Pub Date : 2026-02-09DOI: 10.1186/s12934-026-02946-7
Hugo Fleuriot-Blitman, Katerina Sabatova, Véronique Amstutz, Marketa Jakubickova, Eva Slaninova, Katerina Mrazova, María Celeste Ferrín Mendoza, Kamila Hrubanova, Vladislav Krzyzanek, Stanislav Obruca, Karel Sedlar, Manfred Zinn
Background: Rhodospirillum rubrum owns a dynamic poly(3-hydroxybutyrate) (PHB) cycle: During growth PHB is accumulated and subsequently degraded under carbon starvation. Interestingly, this cycle is typically found for acetate grown R. rubrum but not for fructose grown cells, where no PHB accumulation has been observed. This study aimed to determine whether expression of PHB cycle genes correlates with the phases of PHB accumulation and degradation on acetate in comparison to absence of PHB synthesis during growth on fructose and ΔphaC1ΔphaC2 mutant unable to polymerize PHB on acetate.
Results: Surprisingly, transcriptomic analyses of the wild-type strain demonstrated that PHB cycle genes were not only expressed during growth on acetate but also for growth on fructose, regardless of PHB content. Substrate-specific expression patterns were identified: The PHB depolymerase gene phaZ1 was predominantly expressed on acetate, while phaZ2 and the depolymerase regulator apdA were upregulated on fructose. Interestingly, phaC3 and phaZ3 showed distinct expression patterns compared with other PHB cycle genes, particularly in mutant strains. Despite the absence of PHB granules in the ΔphaC1ΔphaC2 strain, several PHB cycle genes remained expressed, and volatile fatty acid assimilation pathways were transcriptionally impacted.
Conclusions: These findings highlight the complexity of the PHB cycle and suggest that PHB participates in other physiological processes, such as substrate assimilation, potentially via regulatory actions of PHB granule bound regulator PhaR.
{"title":"Gene expression analysis reveals distinct PHB depolymerization mechanisms and broader involvement of the PHB cycle in Rhodospirillum rubrum growing on acetate and fructose.","authors":"Hugo Fleuriot-Blitman, Katerina Sabatova, Véronique Amstutz, Marketa Jakubickova, Eva Slaninova, Katerina Mrazova, María Celeste Ferrín Mendoza, Kamila Hrubanova, Vladislav Krzyzanek, Stanislav Obruca, Karel Sedlar, Manfred Zinn","doi":"10.1186/s12934-026-02946-7","DOIUrl":"https://doi.org/10.1186/s12934-026-02946-7","url":null,"abstract":"<p><strong>Background: </strong>Rhodospirillum rubrum owns a dynamic poly(3-hydroxybutyrate) (PHB) cycle: During growth PHB is accumulated and subsequently degraded under carbon starvation. Interestingly, this cycle is typically found for acetate grown R. rubrum but not for fructose grown cells, where no PHB accumulation has been observed. This study aimed to determine whether expression of PHB cycle genes correlates with the phases of PHB accumulation and degradation on acetate in comparison to absence of PHB synthesis during growth on fructose and ΔphaC1ΔphaC2 mutant unable to polymerize PHB on acetate.</p><p><strong>Results: </strong>Surprisingly, transcriptomic analyses of the wild-type strain demonstrated that PHB cycle genes were not only expressed during growth on acetate but also for growth on fructose, regardless of PHB content. Substrate-specific expression patterns were identified: The PHB depolymerase gene phaZ1 was predominantly expressed on acetate, while phaZ2 and the depolymerase regulator apdA were upregulated on fructose. Interestingly, phaC3 and phaZ3 showed distinct expression patterns compared with other PHB cycle genes, particularly in mutant strains. Despite the absence of PHB granules in the ΔphaC1ΔphaC2 strain, several PHB cycle genes remained expressed, and volatile fatty acid assimilation pathways were transcriptionally impacted.</p><p><strong>Conclusions: </strong>These findings highlight the complexity of the PHB cycle and suggest that PHB participates in other physiological processes, such as substrate assimilation, potentially via regulatory actions of PHB granule bound regulator PhaR.</p>","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146150263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-08DOI: 10.1186/s12934-026-02923-0
Maysa M Ali, Sara M Ibrahim, Mohamed Abdelazim, Abdel-Elnaser A Zohri
{"title":"Statical optimization of cellulase enzymes production by Trichoderma harzianum PP400831 using response surface methodology and their application in production of 2G bioethanol.","authors":"Maysa M Ali, Sara M Ibrahim, Mohamed Abdelazim, Abdel-Elnaser A Zohri","doi":"10.1186/s12934-026-02923-0","DOIUrl":"https://doi.org/10.1186/s12934-026-02923-0","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-04DOI: 10.1186/s12934-026-02948-5
