Microbiological research最新文献

{"title":"Elucidation of PGPR-responsive OsNAM2 regulates salt tolerance in Arabidopsis by AFP2 and SUS protein interaction","authors":"Harshita Joshi ,&nbsp;Klaus Harter ,&nbsp;Leander Rohr ,&nbsp;Shashank Kumar Mishra ,&nbsp;Puneet Singh Chauhan","doi":"10.1016/j.micres.2024.127890","DOIUrl":"10.1016/j.micres.2024.127890","url":null,"abstract":"<div><p>This study investigates the molecular mechanisms underlying salt stress responses in plants, focusing on the regulatory roles of OsNAM2, a gene influenced by the plant growth-promoting rhizobacterium <em>Bacillus amyloliquefaciens</em> (SN13). The study examines how SN13-modulated OsNAM2 enhances salt tolerance in Arabidopsis through physiological, biochemical, and molecular analyses. Overexpression of OsNAM2, especially with SN13 inoculation, improves germination, seedling growth, root length, and biomass under high NaCl concentrations compared to wild-type plants, indicating a synergistic effect. OsNAM2 overexpression enhances relative water content, reduces electrolyte leakage and malondialdehyde accumulation, and increases proline content, suggesting better membrane integrity and stress endurance. Furthermore, SN13 and OsNAM2 overexpression modulates essential metabolic genes involved in glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle, facilitating metabolic adjustments crucial for salt stress adaptation. The interaction of OsNAM2 with SUS, facilitated by SN13, suggests enhanced sucrose metabolism efficiency, providing substrates for protective responses. Additionally, OsNAM2 plays a regulatory role in the ABA signaling pathway through significant protein-protein interactions like with AFP2. This study highlights the intricate interplay between SN13-responsive OsNAM2 and key signaling pathways, suggesting strategies for enhancing crop salt tolerance through targeted genetic and microbial interventions</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"289 ","pages":"Article 127890"},"PeriodicalIF":6.1,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic review on marine carbon source-mannitol: Applications in synthetic biology","authors":"Fengxu Xiao ,&nbsp;Yupeng Zhang ,&nbsp;Lihuan Zhang ,&nbsp;Yanling Wang ,&nbsp;Chenxing Li ,&nbsp;Siyu Li ,&nbsp;Jiawei Lu ,&nbsp;Wei Chen ,&nbsp;Guiyang Shi ,&nbsp;Youran Li","doi":"10.1016/j.micres.2024.127881","DOIUrl":"10.1016/j.micres.2024.127881","url":null,"abstract":"<div><p>Mannitol, one of the most widespread sugar alcohols, has been integral to daily human life for two centuries. Global population growth and competition for freshwater, food, and land have prompted a shift in the fermentation industry from terrestrial to marine raw materials. Mannitol is a readily available carbohydrate in brown seaweed from the ocean and possess a higher reducing power than glucose, making it a promising substrate for biological manufacturing. This has spurred numerous explorations into converting mannitol into high-value chemicals. Researchers have engineered microorganisms to utilize mannitol in various synthetic biological applications, including: (1) employing mannitol as an inducer to control the activation and deactivation of genetic circuits; (2) using mannitol as a carbon source for synthesizing high-value chemicals through biomanufacturing. This review summarizes the latest advances in the application of mannitol in synthetic biology.</p></div><div><h3>Aim of review</h3><p>The aim is to present a thorough and in-depth knowledge of mannitol, a marine carbon source, and then use this carbon source in synthetic biology to improve the competitiveness of biosynthetic processes. We outlined the methods and difficulties of utilizing mannitol in synthetic biology with a variety of microbes serving as hosts. Furthermore, future research directions that could alleviate the carbon catabolite repression (CCR) relationship between glucose and mannitol are also covered.</p></div><div><h3>Expected contributions of review</h3><p>Provide an overview of the current state, drawbacks, and directions for future study on mannitol as a carbon source or genetic circuit inducer in synthetic biology.