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He P, Hu S, Zhang Y, Xiang Z, Zhu A, Chen S. Transcription factor AbrB regulates ROS generation and clearance in Bacillus licheniformis. Microbiol Res 2024; 287:127843. [PMID: 39024796 DOI: 10.1016/j.micres.2024.127843] [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: 04/09/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Oxidative damage caused by the accumulation of reactive oxygen species (ROS) is one of the main obstacles to the improvement of microbial cell growth and fermentation characteristics under adverse environments. And the antioxidant capacity of cells will increase with the cell growth. Here, we found that a transition state transcription factor AbrB related to changes in cell growth status could regulate the accumulation of ROS and antioxidant capacity in Bacillus licheniformis. The results showed that the accumulation of intracellular ROS was reduced by 23.91 % and the cell survival rates were increased by 1.77-fold under 0.5 mM H2O2 when AbrB was knocked out. We further mapped regulatory target genes of AbrB related to ROS generation or clearance based on our previously analyzed transcriptome sequencing. It proved that AbrB could promote ROS generation via upregulating the synthesis of oxidase and siderophores, and negatively regulating the synthesis of iron chelators (pulcherriminic acid, and H2S). Additionally, AbrB could inhibit ROS clearance by negatively regulating the synthesis of antioxidase (superoxide dismutase, catalase, peroxidase, thioredoxin, thioredoxin reductase) and cysteine. Those results illustrated that the inactivation of AbrB during the stationary phase, along with its control over ROS generation and clearance, might represent a vital self-protection mechanism during cell evolution. Overall, the systematic investigation of the multi-pathway regulation network of ROS generation and clearance highlights the important function of AbrB in maintaining intracellular redox balance.
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Affiliation(s)
- Penghui He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shiying Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yongjia Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhengwei Xiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, China
| | - Anting Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, China; Key Laboratory of Green Chemical Technology of Fujian Province University, College of Ecological and Resource Engineering, Wuyi University, Wuyishan 354300, China.
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2
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Wu T, Wei W, Gao C, Wu J, Gao C, Chen X, Liu L, Song W. Synthesis of C-N bonds by nicotinamide-dependent oxidoreductase: an overview. Crit Rev Biotechnol 2024:1-25. [PMID: 39229892 DOI: 10.1080/07388551.2024.2390082] [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: 06/08/2023] [Revised: 11/05/2023] [Accepted: 11/25/2023] [Indexed: 09/05/2024]
Abstract
Compounds containing chiral C-N bonds play a vital role in the composition of biologically active natural products and small pharmaceutical molecules. Therefore, the development of efficient and convenient methods for synthesizing compounds containing chiral C-N bonds is a crucial area of research. Nicotinamide-dependent oxidoreductases (NDOs) emerge as promising biocatalysts for asymmetric synthesis of chiral C-N bonds due to their mild reaction conditions, exceptional stereoselectivity, high atom economy, and environmentally friendly nature. This review aims to present the structural characteristics and catalytic mechanisms of various NDOs, including imine reductases/ketimine reductases, reductive aminases, EneIRED, and amino acid dehydrogenases. Additionally, the review highlights protein engineering strategies employed to modify the stereoselectivity, substrate specificity, and cofactor preference of NDOs. Furthermore, the applications of NDOs in synthesizing essential medicinal chemicals, such as noncanonical amino acids and chiral amine compounds, are extensively examined. Finally, the review outlines future perspectives by addressing challenges and discussing the potential of utilizing NDOs to establish efficient biosynthesis platforms for C-N bond synthesis. In conclusion, NDOs provide an economical, efficient, and environmentally friendly toolbox for asymmetric synthesis of C-N bonds, thus contributing significantly to the field of pharmaceutical chemical development.
