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Hao S, Shen L, Liu P, Yong Q, Wang Y, Zheng X. Development of a prognostic model for muscle-invasive bladder cancer using glutamine metabolism. Comput Biol Med 2024; 171:108223. [PMID: 38430744 DOI: 10.1016/j.compbiomed.2024.108223] [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: 11/07/2023] [Revised: 01/31/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Muscle-invasive bladder cancer (MIBC) is distinguished by its pronounced invasiveness and unfavorable prognosis. Immunotherapy and targeted therapy have emerged as key treatment options for various types of cancer. Altered metabolism is a defining characteristic of cancer cells, and there is mounting evidence suggesting the important role of glutamine metabolism (GM) in tumor metabolism. Nevertheless, the relationship between GM and clinical outcomes, immune microenvironment, and immunotherapy in MIBC remains unknown. METHODS This study employed Mendelian randomization to explore the causal relationship between blood metabolites and bladder tumors. We systematically evaluated 373 glutamine metabolism-related genes and identified prognostic-related genes, leading to the construction of a glutamine-associated prognostic model. Further analysis confirmed the correlation between high and low-risk groups with the tumor microenvironment, immune cell infiltration, and tumor mutation burden. Subsequently, we assessed the relationship between the risk score and the sensitivity to various immunotherapies and anticancer drugs. RESULTS We identified 14 blood metabolites at the molecular level that have a causal relationship with bladder tumors. At the gene level, the study discussed differentially expressed GM genes in MIBC. First, we established a risk model predicting overall survival (OS) based on GM genes, confirming its reliable predictive ability in MIBC patients and validated it in a GEO cohort. Additionally, a reliable column line chart was created. Secondly, two distinct molecular subtypes were identified, and the associations between different risk groups and tumor microenvironment and immune infiltration were observed. In addition, the predicted risk values correlated with responses to a broad range of pharmaceutical agents. CONCLUSION In summary, we confirmed the causal relationship between blood metabolites and bladder tumors. Furthermore, a risk scoring model related to glutamine metabolism consisting of 9 genes was developed. This model could potentially serve as a useful tool for predicting prognosis and guiding the treatment of MIBC patients.
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Affiliation(s)
- Sida Hao
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China; Department of Urology, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, 310003, Zhejiang, China.
| | - Lin Shen
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
| | - Pengju Liu
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
| | - Qin Yong
- Department of Urology, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, 310003, Zhejiang, China.
| | - Yeqiang Wang
- Department of Urology, Zhejiang Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, 310003, Zhejiang, China.
| | - Xiangyi Zheng
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
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Bigi MM, Forrellad MA, García JS, Blanco FC, Vázquez CL, Bigi F. An update on Mycobacterium tuberculosis lipoproteins. Future Microbiol 2023; 18:1381-1398. [PMID: 37962486 DOI: 10.2217/fmb-2023-0088] [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: 04/17/2023] [Accepted: 08/29/2023] [Indexed: 11/15/2023] Open
Abstract
Almost 3% of the proteins of Mycobacterium tuberculosis (M. tuberculosis), the main causative agent of human tuberculosis, are lipoproteins. These lipoproteins are characteristic of the mycobacterial cell envelope and participate in many mechanisms involved in the pathogenesis of M. tuberculosis. In this review, the authors provide an updated analysis of M. tuberculosis lipoproteins and categorize them according to their demonstrated or predicted functions, including transport of compounds to and from the cytoplasm, biosynthesis of the mycobacterial cell envelope, defense and resistance mechanisms, enzymatic activities and signaling pathways. In addition, this updated analysis revealed that at least 40% of M. tuberculosis lipoproteins are glycosylated.