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"289 ","pages":"Article 127881"},"PeriodicalIF":6.1,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Challenges to rhizobial adaptability in a changing climate: Genetic engineering solutions for stress tolerance","authors":"Yunjia Zhang ,&nbsp;Yee-Shan Ku ,&nbsp;Tsz-Yan Cheung ,&nbsp;Sau-Shan Cheng ,&nbsp;Dawei Xin ,&nbsp;Kewin Gombeau ,&nbsp;Yizhi Cai ,&nbsp;Hon-Ming Lam ,&nbsp;Ting-Fung Chan","doi":"10.1016/j.micres.2024.127886","DOIUrl":"10.1016/j.micres.2024.127886","url":null,"abstract":"<div><p>Rhizobia interact with leguminous plants in the soil to form nitrogen fixing nodules in which rhizobia and plant cells coexist. Although there are emerging studies on rhizobium-associated nitrogen fixation in cereals, the legume-rhizobium interaction is more well-studied and usually serves as the model to study rhizobium-mediated nitrogen fixation in plants. Rhizobia play a crucial role in the nitrogen cycle in many ecosystems. However, rhizobia are highly sensitive to variations in soil conditions and physicochemical properties (i.e. moisture, temperature, salinity, pH, and oxygen availability). Such variations directly caused by global climate change are challenging the adaptive capabilities of rhizobia in both natural and agricultural environments. Although a few studies have identified rhizobial genes that confer adaptation to different environmental conditions, the genetic basis of rhizobial stress tolerance remains poorly understood. In this review, we highlight the importance of improving the survival of rhizobia in soil to enhance their symbiosis with plants, which can increase crop yields and facilitate the establishment of sustainable agricultural systems. To achieve this goal, we summarize the key challenges imposed by global climate change on rhizobium-plant symbiosis and collate current knowledge of stress tolerance-related genes and pathways in rhizobia. And finally, we present the latest genetic engineering approaches, such as synthetic biology, implemented to improve the adaptability of rhizobia to changing environmental conditions.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"288 ","pages":"Article 127886"},"PeriodicalIF":6.1,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002878/pdfft?md5=d7c64a7183dfbda5788b5a79fe567e8f&pid=1-s2.0-S0944501324002878-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142130077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enzymatic promiscuity and underground reactions accounted for the capability of Escherichia coli to use the non-natural chemical synthon 2,4-dihydroxybutyric acid as a carbon source for growth","authors":"Thibault Malfoy ,&nbsp;Ceren Alkim ,&nbsp;Manon Barthe ,&nbsp;Julie Fredonnet ,&nbsp;Jean Marie François","doi":"10.1016/j.micres.2024.127888","DOIUrl":"10.1016/j.micres.2024.127888","url":null,"abstract":"<div><p>2,4-dihydroxybutyric acid (DHB) and 2-keto-4-hydroxybutyrate (OHB) are non-natural molecules obtained through synthetic pathways from renewable carbon source. As they are structurally similar to lactate and pyruvate respectively, they could possibly interfere with the metabolic network of <em>Escherichia coli</em>. In fact, we showed that DHB can be easily oxidized by the membrane associated L and D-lactate dehydrogenases encoded by <em>lldD</em>, <em>dld</em> and <em>ykgF</em> into OHB, and the latter being cleaved into pyruvate and formaldehyde by several pyruvate-dependent aldolases, with YagE being the most effective. While formaldehyde was readily detoxified into formate, <em>Escherichia coli</em> K12 MG1655 strain failed to grow on DHB despite of the production of pyruvate. To find out the reason for this failure, we constructed a mutant strain whose growth was rendered dependent on DHB and subjected this strain to adaptive evolution. Genome sequencing of the adapted strain revealed an essential role for <em>ygbI</em> encoding a transcriptional repressor of the threonate operon in this DHB-dependent growth. This critical function was attributed to the derepression of <em>ygbN</em> encoding a putative threonate transporter, which was found to exclusively transport the D form of DHB. A subsequent laboratory evolution was carried out with <em>E. coli</em> K12 MG1655 deleted for <em>ΔygbI</em> to adapt for growth on DHB as sole carbon source. Remarkably, only two additional mutations were disclosed in the