Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.

Nouioui I, Rückert C, Willemse J, van Wezel GP, Klenk H-P, Busche T, Kalinowski J, Bredholt H, Zotchev SB (2017)
Antonie Van Leeuwenhoek. Journal of Microbiology 110(12): 1705-1717.

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Autor*in
Nouioui, Imen; Rückert, ChristianUniBi ; Willemse, Jost; van Wezel, Gilles P.; Klenk, Hans-Peter; Busche, TobiasUniBi; Kalinowski, JörnUniBi; Bredholt, Harald; Zotchev, Sergey B.
Einrichtung
Centrum für Biotechnologie
Abstract / Bemerkung
Two actinobacterial strains, ADI 127-17T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17T (= DSM 46855T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17T = DSM 46855T = CECT 9355T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092T and A. hoggarensis DSM 45943T to unravel unique genome features and biosynthetic potential of the new isolates.
Erscheinungsjahr
2017
Zeitschriftentitel
Antonie Van Leeuwenhoek. Journal of Microbiology
Band
110
Ausgabe
12
Seite(n)
1705-1717
Urheberrecht / Lizenzen
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0)
ISBN
0003-6072
ISSN
0003-6072
Page URI
https://pub.uni-bielefeld.de/record/2913400

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Nouioui I, Rückert C, Willemse J, et al. Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie Van Leeuwenhoek. Journal of Microbiology. 2017;110(12):1705-1717.
Nouioui, I., Rückert, C., Willemse, J., van Wezel, G. P., Klenk, H. - P., Busche, T., Kalinowski, J., et al. (2017). Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie Van Leeuwenhoek. Journal of Microbiology, 110(12), 1705-1717. doi:10.1007/s10482-017-0920-9
Nouioui, Imen, Rückert, Christian, Willemse, Jost, van Wezel, Gilles P., Klenk, Hans-Peter, Busche, Tobias, Kalinowski, Jörn, Bredholt, Harald, and Zotchev, Sergey B. 2017. “Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.”. Antonie Van Leeuwenhoek. Journal of Microbiology 110 (12): 1705-1717.
Nouioui, I., Rückert, C., Willemse, J., van Wezel, G. P., Klenk, H. - P., Busche, T., Kalinowski, J., Bredholt, H., and Zotchev, S. B. (2017). Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie Van Leeuwenhoek. Journal of Microbiology 110, 1705-1717.
Nouioui, I., et al., 2017. Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie Van Leeuwenhoek. Journal of Microbiology, 110(12), p 1705-1717.
I. Nouioui, et al., “Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.”, Antonie Van Leeuwenhoek. Journal of Microbiology, vol. 110, 2017, pp. 1705-1717.
Nouioui, I., Rückert, C., Willemse, J., van Wezel, G.P., Klenk, H.-P., Busche, T., Kalinowski, J., Bredholt, H., Zotchev, S.B.: Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation. Antonie Van Leeuwenhoek. Journal of Microbiology. 110, 1705-1717 (2017).
Nouioui, Imen, Rückert, Christian, Willemse, Jost, van Wezel, Gilles P., Klenk, Hans-Peter, Busche, Tobias, Kalinowski, Jörn, Bredholt, Harald, and Zotchev, Sergey B. “Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.”. Antonie Van Leeuwenhoek. Journal of Microbiology 110.12 (2017): 1705-1717.

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Daten bereitgestellt von Europe PubMed Central.

An orthogonal system for heterologous expression of actinobacterial lasso peptides in Streptomyces hosts.
Mevaere J, Goulard C, Schneider O, Sekurova ON, Ma H, Zirah S, Afonso C, Rebuffat S, Zotchev SB, Li Y., Sci Rep 8(1), 2018
PMID: 29844351
Isolation of Petrocidin A, a New Cytotoxic Cyclic Dipeptide from the Marine Sponge-Derived Bacterium Streptomyces sp. SBT348.
Cheng C, Othman EM, Stopper H, Edrada-Ebel R, Hentschel U, Abdelmohsen UR., Mar Drugs 15(12), 2017
PMID: 29211005

62 References

Daten bereitgestellt von Europe PubMed Central.

