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Liu J, Xie S, Xu M, Jiang X, Wang Q, Zhao H, Zhang B. Screening the Protective Agents Able to Improve the Survival of Lactic Acid Bacteria Strains Subjected to Spray Drying Using Several Key Enzymes Responsible for Carbohydrate Utilization. Microorganisms 2024; 12:1094. [PMID: 38930476 PMCID: PMC11205755 DOI: 10.3390/microorganisms12061094] [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: 04/30/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
The aim of this study was to identify the most effective protectants for enhancing the viability of specific lactic acid bacteria (LAB) strains (Lactobacillus delbrueckii subsp. bulgaricus CICC 6097, Lactiplantibacillus plantarum CICC 21839, Lactobacillus acidophilus NCFM) by assessing their enzymatic activity when exposed to spray drying (inlet/outlet temperature: 135 °C/90 °C). Firstly, it was found that the live cell counts of the selected LAB cells from the 10% (w/v) recovered skim milk (RSM) group remained above 107 CFU/g after spray drying. Among all the three groups (1% w/v RSM group, 10% w/v RSM group, and control group), the two enzymes pyruvate kinase (PK) and lactate dehydrogenase (LDH) were more sensitive to spray drying than hexokinase (HK) and β-galactosidase (β-GAL). Next, transcriptome data of Lb. acidophilus NCFM showed that 10% (w/v) RSM improved the down-regulated expressions of genes encoding PK (pyk) and LDH (ldh) after spray drying compared to 1% (w/v) RSM. Finally, four composite protectants were created, each consisting of 10% (w/v) RSM plus a different additive-sodium glutamate (CP-A group), sucrose (CP-B group), trehalose (CP-C group), or a combination of sodium glutamate, sucrose, and trehalose (CP-D group)-to encapsulate Lb. acidophilus NCFM. It was observed that the viable counts of strain NCFM (8.56 log CFU/g) and enzymatic activity of PK and LDH in the CP-D group were best preserved compared to the other three groups. Therefore, our study suggested that measuring the LDH and PK activity could be used as a promising tool to screen the effective spray-dried protective agent for LAB cells.
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Affiliation(s)
| | | | | | | | | | | | - Bolin Zhang
- Beijing Key Laboratory of Forest Food Processing and Safety, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing 100083, China; (J.L.); (S.X.); (M.X.); (X.J.); (Q.W.); (H.Z.)
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2
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Ekkers DM, Tusso S, Moreno-Gamez S, Rillo MC, Kuipers OP, van Doorn GS. Trade-offs predicted by metabolic network structure give rise to evolutionary specialization and phenotypic diversification. Mol Biol Evol 2022; 39:msac124. [PMID: 35679426 PMCID: PMC9206417 DOI: 10.1093/molbev/msac124] [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: 06/08/2021] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Mitigating trade-offs between different resource-utilization functions is key to an organism's ecological and evolutionary success. These trade-offs often reflect metabolic constraints with a complex molecular underpinning; therefore, their consequences for evolutionary processes have remained elusive. Here, we investigate how metabolic architecture induces resource utilization constraints and how these constraints, in turn, elicit evolutionary specialization and diversification. Guided by the metabolic network structure of the bacterium Lactococcus cremoris, we selected two carbon sources (fructose and galactose) with predicted co-utilization constraints. By evolving L. cremoris on either fructose, galactose or a mix of both sugars, we imposed selection favoring divergent metabolic specializations or co-utilization of both resources, respectively. Phenotypic characterization revealed the evolution of either fructose or galactose specialists in the single-sugar treatments. In the mixed sugar regime, we observed adaptive diversification: both specialists coexisted, and no generalist evolved. Divergence from the ancestral phenotype occurred at key pathway junctions in the central carbon metabolism. Fructose specialists evolved mutations in the fbp and pfk genes that appear to balance anabolic and catabolic carbon fluxes. Galactose specialists evolved increased expression of pgmA (the primary metabolic bottleneck of galactose metabolism) and silencing of ptnABCD (the main glucose transporter) and ldh (regulator/enzyme of downstream carbon metabolism). Overall, our study shows how metabolic network architecture and historical contingency serve to predict targets of selection and inform the functional interpretation of evolved mutations. The elucidation of the relationship between molecular constraints and phenotypic trade-offs contributes to an integrative understanding of evolutionary specialization and diversification.
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Affiliation(s)
- David M Ekkers
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
- Science for Life Laboratories and Department of Evolutionary Biology, Norbyvägen 18D, Uppsala University, 75236 Uppsala, Sweden
| | - Stefany Moreno-Gamez
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Marina C Rillo
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - G Sander van Doorn
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Avci O, Büyüksünetçi YT, Güley Z, Anik Ü. L. Lactis
Subsp
. Lactis
of Cheese Origin Based Microbial Fuel Cell. ChemistrySelect 2021. [DOI: 10.1002/slct.202102229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Okan Avci
- Mugla Sitki Kocman University Faculty of Science Chemistry Department 48000- Kotekli, Mugla Turkey
| | - Yudum T. Büyüksünetçi
- Mugla Sitki Kocman University Faculty of Science Chemistry Department 48000- Kotekli, Mugla Turkey
| | - Ziba Güley
- Alanya Alaaddin Keykubat University Rafet Kayıs Engineering Faculty Department of Food Engineering 07425- Alanya, Antalya Turkey
| | - Ülkü Anik
- Mugla Sitki Kocman University Faculty of Science Chemistry Department 48000- Kotekli, Mugla Turkey
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4
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Sato R, Ikeda M, Tanaka T, Ohara H, Aso Y. Production of R- and S-1,2-propanediol in engineered Lactococcus lactis. AMB Express 2021; 11:117. [PMID: 34398341 PMCID: PMC8368392 DOI: 10.1186/s13568-021-01276-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/11/2022] Open
Abstract
1,2-propanediol (1,2-PDO) is a versatile chemical used in multiple manufacturing processes. To date, some engineered and non-engineered microbes, such as Escherichia coli, Lactobacillus buchneri, and Clostridium thermosaccharolyticum, have been used to produce 1,2-PDO. In this study, we demonstrated the production of R- and S-1,2-PDO using engineered Lactococcus lactis. The L- and D-lactic acid-producing L. lactis strains NZ9000 and AH1 were transformed with the plasmid pNZ8048-ppy harboring pct, pduP, and yahK genes for 1,2-PDO biosynthesis, resulting in L. lactis LL1 and LL2, respectively. These engineered L. lactis produced S- and R-1,2-PDO at concentrations of 0.69 and 0.50 g/L with 94.4 and 78.0% ee optical purities, respectively, from 1% glucose after 72 h of cultivation. Both 1% mannitol and 1% gluconate were added instead of glucose to the culture of L. lactis LL1 to supply NADH and NADPH to the 1,2-PDO production pathway, resulting in 75% enhancement of S-1,2-PDO production. Production of S-1,2-PDO from 5% mannitol and 5% gluconate was demonstrated using L. lactis LL1 with a pH-stat approach. This resulted in S-1,2-PDO production at a concentration of 1.88 g/L after 96 h of cultivation. To our knowledge, this is the first report on the production of R- and S-1,2-PDO using engineered lactic acid bacteria.
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Affiliation(s)
- Rintaro Sato
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Saitama, Japan
| | - Motoyuki Ikeda
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
| | - Tomonari Tanaka
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan.
- JST-Mirai Program, Japan Science and Technology Agency, Saitama, Japan.
