1887

Abstract

Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [ 1 ] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [ 2 ] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-07-01
2024-03-29
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References

  1. Oren A, Garrity GMY. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:10 [View Article] [PubMed]
    [Google Scholar]
  2. Bérdy J. Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot (Tokyo) 2012; 65:385–395 [View Article] [PubMed]
    [Google Scholar]
  3. Gerwick WH, Moore BS. Lessons from the past and charting the future of marine natural products drug discovery and chemical biology. Chem Biol 2012; 19:85–98 [View Article] [PubMed]
    [Google Scholar]
  4. Hutchings MI, Truman AW, Wilkinson B. Antibiotics: past, present and future. Curr Opin Microbiol 2019; 51:72–80 [View Article] [PubMed]
    [Google Scholar]
  5. Chater KF. Recent advances in understanding Streptomyces. F1000Res 2016; 5:2795 [View Article]
    [Google Scholar]
  6. Seipke RF, Kaltenpoth M, Hutchings MI. Streptomyces as symbionts: an emerging and widespread theme?. FEMS Microbiol Rev 2012; 36:862–876 [View Article] [PubMed]
    [Google Scholar]
  7. van der Meij A, Worsley SF, Hutchings MI, van Wezel GP. Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev 2017; 41:392–416 [View Article] [PubMed]
    [Google Scholar]
  8. Loria R, Kers J, Joshi M. Evolution of plant pathogenicity in streptomyces. Annu Rev Phytopathol 2006; 44:469–487
    [Google Scholar]
  9. McCormick JR, Flärdh K. Signals and regulators that govern Streptomyces development. FEMS Microbiol Rev 2012; 36:206–231 [View Article] [PubMed]
    [Google Scholar]
  10. Bush MJ, Tschowri N, Schlimpert S, Flärdh K, Buttner MJ. c-di-GMP signalling and the regulation of developmental transitions in streptomycetes. Nat Rev Microbiol 2015; 13:749–760 [View Article] [PubMed]
    [Google Scholar]
  11. Hull TD, Ryu M-H, Sullivan MJ, Johnson RC, Klena NT et al. Cyclic Di-GMP phosphodiesterases RmdA and RmdB are involved in regulating colony morphology and development in Streptomyces coelicolor. J Bacteriol 2012; 194:4642–4651 [View Article] [PubMed]
    [Google Scholar]
  12. Tschowri N, Schumacher MA, Schlimpert S, Chinnam NB, Findlay KC et al. Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development. Cell 2014; 158:1136–1147 [View Article] [PubMed]
    [Google Scholar]
  13. Schumacher MA, Zeng W, Findlay KC, Buttner MJ, Brennan RG et al. The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex. Nucleic Acids Res 2017; 45:6923–6933 [View Article] [PubMed]
    [Google Scholar]
  14. Schumacher MA, Gallagher KA, Holmes NA, Chandra G, Henderson M et al. Evolution of a σ-(c-di-GMP)-anti-σ switch. Proc Natl Acad Sci U S A 2021; 118:e2105447118 [View Article] [PubMed]
    [Google Scholar]
  15. Chou S-H, Galperin MY. Cyclic di-GMP in Streptomycetes: A New Conformation, New Binding Mode, New Receptor, and A New Mechanism to Control Cell Development. Mol Cell 2020; 77:443–445 [View Article] [PubMed]
    [Google Scholar]
  16. Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C et al. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci U S A 2001; 98:12215–12220 [View Article] [PubMed]
    [Google Scholar]
  17. Bentley SD, Chater KF, Cerdeño-Tárraga A-M, Challis GL, Thomson NR et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002; 417:141–147 [View Article] [PubMed]
    [Google Scholar]
  18. Hoskisson PA, Seipke RF. Cryptic or Silent? The Known Unknowns, Unknown Knowns, and Unknown Unknowns of Secondary Metabolism. mBio 2020; 11:e02642-20 [View Article] [PubMed]
    [Google Scholar]
  19. Lee N, Kim W, Hwang S, Lee Y, Cho S et al. Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters. Sci Data 2020; 7:55 [View Article] [PubMed]
    [Google Scholar]
  20. Rigali S, Anderssen S, Naômé A, van Wezel GP. Cracking the regulatory code of biosynthetic gene clusters as a strategy for natural product discovery. Biochem Pharmacol 2018; 153:24–34 [View Article] [PubMed]
    [Google Scholar]