Improved prediction of signal peptides: SignalP 3.0.
Bendtsen JD, Nielsen H, von Heijne G, Brunak S., J. Mol. Biol. 340(4), 2004
PMID: 15223320
Immense essence of excellence: marine microbial bioactive compounds.
Bhatnagar I, Kim SK., Mar Drugs 8(10), 2010
PMID: 21116414
Prokaryotic gene prediction using GeneMark and GeneMark.hmm
Borodovsky M, Mills R, Besemer J, Lomsadze A., 2003
Actinoalloteichus hoggarensis sp. nov., an actinomycete isolated from Saharan soil.
Boudjelal F, Zitouni A, Bouras N, Schumann P, Sproer C, Sabaou N, Klenk HP., Int. J. Syst. Evol. Microbiol. 65(Pt 6), 2015
PMID: 25825244
Cross-membranes orchestrate compartmentalization and morphogenesis in Streptomyces.
Celler K, Koning RI, Willemse J, Koster AJ, van Wezel GP., Nat Commun 7(), 2016
PMID: 27291257
EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences.
Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW., Int. J. Syst. Evol. Microbiol. 57(Pt 10), 2007
PMID: 17911292
Analysis of isoprenoid quinone
Collins MD., 1985
Introducing the parvome: bioactive compounds in the microbial world.
Davies J, Ryan KS., ACS Chem. Biol. 7(2), 2011
PMID: 22074935
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.
Eddy SR., BMC Bioinformatics 3(), 2002
PMID: 12095421
Reverse transcriptase sequencing of 16S ribosomal RNA from Faenia rectivirgula, Pseudonocardia thermophila and Saccharopolyspora hirsuta, three wall type IV actinomycetes which lack mycolic acids.
Embley TM, Smida J, Stackebrandt E., J. Gen. Microbiol. 134(4), 1988
PMID: 2460582
List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet.
Euzeby JP., Int. J. Syst. Bacteriol. 47(2), 1997
PMID: 9103655
Base-calling of automated sequencer traces using phred. II. Error probabilities.
Ewing B, Green P., Genome Res. 8(3), 1998
PMID: 9521922
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Ewing B, Hillier L, Wendl MC, Green P., Genome Res. 8(3), 1998
PMID: 9521921
Salinosporamide A: a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus salinospora.
Feling RH, Buchanan GO, Mincer TJ, Kauffman CA, Jensen PR, Fenical W., Angew. Chem. Int. Ed. Engl. 42(3), 2003
PMID: 12548698
Cytotoxic bipyridines from the marine-derived actinomycete Actinoalloteichus cyanogriseus WH1-2216-6.
Fu P, Wang S, Hong K, Li X, Liu P, Wang Y, Zhu W., J. Nat. Prod. 74(8), 2011
PMID: 21770434
Cyanogramide with a new spiro[indolinone-pyrroloimidazole] skeleton from Actinoalloteichus cyanogriseus.
Fu P, Kong F, Li X, Wang Y, Zhu W., Org. Lett. 16(14), 2014
PMID: 24968070
Stereochemical Assignment and Biological Evaluation of BE-14106 Unveils the Importance of One Acetate Unit for the Antifungal Activity of Polyene Macrolactams.
Fujita K, Sugiyama R, Nishimura S, Ishikawa N, Arai MA, Ishibashi M, Kakeya H., J. Nat. Prod. 79(7), 2016
PMID: 27331864
Viewing and editing assembled sequences using Consed
Gordon D., 2003
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Rfam: annotating non-coding RNAs in complete genomes.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608160
The biosynthetic gene cluster for a monocyclic beta-lactam antibiotic, nocardicin A.
Gunsior M, Breazeale SD, Lind AJ, Ravel J, Janc JW, Townsend CA., Chem. Biol. 11(7), 2004
PMID: 15271351
Mining and polishing of the treasure trove in the bacterial genus streptomyces.
Horinouchi S., Biosci. Biotechnol. Biochem. 71(2), 2007
PMID: 17284841
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023
Genomics of sponge-associated Streptomyces spp. closely related to Streptomyces albus J1074: insights into marine adaptation and secondary metabolite biosynthesis potential.
Ian E, Malko DB, Sekurova ON, Bredholt H, Ruckert C, Borisova ME, Albersmeier A, Kalinowski J, Gelfand MS, Zotchev SB., PLoS ONE 9(5), 2014
PMID: 24819608
The National Center for Biotechnology Information's Protein Clusters Database.
Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18940865
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Krogh A, Larsson B, von Heijne G, Sonnhammer EL., J. Mol. Biol. 305(3), 2001
PMID: 11152613
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Kumar S, Stecher G, Tamura K., Mol. Biol. Evol. 33(7), 2016
PMID: 27004904
Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum
Kuykendall LD, Roy MA, O’Neill JJ, Devine TE., 1988
Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009.
Labeda DP, Goodfellow M, Chun J, Zhi XY, Li WJ., Int. J. Syst. Evol. Microbiol. 61(Pt 6), 2010
PMID: 20601483
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW., Nucleic Acids Res. 35(9), 2007
PMID: 17452365
16S/23S rRNA sequencing. Nucleic acid techniques
Lane DJ., 1991
Chemical composition as a criterion in the classification of aerobic actinomycetes
Lechevalier MP, Lechevalier HA., 1970
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19914934
