{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T14:24:38Z","timestamp":1788531878083,"version":"build-2803163510"},"reference-count":80,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T00:00:00Z","timestamp":1788480000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry for Science and Higher Education of the Russian Federation","award":["124020500028-4"],"award-info":[{"award-number":["124020500028-4"]}]},{"name":"Ministry for Science and Higher Education of the Russian Federation","award":["122031400671-1"],"award-info":[{"award-number":["122031400671-1"]}]},{"name":"Ministry for Science and Higher Education of the Russian Federation","award":["FSNF-2025-0013"],"award-info":[{"award-number":["FSNF-2025-0013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Non-pathogenic actinomycetes play a key role in the degradation of xenobiotics and the biotransformation of complex organic compounds. Studying gene expression in these bacteria can be challenging due to the rigid cell wall that hinders RNA extraction. Here we present the first comprehensive study of total RNA isolation from Rhodococcus and Gordonia genera, encompassing 21 strains grown under 34 conditions, including n-alkanes C3\u2013C16, terpenoids, non-steroidal anti-inflammatory drugs, used frying oil, and mercury chloride. We compared no lysis strategy and three cell lysis approaches (freezing-thawing, bead beating, and lysozyme treatment) combined with the TRIzol or silica column-based RNA extraction kits. Bead beating, despite aggressive mechanical action, failed to reliably yield intact RNA. We show for the first time that 40 mg\/mL of lysozyme with prolonged exposure (1 h) reliably lyses Rhodococcus and Gordonia cells (96\u2013100% successful isolations), yielding pure integral RNA (118.5\u2013485.8 ng\/\u00b5L) with the RNA Solo Kit, without requiring detergents. We also developed the first protocol for RNA extraction from Rhodococcus cells grown on used frying oil, requiring pre-washing with 0.1 vol.% Tween 80 to disintegrate hard-to-harvest aggregates. These findings establish a robust strategy for RNA isolation from hydrophobic Rhodococcus and Gordonia bacteria.<\/jats:p>","DOI":"10.3390\/ijms27177890","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T13:50:44Z","timestamp":1788529844000},"page":"7890","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cell Disruption and RNA Extraction from Rhodococcus and Gordonia Bacteria Grown in the Presence of Hydrophobic Organic Compounds and Heavy Metal Salts"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3788-217X","authenticated-orcid":false,"given":"Anastasiia V.","family":"Krivoruchko","sequence":"first","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"},{"name":"Microbiology and Immunology Department, Perm State University, 15 Bukirev Str., 614990 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Liliia P.","family":"Komarova","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"},{"name":"Microbiology and Immunology Department, Perm State University, 15 Bukirev Str., 614990 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6353-2975","authenticated-orcid":false,"given":"Polina Y.","family":"Maltseva","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"},{"name":"Microbiology and Immunology Department, Perm State University, 15 Bukirev Str., 614990 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"given":"Semyon M.","family":"Tyan","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"},{"name":"Microbiology and Immunology Department, Perm State University, 15 Bukirev Str., 614990 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4036-9817","authenticated-orcid":false,"given":"Anastasia A.","family":"Golysheva","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9292-5726","authenticated-orcid":false,"given":"Natalia A.","family":"Plotnitskaya","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"},{"name":"Microbiology and Immunology Department, Perm State University, 15 Bukirev Str., 614990 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9165-8363","authenticated-orcid":false,"given":"Maria S.","family":"Kuyukina","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"},{"name":"Microbiology and Immunology Department, Perm State University, 15 Bukirev Str., 614990 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2558-4789","authenticated-orcid":false,"given":"Irina