{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T17:12:18Z","timestamp":1760116338591,"version":"build-2065373602"},"reference-count":81,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2024,12,22]],"date-time":"2024-12-22T00:00:00Z","timestamp":1734825600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Alexander von Humboldt Foundation","award":["871072"],"award-info":[{"award-number":["871072"]}]},{"name":"European Union","award":["871072"],"award-info":[{"award-number":["871072"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Glycopeptide antibiotics (GPAs) are a very successful class of clinically relevant antibacterials, used to treat severe infections caused by Gram-positive pathogens, e.g., multidrug resistant and methicillin-resistant staphylococci. The biosynthesis of GPAs is coded within large biosynthetic gene clusters (BGCs). In recent years, modern DNA sequencing technologies have allowed the identification and characterization of multiple novel GPA BGCs, leading to the discovery of novel compounds. Our previous research anticipated that the genome of Amycolatopsis bartoniae DSM 45807T carries a novel GPA BGC, although the genomic sequence quality available at that time did not allow us to characterize its organization properly. Objectives: To address this gap, in the current work we aimed to produce a complete genome assembly of A. bartoniae DSM 45807, and to identify and analyze the corresponding GPA BGC. Methods: Bioinformatic and microbiological methods were utilized in this research. Results: We de novo sequenced and completely assembled the genome of A. bartoniae DSM 45807, and fully characterized the BGC of interest, named aba. This BGC has an unusual gene organization and it contains four genes for sulfotransferases, which are considered to be rare in GPA BGCs. Our pathway prediction indicated that aba encodes the biosynthesis of a putatively novel GPA, although we were not able to detect any GPA production under different cultivation conditions, implying that aba pathway is inactive. Conclusions: Our results indicate aba as a promising source for new GPA tailoring enzymes.<\/jats:p>","DOI":"10.3390\/genes15121651","type":"journal-article","created":{"date-parts":[[2024,12,23]],"date-time":"2024-12-23T04:33:29Z","timestamp":1734928409000},"page":"1651","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Complete Genome Assembly of Amycolatopsis bartoniae DSM 45807T Allows the Characterization of a Novel Glycopeptide Biosynthetic Gene Cluster"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-5687-1446","authenticated-orcid":false,"given":"Anastasia","family":"Stepanyshyn","sequence":"first","affiliation":[{"name":"Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9722-4435","authenticated-orcid":false,"given":"Christian","family":"R\u00fcckert-Reed","sequence":"additional","affiliation":[{"name":"Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany"},{"name":"Medical School OWL, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9211-8927","authenticated-orcid":false,"given":"Tobias","family":"Busche","sequence":"additional","affiliation":[{"name":"Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bohdan","family":"Yaruta","sequence":"additional","affiliation":[{"name":"Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5446-7544","authenticated-orcid":false,"given":"Andres","family":"Andreo-Vidal","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9195-6777","authenticated-orcid":false,"given":"Flavia","family":"Marinelli","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9052-1998","authenticated-orcid":false,"given":"J\u00f6rn","family":"Kalinowski","sequence":"additional","affiliation":[{"name":"Technology Platform Genomics, CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3296-8297","authenticated-orcid":false,"given":"Oleksandr","family":"Yushchuk","sequence":"additional","affiliation":[{"name":"Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 79005 Lviv, Ukraine"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,12,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1039\/C7NP00012J","article-title":"Targeting a cell wall biosynthesis hot spot","volume":"34","author":"Schneider","year":"2017","journal-title":"Nat. Prod. Rep."