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Aslam A, Zhao S, Lu X, He N, Zhu H, Malik AU, Azam M, Liu W. High-Throughput LC-ESI-MS/MS Metabolomics Approach Reveals Regulation of Metabolites Related to Diverse Functions in Mature Fruit of Grafted Watermelon. Biomolecules 2021; 11:628. [PMID: 33922544 PMCID: PMC8146259 DOI: 10.3390/biom11050628] [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: 02/26/2021] [Revised: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022] Open
Abstract
Grafting has been reported as a factor regulating the metabolome of a plant. Therefore, a comprehensive metabolic profile and comparative analysis of metabolites were conducted from fully mature fruit of pumpkin-grafted watermelon (PGW) and a self-rooted watermelon (SRW). Widely targeted LC-ESI-MS/MS metabolomics approach facilitated the simultaneous identification and quantification of 339 metabolites across PGW and SRW. Regardless of grafting, delta-aminolevulinic acid hydrochloride, sucrose, mannose-6-phosphate (carbohydrates), homocystine, 2-phenylglycine, s-adenosyl-L-homocysteine (amino acids and derivatives), malic, azelaic, H-butanoic acid ethyl ester-hexoside isomer 1, (organic acids), MAG (18:3) isomer1, LysoPC 16:0, LysoPC 18:2 2n isomer (lipids) p-coumaric acid, piperidine, and salicylic acid-o-glycoside (secondary metabolites) were among the dominant metabolite. Dulcitol, mono-, and disaccharide sugars were higher in PGW, while polysaccharides showed complex behavior. In PGW, most aromatic and nitrogen-rich amino acids accumulated greater than 1.5- and 1-fold, respectively. Intermediates of the tricarboxylic acid cycle (TCA), stress-related metabolites, vitamin B5, and several flavonoids were significantly more abundant in PGW. Most lipids were also significantly higher in grafted watermelon. This is the first report providing a comprehensive picture of watermelon metabolic profile and changes induced by grafting. Hence, the untargeted high-throughput LC-ESI-MS/MS metabolomics approach could be suitable to provide significant differences in metabolite contents between grafted and ungrafted plants.
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Affiliation(s)
- Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (A.A.); (S.Z.); (X.L.); (N.H.); (H.Z.)
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (A.A.); (S.Z.); (X.L.); (N.H.); (H.Z.)
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (A.A.); (S.Z.); (X.L.); (N.H.); (H.Z.)
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (A.A.); (S.Z.); (X.L.); (N.H.); (H.Z.)
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (A.A.); (S.Z.); (X.L.); (N.H.); (H.Z.)
| | - Aman Ullah Malik
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38000, Punjab, Pakistan; (A.U.M.); (M.A.)
| | - Muhammad Azam
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38000, Punjab, Pakistan; (A.U.M.); (M.A.)
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China; (A.A.); (S.Z.); (X.L.); (N.H.); (H.Z.)
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Liu G, Qiao Y, Zhang Y, Leng C, Chen H, Sun J, Fan X, Li A, Feng Z. Metabolic Profiles of Carbohydrates in Streptococcus thermophilus During pH-Controlled Batch Fermentation. Front Microbiol 2020; 11:1131. [PMID: 32547529 PMCID: PMC7272703 DOI: 10.3389/fmicb.2020.01131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/05/2020] [Indexed: 02/05/2023] Open
Abstract
Revealing the metabolic profiles of carbohydrates with their regulatory genes and metabolites is conducive to understanding their mechanism of utilization in Streptococcus thermophilus MN-ZLW-002 during pH-controlled batch fermentation. Transcriptomics and metabolomics were used to study carbohydrate metabolism. More than 200 unigenes were involved in carbohydrate transport. Of these unigenes, 55 were involved in the phosphotransferase system (PTS), which had higher expression levels than those involved in ABC protein-dependent systems, permeases, and symporters. The expression levels of the genes involved in the carbohydrate transport systems and phosphate transport system were high at the end-lag and end-exponential growth phases, respectively. In addition, 166 differentially expressed genes (DEGs) associated with carbohydrate metabolism were identified. Most genes had their highest expression levels at the end-lag phase. The pfk, ldh, zwf, and E3.2.1.21 genes involved in the glycolytic pathway had higher expression levels at the end-exponential growth phase than the mid-exponential growth phase. The results showed high expression levels of lacZ and galKTM genes and reabsorption of extracellular galactose. S. thermophilus MN-ZLW-002 can metabolize and utilize galactose. Overall, this comprehensive network of carbohydrate metabolism is useful for further studies of the control of glycolytic pathway during the high-density culture of S. thermophilus.
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Affiliation(s)
- Gefei Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yali Qiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yanjiao Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Cong Leng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Hongyu Chen
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Jiahui Sun
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xuejing Fan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Aili Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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7
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Aslam A, Zhao S, Azam M, Lu X, He N, Li B, Dou J, Zhu H, Liu W. Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development. PeerJ 2020; 8:e8259. [PMID: 31934503 PMCID: PMC6951286 DOI: 10.7717/peerj.8259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/20/2019] [Indexed: 02/05/2023] Open
Abstract
Grafting has been reported as a factor that influences fruit quality. However, a comprehensive study of the metabolic profile related to fruit quality and the underlying molecular mechanism in grafted watermelon has not been carried out. Metabolomics and transcriptome analysis were performed on both pumpkin-grafted watermelon and ungrafted watermelon at different developmental stages. In total, 56 primary metabolites were identified with either high or low abundance between ungrafted and pumpkin-grafted watermelon. The results indicated that ornithine, arginine, lysine (amino acids), glucose, sucrose, glucosamine (sugars), malic acid, fumaric acid and succinic acid (organic acids) were among the dominant metabolites influencing fruit quality. Additionally, comparative RNA sequence analysis on grafted and ungrafted watermelon yielded 729, 174, 128 and 356 differentially expressed genes at 10, 18, 26 and 34 days after pollination (DAP), respectively. Functional annotations of these genes indicated that grafting significantly altered the biological and metabolic processes related to fruit quality. Our comparative metabolomics and transcriptome analysis revealed that FBA2, FK, SuSy, SPS, IAI, AI and sugar transporter gene (SWT3b) might play a central role in the accumulation of glucose and sucrose, whereas higher malic acid content was attributed to high down regulation of ALMT13 and ALMT8 in pumpkin-grafted watermelon. Changes in the ornithine, glutamine, alanine, tyrosine, valine, asparagine, phenylalanine, arginine and tryptophan contents were consistent with the transcript level of their metabolic genes such as NAOD, GS, AGT, TaT, aDH1, OGDH, aDC, 4CL 1, PaL, CaT and two nitrate transporter genes (NRT1) in pumpkin-grafted watermelon. This study provides the basis for understanding the graft-responsive changes in the metabolic profile and regulatory mechanism related to fruit quality.