Marine actinobacteria: an important source of bioactive natural products.
Manivasagan P, Kang KH, Sivakumar K, Li-Chan EC, Oh HM, Kim SK., Environ. Toxicol. Pharmacol. 38(1), 2014
PMID: 24959957
CDD: specific functional annotation with the Conserved Domain Database.
Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18984618
An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal K, Parlett JH., 1984
Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids.
Miller LT., J. Clin. Microbiol. 16(3), 1982
PMID: 7130373
Marine actinomycetes: a new source of compounds against the human malaria parasite.
Prudhomme J, McDaniel E, Ponts N, Bertani S, Fenical W, Jensen P, Le Roch K., PLoS ONE 3(6), 2008
PMID: 18523554
Introducing a Digital Protologue: A timely move towards a database-driven systematics of Archaea and Bacteria.
Rossello-Mora R, Trujillo ME, Sutcliffe IC., Syst. Appl. Microbiol. 40(3), 2017
PMID: 28249694
Complete genome sequence of Streptomyces lividans TK24.
Ruckert C, Albersmeier A, Busche T, Jaenicke S, Winkler A, Friðjonsson OH, Hreggviðsson GO, Lambert C, Badcock D, Bernaerts K, Anne J, Economou A, Kalinowski J., J. Biotechnol. 199(), 2015
PMID: 25680930
Diversity of the ectoines biosynthesis genes in the salt tolerant Streptomyces and evidence for inductive effect of ectoines on their accumulation.
Sadeghi A, Soltani BM, Nekouei MK, Jouzani GS, Mirzaei HH, Sadeghizadeh M., Microbiol. Res. 169(9-10), 2014
PMID: 24629523
Identification of bacteria by gas chromatography of cellular fatty acids
Sasser M., 1990
Neomaclafungins A-I: oligomycin-class macrolides from a marine-derived actinomycete.
Sato S, Iwata F, Yamada S, Katayama M., J. Nat. Prod. 75(11), 2012
PMID: 23102410
Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge.
Schaffert L, Albersmeier A, Winkler A, Kalinowski J, Zotchev SB, Ruckert C., Stand Genomic Sci 11(), 2016
PMID: 28031775
Methods for characterizing Streptomyces species
Shirling EB, Gottlieb D., 1966
Actinoalloteichus spitiensis sp. nov., a novel actinobacterium isolated from a cold desert of the Indian Himalayas.
Singla AK, Mayilraj S, Kudo T, Krishnamurthi S, Prasad GS, Vohra RM., Int. J. Syst. Evol. Microbiol. 55(Pt 6), 2005
PMID: 16280527
Proposal for a new hierarchic classification System, Actinobacteria classis nov
Stackebrandt E, Rainy FA, Ward-Rainy NL., 1997
Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography.
Staneck JL, Roberts GD., Appl Microbiol 28(2), 1974
PMID: 4605116
Marine actinomycetes: an ongoing source of novel bioactive metabolites.
Subramani R, Aalbersberg W., Microbiol. Res. 167(10), 2012
PMID: 22796410
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
Tamura K, Nei M., Mol. Biol. Evol. 10(3), 1993
PMID: 8336541
Actinoalloteichus cyanogriseus gen. nov., sp. nov.
Tamura T, Zhiheng L, Yamei Z, Hatano K., Int. J. Syst. Evol. Microbiol. 50 Pt 4(), 2000
PMID: 10939647
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG., Nucleic Acids Res. 25(24), 1997
PMID: 9396791
Characterization of the maduropeptin biosynthetic gene cluster from Actinomadura madurae ATCC 39144 supporting a unifying paradigm for enediyne biosynthesis.
Van Lanen SG, Oh TJ, Liu W, Wendt-Pienkowski E, Shen B., J. Am. Chem. Soc. 129(43), 2007
PMID: 17918933
Novel cyclopentenone derivatives produced by a rare actinobacterial strain Actinoalloteichus nanshanensis sp. nov. NEAU 119.
Wang XJ, Zhang J, Wang JD, Qian PT, Liu CX, Xiang WS., Nat. Prod. Res. 27(20), 2013
PMID: 23432091
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH., Nucleic Acids Res. 43(W1), 2015
PMID: 25948579
Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa).
Xiang W, Liu C, Wang X, Du J, Xi L, Huang Y., Int. J. Syst. Evol. Microbiol. 61(Pt 5), 2010
PMID: 20562245
Antibiotics as signalling molecules.
Yim G, Wang HH, Davies J., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 362(1483), 2007
PMID: 17360275
Structure and biosynthesis of heat-stable antifungal factor (HSAF), a broad-spectrum antimycotic with a novel mode of action.
Yu F, Zaleta-Rivera K, Zhu X, Huffman J, Millet JC, Harris SD, Yuen G, Li XC, Du L., Antimicrob. Agents Chemother. 51(1), 2006
PMID: 17074795
Actinoalloteichus hymeniacidonis sp. nov., an actinomycete isolated from the marine sponge Hymeniacidon perleve.
Zhang H, Zheng W, Huang J, Luo H, Jin Y, Zhang W, Liu Z, Huang Y., Int. J. Syst. Evol. Microbiol. 56(Pt 10), 2006
PMID: 17012552
Identification of caerulomycin A gene cluster implicates a tailoring amidohydrolase.
Zhu Y, Fu P, Lin Q, Zhang G, Zhang H, Li S, Ju J, Zhu W, Zhang C., Org. Lett. 14(11), 2012
PMID: 22591508
Marine actinomycetes as an emerging resource for the drug development pipelines.
Zotchev SB., J. Biotechnol. 158(4), 2011
PMID: 21683100
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