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Panda S, Jayasinghe YP, Shinde DD, Bueno E, Stastny A, Bertrand BP, Chaudhari SS, Kielian T, Cava F, Ronning DR, Thomas VC. Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575639. [PMID: 38293037 PMCID: PMC10827132 DOI: 10.1101/2024.01.15.575639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Weak organic acids are commonly found in host niches colonized by bacteria, and they can inhibit bacterial growth as the environment becomes acidic. This inhibition is often attributed to the toxicity resulting from the accumulation of high concentrations of organic anions in the cytosol, which disrupts cellular homeostasis. However, the precise cellular targets that organic anions poison and the mechanisms used to counter organic anion intoxication in bacteria have not been elucidated. Here, we utilize acetic acid, a weak organic acid abundantly found in the gut to investigate its impact on the growth of Staphylococcus aureus. We demonstrate that acetate anions bind to and inhibit d-alanyl-d-alanine ligase (Ddl) activity in S. aureus. Ddl inhibition reduces intracellular d-alanyl-d-alanine (d-Ala-d-Ala) levels, compromising staphylococcal peptidoglycan cross-linking and cell wall integrity. To overcome the effects of acetate-mediated Ddl inhibition, S. aureus maintains a substantial intracellular d-Ala pool through alanine racemase (Alr1) activity and additionally limits the flux of d-Ala to d-glutamate by controlling d-alanine aminotransferase (Dat) activity. Surprisingly, the modus operandi of acetate intoxication in S. aureus is common to multiple biologically relevant weak organic acids indicating that Ddl is a conserved target of small organic anions. These findings suggest that S. aureus may have evolved to maintain high intracellular d-Ala concentrations, partly to counter organic anion intoxication.
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Affiliation(s)
- Sasmita Panda
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Yahani P. Jayasinghe
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Dhananjay D. Shinde
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umea SE-90187, Sweden
| | - Amanda Stastny
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Blake P. Bertrand
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Sujata S. Chaudhari
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Tammy Kielian
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umea SE-90187, Sweden
| | - Donald R. Ronning
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Vinai C. Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
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González-González A, Batarseh TN, Rodríguez-Verdugo A, Gaut BS. Patterns of Fitness and Gene Expression Epistasis Generated by Beneficial Mutations in the rho and rpoB Genes of Escherichia coli during High-Temperature Adaptation. Mol Biol Evol 2024; 41:msae187. [PMID: 39235107 PMCID: PMC11414761 DOI: 10.1093/molbev/msae187] [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: 05/12/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Epistasis is caused by genetic interactions among mutations that affect fitness. To characterize properties and potential mechanisms of epistasis, we engineered eight double mutants that combined mutations from the rho and rpoB genes of Escherichia coli. The two genes encode essential functions for transcription, and the mutations in each gene were chosen because they were beneficial for adaptation to thermal stress (42.2 °C). The double mutants exhibited patterns of fitness epistasis that included diminishing returns epistasis at 42.2 °C, stronger diminishing returns between mutations with larger beneficial effects and both negative and positive (sign) epistasis across environments (20.0 °C and 37.0 °C). By assessing gene expression between single and double mutants, we detected hundreds of genes with gene expression epistasis. Previous work postulated that highly connected hub genes in coexpression networks have low epistasis, but we found the opposite: hub genes had high epistasis values in both coexpression and protein-protein interaction networks. We hypothesized that elevated epistasis in hub genes reflected that they were enriched for targets of Rho termination but that was not the case. Altogether, gene expression and coexpression analyses revealed that thermal adaptation occurred in modules, through modulation of ribonucleotide biosynthetic processes and ribosome assembly, the attenuation of expression in genes related to heat shock and stress responses, and with an overall trend toward restoring gene expression toward the unstressed state.
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Affiliation(s)
- Andrea González-González
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Tiffany N Batarseh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
| | | | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
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3
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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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4
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Zhao D, Li C. Multi-omics profiling reveals potential mechanisms of culture temperature modulating biosynthesis of carotenoids, lipids, and exopolysaccharides in oleaginous red yeast Rhodotorula glutinis ZHK. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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5
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Ferreira EGC, Gomes DF, Delai CV, Barreiros MAB, Grange L, Rodrigues EP, Henning LMM, Barcellos FG, Hungria M. Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15). BMC Microbiol 2022; 22:122. [PMID: 35513812 PMCID: PMC9069715 DOI: 10.1186/s12866-022-02527-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/11/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer. RESULTS A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF. CONCLUSIONS All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.