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Affiliation(s)
- María M Bigi
- Instituto de Investigaciones Biomédicas, CONICET, Universidad de Buenos Aires, Paraguay 2155 (C1121ABG), Buenos Aires, Argentina
| | - Marina A Forrellad
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria, Argentina (INTA), N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
| | - Julia S García
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria, Argentina (INTA), N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
| | - Federico C Blanco
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria, Argentina (INTA), N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
| | - Cristina L Vázquez
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria, Argentina (INTA), N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
| | - Fabiana Bigi
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria, Argentina (INTA), N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, N. Repetto & de los Reseros, Hurlingham (1686), Buenos Aires, Argentina
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Xu L, Han F, Zhang X, Yu Q. Ultrasound enhanced biosynthesis of L-theanine from L-glutamine and ethylamine by recombinant γ-glutamyltranspeptidase. BIORESOURCE TECHNOLOGY 2020; 307:123251. [PMID: 32245672 DOI: 10.1016/j.biortech.2020.123251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
A mutant library of the key amino acid residue site E387 in γ-glutamyltranspeptidase was constructed to screen the mutant enzymes with significantly improved thermal stability (E387Q). The reaction temperature of the mutant enzyme (E387Q) was 10℃ higher than that of the parent enzyme. Ultrasound-assisted synthesis of L-theanine by γ-glutamyltranspeptidase was investigated. The effects of ultrasonic power, reaction pH and substrate concentration on the enzymatic synthesis of L-theanine were studied by the response surface method. The results showed that the optimal process conditions are ultrasonic power of 100 W, reaction pH of 9, substrate L-glutamine concentration of 120 mmol/L, reaction temperature of 45℃, and L-theanine yield of 89.1%. The yield of L-theanine is 2.61 times higher than that obtained without ultrasound. Ultrasound can significantly promote the synthesis of L-theanine by γ-glutamyltranspeptidase.
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Affiliation(s)
- Lisheng Xu
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China.
| | - Fangkai Han
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China
| | - Xingtao Zhang
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China
| | - Qiaoling Yu
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China
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Ruwe M, Persicke M, Busche T, Müller B, Kalinowski J. Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum. Front Microbiol 2019; 10:2769. [PMID: 31849906 PMCID: PMC6892785 DOI: 10.3389/fmicb.2019.02769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
The alarmone species ppGpp and pppGpp are elementary components of bacterial physiology as they both coordinate the bacterial stress response and serve as fine-tuners of general metabolism during conditions of balanced growth. Since the regulation of (p)ppGpp metabolism and the effects of (p)ppGpp on cellular processes are highly complex and show massive differences between bacterial species, the underlying molecular mechanisms have so far only been insufficiently investigated for numerous microorganisms. In this study, (p)ppGpp physiology in the actinobacterial model organism Corynebacterium glutamicum was analyzed by phenotypic characterization and RNAseq-based transcriptome analysis. Total nutrient starvation was identified as the most effective method to induce alarmone production, whereas traditional induction methods such as the addition of serine hydroxamate (SHX) or mupirocin did not show a strong accumulation of (p)ppGpp. The predominant alarmone in C. glutamicum represents guanosine tetraphosphate, whose stress-associated production depends on the presence of the bifunctional RSH enzyme Rel. Interestingly, in addition to ppGpp, another substance yet not identified accumulated strongly under inducing conditions. A C. glutamicum triple mutant (Δrel,ΔrelS,ΔrelH) unable to produce alarmones [(p)ppGpp0 strain] exhibited unstable growth characteristics and interesting features such as an influence of illumination on its physiology, production of amino acids as well as differences in vitamin and carotenoid production. Differential transcriptome analysis using RNAseq provided numerous indications for the molecular basis of the observed phenotype. An evaluation of the (p)ppGpp-dependent transcriptional regulation under total nutrient starvation revealed a complex interplay with the involvement of ribosome-mediated transcriptional attenuation, the stress-responsive sigma factors σB and σH and transcription factors such as McbR, the master regulator of sulfur metabolism. In addition to the differential regulation of genes connected with various cell functions, the transcriptome analysis revealed conserved motifs within the promoter regions of (p)ppGpp-dependently and independently regulated genes. In particular, the representatives of translation-associated genes are both (p)ppGpp-dependent transcriptionally downregulated and show a highly conserved and so far unknown TTTTG motif in the -35 region, which is also present in other actinobacterial genera.