B.","family":"Ivshina","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Street., 614081 Perm, Russia"},{"name":"Microbiology and Immunology Department, Perm State University, 15 Bukirev Str., 614990 Perm, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Krivoruchko, A., Kuyukina, M., Peshkur, T., Cunningham, C.J., and Ivshina, I. (2023). Rhodococcus strains from the Specialized Collection of Alkanotrophs for biodegradation of aromatic compounds. Molecules, 28.","DOI":"10.3390\/molecules28052393"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"21559","DOI":"10.1038\/s41598-022-26173-3","article-title":"Adhesion of Rhodococcus bacteria to solid hydrocarbons and enhanced biodegradation of these compounds","volume":"12","author":"Ivshina","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1134\/S0026261724607620","article-title":"The Rhodococcus ruber actinomycetes, key and universal biooxidizers of C2\u2013C4 gaseous alkanes","volume":"94","author":"Ivshina","year":"2025","journal-title":"Microbiology"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Ivshina, I., Kuyukina, M., Krivoruchko, A., Elkin, A., Peshkur, T., and Cunningham, C.J. (2024). Resistant Rhodococcus for biodegradation of diesel fuel at high concentration and low temperature. Microorganisms, 12.","DOI":"10.3390\/microorganisms12122605"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1134\/S0003683816010075","article-title":"The effect of organic solvents on the viability and morphofunctional properties of Rhodococcus","volume":"52","author":"Korshunova","year":"2016","journal-title":"Appl. Biochem. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e14453","DOI":"10.1111\/1751-7915.14453","article-title":"Unravelling the role of the group 6 soluble di-iron monooxygenase (SDIMO) SmoABCD in alkane metabolism and chlorinated alkane degradation","volume":"17","author":"Ferrari","year":"2024","journal-title":"Microb. Biotechnol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Tyumina, E., Bazhutin, G., Kostrikina, N., Sorokin, V., Mulyukin, A., and Ivshina, I. (2023). Phenotypic and metabolic adaptations of Rhodococcus cerastii strain IEGM 1243 to separate and combined effects of diclofenac and ibuprofen. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1275553"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Tyan, S., Kostrikina, N., Sorokin, V., Mulyukin, A., and Ivshina, I. (2025). Adaptive responses of Gordonia alkanivorans IEGM 1277 to the action of meloxicam and its efficient biodegradation. Front. Bioeng. Biotechnol., 13.","DOI":"10.3389\/fbioe.2025.1603975"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"116190","DOI":"10.1016\/j.ecoenv.2024.116190","article-title":"Bioaccumulation of molybdate ions by alkanotrophic Rhodococcus leads to significant alterations in cellular ultrastructure and physiology","volume":"274","author":"Ivshina","year":"2024","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Ivshina, I.B., Luchnikova, N.A., Maltseva, P.Y., Ilyina, I.V., Volcho, K.P., Gatilov, Y.V., Korchagina, D.V., Kostrikina, N.A., Sorokin, V.V., and Mulyukin, A.L. (2022). Biotransformation of (\u2013)-isopulegol by Rhodococcus rhodochrous. Pharmaceuticals, 15.","DOI":"10.3390\/ph15080964"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Maltseva, P.Y., Plotnitskaya, N.A., and Ivshina, I.B. (2024). Transformation of terpenoids and steroids using actinomycetes of the genus Rhodococcus. Molecules, 29.","DOI":"10.3390\/molecules29143378"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.molcatb.2015.10.014","article-title":"Biotransformation of prochiral sulfides into (R)-sulfoxides using immobilized Gordonia terrae IEGM 136 cells","volume":"123","author":"Kylosova","year":"2016","journal-title":"J. Mol. Catal. B Enzym."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.envint.2008.07.018","article-title":"Biodegradation potential of the genus Rhodococcus","volume":"35","year":"2009","journal-title":"Environ. Int."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"8567","DOI":"10.1007\/s00253-020-10861-z","article-title":"Biotechnology of Rhodococcus for the production of valuable compounds","volume":"104","author":"Cappelletti","year":"2020","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"107698","DOI":"10.1016\/j.biotechadv.2021.107698","article-title":"Stress response in Rhodococcus strains","volume":"53","author":"Grulich","year":"2021","journal-title":"Biotechnol. Adv."