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Affiliation(s)
- Tianfu Wu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Changzheng Gao
- Department of Cardiology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
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3
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Benoit SL, Maier RJ. d-aspartate, an amino-acid important for human health, supports anaerobic respiration in several Campylobacter species. Res Microbiol 2024; 175:104219. [PMID: 38945250 DOI: 10.1016/j.resmic.2024.104219] [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: 05/10/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Despite being classified as microaerophilic microorganisms, most Campylobacter species can grow anaerobically, using formate or molecular hydrogen (H2) as electron donors, and various nitrogenous and sulfurous compounds as electron acceptors. Herein, we showed that both l-asparagine (l-Asn) and l-aspartic acid (l-Asp) bolster H2-driven anaerobic growth in several Campylobacter species, whereas the d-enantiomer form of both asparagine (d-Asn) and aspartic acid (d-Asp) only increased anaerobic growth in Campylobacter concisus strain 13826 and Campylobacter ureolyticus strain NCTC10941. A gene annotated as racD encoding for a putative d/l-Asp racemase was identified in the genome of both strains. Disruption of racD in Cc13826 resulted in the inability of the mutant strain to use either d-enantiomer during anaerobic growth. Hence, our results suggest that the racD gene is required for campylobacters to use either d-Asp or d-Asn. The use of d-Asp by various human opportunistic bacterial pathogens, including C. concisus, C. ureolyticus, and also possibly select strains of Campylobacter gracilis, Campylobacter rectus and Campylobacter showae, is significant, because d-Asp is an important signal molecule for both human nervous and neuroendocrine systems. To our knowledge, this is the first report of pathogens scavenging a d-amino acid essential for human health.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, GA, 30602, United States; Center for Metalloenzyme Studies, University of Georgia, Athens, GA, 30602, United States.
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, GA, 30602, United States; Center for Metalloenzyme Studies, University of Georgia, Athens, GA, 30602, United States
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4
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Hallam JC, Sandalli S, Floria I, Turner NCA, Tang-Fichaux M, Oswald E, O'Boyle N, Roe AJ. D-Serine reduces the expression of the cytopathic genotoxin colibactin. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:63-77. [PMID: 36908282 PMCID: PMC9993432 DOI: 10.15698/mic2023.03.793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 03/14/2023]
Abstract
Some Escherichia coli strains harbour the pks island, a 54 kb genomic island encoding the biosynthesis genes for a genotoxic compound named colibactin. In eukaryotic cells, colibactin can induce DNA damage, cell cycle arrest and chromosomal instability. Production of colibactin has been implicated in the development of colorectal cancer (CRC). In this study, we demonstrate the inhibitory effect of D-Serine on the expression of the pks island in both prototypic and clinically-associated colibactin-producing strains and determine the implications for cytopathic effects on host cells. We also tested a comprehensive panel of proteinogenic L-amino acids and corresponding D-enantiomers for their ability to modulate clbB transcription. Whilst several D-amino acids exhibited the ability to inhibit expression of clbB, D-Serine exerted the strongest repressing activity (>3.8-fold) and thus, we focussed additional experiments on D-Serine. To investigate the cellular effect, we investigated if repression of colibactin by D-Serine could reduce the cytopathic responses normally observed during infection of HeLa cells with pks + strains. Levels of γ-H2AX (a marker of DNA double strand breaks) were reduced 2.75-fold in cells infected with D-Serine treatment. Moreover, exposure of pks + E. coli to D-Serine during infection caused a reduction in cellular senescence that was observable at 72 h post infection. The recent finding of an association between pks-carrying commensal E. coli and CRC, highlights the necessity for the development of colibactin targeting therapeutics. Here we show that D-Serine can reduce expression of colibactin, and inhibit downstream cellular cytopathy, illuminating its potential to prevent colibactin-associated disease.
