{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T09:23:29Z","timestamp":1766049809541,"version":"build-2065373602"},"reference-count":54,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T00:00:00Z","timestamp":1636588800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM094157","P20GM103430"],"award-info":[{"award-number":["GM094157","P20GM103430"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","award":["1016013"],"award-info":[{"award-number":["1016013"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Rhodothermus marinus is a halophilic extreme thermophile, with potential as a model organism for studies of the structural basis of antibiotic resistance. In order to facilitate genetic studies of this organism, we have surveyed the antibiotic sensitivity spectrum of R. marinus and identified spontaneous antibiotic-resistant mutants. R. marinus is naturally insensitive to aminoglycosides, aminocylitols and tuberactinomycins that target the 30S ribosomal subunit, but is sensitive to all 50S ribosomal subunit-targeting antibiotics examined, including macrolides, lincosamides, streptogramin B, chloramphenicol, and thiostrepton. It is also sensitive to kirromycin and fusidic acid, which target protein synthesis factors. It is sensitive to rifampicin (RNA polymerase inhibitor) and to the fluoroquinolones ofloxacin and ciprofloxacin (DNA gyrase inhibitors), but insensitive to nalidixic acid. Drug-resistant mutants were identified using rifampicin, thiostrepton, erythromycin, spiramycin, tylosin, lincomycin, and chloramphenicol. The majority of these were found to have mutations that are similar or identical to those previously found in other species, while several novel mutations were identified. This study provides potential selectable markers for genetic manipulations and demonstrates the feasibility of using R. marinus as a model system for studies of ribosome and RNA polymerase structure, function, and evolution.<\/jats:p>","DOI":"10.3390\/antibiotics10111384","type":"journal-article","created":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T23:02:41Z","timestamp":1636671761000},"page":"1384","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["A Survey of Spontaneous Antibiotic-Resistant Mutants of the Halophilic, Thermophilic Bacterium Rhodothermus marinus"],"prefix":"10.3390","volume":"10","author":[{"given":"Sophia","family":"Silvia","sequence":"first","affiliation":[{"name":"Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha A.","family":"Donahue","sequence":"additional","affiliation":[{"name":"Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erin E.","family":"Killeavy","sequence":"additional","affiliation":[{"name":"Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5465-5315","authenticated-orcid":false,"given":"Gerwald","family":"Jogl","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0837-9417","authenticated-orcid":false,"given":"Steven T.","family":"Gregory","sequence":"additional","affiliation":[{"name":"Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI 02881, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1128\/MMBR.00055-15","article-title":"Bacterial transcription as a target for antibacterial drug development","volume":"80","author":"Ma","year":"2016","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"848","DOI":"10.3390\/biom5020848","article-title":"Structural biology of bacterial RNA polymerase","volume":"5","author":"Murakami","year":"2015","journal-title":"Biomolecules"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nrmicro3155","article-title":"Ribosome-targeting antibiotics and mechanisms of bacterial resistance","volume":"12","author":"Wilson","year":"2014","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_4","first-page":"299","article-title":"Rhodothermus marinus, gen. nov., sp. nov., a thermophilic, halophilic bacterium from submarine hot springs in Iceland","volume":"134","author":"Alfredsson","year":"1988","journal-title":"J. Gen. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00792-005-0466-z","article-title":"Rhodothermus marinus: Physiology and molecular biology","volume":"10","author":"Bjornsdottir","year":"2006","journal-title":"Extremophiles"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1099\/00207713-52-2-485","article-title":"Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds","volume":"52","author":"Oren","year":"2002","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"18147","DOI":"10.1073\/pnas.0509073102","article-title":"The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea","volume":"102","author":"Mongodin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2571","DOI":"10.1099\/ijs.0.010892-0","article-title":"Salisaeta longa gen. nov., sp. nov., a red, halophilic member of the Bacteroidetes","volume":"59","author":"Vaisman","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1099\/ijs.0.026294-0","article-title":"Rubricoccus marinus gen. nov., sp. nov., of the family \u2018Rhodothermaceae\u2019, isolated from seawater","volume":"61","author":"Park","year":"2011","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1099\/ijs.0.046318-0","article-title":"Rubrivirga marina gen. nov., sp. nov., a member of the family Rhodothermaceae isolated from deep seawater","volume":"63","author":"Park","year":"2013","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2272","DOI":"10.1099\/ijs.0.000247","article-title":"Longimonas halophila gen. nov., sp. nov., isolated from a marine solar saltern","volume":"65","author":"Xia","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3287","DOI":"10.1099\/ijsem.0.001190","article-title":"Longibacter