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Affiliation(s)
- Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Muhammad Azam
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan, China
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Puvendran K, Jayaraman G. Enhancement of acetyl-CoA by acetate co-utilization in recombinant Lactococcus lactis cultures enables the production of high molecular weight hyaluronic acid. Appl Microbiol Biotechnol 2019; 103:6989-7001. [PMID: 31267232 DOI: 10.1007/s00253-019-09987-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 10/26/2022]
Abstract
The molecular weight of hyaluronic acid (HA) is a critical property which determines its usage in various biomedical applications. This study investigates the correlation between the availability of a critical cofactor, acetyl-CoA, the concentration of a limiting precursor, UDP-N-acetylglucosamine (UDP-GlcNAc), and the molecular weight of HA (MWHA) produced by recombinant Lactococcus lactis MKG6 cultures. This strain expressed three heterologous HA-pathway genes obtained from the has operon of Streptococcus zooepidemicus in an ldh-mutant host strain, L. lactis NZ9020. A flux balance analysis, performed using the L. lactis genome-scale metabolic network, showed a positive correlation of acetyl-CoA flux with the UDP-GlcNAc flux and the experimental data on HA productivity. To increase the intracellular levels of acetyl-CoA, acetate was supplemented as a pulse feed in anaerobic batch cultures. However, acetate is effectively utilized only in the presence of glucose and exhaustion of glucose resulted in decreasing the final MWHA (1.5 MDa). Co-supplementation of acetate resulted in enhancing the acetyl-CoA and UDP-GlcNAc levels as well as the MWHA to 2.5 MDa. This logic was extended to fed-batch cultures, designed with a pH-based feedback control of glucose feeding and pulse acetate supplementation. When the glucose feed concentration was optimally adjusted to prevent glucose exhaustion or accumulation, the acetate utilization was found to be high, resulting in significantly enhanced levels of acetyl-CoA and UDP-GlcNAc as well as a MWHA of 3.4 MDa, which was sustained at this value throughout the process. This study provides the possibility of commercially producing high MWHA using recombinant L. lactis strains.
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Affiliation(s)
- Kirubhakaran Puvendran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Guhan Jayaraman
- Bioprocess and Metabolic Engineering Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
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Sahoo TK, Jayaraman G. Co-culture of Lactobacillus delbrueckii and engineered Lactococcus lactis enhances stoichiometric yield of D-lactic acid from whey permeate. Appl Microbiol Biotechnol 2019; 103:5653-5662. [PMID: 31115633 DOI: 10.1007/s00253-019-09819-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/13/2019] [Accepted: 03/31/2019] [Indexed: 12/18/2022]
Abstract
D-Lactic acid (D-LA) is an enantiomer of lactic acid, which has a niche application in synthesis of poly-lactic acid based (PLA) polymer owing to its contribution to the thermo-stability of stereo-complex PLA polymer. Utilization of renewable substrates such as whey permeate is pivotal to economically viable production of D-LA. In present work, we have demonstrated D-LA production from whey permeate by Lactobacillus delbrueckii and engineered Lactococcus lactis. We observed that lactose fermentation by a monoculture of L. delbrueckii yields D-LA and galactose as major products. The highest yield of D-LA obtained was 0.48 g g-1 when initial lactose concentration was 30 g L-1. Initial lactose concentration beyond 20 g L-1 resulted in accumulation of glucose and galactose, and hence, reduced the stoichiometric yield of D-LA. L. lactis naturally produces L-lactic acid (L-LA), so a mutant strain of L. lactis (L. lactis Δldh ΔldhB ΔldhX) was used to prevent L-LA production and engineer it for D-LA production. Heterologous over-expression of D-lactate dehydrogenase (ldhA) in the recombinant strain L. lactis TSG1 resulted in 0.67 g g-1 and 0.44 g g-1 of D-LA yield from lactose and galactose, respectively. Co-expression of galactose permease (galP) and α-phosphoglucomutase (pgmA) with ldhA in the recombinant strain L. lactis TSG3 achieved a D-LA yield of 0.92 g g-1 from galactose. A co-culture batch process of L. delbrueckii and L. lactis TSG3 achieved an enhanced stoichiometric yield of 0.90 g g-1 and ~45 g L-1D-LA from whey permeate (lactose). This is the highest reported yield of D-LA from lactose substrate, and the titres can be improved further by a suitably designed fed-batch co-culture process.
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Affiliation(s)
- Tridweep K Sahoo
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Guhan Jayaraman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
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Jeeva P, Shanmuga Doss S, Sundaram V, Jayaraman G. Production of controlled molecular weight hyaluronic acid by glucostat strategy using recombinant Lactococcus lactis cultures. Appl Microbiol Biotechnol 2019; 103:4363-4375. [DOI: 10.1007/s00253-019-09769-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
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11
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Zhao L, Liu A, Song T, Jin Y, Xu X, Gao Y, Ye X, Qi H. Transcriptome analysis reveals the effects of grafting on sugar and α-linolenic acid metabolisms in fruits of cucumber with two different rootstocks. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:289-302. [PMID: 30036858 DOI: 10.1016/j.plaphy.2018.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 05/22/2023]
Abstract
Flavor quality in cucumber is affected by different rootstocks, but the molecular mechanism is largely unclean. To clarify the differences of sugar and aromatic compounds, cucumber (cucumis sativus) fruits from plants of self-grafted (SG) or grafted onto figleaf gourd (Cucurbita ficifolia; G1) or 'Weisheng No.1' rootstock (Cucurbita moschata ⅹCucurbita moschata hybrids; G2) were performed the transcriptome analysis. We obtained 1013 and 920 differentially expressed genes (DEGs) from G1 and G2 compared to SG respectively, in which 453 genes were co-expressed. Functional annotations showed many DEGs were involved in glycolysis/gluconeogenesis metabolism, fructose metabolism and α-Linolenic acid metabolisms, 20 DEGs were selected from the 3 pathways to validate sequencing accuracy by quantitative real-time PCR. The gene relative expression levels were concurrent with RNA-seq results and sugar and aromatic compounds content phenotypes. Moreover, some vital transcript factors and transport proteins were analyzed. These findings indicate that different rootstocks could induce significantly changes in the physiological profiling and transcripts of sugar- and aromatic flavor-related genes. This study provides a novel insight into the molecular mechanisms of fruit quality regulated by candidate genes.
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Affiliation(s)
- Lili Zhao
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China; Institute of Vegetable Research, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110866, China.
| | - Aiqun Liu
- Institute of Vegetable Research, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110866, China.
| | - Tiefeng Song
- Institute of Vegetable Research, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110866, China.
| | - Yazhong Jin
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilong Jiang 163319, China.
| | - Xin Xu
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China.
| | - Yang Gao
- Agricultural Technology Extension Centre of Changtu' Country, Tieling, Liaoning 112599, China.
| | - Xueling Ye
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China.
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China.
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12
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Production of a highly concentrated probiotic culture of Lactococcus lactis CECT 539 containing high amounts of nisin. 3 Biotech 2018; 8:292. [PMID: 29963352 DOI: 10.1007/s13205-018-1318-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/18/2018] [Indexed: 10/28/2022] Open
Abstract
In this study, probiotic biomass and nisin productions by Lactococcus lactis CECT 539 were followed in two realkalized fed-batch cultures in diluted whey (DW) supplemented with KH2PO4 up to a total phosphorus concentration of 0.459 g/L. Increased biomass (5.12 g/L, 2.18 × 1010 CFU/mL) and nisin (235.23 BU/mL) concentrations were obtained in the culture fed concentrated whey and concentrated mussel processing waste (CMPW) medium supplemented with glucose up to a concentration of 400 g/L (CMPW + G medium) compared with similar fed-batch fermentations in DW medium. In the second fed-batch fermentation, the feeding medium CMPW + G was supplemented with KH2PO4 up to a TP concentration of 3.21 g/L. With this approach, increased production of biomass (5.49 g/L, 2.33 × 1010 CFU/mL) and nisin (257.59 BU/mL) was obtained. Considering the substantial availability of these wastes at very low prices from local dairy and mussel processing plants in Galicia, their use as culture media could offer an attractive alternative for a low-cost production of probiotic biomass and nisin at a high scale.