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Affiliation(s)
- Jennifer C. Hallam
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Sofia Sandalli
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Iris Floria
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Natasha C. A. Turner
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Min Tang-Fichaux
- IRSD, INSERM, INRAE, Université de Toulouse, ENVT, Toulouse, France
| | - Eric Oswald
- IRSD, INSERM, INRAE, Université de Toulouse, ENVT, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Nicky O'Boyle
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Andrew J. Roe
- School of Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
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5
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D-Amino Acids and Cancer: Friends or Foes? Int J Mol Sci 2023; 24:ijms24043274. [PMID: 36834677 PMCID: PMC9962368 DOI: 10.3390/ijms24043274] [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: 12/12/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
α-amino acids exist in two configurations, named D-(dextro) and L-(levo) enantiomers. L-amino acids are used in protein synthesis and play a central role in cell metabolism. The effects of the L-amino acid composition of foods and the dietary modifications of this composition on the efficacy of cancer therapies have been widely investigated in relation to the growth and reproduction of cancerous cells. However, less is known about the involvement of D-amino acids. In recent decades, D-amino acids have been identified as natural biomolecules that play interesting and specific roles as common components of the human diet. Here, we focus on recent investigations showing altered D-amino acid levels in specific cancer types and on the various roles proposed for these biomolecules related to cancer cell proliferation, cell protection during therapy, and as putative, innovative biomarkers. Notwithstanding recent progress, the relationship between the presence of D-amino acids, their nutritional value, and cancer cell proliferation and survival represents an underrated scientific issue. Few studies on human samples have been reported to date, suggesting a need for routine analysis of D-amino acid content and an evaluation of the enzymes involved in regulating their levels in clinical samples in the near future.
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6
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Liu Q, Tang S, Wang H, Han P. Stereospecific recognition and rapid determination of D-amino acids in human serum based on luminescent metal-organic frameworks. NEW J CHEM 2022. [DOI: 10.1039/d1nj05570d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The current luminescent metal-organic frameworks (MOFs) based fluorescent detection mostly focuses on achiral molecules. The stereospecific recognition and determination of MOF-based detection remain challenging. A novel luminescent terbium-based MOF (Tb-MOF)...
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7
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Genomic plasticity of pathogenic Escherichia coli mediates d-serine tolerance via multiple adaptive mechanisms. Proc Natl Acad Sci U S A 2020; 117:22484-22493. [PMID: 32848072 PMCID: PMC7486766 DOI: 10.1073/pnas.2004977117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pathogens ensure infection of favored sites in the body by responding to chemical signals. One chemical abundant in urine, the amino acid d-Ser, is toxic to EHEC and reduces expression of the machinery used for host cell attachment, making the bladder an unfavorable environment. We observed that under d-Ser stress, EHEC acquires genetic changes that lead to blocking d-Ser uptake into the cell or activating a silent enzyme for degrading d-Ser. This prevents growth inhibition and, critically, inhibits the repression of attachment machinery normally caused by d-Ser. These findings highlight the importance of pathogen evolution in determining how host molecules regulate colonization. These interactions underpin a process known as niche restriction that is important for pathogen success within the host. The molecular environment of the host can have profound effects on the behavior of resident bacterial species. We recently established how the sensing and response of enterohemorrhagic Escherichia coli (EHEC) to d-serine (d-Ser) resulted in down-regulation of type 3 secretion system-dependent colonization, thereby avoiding unfavorable environments abundant in this toxic metabolite. However, this model ignores a key determinant of the success of bacterial pathogens, adaptive evolution. In this study, we have explored the adaptation of EHEC to d-Ser and its consequences for pathogenesis. We rapidly isolated multiple, independent, EHEC mutants whose growth was no longer compromised in the presence of d-Ser. Through a combination of whole-genome sequencing and transcriptomics, we showed that tolerance could be attributed to disruption of one of two d-Ser transporters and/or activation of a previously nonfunctional d-Ser deaminase. While the implication of cytoplasmic transport in d-Ser toxicity was unsurprising, disruption of a single transporter, CycA, was sufficient to completely overcome the repression of type 3 secretion system activity normally associated with exposure to d-Ser. Despite the fact that this reveals a mechanism by which evolution could drive a pathogen to colonize new niches, interrogation of sequenced E. coli O157:H7 genomes showed a high level of CycA conservation, highlighting a strong selective pressure for functionality. Collectively, these data show that CycA is a critically important conduit for d-Ser uptake that is central to the niche restriction of EHEC.