Raghav Acharya, Joshua Hinckley, Rachel Barry, Eugenie Cha, Harini Narayanan, Brittney C Sunday, Hayley Ford, Charles A Whittaker, J Christopher Love
{"title":"Systematic perturbation of cultures of K. phaffii by carbon co-feeding show gene signatures associated with production of recombinant proteins.","authors":"Raghav Acharya, Joshua Hinckley, Rachel Barry, Eugenie Cha, Harini Narayanan, Brittney C Sunday, Hayley Ford, Charles A Whittaker, J Christopher Love","doi":"10.1186/s12934-026-02948-5","DOIUrl":"https://doi.org/10.1186/s12934-026-02948-5","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-03DOI: 10.1186/s12934-026-02939-6
Demian Dietrich, Hang Qi, Sofija Jovanovic Gasovic, Michael Kohlstedt, Christoph Wittmann
{"title":"Defined YNB-free mineral medium improves reproducibility and enables high-titer production in Yarrowia lipolytica.","authors":"Demian Dietrich, Hang Qi, Sofija Jovanovic Gasovic, Michael Kohlstedt, Christoph Wittmann","doi":"10.1186/s12934-026-02939-6","DOIUrl":"https://doi.org/10.1186/s12934-026-02939-6","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-03DOI: 10.1186/s12934-026-02943-w
Jan Benedict Spannenkrebs, Leesa Jane Klau, Marianna Karava, Finn Lillelund Aachmann, Johannes Kabisch
{"title":"Spore immobilized enzymes for the multi-step synthesis of cellobiose.","authors":"Jan Benedict Spannenkrebs, Leesa Jane Klau, Marianna Karava, Finn Lillelund Aachmann, Johannes Kabisch","doi":"10.1186/s12934-026-02943-w","DOIUrl":"https://doi.org/10.1186/s12934-026-02943-w","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-02DOI: 10.1186/s12934-026-02927-w
Mohamed A Awad, Sherif F Hammad, Fahd M Abdelkarem, Amira Elkattan, Samir F El-Mashtoly, Hesham S M Soliman, Kuniyoshi Shimizu
{"title":"Metabolite profiling of Bacillus velezensis DM extract linked to the rhizosphere of Datura metel L. and dermatoprotective potential of an isolated glycoglycerolipid.","authors":"Mohamed A Awad, Sherif F Hammad, Fahd M Abdelkarem, Amira Elkattan, Samir F El-Mashtoly, Hesham S M Soliman, Kuniyoshi Shimizu","doi":"10.1186/s12934-026-02927-w","DOIUrl":"https://doi.org/10.1186/s12934-026-02927-w","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146106232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-02DOI: 10.1186/s12934-026-02922-1
Annalena Sommer, Sarah Pauli, Michael Kohlstedt, Judith Becker, Christoph Wittmann
{"title":"Metabolic engineering of Corynebacterium glutamicum for high-yield de novo biosynthesis of 5-aminovaleramide, a promising bio-based monomer.","authors":"Annalena Sommer, Sarah Pauli, Michael Kohlstedt, Judith Becker, Christoph Wittmann","doi":"10.1186/s12934-026-02922-1","DOIUrl":"https://doi.org/10.1186/s12934-026-02922-1","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146106268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1186/s12934-026-02938-7
Hang Nie, Yajun Feng, Guanghui Sun, Haijie Li, Jingwen Kang, Yanqing Zhang, Chenhui Zhu, Yu Mi, Yuan Guo, Pei Ma
{"title":"Mechanism-guided control of intracellular alkalinization and process pH for production of recombinant human B-type natriuretic peptide under the cSAT scheme in Escherichia coli.","authors":"Hang Nie, Yajun Feng, Guanghui Sun, Haijie Li, Jingwen Kang, Yanqing Zhang, Chenhui Zhu, Yu Mi, Yuan Guo, Pei Ma","doi":"10.1186/s12934-026-02938-7","DOIUrl":"https://doi.org/10.1186/s12934-026-02938-7","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146100416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-01DOI: 10.1186/s12934-026-02941-y
Kameshwara V R Peri, Iván Domenzain, Hanna D Alalam, Luca Torello Pianale, Abril Valverde Rascón, Jens Nielsen, Cecilia Geijer
{"title":"Model-driven exploration of lactose and galactose metabolism via an oxidoreductive pathway in Sungouiella intermedia for cell factory applications.","authors":"Kameshwara V R Peri, Iván Domenzain, Hanna D Alalam, Luca Torello Pianale, Abril Valverde Rascón, Jens Nielsen, Cecilia Geijer","doi":"10.1186/s12934-026-02941-y","DOIUrl":"https://doi.org/10.1186/s12934-026-02941-y","url":null,"abstract":"","PeriodicalId":18582,"journal":{"name":"Microbial Cell Factories","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146100419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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