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13
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Liang S, Gao D, Liu H, Wang C, Wen J. Metabolomic and proteomic analysis of D-lactate-producing Lactobacillus delbrueckii under various fermentation conditions. J Ind Microbiol Biotechnol 2018; 45:681-696. [PMID: 29808292 DOI: 10.1007/s10295-018-2048-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/19/2018] [Indexed: 11/29/2022]
Abstract
As an important feedstock monomer for the production of biodegradable stereo-complex poly-lactic acid polymer, D-lactate has attracted much attention. To improve D-lactate production by microorganisms such as Lactobacillus delbrueckii, various fermentation conditions were performed, such as the employment of anaerobic fermentation, the utilization of more suitable neutralizing agents, and exploitation of alternative nitrogen sources. The highest D-lactate titer could reach 133 g/L under the optimally combined fermentation condition, increased by 70.5% compared with the control. To decipher the potential mechanisms of D-lactate overproduction, the time-series response of intracellular metabolism to different fermentation conditions was investigated by GC-MS and LC-MS/MS-based metabolomic analysis. Then the metabolomic datasets were subjected to weighted correlation network analysis (WGCNA), and nine distinct metabolic modules and eight hub metabolites were identified to be specifically associated with D-lactate production. Moreover, a quantitative iTRAQ-LC-MS/MS proteomic approach was employed to further analyze the change of intracellular metabolism under the combined fermentation condition, identifying 97 up-regulated and 42 down-regulated proteins compared with the control. The in-depth analysis elucidated how the key factors exerted influence on D-lactate biosynthesis. The results revealed that glycolysis and pentose phosphate pathways, transport of glucose, amino acids and peptides, amino acid metabolism, peptide hydrolysis, synthesis of nucleotides and proteins, and cell division were all strengthened, while ATP consumption for exporting proton, cell damage, metabolic burden caused by stress response, and bypass of pyruvate were decreased under the combined condition. These might be the main reasons for significantly improved D-lactate production. These findings provide the first omics view of cell growth and D-lactate overproduction in L. delbrueckii, which can be a theoretical basis for further improving the production of D-lactate.
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Affiliation(s)
- Shaoxiong Liang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Dacheng Gao
- Dalian Research Institute of Petroleum and Petrochemicals, SINOPEC, Dalian, 116000, People's Republic of China
| | - Huanhuan Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, China.,Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Cheng Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
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14
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Nsogning SD, Fischer S, Becker T. Investigating on the fermentation behavior of six lactic acid bacteria strains in barley malt wort reveals limitation in key amino acids and buffer capacity. Food Microbiol 2018. [PMID: 29526209 DOI: 10.1016/j.fm.2018.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding lactic acid bacteria (LAB) fermentation behavior in malt wort is a milestone towards flavor improvement of lactic acid fermented malt beverages. Therefore, this study aims to outline deficiencies that may exist in malt wort fermentation. First, based on six LAB strains, cell viability and vitality were evaluated. Second, sugars, organic acids, amino acids, pH value and buffering capacity (BC) were monitored. Finally, the implication of key amino acids, fructose and wort BC on LAB growth was determined. Short growth phase coupled with prompt cell death and a decrease in metabolic activity was observed. Low wort BC caused rapid pH drop with lactic acid accumulation, which conversely increased the BC leading to less pH change at late-stage fermentation. Lactic acid content (≤3.9 g/L) was higher than the reported inhibitory concentration (1.8 g/L). Furthermore, sugars were still available but fructose and key amino acids lysine, arginine and glutamic acid were considerably exhausted (≤98%). Wort supplementations improved cell growth and viability leading to conclude that key amino acid depletion coupled with low BC limits LAB growth in malt wort. Then, a further increase in organic acid reduces LAB viability. This knowledge opens doors for LAB fermentation process optimization in malt wort.
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Affiliation(s)
- Sorelle Dongmo Nsogning
- Institute of Brewing and Beverage Technology, Technische Universität München, Weihenstephaner Steig 20, 85354 Freising, Germany.
| | - Susann Fischer
- Institute of Brewing and Beverage Technology, Technische Universität München, Weihenstephaner Steig 20, 85354 Freising, Germany.
| | - Thomas Becker
- Institute of Brewing and Beverage Technology, Technische Universität München, Weihenstephaner Steig 20, 85354 Freising, Germany.
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15
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Azizan KA, Ressom HW, Mendoza ER, Baharum SN. 13C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses. PeerJ 2017; 5:e3451. [PMID: 28695065 PMCID: PMC5501154 DOI: 10.7717/peerj.3451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/19/2017] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, 13C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS) were used to measure the flux ratios of active pathways in the central metabolism of L. lactis when subjected to three conditions varying in temperature (30°C, 37°C) and agitation (with and without agitation at 150 rpm). Collectively, the concentrations of proteinogenic amino acids (PAAs) and free fatty acids (FAAs) were compared, and Pearson correlation analysis (r) was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP) pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA). Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of L. lactis’ central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA) from pyruvate (PYR) reaction in all conditions suggested the activation of pyruvate carboxylate (pycA) in L. lactis, in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP) pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in L. lactis. Overall, the integration of systematic analysis of amino acids and flux ratio analysis provides a systems-level understanding of how L. lactis regulates central metabolism under various conditions.
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Affiliation(s)
- Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Habtom W Ressom
- Departments of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Eduardo R Mendoza
- Institute of Mathematics, University of the Philippines Diliman, Quezon City, Metro Manila, Philippines.,Membrane Biochemistry Group, Max Planck Institute of Biochemistry, Planegg, Germany
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
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16
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Paulussen C, Hallsworth JE, Álvarez‐Pérez S, Nierman WC, Hamill PG, Blain D, Rediers H, Lievens B. Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species. Microb Biotechnol 2017; 10:296-322. [PMID: 27273822 PMCID: PMC5328810 DOI: 10.1111/1751-7915.12367] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/08/2016] [Accepted: 04/18/2016] [Indexed: 01/26/2023] Open
Abstract
Fungi of the genus Aspergillus are widespread in the environment. Some Aspergillus species, most commonly Aspergillus fumigatus, may lead to a variety of allergic reactions and life-threatening systemic infections in humans. Invasive aspergillosis occurs primarily in patients with severe immunodeficiency, and has dramatically increased in recent years. There are several factors at play that contribute to aspergillosis, including both fungus and host-related factors such as strain virulence and host pulmonary structure/immune status, respectively. The environmental tenacity of Aspergilllus, its dominance in diverse microbial communities/habitats, and its ability to navigate the ecophysiological and biophysical challenges of host infection are attributable, in large part, to a robust stress-tolerance biology and exceptional capacity to generate cell-available energy. Aspects of its stress metabolism, ecology, interactions with diverse animal hosts, clinical presentations and treatment regimens have been well-studied over the past years. Here, we synthesize these findings in relation to the way in which some Aspergillus species have become successful opportunistic pathogens of human- and other animal hosts. We focus on the biophysical capabilities of Aspergillus pathogens, key aspects of their ecophysiology and the flexibility to undergo a sexual cycle or form cryptic species. Additionally, recent advances in diagnosis of the disease are discussed as well as implications in relation to questions that have yet to be resolved.
