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Luo L, Wei H, Kong D, Wan L, Jiang Y, Qin S, Suo Y. Efficient production of butyric acid from lignocellulosic biomass by revealing the mechanisms of Clostridium tyrobutyricum tolerance to phenolic inhibitors. BIORESOURCE TECHNOLOGY 2024; 396:130427. [PMID: 38336212 DOI: 10.1016/j.biortech.2024.130427] [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: 11/22/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Phenolic compounds (PCs) generated during pretreatment of lignocellulosic biomass severely hinder the biorefinery by Clostridia. As a hyperbutyrate-producing strain, Clostridium tyrobutyricum has excellent tolerance to PCs, but its tolerance mechanism is poorly understood. In this study, a comprehensive transcriptome analysis was applied to elucidate the response of C. tyrobutyricum to four typical PCs. The findings revealed that the expression levels of genes associated with PC reduction, HSPs, and membrane transport were significantly altered under PC stress. Due to PCs being reduced to low-toxicity alcohols/acids by C. tyrobutyricum, enhancing the reduction of PCs by overexpressing reductase genes could enhance the strain's tolerance to PCs. Under 1.0 g/L p-coumaric acid stress, compared with the wild-type strain, ATCC 25755/sdr1 exhibited a 31.2 % increase in butyrate production and a 38.5 % increase in productivity. These insights contribute to the construction of PC-tolerant Clostridia, which holds promise for improving biofuel and chemical production from lignocellulosic biomass.
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Affiliation(s)
- Linshuang Luo
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Hailing Wei
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Deting Kong
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Liqiong Wan
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Yuntao Jiang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China
| | - Shiwen Qin
- School of Agriculture, Yunnan University, Kunming 650500, China.
| | - Yukai Suo
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Yunnan Minzu University, Kunming 650504, China; Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming 650031, China.
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2
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Chen Y, Ying Y, Lalsiamthara J, Zhao Y, Imani S, Li X, Liu S, Wang Q. From bacteria to biomedicine: Developing therapies exploiting NAD + metabolism. Bioorg Chem 2024; 142:106974. [PMID: 37984103 DOI: 10.1016/j.bioorg.2023.106974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) serves as a critical cofactor in cellular metabolism and redox reactions. Bacterial pathways rely on NAD+ participation, where its stability and concentration govern essential homeostasis and functions. This review delves into the role and metabolic regulation of NAD+ in bacteria, highlighting its influence on physiology and virulence. Notably, we explore enzymes linked to NAD+ metabolism as antibacterial drug targets and vaccine candidates. Moreover, we scrutinize NAD+'s medical potential, offering insights for its application in biomedicine. This comprehensive assessment informs future research directions in the dynamic realm of NAD+ and its biomedical significance.
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Affiliation(s)
- Yu Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Yuanyuan Ying
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Jonathan Lalsiamthara
- Molecular Microbiology & Immunology, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Yuheng Zhao
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, Zhejiang 310015, China
| | - Saber Imani
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Xin Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Sijing Liu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Qingjing Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China.
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3
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Wang J, Liang P, Sun H, Wu Z, Gottschalk M, Qi K, Zheng H. Comparative transcriptomic analysis reveal genes involved in the pathogenicity increase of Streptococcus suis epidemic strains. Virulence 2022; 13:1455-1470. [PMID: 36031944 PMCID: PMC9423846 DOI: 10.1080/21505594.2022.2116160] [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] [Indexed: 11/26/2022] Open
Abstract
Streptococcus suis epidemic strains were responsible for two outbreaks in China and possessed increased pathogenicity which was featured prominently by inducing an excessive inflammatory response at the early phase of infection. To discover the critical genes responsible for the pathogenicity increase of S. suis epidemic strains, the genome-wide transcriptional profiles of epidemic strain SC84 were investigated at the early phase of interaction with BV2 cells. The overall low expression levels of 89K pathogenicity island (PAI) and 129 known virulence genes in the SC84 interaction groups indicated that its pathogenicity increase should be attributed to novel mechanisms. Using highly pathogenic strain P1/7 and intermediately pathogenic strain 89–1591 as controls, 11 pathogenicity increase crucial genes (PICGs) and 38 pathogenicity increase-related genes (PIRGs) were identified in the SC84 incubation groups. The PICGs encoded proteins related to the methionine biosynthesis/uptake pathway and played critical roles in the pathogenicity increase of epidemic strains. A high proportion of PIRGs encoded surface proteins related to host cell adherence and immune escape, which may be conducive to the pathogenicity increase of epidemic strains by rapidly initiating infection. The fact that none of PICGs and PIRGs belonged to epidemic strain-specific gene indicated that the pathogenicity increase of epidemic strain may be determined by the expression level of genes, rather than the presence of them. Our results deepened the understanding on the mechanism of the pathogenicity increase of S. suis epidemic strains and provided novel approaches to control the life-threatening infections of S. suis epidemic strains.