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Affiliation(s)
- Matthias Ruwe
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Xu G, Zha J, Cheng H, Ibrahim MHA, Yang F, Dalton H, Cao R, Zhu Y, Fang J, Chi K, Zheng P, Zhang X, Shi J, Xu Z, Gross RA, Koffas MAG. Engineering Corynebacterium glutamicum for the de novo biosynthesis of tailored poly-γ-glutamic acid. Metab Eng 2019; 56:39-49. [PMID: 31449877 DOI: 10.1016/j.ymben.2019.08.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/15/2019] [Accepted: 08/17/2019] [Indexed: 11/17/2022]
Abstract
γ-Polyglutamic acid (γ-PGA) is a biodegradable polymer naturally produced by Bacillus spp. that has wide applications. Fermentation of γ-PGA using Bacillus species often requires the supplementation of L-glutamic acid, which greatly increases the overall cost. Here, we report a metabolically engineered Corynebacterium glutamicum capable of producing γ-PGA from glucose. The genes encoding γ-PGA synthase complex from B. subtilis (pgsB, C, and A) or B. licheniformis (capB, C, and A) were expressed under inducible promoter Ptac in a L-glutamic acid producer C. glutamicum ATCC 13032, which led to low levels of γ-PGA production. Subsequently, C. glutamicum F343 with a strong L-glutamic acid production capability was tested. C. glutamicum F343 carrying capBCA produced γ-PGA up to 11.4 g/L, showing a higher titer compared with C. glutamicum F343 expressing pgsBCA. By introducing B. subtilis glutamate racemase gene racE under Ptac promoter mutants with different expression strength, the percentage of L-glutamic acid units in γ-PGA could be adjusted from 97.1% to 36.9%, and stayed constant during the fermentation process, while the γ-PGA titer reached 21.3 g/L under optimal initial glucose concentrations. The molecular weight (Mw) of γ-PGA in the engineered strains ranged from 2000 to 4000 kDa. This work provides a foundation for the development of sustainable and cost-effective de novo production of γ-PGA from glucose with customized ratios of L-glutamic acid in C. glutamicum.
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Affiliation(s)
- Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Jian Zha
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Hui Cheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Mohammad H A Ibrahim
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Chemistry of Natural and Microbial Products Department, National Research Centre, Al-Bohoos St., Cairo, 12622, Egypt
| | - Fan Yang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Hunter Dalton
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States
| | - Rong Cao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Yaxin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Jiahua Fang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Kaijun Chi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Pu Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiaomei Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; Laboratory of Pharmaceutical Engineering, School of Pharmaceutics, Jiangnan University, Wuxi, 214122, China
| | - Jinsong Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; Laboratory of Pharmaceutical Engineering, School of Pharmaceutics, Jiangnan University, Wuxi, 214122, China
| | - Zhenghong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China; Laboratory of Pharmaceutical Engineering, School of Pharmaceutics, Jiangnan University, Wuxi, 214122, China.
| | - Richard A Gross
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Chemistry of Natural and Microbial Products Department, National Research Centre, Al-Bohoos St., Cairo, 12622, Egypt; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.
| | - Mattheos A G Koffas
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Chemistry of Natural and Microbial Products Department, National Research Centre, Al-Bohoos St., Cairo, 12622, Egypt; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
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Ruwe M, Rückert C, Kalinowski J, Persicke M. Functional Characterization of a Small Alarmone Hydrolase in Corynebacterium glutamicum. Front Microbiol 2018; 9:916. [PMID: 29867827 PMCID: PMC5954133 DOI: 10.3389/fmicb.2018.00916] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/20/2018] [Indexed: 11/13/2022] Open
Abstract
The (pp)pGpp metabolism is an important component of bacterial physiology as it is involved in various stress responses and mechanisms of cell homeostasis, e.g., the regulation of growth. However, in order to better understand the (pp)pGpp associated regulation, it is crucial to study the molecular mechanisms of (pp)pGpp metabolism. In recent years, bioinformatic analyses of the RelA/SpoT homolog (RSH) superfamily have led to the discovery of small monofunctional RSH derivatives in addition to the well-known bifunctional Rel proteins. These are also referred to as small alarmone synthetases (SASs) or small alarmone hydrolases (SAHs). In this study, the ORF cg1485 from C. glutamicum was identified as a putative SAH encoding gene, based on a high similarity of the corresponding amino acid sequence with the (pp)pGpp hydrolysis domain. The characterization of its gene product, designated as RelHCg, represents the first functional investigation of a bacterial representative of the SAH subfamily. The predicted pyrophosphohydrolase activity was demonstrated in vivo by expression in two E. coli strains, characterized by different alarmone basal levels, as well as by in vitro analysis of the purified protein. During the assay-based analysis of hydrolysis activity in relation to the three known alarmone species, both RelHCg and the bifunctional RSH enzyme RelCg were found to exhibit a pronounced substrate inhibition for alarmone concentrations of more than 0.75 mM. This characteristic of (pp)pGpp hydrolases could be an important mechanism for realizing the bistable character of the (pp)pGpp metabolism between a (pp)pGpp basal level and stress-associated alarmone production. The deletion of relHCg caused only a minor effect on growth behavior in both wild-type background and deletion mutants with deletion of (pp)pGpp synthetases. Based on this observation, the protein is probably only present or active under specific environmental conditions. The independent loss of the corresponding gene in numerous representatives of the genus Corynebacterium, which was found by bioinformatic analyses, also supports this hypothesis. Furthermore, growth analysis of all possible deletion combinations of the three active C. glutamicum RSH genes revealed interesting functional relationships which will have to be investigated in more detail in the future.
