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Zhang J, Sun T, Zhang W, Chen L. Identification of acidic stress-responsive genes and acid tolerance engineering in Synechococcus elongatus PCC 7942. Appl Microbiol Biotechnol 2024; 108:115. [PMID: 38204133 PMCID: PMC10781874 DOI: 10.1007/s00253-023-12984-5] [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: 09/22/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Cyanobacteria are excellent autotrophic photosynthetic chassis employed in synthetic biology, and previous studies have suggested that they have alkaline tolerance but low acid tolerance, significantly limiting their productivity as photosynthetic chassis and necessitating investigations into the acid stress resistance mechanism. In this study, differentially expressed genes were obtained by RNA sequencing-based comparative transcriptomic analysis under long-term acidic stress conditions and acidic shock treatment, in the model cyanobacterium Synechococcus elongatus PCC 7942. A pathway enrichment analysis revealed the upregulated and downregulated pathways during long-term acidic and shock stress treatment. The subsequent single gene knockout and phenotype analysis showed that under acidic stress conditions, the strains with chlL, chlN, pex, synpcc7942_2038, synpcc7942_1890, or synpcc7942_2547 knocked out grew worse than the wild type, suggesting their involvement in acid tolerance. This finding was further confirmed by introducing the corresponding genes back into the knockout mutant individually. Moreover, individual overexpression of the chlL and chlN genes in the wild type successfully improved the tolerance of S. elongatus PCC 7942 to acidic stress. This work successfully identified six genes involved in acidic stress responses, and overexpressing chIL or chIN individually successfully improved acid tolerance in S. elongatus PCC 7942, providing valuable information to better understand the acid resistance mechanism in S. elongatus PCC 7942 and novel insights into the robustness and tolerance engineering of cyanobacterial chassis. KEY POINTS: • DEGs were identified by RNA-seq based transcriptomics analysis in response to acidic stress in S. elongatus PCC 7942. • Six genes were identified to be involved in acid tolerance in S. elongatus PCC 7942. • Overexpression of chIL or chIN individually successfully improved the acid tolerance of S. elongatus PCC 7942.
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Affiliation(s)
- Jie Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China.
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Yang H, Hao L, Jin Y, Huang J, Zhou R, Wu C. Functional roles and engineering strategies to improve the industrial functionalities of lactic acid bacteria during food fermentation. Biotechnol Adv 2024; 74:108397. [PMID: 38909664 DOI: 10.1016/j.biotechadv.2024.108397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/20/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
In order to improve the flavor profiles, food security, probiotic effects and shorten the fermentation period of traditional fermented foods, lactic acid bacteria (LAB) were often considered as the ideal candidate to participate in the fermentation process. In general, LAB strains possessed the ability to develop flavor compounds via carbohydrate metabolism, protein hydrolysis and amino acid metabolism, lipid hydrolysis and fatty acid metabolism. Based on the functional properties to inhibit spoilage microbes, foodborne pathogens and fungi, those species could improve the safety properties and prolong the shelf life of fermented products. Meanwhile, influence of LAB on texture and functionality of fermented food were also involved in this review. As for the adverse effect carried by environmental challenges during fermentation process, engineering strategies based on exogenous addition, cross protection, and metabolic engineering to improve the robustness and of LAB were also discussed in this review. Besides, this review also summarized the potential strategies including microbial co-culture and metabolic engineering for improvement of fermentation performance in LAB strains. The authors hope this review could contribute to provide an understanding and insight into improving the industrial functionalities of LAB.
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Affiliation(s)
- Huan Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Liying Hao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.
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Romano P, Simonetti S, Gambi MC, Luckenbach T, Zupo V, Corsi I. Preliminary investigation on the potential involvement of an ABC-like gene in Halomicronema metazoicum (Cyanobacteria) tolerance to low seawater pH in an ocean acidification scenario. MARINE POLLUTION BULLETIN 2024; 205:116584. [PMID: 38878421 DOI: 10.1016/j.marpolbul.2024.116584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 07/24/2024]
Abstract
Decreasing ocean surface pH, called ocean acidification (OA), is among the major risks for marine ecosystems due to human-driven atmospheric pCO2 increase. Understanding the molecular mechanisms of adaptation enabling marine species to tolerate a lowered seawater pH could support predictions of consequences of future OA scenarios for marine life. This study examined whether the ATP-binding cassette (ABC)-like gene slr2019 confers tolerance to the marine cyanobacterium Halomicronema metazoicum to low seawater pH conditions (7.7, 7.2, 6.5) in short- and long-term exposures (7 and 30 d). Photosynthetic pigment content indicated that the species can tolerate all three lowered-pH conditions. At day 7, slr2019 was up-regulated at pH 7.7 while no changes were observed at lower pH. After 30-d exposure, a significant decrease in slr2019 transcript levels was observed in all low-pH treatments. These first results indicate an effect of low pH on the examined transporter expression in H. metazoicum.
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Affiliation(s)
- Patrizia Romano
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Department of BEOM, Napoli, Italy.
| | - Silvia Simonetti
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Integrative Marine Ecology Department, Napoli, Italy.
| | | | - Till Luckenbach
- Department Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Valerio Zupo
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Integrative Marine Ecology Department, Napoli, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy
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Yao S, Tu R, Jin Y, Zhou R, Wu C, Qin J. Improvement of the viability of Tetragenococcus halophilus under acidic stress by forming the biofilm cell structure based on RNA-Seq and iTRAQ analyses. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:3559-3569. [PMID: 38147410 DOI: 10.1002/jsfa.13240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 12/28/2023]
Abstract
BACKGROUND Tetragenococcus halophilus is a halophilic lactic acid bacterium (LAB) isolated from soya sauce moromi. During the production of these fermented foods, acid stress is an inevitable environmental stress. In our previous study, T. halophilus could form biofilms and the cells in the biofilms exhibited higher cell viability under multiple environmental stresses, including acid stress. RESULTS In this study, the effect of preformed T. halophilus biofilms on cell survival, cellular structure, intracellular environment, and the expression of genes and proteins under acid stress was investigated. The result showed that acid stress with pH 4.30 for 1.5 h reduced the live T. halophilus cell count and caused cellular structure damage. However, T. halophilus biofilm cells exhibited greater cell survival under acid stress than the planktonic cells, and biofilm formation reduced the damage of acid stress to the cell membrane and cell wall. The biofilm cells maintained a higher level of H+ -ATPase activity and intracellular ammonia concentration after acid stress. The RNA-Seq and iTRAQ technologies revealed that the genes and proteins associated with ATP production, the uptake of trehalose and N-acetylmuramic acid, the assembly of H+ -ATPase, amino acid biosynthesis and metabolism, ammonia production, fatty acid biosynthesis, CoA biosynthesis, thiamine production, and acetoin biosynthesis might be responsible for the stronger acid tolerance of T. halophilus biofilm cells together. CONCLUSION These findings further explained the mechanisms that allowed LAB biofilm cells to resist environmental stress. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Shangjie Yao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Rongkun Tu
- Luzhou Lao Jiao Co., Ltd., Luzhou, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Jiufu Qin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
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Derunets AS, Selimzyanova AI, Rykov SV, Kuznetsov AE, Berezina OV. Strategies to enhance stress tolerance in lactic acid bacteria across diverse stress conditions. World J Microbiol Biotechnol 2024; 40:126. [PMID: 38446232 DOI: 10.1007/s11274-024-03905-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/21/2024] [Indexed: 03/07/2024]
Abstract
Lactic acid bacteria (LAB) hold significant importance in diverse fields, including food technology, industrial biotechnology, and medicine. As basic components of starter cultures, probiotics, immunomodulators, and live vaccines, LAB cells resist a variety of stressors, including temperature fluctuations, osmotic and pH shocks, exposure to oxidants and ultraviolet radiation, substrate deprivation, mechanical damage, and more. To stay alive in these adversities, LAB employ a wide range of stress response strategies supported by various mechanisms, for example rearrangement of metabolism, expression of specialized biomolecules (e.g., chaperones and antioxidants), exopolysaccharide synthesis, and complex repair and regulatory systems. LAB can coordinate responses to various stressors using global regulators. In this review, we summarize current knowledge about stress response strategies used by LAB and consider mechanisms of response to specific stressful factors, supported by illustrative examples. In addition, we discuss technical approaches to increase the stress resistance of LAB, including pre-adaptation, genetic modification of strains, and adjustment of cultivation conditions. A critical analysis of the recent findings in this field augments comprehension of stress tolerance mechanisms in LAB, paving the way for prospective research directions with implications in fundamental and practical areas.