adapted strain, which were demonstrated by reverse engineering to be necessary and sufficient for robust growth on DHB. One mutation was in <em>nanR</em> encoding the transcription repressor of sialic acid metabolic genes, causing 140-fold increase in expression of <em>nanA</em> encoding N-acetyl neuraminic acid lyase, a pyruvate-dependent aldolase, and the other was in the promoter of <em>dld</em> leading to 14-fold increase in D-lactate dehydrogenase activity on DHB. Taken together, this work illustrates the importance of promiscuous enzymes in underground metabolism and moreover, in the frame of synthetic pathways aiming at producing non-natural products, these underground reactions could potentially penalize yield and title of these bio-based products.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"288 ","pages":"Article 127888"},"PeriodicalIF":6.1,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002891/pdfft?md5=052fb9a2a56f6fdc7c77da67194b214c&pid=1-s2.0-S0944501324002891-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142130040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unearthing the soil-bacteria nexus to enhance potassium bioavailability for global sustainable agriculture: A mechanistic preview","authors":"Saba Babar ,&nbsp;Amanullah Baloch ,&nbsp;Muhammad Qasim ,&nbsp;Jiyuan Wang ,&nbsp;Xiangling Wang ,&nbsp;Yuxuan Li ,&nbsp;Sarmand Khalid ,&nbsp;Cuncang Jiang","doi":"10.1016/j.micres.2024.127885","DOIUrl":"10.1016/j.micres.2024.127885","url":null,"abstract":"<div><p>Established as a plant macronutrient, potassium (K) substantially bestows plant growth and thus, global food production. It is absorbed by plants as potassium cation (K⁺) from soil solution, which is enriched through slow-release from soil minerals or addition of soluble fertilizers. Contribution of bioavailable K⁺ from soil is usually insignificant (&lt; 2 %), although the earth's crust is rich in K-bearing minerals. However, K is fixed largely in interlayer spaces of K-bearing minerals, which can be released by K-solubilizing bacteria (KSB) such as <em>Bacillus, Pseudomonas, Enterobacter,</em> and <em>Acidithiobacillus</em>. The underlying mechanisms of K dissolution by KSB include acidolysis, ion exchange reactions, chelation, complexolysis, and release of various organic and inorganic acids such as citric, oxalic, acetic, gluconic, and tartaric acids. These acids cause disintegration of K-bearing minerals and bring K⁺ into soil solution that becomes available to the plants. Current literature review updates the scientific information about microbial species, factors, and mechanisms governing the bio-intrusion of K-bearing minerals. Moreover, it explores the potential of KSB not only for K-solubilization but also to enhance bioavailability of phosphorus, nitrogen, and micronutrients, as well as its other beneficial impact on plant growth. Thus, in the context of sustainable agricultural production and global food security, utilization of KSB may facilitate plant nutrient availability, conserve natural resources, and reduce environmental impacts caused by chemical fertilizers.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"288 ","pages":"Article 127885"},"PeriodicalIF":6.1,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142130078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The protective role of potassium in the adaptation of Pseudomonas protegens SN15-2 to hyperosmotic stress","authors":"Jian Wang ,&nbsp;Yaping Wang ,&nbsp;Shouquan Lu ,&nbsp;Haibo Lou ,&nbsp;XiaoBing Wang ,&nbsp;Wei Wang","doi":"10.1016/j.micres.2024.127887","DOIUrl":"10.1016/j.micres.2024.127887","url":null,"abstract":"<div><p><em>Pseudomonas protegens</em> is an important biocontrol agent with the ability to suppress plant pathogens and promote plant growth. <em>P. protegens’</em> ability to endure hyperosmotic stress is crucial to its effectiveness as a biocontrol agent. This study elucidated potassium’s role and mechanism of action in enabling the hyperosmotic tolerance of <em>P. protegens</em>. Potassium was observed to significantly improve the growth of <em>P. protegens</em> under hyperosmotic conditions. Four functionally redundant potassium transporters, KdpA1, KdpA2, TrkH, and Kup, were identified in <em>P. protegens</em>, of which KdpA2 and