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Affiliation(s)
- Matthias Ruwe
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Charve J, Manganiello S, Glabasnia A. Analysis of Umami Taste Compounds in a Fermented Corn Sauce by Means of Sensory-Guided Fractionation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:1863-1871. [PMID: 29397710 DOI: 10.1021/acs.jafc.7b05633] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Corn sauce, an ingredient obtained from the fermentation of enzymatically hydrolyzed corn starch and used in culinary applications to provide savory taste, was investigated in this study. The links between its sensory properties and taste compounds were assessed using a combination of analytical and sensory approaches. The analyses revealed that glutamic acid, sodium chloride, and acetic acid were the most abundant compounds, but they could not explain entirely the savory taste. The addition of other compounds, found at subthreshold concentrations (alanine, glutamyl peptides, and one Amadori compound), contributed partly to close the sensory gap between the re-engineered sample and the original product. Further chemical breakdown, by a sensory-guided fractionation approach, led to the isolation of two fractions with taste-modulating effects. Analyses by mass spectrometry and nuclear magnetic resonance showed that the fractions contained glutamyl peptides, pyroglutamic acid, glutamic acid, valine, N-formyl-glutamic acid, and N-acetyl-glutamine.
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Kulis-Horn RK, Rückert C, Kalinowski J, Persicke M. Sequence-based identification of inositol monophosphatase-like histidinol-phosphate phosphatases (HisN) in Corynebacterium glutamicum, Actinobacteria, and beyond. BMC Microbiol 2017; 17:161. [PMID: 28720084 PMCID: PMC5516325 DOI: 10.1186/s12866-017-1069-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/10/2017] [Indexed: 12/30/2022] Open
Abstract
Background The eighth step of l-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized. Moreover, there exist several IMPase-like proteins in bacteria (e.g. CysQ, ImpA, and SuhB) which are very similar to HisN but most likely do not participate in l-histidine biosynthesis. Results Deletion of hisN, the gene encoding the IMPase-like HolPase in C. glutamicum, does not result in complete l-histidine auxotrophy. Out of four hisN homologs present in the genome of C. glutamicum (impA, suhB, cysQ, and cg0911), only cg0911 encodes an enzyme with HolPase activity. The enzymatic properties of HisN and Cg0911 were determined, delivering the first available kinetic data for IMPase-like HolPases. Additionally, we analyzed the amino acid sequences of potential HisN, ImpA, SuhB, CysQ and Cg0911 orthologs from bacteria and identified six conserved sequence motifs for each group of orthologs. Mutational studies confirmed the importance of a highly conserved aspartate residue accompanied by several aromatic amino acid residues present in motif 5 for HolPase activity. Several bacterial proteins containing all identified HolPase motifs, but showing only moderate sequence similarity to HisN from C. glutamicum, were experimentally confirmed as IMPase-like HolPases, demonstrating the value of the identified motifs. Based on the confirmed IMPase-like HolPases two profile Hidden Markov Models (HMMs) were build using an iterative approach. These HMMs allow the fast, reliable detection and differentiation of the two paralog groups from each other and other IMPases. Conclusion The kinetic data obtained for HisN from C. glutamicum, as an example for an IMPase-like HolPases, shows remarkable differences in enzyme properties as compared to HAD- or PHP-type HolPases. The six sequence motifs and the HMMs presented in this study can be used to reliably differentiate between IMPase-like HolPases and IMPase-like proteins with no such activity, with the potential to enhance current and future genome annotations. A phylogenetic analysis reveals that IMPase-like HolPases are not only present in Actinobacteria and plant but can be found in further bacterial phyla, including, among others, Proteobacteria, Chlorobi and Planctomycetes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1069-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert Kasimir Kulis-Horn
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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