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Fu Q, Lv R, Wang S, Wang W, Li Y, Qiu G, Chen X, Sun C. Ndufa8 promotes white fat Browning by improving mitochondrial respiratory chain complex I function to ameliorate obesity by in vitro and in vivo. Cell Signal 2024; 122:111340. [PMID: 39127135 DOI: 10.1016/j.cellsig.2024.111340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/13/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Obesity and its complications have become a global health problem that needs to be addressed urgently. White adipose tissue (WAT) browning contributes to consuming excess energy in WAT, which is important for improving obesity and maintaining a healthy energy homeostasis. Mitochondria, as the energy metabolism center of cells, are extensively involved in many metabolic processes, including the browning of WAT. NADH: Ubiquinone oxidoreductase subunit A8 (NDUFA8) is a constituent subunit of respiratory chain complex I (CI), which has been found to participate in a wide range of physiological processes by affecting the activity of respiratory CI. However, the regulatory effect of Ndufa8 on the browning of WAT has not been reported. Here, we used β3-adrenergic agonis CL316, 243 to construct WAT browning models in vivo and in vitro to investigate the role and mechanism of Ndufa8 in the regulation of WAT browning. Briefly, Ndufa8 significantly increased CI activity and suppressed mitochondrial ROS levels in vitro, thereby improving mitochondrial function. Ndufa8 also increased the transcriptional levels and protein levels of UCP1 in vitro and in vivo, which promoted WAT browning. Our findings provide a new molecular approach for the research of browning of WAT in animals, as well as a new target for animal metabolism improvement and obesity treatments.
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Affiliation(s)
- Qinghua Fu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Lv
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Simeng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wentao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yizhou Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guiping Qiu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinhao Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chao Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Rebnegger C, Coltman BL, Kowarz V, Peña DA, Mentler A, Troyer C, Hann S, Schöny H, Koellensperger G, Mattanovich D, Gasser B. Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates. Microb Cell Fact 2024; 23:43. [PMID: 38331812 PMCID: PMC10851509 DOI: 10.1186/s12934-024-02314-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions. RESULTS By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h-1. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g-1 h-1. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival. CONCLUSIONS In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.
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Affiliation(s)
- Corinna Rebnegger
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Benjamin L Coltman
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Viktoria Kowarz
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - David A Peña
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Axel Mentler
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Harald Schöny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Diethard Mattanovich
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Brigitte Gasser
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria.
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van Winden WA, Mans R, Breestraat S, Verlinden RAJ, Mielgo‐Gómez Á, de Hulster EAF, de Bruijn HMCJ, Noorman HJ. Towards closed carbon loop fermentations: Cofeeding of Yarrowia lipolytica with glucose and formic acid. Biotechnol Bioeng 2022; 119:2142-2151. [PMID: 35451059 PMCID: PMC9540030 DOI: 10.1002/bit.28115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 11/26/2022]
Abstract
A novel fermentation process was developed in which renewable electricity is indirectly used as an energy source in fermentation, synergistically decreasing both the consumption of sugar as a first generation carbon source and emission of the greenhouse gas CO2 . As an illustration, a glucose-based process is co-fed with formic acid, which can be generated by capturing CO2 from fermentation offgas followed by electrochemical reduction with renewable electricity. This "closed carbon loop" concept is demonstrated by a case study in which cofeeding formic acid is shown to significantly increase the yield of biomass on glucose of the industrially relevant yeast species Yarrowia lipolytica. First, the optimal feed ratio of formic acid to glucose is established using chemostat cultivations. Subsequently, guided by a dynamic fermentation process model, a fed-batch protocol is developed and demonstrated on laboratory scale. Finally, the developed fed-batch process is tested and proven to be scalable at pilot scale. Extensions of the concept are discussed to apply the concept to anaerobic fermentations, and to recycle the O2 that is co-generated with the formic acid to aerobic fermentation processes for intensification purposes.