TrkH were particularly important for its growth under hyperosmotic conditions. Potassium enhanced the biofilm formation and cell membrane stability of <em>P. protegens</em> under hyperosmotic conditions. In addition, we revealed that K⁺ stimulates the expression of several genes related to DNA damage repair in <em>P. protegens</em> under hyperosmotic conditions. Further experiments revealed that the DNA repair-related <em>recG</em> induced by potassium contributes to <em>P. protegens</em>’ hyperosmotic tolerance. We also found that the sigma factor RpoN participates in the hyperosmotic adaptation of <em>P. protegens</em>. Furthermore, we revealed that the <em>opuCABCD</em> operon, whose expression is induced by potassium through RpoN, serves as the key pathway through which betaine, choline, and carnitine improve the hyperosmotic tolerance of <em>P. protegens</em>.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"289 ","pages":"Article 127887"},"PeriodicalIF":6.1,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing native-cryptic plasmids for stable overexpression of heterologous genes in Clostridium butyricum DSM 10702 for industrial and medical applications","authors":"Yanchao Zhang ,&nbsp;Ying Cong ,&nbsp;Tom S. Bailey ,&nbsp;Ludwig J. Dubois ,&nbsp;Jan Theys ,&nbsp;Philippe Lambin","doi":"10.1016/j.micres.2024.127889","DOIUrl":"10.1016/j.micres.2024.127889","url":null,"abstract":"<div><p><em>Clostridium butyricum</em> has emerged as a promising candidate for both industrial and medical biotechnologies, underscoring the key pursuit of stable gene overexpression in engineering <em>C. butyricum</em>. Unlike antibiotic-selective vectors, native-cryptic plasmids can be utilized for antibiotic-free expression systems in bacteria but have not been effectively exploited in <em>C. butyricum</em> to date. This study focuses on leveraging these plasmids, pCB101 and pCB102, in <em>C. butyricum</em> DSM10702 for stable gene overexpression without antibiotic selection via efficient gene integration using the SacB-based allelic exchange method. Integration of reporter IFP2.0 and glucuronidase generated sustained near-infrared fluorescence and robust enzyme activity across successive subcultures. Furthermore, successful secretion of a cellulase, Cel9M, and the human interleukin 10 from pCB102 highlights native-cryptic plasmids’ potential in conferring stable gene products for industrial and medical applications in <em>C. butyricum</em>. This work appears to be the first study to harness the <em>Clostridium</em> native-cryptic plasmid for stable gene overexpression without antibiotics, thereby advancing the biotechnological prospects of <em>C. butyricum</em>.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"288 ","pages":"Article 127889"},"PeriodicalIF":6.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002908/pdfft?md5=ac49bfff01f7dc90c408ba08bacad085&pid=1-s2.0-S0944501324002908-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142095508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Repurposing endogenous Type I-D CRISPR-Cas system for genome editing in Synechococcus sp. PCC7002","authors":"Shuxiao Yang,&nbsp;Yongjiu Zhang,&nbsp;Chunyan Li,&nbsp;Xiaoming Tan","doi":"10.1016/j.micres.2024.127884","DOIUrl":"10.1016/j.micres.2024.127884","url":null,"abstract":"<div><p><em>Synechococcus</em> sp. PCC7002 has been considered as a photosynthetic chassis for the conversion of CO₂ into biochemicals through genetic modification. However, conventional genetic manipulation techniques prove inadequate for comprehensive genetic modifications in this strain. Here, we present the development of a genome editing tool tailored for <em>S</em>. PCC7002, leveraging its endogenous type I-D CRISPR-Cas system. Utilizing this novel tool, we successfully deleted the <em>glgA1</em> gene and iteratively edited the genome to obtain a double mutant of <em>glgA1</em> and <em>glgA2</em> genes. Additionally, large DNA fragments encompassing the entire type I-A (∼14 kb) or III-B CRISPR-Cas (∼21 kb) systems were completely knocked-out in <em>S</em>. PCC7002 using our tool. Furthermore, the endogenous pAQ5 plasmid, approximately 38 kb in length, was successfully cured from <em>S</em>. PCC7002. Our work demonstrates the feasibility of harnessing the endogenous CRISPR-Cas system for genome editing in <em>S</em>. PCC7002, thereby enriching the genetic toolkit for this species and providing a foundation for future enhancements in its biosynthetic efficiency.