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Park SY, Jung SR, Kim JY, Kim YW, Sung HK, Park SY, Doh KO, Koh JH. Lactate promotes fatty acid oxidation by the tricarboxylic acid cycle and mitochondrial respiration in muscles of obese mice. Am J Physiol Cell Physiol 2024; 327:C619-C633. [PMID: 38981606 DOI: 10.1152/ajpcell.00060.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/04/2024] [Accepted: 06/20/2024] [Indexed: 07/11/2024]
Abstract
Lower oxidative capacity in skeletal muscles (SKMs) is a prevailing cause of metabolic diseases. Exercise not only enhances the fatty acid oxidation (FAO) capacity of SKMs but also increases lactate levels. Given that lactate may contribute to tricarboxylic acid cycle (TCA) flux and impact monocarboxylate transporter 1 in the SKMs, we hypothesize that lactate can influence glucose and fatty acid (FA) metabolism. To test this hypothesis, we investigated the mechanism underlying lactate-driven FAO regulation in the SKM of mice with diet-induced obesity (DIO). Lactate was administered to DIO mice immediately after exercise for over 3 wk. We found that increased lactate levels enhanced energy expenditure mediated by fat metabolism during exercise recovery and decreased triglyceride levels in DIO mice SKMs. To determine the lactate-specific effects without exercise, we administered lactate to mice on a high-fat diet (HFD) for 8 wk. Similar to our exercise conditions, lactate increased FAO, TCA cycle activity, and mitochondrial respiration in the SKMs of HFD-fed mice. In addition, under sufficient FA conditions, lactate increased uncoupling protein-3 abundance via the NADH-NAD+ shuttle. Conversely, ATP synthase abundance decreased in the SKMs of HFD mice. Taken together, our results suggest that lactate amplifies the adaptive increase in FAO capacity mediated by the TCA cycle and mitochondrial respiration in SKMs under sufficient FA abundance.NEW & NOTEWORTHY Lactate administration post-exercise promotes triglyceride content loss in skeletal muscles (SKMs) and reduced body weight. Lactate enhances fatty acid oxidation in the SKMs of high-fat diet (HFD)-fed mice due to enhanced mitochondrial oxygen consumption. In addition, lactate restores the malate-aspartate shuttle, which is reduced by a HFD, and activates the tricarboxylic acid cycle (TCA) cycle in SKMs. Interestingly, supraphysiological lactate facilitates uncoupling protein-3 expression through NADH/NAD+, which is enhanced under high-fat levels in SKMs.
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Affiliation(s)
- Sol-Yi Park
- Department of Physiology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Su-Ryun Jung
- Department of Physiology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Jong-Yeon Kim
- Department of Physiology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Yong-Woon Kim
- Department of Physiology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Hoon-Ki Sung
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - So-Young Park
- Department of Physiology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Kyung-Oh Doh
- Department of Physiology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Jin-Ho Koh
- Department of Convergence Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
- Department of Global Medical Science, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
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2
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She F, Anderson BW, Khana DB, Zhang S, Steinchen W, Fung DK, Lucas LN, Lesser NG, Stevenson DM, Astmann TJ, Bange G, van Pijkeren JP, Amador-Noguez D, Wang JD. Allosteric Regulation of Pyruvate Kinase Enables Efficient and Robust Gluconeogenesis by Preventing Metabolic Conflicts and Carbon Overflow. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.607825. [PMID: 39211278 PMCID: PMC11361145 DOI: 10.1101/2024.08.15.607825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Glycolysis and gluconeogenesis are reciprocal metabolic pathways that utilize different carbon sources. Pyruvate kinase catalyzes the irreversible final step of glycolysis, yet the physiological function of its regulation is poorly understood. Through metabolomics and enzyme kinetics studies, we discovered that pyruvate kinase activity is inhibited during gluconeogenesis in the soil bacterium Bacillus subtilis . This regulation involves an extra C-terminal domain (ECTD) of pyruvate kinase, which is essential for autoinhibition and regulation by metabolic effectors. Introducing a pyruvate kinase mutant lacking the ECTD into B. subtilis resulted in defects specifically under gluconeogenic conditions, including inefficient carbon utilization, slower growth, and decreased resistance to the herbicide glyphosate. These defects are not caused by the phosphoenolpyruvate-pyruvate-oxaloacetate futile cycle. Instead, we identified two significant metabolic consequences of pyruvate kinase dysregulation during gluconeogenesis: increased carbon overflow into the medium and failure to expand glycolytic intermediates such as phosphoenolpyruvate (PEP). In silico analysis revealed that in wild-type cells, an expanded PEP pool enabled by pyruvate kinase regulation is critical for the thermodynamic feasibility of gluconeogenesis. Our findings underscore the importance of allosteric regulation during gluconeogenesis in coordinating metabolic flux, efficient energy utilization, and antimicrobial resistance.
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Naik R, Gupte S. Optimization of media components for enhanced carotenoid production by Paracoccus marcusii RSPO1 and assessment of their cytotoxicity against A549 and vero cells. Prep Biochem Biotechnol 2024; 54:764-778. [PMID: 38165781 DOI: 10.1080/10826068.2023.2282533] [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] [Indexed: 01/04/2024]
Abstract
In this study, we tried to explore the influence of various tricarboxylic acid (TCA) cycle intermediates on carotenoid production and with a focus on enhancing pigment biosynthesis, we conducted two statistical analysis. In case of TCA intermediates influence on pigment production by Paracoccus marcusii RSPO1; fumaric acid, and malic acid were observed as potent enhancers of pigment biosynthesis. Further, to optimize key media components for enhanced carotenoid production, the Plackett-Burman design was employed encompassing carbon, nitrogen sources, TCA cycle intermediates, and metal salts. The selected factors after Plackett Burman were fine-tuned through Response Surface Methodology and the optimal concentrations that have remarkably elevated carotenoid production were starch-2.24 g/l, MgSO4-0.416 g/l, ZnSO4-0.0157 g/l, and fumaric Acid-16 mM. Further, evaluation of pigment cytotoxicity against normal (Vero) and Non-Small Cell Carcinoma (A549) cells was performed. The resultant IC50 values were quantified as 161.3 µg/ml and 7.623 µg/ml for Vero and A549 cells, respectively. Moreover, a reactive oxygen species (ROS) determination study in A549 cells was done which have shown a noteworthy threefold ROS production in A549 cells through fluorescence spectroscopic observation. This implies that the bacterial carotenoids can act as potent pro-oxidants against cancerous cells while being nontoxic toward normal cells.
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Affiliation(s)
- Raj Naik
- Department of Microbiology, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Science (ARIBAS), CVM University, Anand, Gujarat, India
| | - Shilpa Gupte
- Department of Microbiology, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Science (ARIBAS), CVM University, Anand, Gujarat, India
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4
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Jasinska W, Dindo M, Cordoba SMC, Serohijos AWR, Laurino P, Brotman Y, Bershtein S. Non-consecutive enzyme interactions within TCA cycle supramolecular assembly regulate carbon-nitrogen metabolism. Nat Commun 2024; 15:5285. [PMID: 38902266 PMCID: PMC11189929 DOI: 10.1038/s41467-024-49646-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/14/2024] [Indexed: 06/22/2024] Open
Abstract
Enzymes of the central metabolism tend to assemble into transient supramolecular complexes. However, the functional significance of the interactions, particularly between enzymes catalyzing non-consecutive reactions, remains unclear. Here, by co-localizing two non-consecutive enzymes of the TCA cycle from Bacillus subtilis, malate dehydrogenase (MDH) and isocitrate dehydrogenase (ICD), in phase separated droplets we show that MDH-ICD interaction leads to enzyme agglomeration with a concomitant enhancement of ICD catalytic rate and an apparent sequestration of its reaction product, 2-oxoglutarate. Theory demonstrates that MDH-mediated clustering of ICD molecules explains the observed phenomena. In vivo analyses reveal that MDH overexpression leads to accumulation of 2-oxoglutarate and reduction of fluxes flowing through both the catabolic and anabolic branches of the carbon-nitrogen intersection occupied by 2-oxoglutarate, resulting in impeded ammonium assimilation and reduced biomass production. Our findings suggest that the MDH-ICD interaction is an important coordinator of carbon-nitrogen metabolism.
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Affiliation(s)
- Weronika Jasinska
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mirco Dindo
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Medicine and Surgery, Section of Physiology and Biochemistry, University of Perugia, Perugia, Italy
| | - Sandra M C Cordoba
- Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Adrian W R Serohijos
- Departement de Biochimie, Universite de Montreal, Quebec, Canada
- Centre Robert-Cedergren en Bio-informatique et Genomique, Universite de Montreal, Quebec, Canada
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Institute for Protein Research, Osaka University, Suita, Japan.
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Shimon Bershtein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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5
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Heberle A, Cappuccio E, Andric A, Kuen T, Simonini A, Weiss AKH. Mitochondrial enzyme FAHD1 reduces ROS in osteosarcoma. Sci Rep 2024; 14:9231. [PMID: 38649439 PMCID: PMC11035622 DOI: 10.1038/s41598-024-60012-x] [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: 08/20/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
This study investigated the impact of overexpressing the mitochondrial enzyme Fumarylacetoacetate hydrolase domain-containing protein 1 (FAHD1) in human osteosarcoma epithelial cells (U2OS) in vitro. While the downregulation or knockdown of FAHD1 has been extensively researched in various cell types, this study aimed to pioneer the exploration of how increased catalytic activity of human FAHD1 isoform 1 (hFAHD1.1) affects human cell metabolism. Our hypothesis posited that elevation in FAHD1 activity would lead to depletion of mitochondrial oxaloacetate levels. This depletion could potentially result in a decrease in the flux of the tricarboxylic acid (TCA) cycle, thereby accompanied by reduced ROS production. In addition to hFAHD1.1 overexpression, stable U2OS cell lines were established overexpressing a catalytically enhanced variant (T192S) and a loss-of-function variant (K123A) of hFAHD1. It is noteworthy that homologs of the T192S variant are present in animals exhibiting increased resistance to oxidative stress and cancer. Our findings demonstrate that heightened activity of the mitochondrial enzyme FAHD1 decreases cellular ROS levels in U2OS cells. However, these results also prompt a series of intriguing questions regarding the potential role of FAHD1 in mitochondrial metabolism and cellular development.
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Affiliation(s)
- Anne Heberle
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Elia Cappuccio
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Andreas Andric
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Tatjana Kuen
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Anna Simonini
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Alexander K H Weiss
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria.
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Gulevich AY, Skorokhodova AY, Debabov VG. Biosynthesis of C4-C8 3-Hydroxycarboxylic Acids from Glucose through the Inverted Fatty Acid β-Oxidation by Metabolically Engineered Escherichia coli. Biomolecules 2024; 14:449. [PMID: 38672466 PMCID: PMC11048500 DOI: 10.3390/biom14040449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Inverted fatty acid β-oxidation represents a versatile biochemical platform for biosynthesis by the engineered microbial strains of numerous value-added chemicals from convenient and abundant renewable carbon sources, including biomass-derived sugars. Although, in recent years, significant progress has been made in the production through this pathway of n-alcohols, 1,3-diols, and carboxylic acids and its 2,3-unsaturated derivatives, the potential of the pathway for the biosynthesis of 3-hydroxycarboxylic acids remained almost undisclosed. In this study, we demonstrate the microaerobic production of even-chain-length C4-C8 3-hydroxycarboxylic acids from glucose through the inverted fatty acid β-oxidation by engineered E. coli strains. The notable accumulation of target compounds was achieved upon the strong constitutive expression of the genes atoB, fadA, fadB, fadE/fabI, and tesB, which code for the key enzymes catalysing reactions of aerobic fatty acid β-oxidation and thioesterase II, in strains devoid of mixed-acid fermentation pathways and lacking nonspecific thioesterase YciA. The best performing recombinants were able to synthesise up to 14.5 mM of 3-hydroxycarboxylic acids from glucose with a total yield of 0.34 mol/mol and a C4/C6/C8 ratio averaging approximately 63/28/9. The results provide a framework for the development of highly efficient strains and processes for the bio-based production of valuable 3-hydroxycarboxylates from renewable raw materials.