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Affiliation(s)
| | - Robert Mans
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | | | - Álvaro Mielgo‐Gómez
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | | | - Henk J. Noorman
- DSM Biotechnology Center, DSM N.V.DelftThe Netherlands
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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Dekker WJC, Jürgens H, Ortiz-Merino RA, Mooiman C, van den Berg R, Kaljouw A, Mans R, Pronk JT. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6523363. [PMID: 35137036 PMCID: PMC8862043 DOI: 10.1093/femsyr/foac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha showed its minimum oxygen requirements to be an order of magnitude larger than those reported for the thermotolerant yeast Kluyveromyces marxianus. High oxygen requirements of O. parapolymorpha coincided with a near absence of glycerol, a key NADH/NAD+ redox-cofactor-balancing product in many other yeasts, in oxygen-limited cultures. Genome analysis indicated absence of orthologs of the Saccharomyces cerevisiae glycerol-3-phosphate-phosphatase genes GPP1 and GPP2. Co-feeding of acetoin, whose conversion to 2,3-butanediol enables reoxidation of cytosolic NADH, supported a 2.5-fold increase of the biomass concentration in oxygen-limited cultures. An O. parapolymorpha strain in which key genes involved in mitochondrial reoxidation of NADH were inactivated did produce glycerol, but transcriptome analysis did not reveal a clear candidate for a responsible phosphatase. Expression of S. cerevisiae GPD2, which encodes NAD+-dependent glycerol-3-phosphate dehydrogenase, and GPP1 supported increased glycerol production by oxygen-limited chemostat cultures of O. parapolymorpha. These results identify dependence on respiration for NADH reoxidation as a key contributor to unexpectedly high oxygen requirements of O. parapolymorpha.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Hannes Jürgens
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Remon van den Berg
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Corresponding author: Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands. Tel: +31 15 2783214; E-mail:
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Ploessl D, Zhao Y, Cao M, Ghosh S, Lopez C, Sayadi M, Chudalayandi S, Severin A, Huang L, Gustafson M, Shao Z. A repackaged CRISPR platform increases homology-directed repair for yeast engineering. Nat Chem Biol 2022; 18:38-46. [PMID: 34711982 DOI: 10.1038/s41589-021-00893-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022]
Abstract
Inefficient homology-directed repair (HDR) constrains CRISPR-Cas9 genome editing in organisms that preferentially employ nonhomologous end joining (NHEJ) to fix DNA double-strand breaks (DSBs). Current strategies used to alleviate NHEJ proficiency involve NHEJ disruption. To confer precision editing without NHEJ disruption, we identified the shortcomings of the conventional CRISPR platforms and developed a CRISPR platform-lowered indel nuclease system enabling accurate repair (LINEAR)-which enhanced HDR rates (to 67-100%) compared to those in previous reports using conventional platforms in four NHEJ-proficient yeasts. With NHEJ preserved, we demonstrate its ability to survey genomic landscapes, identifying loci whose spatiotemporal genomic architectures yield favorable expression dynamics for heterologous pathways. We present a case study that deploys LINEAR precision editing and NHEJ-mediated random integration to rapidly engineer and optimize a microbial factory to produce (S)-norcoclaurine. Taken together, this work demonstrates how to leverage an antagonizing pair of DNA DSB repair pathways to expand the current collection of microbial factories.
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Affiliation(s)
- Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Yuxin Zhao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Carmen Lopez
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA
| | - Maryam Sayadi
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Siva Chudalayandi
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Andrew Severin
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Lei Huang
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Marissa Gustafson
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA. .,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA. .,Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA. .,Bioeconomy Institute, Iowa State University, Ames, IA, USA. .,The Ames Laboratory, Ames, IA, USA. .,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Lu H, Li F, Yuan L, Domenzain I, Yu R, Wang H, Li G, Chen Y, Ji B, Kerkhoven EJ, Nielsen J. Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. Mol Syst Biol 2021; 17:e10427. [PMID: 34676984 PMCID: PMC8532513 DOI: 10.15252/msb.202110427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.
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Affiliation(s)
- Hongzhong Lu
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Feiran Li
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Le Yuan
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Iván Domenzain
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Rosemary Yu
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Hao Wang
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- National Bioinformatics Infrastructure SwedenScience for Life LaboratoryChalmers University of TechnologyGothenburgSweden
| | - Gang Li
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Yu Chen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Boyang Ji
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Eduard J Kerkhoven
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
- BioInnovation InstituteCopenhagen NDenmark
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