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Gao S, Liao Y, He H, Yang H, Yang X, Xu S, Wang X, Chen K, Ouyang P. Advance of tolerance engineering on microbes for industrial production. Synth Syst Biotechnol 2023; 8:697-707. [PMID: 38025766 PMCID: PMC10656194 DOI: 10.1016/j.synbio.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Industrial microbes have become the core of biological manufacturing, which utilized as the cell factory for production of plenty of chemicals, fuels and medicine. However, the challenge that the extreme stress conditions exist in production is unavoidable for cell factory. Consequently, to enhance robustness of the chassis cell lays the foundation for development of bio-manufacturing. Currently, the researches on cell tolerance covered various aspects, involving reshaping regulatory network, cell membrane modification and other stress response. In fact, the strategies employed to improve cell robustness could be summarized into two directions, irrational engineering and rational engineering. In this review, the metabolic engineering technologies on enhancement of microbe tolerance to industrial conditions are summarized. Meanwhile, the novel thoughts emerged with the development of biological instruments and synthetic biology are discussed.
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Affiliation(s)
- Siyuan Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Yang Liao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Hao He
- Petrochemical Research Institute of PetroChina Co. Ltd., Beijing, 102206, China
| | - Huiling Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xuewei Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
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Zhang Y, Pan L, Zhang Y, Wang K, Wang L, Zhang H, Zhang J, Chen X. Understanding the Streptomyces albulus response to low-pH stress at the interface of physiology and transcriptomics. Appl Microbiol Biotechnol 2023; 107:2611-2626. [PMID: 36882645 DOI: 10.1007/s00253-023-12449-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/09/2023]
Abstract
Streptomyces albulus is a well-established cell factory for ε-poly-L-lysine (ε-PL) production. It has been reported that ε-PL biosynthesis is strictly regulated by pH and that ε-PL can accumulate at approximately pH 4.0, which is outside of the general pH range for natural product production by Streptomyces species. However, how S. albulus responds to low pH is not clear. In this study, we attempted to explore the response of S. albulus to low-pH stress at the physiological and global gene transcription levels. At the physiological level, S. albulus maintained intracellular pH homeostasis at ~pH 7.5, increased the unsaturated fatty acid ratio, extended the fatty acid chain length, enhanced ATP accumulation, increased H+-ATPase activity, and accumulated the basic amino acids L-lysine and L-arginine. At the global gene transcription level, carbohydrate metabolism, oxidative phosphorylation, macromolecule protection and repair, and the acid tolerance system were found to be involved in combating low-pH stress. Finally, we preliminarily evaluated the effect of the acid tolerance system and cell membrane fatty acid synthesis on low-pH tolerance via gene manipulation. This work provides new insight into the adaptation mechanism of Streptomyces to low-pH stress and a new opportunity for constructing robust S. albulus strains for ε-PL production. KEY POINTS: • S. albulus consistently remained pH i at ~7.4 regardless of the environmental pH. • S. albulus combats low-pH stress by modulating lipid composition of cell membrane. • Overexpression of cfa in S. albulus could improve low-pH tolerance and ɛ-PL titer.
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Affiliation(s)
- Yulin Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Long Pan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
- School of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Yue Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Kaifang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Liang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Hongjian Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Jianhua Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Xusheng Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China.
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Xu J, Guo L, Zhao N, Meng X, Zhang J, Wang T, Wei X, Fan M. Response mechanisms to acid stress of acid-resistant bacteria and biotechnological applications in the food industry. Crit Rev Biotechnol 2023; 43:258-274. [PMID: 35114869 DOI: 10.1080/07388551.2021.2025335] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Acid-resistant bacteria are more and more widely used in industrial production due to their unique acid-resistant properties. In order to survive in various acidic environments, acid-resistant bacteria have developed diverse protective mechanisms such as sensing acid stress and signal transduction, maintaining intracellular pH homeostasis by controlling the flow of H+, protecting and repairing biological macromolecules, metabolic modification, and cross-protection. Acid-resistant bacteria have broad biotechnological application prospects in the food field. The production of fermented foods with high acidity and acidophilic enzymes are the main applications of this kind of bacteria in the food industry. Their acid resistance modules can also be used to construct acid-resistant recombinant engineering strains for special purposes. However, they can also cause negative effects on foods, such as spoilage and toxicity. Herein, the aim of this paper is to summarize the research progress of molecular mechanisms against acid stress of acid-resistant bacteria. Moreover, their effects on the food industry were also discussed. It is useful to lay a foundation for broadening our understanding of the physiological metabolism of acid-resistant bacteria and better serving the food industry.