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1002\/(SICI)1521-3773(19990802)38:15<2096::AID-ANIE2096>3.0.CO;2-F","article-title":"Chemistry, biology, and medicine of the glycopeptide antibiotics","volume":"38","author":"Nicolaou","year":"1999","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.mib.2010.08.011","article-title":"Glycopeptide biosynthesis in the context of basic cellular functions","volume":"13","author":"Stegmann","year":"2010","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"8548","DOI":"10.1073\/pnas.151246498","article-title":"Molecular cloning and sequence analysis of the complestatin biosynthetic gene cluster","volume":"98","author":"Chiu","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_5","first-page":"76","article-title":"The border sequence of the balhimycin biosynthesis gene cluster from Amycolatopsis balhimycina contains bbr, encoding a StrR-like pathway-specific regulator","volume":"13","author":"Shawky","year":"2007","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"ref_6","first-page":"107","article-title":"Biosynthetic gene cluster of the glycopeptide antibiotic teicoplanin: Characterization of two glycosyltransferases and the key acyltransferase","volume":"11","author":"Li","year":"2004","journal-title":"Chem. Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1039\/NP9961300469","article-title":"The glycopeptide story\u2014How to kill the deadly \u201cSuperbugs\u201d","volume":"13","author":"Williams","year":"1996","journal-title":"Nat. Prod. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1016\/j.biotechadv.2018.02.009","article-title":"Old and new glycopeptide antibiotics: Arom product to gene and back in the post-genomic era","volume":"36","author":"Marcone","year":"2018","journal-title":"Biotechnol. Adv."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e00408-13","DOI":"10.1128\/genomeA.00408-13","article-title":"Genome sequence of the vancomycin-producing Amycolatopsis orientalis subsp. orientalis strain KCTC 9412T","volume":"1","author":"Jeong","year":"2013","journal-title":"Genome Announc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1021\/acsinfecdis.2c00253","article-title":"Recent advances in the development of semisynthetic glycopeptide antibiotics: 2014-2022","volume":"8","author":"Innocenti","year":"2022","journal-title":"ACS Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/S1074-5521(98)90060-6","article-title":"Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic","volume":"5","author":"Kirkpatrick","year":"1998","journal-title":"Chem. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/S1074-5521(03)00120-0","article-title":"The gene cluster for the biosynthesis of the glycopeptide antibiotic A40926 by Nonomuraea species","volume":"10","author":"Sosio","year":"2003","journal-title":"Chem. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.7164\/antibiotics.42.1882","article-title":"Proposal to name the vancomycin-ristocetin like glycopeptides as dalbaheptides","volume":"42","author":"Parenti","year":"1989","journal-title":"J. Antibiot."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/s41586-020-1990-9","article-title":"Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling","volume":"578","author":"Culp","year":"2020","journal-title":"Nature"},{"unstructured":"Gavriilidou, A., Adamek, M., Rodler, J.-P., Kubach, N., Kramer, S., Huson, D.H., Cryle, M.J., Stegmann, E., and Ziemert, N. Phylogenetic distance and structural diversity directing a reclassification of glycopeptide antibiotics. bioRxiv.","key":"ref_15"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.jgar.2023.12.021","article-title":"The first vanE-type vancomycin resistant Enterococcus faecalis isolates in Norway\u2014Phenotypic and molecular characteristics","volume":"36","author":"Janice","year":"2024","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1007\/s10096-022-04479-4","article-title":"VanA-Enterococcus faecalis in Poland: Hospital population clonal structure and vanA mobilome","volume":"41","author":"Wardal","year":"2022","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1186\/s12879-024-09797-w","article-title":"Unraveling novel mutation patterns and morphological variations in two dalbavancin-resistant MRSA strains in Austria using whole genome sequencing and transmission electron microscopy","volume":"24","author":"Hotz","year":"2024","journal-title":"BMC Infect. Dis."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1862","DOI":"10.1038\/s41564-019-0531-5","article-title":"Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance","volume":"4","author":"Waglechner","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1021\/acscentsci.1c01389","article-title":"Phylogeny-informed synthetic biology reveals unprecedented structural novelty in Type V glycopeptide antibiotics","volume":"8","author":"Xu","year":"2022","journal-title":"ACS Cent. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"7842","DOI":"10.1038\/s41467-023-43451-4","article-title":"Resurrecting ancestral antibiotics: Unveiling the origins of modern lipid II targeting glycopeptides","volume":"14","author":"Hansen","year":"2023","journal-title":"Nat. Commun."},{"doi-asserted-by":"crossref","unstructured":"Andreo-Vidal, A., Binda, E., Fedorenko, V., Marinelli, F., and Yushchuk, O. (2021). Genomic insights into the distribution and phylogeny of glycopeptide resistance determinants within the Actinobacteria phylum. Antibiotics, 10.","key":"ref_22","DOI":"10.3390\/antibiotics10121533"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"5687","DOI":"10.1128\/AAC.03349-14","article-title":"Antibiotic resistance mechanisms inform discovery: Identification and characterization of a novel Amycolatopsis strain producing ristocetin","volume":"58","author":"Truman","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"5232","DOI":"10.1038\/s41467-020-19138-5","article-title":"GPAHex\u2014A synthetic biology platform for Type IV\u2013V glycopeptide antibiotic production and discovery","volume":"11","author":"Xu","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS ONE"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"D1020","DOI":"10.1093\/nar\/gkaa1105","article-title":"RefSeq: Expanding the prokaryotic genome annotation pipeline reach with protein family model curation","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1093\/nar\/gkh454","article-title":"CD-Search: Protein domain annotations on the fly","volume":"32","author":"Bryant","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"W46","DOI":"10.1093\/nar\/gkad344","article-title":"AntiSMASH 7.0: New and improved predictions for detection, regulation, chemical structures and visualisation","volume":"51","author":"Blin","year":"2023","journal-title":"Nucleic Acids Res."},{"unstructured":"Kieser, T., Bibb, M., Buttner, M., and Chater, K. (2000). Practical Streptomyces Genetics, John Innes Foundation. [2nd ed.].","key":"ref_35"},{"unstructured":"Sambrook, J., and Russell, D.W. (2001). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press. [3rd ed.].","key":"ref_36"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"3507","DOI":"10.1038\/s41598-021-82934-6","article-title":"Eliciting the silent lucensomycin biosynthetic pathway in Streptomyces cyanogenus S136 via manipulation of the global regulatory gene adpA","volume":"11","author":"Yushchuk","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2888","DOI":"10.1128\/AAC.48.8.2888-2896.2004","article-title":"Antibiotic-inducible promoter regulated by the cell envelope stress-sensing two-component system LiaRS of Bacillus subtilis","volume":"48","author":"Mascher","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1046\/j.1365-2958.2003.03786.x","article-title":"Cell wall stress responses in Bacillus subtilis: The regulatory network of the bacitracin stimulon","volume":"50","author":"Mascher","year":"2003","journal-title":"Mol. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"17273","DOI":"10.1073\/pnas.0807564105","article-title":"Cloning and characterization of new glycopeptide gene clusters found in an environmental DNA megalibrary","volume":"105","author":"Banik","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"doi-asserted-by":"crossref","unstructured":"Yushchuk, O., and Ostash, B. (2022). Glycopeptide antibiotics: Genetics, chemistry, and new screening approaches. Nat. Prod. Actinomycetes Divers. Ecol. Drug Discov., 411\u2013444.","key":"ref_41","DOI":"10.1007\/978-981-16-6132-7_16"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"6185","DOI":"10.1128\/AAC.03512-14","article-title":"Overproduction of ristomycin a by activation of a silent gene cluster in Amycolatopsis japonicum MG417-CF17","volume":"58","author":"Spohn","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1016\/S0969-2126(96)00156-6","article-title":"Crystal structure of vancomycin","volume":"4","author":"Schneider","year":"1996","journal-title":"Structure"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.ymben.2010.05.001","article-title":"Increased glycopeptide production after overexpression of shikimate pathway genes being part of the balhimycin biosynthetic gene cluster","volume":"12","author":"Thykaer","year":"2010","journal-title":"Metab. Eng."