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Affiliation(s)
- A S Derunets
- National Research Center Kurchatov Institute, Moscow, Russia.
| | | | - S V Rykov
- National Research Center Kurchatov Institute, Moscow, Russia
| | - A E Kuznetsov
- D. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - O V Berezina
- National Research Center Kurchatov Institute, Moscow, Russia
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Li R, Hu Y, Xu Y, Zhou J, Li Y, Liu Q, Yu B. Safety assessment, whole genome sequence, and metabolome analysis of Streptococcus thermophilus CICC 20372 for bone cement fermentation. Arch Microbiol 2023; 206:21. [PMID: 38095705 DOI: 10.1007/s00203-023-03737-z] [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: 09/11/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Bone is a kind of meat processing by-product with high nutritional value but low in calorie, which is a typical food in China and parts of East Asian countries. Microbial fermentation by lactic acid bacteria showed remarkable advantages to increase the absorption of nutrients from bone cement by human body. Streptococcus thermophilus CICC 20372 is proven to be a good starter for bone cement fermentation. No genes encoding virulence traits or virulence factors were found in the genome of S. thermophilus CICC 20372 by a thorough genomic analysis. Its notable absence of antibiotic resistance further solidifies the safety. Furthermore, the genomic analysis identified four types of gene clusters responsible for the synthesis of antimicrobial metabolites. A comparative metabolomic analysis was performed by cultivating the strain in bone cement at 37 °C for 72 h, with the culture in de Man, Rogosa, and Sharpe (MRS) medium as control. Metabolome analysis results highlighted the upregulation of pathways involved in 2-oxocarboxylic acid metabolism, ATP-binding cassette (ABC) transporters, amino acid synthesis, and nucleotide metabolism during bone cement fermentation. S. thermophilus CICC 20372 produces several metabolites with health-promoting function during bone cement fermentation, including indole-3-lactic acid, which is demonstrated ameliorative effects on intestinal inflammation, tumor growth, and gut dysbiosis. In addition, lots of nucleotide and organic acids were accumulated at higher levels, which enriched the fermented bone cement with a variety of nutrients. Collectively, these features endow S. thermophilus CICC 20372 a great potential strain for bone food processing.
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Affiliation(s)
- Rongshan Li
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yangfan Hu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Xu
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
| | - Jinlong Zhou
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
| | - Yunfang Li
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
| | - Qing Liu
- General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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Sepúlveda-Correa A, Monsalve L, Polania J, Mestanza O, Vanegas J. Effect of salinity on genes involved in the stress response in mangrove soils. Antonie Van Leeuwenhoek 2023; 116:1171-1184. [PMID: 37682363 DOI: 10.1007/s10482-023-01856-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/02/2023] [Indexed: 09/09/2023]
Abstract
Mangroves are a challenging ecosystem for the microorganisms that inhabit them, considering they are subjected to stressful conditions such as high and fluctuating salinity. Metagenomic analysis of mangrove soils under contrasting salinity conditions was performed at the mouth of the Ranchera River to the Caribbean Sea in La Guajira, Colombia, using shotgun sequencing and the Illumina Hiseq 2500 platform. Functional gene analysis demonstrated that salinity could influence the abundance of microbial genes involved in osmoprotectant transport, DNA repair, heat shock proteins (HSP), and Quorum Sensing, among others. In total, 135 genes were discovered to be linked to 12 pathways. Thirty-four genes out of 10 pathways had statistical differences for a p-value and FDR < 0.05. UvrA and uvrB (nucleotide excision repair), groEL (HSP), and secA (bacterial secretion system) genes were the most abundant and were enriched by high salinity. The results of this study showed the prevalence of diverse genetic mechanisms that bacteria use as a response to survive in the challenging mangrove, as well as the presence of various genes that are recruited in order to maintain bacterial homeostasis under conditions of high salinity.
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Affiliation(s)
- Alejandro Sepúlveda-Correa
- Natural Sciences Department, Université du Québec en Outaouais, 58 Rue Principale, Ripon, QC, J0V 1V0, Canada
- Universidad Nacional de Colombia Sede Medellín, Cra. 65 #59a-110, Medellín, Colombia
| | | | - Jaime Polania
- Universidad Nacional de Colombia Sede Medellín, Cra. 65 #59a-110, Medellín, Colombia
| | - Orson Mestanza
- Instituto Nacional de Salud, Cápac Yupanqui 1400 - Jesus María, Lima, Perú
| | - Javier Vanegas
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia.
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Gao L, Shi W, Xia X. Genomic Plasticity of Acid-Tolerant Phenotypic Evolution in Acetobacter pasteurianus. Appl Biochem Biotechnol 2023; 195:6003-6019. [PMID: 36738389 DOI: 10.1007/s12010-023-04353-9] [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] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Acetic acid bacteria have a remarkable capacity to cope with elevated concentrations of cytotoxic acetic acid in their fermentation environment. In particular, the high-level acetate tolerance of Acetobacter pasteurianus that occurs in vinegar industrial settings must be constantly selected for. However, the improved acetic acid tolerance is rapidly lost without a selection pressure. To understand genetic and molecular biology of this acquired acetic acid tolerance in A. pasteurianus, we evolved three strains A. pasteurianus CICIM B7003, CICIM B7003-02, and ATCC 33,445 over 960 generations (4 months) in two initial acetic acids of 20 g·L-1 and 30 g·L-1, respectively. An acetic acid-adapted strain M20 with significantly improved specific growth rate of 0.159 h-1 and acid productivity of 1.61 g·L-1·h-1 was obtained. Comparative genome analysis of six evolved strains revealed that the genetic variations of adaptation were mainly focused on lactate metabolism, membrane proteins, transcriptional regulators, transposases, replication, and repair system. Among of these, lactate dehydrogenase, acetolactate synthase, glycosyltransferase, ABC transporter ATP-binding protein, two-component regulatory systems, the type II toxin-antitoxin system (RelE/RelB/StbE), exodeoxyribonuclease III, type I restriction endonuclease, tRNA-uridine 2-sulfurtransferase, and transposase might collaboratively contribute to the improved acetic acid tolerance in A. pasteurianus strains. The balance between repair factors and transposition variations might be the basis for genomic plasticity of A. pasteurianus strains, allowing the survival of populations and their offspring in acetic acid stress fluctuations. These observations provide important insights into the nature of acquired acetic acid tolerance phenotype and lay a foundation for future genetic manipulation of these strains.