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Affiliation(s)
- Andrey Yu. Gulevich
- Research Center of Biotechnology, Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia; (A.Y.S.); (V.G.D.)
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Peng H, Chen P, Guo R, Zhou Z, Chen Y, Xu P, Su H, Xiao Y, Jiang H. Regulation of the growth performance and the gastrointestinal microbiota community by the addition of defective pear fermentation to feed of small-tailed Han sheep. Front Microbiol 2024; 15:1358033. [PMID: 38638905 PMCID: PMC11024308 DOI: 10.3389/fmicb.2024.1358033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/18/2024] [Indexed: 04/20/2024] Open
Abstract
This study investigated the effects of defective pear fermentation (DPF) diets on growth performance and gastrointestinal microbial communities in 60 healthy male small-tailed Han sheep, aged 90 days. The sheep were randomly divided into four groups, each consisting of three replicates with five sheep per replicate. Initially, all groups received a basal diet for seven days during the adaptation stage. Subsequently, for 60 days, group C (control) was fed a basal diet, group X received a basal diet with 2% DPF, group Y had a basal diet with 4% DPF, and group Z was fed a basal diet with 6% DPF. The results indicated that group Y experienced a significant increase in average daily gain (ADG) and average daily feed intake (ADFI). The addition of DPF significantly elevated the levels of GSH-Px and notably reduced MDA content compared to group C. Analysis of gastrointestinal microbiota showed that groups receiving DPF had increased relative abundances of Lachnospiraceae_NK3A20_group, norank_f p-2534-18B5_gut_group, Acetitomaculum, Actinobacteriota, Bacteroidota and Ruminococcus_gauvreauii_group, and decreased abundances of Proteobacteria, Prevotella, Staphylococcus, and Psychrobacter compared to group C. Group X exhibited the highest relative abundance of Olsenella, while group Y showed a significant increase in unclassified_f Lachnospiraceae compared to the other groups. Bacterial function prediction indicated that pathways related to energy metabolism were more prevalent in group X and Y. This study preliminarily confirms the feasibility of using DPF as feed additives, providing a foundation for further research and evaluation of DPF's application in animal production.
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Affiliation(s)
- Hongxin Peng
- Key Laboratory of Tarim University Husbandry Science and Technology, College of Animal Science and Technology, Tarim University, Alar, China
| | - Pinpin Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Rui Guo
- Key Laboratory of Tarim University Husbandry Science and Technology, College of Animal Science and Technology, Tarim University, Alar, China
| | - Zheng Zhou
- Key Laboratory of Tarim University Husbandry Science and Technology, College of Animal Science and Technology, Tarim University, Alar, China
| | - Yafei Chen
- Key Laboratory of Tarim University Husbandry Science and Technology, College of Animal Science and Technology, Tarim University, Alar, China
| | - Ping Xu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Huawei Su
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuncai Xiao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Hui Jiang
- Key Laboratory of Tarim University Husbandry Science and Technology, College of Animal Science and Technology, Tarim University, Alar, China
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Giacomini JJ, Torres-Morales J, Tang J, Dewhirst FE, Borisy GG, Mark Welch JL. Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity. Microbiol Spectr 2024; 12:e0401723. [PMID: 38488280 PMCID: PMC10986600 DOI: 10.1128/spectrum.04017-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024] Open
Abstract
Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility. IMPORTANCE Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.
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Affiliation(s)
| | | | - Jonathan Tang
- The Forsyth Institute, Cambridge, Massachusetts, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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Zhang Y, Wang X, Odesanmi C, Hu Q, Li D, Tang Y, Liu Z, Mi J, Liu S, Wen T. Model-guided metabolic rewiring to bypass pyruvate oxidation for pyruvate derivative synthesis by minimizing carbon loss. mSystems 2024; 9:e0083923. [PMID: 38315666 PMCID: PMC10949502 DOI: 10.1128/msystems.00839-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Engineering microbial hosts to synthesize pyruvate derivatives depends on blocking pyruvate oxidation, thereby causing severe growth defects in aerobic glucose-based bioprocesses. To decouple pyruvate metabolism from cell growth to improve pyruvate availability, a genome-scale metabolic model combined with constraint-based flux balance analysis, geometric flux balance analysis, and flux variable analysis was used to identify genetic targets for strain design. Using translation elements from a ~3,000 cistronic library to modulate fxpK expression in a bicistronic cassette, a bifido shunt pathway was introduced to generate three molecules of non-pyruvate-derived acetyl-CoA from one molecule of glucose, bypassing pyruvate oxidation and carbon dioxide generation. The dynamic control of flux distribution by T7 RNAP-mediated synthetic small RNA decoupled pyruvate catabolism from cell growth. Adaptive laboratory evolution and multi-omics analysis revealed that a mutated isocitrate dehydrogenase functioned as a metabolic switch to activate the glyoxylate shunt as the only C4 anaplerotic pathway to generate malate from two molecules of acetyl-CoA input and bypass two decarboxylation reactions in the tricarboxylic acid cycle. A chassis strain for pyruvate derivative synthesis was constructed to reduce carbon loss by using the glyoxylate shunt as the only C4 anaplerotic pathway and the bifido shunt as a non-pyruvate-derived acetyl-CoA synthetic pathway and produced 22.46, 27.62, and 6.28 g/L of l-leucine, l-alanine, and l-valine by a controlled small RNA switch, respectively. Our study establishes a novel metabolic pattern of glucose-grown bacteria to minimize carbon loss under aerobic conditions and provides valuable insights into cell design for manufacturing pyruvate-derived products.IMPORTANCEBio-manufacturing from biomass-derived carbon sources using microbes as a cell factory provides an eco-friendly alternative to petrochemical-based processes. Pyruvate serves as a crucial building block for the biosynthesis of industrial chemicals; however, it is different to improve pyruvate availability in vivo due to the coupling of pyruvate-derived acetyl-CoA with microbial growth and energy metabolism via the oxidative tricarboxylic acid cycle. A genome-scale metabolic model combined with three algorithm analyses was used for strain design. Carbon metabolism was reprogrammed using two genetic control tools to fine-tune gene expression. Adaptive laboratory evolution and multi-omics analysis screened the growth-related regulatory targets beyond rational design. A novel metabolic pattern of glucose-grown bacteria is established to maintain growth fitness and minimize carbon loss under aerobic conditions for the synthesis of pyruvate-derived products. This study provides valuable insights into the design of a microbial cell factory for synthetic biology to produce industrial bio-products of interest.
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Affiliation(s)
- Yun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xueliang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Christianah Odesanmi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qitiao Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dandan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuan Tang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Mi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuwen Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tingyi Wen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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10
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Scott KM, Payne RR, Gahramanova A. Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways. Appl Environ Microbiol 2024; 90:e0155723. [PMID: 38299815 PMCID: PMC10880623 DOI: 10.1128/aem.01557-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.
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Affiliation(s)
- Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Ren R. Payne
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Arin Gahramanova
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
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11
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Páez-Watson T, van Loosdrecht MCM, Wahl SA. From metagenomes to metabolism: Systematically assessing the metabolic flux feasibilities for "Candidatus Accumulibacter" species during anaerobic substrate uptake. WATER RESEARCH 2024; 250:121028. [PMID: 38128304 DOI: 10.1016/j.watres.2023.121028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic potential, but also feasibilities of these models under specific environmental conditions. In this study, we present a systematic analysis of the metabolic potential in species of "Candidatus Accumulibacter", a group of polyphosphate-accumulating organisms (PAOs). We constructed a metabolic model of the central carbon metabolism and compared the metabolic potential among available MAGs for "Ca. Accumulibacter" species. By combining Elementary Flux Modes Analysis (EFMA) with max-min driving force (MDF) optimization, we obtained all possible flux distributions of the metabolic network and calculated their individual thermodynamic feasibility. Our findings reveal significant variations in the metabolic potential among "Ca. Accumulibacter" MAGs, particularly in the presence of anaplerotic reactions. EFMA revealed 700 unique flux distributions in the complete metabolic model that enable the anaerobic uptake of acetate and its conversion into polyhydroxyalkanoates (PHAs), a well-known phenotype of "Ca. Accumulibacter". However, thermodynamic constraints narrowed down this solution space to 146 models that were stoichiometrically and thermodynamically feasible (MDF > 0 kJ/mol), of which only 8 were strongly feasible (MDF > 7 kJ/mol). Notably, several novel flux distributions for the metabolic model were identified, suggesting putative, yet unreported, functions within the PAO communities. Overall, this work provides valuable insights into the metabolic variability among "Ca. Accumulibacter" species and redefines the anaerobic metabolic potential in the context of phosphate removal. More generally, the integrated workflow presented in this paper can be applied to any metabolic model obtained from a MAG generated from microbial communities to objectively narrow the expected phenotypes from community members.
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Affiliation(s)
- Timothy Páez-Watson
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | | | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
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Guo T, Sperber AM, Krieger IV, Duan Y, Chemelewski VR, Sacchettini JC, Herman JK. Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization. J Bacteriol 2024; 206:e0020223. [PMID: 38047707 PMCID: PMC10810218 DOI: 10.1128/jb.00202-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023] Open
Abstract
YisK is an uncharacterized protein in Bacillus subtilis previously shown to interact genetically with the elongasome protein Mbl. YisK overexpression leads to cell widening and lysis, phenotypes that are dependent on mbl and suppressed by mbl mutations. In the present work, we characterize YisK's localization, structure, and enzymatic activity. We show that YisK localizes as puncta that depend on Mbl. YisK belongs to the fumarylacetoacetate hydrolase (FAH) superfamily, and crystal structures revealed close structural similarity to two oxaloacetate (OAA) decarboxylases: human mitochondrial FAHD1 and Corynebacterium glutamicum Cg1458. We demonstrate that YisK can also catalyze the decarboxylation of OAA (K m = 134 µM, K cat = 31 min-1). A catalytic dead variant (YisK E148A, E150A) retains wild-type localization and still widens cells following overexpression, indicating these activities are not dependent on YisK catalysis. Conversely, a non-localizing variant (YisK E30A) retains wild-type enzymatic activity in vitro but localizes diffusely and no longer widens cells following overexpression. Together, these results suggest that YisK may be subject to spatial regulation that depends on the cell envelope synthesis machinery. IMPORTANCE The elongasome is a multiprotein complex that guides lengthwise growth in some bacteria. We previously showed that, in B. subtilis, overexpression of an uncharacterized putative enzyme (YisK) perturbed function of the actin-like elongasome protein Mbl. Here, we show that YisK exhibits Mbl-dependent localization. Through biochemical and structural characterization, we demonstrate that, like its mitochondrial homolog FAHD1, YisK can catalyze the decarboxylation of the oxaloacetate to pyruvate and CO2. YisK is the first example of an enzyme implicated in central carbon metabolism with subcellular localization that depends on Mbl.
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Affiliation(s)
- Tingfeng Guo
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Anthony M. Sperber
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Inna V. Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Yi Duan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Veronica R. Chemelewski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Jennifer K. Herman
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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13
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Pešić D, Đukić MM, Stanojević I, Živkovć V, Bolevich S, Bolevich S, Jakovljević V. Cardiorespiratory fitness mediates cortisol and lactate responses to winter and summer marches. J Med Biochem 2024; 43:72-85. [PMID: 38496029 PMCID: PMC10943469 DOI: 10.5937/jomb0-44369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 03/19/2024] Open
Abstract
Background The influence of homeostatically regulated physiological processes, including cardiorespiratory fitness (VO2max), on the response to physical stressors such as acclimatisation and marching, remains understudied. We aimed to investigate the effects of summer and winter acclimatisation and marching on cortisol levels and blood lactate, to gain insight into the role of these physiological processes in the stress response. Methods Two groups of young Europeans, classified as poor (PCF; n=9) and good physical condition (GCF; n=21), based on a VO2MAX threshold of 40 mL O2/ kg/min, underwent 2-h March (6-7 km/h) in winter (5˚C) and summer (32˚C). Commercial tests, UniCel DxI Access Cortisol assay and EKF Biosen Clinic/GP assay were used for cortisol and lactate blood measurements (morning samples and those taken immediately after marches), respectively.