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Affiliation(s)
- Junnan Xu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Li Guo
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Ning Zhao
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Xuemei Meng
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Jie Zhang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Tieru Wang
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
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Jung M, Ahn YJ. Growth-enhancing effect of bacterial and plant heat shock proteins in Escherichia coli. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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Yusof NA, Masnoddin M, Charles J, Thien YQ, Nasib FN, Wong CMVL, Abdul Murad AM, Mahadi NM, Bharudin I. Can heat shock protein 70 (HSP70) serve as biomarkers in Antarctica for future ocean acidification, warming and salinity stress? Polar Biol 2022. [DOI: 10.1007/s00300-022-03006-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractThe Antarctic Peninsula is one of the fastest-warming places on Earth. Elevated sea water temperatures cause glacier and sea ice melting. When icebergs melt into the ocean, it “freshens” the saltwater around them, reducing its salinity. The oceans absorb excess anthropogenic carbon dioxide (CO2) causing decline in ocean pH, a process known as ocean acidification. Many marine organisms are specifically affected by ocean warming, freshening and acidification. Due to the sensitivity of Antarctica to global warming, using biomarkers is the best way for scientists to predict more accurately future climate change and provide useful information or ecological risk assessments. The 70-kilodalton (kDa) heat shock protein (HSP70) chaperones have been used as biomarkers of stress in temperate and tropical environments. The induction of the HSP70 genes (Hsp70) that alter intracellular proteins in living organisms is a signal triggered by environmental temperature changes. Induction of Hsp70 has been observed both in eukaryotes and in prokaryotes as response to environmental stressors including increased and decreased temperature, salinity, pH and the combined effects of changes in temperature, acidification and salinity stress. Generally, HSP70s play critical roles in numerous complex processes of metabolism; their synthesis can usually be increased or decreased during stressful conditions. However, there is a question as to whether HSP70s may serve as excellent biomarkers in the Antarctic considering the long residence time of Antarctic organisms in a cold polar environment which appears to have greatly modified the response of heat responding transcriptional systems. This review provides insight into the vital roles of HSP70 that make them ideal candidates as biomarkers for identifying resistance and resilience in response to abiotic stressors associated with climate change, which are the effects of ocean warming, freshening and acidification in Antarctic organisms.
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Song H, Lou N, Liu J, Xiang H, Shang D. Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture. Proteome Sci 2021; 19:4. [PMID: 33750393 PMCID: PMC7945214 DOI: 10.1186/s12953-021-00172-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/25/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. METHODS To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. RESULTS The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. CONCLUSIONS These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.
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Affiliation(s)
- Huiyi Song
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, 222 Zhongshan Road, Dalian, 116023, P. R. China
| | - Ni Lou
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Jianjun Liu
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, 222 Zhongshan Road, Dalian, 116023, P. R. China
| | - Hong Xiang
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, 222 Zhongshan Road, Dalian, 116023, P. R. China
| | - Dong Shang
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, 222 Zhongshan Road, Dalian, 116023, P. R. China.
- The Third Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, P. R. China.
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Lotfi M, Ghafouri H, Sarikhan S, Shahangian SS, Darvishi R. Cloning, prokaryotic expression, and functional characterization of a novel 70-kDa heat shock protein (DnaK) from Bacillus persicus. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Ahn YJ, Im E. Heterologous expression of heat shock proteins confers stress tolerance in Escherichia coli, an industrial cell factory: A short review. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Characterization and transcriptomic basis of biofilm formation by Lactobacillus plantarum J26 isolated from traditional fermented dairy products. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Goulart MC, Cueva‐Yesquén LG, Hidalgo Martinez KJ, Attili‐Angelis D, Fantinatti‐Garboggini F. Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture-dependent and culture-independent analysis. Microbiologyopen 2019; 8:e896. [PMID: 31454177 PMCID: PMC6813437 DOI: 10.1002/mbo3.896] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/12/2022] Open
Abstract
Plants and endophytic microorganisms have coevolved unique relationships over many generations. Plants show a specific physiological status in each developmental stage, which may determine the occurrence and dominance of specific endophytic populations with a predetermined ecological role. This study aimed to compare and determine the structure and composition of cultivable and uncultivable bacterial endophytic communities in vegetative and reproductive stages (RS) of Passiflora incarnata. To that end, the endophytic communities were assessed by plating and Illumina-based 16S rRNA gene amplicon sequencing. Two hundred and four cultivable bacterial strains were successfully isolated. From the plant's RS, the isolated strains were identified mainly as belonging to the genera Sphingomonas, Curtobacterium, and Methylobacterium, whereas Bacillus was the dominant genus isolated from the vegetative stage (VS). From a total of 133,399 sequences obtained from Illumina-based sequencing, a subset of 25,092 was classified in operational taxonomy units (OTUs). Four hundred and sixteen OTUs were obtained from the VS and 66 from the RS. In the VS, the most abundant families were Pseudoalteromonadaceae and Alicyclobacillaceae, while in the RS, Enterobacteriaceae and Bacillaceae were the most abundant families. The exclusive abundance of specific bacterial populations for each developmental stage suggests that plants may modulate bacterial endophytic community structure in response to different physiological statuses occurring at the different plant developmental stages.
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Affiliation(s)
- Marcela C. Goulart
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Luis G. Cueva‐Yesquén
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Kelly J. Hidalgo Martinez
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Derlene Attili‐Angelis
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Fabiana Fantinatti‐Garboggini
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
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