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Affiliation(s)
- Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Wei Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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Li A, Fan J, Jia Y, Tang X, Chen J, Shen C. Phenotype and metabolism alterations in PCB-degrading Rhodococcus biphenylivorans TG9 T under acid stress. J Environ Sci (China) 2023; 127:441-452. [PMID: 36522076 DOI: 10.1016/j.jes.2022.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 06/17/2023]
Abstract
Environmental acidification impairs microorganism diversity and their functions on substance transformation. Rhodococcus is a ubiquitously distributed genus for contaminant detoxification in the environment, and it can also adapt a certain range of pH. This work interpreted the acid responses from both phenotype and metabolism in strain Rhodococcus biphenylivorans TG9T (TG9) induced at pH 3. The phenotype alterations were described with the number of culturable and viable cells, intracellular ATP concentrations, cell shape and entocyte, degradation efficiency of polychlorinated biphenyl (PCB) 31 and biphenyl. The number of culturable cells maintained rather stable within the first 10 days, even though the other phenotypes had noticeable alterations, indicating that TG9 possesses certain capacities to survive under acid stress. The metabolism responses were interpreted based on transcription analyses with four treatments including log phase (LP), acid-induced (PER), early recovery after removing acid (RE) and later recovery (REL). With the overview on the expression regulations among the 4 treatments, the RE sample presented more upregulated and less downregulated genes, suggesting that its metabolism was somehow more active after recovering from acid stress. In addition, the response mechanism was interpreted on 10 individual metabolism pathways mainly covering protein modification, antioxidation, antipermeability, H+ consumption, neutralization and extrusion. Furthermore, the transcription variations were verified with RT-qPCR on 8 genes with 24-hr, 48-hr and 72-hr acid treatment. Taken together, TG9 possesses comprehensive metabolism strategies defending against acid stress. Consequently, a model was built to provide an integrate insight to understand the acid resistance/tolerance metabolisms in microorganisms.
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Affiliation(s)
- Aili Li
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiahui Fan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yangyang Jia
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xianjin Tang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingwen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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10
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Jiang Z, Lu J, Tong Y, Yang H, Feng S. Enhancement of acid tolerance of Escherichia coli by introduction of molecule chaperone CbpA from extremophile. World J Microbiol Biotechnol 2023; 39:158. [PMID: 37046107 DOI: 10.1007/s11274-023-03613-4] [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: 02/24/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023]
Abstract
Molecular chaperone CbpA from extreme acidophile Acidithiobacillus caldus was applied to improve acid tolerance of Escherichia coli via CRISPR/Cas9. Cell growth and viability of plasmid complementary strain indicated the importance of cbpAAc for bacteria acid tolerance. With in situ gene replacement by CRISPR/Cas9 system, colony formation unit (CFU) of genome recombinant strain BL21-ΔcbpA/AccbpA showed 7.7 times higher cell viability than deficient strain BL21-ΔcbpA and 2.3 times higher than wild type. Cell morphology observation using Field Emission Scanning Electron Microscopy (FESEM) revealed cell breakage of BL21-ΔcbpA and significant recovery of BL21-ΔcbpA/AccbpA. The intracellular ATP level of all strains gradually decreased along with the increased stress time. Particularly, the value of recombinant strain was 56.0% lower than that of deficient strain after 5 h, indicating that the recombinant strain consumed a lot of energy to resist acid stress. The arginine concentration in BL21-ΔcbpA/AccbpA was double that of BL21-ΔcbpA, while the aspartate and glutamate contents were 14.8% and 6.2% higher, respectively, compared to that of wild type. Moreover, RNA-Seq analysis examined 93 genes down-regulated in BL21-ΔcbpA compared to wild type strain, while 123 genes were up-regulated in BL21-ΔcbpA/AccbpA compared to BL21-ΔcbpA, with an emphasis on energy metabolism, transport, and cell components. Finally, the working model in response to acid stress of cbpA from A. caldus was developed. This study constructed a recombinant strain resistant to acid stress and also provided a reference for enhancing microorganisms' robustness to various conditions.
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Affiliation(s)
- Zhenming Jiang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jie Lu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, China
| | - Hailin Yang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Shoushuai Feng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
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11
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Recent advances in genetic tools for engineering probiotic lactic acid bacteria. Biosci Rep 2023; 43:232386. [PMID: 36597861 PMCID: PMC9842951 DOI: 10.1042/bsr20211299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
Synthetic biology has grown exponentially in the last few years, with a variety of biological applications. One of the emerging applications of synthetic biology is to exploit the link between microorganisms, biologics, and human health. To exploit this link, it is critical to select effective synthetic biology tools for use in appropriate microorganisms that would address unmet needs in human health through the development of new game-changing applications and by complementing existing technological capabilities. Lactic acid bacteria (LAB) are considered appropriate chassis organisms that can be genetically engineered for therapeutic and industrial applications. Here, we have reviewed comprehensively various synthetic biology techniques for engineering probiotic LAB strains, such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 mediated genome editing, homologous recombination, and recombineering. In addition, we also discussed heterologous protein expression systems used in engineering probiotic LAB. By combining computational biology with genetic engineering, there is a lot of potential to develop next-generation synthetic LAB with capabilities to address bottlenecks in industrial scale-up and complex biologics production. Recently, we started working on Lactochassis project where we aim to develop next generation synthetic LAB for biomedical application.
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Zaccaria E, Klaassen T, Alleleyn AM, Boekhorst J, Chervaux C, Smokvina T, Troost FJ, Kleerebezem M. L. rhamnosus CNCM I-3690 survival, adaptation, and small bowel microbiome impact in human. Gut Microbes 2023; 15:2244720. [PMID: 37589280 PMCID: PMC10438856 DOI: 10.1080/19490976.2023.2244720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/05/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
Fermented foods and beverages are a significant source of dietary bacteria that enter the gastrointestinal (GI) tract. However, little is known about how these microbes survive and adapt to the small intestinal environment. Colony-forming units (CFU) enumeration and viability qPCR of Lacticaseibacillus rhamnosus CNCM I-3690 in the ileal effluent of 10 ileostomy subjects during 12-h post consumption of a dairy product fermented with this strain demonstrated the high level of survival of this strain during human small intestine passage. Metatranscriptome analyses revealed the in situ transcriptome of L. rhamnosus in the small intestine, which was contrasted with transcriptome data obtained from in vitro cultivation. These comparative analyses revealed substantial metabolic adaptations of L. rhamnosus during small intestine transit, including adjustments of carbohydrate metabolism, surface-protein expression, and translation machinery. The prominent presence of L. rhamnosus in the effluent samples did not elicit an appreciable effect on the composition of the endogenous small intestine microbiome, but significantly altered the ecosystem's overall activity profile, particularly of pathways associated with carbohydrate metabolism. Strikingly, two of the previously recognized gut-brain metabolic modules expressed in situ by L. rhamnosus (inositol degradation and glutamate synthesis II) are among the most dominantly enriched activities in the ecosystem's activity profile. This study establishes the survival capacity of L. rhamnosus in the human small intestine and highlights its functional adjustment in situ, which we postulate to play a role in the probiotic effects associated with this strain.