salinarum gen. nov., sp. nov., isolated from a marine solar saltern","volume":"66","author":"Xia","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1128\/aem.52.6.1313-1316.1986","article-title":"Isolation of halotolerant Thermus spp. from submarine hot springs in Iceland","volume":"52","author":"Kristjansson","year":"1986","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1038\/s41467-018-04141-8","article-title":"Structural basis for energy transduction by respiratory alternative complex III","volume":"9","author":"Sousa","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1038\/nature13263","article-title":"Ribosomal oxygenases are structurally conserved from prokaryotes to humans","volume":"510","author":"Chowdhury","year":"2014","journal-title":"Nature"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"6165","DOI":"10.1128\/jb.176.20.6165-6169.1994","article-title":"The sequence of the single 16S rRNA gene of the thermophilic eubacterium Rhodothermus marinus reveals a distant relationship to the group containing Flexibacter, Bacteroides, and Cytophaga species","volume":"176","year":"1994","journal-title":"J. Bacteriol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"283","DOI":"10.4056\/sigs.46736","article-title":"Complete genome sequence of Rhodothermus marinus type strain (R-10)","volume":"1","author":"Nolan","year":"2009","journal-title":"Stand. Genom. Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4653","DOI":"10.1093\/nar\/12.11.4653","article-title":"Antibiotic resistance mutations in 16S and 23S ribosomal RNA genes of Escherichia coli","volume":"12","author":"Sigmund","year":"1984","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1073\/pnas.96.5.1971","article-title":"An Escherichia coli strain with all chromosomal rRNA operons inactivated: Complete exchange of rRNA genes between bacteria","volume":"96","author":"Asai","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/j.biochi.2006.04.008","article-title":"A genetic model to investigate drug-target interactions at the ribosomal decoding site","volume":"88","author":"Hobbie","year":"2006","journal-title":"Biochimie"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1261\/rna.1374809","article-title":"Genetic and structural analysis of base substitutions in the central pseudoknot of Thermus thermophilus 16S ribosomal RNA","volume":"15","author":"Gregory","year":"2009","journal-title":"RNA"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"4804","DOI":"10.1128\/JB.187.14.4804-4812.2005","article-title":"Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus","volume":"187","author":"Gregory","year":"2005","journal-title":"J. Bacteriol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1007\/s00253-004-1730-3","article-title":"Establishment of a gene transfer system for Rhodothermus marinus","volume":"66","author":"Bjornsdottir","year":"2005","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"5505","DOI":"10.1128\/AEM.02070-10","article-title":"Generation of targeted deletions in the genome of Rhodothermus marinus","volume":"77","author":"Bjornsdottir","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/s00792-006-0037-y","article-title":"Cloning and expression of heterologous genes in Rhodothermus marinus","volume":"11","author":"Bjornsdottir","year":"2007","journal-title":"Extremophiles"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3192","DOI":"10.1128\/AAC.49.8.3192-3197.2005","article-title":"Molecular analysis of cross-resistance to capreomycin, kanamycin, amikacin, and viomycin in Mycobacterium tuberculosis","volume":"49","author":"Maus","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1038\/ja.2014.107","article-title":"Resistance to rifampicin: A review","volume":"67","author":"Goldstein","year":"2014","journal-title":"J. Antibiot."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4147","DOI":"10.1038\/s41467-018-06587-2","article-title":"Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism","volume":"9","author":"Peek","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.molcel.2008.01.009","article-title":"Translational regulation via L11: Molecular switches on the ribosome turned on and off by thiostrepton and micrococcin","volume":"30","author":"Harms","year":"2008","journal-title":"Mol. Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1126\/science.289.5481.905","article-title":"The complete atomic structure of the large ribosomal subunit at 2.4 \u00c5 resolution","volume":"289","author":"Ban","year":"2000","journal-title":"Science"},{"key":"ref_31","unstructured":"Gale, E.F., Cundliffe, P.E., Reynolds, M.H., and Richmond, M.J. (1981). Waring. The Molecular Basis of Antibiotic Action, John Wiley & Sons."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.tibs.2018.06.011","article-title":"How macrolide antibiotics work","volume":"43","author":"Mankin","year":"2018","journal-title":"Trends Biochem. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1261\/rna.069260.118","article-title":"High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition","volume":"25","author":"Svetlov","year":"2019","journal-title":"RNA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"a025395","DOI":"10.1101\/cshperspect.a025395","article-title":"Resistance to macrolide antibiotics in public health pathogens","volume":"6","author":"Fyfe","year":"2016","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.jmb.2008.12.064","article-title":"Recombineering reveals a diverse collection of ribosomal proteins L4 and L22 that confer resistance to macrolide antibiotics","volume":"386","author":"Diner","year":"2009","journal-title":"J. Mol. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/BF00333665","article-title":"Biochemical and genetic studies of two different types of erythromycin resistant mutants of Escherichia coli with altered ribosomal proteins","volume":"127","author":"Wittmann","year":"1973","journal-title":"Mol. Gen. Genet."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"6192","DOI":"10.1128\/jb.176.20.6192-6198.1994","article-title":"Ribosomal protein gene sequence changes in erythromycin-resistant mutants of Escherichia coli","volume":"176","author":"Chittum","year":"1994","journal-title":"J. Bacteriol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1261\/rna.5400703","article-title":"The extended loops of ribosomal proteins L4 and L22 are not required for ribosome assembly or L4-mediated autogenous control","volume":"9","author":"Zengel","year":"2003","journal-title":"RNA"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1111\/j.1365-2958.2007.05975.x","article-title":"Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli","volume":"66","author":"Zaman","year":"2007","journal-title":"Mol. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"5798","DOI":"10.1093\/nar\/gkw493","article-title":"The extended loops of ribosomal proteins uL4 and uL22 of Escherichia coli contribute to ribosome assembly and protein translation","volume":"44","author":"Lawrence","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1126\/science.1069594","article-title":"Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 \u00c5 resolution","volume":"296","author":"Murakami","year":"2002","journal-title":"Science"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1038\/nature752","article-title":"Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 \u00c5 resolution","volume":"417","author":"Vassylyev","year":"2002","journal-title":"Nature"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/S0959-440X(02)00005-2","article-title":"Bacterial RNA polymerases: The wholo story","volume":"13","author":"Murakami","year":"2003","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1016\/S0092-8674(01)00286-0","article-title":"Structural mechanism for rifampicin inhibition of bacterial RNA polymerase","volume":"104","author":"Campbell","year":"2001","journal-title":"Cell"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.cell.2005.02.005","article-title":"Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance","volume":"121","author":"Tu","year":"2005","journal-title":"Cell"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"5750","DOI":"10.1093\/nar\/gkh913","article-title":"Multiple defects in translation associated with altered ribosomal protein L4","volume":"32","author":"Gregory","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1006\/jmbi.1999.2839","article-title":"Erythromycin resistance mutations in ribosomal protein L22 and L4 perturb the higher order structure of 23S ribosomal RNA","volume":"289","author":"Gregory","year":"1999","journal-title":"J. Mol. Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/S1097-2765(01)00293-3","article-title":"The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22","volume":"8","author":"Gabashvili","year":"2001","journal-title":"Mol. Cell"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1128\/AAC.15.1.7","article-title":"Mechanism of aminoglycoside antibiotic resistance in anaerobic bacteria: Clostridium perfringens and Bacteroides fragilis","volume":"15","author":"Bryan","year":"1979","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D\u2019Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., and M\u00fcller, K.M. (2002). The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinform., 3.","DOI":"10.1186\/1471-2105-3-2"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"The RNAcentral Consortium, Petrov, A.I., Kay, S.J.E., Kalvari, I., Howe, K.L., Gray, K.A., Bruford, E.A., Kersey, P.J., Cochrane, G., and Finn, R.D. (2017). RNAcentral: A comprehensive database of non-coding RNA sequences. Nucleic Acids Res., 45, D128\u2013D134.","DOI":"10.1093\/nar\/gkw1008"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"5921","DOI":"10.1016\/S0021-9258(19)83867-X","article-title":"Identification of the paromomycin-resistance mutation in the 15 S rRNA gene of yeast mitochondria","volume":"257","author":"Li","year":"1982","journal-title":"J. Biol. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"6334","DOI":"10.1016\/S0021-9258(18)88976-1","article-title":"The nucleotide sequence of the 17S ribosomal RNA gene of Tetrahymena thermophila and the identification of point mutations resulting in resistance to the antibiotics paromomycin and hygromycin","volume":"260","author":"Spangler","year":"1985","journal-title":"J. Biol. Chem."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"W636","DOI":"10.1093\/nar\/gkz268","article-title":"The EMBL-EBI search and sequence analysis tools APIs in 2019","volume":"47","author":"Madeira","year":"2019","journal-title":"Nucleic Acids Res."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/11\/1384\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:28:34Z","timestamp":1760167714000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/11\/1384"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,11]]},"references-count":54,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2021,11]]}},"alternative-id":["antibiotics10111384"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics10111384","relation":{},"ISSN":["2079-6382"],"issn-type":[{"type":"electronic","value":"2079-6382"}],"subject":[],"published":{"date-parts":[[2021,11,11]]}}}