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8
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Yu Y, Yang J, Zheng LY, Sheng Q, Li CY, Wang M, Zhang XY, McMinn A, Zhang YZ, Song XY, Chen XL. Diversity of D-Amino Acid Utilizing Bacteria From Kongsfjorden, Arctic and the Metabolic Pathways for Seven D-Amino Acids. Front Microbiol 2020; 10:2983. [PMID: 31998270 PMCID: PMC6965332 DOI: 10.3389/fmicb.2019.02983] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022] Open
Abstract
D-amino acids (DAAs) are an important component of the refractory dissolved organic matter pool in the ocean. Microbes play a vital role in promoting the recycling of DAAs in the ocean. However, the diversity of marine DAA-utilizing bacteria and how they metabolize DAAs are seldom studied. Here, by enrichment culture with DAAs as the sole nitrogen source, bacteria of 12 families from three phyla were recovered from surface seawater and sediment from Kongsfjorden, Arctic, and seven DAA-utilizing bacterial strains were isolated. These strains have different DAA-utilizing abilities. Of the seven DAAs used, Halomonas titanicae SM1922 and Pseudoalteromonas neustonica SM1927 were able to utilize seven and five of them, respectively, while the other strains were able to utilize only one or two. Based on genomic, transcriptional and biochemical analyses, the key genes involved in DAA metabolism in each strain were identified and the metabolic pathways for the seven DAAs in these marine bacteria were identified. Conversion of DAAs into α-keto acids is generally the main pathway in marine DAA-utilizing bacteria, which is performed by several key enzymes, including DAA oxidoreductases/dehydrogenases, D-serine ammonia-lyases, D-serine ammonia-lyase DSD1s and DAA transaminases. In addition, conversion of DAAs into LAAs is another pathway, which is performed by amino acid racemases. Among the identified key enzymes, D-serine ammonia-lyase DSD1 and Asp racemase are first found to be employed by bacteria for DAA utilization. These results shed light on marine DAA-utilizing bacteria and the involved DAA metabolism pathways, offering a better understanding of the DAA recycling in the ocean.
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Affiliation(s)
- Yang Yu
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Li-Yuan Zheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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9
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Queiroz PS, Ruas FAD, Barboza NR, de Castro Borges W, Guerra-Sá R. Alterations in the proteomic composition of Serratia marcescens in response to manganese (II). BMC Biotechnol 2018; 18:83. [PMID: 30594179 PMCID: PMC6311052 DOI: 10.1186/s12896-018-0493-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/17/2018] [Indexed: 02/03/2023] Open
Abstract
Background Proteomics is an important tool for the investigation of dynamic physiological responses of microbes under heavy metal stress. To gain insight into how bacteria respond to manganese (II) and identify the proteins involved in Mn (II) oxidation, the shotgun proteomics approach was applied to a potential Mn (II)-oxidizing Serratia marcescens strain cultivated in the absence and presence of Mn (II). Results The LG1 strain, which grew equally well in the two conditions, was found to express a set of proteins related to cellular processes vital for survival, as well as proteins involved in adaptation and tolerance to Mn (II). The multicopper oxidase CueO was identified, indicating its probable participation in the Mn (II) bio-oxidation; however, its expression was not modulated by the presence of Mn (II). A set of proteins related to cell and metabolic processes vital to the cells were downregulated in the presence of Mn (II), while cell membrane-related proteins involved in the maintenance of cell integrity and survival under stress were upregulated under this condition. Conclusions These findings indicate that the LG1 strain may be applied successfully in the bioremediation of Mn (II), and the shotgun approach provides an efficient means for obtaining the total proteome of this species.