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Affiliation(s)
- Edoardo Zaccaria
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Tim Klaassen
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
- Food Innovation and Health, Department of Human Biology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Venlo, The Netherlands
| | - Annick M.E. Alleleyn
- Food Innovation and Health, Department of Human Biology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Venlo, The Netherlands
| | - Jos Boekhorst
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Tamara Smokvina
- Danone Nutricia Research, Centre Daniel Carasso, Palaiseau, France
| | - Freddy J. Troost
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Michiel Kleerebezem
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
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Hu M, Bao W, Peng Q, Hu W, Yang X, Xiang Y, Yan X, Li M, Xu P, He Q, Yang S. Metabolic engineering of Zymomonas mobilis for co-production of D-lactic acid and ethanol using waste feedstocks of molasses and corncob residue hydrolysate. Front Bioeng Biotechnol 2023; 11:1135484. [PMID: 36896016 PMCID: PMC9989019 DOI: 10.3389/fbioe.2023.1135484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Lactate is the precursor for polylactide. In this study, a lactate producer of Z. mobilis was constructed by replacing ZMO0038 with LmldhA gene driven by a strong promoter PadhB, replacing ZMO1650 with native pdc gene driven by Ptet, and replacing native pdc with another copy of LmldhA driven by PadhB to divert carbon from ethanol to D-lactate. The resultant strain ZML-pdc-ldh produced 13.8 ± 0.2 g/L lactate and 16.9 ± 0.3 g/L ethanol using 48 g/L glucose. Lactate production of ZML-pdc-ldh was further investigated after fermentation optimization in pH-controlled fermenters. ZML-pdc-ldh produced 24.2 ± 0.6 g/L lactate and 12.9 ± 0.8 g/L ethanol as well as 36.2 ± 1.0 g/L lactate and 40.3 ± 0.3 g/L ethanol, resulting in total carbon conversion rate of 98.3% ± 2.5% and 96.2% ± 0.1% with final product productivity of 1.9 ± 0.0 g/L/h and 2.2 ± 0.0 g/L/h in RMG5 and RMG12, respectively. Moreover, ZML-pdc-ldh produced 32.9 ± 0.1 g/L D-lactate and 27.7 ± 0.2 g/L ethanol as well as 42.8 ± 0.0 g/L D-lactate and 53.1 ± 0.7 g/L ethanol with 97.1% ± 0.0% and 99.1% ± 0.8% carbon conversion rate using 20% molasses or corncob residue hydrolysate, respectively. Our study thus demonstrated that it is effective for lactate production by fermentation condition optimization and metabolic engineering to strengthen heterologous ldh expression while reducing the native ethanol production pathway. The capability of recombinant lactate-producer of Z. mobilis for efficient waste feedstock conversion makes it a promising biorefinery platform for carbon-neutral biochemical production.
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Affiliation(s)
- Mimi Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Weiwei Bao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Qiqun Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Wei Hu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Xinyu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Yan Xiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Xiongying Yan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd., Kaihua County, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiaoning He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
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Tian W, Qin J, Lian C, Yao Q, Wang X. Identification of a major facilitator superfamily protein that is beneficial to L-lactic acid production by Bacillus coagulans at low pH. BMC Microbiol 2022; 22:310. [PMID: 36536285 PMCID: PMC9764580 DOI: 10.1186/s12866-022-02736-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Product inhibition is one of the major problems in lactic acid (LA) fermentation. Our previous study revealed that Bacillus coagulans 2-6 was an efficient producer of high-optical-purity L-LA. Its mutant strain B. coagulans Na-2 has better resistance to sodium lactate stress but the resistance mechanism has not been understood. RESULTS In this study, the whole-genome sequencing of B. coagulans Na-2 was performed and one mutant gene mfs coding for the major facilitator superfamily (MFS) protein was revealed by comparative genome analysis. Ten mutation sites were identified between the wild (MFS-2-6) and mutant (MFS-Na-2) proteins, among which T127A and N154T were predicted locating in the center of the transmembrane transport channel. The MFS-2-6 and MFS-Na-2 were expressed separately in a genetically operable strain, B. coagulans DSM1, using the genes' native promoter. The expression of the two MFS proteins had no effect and a negative effect on L-LA production when the pH was controlled at 6.0 and 7.0 by sodium hydroxide, respectively. However, 4.2 and 4.6-fold of L-LA concentrations were obtained at pH 5.0 by the strains expressing MFS-2-6 and MFS-Na-2 than that by the control strain, respectively. The intracellular pH values of the strains expressing MFS-2-6 and MFS-Na-2 were approximately 0.69 and 0.45 higher than that of the control strain during pH-controlled fermentation at 5.0. Results suggest that the expression of MFS-2-6 and MFS-Na-2 were both conducive to L-LA production at low pH, while the better performance of the latter was probably due to the more appropriate intracellular pH during the whole fermentation process. CONCLUSIONS The MFS protein identified here can improve the ability of B. coagulans to resist acidic environments and produce more L-LA at low pH. The MFS protein has an application potential in environment-friendly L-LA production.
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Affiliation(s)
- Wenzhe Tian
- grid.440653.00000 0000 9588 091XCollege of Pharmacy, Binzhou Medical University, Yantai, 264003 China
| | - Jiayang Qin
- grid.440653.00000 0000 9588 091XCollege of Pharmacy, Binzhou Medical University, Yantai, 264003 China
| | - Congcong Lian
- grid.440653.00000 0000 9588 091XCollege of Pharmacy, Binzhou Medical University, Yantai, 264003 China
| | - Qingshou Yao
- grid.440653.00000 0000 9588 091XCollege of Pharmacy, Binzhou Medical University, Yantai, 264003 China
| | - Xiuwen Wang
- grid.440653.00000 0000 9588 091XCollege of Pharmacy, Binzhou Medical University, Yantai, 264003 China
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Simonetti S, Zupo V, Gambi MC, Luckenbach T, Corsi I. Unraveling cellular and molecular mechanisms of acid stress tolerance and resistance in marine species: New frontiers in the study of adaptation to ocean acidification. MARINE POLLUTION BULLETIN 2022; 185:114365. [PMID: 36435021 DOI: 10.1016/j.marpolbul.2022.114365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Since the industrial revolution, fossil fuel combustion has led to a 30 %-increase of the atmospheric CO2 concentration, also increasing the ocean partial CO2 pressure. The consequent lowered surface seawater pH is termed ocean acidification (OA) and severely affects marine life on a global scale. Cellular and molecular responses of marine species to lowered seawater pH have been studied but information on the mechanisms driving the tolerance of adapted species to comparatively low seawater pH is limited. Such information may be obtained from species inhabiting sites with naturally low water pH that have evolved remarkable abilities to tolerate such conditions. This review gathers information on current knowledge about species naturally facing low water pH conditions and on cellular and molecular adaptive mechanisms enabling the species to survive under, and even benefit from, adverse pH conditions. Evidences derived from case studies on naturally acidified systems and on resistance mechanisms will guide predictions on the consequences of future adverse OA scenarios for marine biodiversity.
