Russian version English version
About the Journal
Editorial Board
Instructions for Authors
Information for Readers and Authors
Current Issue
Archive
Contact Us
Search

Send manuscript
 


Volume 18   Issue 2   Year 2023
References

  1. Subramani R., Aalbersberg W. Culturable rare Actinomycetes: diversity, isolation and marine natural product discovery. Appl. Microbiol. Biotechnol. 2013;97:9291–9321. doi: 10.1007/s00253-013-5229-7
  2. Mohammadipanah F., Wink J. Actinobacteria from arid and desert habitats: diversity and biological activity. Front. Microbiol. 2016;6. Article No. 1541. doi: 10.3389/fmicb.2015.01541
  3. Azman A.S., Othman I., Velu S.S., Chan K.G., Lee L.H. Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity. Front. Microbiol. 2015;6. Article No. 856. doi: 10.3389/fmicb.2015.00856
  4. Nouioui I., Carro L., Garcia-Lopez M., Meier-Kolthoff J.P., Woyke T., Kyrpides N.C., Pukall R., Klenk H.P., Goodfellow M., Goker M. Genome-based taxonomic classification of the phylum Actinobacteria. Front. Microbiol. 2018;9. Article No. 2007. doi: 10.3389/fmicb.2018.02007
  5. Amin D.H., Abdallah N.A., Abolmaaty A., Tolba S., Wellington E.M.H. Microbiological and molecular insights on rare actinobacteria harboring bioactive prospective. Bull. Natl. Res. Cent. 2020;44. Article No. 5. doi: 10.1186/s42269-019-0266-8
  6. Subramani R., Sipkema D. Marine rare actinomycetes: a promising source of structurally diverse and unique novel natural products. Mar. Drugs. 2019;17. Article No. 249. doi: 10.3390/md17050249
  7. Chaturvedi S., Khurana S.M.P. In: Plant Biotechnology: Progress in Genomic Era. Ed. Khurana S., Gaur R. Singapore: Springer, 2019. P. 277–307. doi: 10.1007/978-981-13-8499-8_13
  8. Zinder N.D., Lederberg J. Genetic exchange in Salmonella. J. Bacteriol. 1952;64:679–699. doi: 10.1128/jb.64.5.679-699.1952
  9. Thierauf A., Perez G., Maloy A.S. Generalized transduction. Methods Mol. Biol. 2009;501:267–286. doi: 10.1007/978-1-60327-164-6_23
  10. Chen J., Quiles-Puchalt N., Chiang Y.N., Bacigalupe R., Fillol-Salom A., Chee M., Fitzgerald J.R., Penades J.R. Genome hypermobility by lateral transduction. Science. 2018;362:207–212. doi: 10.1126/science.aat5867
  11. Moore S.D. Assembling new Escherichia coli strains by transduction using phage P1. Methods Mol. Biol. 2011;765:155–169. doi: 10.1007/978-1-61779-197-0_10
  12. Thomason L.C., Costantino N., Court D.L. E. coli genome manipulation by P1 transduction. Curr. Protoc. Mol. Biol. 2007. Chapter 1:1.17.1–1.17.8. doi: 10.1002/0471142727.mb0117s79
  13. Russell D.A., Hatfull G.F. PhagesDB: the actinobacteriophage database. Bioinformatics. 2017;33:784–786. doi: 10.1093/bioinformatics/btw71
  14. Brettin T., Davis J. J., Disz T., Edwards R.A., Gerdes S., Olsen G.J., Olson R., Overbeek R., Parrello B., Pusch G.D. et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 2015;5. Article No. 8365. doi: 10.1038/srep08365
  15. Davis J.J., Wattam A.R., Aziz R.K., Brettin T., Butler R., Butler R.M., Chlenski P., Conrad N., Dickerman A., Dietrich E.M. et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 2020;48. P. D606–D612. doi: 10.1093/nar/gkz943
  16. Tanizawa Y., Fujisawa T., Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018;34:1037–1039. doi: 10.1093/bioinformatics/btx713
  17. Contreras-Moreira B., Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol. 2013;79:7696–7701. doi: 10.1128/AEM.02411-13
  18. Kristensen D.M., Kannan L., Coleman M.K., Wolf Y.I., Sorokin A., Koonin E.V., Mushegian A. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics. 2010;26:1481–1487. doi: 10.1093/bioinformatics/btq229
  19. Vinuesa P., Ochoa-Sanchez L.E., Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front. Microbiol. 2018;9. Article No. 771. doi: 10.3389/fmicb.2018.00771
  20. Meier-Kolthoff J.P., Goker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics. 2017;33:3396–3404. doi: 10.1093/bioinformatics/btx440