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Affiliation(s)
- Pollyana Santos Queiroz
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Ciências Biológicas (DECBI) & Instituto de Ciências Exatas e Biológica (NUPEB), Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - France Anne Dias Ruas
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Ciências Biológicas (DECBI) & Instituto de Ciências Exatas e Biológica (NUPEB), Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Natália Rocha Barboza
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Ciências Biológicas (DECBI) & Instituto de Ciências Exatas e Biológica (NUPEB), Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - William de Castro Borges
- Laboratório de Enzimologia e Proteômica, Departamento de Ciências Biológicas (DECBI), Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Renata Guerra-Sá
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Ciências Biológicas (DECBI) & Instituto de Ciências Exatas e Biológica (NUPEB), Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
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10
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Aliashkevich A, Alvarez L, Cava F. New Insights Into the Mechanisms and Biological Roles of D-Amino Acids in Complex Eco-Systems. Front Microbiol 2018; 9:683. [PMID: 29681896 PMCID: PMC5898190 DOI: 10.3389/fmicb.2018.00683] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/22/2018] [Indexed: 01/22/2023] Open
Abstract
In the environment bacteria share their habitat with a great diversity of organisms, from microbes to humans, animals and plants. In these complex communities, the production of extracellular effectors is a common strategy to control the biodiversity by interfering with the growth and/or viability of nearby microbes. One of such effectors relies on the production and release of extracellular D-amino acids which regulate diverse cellular processes such as cell wall biogenesis, biofilm integrity, and spore germination. Non-canonical D-amino acids are mainly produced by broad spectrum racemases (Bsr). Bsr’s promiscuity allows it to generate high concentrations of D-amino acids in environments with variable compositions of L-amino acids. However, it was not clear until recent whether these molecules exhibit divergent functions. Here we review the distinctive biological roles of D-amino acids, their mechanisms of action and their modulatory properties of the biodiversity of complex eco-systems.
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Affiliation(s)
- Alena Aliashkevich
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Laura Alvarez
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
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11
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Zhang Z, Liu Y, Liu P, Yang L, Jiang X, Luo D, Yang D. Non-invasive detection of gastric cancer relevant d-amino acids with luminescent DNA/silver nanoclusters. NANOSCALE 2017; 9:19367-19373. [PMID: 29199749 DOI: 10.1039/c7nr07337b] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Chirality plays essential roles in life systems such that l-amino acids (LAAs) are predominantly found as the building units of protein for organisms. The presence of the d-enantiomer (DAA) has been found to be specifically relevant to gastric cancer. We herein construct a luminescent DNA/silver nanocluster based biosensing system to achieve rapid and specific detection of DAAs. As a proof of application, we detected DAAs in saliva samples from patients with gastric cancer, and the test results exhibited excellent specificity. Our detection system has the following major advantages: (i) the detection is rapid, being completed in less than 1 hour; (ii) the limit of detection falls in the effective range of DAA concentrations of gastric cancer at an early stage, indicating that our method is potentially suitable for early diagnosis of gastric cancer; (iii) the non-invasive sampling manner provides an adaptable system for point-of-care testing (POCT); and (iv) the system does not require any massive instruments or expensive reagents, which enables POCT as well.
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Affiliation(s)
- Zhikun Zhang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300350, China.