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Affiliation(s)
- Deniel Pešić
- Military Medical Academy, Institute of Hygiene, Department of Exercise Physiology, Belgrade
| | - Mirjana M. Đukić
- University of Belgrade, Faculty of Pharmacy, Department of Toxicology, Belgrade
| | - Ivan Stanojević
- Military Medical Academy, Institute of Medical Research, Belgrade
| | - Vladimir Živkovć
- University of Kragujevac, Faculty of Medical Sciences, Department of Physiology, Kragujevac
| | - Sergey Bolevich
- First Moscow State Medical University I. M. Sechenov, Department of Pharmacology, Moscow, Russia
| | - Stefani Bolevich
- First Moscow State Medical University I. M. Sechenov, Department of Pharmacology, Moscow, Russia
| | - Vladimir Jakovljević
- University of Kragujevac, Faculty of Medical Sciences, Department of Physiology, Kragujevac
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14
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Han S, Kim D, Kim Y, Yoon SH. Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12. BMC Genomics 2024; 25:63. [PMID: 38229031 DOI: 10.1186/s12864-023-09940-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/25/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Pseudomonas putida S12 is a gram-negative bacterium renowned for its high tolerance to organic solvents and metabolic versatility, making it attractive for various applications, including bioremediation and the production of aromatic compounds, bioplastics, biofuels, and value-added compounds. However, a metabolic model of S12 has yet to be developed. RESULTS In this study, we present a comprehensive and highly curated genome-scale metabolic network model of S12 (iSH1474), containing 1,474 genes, 1,436 unique metabolites, and 2,938 metabolic reactions. The model was constructed by leveraging existing metabolic models and conducting comparative analyses of genomes and phenomes. Approximately 2,000 different phenotypes were measured for S12 and its closely related KT2440 strain under various nutritional and environmental conditions. These phenotypic data, combined with the reported experimental data, were used to refine and validate the reconstruction. Model predictions quantitatively agreed well with in vivo flux measurements and the batch cultivation of S12, which demonstrated that iSH1474 accurately represents the metabolic capabilities of S12. Furthermore, the model was simulated to investigate the maximum theoretical metabolic capacity of S12 growing on toxic organic solvents. CONCLUSIONS iSH1474 represents a significant advancement in our understanding of the cellular metabolism of P. putida S12. The combined results of metabolic simulation and comparative genome and phenome analyses identified the genetic and metabolic determinants of the characteristic phenotypes of S12. This study could accelerate the development of this versatile organism as an efficient cell factory for various biotechnological applications.
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Affiliation(s)
- Sol Han
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dohyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngshin Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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15
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Lai A, Huang Y, Luo H, Jin Y, Wang L, Chen B, Deng K, Huang W, Zhang Y. Ruminal degradation characteristics of bagasse with different fermentation treatments in the rumen of beef cattle. Anim Sci J 2024; 95:e13937. [PMID: 38500367 DOI: 10.1111/asj.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 12/28/2023] [Accepted: 01/29/2024] [Indexed: 03/20/2024]
Abstract
This experiment aimed to study the degradation characteristics of bagasse after three fermentation treatments in beef cattle. Bagasse 1 was treated with 0.3% lactic acid bacteria (w/w). Bagasse 2 was treated with 0.3% mixed strains (Saccharomyces cerevisiae, Aspergillus niger, Aspergillus oryzae, and lactic acid bacteria at 2:1:1:1). Bagasse 3 was treated with 0.1% cellulase and 0.1% xylanase in addition to 0.3% mixed strains of bagasse 2. The dry matter (DM), crude ash (ASH), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) in the bagasses were determined. Compared to the control bagasse (without the strain and enzyme treatments), three fermented bagasses showed higher DM after 4 h fermentation. The CP and ASH contents in fermented bagasse 3 were the highest, while the contents of NDF and ADF in fermented bagasse 3 were the lowest among all the groups. The effective degradability of DM, CP, NDF, and ADF was highest in fermented bagasse 3 among the evaluated bagasse feed, followed by fermented bagasse 2 > fermented bagasse 1 > bagasse. Overall, fermented bagasse 3 was better than the control and other treated bagasses, thus fermented bagasse 3 is a hopeful source for ruminant diet of beef cattle.
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Affiliation(s)
- Anqiang Lai
- College of Animal Science, Xichang University, Xichang, China
| | - Yanru Huang
- College of Animal Science, Xichang University, Xichang, China
| | - Haocen Luo
- College of Animal Science, Xichang University, Xichang, China
| | - Yadong Jin
- College of Animal Science, Xichang University, Xichang, China
| | - Langzhou Wang
- College of Animal Science, Xichang University, Xichang, China
| | - Binlong Chen
- College of Animal Science, Xichang University, Xichang, China
| | - Kaimei Deng
- Rural Industrial Technology Service Center of Ningnan County, Liangshan, China
| | - Wenming Huang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yi Zhang
- College of Animal Science, Xichang University, Xichang, China
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16
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Shakoor A, Alam A, Jan F, Khan M, Ali M, Ullah S, Khan A, AlAsmari AF, Alasmari F, Al-Ghafri A, Al-Harrasi A. Novel benzimidazole derivatives as effective inhibitors of prolyl oligopeptidase: synthesis, in vitro and in silico analysis. Future Med Chem 2024; 16:43-58. [PMID: 38054466 DOI: 10.4155/fmc-2023-0267] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
Background: This research aims to discover novel derivatives having potential therapeutic applications in treating conditions related to prolyl oligopeptidase (POP) dysfunction. Method: Novel benzimidazole derivatives have been synthesized, characterized and screened for their in vitro POP inhibition. Results: All these derivatives showed excellent-to-good inhibitory activities in the range of IC50 values of 3.61 ± 0.15 to 43.72 ± 1.18 μM, when compared with standard Z-prolyl-prolinal. The docking analysis revealed the strong interactions between our compounds and the target enzyme, providing critical insights into their binding affinities and potential implications for drug development. Conclusion: The significance of these compounds in targeting POP enzyme offers promising prospects for future research in the field of neuropharmacology.
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Affiliation(s)
- Abdul Shakoor
- Department of Chemistry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Aftab Alam
- Department of Chemistry, University of Malakand, PO Box 18800, Khyber Pakhtunkhwa, Pakistan
| | - Faheem Jan
- Shenyang National Laboratory for Materials Science, Institute of Metal Research Chinese Academy of Sciences, Shenyang, Liaoning, 110016, People's Republic of China
| | - Momin Khan
- Department of Chemistry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Mumtaz Ali
- Department of Chemistry, University of Malakand, PO Box 18800, Khyber Pakhtunkhwa, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, PO Box 33, Nizwa, Oman
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, PO Box 33, Nizwa, Oman
| | - Abdullah F AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Fawaz Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ahmed Al-Ghafri
- Natural and Medical Sciences Research Center, University of Nizwa, PO Box 33, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, PO Box 33, Nizwa, Oman
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Hongo Y, Hano T, Yamaguchi H, Tomaru Y. Transcriptional responses of the marine diatom Chaetoceros tenuissimus to phosphate deficiency. Gene 2023; 884:147695. [PMID: 37549856 DOI: 10.1016/j.gene.2023.147695] [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: 06/07/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The planktonic diatom Chaetoceros tenuissimus sometimes forms blooms in coastal surface waters where dissolved inorganic phosphorus (P) is typically deficient. To understand the molecular mechanisms for survival under P-deficient conditions, we compared whole transcripts and metabolites with P-sufficient conditions using stationary growth cells. Under P-deficient conditions, cell numbers and photosynthetic activities decreased as cells entered the stationary growth phase, with downregulation of transcripts related to the Calvin cycle and glycolysis/gluconeogenesis. Therefore, metabolites varied across nutritional conditions. Alkaline phosphatase, phosphodiesterase, phytase, phosphate transporter, and transcription factor genes were drastically upregulated under dissolved inorganic P deficiency. Genes related to phospholipid degradation and nonphospholipid synthesis were also upregulated. These results indicate that C. tenuissimus rearranges its membrane composition from phospholipids to nonphospholipids to conserve phosphate. To endure in P-deficient conditions, C. tenuissimus modifies its gene responses, suggesting a potential survival strategy in nature.
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Affiliation(s)
- Yuki Hongo
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan.
| | - Takeshi Hano
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Yuji Tomaru
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
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Vila JC, Goldford J, Estrela S, Bajic D, Sanchez-Gorostiaga A, Damian-Serrano A, Lu N, Marsland R, Rebolleda-Gomez M, Mehta P, Sanchez A. Metabolic similarity and the predictability of microbial community assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564019. [PMID: 37961608 PMCID: PMC10634833 DOI: 10.1101/2023.10.25.564019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
When microbial communities form, their composition is shaped by selective pressures imposed by the environment. Can we predict which communities will assemble under different environmental conditions? Here, we hypothesize that quantitative similarities in metabolic traits across metabolically similar environments lead to predictable similarities in community composition. To that end, we measured the growth rate and by-product profile of a library of proteobacterial strains in a large number of single nutrient environments. We found that growth rates and secretion profiles were positively correlated across environments when the supplied substrate was metabolically similar. By analyzing hundreds of in-vitro communities experimentally assembled in an array of different synthetic environments, we then show that metabolically similar substrates select for taxonomically similar communities. These findings lead us to propose and then validate a comparative approach for quantitatively predicting the effects of novel substrates on the composition of complex microbial consortia.
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Affiliation(s)
- Jean C.C. Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joshua Goldford
- Division of Geophysical and Planetary sciences,California Institute of Technology, Pasadena, CA, USA
| | - Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Djordje Bajic
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Section of Industrial Microbiology, Department of Biotechnology, Technical University Delft, Delft, The Netherlands
| | - Alicia Sanchez-Gorostiaga
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Alcalá de Henares, Spain
| | - Alejandro Damian-Serrano
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Department of Biology, University of Oregon, Eugene, OR, USA
| | - Nanxi Lu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Robert Marsland
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Maria Rebolleda-Gomez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbial Biotechnology, National Center for Biotechnology CNB-CSIC; Madrid, Spain
- New address: Institute of Functional Biology & Genomics IBFG, CSIC & University of Salamanca; Salamanca, Spain
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Xiang J, Wang SW, Tao Y, Ye JZ, Liang Y, Peng XX, Yang LF, Li H. A glucose-mediated antibiotic resistance metabolic flux from glycolysis, the pyruvate cycle, and glutamate metabolism to purine metabolism. Front Microbiol 2023; 14:1267729. [PMID: 37915850 PMCID: PMC10616527 DOI: 10.3389/fmicb.2023.1267729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/18/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction Bacterial metabolic environment influences antibiotic killing efficacy. Thus, a full understanding for the metabolic resistance mechanisms is especially important to combat antibiotic-resistant bacteria. Methods Isobaric tags for relative and absolute quantification-based proteomics approach was employed to compare proteomes between ceftazidime-resistant and -sensitive Edwarsiella tarda LTB4 (LTB4-RCAZ and LTB4-S, respectively). Results This analysis suggested the possibility that the ceftazidime resistance mediated by depressed glucose is implemented through an inefficient metabolic flux from glycolysis, the pyruvate cycle, glutamate metabolism to purine metabolism. The inefficient flux was demonstrated by the reduced expression of genes and the decreased activity of enzymes in the four metabolic pathways. However, supplement upstream glucose and downstream guanosine separately restored ceftazidime killing, which not only supports the conclusion that the inefficient metabolic flux is responsible for the resistance, but also provides an effective approach to reverse the resistance. In addition, the present study showed that ceftazidime is bound to pts promoter in E. tarda. Discussion Our study highlights the way in fully understanding metabolic resistance mechanisms and establishing metabolites-based metabolic reprogramming to combat antibiotic resistance.
