, K.; Heilmann, C.; Peters, G. Coagulase-negative staphylococci. Clin. Microbiol. Rev. 2014, 27, 870–926. [Google Scholar] [CrossRef]
- De Buck, J.; Ha, V.; Naushad, S.; Nobrega, D.B.; Luby, C.; Middleton, J.R.; De Vliegher, S.; Barkema, H.W. Non-aureus staphylococci and bovine udder health: Current understanding and knowledge gaps. Front. Vet. Sci. 2021, 8, 658031. [Google Scholar] [CrossRef]
- Al-harbi, H.; Ranjbar, S.; Moore, R.J.; Alawneh, J.I. Bacteria isolated from milk of dairy cows with and without clinical mastitis in different regions of Australia and their amr profiles. Front. Vet. Sci. 2021, 8, 743725. [Google Scholar] [CrossRef] [PubMed]
- Hatoum-Aslan, A. The phages of staphylococci: Critical catalysts in health and disease. Trends Microbiol. 2021, 29, 1117–1129. [Google Scholar] [CrossRef] [PubMed]
- Sofy, A.R.; Abd El Haliem, N.F.; Refaey, E.E.; Hmed, A.A. Polyvalent phage conshp-3 as a natural antimicrobial agent showing lytic and antibiofilm activities against antibiotic-resistant coagulase-negative staphylococci strains. Foods 2020, 9, 673. [Google Scholar] [CrossRef] [PubMed]
- Argemi, X.; Martin, V.; Loux, V.; Dahyot, S.; Lebeurre, J.; Guffroy, A.; Martin, M.; Velay, A.; Keller, D.; Riegel, P.; et al. Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements. Genome Biol. Evol. 2017, 9, 1183–1189. [Google Scholar] [CrossRef] [PubMed]
- Deghorain, M.; Bobay, L.; Smeesters, P.R.; Bousbata, S.; Vermeersch, M.; Perez-Morga, D.; Drèze, P.; Rocha, E.P.C.; Touchon, M.; Van Melderen, L. Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. J. Bacteriol. 2012, 194, 5829–5839. [Google Scholar] [CrossRef]
- Pantůček, R.; Sedláček, I.; Indráková, A.; Vrbovská, V.; Mašlaňová, I.; Kovařovic, V.; Švec, P.; Králová, S.; Krištofová, L.; Kekláková, J.; et al. Staphylococcus edaphicus sp. nov., isolated in antarctica, harbors themecc gene and genomic islands with a suspected role in adaptation to extreme environments. Appl. Environ. Microb. 2018, 84, e01746-17. [Google Scholar] [CrossRef]
- Jun, J.W.; Giri, S.S.; Kim, H.J.; Chi, C.; Yun, S.; Kim, S.G.; Kim, S.W.; Kang, J.W.; Park, S.C. Complete genome sequence of the novel bacteriophage pSco-10 Infecting Staphylococcus cohnii. Genome Announc. 2017, 5, e1017–e1032. [Google Scholar] [CrossRef]
- Wipf, J.R.K.; Schwendener, S.; Perreten, V. The novel macrolide-lincosamide-streptogramin b resistance geneerm is associated with a prophage in Staphylococcus xylosus. Antimicrob. Agents Chin. 2014, 58, 6133–6138. [Google Scholar] [CrossRef]
- Tian, F.; Li, J.; Li, F.; Tong, Y. Characteristics and genome analysis of a novel bacteriophage IME1323_01, the first temperate bacteriophage induced from Staphylococcus caprae. Virus Res. 2021, 305, 198569. [Google Scholar] [CrossRef]
- Deghorain, M.; Van Melderen, L. The staphylococci phages family: An overview. Viruses 2012, 4, 3316–3335. [Google Scholar] [CrossRef]
- Turner, D.; Shkoporov, A.N.; Lood, C.; Millard, A.D.; Dutilh, B.E.; Alfenas-Zerbini, P.; van Zyl, L.J.; Aziz, R.K.; Oksanen, H.M.; Poranen, M.M.; et al. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch. Virol. 2023, 168, 74. [Google Scholar] [CrossRef] [PubMed]
- Winstel, V.; Liang, C.; Sanchez-Carballo, P.; Steglich, M.; Munar, M.; Bröker, B.M.; Penadés, J.R.; Nübel, U.; Holst, O.; Dandekar, T.; et al. Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens. Nat. Commun. 2013, 4, 2345. [Google Scholar] [CrossRef]