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12
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Xu J, Bai Y, Fan T, Zheng X, Cai Y. Expression, purification, and characterization of a membrane-bound D-amino acid dehydrogenase from Proteus mirabilis JN458. Biotechnol Lett 2017; 39:1559-1566. [PMID: 28676939 DOI: 10.1007/s10529-017-2388-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/19/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To characterize a novel membrane-bound D -amino acid dehydrogenase from Proteus mirabilis JN458 (PmDAD). RESULTS The recombinant PmDAD protein, encoding a peptide of 434 amino acids with a MW of 47.7 kDa, exhibited broad substrate specificity with D -alanine the most preferred substrate. The K m and V max values for D -alanine were 9 mM and 20 μmol min-1 mg-1, respectively. Optimal activity was at pH 8 and 45 °C. Additionally, this PmDAD generated H2O2 and exhibited 68 and 60% similarity with E. coli K12 DAD and Pseudomonas aeruginosa DAD, respectively, with low degrees of sequence similarity with other bacterial DADs. CONCLUSIONS D-Amino acid dehydrogenase from Proteus mirabilis JN458 was expressed and characterized for the first time, DAD was confirmed to be an alanine dehydrogenase.
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Affiliation(s)
- Jinjin Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Taiping Fan
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China.,Department of Pharmacology, University of Cambridge, Cambridge, CB2 1T, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Kubota T, Kobayashi T, Nunoura T, Maruyama F, Deguchi S. Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms. Front Microbiol 2016; 7:511. [PMID: 27148200 PMCID: PMC4836201 DOI: 10.3389/fmicb.2016.00511] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/29/2016] [Indexed: 12/27/2022] Open
Abstract
Microorganisms that utilize various D-amino acids (DAAs) were successfully isolated from deep-sea sediments. The isolates were phylogenetically assigned to Alphaproteobacteria, Gammmaproteobacteria, and Bacilli. Some of the isolates exhibited high enantioselective degradation activities to various DAAs. In particular, the Alphaproteobacteria Nautella sp. strain A04V exhibited robust growth in minimal medium supplemented with D-Val as a sole carbon and nitrogen source, whereas its growth was poor on minimal medium supplemented with L-Val instead of D-Val. Its growth was facilitated most when racemic mixtures of valine were used. In contrast, the Nautella strains isolated from shallow-sea grew only with L-Val. No significant differences were found among the strains in the genome sequences including genes possibly related to DAA metabolisms.
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Affiliation(s)
- Takaaki Kubota
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Tohru Kobayashi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Shigeru Deguchi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
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Kobori H, Tanigawa M, Maeda S, Hori H, Yubisui T, Nagata Y. Methemoglobin reduction mediated by D-amino acid dehydrogenase in Propsilocerus akamusi (Tokunaga) larvae. JOURNAL OF INSECT PHYSIOLOGY 2015; 77:33-38. [PMID: 25896287 DOI: 10.1016/j.jinsphys.2015.04.002] [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: 10/17/2014] [Revised: 03/06/2015] [Accepted: 04/12/2015] [Indexed: 06/04/2023]
Abstract
A methemoglobin (metHb) reduction system is required for aerobic respiration. In humans, Fe(III)-heme-bearing metHb (the oxidized form of hemoglobin), which cannot bind oxygen, is converted to Fe(II)-heme-bearing oxyhemoglobin (oxyHb, the reduced form), which can bind oxygen, in a system comprising NADH, NADH-cytochrome b5 reductase, and cytochrome b5. However, the mechanism of metHb reduction in organisms that inhabit oxygen-deficient environments is unknown. In the coelomic fluid of the larvae of Propsilocerus akamusi, which inhabit a microaerobic environment, we found that metHb was reduced by D-alanine. We purified an FAD-containing enzyme, D-amino acid dehydrogenase (DAD), and component V hemoglobin from the larvae. Using the purified components and spectrophotometric analyses, we showed a novel function of DAD: DAD-mediation of P. akamusi component V metHb reduction with using D-alanine as an electron donor. P. akamusi larvae possess this D-alanine-DAD metHb reduction system in addition to a previously discovered NADH-NADH-cytochrome b5 reductase system. This is the first report of the presence of DAD in a multicellular organism. The molecular mass of DAD was estimated to be 45 kDa. The optimal pH and temperature of the enzyme were 7.4 and 20 °C, respectively, and the optimal substrate was D-alanine. The enzyme activity was inhibited by benzoate and sulfhydryl-binding reagents.