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Affiliation(s)
- Jiao Xiang
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi-wen Wang
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuan Tao
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jing-zhou Ye
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Liang
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuan-xian Peng
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Guangdong Litai Pharmaceutical Co., Ltd., Jieyang, China
| | - Li-fen Yang
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hui Li
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Zumsteg J, Hirschler A, Carapito C, Maurer L, Villette C, Heintz D, Dahl C, El Nayal A, Sangal V, Mahmoud H, Van Dorsselaer A, Ismail W. Mechanistic insights into sulfur source-driven physiological responses and metabolic reorganization in the fuel-biodesulfurizing Rhodococcus qingshengii IGTS8. Appl Environ Microbiol 2023; 89:e0082623. [PMID: 37655899 PMCID: PMC10537767 DOI: 10.1128/aem.00826-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Comparative proteomics and untargeted metabolomics were combined to study the physiological and metabolic adaptations of Rhodococcus qingshengii IGTS8 under biodesulfurization conditions. After growth in a chemically defined medium with either dibenzothiophene (DBT) or MgSO4 as the sulfur source, many differentially produced proteins and metabolites associated with several metabolic and physiological processes were detected including the metabolism of carbohydrates, amino acids, lipids, nucleotides, vitamins, protein synthesis, transcriptional regulation, cell envelope biogenesis, and cell division. Increased production of the redox cofactor mycofactocin and associated proteins was one of the most striking adaptations under biodesulfurization conditions. While most central metabolic enzymes were less abundant in the presence of DBT, a key enzyme of the glyoxylate shunt, isocitrate lyase, was up to 26-fold more abundant. Several C1 metabolism and oligotrophy-related enzymes were significantly more abundant in the biodesulfurizing culture. R. qingshengii IGTS8 exhibited oligotrophic growth in liquid and solid media under carbon starvation. Moreover, the oligotrophic growth was faster on the solid medium in the presence of DBT compared to MgSO4 cultures. In the DBT culture, the cell envelope and phospholipids were remodeled, with lower levels of phosphatidylethanolamine and unsaturated and short-chain fatty acids being the most prominent changes. Biodesulfurization increased the biosynthesis of osmoprotectants (ectoine and mannosylglycerate) as well as glutamate and induced the stringent response. Our findings reveal highly diverse and overlapping stress responses that could protect the biodesulfurizing culture not only from the associated sulfate limitation but also from chemical, oxidative, and osmotic stress, allowing efficient resource management. IMPORTANCE Despite decades of research, a commercially viable bioprocess for fuel desulfurization has not been developed yet. This is mainly due to lack of knowledge of the physiology and metabolism of fuel-biodesulfurizing bacteria. Being a stressful condition, biodesulfurization could provoke several stress responses that are not understood. This is particularly important because a thorough understanding of the microbial stress response is essential for the development of environmentally friendly and industrially efficient microbial biocatalysts. Our comparative systems biology studies provide a mechanistic understanding of the biology of biodesulfurization, which is crucial for informed developments through the rational design of recombinant biodesulfurizers and optimization of the bioprocess conditions. Our findings enhance the understanding of the physiology, metabolism, and stress response not only in biodesulfurizing bacteria but also in rhodococci, a precious group of biotechnologically important bacteria.
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Affiliation(s)
- Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Loïc Maurer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Département mécanique, ICube Laboratoire des sciences de l’ingénieur, de l’informatique et de l’imagerie, UNISTRA/CNRS/ENGEES/INSA, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ashraf El Nayal
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Huda Mahmoud
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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21
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Gu P, Zhao S, Niu H, Li C, Jiang S, Zhou H, Li Q. Synthesis of isobutanol using acetate as sole carbon source in Escherichia coli. Microb Cell Fact 2023; 22:196. [PMID: 37759284 PMCID: PMC10537434 DOI: 10.1186/s12934-023-02197-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND With concerns about depletion of fossil fuel and environmental pollution, synthesis of biofuels such as isobutanol from low-cost substrate by microbial cell factories has attracted more and more attention. As one of the most promising carbon sources instead of food resources, acetate can be utilized by versatile microbes and converted into numerous valuable chemicals. RESULTS An isobutanol synthetic pathway using acetate as sole carbon source was constructed in E. coli. Pyruvate was designed to be generated via acetyl-CoA by pyruvate-ferredoxin oxidoreductase YdbK or anaplerotic pathway. Overexpression of transhydrogenase and NAD kinase increased the isobutanol titer of recombinant E. coli from 121.21 mg/L to 131.5 mg/L under batch cultivation. Further optimization of acetate supplement concentration achieved 157.05 mg/L isobutanol accumulation in WY002, representing the highest isobutanol titer by using acetate as sole carbon source. CONCLUSIONS The utilization of acetate as carbon source for microbial production of valuable chemicals such as isobutanol could reduce the consumption of food-based substrates and save production cost. Engineering strategies applied in this study will provide a useful reference for microbial production of pyruvate derived chemical compounds from acetate.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Hao Niu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Chengwei Li
- RZBC GROUP CO., LTD, Rizhao, 276800, Shandong, China
| | | | - Hao Zhou
- RZBC GROUP CO., LTD, Rizhao, 276800, Shandong, China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
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22
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Yan J, Yang B, Xue X, Li J, Li Y, Li A, Ding P, Cao B. Transcriptome Analysis Reveals the Effect of PdhR in Plesiomonas shigelloides. Int J Mol Sci 2023; 24:14473. [PMID: 37833920 PMCID: PMC10572922 DOI: 10.3390/ijms241914473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The pyruvate dehydrogenase complex regulator (PdhR) was originally identified as a repressor of the pdhR-aceEF-lpd operon, which encodes the pyruvate dehydrogenase complex (PDHc) and PdhR itself. According to previous reports, PdhR plays a regulatory role in the physiological and metabolic pathways of bacteria. At present, the function of PdhR in Plesiomonas shigelloides is still poorly understood. In this study, RNA sequencing (RNA-Seq) of the wild-type strain and the ΔpdhR mutant strains was performed for comparison to identify the PdhR-controlled pathways, revealing that PdhR regulates ~7.38% of the P. shigelloides transcriptome. We found that the deletion of pdhR resulted in the downregulation of practically all polar and lateral flagella genes in P. shigelloides; meanwhile, motility assay and transmission electron microscopy (TEM) confirmed that the ΔpdhR mutant was non-motile and lacked flagella. Moreover, the results of RNA-seq and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) showed that PdhR positively regulated the expression of the T3SS cluster, and the ΔpdhR mutant significantly reduced the ability of P. shigelloides to infect Caco-2 cells compared with the WT. Consistent with previous research, pyruvate-sensing PdhR directly binds to its promoter and inhibits pdhR-aceEF-lpd operon expression. In addition, we identified two additional downstream genes, metR and nuoA, that are directly negatively regulated by PdhR. Furthermore, we also demonstrated that ArcA was identified as being located upstream of pdhR and lpdA and directly negatively regulating their expression. Overall, we revealed the function and regulatory pathway of PdhR, which will allow for a more in-depth investigation into P. shigelloides pathogenicity as well as the complex regulatory network.
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Affiliation(s)
- Junxiang Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Xinke Xue
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Jinghao Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Yuehua Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Ang Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
- College of Pharmacy Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Peng Ding
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
| | - Boyang Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin 300457, China
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23
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Kurpejović E, Wibberg D, Bastem GM, Burgardt A, Busche T, Kaya FEA, Dräger A, Wendisch VF, Akbulut BS. Can Genome Sequencing Coupled to Flux Balance Analyses Offer Precision Guidance for Industrial Strain Development? The Lessons from Carbon Trafficking in Corynebacterium glutamicum ATCC 21573. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:434-443. [PMID: 37707996 DOI: 10.1089/omi.2023.0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Systems biology tools offer new prospects for industrial strain selection. For bacteria that are significant for industrial applications, whole-genome sequencing coupled to flux balance analysis (FBA) can help unpack the complex relationships between genome mutations and carbon trafficking. This work investigates the l-tyrosine (l-Tyr) overproducing model system Corynebacterium glutamicum ATCC 21573 with an eye to more rational and precision strain development. Using genome-wide mutational analysis of C. glutamicum, we identified 27,611 single nucleotide polymorphisms and 479 insertion/deletion mutations. Mutations in the carbon uptake machinery have led to phosphotransferase system-independent routes as corroborated with FBA. Mutations within the central carbon metabolism of C. glutamicum impaired the carbon flux, as evidenced by the lower growth rate. The entry to and flow through the tricarboxylic acid cycle was affected by mutations in pyruvate and α-ketoglutarate dehydrogenase complexes, citrate synthase, and isocitrate dehydrogenase. FBA indicated that the estimated flux through the shikimate pathway became larger as the l-Tyr production rate increased. In addition, protocatechuate export was probabilistically impossible, which could have contributed to the l-Tyr accumulation. Interestingly, aroG and cg0975, which have received previous attention for aromatic amino acid overproduction, were not mutated. From the branch point molecule, prephenate, the change in the promoter region of pheA could be an influential contributor. In summary, we suggest that genome sequencing coupled with FBA is well poised to offer rational guidance for industrial strain development, as evidenced by these findings on carbon trafficking in C. glutamicum ATCC 21573.
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Affiliation(s)
- Eldin Kurpejović
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Arthur Burgardt
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Bielefeld, Germany
| | - Fatma Ece Altinisik Kaya
- Department of Bioengineering, Marmara University, Istanbul, Turkey
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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24
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Fry B, Carter JF, O'Mara K. Fingerprinting eukaryotic metabolism across the animal kingdom using position-specific isotope analysis (PSIA) 13C/ 12C measurements. SCIENCE ADVANCES 2023; 9:eadg1549. [PMID: 37406114 DOI: 10.1126/sciadv.adg1549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/01/2023] [Indexed: 07/07/2023]
Abstract
Despite differences in their overall metabolism, eukaryotes share a common mitochondrial biochemistry. We investigated how this fundamental biochemistry supports overall metabolism using a high-resolution carbon isotope approach, position-specific isotope analysis. We measured carbon isotope 13C/12C cycling in animals, focusing on amino acids that are formed in mitochondrial reactions and are most metabolically active. Carboxyl isotope determinations for amino acids showed strong signals related to common biochemical pathways. Contrasting isotope patterns were measured for metabolism associated with major life history patterns, including growth and reproduction. Turnover of proteins and lipids as well as gluoconeogensis dynamics could be estimated for these metabolic life histories. The high-resolution isotomics measurements fingerprinted metabolism and metabolic strategies across the eukaryotic animal kingdom, yielding results for humans, ungulates, whales, and diverse fish and invertebrates in a nearshore marine food web.
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Affiliation(s)
- Brian Fry
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - James F Carter
- Queensland Health, Forensic and Scientific Services, Coopers Plains, Queensland 4108, Australia
| | - Kaitlyn O'Mara
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia
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25
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Khandelwal R, Srivastava P, Bisaria VS. Recent advances in the production of malic acid by native fungi and engineered microbes. World J Microbiol Biotechnol 2023; 39:217. [PMID: 37269376 DOI: 10.1007/s11274-023-03666-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Malic acid is mainly produced by chemical methods which lead to various environmental sustainability concerns associated with CO2 emissions and resulting global warming. Since malic acid is naturally synthesized, microorganisms offer an eco-friendly and cost-effective alternative for its production. An additional advantage of microbial production is the synthesis of pure L-form of malic acid. Due to its numerous applications, biotechnologically- produced L-malic acid is a much sought-after platform chemical. Malic acid can be produced by microbial fermentation via oxidative/reductive TCA and glyoxylate pathways. This article elaborates the potential and limitations of high malic acid producing native fungi belonging to Aspergillus, Penicillium, Ustilago and Aureobasidium spp. The utilization of industrial side streams and low value renewable substrates such as crude glycerol and lignocellulosic biomass is also discussed with a view to develop a competitive bio-based production process. The major impediments present in the form of toxic compounds from lignocellulosic residues or synthesized during fermentation along with their remedial measures are also described. The article also focuses on production of polymalic acid from renewable substrates which opens up a cost-cutting dimension in production of this biodegradable polymer. Finally, the recent strategies being employed for its production in recombinant organisms have also been covered.