  21. Gavriilidou A, Kautsar SA, Zaburannyi N, Krug D, Müller R et al. A global survey of specialized metabolic diversity encoded in bacterial genomes; 2021 https://www.biorxiv.org/content/10.1101/2021.08.11.455920v1 accessed 3 January 2022
  22. Yushchuk O, Ostash I, Mösker E, Vlasiuk I, Deneka M et al. Eliciting the silent lucensomycin biosynthetic pathway in Streptomyces cyanogenus S136 via manipulation of the global regulatory gene adpA. Sci Rep 2021; 11:3507 [View Article] [PubMed]
    [Google Scholar]
  23. Currie CR. A community of ants, fungi, and bacteria: A multilateral approach to studying symbiosis. Annu Rev Microbiol 2001; 55:357–380 [View Article] [PubMed]
    [Google Scholar]
  24. Jensen PR, Moore BS, Fenical W. The marine actinomycete genus Salinispora: A model organism for secondary metabolite discovery. Nat Prod Rep 2015; 32:738–751 [View Article] [PubMed]
    [Google Scholar]
  25. Heine D, Holmes NA, Worsley SF, Santos ACA, Innocent TM et al. Chemical warfare between leafcutter ant symbionts and a co-evolved pathogen. Nat Commun 2018; 9:2208 [View Article] [PubMed]
    [Google Scholar]
  26. Holmes NA, Devine R, Qin Z, Seipke RF, Wilkinson B et al. Complete genome sequence of Streptomyces formicae KY5, the formicamycin producer. J Biotechnol 2018; 265:116–118 [View Article] [PubMed]
    [Google Scholar]
  27. Li H, Sosa-Calvo J, Horn HA, Pupo MT, Clardy J et al. Convergent evolution of complex structures for ant-bacterial defensive symbiosis in fungus-farming ants. Proc Natl Acad Sci U S A 2018; 115:10720–10725 [View Article] [PubMed]
    [Google Scholar]
  28. Parra J, Soldatou S, Rooney LM, Duncan KRY. Pseudonocardia abyssalis sp. nov. and Pseudonocardia oceani sp. nov., two novel actinomycetes isolated from the deep Southern Ocean. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  29. Qin Z, Munnoch JT, Devine R, Holmes NA, Seipke RF et al. Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chem Sci 2017; 8:3218–3227 [View Article] [PubMed]
    [Google Scholar]
  30. Rutledge PJ, Challis GL. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 2015; 13:509–523 [View Article] [PubMed]
    [Google Scholar]
  31. van Bergeijk DA, Terlouw BR, Medema MH, van Wezel GP. Ecology and genomics of Actinobacteria: new concepts for natural product discovery. Nat Rev Microbiol 2020; 18:546–558 [View Article] [PubMed]
    [Google Scholar]
  32. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C et al. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016; 80:1–43 [View Article] [PubMed]
    [Google Scholar]
  33. Takahashi Y, Matsumoto A, Seino A, Ueno J, Iwai Y et al. Streptomyces avermectinius sp. nov., an avermectin-producing strain. Int J Syst Evol Microbiol 2002; 52:2163–2168 [View Article] [PubMed]
    [Google Scholar]
  34. Weinstein MJ, Luedemann GM, Oden EM, Wagman GH, Rosselet JP et al. Gentamicin, a new antibiotic complex from Micromonospora. J Med Chem 1963; 6:463–464 [View Article] [PubMed]
    [Google Scholar]
  35. Woodward TE, Raby WT. Aureomycin in treatment of experimental and human tularemia. J Am Med Assoc 1949; 139:830–832 [View Article] [PubMed]
    [Google Scholar]
  36. Ehrlich J, Bartz QR, Smith RM, Joslyn DA, Burkholder PR. Chloromycetin, a New Antibiotic From a Soil Actinomycete. Science 1947; 106:417 [View Article] [PubMed]
    [Google Scholar]
  37. Hopwood DA. Streptomyces in nature and medicine: The antibiotic makers Oxford, New York: Oxford University Press; 2007 p 272 p
    [Google Scholar]
  38. Kieser T, Bibb M, Chater K, Butter M, Hopwood D et al. Practical Streptomyces genetics: A laboratory manual; 2000
  39. Cobb RE, Wang Y, Zhao H. High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 2015; 4:723–728 [View Article] [PubMed]
    [Google Scholar]
  40. Tong Y, Charusanti P, Zhang L, Weber T, Lee SY. CRISPR-Cas9 Based Engineering of Actinomycetal Genomes. ACS Synth Biol 2015; 4:1020–1029 [View Article] [PubMed]
    [Google Scholar]
  41. Tong Y, Whitford CM, Blin K, Jørgensen TS, Weber T et al. CRISPR-Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in Streptomycetes. Nat Protoc 2020; 15:2470–2502 [View Article] [PubMed]
    [Google Scholar]