},{"key":"ref_16","unstructured":"Kurtb\u00f6ke, I. (2024). Extremotolerant Rhodococcus as an important resource for environmental biotechnology. Actinomycetes in Marine and Extreme Environments: Unexhausted Sources for Microbial Biotechnology, Science Publishers, CRC Press."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Krivoruchko, A., Nurieva, D., Luppov, V., Kuyukina, M., and Ivshina, I. (2025). The lipid- and polysaccharide-rich extracellular polymeric substances of Rhodococcus support biofilm formation and protection from toxic hydrocarbons. Polymers, 17.","DOI":"10.3390\/polym17141912"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/0003-2697(87)90021-2","article-title":"Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction","volume":"162","author":"Chomczynski","year":"1987","journal-title":"Anal. Biochem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1023\/B:MICI.0000032247.34014.a0","article-title":"Changes in the fine structure of microbial cells induced by chaotropic salts","volume":"73","author":"Duda","year":"2004","journal-title":"Microbiology"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.ab.2016.08.001","article-title":"RNASwift: A rapid, versatile RNA extraction method free from phenol and chloroform","volume":"512","author":"Nwokeoji","year":"2016","journal-title":"Anal. Biochem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"105311","DOI":"10.1016\/j.isci.2022.105311","article-title":"Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples","volume":"25","author":"Verbeelen","year":"2022","journal-title":"iScience"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.forsciint.2005.02.020","article-title":"Multiplex mRNA profiling for the identification of body fluids","volume":"152","author":"Juusola","year":"2005","journal-title":"Forensic Sci. Int."},{"key":"ref_23","first-page":"1","article-title":"Effective RNA isolation method for gram-positive and acid-fast bacteria: Metamorphosed from conventional RNA isolation techniques","volume":"206","author":"Bera","year":"2024","journal-title":"Arch. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"6757","DOI":"10.1007\/s11033-021-06673-7","article-title":"A modified approach for high-quality RNA extraction of spore-forming Bacillus subtilis at varied physiological stages","volume":"48","author":"Jaiaue","year":"2021","journal-title":"Mol. Biol. Rep."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Cho, H.-s., Choi, M., Lee, Y., Jeon, H., Ahn, B., Soundrarajan, N., Hong, K., Kim, J.-H., and Park, C. (2021). High-quality nucleic acid isolation from hard-to-lyse bacterial strains using PMAP-36, a broad-spectrum antimicrobial peptide. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22084149"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.gene.2011.12.010","article-title":"Improved method for the isolation of RNA from bacteria refractory to disruption, including S. aureus producing biofilm","volume":"494","author":"Atshan","year":"2012","journal-title":"Gene"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e03077-25","DOI":"10.1128\/spectrum.03077-25","article-title":"Enzyme-enhanced RNA isolation from biofilm-producing bacteria","volume":"14","author":"Felton","year":"2026","journal-title":"Microbiol. Spectr."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Maurer, M., Klassert, T.E., L\u00f6ffler, B., Slevogt, H., and Tuchscherr, L. (2023). Extraction of high-quality RNA from S. aureus internalized by endothelial cells. Microorganisms, 11.","DOI":"10.3390\/microorganisms11041020"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"107318","DOI":"10.1016\/j.mimet.2025.107318","article-title":"A workflow for selective isolation of bacterial RNA from Streptococcus agalactiae during in vivo infection","volume":"239","author":"Lentini","year":"2025","journal-title":"J. Microbiol. Methods"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1271\/bbb.70493","article-title":"Detection of bphAa gene expression of Rhodococcus sp. strain RHA1 in soil using a new method of RNA preparation from soil","volume":"72","author":"Wang","year":"2008","journal-title":"Biosci. Biotechnol. Biochem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1016\/j.jmoldx.2011.06.007","article-title":"Paraffin embedding contributes to RNA aggregation, reduced RNA yield, and low RNA quality","volume":"13","author":"Evers","year":"2011","journal-title":"J. Mol. Diagn."