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Affiliation(s)
- Rohit Khandelwal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
- Corporate Research & Development Centre, Bharat Petroleum Corporation Limited, Udyog Kendra, P. O. Surajpur, Greater Noida, 201306, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Virendra Swarup Bisaria
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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26
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Hwang Y, Harshey RM. A Second Role for the Second Messenger Cyclic-di-GMP in E. coli: Arresting Cell Growth by Altering Metabolic Flow. mBio 2023; 14:e0061923. [PMID: 37036337 PMCID: PMC10127611 DOI: 10.1128/mbio.00619-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/11/2023] Open
Abstract
c-di-GMP primarily controls motile to sessile transitions in bacteria. Diguanylate cyclases (DGCs) catalyze the synthesis of c-di-GMP from two GTP molecules. Typically, bacteria encode multiple DGCs that are activated by specific environmental signals. Their catalytic activity is modulated by c-di-GMP binding to autoinhibitory sites (I-sites). YfiN is a conserved inner membrane DGC that lacks these sites. Instead, YfiN activity is directly repressed by periplasmic YfiR, which is inactivated by redox stress. In Escherichia coli, an additional envelope stress causes YfiN to relocate to the mid-cell to inhibit cell division by interacting with the division machinery. Here, we report a third activity for YfiN in E. coli, where cell growth is inhibited without YfiN relocating to the division site. This action of YfiN is only observed when the bacteria are cultured on gluconeogenic carbon sources, and is dependent on absence of the autoinhibitory sites. Restoration of I-site function relieves the growth-arrest phenotype, and disabling this function in a heterologous DGC causes acquisition of this phenotype. Arrested cells are tolerant to a wide range of antibiotics. We show that the likely cause of growth arrest is depletion of cellular GTP from run-away synthesis of c-di-GMP, explaining the dependence of growth arrest on gluconeogenic carbon sources that exhaust more GTP during production of glucose. This is the first report of c-di-GMP-mediated growth arrest by altering metabolic flow. IMPORTANCE The c-di-GMP signaling network in bacteria not only controls a variety of cellular processes such as motility, biofilms, cell development, and virulence, but does so by a dizzying array of mechanisms. The DGC YfiN singularly represents the versatility of this network in that it not only inhibits motility and promotes biofilms, but also arrests growth in Escherichia coli by relocating to the mid-cell and blocking cell division. The work described here reveals that YfiN arrests growth by yet another mechanism in E. coli, changing metabolic flow. This function of YfiN, or of DGCs without autoinhibitory I-sites, may contribute to antibiotic tolerant persisters in relevant niches such as the gut where gluconeogenic sugars are found.
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Affiliation(s)
- YuneSahng Hwang
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, Texas, USA
| | - Rasika M. Harshey
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, Texas, USA
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27
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Sannelli F, Jensen PR, Meier S. In-Cell NMR Approach for Real-Time Exploration of Pathway Versatility: Substrate Mixtures in Nonengineered Yeast. Anal Chem 2023; 95:7262-7270. [PMID: 37097609 DOI: 10.1021/acs.analchem.3c00225] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The central carbon metabolism of microbes will likely be used in future sustainable bioproduction. A sufficiently deep understanding of central metabolism would advance the control of activity and selectivity in whole-cell catalysis. Opposite to the more obvious effects of adding catalysts through genetic engineering, the modulation of cellular chemistry through effectors and substrate mixtures remains less clear. NMR spectroscopy is uniquely suited for in-cell tracking to advance mechanistic insight and to optimize pathway usage. Using a comprehensive and self-consistent library of chemical shifts, hyperpolarized NMR, and conventional NMR, we probe the versatility of cellular pathways to changes in substrate composition. Conditions for glucose influx into a minor pathway to an industrial precursor (2,3-butanediol) can thus be designed. Changes to intracellular pH can be followed concurrently, while mechanistic details for the minor pathway can be derived using an intermediate-trapping strategy. Overflow at the pyruvate level can be induced in nonengineered yeast with suitably mixed carbon sources (here glucose with auxiliary pyruvate), thus increasing glucose conversion to 2,3-butanediol by more than 600-fold. Such versatility suggests that a reassessment of canonical metabolism may be warranted using in-cell spectroscopy.
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Affiliation(s)
- Francesca Sannelli
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs Lyngby, Denmark
| | - Pernille Rose Jensen
- Department of Health Technology, Technical University of Denmark, Elektrovej 349, 2800 Kgs Lyngby, Denmark
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs Lyngby, Denmark
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28
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Wu Z, Liang X, Li M, Ma M, Zheng Q, Li D, An T, Wang G. Advances in the optimization of central carbon metabolism in metabolic engineering. Microb Cell Fact 2023; 22:76. [PMID: 37085866 PMCID: PMC10122336 DOI: 10.1186/s12934-023-02090-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
Central carbon metabolism (CCM), including glycolysis, tricarboxylic acid cycle and the pentose phosphate pathway, is the most fundamental metabolic process in the activities of living organisms that maintains normal cellular growth. CCM has been widely used in microbial metabolic engineering in recent years due to its unique regulatory role in cellular metabolism. Using yeast and Escherichia coli as the representative organisms, we summarized the metabolic engineering strategies on the optimization of CCM in eukaryotic and prokaryotic microbial chassis, such as the introduction of heterologous CCM metabolic pathways and the optimization of key enzymes or regulatory factors, to lay the groundwork for the future use of CCM optimization in metabolic engineering. Furthermore, the bottlenecks in the application of CCM optimization in metabolic engineering and future application prospects are summarized.
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Affiliation(s)
- Zhenke Wu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mengyu Ma
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
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29
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Zhang X, Xia L, Liu J, Wang Z, Yang Y, Wu Y, Yang Q, Huang L, Shen P. Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria. Int J Mol Sci 2023; 24:ijms24087521. [PMID: 37108681 PMCID: PMC10138955 DOI: 10.3390/ijms24087521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Methylotrophic bacteria are widely distributed in nature and can be applied in bioconversion because of their ability to use one-carbon source. The aim of this study was to investigate the mechanism underlying utilization of high methanol content and other carbon sources by Methylorubrum rhodesianum strain MB200 via comparative genomics and analysis of carbon metabolism pathway. The genomic analysis revealed that the strain MB200 had a genome size of 5.7 Mb and two plasmids. Its genome was presented and compared with that of the 25 fully sequenced strains of Methylobacterium genus. Comparative genomics revealed that the Methylorubrum strains had closer collinearity, more shared orthogroups, and more conservative MDH cluster. The transcriptome analysis of the strain MB200 in the presence of various carbon sources revealed that a battery of genes was involved in the methanol metabolism. These genes are involved in the following functions: carbon fixation, electron transfer chain, ATP energy release, and resistance to oxidation. Particularly, the central carbon metabolism pathway of the strain MB200 was reconstructed to reflect the possible reality of the carbon metabolism, including ethanol metabolism. Partial propionate metabolism involved in ethyl malonyl-CoA (EMC) pathway might help to relieve the restriction of the serine cycle. In addition, the glycine cleavage system (GCS) was observed to participate in the central carbon metabolism pathway. The study revealed the coordination of several metabolic pathways, where various carbon sources could induce associated metabolic pathways. To the best of our knowledge, this is the first study providing a more comprehensive understanding of the central carbon metabolism in Methylorubrum. This study provided a reference for potential synthetic and industrial applications of this genus and its use as chassis cells.
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Affiliation(s)
- Xi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Liqing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Jianyi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zihao Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Yanni Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Yiting Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Qingshan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Luodong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Peihong Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
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30
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Ceron-Chafla P, de Vrieze J, Rabaey K, van Lier JB, Lindeboom REF. Steering the product spectrum in high-pressure anaerobic processes: CO 2 partial pressure as a novel tool in biorefinery concepts. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:27. [PMID: 36803622 PMCID: PMC9938588 DOI: 10.1186/s13068-023-02262-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/05/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Elevated CO2 partial pressure (pCO2) has been proposed as a potential steering parameter for selective carboxylate production in mixed culture fermentation. It is anticipated that intermediate product spectrum and production rates, as well as changes in the microbial community, are (in)directly influenced by elevated pCO2. However, it remains unclear how pCO2 interacts with other operational conditions, namely substrate specificity, substrate-to-biomass (S/X) ratio and the presence of an additional electron donor, and what effect pCO2 has on the exact composition of fermentation products. Here, we investigated possible steering effects of elevated pCO2 combined with (1) mixed substrate (glycerol/glucose) provision; (2) subsequent increments in substrate concentration to increase the S/X ratio; and (3) formate as an additional electron donor. RESULTS Metabolite predominance, e.g., propionate vs. butyrate/acetate, and cell density, depended on interaction effects between pCO2-S/X ratio and pCO2-formate. Individual substrate consumption rates were negatively impacted by the interaction effect between pCO2-S/X ratio and were not re-established after lowering the S/X ratio and adding formate. The product spectrum was influenced by the microbial community composition, which in turn, was modified by substrate type and the interaction effect between pCO2-formate. High propionate and butyrate levels strongly correlated with Negativicutes and Clostridia predominance, respectively. After subsequent pressurized fermentation phases, the interaction effect between pCO2-formate enabled a shift from propionate towards succinate production when mixed substrate was provided. CONCLUSIONS Overall, interaction effects between elevated pCO2, substrate specificity, high S/X ratio and availability of reducing equivalents from formate, rather than an isolated pCO2 effect, modified the proportionality of propionate, butyrate and acetate in pressurized mixed substrate fermentations at the expense of reduced consumption rates and increased lag-phases. The interaction effect between elevated pCO2 and formate was beneficial for succinate production and biomass growth with a glycerol/glucose mixture as the substrate. The positive effect may be attributed to the availability of extra reducing equivalents, likely enhanced carbon fixating activity and hindered propionate conversion due to increased concentration of undissociated carboxylic acids.
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Affiliation(s)
- Pamela Ceron-Chafla
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands.
| | - Jo de Vrieze
- grid.5342.00000 0001 2069 7798Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Korneel Rabaey
- grid.5342.00000 0001 2069 7798Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium ,grid.510907.aCenter for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Coupure Links 653, 9000 Ghent, Belgium
| | - Jules B. van Lier
- grid.5292.c0000 0001 2097 4740Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Ralph E. F. Lindeboom
- grid.5292.c0000 0001 2097 4740Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
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The inside scoop: Comparative genomics of two intranuclear bacteria, "Candidatus Berkiella cookevillensis" and "Candidatus Berkiella aquae". PLoS One 2022; 17:e0278206. [PMID: 36584052 PMCID: PMC9803151 DOI: 10.1371/journal.pone.0278206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/12/2022] [Indexed: 12/31/2022] Open
Abstract
"Candidatus Berkiella cookevillensis" (strain CC99) and "Candidatus Berkiella aquae" (strain HT99), belonging to the Coxiellaceae family, are gram-negative bacteria isolated from amoebae in biofilms present in human-constructed water systems. Both bacteria are obligately intracellular, requiring host cells for growth and replication. The intracellular bacteria-containing vacuoles of both bacteria closely associate with or enter the nuclei of their host cells. In this study, we analyzed the genome sequences of CC99 and HT99 to better understand their biology and intracellular lifestyles. The CC99 genome has a size of 2.9Mb (37.9% GC) and contains 2,651 protein-encoding genes (PEGs) while the HT99 genome has a size of 3.6Mb (39.4% GC) and contains 3,238 PEGs. Both bacteria encode high proportions of hypothetical proteins (CC99: 46.5%; HT99: 51.3%). The central metabolic pathways of both bacteria appear largely intact. Genes for enzymes involved in the glycolytic pathway, the non-oxidative branch of the phosphate pathway, the tricarboxylic acid pathway, and the respiratory chain were present. Both bacteria, however, are missing genes for the synthesis of several amino acids, suggesting reliance on their host for amino acids and intermediates. Genes for type I and type IV (dot/icm) secretion systems as well as type IV pili were identified in both bacteria. Moreover, both bacteria contain genes encoding large numbers of putative effector proteins, including several with eukaryotic-like domains such as, ankyrin repeats, tetratricopeptide repeats, and leucine-rich repeats, characteristic of other intracellular bacteria.