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"288 ","pages":"Article 127884"},"PeriodicalIF":6.1,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142122274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virulence regulation in plant-pathogenic bacteria by host-secreted signals","authors":"Muhammad Asif,&nbsp;Xin Xie,&nbsp;Zhibo Zhao","doi":"10.1016/j.micres.2024.127883","DOIUrl":"10.1016/j.micres.2024.127883","url":null,"abstract":"<div><p>Bacterial pathogens manipulate host signaling pathways and evade host defenses using effector molecules, coordinating their deployment to ensure successful infection. However, host-derived metabolites as signals, and their critical role in regulating bacterial virulence requires further insights. Effective regulation of virulence, which is essential for pathogenic bacteria, involves controlling factors that enable colonization, defense evasion, and tissue damage. This regulation is dynamic, influenced by environmental cues including signals from host plants like exudates. Plant exudates, comprising of diverse compounds released by roots and tissues, serve as rich chemical signals affecting the behavior and virulence of associated bacteria. Plant nutrients act as signaling molecules that are sensed through membrane-localized receptors and intracellular response mechanisms in bacteria. This review explains how different bacteria detect and answer to secreted chemical signals, regulating virulence gene expression. Our main emphasis is exploring the recognition process of host-originated signaling molecules through molecular sensors on cellular membranes and intracellular signaling pathways. This review encompasses insights into how bacterial strains individually coordinate their virulence in response to various distinct host-derived signals that can positively or negatively regulate their virulence. Furthermore, we explained the interruption of plant defense with the perception of host metabolites to dampen pathogen virulence. The intricate interplay between pathogens and plant signals, particularly in how pathogens recognize host metabolic signals to regulate virulence genes, portrays a crucial initial interaction leading to profound influences on infection outcomes. This work will greatly aid researchers in developing new strategies for preventing and treating infections.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"288 ","pages":"Article 127883"},"PeriodicalIF":6.1,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002842/pdfft?md5=72a8c201696e6bf77a88ebaf7f4d85a9&pid=1-s2.0-S0944501324002842-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142088980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB","authors":"Unai Fernández-Arévalo ,&nbsp;Jonathan Fuchs ,&nbsp;Matthias Boll ,&nbsp;Eduardo Díaz","doi":"10.1016/j.micres.2024.127882","DOIUrl":"10.1016/j.micres.2024.127882","url":null,"abstract":"<div><p>Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of <em>m</em>-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the <em>hbd</em> genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium <em>Aromatoleum</em> sp. CIB. The <em>hbd</em> cluster is organized in three catabolic operons and a regulatory <em>hbdR</em> gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (<em>P</em>_{<em>hbdN</em>}<em>, P</em>_{<em>hbdE</em>} and <em>P</em>_{<em>hbdH</em>}) by binding to a conserved palindromic operator box (ATGAATGAN₄TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the <em>hbd</em> genes. Moreover, the <em>hbd</em> genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the <em>hbd</em> cluster among members of the <em>Aromatoleum/Thauera</em> bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the <em>hbd</em> gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"288 ","pages":"Article 127882"},"PeriodicalIF":6.1,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002830/pdfft?md5=badde5561632685d11a12c9bf2bd39da&pid=1-s2.0-S0944501324002830-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142095509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}