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Affiliation(s)
- Silvia Simonetti
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Dep.t of BluBioTech, Napoli, Italy.
| | - Valerio Zupo
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Dep.t of BluBioTech, Napoli, Italy.
| | | | - Till Luckenbach
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy.
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Revealing novel synergistic defense and acid tolerant performance of Escherichia coli in response to organic acid stimulation. Appl Microbiol Biotechnol 2022; 106:7577-7594. [DOI: 10.1007/s00253-022-12241-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
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Zhang X, Zheng Y, Kumar Awasthi M, Zhou C, Barba FJ, Cai Z, Liu L, Rene ER, Pan D, Cao J, Sindhu R, Xia Q. Strategic thermosonication-mediated modulation of lactic acid bacteria acidification kinetics for enhanced (post)-fermentation performance. BIORESOURCE TECHNOLOGY 2022; 361:127739. [PMID: 35940323 DOI: 10.1016/j.biortech.2022.127739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
This study explored the feasibility of thermosonication (TS)-prestressed inoculum with different fermentation patterns for regulating microbial (post)-fermentation acidification kinetics. Through a Box-Behnken design, stimulative (20 min, 400 W, 33 kHz, 25 °C) and inhibitive (10 min, 600 W, 33 kHz, 20 °C) effects on the acidification capability of Lactobacillus plantarum A3 were achieved without observing greatly activated/inactivated strains growth, further confirmed by lactose fermentation performed by Streptococcus thermophilus and Lactobacillus bulgaricus. Lactic acid was the major contributing factor responsible for TS-induced acidification modifications corresponding to the potential fluctuations of CoA biosynthesis, fatty acid degradation and chain elongation pathways to TS prestress. Microscopy observations and quantitative extracellular substance assays showed palpable stress disturbance on microbes, but causing insignificant effects on product characteristics. This investigation demonstrated the potential of controlled sonication prestress strategies to achieve dual engineering effects on microbial metabolic behavior, for alleviating post-acidification problem or enhancing process efficiencies.
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Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Yuanrong Zheng
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, Shaanxi Province, China
| | - Changyu Zhou
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Francisco J Barba
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine Department, Faculty of Pharmacy, Universitat de València, Avda. Vicent Andrés Estellés, s/n, 46100 Burjassot, València, Spain
| | - Zhendong Cai
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Lianliang Liu
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2601DA Delft, the Netherlands
| | - Daodong Pan
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China
| | - Jinxuan Cao
- School of Food and Health, Beijing Technology and Business University, 11 Fucheng Road, Beijing 100048, China
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 691 505, Kerala, India
| | - Qiang Xia
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo 315211, China; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa 999078, Macau.
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18
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Comparative transcriptome analysis reveals the contribution of membrane transporters to acid tolerance in Lactococcus lactis. J Biotechnol 2022; 357:9-17. [PMID: 35963594 DOI: 10.1016/j.jbiotec.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/08/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022]
Abstract
Acid stress caused by the accumulation of acidic metabolites severely affects the fermentation performance of lactic acid bacteria. In this study, to overcome the impact of acid stress during growth, nine membrane transporters were introduced in Lactococcus lactis NZ9000 to study their effects on acid tolerance. The engineered strains that overexpressed the metal ATP-binding cassette (ABC) transporters zitP (metal ABC transporter permease) and zitQ (metal ABC transporter ATP-binding protein) exhibited 14.5 and 9.5-fold higher survival rates, respectively, at pH 4.0 for 4 h than the control strain. During acid stress, the two recombinant strains maintained relatively higher ATP concentrations, i.e., 7.7- and 11.7-fold higher, respectively, than the control strain at pH 4.0 for 3 h. Subsequently, transcriptome analysis revealed that genes associated with ABC transporters, metal ion transport, transcriptional regulation, and stress response exhibited differentially expressed. The transcriptional level of ecfA2 gene (energy-coupling factor transporter ATPase) was substantially higher in L. lactis (ZitQ) during acid stress, and the ecfA2 gene was overexpressed in L. lactis. This recombinant strain L. lactis (EcfA2) exhibited a 598.7-fold higher survival rate than the control strain at pH 4.0 for 4 h. This study showed that the membrane transporters ZitP and ZitQ could increase acid tolerance and provided a strategy for constructing robust strains that can be used in food industry.
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Dai C, Wu H, Wang X, Zhao K, Lu Z. Network and meta-omics reveal the cooperation patterns and mechanisms in an efficient 1,4-dioxane-degrading microbial consortium. CHEMOSPHERE 2022; 301:134723. [PMID: 35489450 DOI: 10.1016/j.chemosphere.2022.134723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/09/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
1,4-Dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mixed cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial consortium CH1. A 1,4-dioxane-degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and had a potential of being one of the important degraders due to its high relative abundance, highly expressed monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium could be involved in the intermediates metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) differentially high-expressed. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators cooperated with ZM13 in the way of providing amino acids or fatty acids, as well as relieving environmental stresses to promote biodegradation. These results provide new insights into our understandings of the microbial interactions during 1,4-dioxane degradation, and have important implications for predicting microbial cooperation and constructing efficient and stable synthetic 1,4-dioxane-degrading consortia for practical remediation.
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Affiliation(s)
- Chuhan Dai
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China.
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Yao S, Li S, Zhan Y, Wan C. Proteome-wide analysis of stress response to temperature in Sulfolobus islandicus. J Proteomics 2022; 266:104681. [PMID: 35842219 DOI: 10.1016/j.jprot.2022.104681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 10/17/2022]
Abstract
Sulfolobus islandicus is thermophilic archaea that live in an extreme environment of 75 °C-80 °C and pH 2-3. Currently, the molecular mechanism of archaeal adaptation to high temperatures and the stability of proteins at high temperatures are still unclear. This study utilizes proteomics to analyze the differential expression of S. islandicus proteins at different temperatures. We found that ribosomes, glycolysis, nucleotide metabolism, RNA metabolism, transport system, and sulfur metabolism are all affected by temperature. Methylation modification of some proteins changed with temperature. Thermal proteome profiling (TPP) was used to analyze the thermal stability of proteins under 65 °C-85 °C growth conditions. It is suggested that the Tm values of proteins are mainly distributed around the optimum growth temperature (OGT). The proteins in the glycolysis pathway had high thermal stability. Meanwhile, proteins related to DNA replication and translation showed low thermal stability. The protein thermal stability of S. islandicus cultured under 65 °C and 85 °C was higher than that of 75 °C. Our study reveals that S. islandicus may adapt to temperature changes by regulating protein synthesis and carbon metabolism pathways, changing post-translational modifications, and improving protein stability at the same time. SIGNIFICANCE: The molecular mechanism of archaeal adaptation to high temperatures and the stability of proteins at high temperatures are still unclear. Our proteomics study identified 477 differentially expressed proteins of S. islandicus at different temperatures, suggesting that ribosomes, glycolysis, nucleotide metabolism, RNA metabolism, transport system, and sulfur metabolism are affected by temperature. Meanwhile, we found that methylation modification of some proteins changed with temperature. To evaluate the thermal stability of the proteome, we performed thermal proteome profiling to analyze the Tm of proteins under 65 °C-85 °C growth conditions. Tm values of proteins are mainly distributed around the optimum growth temperature. The proteins in the glycolysis pathway had high thermal stability. Meanwhile, proteins related to DNA replication and translation showed low thermal stability. Our study reveals that S. islandicus may adapt to temperature changes by regulating protein synthesis and carbon metabolism pathways, changing post-translational modifications, and improving protein stability at the same time.
