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Yamada M. Molecular basis and functional development of membrane-based microbial metabolism. Biosci Biotechnol Biochem 2024; 88:461-474. [PMID: 38366612 DOI: 10.1093/bbb/zbae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Abstract
My research interest has so far been focused on metabolisms related to the "membrane" of microorganisms, such as the respiratory chain, membrane proteins, sugar uptake, membrane stress and cell lysis, and fermentation. These basic metabolisms are important for the growth and survival of cell, and their knowledge can be used for efficient production of useful materials. Notable achievements in research on metabolisms are elucidation of the structure and function of membrane-bound glucose dehydrogenase as a primary enzyme in the respiratory chain, elucidation of ingenious expression regulation of several operons or by divergent promoters, elucidation of stress-induced programed-cell lysis and its requirement for survival during a long-term stationary phase, elucidation of molecular mechanism of survival at a critical high temperature, elucidation of thermal adaptation and its limit, isolation of thermotolerant fermenting yeast strains, and development of high-temperature fermentation and green energy production technologies. These achievements are described together in this review.
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Affiliation(s)
- Mamoru Yamada
- Graduate School of Sciences and Technology for Innovation, and Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
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Chang F, Wang Y, Zhang J, Tu T, Luo H, Huang H, Bai Y, Qin X, Wang Y, Yao B, Wang Y, Wang X. Efficient production of γ-aminobutyric acid using engineered Escherichia coli whole-cell catalyst. Enzyme Microb Technol 2024; 174:110379. [PMID: 38103484 DOI: 10.1016/j.enzmictec.2023.110379] [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: 10/31/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
γ-Aminobutyric acid (GABA) has been widely used in the food, feed, pharmaceutical, and chemical industry fields. Previously, we developed a whole-cell catalyst capable of converting L-glutamate (L-Glu) into GABA by overexpressing the glutamate decarboxylase gene (gadz11) from Bacillus sp. Z11 in Escherichia coli BL21(DE3). However, to enhance cell permeability, a freeze-thaw treatment is required, and to enhance GADZ11 activity, pyridoxal 5'-phosphate (PLP) must be added to the reaction system. The aim of this study is to provide a more efficient approach for GABA production by engineering the recombinant E. coli above. First, the inducible expression conditions of the gadz11 in E. coli were optimized to 37 °C for 6 h. Next, an ideal engineered strain was produced via increasing cell permeability by overexpressing sulA and eliminating PLP dependence by constructing a self-sufficient system. Furthermore, an efficient whole-cell biocatalytic process was optimized. The optimal substrate concentration, cell density, and reaction temperature were 1.0 mol/L (the molecular ratio of L-Glu to L-monosodium glutamate (L-MSG) was 4:1), 15 and 37 °C, respectively. Finally, a whole-cell bioconversion procedure was performed in a 3-L bioreactor under optimal conditions. The strain could be reused for at least two cycles with GABA yield, productivity and conversion ratio of 206.2 g/L, 117.8 g/L/h and 100.0%, respectively. This is currently the highest GABA productivity from a mixture of L-Glu and L-MSG reported without the addition of cofactors or additional treatment of cells. This work demonstrates that the novel engineered E. coli strain has the potential for application in large-scale industrial GABA production.
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Affiliation(s)
- Fangfang Chang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuheng Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Salas-Orozco MF, Lorenzo-Leal AC, de Alba Montero I, Marín NP, Santana MAC, Bach H. Mechanism of escape from the antibacterial activity of metal-based nanoparticles in clinically relevant bacteria: A systematic review. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 55:102715. [PMID: 37907198 DOI: 10.1016/j.nano.2023.102715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/05/2023] [Accepted: 10/05/2023] [Indexed: 11/02/2023]
Abstract
The emergency of antibiotic-resistant bacteria in severe infections is increasing, especially in nosocomial environments. The ESKAPE group is of special importance in the groups of multi-resistant bacteria due to its high capacity to generate resistance to antibiotics and bactericides. Therefore, metal-based nanomaterials are an attractive alternative to combat them because they have been demonstrated to damage biomolecules in the bacterial cells. However, there is a concern about bacteria developing resistance to NPs and their harmful effects due to environmental accumulation. Therefore, this systematic review aims to report the clinically relevant bacteria that have developed resistance to the NPs. According to the results of this systematic review, various mechanisms to counteract the antimicrobial activity of various NP types have been proposed. These mechanisms can be grouped into the following categories: production of extracellular compounds, metal efflux pumps, ROS response, genetic changes, DNA repair, adaptative morphogenesis, and changes in the plasma membrane.
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Affiliation(s)
- Marco Felipe Salas-Orozco
- Facultad de Estomatología, Doctorado en Ciencias Odontológicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
| | - Ana Cecilia Lorenzo-Leal
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Nuria Patiño Marín
- Facultad de Estomatología, Laboratorio de Investigación Clinica, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Miguel Angel Casillas Santana
- Maestría en Estomatología con Opcion Terminal en Ortodoncia, Facultad de Estomatología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Horacio Bach
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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T N, Govindarajan S, Munavar MH. trans-translation system is important for maintaining genome integrity during DNA damage in bacteria. Res Microbiol 2023; 174:104136. [PMID: 37690591 DOI: 10.1016/j.resmic.2023.104136] [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: 04/21/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
DNA integrity in bacteria is regulated by various factors that act on the DNA. trans-translation has previously been shown to be important for the survival of Escherichia coli cells exposed to certain DNA-damaging agents. However, the mechanisms underlying this sensitivity are poorly understood. In this study, we explored the involvement of the trans-translation system in the maintenance of genome integrity using various DNA-damaging agents and mutant backgrounds. Relative viability assays showed that SsrA-defective cells were sensitive to DNA-damaging agents, such as nalidixic acid (NA), ultraviolet radiation (UV), and methyl methanesulfonate (MMS). The viability of SsrA-defective cells was rescued by deleting sulA, although the expression of SulA was not more pronounced in SsrA-defective cells than in wild-type cells. Live cell imaging using a Gam-GFP fluorescent reporter showed increased double-strand breaks (DSBs) in SsrA-defective cells during DNA damage. We also showed that the ribosome rescue function of SsrA was sufficient for DNA damage tolerance. DNA damage sensitivity can be alleviated by partial uncoupling of transcription and translation by using sub-lethal concentrations of ribosome inhibiting antibiotic (tetracycline) or by mutating the gene coding for RNase H (rnhA). Taken together, our results highlight the importance of trans-translation system in maintaining genome integrity and bacterial survival during DNA damage.
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Affiliation(s)
- Nagarajan T
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India; Department of Biological Sciences, SRM University-AP, Amaravati, India
| | | | - M Hussain Munavar
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India.
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Shen Z, Tang CM, Liu GY. Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids? Mil Med Res 2022; 9:3. [PMID: 35012680 PMCID: PMC8744291 DOI: 10.1186/s40779-021-00362-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/26/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.
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Affiliation(s)
- Zhen Shen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.,Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Guang-Yu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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