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Affiliation(s)
- Everton Geraldo Capote Ferreira
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
| | | | - Caroline Vanzzo Delai
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | | | - Luciana Grange
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | - Elisete Pains Rodrigues
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | | | - Fernando Gomes Barcellos
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | - Mariangela Hungria
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
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6
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Mangalea MR, Borlee BR. The NarX-NarL two-component system regulates biofilm formation, natural product biosynthesis, and host-associated survival in Burkholderia pseudomallei. Sci Rep 2022; 12:203. [PMID: 34997073 PMCID: PMC8742066 DOI: 10.1038/s41598-021-04053-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/14/2021] [Indexed: 01/10/2023] Open
Abstract
Burkholderia pseudomallei is a saprophytic bacterium endemic throughout the tropics causing severe disease in humans and animals. Environmental signals such as the accumulation of inorganic ions mediates the biofilm forming capabilities and survival of B. pseudomallei. We have previously shown that B. pseudomallei responds to nitrate and nitrite by inhibiting biofilm formation and altering cyclic di-GMP signaling. To better understand the roles of nitrate-sensing in the biofilm inhibitory phenotype of B. pseudomallei, we created in-frame deletions of narX (Bp1026b_I1014) and narL (Bp1026b_I1013), which are adjacent components of a conserved nitrate-sensing two-component system. We observed transcriptional downregulation in key components of the biofilm matrix in response to nitrate and nitrite. Some of the most differentially expressed genes were nonribosomal peptide synthases (NRPS) and/or polyketide synthases (PKS) encoding the proteins for the biosynthesis of bactobolin, malleilactone, and syrbactin, and an uncharacterized cryptic NRPS biosynthetic cluster. RNA expression patterns were reversed in ∆narX and ∆narL mutants, suggesting that nitrate sensing is an important checkpoint for regulating the diverse metabolic changes occurring in the biofilm inhibitory phenotype. Moreover, in a macrophage model of infection, ∆narX and ∆narL mutants were attenuated in intracellular replication, suggesting that nitrate sensing contributes to survival in the host.
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Affiliation(s)
- Mihnea R Mangalea
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Bradley R Borlee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA.
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7
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Yang M, Meng F, Gu W, Fu L, Zhang F, Li F, Tao Y, Zhang Z, Wang X, Yang X, Li J, Yu J. Influence of Polysaccharides From Polygonatum kingianum on Short-Chain Fatty Acid Production and Quorum Sensing in Lactobacillus faecis. Front Microbiol 2021; 12:758870. [PMID: 34867887 PMCID: PMC8635744 DOI: 10.3389/fmicb.2021.758870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/19/2021] [Indexed: 01/09/2023] Open
Abstract
Polysaccharide is one of the main active ingredients of Polygonatum kingianum, which has been proven to regulate the balance of gut microbiota. For the first time, this study focused on the regulation of polysaccharides from Polygonatum kingianum (PS) on Lactobacillus faecis, a specific probiotic in the intestinal tract. PS effectively promoted the biomass, biofilm and acetic acid production in L. faecis 2-84, and enhanced quorum sensing (QS) signaling. The characteristics of gene sequence were analyzed using genomics approaches, and L. faecis 2-84 was found to encode 18 genes that are closely related to QS and 10 genes related to short-chain fatty acids (SCFAs). Additionally, transcriptome and proteome analysis demonstrated that PS could promote the QS system of L. faecis by enhancing the transcription of oppA gene and expression of oppD protein. PS also regulated the production and metabolism of SCFAs of L. faecis by upregulating the expression of ldh and metE gene and adh2 protein, and downregulating the expression of mvK gene. In conclusion, it was speculated that PS could affect intestinal SCFAs production by affecting the QS system and SCFAs production in L. faecis. The present study implied that PS might have a role in promoting the growth of intestinal probiotics, where the QS system and SCFAs might be two of the important mechanisms for the probiotic activity of PS.