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Systems-Wide Dissection of Organic Acid Assimilation in Pseudomonas aeruginosa Reveals a Novel Path To Underground Metabolism. mBio 2022; 13:e0254122. [PMID: 36377867 PMCID: PMC9765439 DOI: 10.1128/mbio.02541-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The human pathogen Pseudomonas aeruginosa (Pa) is one of the most frequent and severe causes of nosocomial infection. This organism is also a major cause of airway infections in people with cystic fibrosis (CF). Pa is known to have a remarkable metabolic plasticity, allowing it to thrive under diverse environmental conditions and ecological niches; yet, little is known about the central metabolic pathways that sustain its growth during infection or precisely how these pathways operate. In this work, we used a combination of 'omics approaches (transcriptomics, proteomics, metabolomics, and 13C-fluxomics) and reverse genetics to provide systems-level insight into how the infection-relevant organic acids succinate and propionate are metabolized by Pa. Moreover, through structural and kinetic analysis of the 2-methylcitrate synthase (2-MCS; PrpC) and its paralogue citrate (CIT) synthase (GltA), we show how these two crucial enzymatic steps are interconnected in Pa organic acid assimilation. We found that Pa can rapidly adapt to the loss of GltA function by acquiring mutations in a transcriptional repressor, which then derepresses prpC expression. Our findings provide a clear example of how "underground metabolism," facilitated by enzyme substrate promiscuity, "rewires" Pa metabolism, allowing it to overcome the loss of a crucial enzyme. This pathogen-specific knowledge is critical for the advancement of a model-driven framework to target bacterial central metabolism. IMPORTANCE Pseudomonas aeruginosa is an opportunistic human pathogen that, due to its unrivalled resistance to antibiotics, ubiquity in the built environment, and aggressiveness in infection scenarios, has acquired the somewhat dubious accolade of being designated a "critical priority pathogen" by the WHO. In this work, we uncover the pathways and mechanisms used by P. aeruginosa to grow on a substrate that is abundant at many infection sites: propionate. We found that if the organism is prevented from metabolizing propionate, the substrate turns from being a convenient nutrient source into a potent poison, preventing bacterial growth. We further show that one of the enzymes involved in these reactions, 2-methylcitrate synthase (PrpC), is promiscuous and can moonlight for another essential enzyme in the cell (citrate synthase). Indeed, mutations that abolish citrate synthase activity (which would normally prevent the cell from growing) can be readily overcome if the cell acquires additional mutations that increase the expression of PrpC. This is a nice example of the evolutionary utility of so-called "underground metabolism."
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Engineering Escherichia coli for Efficient Aerobic Conversion of Glucose to Malic Acid through the Modified Oxidative TCA Cycle. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Malic acid is a versatile building-block chemical that can serve as a precursor of numerous valuable products, including food additives, pharmaceuticals, and biodegradable plastics. Despite the present petrochemical synthesis, malic acid, being an intermediate of the TCA cycle of a variety of living organisms, can also be produced from renewable carbon sources using wild-type and engineered microbial strains. In the current study, Escherichia coli was engineered for efficient aerobic conversion of glucose to malic acid through the modified oxidative TCA cycle resembling that of myco- and cyanobacteria and implying channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation. The formation of succinate semialdehyde was enabled in the core strain MAL 0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP, ∆aceBAK, ∆glcB) by the expression of Mycobacterium tuberculosis kgd gene. The secretion of malic acid by the strain was ensured, resulting from the deletion of the mdh, maeA, maeB, and mqo genes. The Bacillus subtilis pycA gene was expressed in the strain to allow pyruvate to oxaloacetate conversion. The corresponding recombinant was able to synthesise malic acid from glucose aerobically with a yield of 0.65 mol/mol. The yield was improved by the derepression in the strain of the electron transfer chain and succinate dehydrogenase due to the enforcement of ATP hydrolysis and reached 0.94 mol/mol, amounting to 94% of the theoretical maximum. The implemented strategy offers the potential for the development of highly efficient strains and processes of bio-based malic acid production.
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Study on spoilage potential and its molecular basis of Shewanella putrefaciens in response to cold conditions by Label-free quantitative proteomic analysis. World J Microbiol Biotechnol 2022; 39:40. [PMID: 36512125 DOI: 10.1007/s11274-022-03479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
To elucidate how Shewanella putrefaciens survives and produces spoilage products in response to cold conditions, the metabolic and protease activity of S. putrefaciens DSM6067 cultured at three different temperatures (30 °C, 10 °C, and 4 °C) was studied by determining the bacterial growth, total volatile basic nitrogen (TVB-N), biogenic amines, extracellular protease activity, as well as the differential expressed proteins via Label-free quantitative proteomics analysis. The lag phase of the strain cultured at 10 °C and 4 °C was about 20 h and 120 h longer than at 30 °C, respectively. The TVB-N increased to 89.23 mg N/100 g within 28 h at 30 °C, and it needed at least 72 h and 224 h at 10 °C and 4 °C, respectively. Cold temperatures (10 °C and 4 °C) also inhibited the yield factors and the extracellular protease activity per cell at the lag phase. However, the protease activity per cell and the yield factors of the sample cultivated at 10 °C and 4 °C well recovered, especially at the mid and latter stages of the log phase. The further quantitative proteomic analysis displayed a complex biological network to tackle cold stress: cold stress responses, nutrient uptake, and energy conservation strategy. It was observed that the protease and peptidase were upregulated, so as to the degradation pathways of serine, arginine, and aspartate, which might lead to the accumulation of spoilage products. This study highlighted the spoilage potential of S. putrefaciens still should be concerned even at low temperatures.
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Orsi E, Claassens NJ, Nikel PI, Lindner SN. Optimizing microbial networks through metabolic bypasses. Biotechnol Adv 2022; 60:108035. [PMID: 36096403 DOI: 10.1016/j.biotechadv.2022.108035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
Metabolism has long been considered as a relatively stiff set of biochemical reactions. This somewhat outdated and dogmatic view has been challenged over the last years, as multiple studies exposed unprecedented plasticity of metabolism by exploring rational and evolutionary modifications within the metabolic network of cell factories. Of particular importance is the emergence of metabolic bypasses, which consist of enzymatic reaction(s) that support unnatural connections between metabolic nodes. Such novel topologies can be generated through the introduction of heterologous enzymes or by upregulating native enzymes (sometimes relying on promiscuous activities thereof). Altogether, the adoption of bypasses resulted in an expansion in the capacity of the host's metabolic network, which can be harnessed for bioproduction. In this review, we discuss modifications to the canonical architecture of central carbon metabolism derived from such bypasses towards six optimization purposes: stoichiometric gain, overcoming kinetic limitations, solving thermodynamic barriers, circumventing toxic intermediates, uncoupling product synthesis from biomass formation, and altering redox cofactor specificity. The metabolic costs associated with bypass-implementation are likewise discussed, including tailoring their design towards improving bioproduction.
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Affiliation(s)
- Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany.
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Wang W, Sudun, Hu H, An J, Zhang H, Zhao Z, Hao Y, Zhai Z. Unraveling the mechanism of raffinose utilization in Ligilactobacillus salivarius Ren by transcriptomic analysis. 3 Biotech 2022; 12:229. [PMID: 35992897 PMCID: PMC9385920 DOI: 10.1007/s13205-022-03280-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022] Open
Abstract
In the gastrointestinal tract, some dietary carbohydrates, such as xylose, raffinose and arabinose, are able to stimulate the growth of Lactobacillus and Bifidobacterium. In this study, the growth rate of Ligilactobacillus salivarius Ren in raffinose was 0.91 ± 0.03 h-1, which was higher than that in glucose (0.83 ± 0.01 h-1). However, limited information is available on specific transporters and glycoside hydrolases responsible for raffinose uptake and catabolism in L. salivarius. Transcriptomic analysis revealed the differential expression of 236 genes (∣log2FoldChange∣ > 0.8) in response to raffinose, which were mainly associated with raffinose transport, raffinose hydrolysis, galactose metabolism and pyruvate metabolism. Notably, gene rafP encoding lactose/raffinose permease was 101.86-fold up-regulated. Two α-galactosidase gene galA1 and galA2 were 117.82-fold and 2.66-fold up-regulated, respectively. To further investigate the role of these genes in raffinose utilization, insertional inactivation was performed using the pORI28-pTRK669 system. The growth assay of these mutants in modified MRS containing 2% (w/v) raffinose indicated that RafP played an important role in raffinose transport and GalA1 was the primary enzyme involved in raffinose hydrolysis. To our knowledge, this is the first report on the molecular mechanism of raffinose utilization in L. salivarius. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03280-6.
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Affiliation(s)
- Weizhe Wang
- Key Laboratory of Functional Dairy, Co-Constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Sudun
- HUA Cloud Intelligent Healthcare Co., Ltd, Shenzhen, China
| | - Huizhong Hu
- Key Laboratory of Functional Dairy, Co-Constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jieran An
- Key Laboratory of Functional Dairy, Co-Constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hongxing Zhang
- Department of Food Science, Beijing University of Agriculture, Beijing, China
| | - Zigang Zhao
- Department of Dermatology, Hainan Hospital of PLA General Hospital, Sanya, Hainan China
| | - Yanling Hao
- Key Laboratory of Functional Dairy, Co-Constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhengyuan Zhai
- Key Laboratory of Functional Dairy, Co-Constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Present Address: College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083 China
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Hobmeier K, Oppermann M, Stasinski N, Kremling A, Pflüger-Grau K, Kunte HJ, Marin-Sanguino A. Metabolic engineering of Halomonas elongata: Ectoine secretion is increased by demand and supply driven approaches. Front Microbiol 2022; 13:968983. [PMID: 36090101 PMCID: PMC9453808 DOI: 10.3389/fmicb.2022.968983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022] Open
Abstract
The application of naturally-derived biomolecules in everyday products, replacing conventional synthetic manufacturing, is an ever-increasing market. An example of this is the compatible solute ectoine, which is contained in a plethora of treatment formulations for medicinal products and cosmetics. As of today, ectoine is produced in a scale of tons each year by the natural producer Halomonas elongata. In this work, we explore two complementary approaches to obtain genetically improved producer strains for ectoine production. We explore the effect of increased precursor supply (oxaloacetate) on ectoine production, as well as an implementation of increased ectoine demand through the overexpression of a transporter. Both approaches were implemented on an already genetically modified ectoine-excreting strain H. elongata KB2.13 (ΔteaABC ΔdoeA) and both led to new strains with higher ectoine excretion. The supply driven approach led to a 45% increase in ectoine titers in two different strains. This increase was attributed to the removal of phosphoenolpyruvate carboxykinase (PEPCK), which allowed the conversion of 17.9% of the glucose substrate to ectoine. For the demand driven approach, we investigated the potential of the TeaBC transmembrane proteins from the ectoine-specific Tripartite ATP-Independent Periplasmic (TRAP) transporter as export channels to improve ectoine excretion. In the absence of the substrate-binding protein TeaA, an overexpression of both subunits TeaBC facilitated a three-fold increased excretion rate of ectoine. Individually, the large subunit TeaC showed an approximately five times higher extracellular ectoine concentration per dry weight compared to TeaBC shortly after its expression was induced. However, the detrimental effect on growth and ectoine titer at the end of the process hints toward a negative impact of TeaC overexpression on membrane integrity and possibly leads to cell lysis. By using either strategy, the ectoine synthesis and excretion in H. elongata could be boosted drastically. The inherent complementary nature of these approaches point at a coordinated implementation of both as a promising strategy for future projects in Metabolic Engineering. Moreover, a wide variation of intracelllular ectoine levels was observed between the strains, which points at a major disruption of mechanisms responsible for ectoine regulation in strain KB2.13.