- Kwan, T.; Liu, J.; DuBow, M.; Gros, P.; Pelletier, J.; Siminovitch, L. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc. Natl. Acad. Sci. USA 2005, 102, 5174–5179. [Google Scholar] [CrossRef] [PubMed]
- Oliveira, H.; Sampaio, M.; Melo, L.D.R.; Dias, O.; Pope, W.H.; Hatfull, G.F.; Azeredo, J. Staphylococci phages display vast genomic diversity and evolutionary relationships. BMC Genom. 2019, 20, 1–14. [Google Scholar] [CrossRef]
- Beloglazova, N.; Brown, G.; Zimmerman, M.D.; Proudfoot, M.; Makarova, K.S.; Kudritska, M.; Kochinyan, S.; Wang, S.; Chruszcz, M.; Minor, W.; et al. A novel family of sequence-specific endoribonucleases associated with the clustered regularly. J. Biol. Chem. 2008, 283, 20361–20371. [Google Scholar] [CrossRef]
- Bryan, M.J.; Burroughs, N.J.; Spence, E.M.; Clokie, M.R.; Mann, N.H.; Bryan, S.J. Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer. PLoS ONE 2008, 3, e2048. [Google Scholar] [CrossRef]
- Kala, S.; Cumby, N.; Sadowski, P.D.; Hyder, B.Z.; Kanelis, V.; Davidson, A.R.; Maxwell, K.L. HNH proteins are a widespread component of phage DNA packaging machines. Proc. Natl. Acad. Sci. USA 2014, 111, 6022–6027. [Google Scholar] [CrossRef] [PubMed]
- Zhang, L.; Xu, D.; Huang, Y.; Zhu, X.; Rui, M.; Wan, T.; Zheng, X.; Shen, Y.; Chen, X.; Ma, K.; et al. Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease. Sci. Rep. 2017, 7, 42542. [Google Scholar] [CrossRef]
- Baumann, R.G.; Black, L.W. Isolation and Characterization of T4 Bacteriophage gp17 Terminase, a Large Subunit Multimer with Enhanced ATPase Activity. J. Biol. Chem. 2003, 278, 4618–4627. [Google Scholar] [CrossRef]
- Rao, V.B.; Mitchell, M.S. The N-terminal ATPase site in the large terminase protein gp17 is critically required for DNA packaging in bacteriophage T4 1 1Edited by M. Gottesman. J. Mol. Biol. 2001, 314, 401–411. [Google Scholar] [CrossRef]
- Xu, J.; Hendrix, R.W.; Duda, R.L. Conserved translational frameshift in dsdna bacteriophage tail assembly genes. Mol. Cell. 2004, 16, 11–21. [Google Scholar] [CrossRef] [PubMed]
- Gesteland, R.F.; Atkins, J.F. Recoding: Dynamic reprogramming of translation. Annu. Rev. Biochem. 1996, 65, 741–768. [Google Scholar] [CrossRef] [PubMed]
- Levin, M.E.; Hendrix, R.W.; Casjens, S.R. A programmed translational frameshift is required for the synthesis of a bacteriophage λ tail assembly protein. J. Mol. Biol. 1993, 234, 124–139. [Google Scholar] [CrossRef] [PubMed]
- Casjens, S.R.; Gilcrease, E.B.; Winn-Stapley, D.A.; Schicklmaier, P.; Schmieger, H.; Pedulla, M.L.; Ford, M.E.; Houtz, J.M.; Hatfull, G.F.; Hendrix, R.W. The generalized transducing Salmonella bacteriophage ES18: Complete genome sequence and DNA packaging strategy. J. Bacteriol. 2005, 187, 1091–1104. [Google Scholar] [CrossRef]
- Paul, J.H. Prophages in marine bacteria: Dangerous molecular time bombs or the key to survival in the seas? ISME J. 2008, 2, 579–589. [Google Scholar] [CrossRef]
- Dodd, I.B.; Perkins, A.J.; Tsemitsidis, D.; Egan, J.B. Octamerization of lambda CI repressor is needed for effective repression of P (RM) and efficient switching from lysogeny. Gene Dev. 2001, 15, 3013–3022. [Google Scholar] [CrossRef] [PubMed]