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Affiliation(s)
- Min Yang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China.,Kunming Third People's Hospital, Kunming, China
| | - Fanying Meng
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Wen Gu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Lihui Fu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Fan Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Fengjiao Li
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Yating Tao
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Zhengyang Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Xi Wang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Xingxin Yang
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Jingping Li
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
| | - Jie Yu
- Yunnan Key Laboratory of Southern Medicine Utilization, College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming, China
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Mudge MC, Nunn BL, Firth E, Ewert M, Hales K, Fondrie WE, Noble WS, Toner J, Light B, Junge KA. Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. Environ Microbiol 2021; 23:3840-3866. [PMID: 33760340 PMCID: PMC8475265 DOI: 10.1111/1462-2920.15485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Colwellia psychrerythraea is a marine psychrophilic bacterium known for its remarkable ability to maintain activity during long-term exposure to extreme subzero temperatures and correspondingly high salinities in sea ice. These microorganisms must have adaptations to both high salinity and low temperature to survive, be metabolically active, or grow in the ice. Here, we report on an experimental design that allowed us to monitor culturability, cell abundance, activity and proteomic signatures of C. psychrerythraea strain 34H (Cp34H) in subzero brines and supercooled sea water through long-term incubations under eight conditions with varying subzero temperatures, salinities and nutrient additions. Shotgun proteomics found novel metabolic strategies used to maintain culturability in response to each independent experimental variable, particularly in pathways regulating carbon, nitrogen and fatty acid metabolism. Statistical analysis of abundances of proteins uniquely identified in isolated conditions provide metabolism-specific protein biosignatures indicative of growth or survival in either increased salinity, decreased temperature, or nutrient limitation. Additionally, to aid in the search for extant life on other icy worlds, analysis of detected short peptides in -10°C incubations after 4 months identified over 500 potential biosignatures that could indicate the presence of terrestrial-like cold-active or halophilic metabolisms on other icy worlds.
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Affiliation(s)
- Miranda C. Mudge
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA
| | - Brook L. Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA
- Astrobiology Program, University of Washington, Seattle, WA
| | - Erin Firth
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
| | - Marcela Ewert
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
| | - Kianna Hales
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA
| | - Jonathan Toner
- Department of Earth and Space Sciences, University of Washington, Seattle, WA
| | - Bonnie Light
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
| | - Karen A. Junge
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
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Wang S, Fang Y, Wang Z, Zhang S, Wang L, Guo Y, Wang X. Improving L-threonine production in Escherichia coli by elimination of transporters ProP and ProVWX. Microb Cell Fact 2021; 20:58. [PMID: 33653345 PMCID: PMC7927397 DOI: 10.1186/s12934-021-01546-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
Background Betaine, an osmoprotective compatible solute, has been used to improve l-threonine production in engineered Escherichia colil-threonine producer. Betaine supplementation upregulates the expression of zwf encoding glucose-6-phosphate dehydrogenase, leading to the increase of NADPH, which is beneficial for l-threonine production. In E. coli, betaine can be taken through ProP encoded by proP or ProVWX encoded by proVWX. ProP is a H+-osmolyte symporter, whereas ProVWX is an ABC transporter. ProP and ProVWX mediate osmotic stress protection by transporting zwitterionic osmolytes, including glycine betaine. Betaine can also be synthesized in E. coli by enzymes encoded by betABIT. However, the influence of ProP, ProVWX and betABIT on l-threonine production in E. coli has not been investigated. Results In this study, the influence of ProP, ProVWX and betABIT on l-threonine production in E. coli has been investigated. Addition of betaine slightly improved the growth of the l-threonine producing E. coli strain TWF001 as well as the l-threonine production. Deletion of betABIT retarded the growth of TWF001 and slightly decreased the l-threonine production. However, deletion of proP or/and proVWX significantly increased the l-threonine production. When proP was deleted, the l-threonine production increased 33.3%; when proVWX was deleted, the l-threonine production increased 40.0%. When both proP and proVWX were deleted, the resulting strain TSW003 produced 23.5 g/l l-threonine after 36 h flask cultivation. The genes betABIT, proC, fadR, crr and ptsG were individually deleted from TSW003, and it was found that further absence of either crr (TWS008) or ptsG (TWS009) improved l-threonine production. TSW008 produced 24.9 g/l l-threonine after 36 h flask cultivation with a yield of 0.62 g/g glucose and a productivity of 0.69 g/l/h. TSW009 produced 26 g/l l-threonine after 48 h flask cultivation with a yield of 0.65 g/g glucose and a productivity of 0.54 g/l/h, which is 116% increase compared to the control TWF001. Conclusions In this study, l-threonine-producing E. coli strains TSW008 and TSW009 with high l-threonine productivity were developed by regulating the intracellular osmotic pressure. This strategy could be used to improve the production of other products in microorganisms.