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Affiliation(s)
- Caroline Paulussen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - John E. Hallsworth
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Sergio Álvarez‐Pérez
- Faculty of Veterinary MedicineDepartment of Animal HealthUniversidad Complutense de MadridMadridE‐28040Spain
| | | | - Philip G. Hamill
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - David Blain
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Hans Rediers
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
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17
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Enhancement of fructose utilization from sucrose in the cell for improved l-serine production in engineered Corynebacterium glutamicum. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Terakawa A, Natsume A, Okada A, Nishihata S, Kuse J, Tanaka K, Takenaka S, Ishikawa S, Yoshida KI. Bacillus subtilis 5'-nucleotidases with various functions and substrate specificities. BMC Microbiol 2016; 16:249. [PMID: 27784292 PMCID: PMC5080769 DOI: 10.1186/s12866-016-0866-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Escherichia coli, nagD, yrfG, yjjG, yieH, yigL, surE, and yfbR encode 5'-nucleotidases that hydrolyze the phosphate group of 5'-nucleotides. In Bacillus subtilis, genes encoding 5'-nucleotidase have remained to be identified. RESULTS We found that B. subtilis ycsE, araL, yutF, ysaA, and yqeG show suggestive similarities to nagD. Here, we expressed them in E. coli to purify the respective His6-tagged proteins. YcsE exhibited significant 5'-nucleotidase activity with a broader specificity, whereas the other four enzymes had rather weak but suggestive activities with various capacities and substrate specificities. In contrast, B. subtilis yktC shares high similarity with E. coli suhB encoding an inositol monophosphatase. YktC exhibited inositol monophosphatase activity as well as 5'-nucleotidase activity preferential for GMP and IMP. The ycsE, yktC, and yqeG genes are induced by oxidative stress and were dispensable, although yqeG was required to maintain normal growth on solid medium. In the presence of diamide, only mutants lacking yktC exhibited enhanced growth defects, whereas the other mutants without ycsE or yqeG did not. CONCLUSIONS Accordingly, in B. subtilis, at least YcsE and YktC acted as major 5'-nucleotidases and the four minor enzymes might function when the intracellular concentrations of substrates are sufficiently high. In addition, YktC is involved in resistance to oxidative stress caused by diamide, while YqeG is necessary for normal colony formation on solid medium.
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Affiliation(s)
- Ayako Terakawa
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Ayane Natsume
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Atsushi Okada
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Shogo Nishihata
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Junko Kuse
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kosei Tanaka
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.,Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Ken-Ichi Yoshida
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan. .,Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.
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19
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Muzika F, Schreiberová L, Schreiber I. Discrete Turing patterns in coupled reaction cells in a cyclic array. REACTION KINETICS MECHANISMS AND CATALYSIS 2016. [DOI: 10.1007/s11144-016-1004-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Hartmann A, Lemos JM, Vinga S. Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics. Comput Biol Med 2015; 63:301-9. [DOI: 10.1016/j.compbiomed.2014.08.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/27/2014] [Accepted: 08/28/2014] [Indexed: 11/26/2022]
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21
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Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R. Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS One 2014; 9:e106453. [PMID: 25268481 PMCID: PMC4182131 DOI: 10.1371/journal.pone.0106453] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 08/07/2014] [Indexed: 11/18/2022] Open
Abstract
Metabolic pathways are complex dynamic systems whose response to perturbations and environmental challenges are governed by multiple interdependencies between enzyme properties, reactions rates, and substrate levels. Understanding the dynamics arising from such a network can be greatly enhanced by the construction of a computational model that embodies the properties of the respective system. Such models aim to incorporate mechanistic details of cellular interactions to mimic the temporal behavior of the biochemical reaction system and usually require substantial knowledge of kinetic parameters to allow meaningful conclusions. Several approaches have been suggested to overcome the severe data requirements of kinetic modeling, including the use of approximative kinetics and Monte-Carlo sampling of reaction parameters. In this work, we employ a probabilistic approach to study the response of a complex metabolic system, the central metabolism of the lactic acid bacterium Lactococcus lactis, subject to perturbations and brief periods of starvation. Supplementing existing methodologies, we show that it is possible to acquire a detailed understanding of the control properties of a corresponding metabolic pathway model that is directly based on experimental observations. In particular, we delineate the role of enzymatic regulation to maintain metabolic stability and metabolic recovery after periods of starvation. It is shown that the feedforward activation of the pyruvate kinase by fructose-1,6-bisphosphate qualitatively alters the bifurcation structure of the corresponding pathway model, indicating a crucial role of enzymatic regulation to prevent metabolic collapse for low external concentrations of glucose. We argue that similar probabilistic methodologies will help our understanding of dynamic properties of small-, medium- and large-scale metabolic networks models.
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Affiliation(s)
- Ettore Murabito
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Sciences (CEAS), Manchester Centre for Integrative Systems Biology (MCISB), The University of Manchester, Manchester, United Kingdom
- * E-mail: (EM); (RS)
| | - Malkhey Verma
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Sciences (CEAS), Manchester Centre for Integrative Systems Biology (MCISB), The University of Manchester, Manchester, United Kingdom
| | - Martijn Bekker
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Domenico Bellomo
- Systems Bioinformatics IBIVU and Netherlands Institute for Systems Biology (NISB), VU University Amsterdam, Amsterdam, The Netherlands
| | - Hans V. Westerhoff
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Sciences (CEAS), Manchester Centre for Integrative Systems Biology (MCISB), The University of Manchester, Manchester, United Kingdom
- Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Molecular Cell Physiology, FALW, VU University Amsterdam, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Bioinformatics IBIVU and Netherlands Institute for Systems Biology (NISB), VU University Amsterdam, Amsterdam, The Netherlands
| | - Ralf Steuer
- CzechGlobe - Global Change Research Center, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Humboldt-University Berlin, Institute for Theoretical Biology, Berlin, Germany
- * E-mail: (EM); (RS)
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22
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Papagianni M, Legiša M. Increased mannitol production in Lactobacillus reuteri ATCC 55730 production strain with a modified 6-phosphofructo-1-kinase. J Biotechnol 2014; 181:20-6. [DOI: 10.1016/j.jbiotec.2014.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
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23
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Maier T, Marcos J, Wodke JAH, Paetzold B, Liebeke M, Gutiérrez-Gallego R, Serrano L. Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae. MOLECULAR BIOSYSTEMS 2013; 9:1743-55. [PMID: 23598864 DOI: 10.1039/c3mb70113a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Systems metabolomics, the identification and quantification of cellular metabolites and their integration with genomics and proteomics data, promises valuable functional insights into cellular biology. However, technical constraints, sample complexity issues and the lack of suitable complementary quantitative data sets prevented accomplishing such studies in the past. Here, we present an integrative metabolomics study of the genome-reduced bacterium Mycoplasma pneumoniae. We experimentally analysed its metabolome using a cross-platform approach. We explain intracellular metabolite homeostasis by quantitatively integrating our results with the cellular inventory of proteins, DNA and other macromolecules, as well as with available building blocks from the growth medium. We calculated in vivo catalytic parameters of glycolytic enzymes, making use of measured reaction velocities, as well as enzyme and metabolite pool sizes. A quantitative, inter-species comparison of absolute and relative metabolite abundances indicated that metabolic pathways are regulated as functional units, thereby simplifying adaptive responses. Our analysis demonstrates the potential for new scientific insight by integrating different types of large-scale experimental data from a single biological source.
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Affiliation(s)
- Tobias Maier
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.