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Affiliation(s)
- Karina Hobmeier
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Martin Oppermann
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Natalie Stasinski
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Andreas Kremling
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Katharina Pflüger-Grau
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Hans Jörg Kunte
- Division Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und-prüfung (BAM), Berlin, Germany
| | - Alberto Marin-Sanguino
- Professorship for Systems Biotechnology, Technical University of Munich, Garching, Germany
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
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Zhang Z, Su W, Bao Y, Huang Q, Ye K, Liu P, Chu X. Modular reconstruction and optimization of the trans-4-hydroxy-L-proline synthesis pathway in Escherichia coli. Microb Cell Fact 2022; 21:159. [PMID: 35953819 PMCID: PMC9367115 DOI: 10.1186/s12934-022-01884-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
Background In recent years, there has been a growing demand for microbial production of trans-4-hydroxy-L-proline (t4Hyp), which is a value-added amino acid and has been widely used in the fields of medicine, food, and cosmetics. In this study, a multivariate modular metabolic engineering approach was used to remove the bottleneck in the synthesis pathway of t4Hyp. Results Escherichia coli t4Hyp synthesis was performed using two modules: a α-ketoglutarate (α-KG) synthesis module (K module) and L-proline synthesis with hydroxylation module (H module). First, α-KG attrition was reduced, and then, L-proline consumption was inhibited. Subsequently, to improve the contribution to proline synthesis with hydroxylation, optimization of gene overexpression, promotor, copy number, and the fusion system was performed. Finally, optimization of the H and K modules was performed in combination to balance metabolic flow. Using the final module H1K4 in a shaking flask culture, 8.80 g/L t4Hyp was produced, which was threefold higher than that produced by the W0 strain. Conclusions These strategies demonstrate that a microbial cell factory can be systematically optimized by modular engineering for efficient production of t4Hyp. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01884-4.
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Affiliation(s)
- Zhenyu Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.,School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Yunyun Bao
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Qianqian Huang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Kai Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Pengfu Liu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
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Jo HG, Adidjaja JJ, Kim DK, Park BS, Lee N, Cho BK, Kim HU, Oh MK. Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin. Sci Rep 2022; 12:10302. [PMID: 35717543 PMCID: PMC9206652 DOI: 10.1038/s41598-022-14199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Streptomyces rapamycinicus NRRL 5491 is a well-known producer of rapamycin, a secondary metabolite with useful bioactivities, including antifungal, antitumor, and immunosuppressive functions. For the enhanced rapamycin production, a rapamycin-overproducing strain SRMK07 was previously obtained as a result of random mutagenesis. To identify genomic changes that allowed the SRMK07 strain’s enhanced rapamycin production, genomes of the NRRL 5491 and SRMK07 strains were newly sequenced in this study. The resulting genome sequences of the wild-type and SRMK07 strains showed the size of 12.47 Mbp and 9.56 Mbp, respectively. Large deletions were observed at both end regions of the SRMK07 strain’s genome, which cover 17 biosynthetic gene clusters (BGCs) encoding secondary metabolites. Also, genes in a genomic region containing the rapamycin BGC were shown to be duplicated. Finally, comparative metabolic network analysis using these two strains’ genome-scale metabolic models revealed biochemical reactions with different metabolic fluxes, which were all associated with NADPH generation. Taken together, the genomic and computational approaches undertaken in this study suggest biological clues for the enhanced rapamycin production of the SRMK07 strain. These clues can also serve as a basis for systematic engineering of a production host for further enhanced rapamycin production.
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Affiliation(s)
- Hee-Geun Jo
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Joshua Julio Adidjaja
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Do-Kyung Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Bu-Soo Park
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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Liu R, Wei X, Song W, Wang L, Cao J, Wu J, Thomas T, Jin T, Wang Z, Wei W, Wei Y, Zhai H, Yao C, Shen Z, Du J, Fang J. Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats. MICROBIOME 2022; 10:75. [PMID: 35538590 PMCID: PMC9088039 DOI: 10.1186/s40168-022-01263-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 03/24/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND The deep sea harbors the majority of the microbial biomass in the ocean and is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches-the deepest part of the ocean. RESULTS In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. In total, 62 metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family, and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g., benzoate), polyaromatic hydrocarbons (e.g., fluorene), polychlorobiphenyl (e.g., 4-chlorobiphenyl), and organochlorine compounds (e.g., chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g., trehalose) and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits suggest that Chloroflexi may follow a "feast-or-famine" metabolic strategy, i.e., preferentially consume labile OM and store the energy intracellularly under OM-rich conditions, and utilize the stored energy or degrade recalcitrant OM for survival under OM-limited condition. CONCLUSION This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi and highlights their significance in deep-sea carbon, sulfur, and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for survival under variable and heterogenic OM inputs in the deep ocean. Video Abstract.
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Affiliation(s)
- Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China.
| | - Xing Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Weizhi Song
- Centre for Marine Science & Innovation and School of Biological Earth and Environmental Science, University of New South Wales, Kensington, Australia
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiaxin Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Torsten Thomas
- Centre for Marine Science & Innovation and School of Biological Earth and Environmental Science, University of New South Wales, Kensington, Australia
| | - Tao Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zixuan Wang
- Tidal Flat Research Center of Jiangsu Province, Nanjing, Jiangsu, China
| | - Wenxia Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Haofeng Zhai
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Cheng Yao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Ziyi Shen
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiangtao Du
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI, USA.
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41
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Theodosiou E, Tüllinghoff A, Toepel J, Bühler B. Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis. Front Bioeng Biotechnol 2022; 10:855715. [PMID: 35497353 PMCID: PMC9043136 DOI: 10.3389/fbioe.2022.855715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.
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Affiliation(s)
- Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Adrian Tüllinghoff
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
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Zannier F, Portero LR, Douki T, Gärtner W, Farías ME, Albarracín VH. Proteomic Signatures of Microbial Adaptation to the Highest Ultraviolet-Irradiation on Earth: Lessons From a Soil Actinobacterium. Front Microbiol 2022; 13:791714. [PMID: 35369494 PMCID: PMC8965627 DOI: 10.3389/fmicb.2022.791714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
In the Central Andean region in South America, high-altitude ecosystems (3500-6000 masl) are distributed across Argentina, Chile, Bolivia, and Peru, in which poly-extremophilic microbes thrive under extreme environmental conditions. In particular, in the Puna region, total solar irradiation and UV incidence are the highest on Earth, thus, restraining the physiology of individual microorganisms and the composition of microbial communities. UV-resistance of microbial strains thriving in High-Altitude Andean Lakes was demonstrated and their mechanisms were partially characterized by genomic analysis, biochemical and physiological assays. Then, the existence of a network of physiological and molecular mechanisms triggered by ultraviolet light exposure was hypothesized and called "UV-resistome". It includes some or all of the following subsystems: (i) UV sensing and effective response regulators, (ii) UV-avoidance and shielding strategies, (iii) damage tolerance and oxidative stress response, (iv) energy management and metabolic resetting, and (v) DNA damage repair. Genes involved in the described UV-resistome were recently described in the genome of Nesterenkonia sp. Act20, an actinobacterium which showed survival to high UV-B doses as well as efficient photorepairing capability. The aim of this work was to use a proteomic approach together with photoproduct measurements to help dissecting the molecular events involved in the adaptive response of a model High-Altitude Andean Lakes (HAAL) extremophilic actinobacterium, Nesterenkonia sp. Act20, under artificial UV-B radiation. Our results demonstrate that UV-B exposure induced over-abundance of a well-defined set of proteins while recovery treatments restored the proteomic profiles present before the UV-challenge. The proteins involved in this complex molecular network were categorized within the UV-resistome subsystems: damage tolerance and oxidative stress response, energy management and metabolic resetting, and DNA damage repair.
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Affiliation(s)
- Federico Zannier
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Luciano R. Portero
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Thierry Douki
- Université Grenoble Alpes, Commissariat a l’Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Institut de Recherche Interdisciplinaire de Grenoble–Systèmes Moléculaires et nanoMatériaux p our l’Énergie et la Santé, Grenoble, France
| | - Wolfgang Gärtner
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - María E. Farías
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
| | - Virginia H. Albarracín
- Laboratorio de Microbiología Ultraestructural y Molecular, Centro Integral de Microscopía Electrónica, Facultad de Agronomía y Zootecnia, UNT y Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales y Microbiológicos, Centro Científico Tecnológico, CONICET NOASUR, San Miguel de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
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Kumar K, Bruheim P. Nutrient-depended metabolic switching during batch cultivation of Streptomyces coelicolor explored with absolute quantitative mass spectrometry-based metabolite profiling. 3 Biotech 2022; 12:80. [PMID: 35242495 PMCID: PMC8882213 DOI: 10.1007/s13205-022-03146-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/10/2022] [Indexed: 11/27/2022] Open
Abstract
The well-known secondary metabolite-producing bacterium Streptomyces coelicolor is a natural choice for the development of super-hosts optimized for the heterologous expression of antibiotic biosynthetic gene clusters (BGCs). In this study, we used S. coelicolor M145 and its derivative strain M1146 where all active BGCs have been deleted and generated high-resolution quantitative time series metabolite profiles under two cultivation conditions (phosphate and nitrogen limitation to cease growth and trigger secondary metabolism). Five targeted LC-MS/MS-based methods were used to quantify intracellular primary metabolites covering phosphorylated metabolites, amino acids, organic acids, (deoxy) nucleoside/sugar phosphates, Nicotinamide adenine dinucleotide (NAD), and Coenzyme A (CoA). The nitrogen limitation resulted in a sharp decline in respiration and an immediate drop in the cell mass concentration. Intracellularly, a reduction in the level of the metabolites next to α-ketoglutarate in the tricarboxylic acid cycle and a decrease in the NADH pool were among the most prominent adaptation to this nutrient limitation. Phosphate limitation evoked a different adaptation of the metabolite pools as most of the phosphorylated metabolite pools except 6-phosphogluconic acid (6PG) pool were downregulated. 13C-isotope-labeling experiments revealed the simultaneous activity of both glycolysis and gluconeogenesis during the co-utilization of glucose and glutamate. The S. coelicolor M1146 strain had similar time-series metabolite profile dynamics as the parent M145 strain, except for a visibly increased 6PG pool in the stationary phase. In general, the nutrient limitation had a larger effect on the metabolite pool levels than the absence of secondary metabolite production in M1146. This study provides new insight into the primary carbon metabolism and its link to the secondary metabolism which is needed for further optimization of both super-host genotype and cultivation conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03146-x.
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Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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44
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Skorokhodova AY, Gulevich AY, Debabov VG. Engineering Escherichia coli for efficient aerobic conversion of glucose to fumaric acid. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 33:e00703. [PMID: 35145886 PMCID: PMC8801760 DOI: 10.1016/j.btre.2022.e00703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/09/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022]
Abstract
Escherichia coli was engineered for efficient aerobic conversion of glucose to fumaric acid. A novel design for biosynthesis of the target product through the modified TCA cycle rather than via glyoxylate shunt, implying oxaloacetate formation from pyruvate and artificial channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation, was implemented. The main fumarases were inactivated in the core strain MSG1.0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP) by the deletion of the fumA, fumB, and fumC genes. The Bacillus subtilis pycA gene was expressed in the strain to ensure pyruvate to oxaloacetate conversion. The Mycobacterium tuberculosis kgd gene was expressed to enable succinate semialdehyde formation. The resulting strain was able to convert glucose to fumaric acid with a yield of 0.86 mol/mol, amounting to 86% of the theoretical maximum. The results demonstrated the high potential of the implemented strategy for development of efficient strains for bio-based fumaric acid production.