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Affiliation(s)
- Sheng Yao
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Sige Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yuyue Zhan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.
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Ribosome Profiling Reveals Genome-Wide Cellular Translational Regulation in Lacticaseibacillus rhamnosus ATCC 53103 under Acid Stress. Foods 2022; 11:foods11101411. [PMID: 35626981 PMCID: PMC9140532 DOI: 10.3390/foods11101411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
During fermentation and food processing, Lacticaseibacillus rhamnosus ATCC 53103 can encounter many adverse conditions, and acid stress is one of them. The purpose of the present study was to investigate the influence of acid stress on the global translational and transcriptional regulation of Lacticaseibacillus rhamnosus ATCC 53103. Two pH values (pH 6.0 vs. pH 5.0) were applied, the effects of which were studied via ribosome profiling and RNA sequencing assay. Under acid stress, many genes showed differential changes at the translational and transcriptional levels. A total of 10 genes showed different expression trends at the two levels. The expression of 337 genes—which mainly participated in the ABC transporters, amino acid metabolism, and ribosome functional group assembly pathways—was shown to be regulated only at the translational level. The translational efficiency of a few genes participating in the pyrimidine and amino acid metabolism pathways were upregulated. Ribosome occupancy data suggested that ribosomes accumulated remarkably in the elongation region of open reading frame regions under acid stress. This study provides new insights into Lacticaseibacillus rhamnosus ATCC 53103 gene expression under acid stress, and demonstrates that the bacterium can respond to acid stress with synergistic translational and transcriptional regulation mechanisms, improving the vitality of cells.
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22
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Characterization of two new strains of Lactococcus lactis for their probiotic efficacy over commercial synbiotics consortia. Braz J Microbiol 2022; 53:903-920. [PMID: 35138631 PMCID: PMC9151986 DOI: 10.1007/s42770-022-00685-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 01/02/2022] [Indexed: 02/01/2023] Open
Abstract
Lactococcus spp. are industrially crucial lactic acid bacteria (LAB) used to manufacture lactic acid, pickled vegetables, buttermilk, cheese, and many kinds of delicious dairy foods and drinks. In addition to these, they are also being used as probiotics in specific formulations. However, their uses as probiotics are comparatively less than the other LAB genera. The present communication hypothesizes to validate the probiotic potentiality of two new Lactococcus lactis subsp. lactis strains for their future uses. These native food fermenting strains were characterized for in vitro acid tolerance, tolerance to simulated gastric and pancreatic juices, autoaggregation and co-aggregation, hydrophobicity, haemolytic activity, bile salt deconjugation, cholesterol removal, antimicrobial spectrum, and antibiotic sensitivity. The in vivo live bacterial feeding of these strains for 30 days was done in Swiss albino mice either singly or in combination with prebiotic inulin and evaluated for hypocholesterolemic activity, immune enhancement, and gut colonization efficiency and compared with the commercial probiotic consortia. The study revealed that the strains could survive in human gut bile concentration, gastric pH conditions at pH 2.0, 3.0, and 8.0 for 6 h, had a broad antibacterial spectrum, and cholesterol binding efficacy. The strains could survive with higher colony-forming units (CFU/mL) when amended with sodium caseinate. The strains had autoaggregation ranges from 15 to 25% over 24 h and had a significant co-aggregation with both lactic acid and Gram-positive and Gram-negative bacterial strains related to human illness. The strains also showed solvent and media-specific hydrophobicity against n-hexane and xylene. The live bacterial feeding either singly or in combination with prebiotic inulin resulted in a significant reduction of LDL (low-density lipoprotein), VLDL (very low-density lipoprotein) cholesterol and triglyceride (TG), and a significant increase in HDL (high-density lipoprotein) cholesterol level, and improved gut colonization and gut immunomodulation. The results prove that these non-haemolytic, non-toxic strains had significant health benefits than the commercial probiotics consortium with the recommended prebiotics mix. Thus, these new Lactococcus lactis subsp. lactis strains could be trialled as a new probiotic combination for human and animal feeds.
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Kang J, Zhou X, Zhang W, Pei F, Ge J. Transcriptomic analysis of bacteriocin synthesis and stress response in Lactobacillus paracasei HD1.7 under acetic acid stress. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Chang D, Islam ZU, Zheng J, Zhao J, Cui X, Yu Z. Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: The proteomics-guided metabolic engineering. Synth Syst Biotechnol 2021; 6:384-395. [PMID: 34853817 PMCID: PMC8605246 DOI: 10.1016/j.synbio.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023] Open
Abstract
Pretreatment of lignocellulosic biomass is crucial for the release of biofermentable sugars for biofuels production, which could greatly alleviate the burgeoning environment and energy crisis caused by the massive usage of traditional fossil fuels. Pyrolysis is a cost-saving pretreatment process that can readily decompose biomass into levoglucosan, a promising anhydrosugar; however, many undesired toxic compounds inhibitory to downstream microbial fermentation are also generated during the pyrolysis, immensely impeding the bioconversion of levoglucosan-containing pyrolysate. Here, we took the first insight into the proteomic responses of a levoglucosan-utilizing and ethanol-producing Escherichia coli to three representative biomass-derived inhibitors, identifying large amounts of differentially expressed proteins (DEPs) that could guide the downstream metabolic engineering for the development of inhibitor-resistant strains. Fifteen up- and eight down-regulated DEPs were further identified as the biomarker stress-responsive proteins candidate for cellular tolerance to multiple inhibitors. Among these biomarker proteins, YcfR exhibiting the highest expression fold-change level was chosen as the target of overexpression to validate proteomics results and develop robust strains with enhanced inhibitor tolerance and fermentation performance. Finally, based on four plasmid-borne genes encoding the levoglucosan kinase, pyruvate decarboxylase, alcohol dehydrogenase, and protein YcfR, a new recombinant strain E. coli LGE-ycfR was successfully created, showing much higher acetic acid-, furfural-, and phenol-tolerance levels compared to the control without overexpression of ycfR. The specific growth rate, final cell density, ethanol concentration, ethanol productivity, and levoglucosan consumption rate of the recombinant were also remarkably improved. From the proteomics-guided metabolic engineering and phenotypic observations, we for the first time corroborated that YcfR is a stress-induced protein responsive to multiple biomass-derived inhibitors, and also developed an inhibitors-resistant strain that could produce bioethanol from levoglucosan in the presence of inhibitors of relatively high concentration. The newly developed E. coli LGE-ycfR strain that could eliminate the commonly-used costly detoxicification processes, is of great potential for the in situ cost-effective bioethanol production from the biomass-derived pyrolytic substrates.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zia Ul Islam
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Junfang Zheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, PR China
| | - Jie Zhao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiaoyong Cui
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, No. 380 Huaibei Town, Huairou District, Beijing, 101408, PR China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, PR China
- Corresponding author. College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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Lu S, Jin H, Wang Y, Tao Y. Genome-Wide Transcriptomic Analysis of n-Caproic Acid Production in Ruminococcaceae Bacterium CPB6 with Lactate Supplementation. J Microbiol Biotechnol 2021; 31:1533-1544. [PMID: 34489376 PMCID: PMC9705837 DOI: 10.4014/jmb.2107.07009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022]
Abstract
n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Ruminococcaceae bacterium strain CPB6 is an anaerobic mesophilic bacterium that is highly prolific in its ability to perform chain elongation of lactate to CA. However, little is known about the genome-wide transcriptional analysis of strain CPB6 for CA production triggered by the supplementation of exogenous lactate. In this study, cultivation of strain CPB6 was carried out in the absence and presence of lactate. Transcriptional profiles were analyzed using RNA-seq, and differentially expressed genes (DEGs) between the lactate-supplemented cells and control cells without lactate were analyzed. The results showed that lactate supplementation led to earlier CA p,roduction, and higher final CA titer and productivity. 295 genes were substrate and/or growth dependent, and these genes cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP), and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. The findings presented herein reveal unique insights into the biomolecular effect of lactate on CA production at the transcriptional level.