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Affiliation(s)
- Hiroki Kobori
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Kanda-Surugadai, Chiyoda Ward, Tokyo 101-8308, Japan
| | - Minoru Tanigawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Kanda-Surugadai, Chiyoda Ward, Tokyo 101-8308, Japan
| | - Shintaro Maeda
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Kanda-Surugadai, Chiyoda Ward, Tokyo 101-8308, Japan
| | - Hiroshi Hori
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Toshitsugu Yubisui
- Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Yoko Nagata
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Kanda-Surugadai, Chiyoda Ward, Tokyo 101-8308, Japan.
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Maeda S, Kobori H, Tanigawa M, Sato K, Yubisui T, Hori H, Nagata Y. Methemoglobin reduction by NADH-cytochrome b(5) reductase in Propsilocerus akamusi larvae. Comp Biochem Physiol B Biochem Mol Biol 2015; 185:54-61. [PMID: 25829149 DOI: 10.1016/j.cbpb.2015.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 03/17/2015] [Accepted: 03/22/2015] [Indexed: 10/23/2022]
Abstract
For oxygen respiration, a methemoglobin (metHb) reduction system is needed in the cell because metHb cannot bind oxygen. We examined the insect Propsilocerus akamusi larvae to elucidate the metHb reduction system in an organism that inhabits an oxygen-deficient environment. NADH-dependent reduction of metHb in coelomic fluid suggested the coexistence of cytochrome b5 reductase (b5R) and cytochrome b5 with hemoglobin in the fluid and that these proteins were involved in physiological metHb reduction in the larvae. The presence of b5R was revealed by purifying b5R to homogeneity from the midge larvae. Using purified components, we showed that larval metHb was reduced via the NADH-b5R (FAD)-cytochrome b5-metHb pathway, a finding consistent with that in aerobic vertebrates, specifically humans and rabbits, and b5R function between mammal and insect was conserved. b5R was identified as a monomeric FAD-containing enzyme; it had a molecular mass of 33.2 kDa in gel-filtration chromatography and approximately 37 kDa in SDS-PAGE analysis. The enzyme's optimal pH and temperature were 6.4 and 25 °C, respectively. The apparent Km and Vmax values were 345 μM and 160 μmol min(-1) mg(-1), respectively, for ferricyanide and 328 μM and 500 μmol min(-1) mg(-1), respectively, for 2,6-dichlorophenolindophenol. The enzyme reaction was inhibited by benzoate, p-hydroxymercuribenzoate, iodoacetamide, and iodoacetate, and was not inhibited by metal ions or EDTA.
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Affiliation(s)
- Shintaro Maeda
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Tokyo 101-8308, Japan
| | - Hiroki Kobori
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Tokyo 101-8308, Japan
| | - Minoru Tanigawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Tokyo 101-8308, Japan
| | - Katsuya Sato
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Tokyo 101-8308, Japan
| | - Toshitsugu Yubisui
- Department of Biochemistry, Faculty of Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Hiroshi Hori
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan
| | - Yoko Nagata
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Tokyo 101-8308, Japan.