  21. Sorensen T. A method of establishing groups of equal amplitudes in plant sociology based on similarity of species content and its application to analyses of the vegetation on danish commons. Kongelige Danske Videnskabernes Selskab, Biologiske Skrifter. 1948;5:1–34.
  22. Bray J.R., Curtis J.T. An ordination of the upland forest communities of Southern Wisconsin. Ecological Monographs. 1957;27:325–349. doi: 10.2307/1942268
  23. Panyukov V.V., Kiselev S.S., Ozoline O.N. Unique k-mers as strain-specific barcodes for phylogenetic analysis and natural microbiome profiling. Int. J. Mol. Sci. 2020;21. Article No. 944. doi: 10.3390/ijms21030944
  24. Kumar S., Stecher G., Li M., Knyaz C., Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 2018;35:1547–1549. doi: 10.1093/molbev/msy096
  25. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987;4:406–425. doi: 10.1093/oxfordjournals.molbev.a040454
  26. 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. doi: 10.1016/S0022-2836(05)80360-2
  27. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 1992;89:10915–10919. doi: 10.1073/pnas.89.22.10915
  28. Sullivan M.J., Petty N.K., Beatson S.A., Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27:1009–1010. doi: 10.1093/bioinformatics/btr039
  29. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–2504. doi: 10.1101/gr.1239303
  30. Hagberg A.A., Schult D.A., Swart P.J. In: Proceedings of the 7th Python in Science Conference. Ed. Varoquaux G., Vaught T., Millman J. Pasadena, 2008. P. 11–15.
  31. Latapy M., Magnien C., Del Vecchio N. Basic notions for the analysis of large two-mode networks. Social Netw. 2008;30:31–48. doi: 10.1016/j.socnet.2007.04.006
  32. Holm S. A simple sequentially rejective multiple test procedure. Scand. J. Statist. 1979;6:65–70.
  33. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 1981;17:368–376. doi: 10.1007/BF01734359
  34. Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 2015;32:268–274. doi: 10.1093/molbev/msu300
  35. Edgar R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340
  36. Kalyaanamoorthy S., Minh B.Q., Wong T.K.F., von Haeseler A, Jermiin L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017;14:587–589. doi: 10.1038/nmeth.4285
  37. Schwarz G. Estimating the dimension of a model. Ann. Stat. 1978;6:461–464. doi: 10.1214/aos/1176344136
  38. Hoang D.T., Chernomor O., von Haeseler A., Minh B.Q., Vinh L.S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 2018;35:518–522. doi: 10.1093/molbev/msx281
  39. Ventura M., Canchaya C., Tauch A., Chandra G., Fitzgerald G.F., Chater K.F., van Sinderen D. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. Rev. 2007;71:495–548. doi: 10.1128/MMBR.00005-07
  40. Heinsch S.C., Hsu S.Y., Otto-Hanson L., Kinkel L., Smanski M.J. Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils. BMC Genomics. 2019;20. Article No. 994. doi: 10.1186/s12864-019-6279-8
  41. Subramaniam G., Thakur V., Saxena R.K., Vadlamudi S., Purohit S., Kumar V., Rathore A., Chitikineni A., Varshney R.K. Complete genome sequence of sixteen plant growth promoting Streptomyces strains. Sci. Rep. 2020;10. Article No. 10294. doi: 10.1038/s41598-020-67153-9
  42. Zhong L., Cheng Q., Tian X., Zhao L., Qin Z. Characterization of the replication, transfer, and plasmid/lytic phage cycle of the Streptomyces plasmid-phage pZL12. J. Bacteriol. 2010;192:3747–3754. doi: 10.1128/JB.00123-10
  43. Pfeifer E., Moura de Sousa J.A., Touchon M., Rocha E.P.C. Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. Nucleic Acids Res. 2021;49:2655–2673. doi: 10.1093/nar/gkab064
  44. Nikulin N.A., Zimin A.A. Influence of non-canonical DNA bases on the genomic diversity of Tevenvirinae. Front. Microbiol. 2021;12. Article No. 632686. doi: 10.3389/fmicb.2021.632686
  45. Falkow S., Baron L.S. Plasmid formation after lambda bacteriophage infection of Escherichia coli-Salmonella typhosa hybrids. J. Bacteriol. 1970;102:288–290. doi: 10.1128/jb.102.1.288-290.1970
  46. Lieb M. λ mutants which persist as plasmids. J. Virol. 1970;6:218–225. doi: 10.1128/jvi.6.2.218-225.1970