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Affiliation(s)
- Shaowen Lu
- CAS Key Laboratory of Environmental and Applied Microbiology and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Hong Jin
- School of Basic Medical Science, Chengdu Medical College, Chengdu 610083, P.R. China
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, Alabama, Alabama 36849, USA
| | - Yong Tao
- CAS Key Laboratory of Environmental and Applied Microbiology and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China,Faculty of Bioengineering, Sichuan University of Science and Engineering, Xueyuan Street 180#, Huixing Rd. Zigong 643000, P.R. China,Corresponding author Phone: 86-028-82890211 Fax: 86-028-82890211 E-mail:
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Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040248] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.
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Tran VG, Zhao H. Engineering robust microorganisms for organic acid production. J Ind Microbiol Biotechnol 2021; 49:6373449. [PMID: 34549297 PMCID: PMC9118992 DOI: 10.1093/jimb/kuab067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/11/2021] [Indexed: 11/24/2022]
Abstract
Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.
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Affiliation(s)
- Vinh G Tran
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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Differences in Acid Stress Response of Lacticaseibacillus paracasei Zhang Cultured from Solid-State Fermentation and Liquid-State Fermentation. Microorganisms 2021; 9:microorganisms9091951. [PMID: 34576848 PMCID: PMC8465097 DOI: 10.3390/microorganisms9091951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Abstract
Liquid-state fermentation (LSF) and solid-state fermentation (SSF) are two forms of industrial production of lactic acid bacteria (LAB). The choice of two fermentations for LAB production has drawn wide concern. In this study, the tolerance of bacteria produced by the two fermentation methods to acid stress was compared, and the reasons for the tolerance differences were analyzed at the physiological and transcriptional levels. The survival rate of the bacterial agent obtained from solid-state fermentation was significantly higher than that of bacteria obtained from liquid-state fermentation after spray drying and cold air drying. However, the tolerance of bacterial cells obtained from liquid-state fermentation to acid stress was significantly higher than that from solid-state fermentation. The analysis at physiological level indicated that under acid stress, cells from liquid-state fermentation displayed a more solid and complete membrane structure, higher cell membrane saturated fatty acid, more stable intracellular pH, and more stable activity of ATPase and glutathione reductase, compared with cells from solid-state fermentation, and these physiological differences led to better tolerance to acid stress. In addition, transcriptomic analysis showed that in the cells cultured from liquid-state fermentation, the genes related to glycolysis, inositol phosphate metabolism, and carbohydrate transport were down-regulated, whereas the genes related to fatty acid synthesis and glutamate metabolism were upregulated, compared with those in cells from solid-state fermentation. In addition, some genes related to acid stress response such as cspA, rimP, rbfA, mazF, and nagB were up-regulated. These findings provide a new perspective for the study of acid stress tolerance of L. paracasei Zhang and offer a reference for the selection of fermentation methods of LAB production.
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Ma M, Zhao Z, Liang Q, Shen H, Zhao Z, Chen Z, He R, Feng S, Cao D, Gan G, Ye H, Qiu W, Deng J, Ming F, Jia J, Sun C, Li J, Zhang L. Overexpression of pEGF improved the gut protective function of Clostridium butyricum partly through STAT3 signal pathway. Appl Microbiol Biotechnol 2021; 105:5973-5991. [PMID: 34396488 DOI: 10.1007/s00253-021-11472-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 12/25/2022]
Abstract
Clostridium butyricum (C. butyricum) is a probiotic that could promote animal growth and protect gut health. So far, current studies mainly keep up with the basic biological functions of C. butyricum, missing the effective strategy to further improve its protective efficiency. A recent report about C. butyricum alleviating intestinal injury through epidermal growth factor receptor (EGFR) inspired us to bridge this gap by porcine epidermal growth factor (EGF) overexpression. Lacking a secretory overexpression system, we constructed the recombinant strains overexpressing pEGF in C. butyricum for the first time and obtained 4 recombinant strains for highly efficient secretion of pEGF (BC/pPD1, BC/pSPP, BC/pGHF, and BC/pDBD). Compared to the wild-type strain, we confirmed that the expression level ranges of the intestinal development-related genes (Claudin-1, GLUT-2, SUC, GLP2R, and EGFR) and anti-inflammation-related gene (IL-10) in IPECs were upregulated under recombinant strain stimulation, and the growth of Staphylococcus aureus and Salmonella typhimurium was significantly inhibited as well. Furthermore, a particular inhibitor (stattic) was used to block STAT3 tyrosine phosphorylation, resulting in the downregulation on antibacterial effect of recombinant strains. This study demonstrated that the secretory overexpression of pEGF in C. butyricum could upregulate the expression level of EGFR, consequently improving the intestinal protective functions of C. butyricum partly following STAT3 signal activation in IPECs and making it a positive loop. These findings on the overexpression strains pointed out a new direction for further development and utilization of C. butyricum. KEY POINTS: • By 12 signal peptide screening in silico, 4 pEGF overexpression strains of C. butyricum/pMTL82151-pEGF for highly efficient secretion of pEGF were generated for the first time. • The secretory overexpression of pEGF promoted the intestinal development, antimicrobial action, and anti-inflammatory function of C. butyricum. • The overexpressed pEGF upregulated the expression level of EGFR and further magnified the gut protective function of recombinant strains which in turn partly depended on STAT3 signal pathway in IPECs.
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Affiliation(s)
- Miaopeng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Zitong Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Qianyi Liang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Haokun Shen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Zengjue Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Zhiyang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Rongxiao He
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Saixiang Feng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Ding Cao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Guanhua Gan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Hejia Ye
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Weihong Qiu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Jinbo Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Feiping Ming
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Junhao Jia
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Chongjun Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Jiayi Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Linghua Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China.