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Affiliation(s)
- Shuaiwen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Liangjia Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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10
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Kutscha R, Pflügl S. Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches. Int J Mol Sci 2020; 21:ijms21228777. [PMID: 33233586 PMCID: PMC7699770 DOI: 10.3390/ijms21228777] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 01/20/2023] Open
Abstract
Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.
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11
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Kiefer D, Merkel M, Lilge L, Henkel M, Hausmann R. From Acetate to Bio-Based Products: Underexploited Potential for Industrial Biotechnology. Trends Biotechnol 2020; 39:397-411. [PMID: 33036784 DOI: 10.1016/j.tibtech.2020.09.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022]
Abstract
Currently, most biotechnological products are based on microbial conversion of carbohydrate substrates that are predominantly generated from sugar- or starch-containing plants. However, direct competitive uses of these feedstocks in the food and feed industry represent a dilemma, so using alternative carbon sources has become increasingly important in industrial biotechnology. A promising alternative carbon source that may be generated in substantial amounts from lignocellulosic biomass and C1 gases is acetate. This review discusses the underexploited potential of acetate to become a next-generation platform substrate in future industrial biotechnology and summarizes alternative sources and routes for acetate production. Furthermore, biotechnological aspects of microbial acetate utilization and the state of the art of biotechnological acetate conversion into value-added bioproducts are highlighted.
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Affiliation(s)
- Dirk Kiefer
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
| | - Manuel Merkel
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
| | - Lars Lilge
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
| | - Marius Henkel
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany.
| | - Rudolf Hausmann
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, Fruwirthstrasse 12, 70599 Stuttgart, Germany
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Noh MH, Lim HG, Moon D, Park S, Jung GY. Auxotrophic Selection Strategy for Improved Production of Coenzyme B 12 in Escherichia coli. iScience 2020; 23:100890. [PMID: 32086013 PMCID: PMC7033360 DOI: 10.1016/j.isci.2020.100890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/17/2020] [Accepted: 02/03/2020] [Indexed: 02/02/2023] Open
Abstract
The production of coenzyme B12 using well-characterized microorganisms, such as Escherichia coli, has recently attracted considerable attention to meet growing demands of coenzyme B12 in various applications. In the present study, we designed an auxotrophic selection strategy and demonstrated the enhanced production of coenzyme B12 using a previously engineered coenzyme B12-producing E. coli strain. To select a high producer, the coenzyme B12-independent methionine synthase (metE) gene was deleted in E. coli, thus limiting its methionine synthesis to only that via coenzyme B12-dependent synthase (encoded by metH). Following the deletion of metE, significantly enhanced production of the specific coenzyme B12 validated the coenzyme B12-dependent auxotrophic growth. Further precise tuning of the auxotrophic system by varying the expression of metH substantially increased the cell biomass and coenzyme B12 production, suggesting that our strategy could be effectively applied to E. coli and other coenzyme B12-producing strains. The auxotrophic selection strategy was applied to coenzyme B12 production Coenzyme B12-independent methionine synthase was deleted for auxotroph system The auxotrophic strategy could significantly enhance the coenzyme B12 production Optimization of the auxotroph system further enhanced the coenzyme B12 production
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Affiliation(s)
- Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Daeyeong Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-Ro, Ulju-gun, Ulsan, Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Korea.