  47. Jaffe-Brachet A., D'Ari R. Maintenance of bacteriophage P1 plasmid. J. Virol. 1977;23:476–482. doi: 10.1128/jvi.23.3.476-482.1977
  48. Sternberg N., Hoess R. The molecular genetics of bacteriophage P1. Annu. Rev. Genet. 1983;17:123–154. doi: 10.1146/annurev.ge.17.120183.001011
  49. Jacob A.E., Barth P.T., Grinter N.J. Compatibility properties of P1 and φAMP prophages. Mol. Gen. Genet. 1975;141:263–267. doi: 10.1007/BF00341804
  50. Goldstein R., Sedivy J., Ljungquist E. Propagation of satellite phage P4 as a plasmid. Proc. Natl. Acad. Sci. USA. 1982;75:515–519. doi: 10.1073/pnas.79.2.515
  51. Ghisotti D., Briani F., Forti F., Piazza F., Polo S., Sabbattini P., Sturniolo T., Terzano S., Zangrossi S., Zappone M., Sironi G., Deho G. Multiple regulatory mechanisms controlling phage-plasmid P4 propagation. FEMS Microbiol. Rev. 1995;17:127–134. doi: 10.1111/j.1574-6976.1995.tb00194.x
  52. Ravin V.K., Shulga M.G. Evidence for extrachromosomal location of prophage N15. Virology. 1970;40:800–807. doi: 10.1016/0042-6822(70)90125-X
  53. Rybchin V.N., Svarchevsky A.N. The plasmid prophage N15: à linear DNA with covalently closed ends. Mol. Microbiol. 1999;33:895–903. doi: 10.1046/j.1365-2958.1999.01533.x
  54. Ravin N.V. N15: the linear phage-plasmid. Plasmid. 2011;65:102–109. doi: 10.1016/j.plasmid.2010.12.004
  55. Strizhov N., Tikhomirova L. Construction of recombinant plasmid carrying the λ DNA fragment responsible for prophage integration. Nucleic Acids Res. 1978;5:1767–1777. doi: 10.1093/nar/5.6.1767
  56. Donoghue D.J., Sharp P.A. Construction of a hybrid bacteriophage-plasmid recombinant DNA vector. J. Bacteriol. 1978;136:1192–1196. doi: 10.1128/jb.136.3.1192-1196.1978
  57. Mel'nikov A.A., Chernov A.P., Fodor I.I. Lambda plasmidophages and their properties. Mol. Biol. (Moscow). 1985;19:610–616 (in Russ.).
  58. Cheng Q., Zhong L., Qin Z. Plasmid pCQ4 and its phage ΦCQ4 of endophytic Streptomyces sp. from Artemisia annua L. Acta Microbiologica Sinica (Wei Sheng Wu Xue Bao). 2012;52:825–831.
  59. Dedrick R.M., Mavrich T.N., Ng W.L., Cervantes Reyes J.C., Olm M.R., Rush R.E., Jacobs-Sera D., Russell D.A., Hatfull G.F. Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. Mol. Microbiol. 2016;101:625–644. doi: 10.1111/mmi.13414
  60. Klyczek K.K., Bonilla J.A., Jacobs-Sera D., Adair T.L., Afram P., Allen K.G., Archambault M.L., Aziz R.M., Bagnasco F.G., Ball S.L. et al. Tales of diversity: genomic and morphological characteristics of forty-six Arthrobacter phages. PLoS ONE. 2017;12. Article No. e0180517. doi: 10.1371/journal.pone.0180517
  61. Smith M.C., Hendrix R.W., Dedrick R., Mitchell K., Ko C.C., Russell D., Bell E., Gregory M., Bibb M.J., Pethick F. et al. Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp. J. Bacteriol. 2013;195:4924–4935. doi: 10.1128/JB.00618-13
  62. Bajpai R., Soni V., Khandrika L., Jangir P.K., Sharma R., Agrawal P. Genome sequence of a novel actinophage PIS136 isolated from a strain of Saccharomonospora sp. J. Virol. 2012;86. Article No. 9552. doi: 10.1128/JVI.01529-12
  63. Cheepudom J., Lee C.C., Cai B., Meng M. Isolation, characterization, and complete genome analysis of P1312, a thermostable bacteriophage that infects Thermobifida fusca. Front. Microbiol. 2015;6. Article No. 959. doi: 10.3389/fmicb.2015.00959
  64. Wilson G.G., Young K.Y., Edlin G.J., Konigsberg W. High-frequency generalized transduction by bacteriophage T4. Nature. 1979;280:80–82. doi: 10.1038/280080a0
  65. 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. doi: 10.1128/JB.187.3.1091-1104.2005
Table of Contents
Original Article
Nikulin N.A., Kiselev S.S., Panyukov V.V., Lu Y., Zimin A.A. Comparative analysis of Actinobacteria phage-plasmids and their transduction potential. Ìàthematical biology and bioinformatics. 2023;18(2):323-346. doi: 10.17537/2023.18.323
(published in English)

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
References
Supplementary data

 
  Copyright IMPB RAS © 2005-2025