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Gao X, Kong J, Zhu H, Mao B, Cui S, Zhao J. Lactobacillus, Bifidobacterium and Lactococcus response to environmental stress: Mechanisms and application of cross-protection to improve resistance against freeze-drying. J Appl Microbiol 2021; 132:802-821. [PMID: 34365708 DOI: 10.1111/jam.15251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/12/2021] [Accepted: 07/07/2021] [Indexed: 01/30/2023]
Abstract
The review deals with lactic acid bacteria in characterizing the stress adaptation with cross-protection effects, mainly associated with Lactobacillus, Bifidobacterium and Lactococcus. It focuses on adaptation and cross-protection in Lactobacillus, Bifidobacterium and Lactococcus, including heat shocking, cold stress, acid stress, osmotic stress, starvation effect, etc. Web of Science, Google Scholar, Science Direct, and PubMed databases were used for the systematic search of literature up to the year 2020. The literature suggests that a lower survival rate during freeze-drying is linked to environmental stress. Protective pretreatment under various mild stresses can be applied to lactic acid bacteria which may enhance resistance in a strain-dependent manner. We investigate the mechanism of damage and adaptation under various stresses including heat, cold, acidic, osmotic, starvation, oxidative and bile stress. Adaptive mechanisms include synthesis of stress-induced proteins, adjusting the composition of cell membrane fatty acids, accumulating compatible substances, etc. Next, we reveal the cross-protective effect of specific stress on the other environmental stresses. Freeze-drying is discussed from three perspectives including the regulation of membrane, accumulation of compatible solutes and the production of chaperones and stress-responsive proteases. The resistance of lactic acid bacteria against technological stress can be enhanced via cross-protection, which improves industrial efficiency concerning the survival of probiotics. However, the adaptive responses and cross-protection are strain-dependent and should be optimized case by case.
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Affiliation(s)
- Xinwei Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jie Kong
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongkang Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
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Biodegradation of aromatic pollutants meets synthetic biology. Synth Syst Biotechnol 2021; 6:153-162. [PMID: 34278013 PMCID: PMC8260767 DOI: 10.1016/j.synbio.2021.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/02/2023] Open
Abstract
Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.
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Qiao W, Qiao Y, Liu F, Zhang Y, Li R, Wu Z, Xu H, Saris PEJ, Qiao M. Engineering Lactococcus lactis as a multi-stress tolerant biosynthetic chassis by deleting the prophage-related fragment. Microb Cell Fact 2020; 19:225. [PMID: 33298073 PMCID: PMC7727215 DOI: 10.1186/s12934-020-01487-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/28/2020] [Indexed: 01/02/2023] Open
Abstract
Background In bioengineering, growth of microorganisms is limited because of environmental and industrial stresses during fermentation. This study aimed to construct a nisin-producing chassis Lactococcus lactis strain with genome-streamlined, low metabolic burden, and multi-stress tolerance characteristics. Results The Cre-loxP recombination system was applied to reduce the genome and obtain the target chassis strain. A prophage-related fragment (PRF; 19,739 bp) in the L. lactis N8 genome was deleted, and the mutant strain L. lactis N8-1 was chosen for multi-stress tolerance studies. Nisin immunity of L. lactis N8-1 was increased to 6500 IU/mL, which was 44.44% higher than that of the wild-type L. lactis N8 (4500 IU/mL). The survival rates of L. lactis N8-1 treated with lysozyme for 2 h and lactic acid for 1 h were 1000- and 10,000-fold higher than that of the wild-type strain, respectively. At 39 ℃, the L. lactis N8-1 could still maintain its growth, whereas the growth of the wild-type strain dramatically dropped. Scanning electron microscopy showed that the cell wall integrity of L. lactis N8-1 was well maintained after lysozyme treatment. Tandem mass tags labeled quantitative proteomics revealed that 33 and 9 proteins were significantly upregulated and downregulated, respectively, in L. lactis N8-1. These differential proteins were involved in carbohydrate and energy transport/metabolism, biosynthesis of cell wall and cell surface proteins. Conclusions PRF deletion was proven to be an efficient strategy to achieve multi-stress tolerance and nisin immunity in L. lactis, thereby providing a new perspective for industrially obtaining engineered strains with multi-stress tolerance and expanding the application of lactic acid bacteria in biotechnology and synthetic biology. Besides, the importance of PRF, which can confer vital phenotypes to bacteria, was established.
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Affiliation(s)
- Wanjin Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.,Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Yu Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Fulu Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Yating Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Ran Li
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Zhenzhou Wu
- State Key Laboratory of Medicinal Chemical Biology & Tianjin Key Laboratory of Protein Sciences, College of Life Sciences, Nankai University, Tianjin, China
| | - Haijin Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mingqiang Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
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Liu T, Zhao Q, Li Y, Zhu L, Jiang L, Huang H. Transcriptomics and Proteomics Analyses of the Responses of Propionibacterium acidipropionici to Metabolic and Evolutionary Manipulation. Front Microbiol 2020; 11:1564. [PMID: 32903527 PMCID: PMC7438477 DOI: 10.3389/fmicb.2020.01564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/16/2020] [Indexed: 01/12/2023] Open
Abstract
We first performed a combination of metabolic engineering (deletion of ldh and poxB and overexpression of mmc) with evolutionary engineering (selection under oxygen stress, acid stress and osmotic stress) in Propionibacterium acidipropionici. The results indicated that the mutants had superior physiological activity, especially the mutant III obtained from P. acidipropionici-Δldh-ΔpoxB+mmc by evolutionary engineering, with 1.5-3.5 times higher growth rates, as well as a 37.1% increase of propionic acid (PA) titer and a 37.8% increase PA productivity compared to the wild type. Moreover, the integrative transcriptomics and proteomics analyses revealed that the differentially expressed genes (DEGs) and proteins (DEPs) in the mutant III were involved in energy metabolism, including the glycolysis pathway and tricarboxylic acid cycle (TCA cycle). These genes were up-regulated to supply increased amounts of energy and precursors for PA synthesis compared to the wild type. In addition, the down-regulation of fatty acid biosynthesis and fatty acid metabolism may indicate that the repressed metabolic flux was related to the production of PA. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to verify the differential expression levels of 16 selected key genes. The results offer deep insights into the mechanism of high PA production, which provides the theoretical foundation for the construction of advanced microbial cell factories.
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Affiliation(s)
- Tingting Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Qianru Zhao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Yang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - He Huang
- College of Pharmaceutical Science, Nanjing Tech University, Nanjing, China
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Ma Y, Li L, Awasthi MK, Tian H, Lu M, Megharaj M, Pan Y, He W. Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations. Appl Microbiol Biotechnol 2020; 104:5873-5887. [PMID: 32415321 DOI: 10.1007/s00253-020-10672-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 01/02/2023]
Abstract
Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.
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Affiliation(s)
- Yinghui Ma
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xi'an, 710043, Shaanxi, PR China.,College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Lijun Li
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xi'an, 710043, Shaanxi, PR China.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Haixia Tian
- College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Meihuan Lu
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xi'an, 710043, Shaanxi, PR China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia
| | - Yalei Pan
- Shaanxi Collaborative Innovation Center of Chinese Medicine Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang, 712046, PR China
| | - Wenxiang He
- College of Natural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
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