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Pinhal S, Ropers D, Geiselmann J, de Jong H. Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate. J Bacteriol 2019; 201:e00147-19. [PMID: 30988035 PMCID: PMC6560135 DOI: 10.1128/jb.00147-19] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/26/2019] [Indexed: 11/24/2022] Open
Abstract
During aerobic growth on glucose, Escherichia coli excretes acetate, a mechanism called "overflow metabolism." At high concentrations, the secreted acetate inhibits growth. Several mechanisms have been proposed for explaining this phenomenon, but a thorough analysis is hampered by the diversity of experimental conditions and strains used in these studies. Here, we describe the construction of a set of isogenic strains that remove different parts of the metabolic network involved in acetate metabolism. Analysis of these strains reveals that (i) high concentrations of acetate in the medium inhibit growth without significantly perturbing central metabolism; (ii) growth inhibition persists even when acetate assimilation is completely blocked; and (iii) regulatory interactions mediated by acetyl-phosphate play a small but significant role in growth inhibition by acetate. The major contribution to growth inhibition by acetate may originate in systemic effects like the uncoupling effect of organic acids or the perturbation of the anion composition of the cell, as previously proposed. Our data suggest, however, that under the conditions considered here, the uncoupling effect plays only a limited role.IMPORTANCE High concentrations of organic acids such as acetate inhibit growth of Escherichia coli and other bacteria. This phenomenon is of interest for understanding bacterial physiology but is also of practical relevance. Growth inhibition by organic acids underlies food preservation and causes problems during high-density fermentation in biotechnology. What causes this phenomenon? Classical explanations invoke the uncoupling effect of acetate and the establishment of an anion imbalance. Here, we propose and investigate an alternative hypothesis: the perturbation of acetate metabolism due to the inflow of excess acetate. We find that this perturbation accounts for 20% of the growth-inhibitory effect through a modification of the acetyl phosphate concentration. Moreover, we argue that our observations are not expected based on uncoupling alone.
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Affiliation(s)
- Stéphane Pinhal
- Univ. Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | | | - Johannes Geiselmann
- Univ. Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, Grenoble, France
- Univ. Grenoble Alpes, Inria, Grenoble, France
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Lim HG, Lee JH, Noh MH, Jung GY. Rediscovering Acetate Metabolism: Its Potential Sources and Utilization for Biobased Transformation into Value-Added Chemicals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3998-4006. [PMID: 29637770 DOI: 10.1021/acs.jafc.8b00458] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the great advantages of microbial fermentation is the capacity to convert various carbon compounds into value-added chemicals. In this regard, there have been many efforts to engineer microorganisms to facilitate utilization of abundant carbon sources. Recently, the potential of acetate as a feedstock has been discovered; efforts have been made to produce various biochemicals from acetate based on understanding of its metabolism. In this review, we discuss the potential sources of acetate and summarized the recent progress to improve acetate utilization with microorganisms. Furthermore, we also describe representative studies that engineered microorganisms for the production of biochemicals from acetate.
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Adenine Addition Restores Cell Viability and Butanol Production in Clostridium saccharoperbutylacetonicum N1-4 (ATCC 13564) Cultivated at 37°C. Appl Environ Microbiol 2017; 83:AEM.02960-16. [PMID: 28130303 DOI: 10.1128/aem.02960-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/20/2017] [Indexed: 12/11/2022] Open
Abstract
We have developed butanol-producing consolidated bioprocessing from cellulosic substrates through coculture of cellulolytic clostridia and butanol-producing Clostridium saccharoperbutylacetonicum strain N1-4. However, the butanol fermentation by strain N1-4 (which has an optimal growth temperature of 30°C) is sensitive to the higher cultivation temperature of 37°C; the nature of this deleterious effect remains unclear. Comparison of the intracellular metabolites of strain N1-4 cultivated at 30°C and 37°C revealed decreased levels of multiple primary metabolites (notably including nucleic acids and cofactors) during growth at the higher temperature. Supplementation of the culture medium with 250 mg/liter adenine enhanced both cell growth (with the optical density at 600 nm increasing from 4.3 to 10.2) and butanol production (increasing from 3.9 g/liter to 9.6 g/liter) at 37°C, compared to those obtained without adenine supplementation, such that the supplemented 37°C culture exhibited growth and butanol production approaching those observed at 30°C in the absence of adenine supplementation. These improved properties were based on the maintenance of cell viability. We further showed that adenine supplementation enhanced cell viability during growth at 37°C by maintaining ATP levels and inhibiting spore formation. This work represents the first demonstration (to our knowledge) of the importance of adenine-related metabolism for clostridial butanol production, suggesting a new means of enhancing target pathways based on metabolite levels.IMPORTANCE Metabolomic analysis revealed decreased levels of multiple primary metabolites during growth at 37°C, compared to 30°C, in C. saccharoperbutylacetonicum strain N1-4. We found that adenine supplementation restored the cell growth and butanol production of strain N1-4 at 37°C. The effects of adenine supplementation reflected the maintenance of cell viability originating from the maintenance of ATP levels and the inhibition of spore formation. Thus, our metabolomic analysis identified the depleted metabolites that were required to maintain cell viability. Our strategy, which is expected to be applicable to a wide range of organisms, permits the identification of the limiting metabolic pathway, which can serve as a new target for molecular breeding. The other novel finding of this work is that adenine supplementation inhibits clostridial spore formation. The mechanism linking spore formation and metabolomic status in butanol-producing clostridia is expected to be the focus of further research.