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Affiliation(s)
- Jianping Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Pujun Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- OIE Reference Lab for Swine Streptococcosis, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Zongfu Wu
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada
| | - Marcelo Gottschalk
- Department of Clinical Laboratory, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi Zhuang Autonomous Region, China
| | - Kexin Qi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
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Minazzato G, Gasparrini M, Heroux A, Sernova NV, Rodionov DA, Cianci M, Sorci L, Raffaelli N. Bacterial NadQ (COG4111) is a Nudix-like, ATP-responsive regulator of NAD biosynthesis. J Struct Biol 2022; 214:107917. [PMID: 36332744 DOI: 10.1016/j.jsb.2022.107917] [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: 03/21/2022] [Revised: 10/13/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Nicotinamide-adenine dinucleotide (NAD) is centrally important to metabolic reactions that involve redox chemistry. In bacteria, NAD biosynthesis is controlled by different transcription factors, depending on the species. Among the four regulators identified so far, the protein NadQ is reported to act as a repressor of the de novo NAD biosynthetic pathway in proteobacteria. Using comparative genomics, a systematic reconstruction of NadQ regulons in thousands of fully sequenced bacterial genomes has been performed, confirming that NadQ is present in α-proteobacteria and some β- and γ-proteobacteria, including pathogens like Bordetella pertussis and Neisseria meningitidis, where it likely controls de novo NAD biosynthesis. Through mobility shift assay and mutagenesis, the DNA binding activity of NadQ from Agrobacterium tumefaciens was experimentally validated and determined to be suppressed by ATP. The crystal structures of NadQ in native form and in complex with ATP were determined, indicating that NadQ is a dimer, with each monomer composed of an N-terminal Nudix domain hosting the effector binding site and a C-terminal winged helix-turn-helix domain that binds DNA. Within the dimer, we found one ATP molecule bound, at saturating concentration of the ligand, in keeping with an intrinsic asymmetry of the quaternary structure. Overall, this study provided the basis for depicting a working model of NadQ regulation mechanism.
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Affiliation(s)
- Gabriele Minazzato
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Massimiliano Gasparrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Annie Heroux
- Elettra - Sincrotrone Trieste S.C.P.A., Basovizza, Italy
| | - Natalia V Sernova
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Leonardo Sorci
- Department of Materials, Environmental Sciences and Urban Planning, Division of Bioinformatics and Biochemistry, Polytechnic University of Marche, Ancona, Italy.
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
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5
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Li Y, Wang Y, Liu J. Genomic Insights Into the Interspecific Diversity and Evolution of Mobiluncus, a Pathogen Associated With Bacterial Vaginosis. Front Microbiol 2022; 13:939406. [PMID: 35865929 PMCID: PMC9294530 DOI: 10.3389/fmicb.2022.939406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial vaginosis (BV) is a common vaginal infection and has been associated with increased risk for a wide array of health issues. BV is linked with a variety of heterogeneous pathogenic anaerobic bacteria, among which Mobiluncus is strongly associated with BV diagnosis. However, their genetic features, pathogenicity, interspecific diversity, and evolutionary characters have not been illustrated at genomic level. The current study performed phylogenomic and comparative genomic analyses of Mobiluncus. Phylogenomic analyses revealed remarkable phylogenetic distinctions among different species. Compared with M. curtisii, M. mulieris had a larger genome and pangenome size with more insertion sequences but less CRISPR-Cas systems. In addition, these two species were diverse in profile of virulence factors, but harbored similar antibiotic resistance genes. Statistically different functional genome profiles between strains from the two species were determined, as well as correlations of some functional genes/pathways with putative pathogenicity. We also showed that high levels of horizontal gene transfer might be an important strategy for species diversification and pathogenicity. Collectively, this study provides the first genome sequence level description of Mobiluncus, and may shed light on its virulence/pathogenicity, functional diversification, and evolutionary dynamics. Our study could facilitate the further investigations of this important pathogen, and might improve the future treatment of BV.
