{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:43:34Z","timestamp":1792590214687,"version":"4.5.0"},"reference-count":101,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100009606","name":"Arabian Gulf University","doi-asserted-by":"publisher","award":["LS_WE_2018"],"award-info":[{"award-number":["LS_WE_2018"]}],"id":[{"id":"10.13039\/100009606","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2026,10,21]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Recent proteomics and metabolomics studies have confirmed the significance of understanding the fuel biodesulfurization phenotype at a global scale beyond the desulfurization 4S pathway. To reveal the transcriptomic adaptations in the model strain\n                      <jats:italic toggle=\"yes\">Rhodococcus qingshengii<\/jats:italic>\n                      IGTS8 under biodesulfurization conditions, we conducted a time series comparative RNA-seq study using cultures of IGTS8 grown on either dibenzothiophene (DBT) or MgSO\n                      <jats:sub>4<\/jats:sub>\n                      as the sulfur source. The RNA-seq data revealed many differentially expressed genes (DEGs) depending on the sulfur source and growth phase, and the strongest transcriptomic response was evident during the late-log phase. In total, 6,690 transcripts were detected in the DBT and MgSO\n                      <jats:sub>4<\/jats:sub>\n                      cultures, representing 99.5% of the total protein-coding genes. A substantial fraction of the DEGs encodes ABC-type transporters and hypothetical proteins. In the DBT culture, 623 DEGs were upregulated, and 587 DEGs were downregulated. Generally, the DEGs covered key physiological processes, such as stress response, regulation of gene expression, uptake of nutrients, metabolism of lipids, amino acids, carbohydrates, proteins, nucleotides, cell division, and cell wall biosynthesis\/degradation. While genes of carbohydrate metabolism were mostly downregulated in the DBT culture, those encoding amino acid and fatty acid degradation, as well as energy conservation, were upregulated. Moreover, genes encoding mobile genetic elements, C1 metabolism enzymes, carbonic anhydrase, and nitrile hydratase were upregulated under biodesulfurization conditions. In contrast, dihydrofolate reductase was strongly downregulated. The growth phase-dependent transcriptomic rearrangements under biodesulfurization conditions appear to prioritize cellular homeostasis and protection rather than proliferation.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Commercial application of fuel biodesulfurization requires exceptionally robust and catalytically active desulfurizing microbes that can tolerate and sustain activity under the harsh operational conditions in oil refineries. It is generally accepted that naturally occurring bacteria may not meet these industrial requirements. Therefore, synthetic biology and metabolic engineering hold promise. However, a thorough understanding of the physiology, metabolism, and stress response of fuel-desulfurizing bacteria, which is currently lacking, is key toward further developments in this field. Considering these knowledge gaps, our findings provide mechanistic insights into the transcriptional responses of the reference biodesulfurizing strain\n                      <jats:italic toggle=\"yes\">Rhodococcus qingshengii<\/jats:italic>\n                      IGTS8, which, when integrated together with our recently reported proteomics and metabolomics data, enable a multifaceted and deeper understanding of the biodesulfurization phenotype, facilitating rational design of more efficient recombinant biodesulfurizers. Hence, this study represents a step forward toward developing a commercially viable fuel biodesulfurization process.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/aem.01549-26","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T13:01:22Z","timestamp":1790168482000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Sulfur source-driven global remodeling of gene expression in the fuel-biodesulfurizing\n                    <i>Rhodococcus qingshengii<\/i>\n                    IGTS8"],"prefix":"10.1128","volume":"92","author":[{"given":"Ashraf","family":"El Nayal","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04gd4wn47","id-type":"ROR","asserted-by":"publisher"}],"name":"Center of Environmental and Biological Studies, Arabian Gulf University","place":["Manama, Bahrain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7405-8446","authenticated-orcid":true,"given":"Vartul","family":"Sangal","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/049e6bc10","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Geography and Natural Sciences, Northumbria University","place":["Newcastle upon Tyne, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdelmalek","family":"Alioua","sequence":"additional","affiliation":[{"name":"Institut de biologie de mol\u00e9culaire des plantes CNRS","place":["Strasbourg, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aur\u00e9lie","family":"Hirschler","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00pg6eq24","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratoire de Spectrom\u00e9trie de Masse BioOrganique, CNRS, Universit\u00e9 de Strasbourg, IPHC UMR 7178","place":["Strasbourg, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandrine","family":"Koechler","sequence":"additional","affiliation":[{"name":"Institut de biologie de mol\u00e9culaire des plantes CNRS","place":["Strasbourg, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimitri","family":"Heintz","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00pg6eq24","id-type":"ROR","asserted-by":"publisher"}],"name":"Universit\u00e9 de Strasbourg, CNRS, IPHC UMR 7178","place":["Strasbourg, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0079-319X","authenticated-orcid":true,"given":"Christine","family":"Carapito","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00pg6eq24","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratoire de Spectrom\u00e9trie de Masse BioOrganique, CNRS, Universit\u00e9 de Strasbourg, IPHC UMR 7178","place":["Strasbourg, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain","family":"Van Dorsselaer","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00pg6eq24","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratoire de Spectrom\u00e9trie de Masse BioOrganique, CNRS, Universit\u00e9 de Strasbourg, IPHC UMR 7178","place":["Strasbourg, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3027-928X","authenticated-orcid":true,"given":"Wael","family":"Ismail","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04gd4wn47","id-type":"ROR","asserted-by":"publisher"}],"name":"Center of Environmental and Biological Studies, Arabian Gulf University","place":["Manama, Bahrain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ibiod.2016.03.011"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.3390\/environments4040085"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.procbio.2025.01.018"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2006.04.005"},{"key":"e_1_3_4_6_2","first-page":"235","volume-title":"Advances in chemical and materials engineering","author":"Paix\u00e3o SM","year":"2020","unstructured":"Paix\u00e3o SM, Silva TP, Arez BF, Alves L. 2020. 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