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Affiliation(s)
- Alexandra Yu. Skorokhodova
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Andrey Yu. Gulevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Vladimir G. Debabov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
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45
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Liu J, Liu M, Shi T, Sun G, Gao N, Zhao X, Guo X, Ni X, Yuan Q, Feng J, Liu Z, Guo Y, Chen J, Wang Y, Zheng P, Sun J. CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an L-proline exporter for L-proline hyperproduction. Nat Commun 2022; 13:891. [PMID: 35173152 PMCID: PMC8850433 DOI: 10.1038/s41467-022-28501-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Development of hyperproducing strains is important for biomanufacturing of biochemicals and biofuels but requires extensive efforts to engineer cellular metabolism and discover functional components. Herein, we optimize and use the CRISPR-assisted editing and CRISPRi screening methods to convert a wild-type Corynebacterium glutamicum to a hyperproducer of L-proline, an amino acid with medicine, feed, and food applications. To facilitate L-proline production, feedback-deregulated variants of key biosynthetic enzyme γ-glutamyl kinase are screened using CRISPR-assisted single-stranded DNA recombineering. To increase the carbon flux towards L-proline biosynthesis, flux-control genes predicted by in silico analysis are fine-tuned using tailored promoter libraries. Finally, an arrayed CRISPRi library targeting all 397 transporters is constructed to discover an L-proline exporter Cgl2622. The final plasmid-, antibiotic-, and inducer-free strain produces L-proline at the level of 142.4 g/L, 2.90 g/L/h, and 0.31 g/g. The CRISPR-assisted strain development strategy can be used for engineering industrial-strength strains for efficient biomanufacturing.
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Affiliation(s)
- Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Moshi Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tuo Shi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Guannan Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojia Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Qianqian Yuan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jinhui Feng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhemin Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Wells RK, Kunihiro BP, Phankitnirundorn K, Peres R, McCracken TA, Umeda L, Lee RH, Kim DY, Juarez R, Maunakea AK. Gut microbial indicators of metabolic health underlie age-related differences in obesity and diabetes risk among Native Hawaiians and Pacific Islanders. Front Cell Infect Microbiol 2022; 12:1035641. [PMID: 36619744 PMCID: PMC9812644 DOI: 10.3389/fcimb.2022.1035641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022] Open
Abstract
Native Hawaiians and Pacific Islanders (NHPIs) suffer from higher prevalence of and mortality to type 2 diabetes mellitus (T2DM) than any other major race/ethnic group in Hawaii. Health inequities in this indigenous population was further exacerbated by the SARS-CoV-2 pandemic. T2DM progression and medical complications exacerbated by COVID-19 are partially regulated by the gut microbiome. However, there is limited understanding of the role of gut bacteria in the context of inflammation-related diseases of health disparities including T2DM and obesity. To address these gaps, we used a community-based research approach from a cohort enriched with NHPI residents on the island of Oahu, Hawaii (N=138). Gut microbiome profiling was achieved via 16s rDNA metagenomic sequencing analysis from stool DNA. Gut bacterial capacity for butyrate-kinase (BUK)-mediated fiber metabolism was assessed using quantitative PCR to measure the abundance of BUK DNA and RNA relative to total bacterial load per stool sample. In our cohort, age positively correlated with hemoglobin A1c (%; R=0.39; P<0.001) and body mass index (BMI; R=0.28; P<0.001). The relative abundance of major gut bacterial phyla significantly varied across age groups, including Bacteroidetes (P<0.001), Actinobacteria (P=0.007), and Proteobacteria (P=0.008). A1c was negatively correlated with the relative levels of BUK DNA copy number (R=-0.17; P=0.071) and gene expression (R=-0.33; P=0.003). Interestingly, we identified specific genera of gut bacteria potentially mediating the effects of diet on metabolic health in this cohort. Additionally, α-diversity among gut bacterial genera significantly varied across T2DM and BMI categories. Together, these results provide insight into age-related differences in gut bacteria that may influence T2DM and obesity in NHPIs. Furthermore, we observed overlapping patterns between gut bacteria and T2DM risk factors, indicating more nuanced, interdependent interactions among these factors as partial determinants of health outcomes. This study adds to the paucity of NHPI-specific data to further elucidate the biological characteristics associated with pre-existing health inequities in this racial/ethnic group that is significantly underrepresented in biomedical research.
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Affiliation(s)
- Riley K Wells
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States.,Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States
| | - Braden P Kunihiro
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States.,Institutional Development Awards (IDeA) Networks of Biomedical Research Excellence (INBRE), University of Hawaii at Manoa, Honolulu, HI, United States
| | - Krit Phankitnirundorn
- Department of Economics, University of Hawaii at Manoa, Honolulu, HI, United States.,University of Hawaii Economic Research Organization (UHERO), University of Hawaii at Manoa, Honolulu, HI, United States
| | - Rafael Peres
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States.,Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States
| | - Trevor A McCracken
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States
| | - Lesley Umeda
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States.,Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States
| | - Rosa H Lee
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States
| | - Dong Yoon Kim
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States
| | - Ruben Juarez
- Department of Economics, University of Hawaii at Manoa, Honolulu, HI, United States.,University of Hawaii Economic Research Organization (UHERO), University of Hawaii at Manoa, Honolulu, HI, United States
| | - Alika K Maunakea
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States.,Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Honolulu, HI, United States
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47
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Advances in microbial production of feed amino acid. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:1-33. [DOI: 10.1016/bs.aambs.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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48
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Thoma F, Schulze C, Gutierrez-Coto C, Hädrich M, Huber J, Gunkel C, Thoma R, Blombach B. Metabolic engineering of Vibrio natriegens for anaerobic succinate production. Microb Biotechnol 2021; 15:1671-1684. [PMID: 34843164 PMCID: PMC9151343 DOI: 10.1111/1751-7915.13983] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
Abstract
The biotechnological production of succinate bears serious potential to fully replace existing petrochemical approaches in the future. In order to establish an economically viable bioprocess, obtaining high titre, yield and productivity is of central importance. In this study, we present a straightforward engineering approach for anaerobic succinate production with Vibrio natriegens, consisting of essential metabolic engineering and optimization of process conditions. The final producer strain V. natriegens Δlldh Δdldh Δpfl Δald Δdns::pycCg (Succ1) yielded 1.46 mol of succinate per mol of glucose under anaerobic conditions (85% of the theoretical maximum) and revealed a particularly high biomass‐specific succinate production rate of 1.33 gSucc gCDW−1 h−1 compared with well‐established production systems. By applying carbon and redox balancing, we determined the intracellular flux distribution and show that under the tested conditions the reductive TCA as well as the oxidative TCA/glyoxylate pathway contributed to succinate formation. In a zero‐growth bioprocess using minimal medium devoid of complex additives and expensive supplements, we obtained a final titre of 60.4 gSucc l−1 with a maximum productivity of 20.8 gSucc l−1 h−1 and an overall volumetric productivity of 8.6 gSucc l−1 h−1 during the 7 h fermentation. The key performance indicators (titre, yield and productivity) of this first engineering approach in V. natriegens are encouraging and compete with costly tailored microbial production systems.
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Affiliation(s)
- Felix Thoma
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany.,SynBiofoundry@TUM, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 22, Straubing, 94315, Germany
| | - Clarissa Schulze
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany
| | - Carolina Gutierrez-Coto
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany
| | - Maurice Hädrich
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany
| | - Janine Huber
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany
| | - Christoph Gunkel
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany
| | - Rebecca Thoma
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, Straubing, 94315, Germany.,SynBiofoundry@TUM, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 22, Straubing, 94315, Germany
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49
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Rodríguez-Esperón MC, Eastman G, Sandes L, Garabato F, Eastman I, Iriarte A, Fabiano E, Sotelo-Silveira JR, Platero R. Genomics and transcriptomics insights into luteolin effects on the beta-rhizobial strain Cupriavidus necator UYPR2.512. Environ Microbiol 2021; 24:240-264. [PMID: 34811861 DOI: 10.1111/1462-2920.15845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
Cupriavidus necator UYPR2.512 is a rhizobial strain that belongs to the Beta-subclass of proteobacteria, able to establish successful symbiosis with Mimosoid legumes. The initial steps of rhizobium-legumes symbioses involve the reciprocal recognition by chemical signals, being luteolin one of the molecules involved. However, there is a lack of information on the effect of luteolin in beta-rhizobia. In this work, we used long-read sequencing to complete the genome of UYPR2.512 providing evidence for the existence of four closed circular replicons. We used an RNA-Seq approach to analyse the response of UYPR2.512 to luteolin. One hundred and forty-five genes were differentially expressed, with similar numbers of downregulated and upregulated genes. Most repressed genes were mapped to the main chromosome, while the upregulated genes were overrepresented among pCne512e, containing the symbiotic genes. Induced genes included the nod operon and genes implicated in exopolysaccharides and flagellar biosynthesis. We identified many genes involved in iron, copper and other heavy metals metabolism. Among repressed genes, we identified genes involved in basal carbon and nitrogen metabolism. Our results suggest that in response to luteolin, C. necator strain UYPR2.512 reshapes its metabolism in order to be prepared for the forthcoming symbiotic interaction.
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Affiliation(s)
- M C Rodríguez-Esperón
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - G Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - L Sandes
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - F Garabato
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - I Eastman
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Montevideo, Uruguay
| | - E Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - J R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - R Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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50
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Lima VF, Erban A, Daubermann AG, Freire FBS, Porto NP, Cândido-Sobrinho SA, Medeiros DB, Schwarzländer M, Fernie AR, Dos Anjos L, Kopka J, Daloso DM. Establishment of a GC-MS-based 13 C-positional isotopomer approach suitable for investigating metabolic fluxes in plant primary metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1213-1233. [PMID: 34486764 DOI: 10.1111/tpj.15484] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
13 C-Metabolic flux analysis (13 C-MFA) has greatly contributed to our understanding of plant metabolic regulation. However, the generation of detailed in vivo flux maps remains a major challenge. Flux investigations based on nuclear magnetic resonance have resolved small networks with high accuracy. Mass spectrometry (MS) approaches have broader potential, but have hitherto been limited in their power to deduce flux information due to lack of atomic level position information. Herein we established a gas chromatography (GC) coupled to MS-based approach that provides 13 C-positional labelling information in glucose, malate and glutamate (Glu). A map of electron impact (EI)-mediated MS fragmentation was created and validated by 13 C-positionally labelled references via GC-EI-MS and GC-atmospheric pressure chemical ionization-MS technologies. The power of the approach was revealed by analysing previous 13 C-MFA data from leaves and guard cells, and 13 C-HCO3 labelling of guard cells harvested in the dark and after the dark-to-light transition. We demonstrated that the approach is applicable to established GC-EI-MS-based 13 C-MFA without the need for experimental adjustment, but will benefit in the future from paired analyses by the two GC-MS platforms. We identified specific glucose carbon atoms that are preferentially labelled by photosynthesis and gluconeogenesis, and provide an approach to investigate the phosphoenolpyruvate carboxylase (PEPc)-derived 13 C-incorporation into malate and Glu. Our results suggest that gluconeogenesis and the PEPc-mediated CO2 assimilation into malate are activated in a light-independent manner in guard cells. We further highlight that the fluxes from glycolysis and PEPc toward Glu are restricted by the mitochondrial thioredoxin system in illuminated leaves.
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Affiliation(s)
- Valéria F Lima
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - Alexander Erban
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - André G Daubermann
- Departamento de Biologia, Setor de Fisiologia Vegetal, Universidade Federal de Lavras, Lavras-MG, 37200-900, Brazil
| | - Francisco Bruno S Freire
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - Nicole P Porto
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - Silvio A Cândido-Sobrinho
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
| | - David B Medeiros
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, Westfälische-Wilhelms-Universität Münster, Münster, D-48143, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Leticia Dos Anjos
- Departamento de Biologia, Setor de Fisiologia Vegetal, Universidade Federal de Lavras, Lavras-MG, 37200-900, Brazil
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Danilo M Daloso
- LabPLant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CE, 60451-970, Brazil
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