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"14901","DOI":"10.1073\/pnas.221582098","article-title":"Glycopeptide antibiotic biosynthesis: Enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine","volume":"98","author":"Chen","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"38370","DOI":"10.1074\/jbc.M106580200","article-title":"A polyketide synthase in glycopeptide biosynthesis. The biosynthesis of the non-proteinogenic amino acid (S)-3,5-dihydroxyphenylglycine","volume":"276","author":"Pfeifer","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1039\/b103668h","article-title":"Biosynthesis of the l-p-hydroxyphenylglycine constituent of the vancomycin-group antibiotic chloroeremomycin","volume":"7","author":"Sandercock","year":"2001","journal-title":"Chem. Commun."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4042","DOI":"10.1074\/jbc.M512223200","article-title":"New insights into the evolutionary links relating to the 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subfamilies","volume":"281","author":"Wu","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1016\/S1074-5521(00)00043-0","article-title":"Biosynthesis of l-p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics","volume":"7","author":"Hubbard","year":"2000","journal-title":"Chem. Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1099\/00221287-148-4-1105","article-title":"Nonribosomal biosynthesis of vancomycin-type antibiotics: A heptapeptide backbone and eight peptide synthetase modules","volume":"148","author":"Recktenwald","year":"2002","journal-title":"Microbiology"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"6093","DOI":"10.1128\/JB.186.18.6093-6100.2004","article-title":"Biosynthesis of chloro-\u03b2-hydroxytyrosine, a nonproteinogenic amino acid of the peptidic backbone of glycopeptide antibiotics","volume":"186","author":"Puk","year":"2004","journal-title":"J. Bacteriol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/cbic.200900600","article-title":"The thioesterase Bhp is involved in the formation of \u03b2-hydroxytyrosine during balhimycin biosynthesis in Amycolatopsis balhimycina","volume":"11","author":"Mulyani","year":"2010","journal-title":"ChemBioChem"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1016\/j.jbiotec.2006.04.009","article-title":"Genetic analysis of the balhimycin (vancomycin-type) oxygenase genes","volume":"124","author":"Stegmann","year":"2006","journal-title":"J. Biotechnol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1016\/j.chembiol.2007.08.014","article-title":"The biosynthesis of teicoplanin-type glycopeptide antibiotics: Assignment of P450 mono-oxygenases to side chain cyclizations of glycopeptide A47934","volume":"14","author":"Hadatsch","year":"2007","journal-title":"Chem. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1021\/acsinfecdis.6b00105","article-title":"How to make a glycopeptide: A synthetic biology approach to expand antibiotic chemical diversity","volume":"2","author":"Yim","year":"2016","journal-title":"ACS Infect. Dis."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1002\/cbic.200900665","article-title":"The biosynthesis of liposidomycin-like A-90289 antibiotics featuring a new type of sulfotransferase","volume":"11","author":"Funabashi","year":"2010","journal-title":"ChemBioChem"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1002\/cbic.200900637","article-title":"Analysis of the liposidomycin gene cluster leads to the identification of new caprazamycin derivatives","volume":"11","author":"Kaysser","year":"2010","journal-title":"ChemBioChem"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"22208","DOI":"10.1021\/acs.jafc.4c06771","article-title":"New bacterial aryl sulfotransferases: Effective tools for sulfation of polyphenols","volume":"72","author":"Brodsky","year":"2024","journal-title":"J. Agric. Food Chem."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"858708","DOI":"10.3389\/fchem.2022.858708","article-title":"Genetics behind the glycosylation patterns in the biosynthesis of dalbaheptides","volume":"10","author":"Yushchuk","year":"2022","journal-title":"Front. Chem."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.chembiol.2004.12.013","article-title":"The neocarzinostatin biosynthetic gene cluster from Streptomyces carzinostaticus ATCC 15944 involving two iterative type I polyketide synthases","volume":"12","author":"Liu","year":"2005","journal-title":"Chem. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"4089","DOI":"10.1007\/s00253-019-09789-w","article-title":"Regulation of teicoplanin biosynthesis: Refining the roles of tei cluster-situated regulatory genes","volume":"103","author":"Yushchuk","year":"2019","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/s00253-007-1139-x","article-title":"The ABC transporter Tba of Amycolatopsis balhimycina is required for efficient export of the glycopeptide antibiotic balhimycin","volume":"77","author":"Menges","year":"2007","journal-title":"Appl. Microbiol. Biotechnol."