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NrtR Mediated Regulation of H1-T6SS in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0185821. [PMID: 35196795 PMCID: PMC8865458 DOI: 10.1128/spectrum.01858-21] [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] [Indexed: 12/02/2022] Open
Abstract
NrtR is a Nudix-related transcriptional regulator that is distributed among diverse bacteria and plays an important role in modulating bacterial intracellular NAD homeostasis. Previously, we showed that NrtR influences the T3SS expression and pathogenesis of Pseudomonas aeruginosa and demonstrated that NrtR mediates T3SS regulation through the cAMP/Vfr pathway. In the present study, we found that mutation of the nrtR gene leads to upregulation of the Hcp secretion island-I type VI secretion system (H1-T6SS). Further analysis revealed that mutation of the nrtR gene results in upregulation of regulatory RNAs (RsmY/RsmZ) that are known to control the H1-T6SS by sequestration of RsmA or RsmN. Simultaneous deletion of rsmY/rsmZ reduced the expression of H1-T6SS in the ΔnrtR mutant. In addition, overexpression of either rsmA or rsmN in ΔnrtR decreased H1-T6SS expression. Chromatin immunoprecipitation (ChIP)-Seq and electrophoretic mobility shift assay (EMSA) analyses revealed that NrtR directly binds to the promoters of rsmY, rsmZ and tssA1 (first gene of the H1-T6SS operon). Overall, the results from this study reveal the molecular details of NrtR-mediated regulation of H1-T6SS in P. aeruginosa. IMPORTANCE NrtR is a Nudix-related transcriptional regulator and controls the NAD cofactor biosynthesis in bacteria. P. aeruginosa NrtR binds to the intergenic region between nadD2 and pcnA to repress the expression of the two operons, therefore controlling the NAD biosynthesis. We have previously reported that NrtR controls T3SS expression via the cAMP/Vfr pathway in P. aeruginosa. However, the global regulatory function and direct binding targets of the NrtR remain elusive in P. aeruginosa. This study reveals novel direct regulatory targets of the NrtR in P. aeruginosa, elucidating the molecular mechanism of NrtR-mediated regulation of H1-T6SS.
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7
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Xu Q, Chen H, Sun W, Zhang Y, Zhu D, Rai KR, Chen JL, Chen Y. sRNA23, a novel small RNA, regulates to the pathogenesis of Streptococcus suis serotype 2. Virulence 2021; 12:3045-3061. [PMID: 34882070 PMCID: PMC8667912 DOI: 10.1080/21505594.2021.2008177] [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] [Indexed: 11/02/2022] Open
Abstract
ABBREVIATION sRNA: small noncoding RNA; FBA: fructose diphosphate aldolase; rplB: 50S ribosomal protein L2; RACE: rapid amplification of cDNA ends; EMSA: electrophoretic mobility shift assay; THB: Todd-Hewitt broth; FBS: fetal bovine serum; BIP: 2,2'-Bipyridine.
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Affiliation(s)
- Quanming Xu
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong Chen
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen Sun
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongyi Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dewen Zhu
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kul Raj Rai
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Chen
- Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Fujian- Fujian Agriculture and Forestry University, Fuzhou, China
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8
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Guo G, Kong X, Du D, Wei D, Yu Y, Zhang W. Genome-wide association study identifies the virulence-associated marker in Streptococcus suis serotype 2. INFECTION GENETICS AND EVOLUTION 2021; 92:104894. [PMID: 33964473 DOI: 10.1016/j.meegid.2021.104894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022]
Abstract
Streptococcus suis (S. suis) has been reported to be a highly invasive pathogen in swine, which causes severe infections like meningitis, arthritis and septicemia, and also a zoonotic agent for humans. Although many putative virulence factors (VFs) have been identified, the exact and wildly accepted virulence associated marker and pathogenesis mechanism of S. suis are still unclear. To establish connection of the genotypes with virulence phenotypes, we performed an "internal standard" method based on the zebrafish model to assess the virulence phenotypes of S. suis and did the genome-wide association study (GWAS) based on the genomes of 68 S. suis isolates. Through GWAS, a total number of 172 genes were identified. Among these genes, 143 of them distribute in virulent isolates. Further VFs interaction network analysis based on protein-protein interaction database found that 71 genes identified in this study could interact with known VFs and some of them even played an important role as the bridge between known VFs or formed important hub. In addition, 12 genes were found conserved in virulent isolates and 3 genes were conserved in avirulent isolates, 8 genes of the virulent conserved genes were belonging to a srtBCD pili cluster. Considering that sbp2', a member of the srtBCD pili cluster has been reported as a virulence-associated factor, we predict that sbp2' could be a fitness virulence-associated marker of virulent isolates. Taken together, our findings contribute to the insights in S. suis pathogenesis, enhance the knowledge of the genomic evolution of S. suis and provide several novel virulence-associated candidates.
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Affiliation(s)
- Genglin Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China.
| | - Xuewei Kong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Dechao Du
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China.
| | - Dan Wei
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China.
| | - Yanfei Yu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Veterinary Biological Engineering and Technology of Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China.
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Kraszewska E, Drabinska J. Nudix proteins affecting microbial pathogenesis. MICROBIOLOGY (READING, ENGLAND) 2020; 166:1110-1114. [PMID: 33253082 DOI: 10.1099/mic.0.000993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nudix proteins catalyse hydrolysis of pyrophosphate bonds in a variety of substrates and are ubiquitous in all domains of life. Their widespread presence and broad substrate specificity suggest that they have important cellular functions. In this review, we summarize the state of knowledge on microbial Nudix proteins involved in pathogenesis.