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24
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Carvalho SM, Kuipers OP, Neves AR. Environmental and nutritional factors that affect growth and metabolism of the pneumococcal serotype 2 strain D39 and its nonencapsulated derivative strain R6. PLoS One 2013; 8:e58492. [PMID: 23505518 PMCID: PMC3591343 DOI: 10.1371/journal.pone.0058492] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/05/2013] [Indexed: 01/06/2023] Open
Abstract
Links between carbohydrate metabolism and virulence in Streptococcus pneumoniae have been recurrently established. To investigate these links further we developed a chemically defined medium (CDM) and standardized growth conditions that allowed for high growth yields of the related pneumococcal strains D39 and R6. The utilization of the defined medium enabled the evaluation of different environmental and nutritional factors on growth and fermentation patterns under controlled conditions of pH, temperature and gas atmosphere. The same growth conditions impacted differently on the nonencapsulated R6, and its encapsulated progenitor D39. A semi-aerobic atmosphere and a raised concentration of uracil, a fundamental component of the D39 capsule, improved considerably D39 growth rate and biomass. In contrast, in strain R6, the growth rate was enhanced by strictly anaerobic conditions and uracil had no effect on biomass. In the presence of oxygen, the difference in the growth rates was mainly attributed to a lower activity of pyruvate oxidase in strain D39. Our data indicate an intricate connection between capsule production in strain D39 and uracil availability. In this study, we have also successfully applied the in vivo NMR technique to study sugar metabolism in S. pneumoniae R6. Glucose consumption, end-products formation and evolution of intracellular metabolite pools were monitored online by (13)C-NMR. Additionally, the pools of NTP and inorganic phosphate were followed by (31)P-NMR after a pulse of glucose. These results represent the first metabolic profiling data obtained non-invasively for S. pneumoniae, and pave the way to a better understanding of regulation of central metabolism.
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Affiliation(s)
- Sandra M. Carvalho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ana Rute Neves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
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25
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Sriyudthsak K, Shiraishi F, Hirai MY. Identification of a metabolic reaction network from time-series data of metabolite concentrations. PLoS One 2013; 8:e51212. [PMID: 23326311 PMCID: PMC3542379 DOI: 10.1371/journal.pone.0051212] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
Abstract
Recent development of high-throughput analytical techniques has made it possible to qualitatively identify a number of metabolites simultaneously. Correlation and multivariate analyses such as principal component analysis have been widely used to analyse those data and evaluate correlations among the metabolic profiles. However, these analyses cannot simultaneously carry out identification of metabolic reaction networks and prediction of dynamic behaviour of metabolites in the networks. The present study, therefore, proposes a new approach consisting of a combination of statistical technique and mathematical modelling approach to identify and predict a probable metabolic reaction network from time-series data of metabolite concentrations and simultaneously construct its mathematical model. Firstly, regression functions are fitted to experimental data by the locally estimated scatter plot smoothing method. Secondly, the fitted result is analysed by the bivariate Granger causality test to determine which metabolites cause the change in other metabolite concentrations and remove less related metabolites. Thirdly, S-system equations are formed by using the remaining metabolites within the framework of biochemical systems theory. Finally, parameters including rate constants and kinetic orders are estimated by the Levenberg–Marquardt algorithm. The estimation is iterated by setting insignificant kinetic orders at zero, i.e., removing insignificant metabolites. Consequently, a reaction network structure is identified and its mathematical model is obtained. Our approach is validated using a generic inhibition and activation model and its practical application is tested using a simplified model of the glycolysis of Lactococcus lactis MG1363, for which actual time-series data of metabolite concentrations are available. The results indicate the usefulness of our approach and suggest a probable pathway for the production of lactate and acetate. The results also indicate that the approach pinpoints a probable strong inhibition of lactate on the glycolysis pathway.
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Affiliation(s)
- Kansuporn Sriyudthsak
- RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
| | - Fumihide Shiraishi
- Graduate school of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
- * E-mail: (FS); (MYH)
| | - Masami Yokota Hirai
- RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
- * E-mail: (FS); (MYH)
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Papagianni M. Metabolic engineering of lactic acid bacteria for the production of industrially important compounds. Comput Struct Biotechnol J 2012; 3:e201210003. [PMID: 24688663 PMCID: PMC3962192 DOI: 10.5936/csbj.201210003] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/10/2012] [Accepted: 09/15/2012] [Indexed: 01/21/2023] Open
Abstract
Lactic acid bacteria (LAB) are receiving increased attention for use as cell factories for the production of metabolites with wide use by the food and pharmaceutical industries. The availability of efficient tools for genetic modification of LAB during the past decade permitted the application of metabolic engineering strategies at the levels of both the primary and the more complex secondary metabolism. The recent developments in the area with a focus on the production of industrially important metabolites will be discussed in this review.
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Affiliation(s)
- Maria Papagianni
- Department of Hygiene and Technology of Food of Animal Origin, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
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Engineering the central pathways in Lactococcus lactis: Functional expression of the phosphofructokinase (pfk) and alternative oxidase (aox1) genes from Aspergillus niger in Lactococcus lactis facilitates improved carbon conversion rates under oxidizing conditions. Enzyme Microb Technol 2012; 51:125-30. [DOI: 10.1016/j.enzmictec.2012.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/23/2012] [Accepted: 04/23/2012] [Indexed: 11/21/2022]
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Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb Cell Fact 2012; 11:50. [PMID: 22545791 PMCID: PMC3461431 DOI: 10.1186/1475-2859-11-50] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/30/2012] [Indexed: 01/19/2023] Open
Abstract
This paper gives an overview of the recent advances in engineering the central carbon metabolism of the industrially important bacteria Escherichia coli, Bacillus subtilis, Corynobacterium glutamicum, Streptomyces spp., Lactococcus lactis and other lactic acid bacteria. All of them are established producers of important classes of products, e.g. proteins, amino acids, organic acids, antibiotics, high-value metabolites for the food industry and also, promising producers of a large number of industrially or therapeutically important chemicals. Optimization of existing or introduction of new cellular processes in these microorganisms is often achieved through manipulation of targets that reside at major points of central metabolic pathways, such as glycolysis, gluconeogenesis, the pentose phosphate pathway and the tricarboxylic acid cycle with the glyoxylate shunt. Based on the huge progress made in recent years in biochemical, genetic and regulatory studies, new fascinating engineering approaches aim at ensuring an optimal carbon and energy flow within central metabolism in order to achieve optimized metabolite production.
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Guo T, Kong J, Zhang L, Zhang C, Hu S. Fine tuning of the lactate and diacetyl production through promoter engineering in Lactococcus lactis. PLoS One 2012; 7:e36296. [PMID: 22558426 PMCID: PMC3338672 DOI: 10.1371/journal.pone.0036296] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 03/30/2012] [Indexed: 01/08/2023] Open
Abstract
Lactococcus lactis is a well-studied bacterium widely used in dairy fermentation and capable of producing metabolites with organoleptic and nutritional characteristics. For fine tuning of the distribution of glycolytic flux at the pyruvate branch from lactate to diacetyl and balancing the production of the two metabolites under aerobic conditions, a constitutive promoter library was constructed by randomizing the promoter sequence of the H2O-forming NADH oxidase gene in L. lactis. The library consisted of 30 promoters covering a wide range of activities from 7,000 to 380,000 relative fluorescence units using a green fluorescent protein as reporter. Eleven typical promoters of the library were selected for the constitutive expression of the H2O-forming NADH oxidase gene in L. lactis, and the NADH oxidase activity increased from 9.43 to 58.17-fold of the wild-type strain in small steps of activity change under aerobic conditions. Meanwhile, the lactate yield decreased from 21.15±0.08 mM to 9.94±0.07 mM, and the corresponding diacetyl production increased from 1.07±0.03 mM to 4.16±0.06 mM with the intracellular NADH/NAD+ ratios varying from 0.711±0.005 to 0.383±0.003. The results indicated that the reduced pyruvate to lactate flux was rerouted to the diacetyl with an almost linear flux variation via altered NADH/NAD+ ratios. Therefore, we provided a novel strategy to precisely control the pyruvate distribution for fine tuning of the lactate and diacetyl production through promoter engineering in L. lactis. Interestingly, the increased H2O-forming NADH oxidase activity led to 76.95% lower H2O2 concentration in the recombinant strain than that of the wild-type strain after 24 h of aerated cultivation. The viable cells were significantly elevated by four orders of magnitude within 28 days of storage at 4°C, suggesting that the increased enzyme activity could eliminate H2O2 accumulation and prolong cell survival.