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"52","DOI":"10.55705\/cmbr.2021.142436.1014","article-title":"Antisense RNA, the modified CRISPR-Cas9, and metal\/metal oxide nanoparticles to inactivate pathogenic bacteria","volume":"1","author":"Alavi","year":"2021","journal-title":"Cell. Mol. Biomed. Rep."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Espinosa, M.J.C., Schmidgall, T., Wagner, G., Kappelmeyer, U., Schreiber, S., Heipieper, H.J., and Eberlein, C. (2021). An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0260002"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"101503","DOI":"10.1016\/j.mex.2021.101503","article-title":"Advanced methods for RNA recovery from petroleum impacted soils","volume":"8","author":"Sale","year":"2021","journal-title":"MethodsX"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1111\/1751-7915.13615","article-title":"The guanidine thiocyanate-high EDTA method for total microbial RNA extraction from severely heavy metal-contaminated soils","volume":"14","author":"Pei","year":"2021","journal-title":"Microb. Biotechnol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3564","DOI":"10.1021\/acs.est.1c08468","article-title":"Metal-catalyzed hydrolysis of RNA in aqueous environments","volume":"56","author":"Chatterjee","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"8135","DOI":"10.3390\/s120608135","article-title":"Novel platform development using an assembly of carbon nanotube, nanogold and immobilized RNA capture element towards rapid, selective sensing of bacteria","volume":"12","author":"Maurer","year":"2012","journal-title":"Sensors"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Saleh, L.Y., Ora, M., and L\u00f6nnberg, T. (2020). Mercury(II)-catalyzed cleavage, isomerization and depurination of RNA and DNA model compounds and desulfurization of their phosphoromonothioate analogs. Catalysts, 10.","DOI":"10.3390\/catal10020219"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1046\/j.1472-765X.1997.00179.x","article-title":"New method for RNA isolation from actinomycetes: Application to the transcriptional analysis of the alcohol oxidoreductase gene thcE in Rhodococcus and Mycobacterium","volume":"25","author":"Nagy","year":"1997","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.jhazmat.2012.04.010","article-title":"Biodegradation of di-n-butyl phthalate by an isolated Gordonia sp. strain QH-11: Genetic identification and degradation kinetics","volume":"221\u2013222","author":"Jin","year":"2012","journal-title":"J. Hazard. Mater."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1139\/gen-2014-0030","article-title":"Identification of gene expression profiles in the actinomycete Gordonia neofelifaecis grown with different steroids","volume":"57","author":"Li","year":"2014","journal-title":"Genome"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.jhazmat.2013.11.061","article-title":"Endosulfan induced alteration in bacterial protein profile and RNA yield of Klebsiella sp. M3, Achromobacter sp. M6, and Rhodococcus sp. M2","volume":"265","author":"Singh","year":"2014","journal-title":"J. Hazard. Mater."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Su, X., Guo, L., Ding, L., Qu, K., and Shen, C. (2016). Induction of viable but nonculturable state in Rhodococcus and transcriptome analysis using RNA-Seq. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0147593"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.ecoenv.2018.03.074","article-title":"Global transcriptomic analysis of Rhodococcus erythropolis D310-1 in responding to chlorimuron-ethyl","volume":"157","author":"Cheng","year":"2018","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"6019","DOI":"10.1038\/s41598-018-24486-w","article-title":"Selection of stable reference genes for RT-qPCR in Rhodococcus opacus PD630","volume":"8","author":"Delorenzo","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Levy-Booth, D.J., Fetherolf, M.M., Stewart, G.R., Liu, J., Eltis, L.D., and Mohn, W.W. (2019). Catabolism of alkylphenols in Rhodococcus via a meta-cleavage pathway associated with genomic islands. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01862"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1007\/s10532-020-09917-8","article-title":"Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6:2 fluorotelomer sulfonamidoalkyl betaine or 6:2 fluorotelomer sulfonate as sole sulfur source","volume":"31","author":"Bottos","year":"2020","journal-title":"Biodegradation"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Zampolli, J., Di Canito, A., Manconi, A., Milanesi, L., Di Gennaro, P., and Orro, A. (2020). Transcriptomic analysis of Rhodococcus opacus R7 grown on o-xylene by RNA-Seq. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01808"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"21311","DOI":"10.1038\/s41598-021-00525-x","article-title":"Transcriptomic analysis of Rhodococcus opacus R7 grown on polyethylene by RNA-Seq","volume":"11","author":"Zampolli","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1007\/s13258-021-01101-3","article-title":"Genome and transcriptome sequencing of a newly isolated 2,4-dinitrophenol-degrading strain Rhodococcus imtechensis XM24D","volume":"43","author":"Hu","year":"2021","journal-title":"Genes Genom."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"fnac014","DOI":"10.1093\/femsle\/fnac014","article-title":"Sigma regulatory network in Rhodococcus erythropolis CCM2595","volume":"369","author":"Busche","year":"2022","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1007\/s00300-022-03049-w","article-title":"Transcriptome analysis of Antarctic Rhodococcus sp. NJ-530 in the response to dimethylsulfoniopropionate","volume":"45","author":"Zhang","year":"2022","journal-title":"Polar Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"001353","DOI":"10.1099\/mic.0.001353","article-title":"Evaluation of distinct molecular architectures and coordinated regulation of the catabolic pathways of oestrogenic dioctyl phthalate isomers in Gordonia sp.","volume":"169","author":"Dhar","year":"2023","journal-title":"Microbiology"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Willner, D.L., Paudel, S., Halleran, A.D., Solini, G.E., Gray, V., and Saha, M.S. (2024). Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1. BMC Microbiol., 24.","DOI":"10.1186\/s12866-024-03241-4"},{"key":"ref_55","first-page":"1","article-title":"The detection and phylogenetic analysis of the alkane 1-monooxygenase gene of members of the genus Rhodococcus","volume":"38","author":"Benedek","year":"2015","journal-title":"Syst. Appl. Microbiol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"10","DOI":"10.7243\/2052-6180-1-10","article-title":"Determining RNA quality for NextGen sequencing: Some exceptions to the gold standard rule of 23S to 16S rRNA ratio","volume":"1","author":"Bhagwat","year":"2013","journal-title":"Microbiol. Discov."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1023\/A:1001747726820","article-title":"Cell envelope composition and organisation in the genus Rhodococcus","volume":"74","author":"Sutcliffe","year":"1998","journal-title":"Antonie Leeuwenhoek"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Alvarez, H.M. (2010). The rhodococcal cell envelope: Composition, organisation and biosynthesis. Biology of Rhodococcus, Springer.","DOI":"10.1007\/978-3-642-12937-7"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Whitman, W., Goodfellow, M., K\u00e4mpfer, P., Busse, H.-J., Trujillo, M., Ludwig, W., Suzuki, K.-I., and Parte, A. (2012). Bergey\u2019s Manual of Systematic Bacteriology. Volume 5: The Actinobacteria, Springer. [2nd ed.].","DOI":"10.1007\/978-0-387-68233-4"},{"key":"ref_60","first-page":"97","article-title":"High-throughput RNA extraction method for P. aeruginosa and S. pyogenes biofilms","volume":"13","author":"Aburayyan","year":"2023","journal-title":"J. Appl. Pharm. Sci."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.1021\/ja211540z","article-title":"Single molecule dynamics of lysozyme processing distinguishes linear and cross-linked peptidoglycan substrates","volume":"134","author":"Choi","year":"2012","journal-title":"J. Am. Chem. Soc."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1111\/j.1574-6976.2007.00094.x","article-title":"Peptidoglycan structure and architecture","volume":"32","author":"Vollmer","year":"2008","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Gumbart, J.C., Beeby, M., Jensen, G.J., and Roux, B. (2014). Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. PLoS Comput. Biol., 10.","DOI":"10.1371\/journal.pcbi.1003475"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"18953","DOI":"10.1073\/pnas.0808035105","article-title":"Molecular organization of Gram-negative peptidoglycan","volume":"105","author":"Gan","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Krivoruchko, A., Nurieva, D., and Ivshina, I. (2026). Extracellular polymeric substances produced by actinomycetes of the genus Rhodococcus for biomedical and environmental applications. Int. J. Mol. Sci., 27.","DOI":"10.3390\/ijms27010498"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1128\/jb.63.5.665-674.1952","article-title":"Factors affecting the lytic activity of lysozyme","volume":"63","author":"Smolelis","year":"1952","journal-title":"J. Bacteriol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Gill, A., Scanlon, T.C., Osipovitch, D.C., Madden, D.R., and Griswold, K.E. (2011). Crystal structure of a charge engineered human lysozyme having enhanced bactericidal activity. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0016788"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1007\/s00284-013-0483-6","article-title":"Study of lysozyme resistance in Rhodococcus equi","volume":"68","author":"Bidaud","year":"2014","journal-title":"Curr. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Alvarez, H.M. (2019). Production of trehalolipid biosurfactants by Rhodococcus. Biology of Rhodococcus, Springer Nature. Microbiology Monographs 16.","DOI":"10.1007\/978-3-030-11461-9"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1128\/jcm.28.3.495-503.1990","article-title":"Rapid and simple method for purification of nucleic acids","volume":"28","author":"Boom","year":"1990","journal-title":"J. Clin. Microbiol."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Alvarez, H.M. (2019). Application of Rhodococcus in bioremediation of contaminated environments. Biology of Rhodococcus, Springer Nature. Microbiology Monographs 16.","DOI":"10.1007\/978-3-030-11461-9"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"3193","DOI":"10.1128\/aem.57.11.3193-3199.1991","article-title":"Hydrophobicity, adhesion, and surface-exposed proteins of gliding bacteria","volume":"57","author":"Sorongon","year":"1991","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/PL00006769","article-title":"Cell surface hydrophobicity of sucrose fermenting and nonfermenting Corynebacterium diphtheriae strains evaluated by different methods","volume":"38","author":"Formiga","year":"1999","journal-title":"Curr. Microbiol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.mimet.2009.08.003","article-title":"Selective adsorption of hydrocarbon-oxidizing Rhodococcus cells in a column with hydrophobized poly(acrylamide) cryogel","volume":"79","author":"Kuyukina","year":"2009","journal-title":"J. Microbiol. Methods"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1134\/S0003683814030144","article-title":"Adaptation of coimmobilized Rhodococcus cells to oil hydrocarbons in a column bioreactor","volume":"50","author":"Serebrennikova","year":"2014","journal-title":"Appl. Biochem. Microbiol."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Tomlinson, C., Rajasekaran, A., Brochu-Gaudreau, K., Dubois, C., Farmilo, A.J., Gris, P., Khatiz, A., Matthews, A., Piltonen, M., and Amrani, A. (2024). A convenient analytic method for gel quantification using ImageJ paired with Python or R. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0308297"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"3233","DOI":"10.1128\/aem.63.8.3233-3241.1997","article-title":"Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients","volume":"63","author":"Heuer","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"2002","DOI":"10.1093\/nar\/29.9.e45","article-title":"A new mathematical model for relative quantification in real-time RT-PCR","volume":"29","author":"Pfaffl","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1373\/clinchem.2008.112797","article-title":"The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments","volume":"55","author":"Bustin","year":"2009","journal-title":"Clin. Chem."},{"key":"ref_80","unstructured":"R Core Team (2026). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7890\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T13:52:40Z","timestamp":1788529960000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7890"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,4]]},"references-count":80,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27177890"],"URL":"https:\/\/doi.org\/10.3390\/ijms27177890","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,4]]}}}