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Affiliation(s)
- Elzbieta Kraszewska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Joanna Drabinska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
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10
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Gao R, Wei W, Hassan BH, Li J, Deng J, Feng Y. A single regulator NrtR controls bacterial NAD + homeostasis via its acetylation. eLife 2019; 8:51603. [PMID: 31596237 PMCID: PMC6800001 DOI: 10.7554/elife.51603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/04/2019] [Indexed: 12/27/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an indispensable cofactor in all domains of life, and its homeostasis must be regulated tightly. Here we report that a Nudix-related transcriptional factor, designated MsNrtR (MSMEG_3198), controls the de novo pathway of NAD+biosynthesis in M. smegmatis, a non-tuberculosis Mycobacterium. The integrated evidence in vitro and in vivo confirms that MsNrtR is an auto-repressor, which negatively controls the de novo NAD+biosynthetic pathway. Binding of MsNrtR cognate DNA is finely mapped, and can be disrupted by an ADP-ribose intermediate. Unexpectedly, we discover that the acetylation of MsNrtR at Lysine 134 participates in the homeostasis of intra-cellular NAD+ level in M. smegmatis. Furthermore, we demonstrate that NrtR acetylation proceeds via the non-enzymatic acetyl-phosphate (AcP) route rather than by the enzymatic Pat/CobB pathway. In addition, the acetylation also occurs on the paralogs of NrtR in the Gram-positive bacterium Streptococcus and the Gram-negative bacterium Vibrio, suggesting that these proteins have a common mechanism of post-translational modification in the context of NAD+ homeostasis. Together, these findings provide a first paradigm for the recruitment of acetylated NrtR to regulate bacterial central NAD+ metabolism.
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Affiliation(s)
- Rongsui Gao
- Department of Pathogen Biology & Microbiology, and Department General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhui Wei
- Department of Pathogen Biology & Microbiology, and Department General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Jun Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jiaoyu Deng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology, and Department General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,College of Animal Sciences, Zhejiang University, Hangzhou, China
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11
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Wang Q, Hassan BH, Lou N, Merritt J, Feng Y. Functional definition of NrtR, a remnant regulator of NAD + homeostasis in the zoonotic pathogen Streptococcus suis. FASEB J 2019; 33:6055-6068. [PMID: 30759348 PMCID: PMC8793812 DOI: 10.1096/fj.201802179rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/15/2019] [Indexed: 12/16/2022]
Abstract
NAD+ is an enzyme cofactor required for the 3 domains of life. However, little is known about the NAD+ biosynthesis and salvage pathways in the opportunistic pathogen Streptococcus suis. A genome-wide search allows us to identify the NAD+ salvage pathway encoded by an operon of nadR-pnuC-nrtR (from SSU05_1973 to SSU05_1971 on the reverse strand) in the S. suis 05ZYH33 that causes streptococcal toxin shock-like syndrome. The regulator of this pathway is Nudix-related transcriptional regulator (NrtR), a transcription regulator of the Nudix family comprising an N-terminal Nudix-like effector domain, and a C-terminal DNA-binding winged helix-turn-helix-like domain. Intriguingly, the S. suis NrtR naturally contains a single amino acid substitution (K92E) in the catalytic site of its Nudix domain that renders it catalytically inactive but does not influence its ability to bind DNA. Despite its lack of enzymatic activity, DNA-binding activity of NrtR is antagonized by the effector ADP-ribose. Furthermore, nrtR knockout in S. suis serotype 2 reduces its capacity to form biofilms and attenuates its virulence in a mouse infection model. Genome mining indicates that nrtR appears in a strain-specific manner whose occupancy is correlated to bacterial infectivity. Unlike the paradigmatic member of NrtR family having 2 unrelated functions (Nudix hydrolase and DNA binding), S. suis 2 retains a single regulatory role in the modulation of NAD+ salvage. This control of NAD+ homeostasis contributes to S. suis virulence.-Wang, Q., Hassan, B. H., Lou, N., Merritt, J., Feng, Y. Functional definition of NrtR, a remnant regulator of NAD+ homeostasis in the zoonotic pathogen Streptococcus suis.
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Affiliation(s)
- Qingjing Wang
- Department of Pathogen Biology and MicrobiologyDepartment of General Intensive Care Unit of Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Bachar H. Hassan
- Stony Brook Cancer CenterStony Brook UniversityStony BrookNew YorkUSA
| | - Ningjie Lou
- Department of Pathogen Biology and MicrobiologyDepartment of General Intensive Care Unit of Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Justin Merritt
- Department of Restorative DentistryOregon Health and Science UniversityPortlandOregonUSA
| | - Youjun Feng
- Department of Pathogen Biology and MicrobiologyDepartment of General Intensive Care Unit of Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
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