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Affiliation(s)
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
- * E-mail:
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Papagianni M, Avramidis N. Cloning and functional expression of the mitochondrial alternative oxidase gene (aox1) of Aspergillus niger in Lactococcus lactis and its induction by oxidizing conditions. Enzyme Microb Technol 2012; 50:17-21. [DOI: 10.1016/j.enzmictec.2011.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/23/2011] [Accepted: 09/26/2011] [Indexed: 10/16/2022]
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Growth rate-dependent control in Enterococcus faecalis: effects on the transcriptome and proteome, and strong regulation of lactate dehydrogenase. Appl Environ Microbiol 2011; 78:170-6. [PMID: 22038603 DOI: 10.1128/aem.06604-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecalis V583 was grown in a glucose-limited chemostat at three different growth rates (0.05, 0.15, and 0.4 h⁻¹). The fermentation pattern changed with growth rate, from a mostly homolactic profile at a high growth rate to a fermentation dominated by formate, acetate, and ethanol production at a low growth rate. A number of amino acids were consumed at the lower growth rates but not by fast-growing cells. The change in metabolic profile was caused mainly by decreased flux through lactate dehydrogenase. The transcription of ldh-1, encoding the principal lactate dehydrogenase, showed very strong growth rate dependence and differed by three orders of magnitude between the highest and the lowest growth rates. Despite the increase in ldh-1 transcript, the content of the Ldh-1 protein was the same under all conditions. Using microarrays and quantitative PCR, the levels of 227 gene transcripts were found to be affected by the growth rate, and 56 differentially expressed proteins were found by proteomic analyses. Few genes or proteins showed a growth rate-dependent increase or decrease in expression across the whole range of conditions, and many showed a maximum or minimum at the middle growth rate (i.e., 0.15 h⁻¹). For many gene products, a discrepancy between transcriptomic and proteomic data were seen, indicating posttranscriptional regulation of expression.
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Microcalorimetric study of the growth of bacterial colonies of Lactococcus lactis IL1403 in agar gels. Food Microbiol 2011; 29:67-79. [PMID: 22029920 DOI: 10.1016/j.fm.2011.08.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 08/01/2011] [Accepted: 08/16/2011] [Indexed: 11/20/2022]
Abstract
Growth of Lactococcus lactis IL1403 in solid agar gels and liquid cultures at different glucose concentrations of 2, 10 and 20 g/L and different inoculation rates from 10(0) to 10(6) cfu/mL with the 10-fold increment was studied using thermal activity monitor TAM III. In parallel to calorimetric measurements the changes of glucose and lactic acid concentrations and pH of culture media were measured in order to obtain additional information for the interpretation of calorimetric power-time curves. Maximal specific growth rates of heat evolution proportional to growth rates of biomass μ(max) (W/h), heat produced during different growth stages Q(TOT) (J/mL), Q(ExP) (J/mL) and duration of lag-phases λ (h) were obtained by processing calorimetric curves. The sizes of colonies were measured also at the end of growth using microscope. The data obtained together with calculated heat yield coefficient Y(Q) (J/cfu) allowed to analyze and describe quantitatively the growth of individual colonies and develop a model of multistage growth of a typical colony of L. lactis in 1% agar gel. Microcalorimetry used in combination with other relevant methods is a very powerful and precise tool in studying solid-state fermentations.
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Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 2011; 476:355-9. [PMID: 21832992 DOI: 10.1038/nature10333] [Citation(s) in RCA: 405] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 06/23/2011] [Indexed: 01/19/2023]
Abstract
Advanced (long-chain) fuels and chemicals are generated from short-chain metabolic intermediates through pathways that require carbon-chain elongation. The condensation reactions mediating this carbon-carbon bond formation can be catalysed by enzymes from the thiolase superfamily, including β-ketoacyl-acyl-carrier protein (ACP) synthases, polyketide synthases, 3-hydroxy-3-methylglutaryl-CoA synthases, and biosynthetic thiolases. Pathways involving these enzymes have been exploited for fuel and chemical production, with fatty-acid biosynthesis (β-ketoacyl-ACP synthases) attracting the most attention in recent years. Degradative thiolases, which are part of the thiolase superfamily and naturally function in the β-oxidation of fatty acids, can also operate in the synthetic direction and thus enable carbon-chain elongation. Here we demonstrate that a functional reversal of the β-oxidation cycle can be used as a metabolic platform for the synthesis of alcohols and carboxylic acids with various chain lengths and functionalities. This pathway operates with coenzyme A (CoA) thioester intermediates and directly uses acetyl-CoA for acyl-chain elongation (rather than first requiring ATP-dependent activation to malonyl-CoA), characteristics that enable product synthesis at maximum carbon and energy efficiency. The reversal of the β-oxidation cycle was engineered in Escherichia coli and used in combination with endogenous dehydrogenases and thioesterases to synthesize n-alcohols, fatty acids and 3-hydroxy-, 3-keto- and trans-Δ(2)-carboxylic acids. The superior nature of the engineered pathway was demonstrated by producing higher-chain linear n-alcohols (C ≥ 4) and extracellular long-chain fatty acids (C > 10) at higher efficiency than previously reported. The ubiquitous nature of β-oxidation, aldehyde/alcohol dehydrogenase and thioesterase enzymes has the potential to enable the efficient synthesis of these products in other industrial organisms.
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Papagianni M, Avramidis N. Lactococcus lactis as a cell factory: A twofold increase in phosphofructokinase activity results in a proportional increase in specific rates of glucose uptake and lactate formation. Enzyme Microb Technol 2011; 49:197-202. [DOI: 10.1016/j.enzmictec.2011.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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Godinho LM, de Sá-Nogueira I. Characterization and regulation of a bacterial sugar phosphatase of the haloalkanoate dehalogenase superfamily, AraL, from Bacillus subtilis. FEBS J 2011; 278:2511-24. [PMID: 21575135 PMCID: PMC3207120 DOI: 10.1111/j.1742-4658.2011.08177.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AraL from Bacillus subtilis is a member of the ubiquitous haloalkanoate dehalogenase superfamily. The araL gene has been cloned, over-expressed in Escherichia coli and its product purified to homogeneity. The enzyme displays phosphatase activity, which is optimal at neutral pH (7.0) and 65 °C. Substrate screening and kinetic analysis showed AraL to have low specificity and catalytic activity towards several sugar phosphates, which are metabolic intermediates of the glycolytic and pentose phosphate pathways. On the basis of substrate specificity and gene context within the arabinose metabolic operon, a putative physiological role of AraL in the detoxification of accidental accumulation of phosphorylated metabolites has been proposed. The ability of AraL to catabolize several related secondary metabolites requires regulation at the genetic level. In the present study, using site-directed mutagenesis, we show that the production of AraL is regulated by a structure in the translation initiation region of the mRNA, which most probably blocks access to the ribosome-binding site, preventing protein synthesis. Members of haloalkanoate dehalogenase subfamily IIA and IIB are characterized by a broad-range and overlapping specificity anticipating the need for regulation at the genetic level. We provide evidence for the existence of a genetic regulatory mechanism controlling the production of AraL.