},{"doi-asserted-by":"crossref","unstructured":"Chen, J., Zhang, S., Chen, Y., Tian, X., Gu, Y., and Ju, J. (2021). Identification and heterologous expression of the kendomycin B biosynthetic gene cluster from Verrucosispora sp. SCSIO 07399. Mar. Drugs, 19.","key":"ref_63","DOI":"10.3390\/md19120673"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1038\/nbt.2685","article-title":"Identifying producers of antibacterial compounds by screening for antibiotic resistance","volume":"31","author":"Thaker","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"e01540-18","DOI":"10.1128\/AAC.01540-18","article-title":"Trichlorination of a teicoplanin-type glycopeptide antibiotic by the halogenase StaI evades resistance","volume":"62","author":"Yim","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1111\/j.1574-6968.2006.00120.x","article-title":"A derivative of the glycopeptide A40926 produced by inactivation of the \u03b2-hydroxylase gene in Nonomuraea sp. ATCC39727","volume":"256","author":"Stinchi","year":"2006","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/s10482-012-9716-0","article-title":"Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils","volume":"102","author":"Zucchi","year":"2012","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/s00253-008-1530-2","article-title":"Optimization of culture conditions and scale-up to plant scales for teicoplanin production by Actinoplanes teichomyceticus","volume":"80","author":"Jung","year":"2008","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1475-2859-10-82","article-title":"Actinoplanes teichomyceticus ATCC 31121 as a cell factory for producing teicoplanin","volume":"10","author":"Taurino","year":"2011","journal-title":"Microb. Cell Fact."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"8","DOI":"10.3389\/fmicb.2020.00008","article-title":"New molecular tools for regulation and improvement of A40926 glycopeptide antibiotic production in Nonomuraea gerenzanensis ATCC 39727","volume":"11","author":"Yushchuk","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1021\/acschembio.1c00170","article-title":"Genomic-led discovery of a novel glycopeptide antibiotic by Nonomuraea coxensis DSM 45129","volume":"16","author":"Yushchuk","year":"2021","journal-title":"ACS Chem. Biol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1021\/sb300092n","article-title":"Opportunities for synthetic biology in antibiotics: Expanding glycopeptide chemical diversity","volume":"4","author":"Thaker","year":"2015","journal-title":"ACS Synth. Biol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"8962","DOI":"10.1073\/pnas.102285099","article-title":"Assembling the glycopeptide antibiotic scaffold: The biosynthesis of A47934 from Streptomyces toyocaensis NRRL15009","volume":"99","author":"Pootoolal","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1111\/j.1574-6976.2011.00317.x","article-title":"Signals and regulators that govern Streptomyces development","volume":"36","author":"McCormick","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1007\/s11274-015-1882-6","article-title":"The adpA-like regulatory gene from Actinoplanes teichomyceticus: In silico analysis and heterologous expression","volume":"31","author":"Ostash","year":"2015","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"5191","DOI":"10.1128\/AAC.02626-14","article-title":"Relationship between glycopeptide production and resistance in the actinomycete Nonomuraea sp. ATCC 39727","volume":"58","author":"Marcone","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1111\/mmi.14266","article-title":"Gene miaA for post-transcriptional modification of tRNAXXA is important for morphological and metabolic differentiation in Streptomyces","volume":"112","author":"Koshla","year":"2019","journal-title":"Mol. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"3.13.1","DOI":"10.1002\/0471250953.bi0313s48","article-title":"Clustal Omega","volume":"48","author":"Sievers","year":"2014","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1093\/bioinformatics\/8.3.275","article-title":"The rapid generation of mutation data matrices from protein sequences","volume":"8","author":"Jones","year":"1992","journal-title":"Bioinformatics"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1093\/oxfordjournals.molbev.a003851","article-title":"A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach","volume":"18","author":"Whelan","year":"2001","journal-title":"Mol. Biol. Evol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"Le","year":"2008","journal-title":"Mol. Biol. 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