  42. Gomez-Escribano JP, Algora Gallardo L, Bozhüyük KAJ, Kendrew SG, Huckle BD et al. Genome editing reveals that pSCL4 is required for chromosome linearity in Streptomyces clavuligerus. Microb Genom 2021; 7: [View Article] [PubMed]
    [Google Scholar]
  43. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–46 [View Article] [PubMed]
    [Google Scholar]
  44. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  45. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
    [Google Scholar]
  46. Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 2014; 158:412–421 [View Article] [PubMed]
    [Google Scholar]
  47. Lithgow GJ, Driscoll M, Phillips P. A long journey to reproducible results. Nature 2017; 548:387–388 [View Article] [PubMed]
    [Google Scholar]
  48. Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH et al. A computational framework to explore large-scale biosynthetic diversity. Nat Chem Biol 2020; 16:60–68 [View Article] [PubMed]
    [Google Scholar]
  49. Kautsar SA, van der Hooft JJJ, de Ridder D, Medema MH. BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. Gigascience 2021; 10:giaa154 [View Article] [PubMed]
    [Google Scholar]
  50. Blin K, Shaw S, Kautsar SA, Medema MH, Weber T. The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes. Nucleic Acids Res 2021; 49:D639–D643 [View Article] [PubMed]
    [Google Scholar]
  51. Kautsar SA, Blin K, Shaw S, Weber T, Medema MH. BiG-FAM: the biosynthetic gene cluster families database. Nucleic Acids Res 2021; 49:D490–D497 [View Article] [PubMed]
    [Google Scholar]
  52. Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR et al. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res 2020; 48:D454–D458 [View Article] [PubMed]
    [Google Scholar]
  53. Kautsar SA, van der Hooft JJJ, de Ridder D, Medema MH. BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. Gigascience 2021; 10:giaa154 [View Article] [PubMed]
    [Google Scholar]
  54. Fernández-Martínez LT, Bibb MJ. Use of the meganuclease I-SceI of Saccharomyces cerevisiae to select for gene deletions in actinomycetes. Sci Rep 2014; 4:7100 [View Article] [PubMed]
    [Google Scholar]
  55. Higo A, Hara H, Horinouchi S, Ohnishi Y. Genome-wide distribution of AdpA, a global regulator for secondary metabolism and morphological differentiation in Streptomyces, revealed the extent and complexity of the AdpA regulatory network. DNA Res 2012; 19:259–273 [View Article] [PubMed]
    [Google Scholar]
  56. Bush MJ, Bibb MJ, Chandra G, Findlay KC, Buttner MJ. Genes required for aerial growth, cell division, and chromosome segregation are targets of WhiA before sporulation in Streptomyces venezuelae. mBio 2013; 4:e00684-13 [View Article] [PubMed]
    [Google Scholar]
  57. Som NF, Heine D, Holmes N, Knowles F, Chandra G et al. The MtrAB two-component system controls antibiotic production in Streptomyces coelicolor A3(2). Microbiology (Reading) 2017; 163:1415–1419 [View Article] [PubMed]
    [Google Scholar]
  58. Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2016; 34:828–837 [View Article] [PubMed]
    [Google Scholar]
  59. Männle D, McKinnie SMK, Mantri SS, Steinke K, Lu Z et al. Comparative genomics and metabolomics in the genus Nocardia. mSystems. n.d https://journals.asm.org/doi/abs/10.1128/mSystems.00125-20 accessed 3 January 2022
  60. Caesar LK, Montaser R, Keller NP, Kelleher NL. Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities. Nat Prod Rep 2021; 38:2041–2065 [View Article] [PubMed]
    [Google Scholar]
  61. Hjörleifsson Eldjárn G, Ramsay A, van der Hooft JJJ, Duncan KR, Soldatou S et al. Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLOS Comput Biol 2021; 17:e1008920 [View Article] [PubMed]
    [Google Scholar]
  62. Handayani I, Saad H, Ratnakomala S, Lisdiyanti P, Kusharyoto W et al. Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach. Mar Drugs 2021; 19:316 [View Article] [PubMed]
    [Google Scholar]
  63. Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD et al. A community resource for paired genomic and metabolomic data mining. Nat Chem Biol 2021; 17:363–368 [View Article] [PubMed]
    [Google Scholar]