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Taïbi K, del Campo AD, Vilagrosa A, Bellés JM, López-Gresa MP, Pla D, Calvete JJ, López-Nicolás JM, Mulet JM. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:1202. [PMID: 28791030 PMCID: PMC5523154 DOI: 10.3389/fpls.2017.01202] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 05/13/2023]
Abstract
Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.
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Affiliation(s)
- Khaled Taïbi
- Faculty of Natural Sciences and Life, Ibn Khaldoun UniversityTiaret, Algeria
- Re-ForeST, Research Institute of Water and Environmental Engineering, Universitat Politècnica de ValènciaValencia, Spain
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València – Consejo Superior de Investigaciones CientíficasValencia, Spain
- *Correspondence: José M. Mulet, Khaled Taïbi,
| | - Antonio D. del Campo
- Re-ForeST, Research Institute of Water and Environmental Engineering, Universitat Politècnica de ValènciaValencia, Spain
| | - Alberto Vilagrosa
- Fundación Centro de Estudios Ambientales del Mediterráneo, Joint Research Unit University of Alicante – CEAM, University of AlicanteAlicante, Spain
| | - José M. Bellés
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València – Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - María Pilar López-Gresa
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València – Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Davinia Pla
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Juan J. Calvete
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - José M. López-Nicolás
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Biología, Universidad de MurciaMurcia, Spain
| | - José M. Mulet
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València – Consejo Superior de Investigaciones CientíficasValencia, Spain
- *Correspondence: José M. Mulet, Khaled Taïbi,
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Kunjapur AM, Hyun JC, Prather KLJ. Deregulation of S-adenosylmethionine biosynthesis and regeneration improves methylation in the E. coli de novo vanillin biosynthesis pathway. Microb Cell Fact 2016; 15:61. [PMID: 27067813 PMCID: PMC4828866 DOI: 10.1186/s12934-016-0459-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/28/2016] [Indexed: 12/31/2022] Open
Abstract
Background Vanillin is an industrially valuable molecule that can be produced from simple carbon sources in engineered microorganisms such as Saccharomyces cerevisiae and Escherichia coli. In E. coli, de novo production of vanillin was demonstrated previously as a proof of concept. In this study, a series of data-driven experiments were performed in order to better understand limitations associated with biosynthesis of vanillate, which is the immediate precursor to vanillin. Results Time-course experiments monitoring production of heterologous metabolites in the E. coli de novo vanillin pathway revealed a bottleneck in conversion of protocatechuate to vanillate. Perturbations in central metabolism intended to increase flux into the heterologous pathway increased average vanillate titers from 132 to 205 mg/L, but protocatechuate remained the dominant heterologous product on a molar basis. SDS-PAGE, in vitro activity measurements, and l-methionine supplementation experiments suggested that the decline in conversion rate was influenced more by limited availability of the co-substrate S-adenosyl-l-methionine (AdoMet or SAM) than by loss of activity of the heterologous O-methyltransferase. The combination of metJ deletion and overexpression of feedback-resistant variants of metA and cysE, which encode enzymes involved in SAM biosynthesis, increased average de novo vanillate titers by an additional 33 % (from 205 to 272 mg/L). An orthogonal strategy intended to improve SAM regeneration through overexpression of native mtn and luxS genes resulted in a 25 % increase in average de novo vanillate titers (from 205 to 256 mg/L). Vanillate production improved further upon supplementation with methionine (as high as 419 ± 58 mg/L), suggesting potential for additional enhancement by increasing SAM availability. Conclusions Results from this study demonstrate context dependency of engineered pathways and highlight the limited methylation capacity of E. coli. Unlike in previous efforts to improve SAM or methionine biosynthesis, we pursued two orthogonal strategies that are each aimed at deregulating multiple reactions. Our results increase the working knowledge of SAM biosynthesis engineering and provide a framework for improving titers of metabolic products dependent upon methylation reactions. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0459-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aditya M Kunjapur
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E17-504G, Cambridge, MA, 02139, USA.,Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jason C Hyun
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E17-504G, Cambridge, MA, 02139, USA.,Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E17-504G, Cambridge, MA, 02139, USA. .,Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Zou H, Chen N, Shi M, Xian M, Song Y, Liu J. The metabolism and biotechnological application of betaine in microorganism. Appl Microbiol Biotechnol 2016; 100:3865-76. [PMID: 27005411 DOI: 10.1007/s00253-016-7462-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 11/29/2022]
Abstract