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Affiliation(s)
- Lia M Godinho
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, Caparica, Portugal
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Cao R, Zeidan AA, Rådström P, van Niel EWJ. Inhibition kinetics of catabolic dehydrogenases by elevated moieties of ATP and ADP--implication for a new regulation mechanism in Lactococcus lactis. FEBS J 2010; 277:1843-52. [PMID: 20193044 DOI: 10.1111/j.1742-4658.2010.07601.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
ATP and ADP inhibit, in varying degrees, several dehydrogenases of the central carbon metabolism of Lactococcus lactis ATCC 19435 in vitro, i.e. glyceraldehyde-3-phosphate dehydrogenase (GAPDH), lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH). Here we demonstrate mixed inhibition for GAPDH and competitive inhibition for LDH and ADH by adenine nucleotides in single inhibition studies. The nonlinear negative co-operativity was best modelled with Hill-type kinetics, showing greater flexibility than the usual parabolic inhibition equation. Because these natural inhibitors are present simultaneously in the cytoplasm, multiple inhibition kinetics was determined for each dehydrogenase. For ADH and LDH, the inhibitor combinations ATP plus NAD and ADP plus NAD are indifferent to each other. Model discrimination suggested that the weak allosteric inhibition of GAPDH had no relevance when multiple inhibitors are present. Interestingly, with ADH and GAPDH the combination of ATP and ADP exhibits lower dissociation constants than with either inhibitor alone. Moreover, the concerted inhibition of ADH and GAPDH, but not of LDH, shows synergy between the two nucleotides. Similar kinetics, but without synergies, were found for horse liver and yeast ADHs, indicating that dehydrogenases can be modulated by these nucleotides in a nonlinear manner in many organisms. The action of an elevated pool of ATP and ADP may effectively inactivate lactococcal ADH, but not GAPDH and LDH, providing leverage for the observed metabolic shift to homolactic acid formation in lactococcal resting cells on maltose. Therefore, we interpret these results as a regulation mechanism contributing to readjusting the flux of ATP production in L. lactis.
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Affiliation(s)
- Rong Cao
- Department of Applied Microbiology, Lund University, Lund, Sweden
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Romero-Garcia S, Hernández-Bustos C, Merino E, Gosset G, Martinez A. Homolactic fermentation from glucose and cellobiose using Bacillus subtilis. Microb Cell Fact 2009; 8:23. [PMID: 19383131 PMCID: PMC2680810 DOI: 10.1186/1475-2859-8-23] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 04/21/2009] [Indexed: 11/15/2022] Open
Abstract
Backgroung Biodegradable plastics can be made from polylactate, which is a polymer made from lactic acid. This compound can be produced from renewable resources as substrates using microorganisms. Bacillus subtilis is a Gram-positive bacterium recognized as a GRAS microorganism (generally regarded as safe) by the FDA. B. subtilis produces and secretes different kind of enzymes, such as proteases, cellulases, xylanases and amylases to utilize carbon sources more complex than the monosaccharides present in the environment. Thus, B. subtilis could be potentially used to hydrolyze carbohydrate polymers contained in lignocellulosic biomass to produce chemical commodities. Enzymatic hydrolysis of the cellulosic fraction of agroindustrial wastes produces cellobiose and a lower amount of glucose. Under aerobic conditions, B. subtilis grows using cellobiose as substrate. Results In this study, we proved that under non-aerated conditions, B. subtilis ferments cellobiose to produce L-lactate with 82% of the theoretical yield, and with a specific rate of L-lactate production similar to that one obtained fermenting glucose. Under fermentative conditions in a complex media supplemented with glucose, B. subtilis produces L-lactate and a low amount of 2,3-butanediol. To increase the L-lactate production of this organism, we generated the B subtilis CH1 alsS- strain that lacks the ability to synthesize 2,3-butanediol. Inactivation of this pathway, that competed for pyruvate availability, let a 15% increase in L-lactate yield from glucose compared with the parental strain. CH1 alsS- fermented 5 and 10% of glucose to completion in mineral medium supplemented with yeast extract in four and nine days, respectively. CH1 alsS- produced 105 g/L of L-lactate in this last medium supplemented with 10% of glucose. The L-lactate yield was up to 95% using mineral media, and the optical purity of L-lactate was of 99.5% since B. subtilis has only one gene (lctE) that exclusively encodes a L-lactate deshydrogenase. Conclusion This study shows that by taking advantage of the cellobiose utilization capability and osmotic stress high resistance of B. subtilis, a robust process for L-lactate production can be developed.
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Affiliation(s)
- Susana Romero-Garcia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A,P, 510-3 Cuernavaca, Mor, 62250, México.
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Razvi A, Zhang Z, Lan CQ. Effects of glucose and nitrogen source concentration on batch fermentation kinetics ofLactococcus lactisunder hemin-stimulated respirative condition. Biotechnol Prog 2008; 24:852-8. [DOI: 10.1002/btpr.16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Orencio-Trejo M, Flores N, Escalante A, Hernández-Chávez G, Bolívar F, Gosset G, Martinez A. Metabolic regulation analysis of an ethanologenic Escherichia coli strain based on RT-PCR and enzymatic activities. BIOTECHNOLOGY FOR BIOFUELS 2008; 1:8. [PMID: 18471274 PMCID: PMC2396614 DOI: 10.1186/1754-6834-1-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 05/01/2008] [Indexed: 05/07/2023]
Abstract
BACKGROUND A metabolic regulation study was performed, based upon measurements of enzymatic activities, fermentation performance, and RT-PCR analysis of pathways related to central carbon metabolism, in an ethanologenic Escherichia coli strain (CCE14) derived from lineage C. In comparison with previous engineered strains, this E coli derivative has a higher ethanol production rate in mineral medium, as a result of the elevated heterologous expression of the chromosomally integrated genes encoding PDCZm and ADHZm (pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis). It is suggested that this behavior might be due to lineage differences between E. coli W and C. RESULTS This study demonstrated that the glycolytic flux is controlled, in this case, by reactions outside glycolysis, i.e., the fermentative pathways. Changes in ethanol production rate in this ethanologenic strain result in low organic acid production rates, and high glycolytic and ethanologenic fluxes, that correlate with enhanced transcription and enzymatic activity levels of PDCZm and ADHZm. Furthermore, a higher ethanol yield (90% of the theoretical) in glucose-mineral media was obtained with CCE14 in comparison with previous engineered E. coli strains, such as KO11, that produces a 70% yield under the same conditions. CONCLUSION Results suggest that a higher ethanol formation rate, caused by ahigher PDCZm and ADHZm activities induces a metabolic state that cells compensate through enhanced glucose transport, ATP synthesis, and NAD-NADH+H turnover rates. These results show that glycolytic enzymatic activities, present in E. coli W and C under fermentative conditions, are sufficient to contend with increases in glucose consumption and product formation rates.
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Affiliation(s)
- Montserrat Orencio-Trejo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Georgina Hernández-Chávez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
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