  64. Um S, Guo H, Thiengmag S, Benndorf R, Murphy R et al. Comparative Genomic and Metabolic Analysis of Streptomyces sp. RB110 Morphotypes Illuminates Genomic Rearrangements and Formation of a New 46-Membered Antimicrobial Macrolide. ACS Chem Biol 2021; 16:1482–1492 [View Article] [PubMed]
    [Google Scholar]
  65. Remmel A. Scientists want virtual meetings to stay after the COVID pandemic. Nature 2021; 591:185–186 [View Article] [PubMed]
    [Google Scholar]
  66. Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A. In living color: bacterial pigments as an untapped resource in the classroom and beyond. PLoS Biol 2010; 8:e1000510 [View Article] [PubMed]
    [Google Scholar]
  67. Genilloud O. Actinomycetes: still a source of novel antibiotics. Nat Prod Rep 2017; 34:1203–1232 [View Article] [PubMed]
    [Google Scholar]
  68. Schlimpert S, Flärdh K, Buttner M. Fluorescence Time-lapse Imaging of the Complete S. venezuelae Life Cycle Using a Microfluidic Device. J Vis Exp 201653863 [View Article] [PubMed]
    [Google Scholar]
  69. Liu G, Chater KF, Chandra G, Niu G, Tan H. Molecular regulation of antibiotic biosynthesis in Streptomyces. Microbiol Mol Biol Rev 2013; 77:112–143 [View Article] [PubMed]
    [Google Scholar]
  70. Romero-Rodríguez A, Robledo-Casados I, Sánchez S. An overview on transcriptional regulators in Streptomyces. Biochim Biophys Acta 2015; 1849:1017–1039 [View Article] [PubMed]
    [Google Scholar]
  71. Hoskisson PA, Fernández-Martínez LT. Regulation of specialised metabolites in Actinobacteria - expanding the paradigms. Environ Microbiol Rep 2018; 10:231–238 [View Article] [PubMed]
    [Google Scholar]
  72. van der Meij A, Willemse J, Schneijderberg MA, Geurts R, Raaijmakers JM et al. Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity. Antonie Van Leeuwenhoek 2018; 111:679–690 [View Article] [PubMed]
    [Google Scholar]
  73. Worsley SF, Newitt J, Rassbach J, Batey SFD, Holmes NA et al. Streptomyces endophytes promote host health and enhance growth across plant species. Appl Environ Microbiol 2020; 86:e01053-20 [View Article] [PubMed]
    [Google Scholar]
  74. Prudence SM, Newitt JT, Worsley SF, Macey MC, Murrell JC et al. Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome. Environ Microbiome 2021; 16:12 [View Article] [PubMed]
    [Google Scholar]
  75. Barke J, Seipke RF, Yu DW, Hutchings MI. A mutualistic microbiome: How do fungus-growing ants select their antibiotic-producing bacteria?. Commun Integr Biol 2011; 4:41–43 [View Article] [PubMed]
    [Google Scholar]
  76. Abdelmohsen UR, Yang C, Horn H, Hajjar D, Ravasi T et al. Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity. Mar Drugs 2014; 12:2771–2789 [View Article] [PubMed]
    [Google Scholar]
  77. Larran S, Perelló A, Simón MR, Moreno V. Isolation and analysis of endophytic microorganisms in wheat (Triticum aestivum L.) leaves. World J Microbiol Biotechnol 2002; 18:683–686 [View Article]
    [Google Scholar]
  78. Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 2012; 488:91–95 [View Article] [PubMed]
    [Google Scholar]
  79. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J et al. Defining the core Arabidopsis thaliana root microbiome. Nature 2012; 488:86–90 [View Article] [PubMed]
    [Google Scholar]
  80. Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J et al. Plant microbiome. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 2015; 349:860–864 [View Article] [PubMed]
    [Google Scholar]
  81. Termini CM, Traver D. Impact of COVID-19 on early career scientists: an optimistic guide for the future. BMC Biol 2020; 18:95 [View Article] [PubMed]
    [Google Scholar]
  82. Prudence SMM, Addington E, Castaño-Espriu L, Mark DR, Pintor-Escobar L et al. Advances in actinomycete research: an ActinoBase review of 2019. Microbiology 2020; 166:683–694 [View Article] [PubMed]
    [Google Scholar]
  83. Undabarrena A, Pereira CF, Kruasuwan W, Parra J, Sélem-Mojica N et al. Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21. Microbiology 2021; 167: [View Article] [PubMed]
    [Google Scholar]
  84. Nodwell JR. Microbe Profile: Streptomyces coelicolor: a burlesque of pigments and phenotypes. Microbiology 2019; 165:953–955 [View Article] [PubMed]
    [Google Scholar]
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