- Lewis, D.; Le, P.; Zurla, C.; Finzi, L.; Adhya, S. Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc. Natl. Acad. Sci. USA 2011, 108, 14807–14812. [Google Scholar] [CrossRef]
- Rosinski, J.A.; Atchley, W.R. Molecular evolution of helix-turn-helix proteins. J. Mol. Evol. 1999, 49, 301–309. [Google Scholar] [CrossRef]
- Panyakampol, J.; Cheevadhanarak, S.; Sutheeworapong, S.; Chaijaruwanich, J.; Senachak, J.; Siangdung, W.; Jeamton, W.; Tanticharoen, M.; Paithoonrangsarid, K. Physiological and transcriptional responses to high temperature in arthrospira (spirulina) platensis C1. Plant Cell Physiol. 2015, 56, 481–496. [Google Scholar] [CrossRef]
- Hu, Y.; Hu, Q.; Wei, R.; Li, R.; Zhao, D.; Ge, M.; Yao, Q.; Yu, X. The XRE Family Transcriptional regulator SrtR in Streptococcus suis is involved in oxidant tolerance and virulence. Front. Cell. Infect. Mi. 2019, 8, 452. [Google Scholar] [CrossRef]
- Harrison, S.C.; Aggarwal, A.K. DNA recognition by proteins with the helix-turn-helix motif. Annu. Rev. Biochem. 1990, 59, 933–969. [Google Scholar] [CrossRef] [PubMed]
- Pabo, C.O.; Lewis, M. The operator-binding domain of λ repressor: Structure and DNA recognition. Nature 1982, 298, 443–447. [Google Scholar] [CrossRef] [PubMed]
- Yuan, L.; Liu, Q.; Xu, L.; Wu, B.; Feng, Y. Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase. Nat. Commun. 2024, 15, 4850. [Google Scholar] [CrossRef] [PubMed]
- Woese, C.R.; Olsen, G.J.; Ibba, M.; Soll, D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. R 2000, 64, 202–236. [Google Scholar] [CrossRef] [PubMed]
- Stark, W.M. Making serine integrases work for us. Curr. Opin. Microbiol. 2017, 38, 130–136. [Google Scholar] [CrossRef]
- Grindley, N.D.; Whiteson, K.L.; Rice, P.A. Mechanisms of site-specific recombination. Annu. Rev. Biochem. 2006, 75, 567–605. [Google Scholar] [CrossRef]
- Young, R. Bacteriophage lysis: Mechanism and regulation. Microbiol. Rev. 1992, 56, 430–481. [Google Scholar] [CrossRef]
- Fischetti, V.A. Bacteriophage lysins as effective antibacterials. Curr. Opin. Microbiol. 2008, 11, 393–400. [Google Scholar] [CrossRef]
- Fernandes, S.; São José, C. More than a hole: The holin lethal function may be required to fully sensitize bacteria to the lytic action of canonical endolysins. Mol. Microbiol. 2016, 102, 92–106. [Google Scholar] [CrossRef]
- Dion, M.B.; Oechslin, F.; Moineau, S. Phage diversity, genomics and phylogeny. Nature reviews. Microbiology 2020, 18, 125–138. [Google Scholar] [CrossRef]
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Pu, F.; Zhang, N.; Pang, J.; Zeng, N.; Baloch, F.B.; Li, Z.; Li, B. Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis. Viruses 2024, 16, 1631. https://doi.org/10.3390/v16101631
Pu F, Zhang N, Pang J, Zeng N, Baloch FB, Li Z, Li B. Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis. Viruses. 2024; 16(10):1631. https://doi.org/10.3390/v16101631
Chicago/Turabian StylePu, Fangxiong, Ning Zhang, Jiahe Pang, Nan Zeng, Faryal Babar Baloch, Zijing Li, and Bingxue Li. 2024. "Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis" Viruses 16, no. 10: 1631. https://doi.org/10.3390/v16101631
APA StylePu, F., Zhang, N., Pang, J., Zeng, N., Baloch, F. B., Li, Z., & Li, B. (2024). Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis. Viruses, 16(10), 1631. https://doi.org/10.3390/v16101631