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Zhang D, Chen X, Zhang R, Yao P, Wu Q, Zhu D. Development of β-Amino Acid Dehydrogenase for the Synthesis of β-Amino Acids via Reductive Amination of β-Keto Acids. ACS Catal 2015. [DOI: 10.1021/cs5017358] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dalong Zhang
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Xi Chen
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Rui Zhang
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Center for Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
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Watanabe S, Morimoto D, Fukumori F, Shinomiya H, Nishiwaki H, Kawano-Kawada M, Sasai Y, Tozawa Y, Watanabe Y. Identification and characterization of D-hydroxyproline dehydrogenase and Delta1-pyrroline-4-hydroxy-2-carboxylate deaminase involved in novel L-hydroxyproline metabolism of bacteria: metabolic convergent evolution. J Biol Chem 2012; 287:32674-88. [PMID: 22833679 DOI: 10.1074/jbc.m112.374272] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
L-hydroxyproline (4-hydroxyproline) mainly exists in collagen, and most bacteria cannot metabolize this hydroxyamino acid. Pseudomonas putida and Pseudomonas aeruginosa convert L-hydroxyproline to α-ketoglutarate via four hypothetical enzymatic steps different from known mammalian pathways, but the molecular background is rather unclear. Here, we identified and characterized for the first time two novel enzymes, D-hydroxyproline dehydrogenase and Δ(1)-pyrroline-4-hydroxy-2-carboxylate (Pyr4H2C) deaminase, involved in this hypothetical pathway. These genes were clustered together with genes encoding other catalytic enzymes on the bacterial genomes. D-hydroxyproline dehydrogenases from P. putida and P. aeruginosa were completely different from known bacterial proline dehydrogenases and showed similar high specificity for substrate (D-hydroxyproline) and some artificial electron acceptor(s). On the other hand, the former is a homomeric enzyme only containing FAD as a prosthetic group, whereas the latter is a novel heterododecameric structure consisting of three different subunits (α(4)β(4)γ(4)), and two FADs, FMN, and [2Fe-2S] iron-sulfur cluster were contained in αβγ of the heterotrimeric unit. These results suggested that the L-hydroxyproline pathway clearly evolved convergently in P. putida and P. aeruginosa. Pyr4H2C deaminase is a unique member of the dihydrodipicolinate synthase/N-acetylneuraminate lyase protein family, and its activity was competitively inhibited by pyruvate, a common substrate for other dihydrodipicolinate synthase/N-acetylneuraminate lyase proteins. Furthermore, disruption of Pyr4H2C deaminase genes led to loss of growth on L-hydroxyproline (as well as D-hydroxyproline) but not L- and D-proline, indicating that this pathway is related only to L-hydroxyproline degradation, which is not linked to proline metabolism.
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Affiliation(s)
- Seiya Watanabe
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan.
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Purification of Helicobacter pylori NCTC 11637 cytochrome bc1 and respiration with D-proline as a substrate. J Bacteriol 2009; 192:1410-5. [PMID: 20023020 DOI: 10.1128/jb.01111-09] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori is a microaerophilic bacterium associated with gastric inflammation and peptic ulcers. Knowledge of how pathogenic organisms produce energy is important from a therapeutic point of view. We found d-amino acid dehydrogenase-mediated electron transport from d-proline or d-alanine to oxygen via the respiratory chain in H. pylori. Coupling of the electron transport to ATP synthesis was confirmed by using uncoupler reagents. We reconstituted the electron transport chain to demonstrate the electron flow from the d-amino acids to oxygen using the recombinant cytochrome bc(1) complex, cytochrome c-553, and the terminal oxidase cytochrome cbb(3) complex. Upon addition of the recombinant d-amino acid dehydrogenase and d-proline or d-alanine to the reconstituted electron transport system, reduction of cytochrome cbb(3) and oxygen consumption was revealed spectrophotometrically and polarographically, respectively. Among the constituents of H. pylori's electron transport chain, only the cytochrome bc(1) complex had been remained unpurified. Therefore, we cloned and sequenced the H. pylori NCTC 11637 cytochrome bc(1) gene clusters encoding Rieske Fe-S protein, cytochrome b, and cytochrome c(1), with calculated molecular masses of 18 kDa, 47 kDa, and 32 kDa, respectively, and purified the recombinant monomeric protein complex with a molecular mass of 110 kDa by gel filtration. The absorption spectrum of the recombinant cytochrome bc(1) complex showed an alpha peak at 561 nm with a shoulder at 552 nm.
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