Glycine betaine (betaine) is widely distributed in nature and can be found in many microorganisms, including bacteria, archaea, and fungi. Due to its particular functions, many microorganisms utilize betaine as a functional chemical and have evolved different metabolic pathways for the biosynthesis and catabolism of betaine. As in animals and plants, the principle role of betaine is to protect microbial cells against drought, osmotic stress, and temperature stress. In addition, the role of betaine in methyl group metabolism has been observed in a variety of microorganisms. Recent studies have shown that betaine supplementation can improve the performance of microbial strains used for the fermentation of lactate, ethanol, lysine, pyruvate, and vitamin B12, during which betaine can act as stress protectant or methyl donor for the biosynthesis of structurally complex compounds. In this review, we summarize the transport, synthesis, catabolism, and functions of betaine in microorganisms and discuss potential engineering strategies that employ betaine as a methyl donor for the biosynthesis of complex secondary metabolites such as a variety of vitamins, coenzymes, and antibiotics. In conclusion, the biocompatibility, C/N ratio, abundance, and comprehensive metabolic information of betaine collectively indicate that this molecule has great potential for broad applications in microbial biotechnology.
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Affiliation(s)
- Huibin Zou
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China. .,CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
| | - Ningning Chen
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yimin Song
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Junhong Liu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
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Kalloniati C, Krompas P, Karalias G, Udvardi MK, Rennenberg H, Herschbach C, Flemetakis E. Nitrogen-Fixing Nodules Are an Important Source of Reduced Sulfur, Which Triggers Global Changes in Sulfur Metabolism in Lotus japonicus. THE PLANT CELL 2015; 27:2384-400. [PMID: 26296963 PMCID: PMC4815097 DOI: 10.1105/tpc.15.00108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/20/2015] [Accepted: 08/03/2015] [Indexed: 05/09/2023]
Abstract
We combined transcriptomic and biochemical approaches to study rhizobial and plant sulfur (S) metabolism in nitrogen (N) fixing nodules (Fix(+)) of Lotus japonicus, as well as the link of S-metabolism to symbiotic nitrogen fixation and the effect of nodules on whole-plant S-partitioning and metabolism. Our data reveal that N-fixing nodules are thiol-rich organs. Their high adenosine 5'-phosphosulfate reductase activity and strong (35)S-flux into cysteine and its metabolites, in combination with the transcriptional upregulation of several rhizobial and plant genes involved in S-assimilation, highlight the function of nodules as an important site of S-assimilation. The higher thiol content observed in nonsymbiotic organs of N-fixing plants in comparison to uninoculated plants could not be attributed to local biosynthesis, indicating that nodules are an important source of reduced S for the plant, which triggers whole-plant reprogramming of S-metabolism. Enhanced thiol biosynthesis in nodules and their impact on the whole-plant S-economy are dampened in plants nodulated by Fix(-) mutant rhizobia, which in most respects metabolically resemble uninoculated plants, indicating a strong interdependency between N-fixation and S-assimilation.
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Affiliation(s)
- Chrysanthi Kalloniati
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Panagiotis Krompas
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Georgios Karalias
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Heinz Rennenberg
- Institute of Forest Sciences, Chair of Tree Physiology, Faculty of Environment and Natural Resources, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Cornelia Herschbach
- Institute of Forest Sciences, Chair of Tree Physiology, Faculty of Environment and Natural Resources, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany
| | - Emmanouil Flemetakis
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
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Proteomic insights into metabolic adaptation to deletion of metE in Saccharopolyspora spinosa. Appl Microbiol Biotechnol 2015; 99:8629-41. [PMID: 26266753 DOI: 10.1007/s00253-015-6883-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/20/2015] [Accepted: 07/26/2015] [Indexed: 12/19/2022]
Abstract
Saccharopolyspora spinosa can produce spinosad as a major secondary metabolite, which is an environmentally friendly agent for insect control. Cobalamin-independent methionine synthase (MetE) is an important enzyme in methionine biosynthesis, and this enzyme is probably closely related to spinosad production. In this study, its corresponding gene metE was inactivated, which resulted in a rapid growth and glucose utilisation rate and almost loss of spinosad production. A label-free quantitative proteomics-based approach was employed to obtain insights into the mechanism by which the metabolic network adapts to the absence of MetE. A total of 1440 proteins were detected from wild-type and ΔmetE mutant strains at three time points: stationary phase of ΔmetE mutant strain (S1ΔmetE , 67 h), first stationary phase of wild-type strain (S1WT, 67 h) and second stationary phase of wild-type strain (S2WT, 100 h). Protein expression patterns were determined using an exponentially modified protein abundance index (emPAI) and analysed by comparing S1ΔmetE /S1WT and S1ΔmetE /S2WT. Results showed that differentially expressed enzymes were mainly involved in primary metabolism and genetic information processing. This study demonstrated that the role of MetE is not restricted to methionine biosynthesis but rather is involved in global metabolic regulation in S. spinosa.
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Ran S, Liu B, Jiang W, Sun Z, Liang J. Transcriptome analysis of Enterococcus faecalis in response to alkaline stress. Front Microbiol 2015; 6:795. [PMID: 26300863 PMCID: PMC4528170 DOI: 10.3389/fmicb.2015.00795] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
Enterococcus faecalis is the most commonly isolated species from endodontic failure root canals; its persistence in treated root canals has been attributed to its ability to resist high pH stress. The goal of this study was to characterize the E. faecalis transcriptome and to identify candidate genes for response and resistance to alkaline stress using Illumina HiSeq 2000 sequencing. We found that E. faecalis could survive and form biofilms in a pH 10 environment and that alkaline stress had a great impact on the transcription of many genes in the E. faecalis genome. The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated. Many of the down-regulated genes found are involved in cell energy production and metabolism and carbohydrate and amino acid metabolism, and the up-regulated genes are mostly related to nucleotide transport and metabolism. The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome. The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress. A number of the regulated genes may be useful candidates for the development of new therapeutic approaches for the treatment of E. faecalis infections.
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Affiliation(s)
- Shujun Ran
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Bin Liu
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Wei Jiang
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Zhe Sun
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Jingping Liang
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
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22
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Adaptation and tolerance of bacteria against acetic acid. Appl Microbiol Biotechnol 2015; 99:6215-29. [DOI: 10.1007/s00253-015-6762-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/05/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
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Wang H, Wang F, Wang W, Yao X, Wei D, Cheng H, Deng Z. Improving the expression of recombinant proteins in E. coli BL21 (DE3) under acetate stress: an alkaline pH shift approach. PLoS One 2014; 9:e112777. [PMID: 25402470 PMCID: PMC4234529 DOI: 10.1371/journal.pone.0112777] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 10/20/2014] [Indexed: 11/23/2022] Open
Abstract
Excess acetate has long been an issue for the production of recombinant proteins in E. coli cells. Recently, improvements in acetate tolerance have been achieved through the use of genetic strategies and medium supplementation with certain amino acids and pyrimidines. The aim of our study was to evaluate an alternative to improve the acetate tolerance of E. coli BL21 (DE3), a popular strain used to express recombinant proteins. In this work we reported the cultivation of BL21 (DE3) in complex media containing acetate at high concentrations. In the presence of 300 mM acetate, compared with pH 6.5, pH 7.5 improved cell growth by approximately 71%, reduced intracellular acetate by approximately 50%, and restored the expression of glutathione S-transferase (GST), green fluorescent protein (GFP) and cytochrome P450 monooxygenase (CYP). Further experiments showed that alkaline pHs up to 8.5 had little inhibition in the expression of GST, GFP and CYP. In addition, the detrimental effect of acetate on the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) by the cell membrane, an index of cellular metabolic capacity, was substantially alleviated by a shift to alkaline pH values of 7.5–8.0. Thus, we suggest an approach of cultivating E. coli BL21 (DE3) at pH 8.0±0.5 to minimize the effects caused by acetate stress. The proposed strategy of an alkaline pH shift is a simple approach to solving similar bioprocessing problems in the production of biofuels and biochemicals from sugars.
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Affiliation(s)
- Hengwei Wang
- Innovation & Application Institute (IAI), Zhejiang Ocean University, Zhoushan, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fengqing Wang
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Wang
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xueling Yao
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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