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Li S, Chen F, Li Y, Wang L, Li H, Gu G, Li E. Rhamnose-Containing Compounds: Biosynthesis and Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165315. [PMID: 36014553 PMCID: PMC9415975 DOI: 10.3390/molecules27165315] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Rhamnose-associated molecules are attracting attention because they are present in bacteria but not mammals, making them potentially useful as antibacterial agents. Additionally, they are also valuable for tumor immunotherapy. Thus, studies on the functions and biosynthetic pathways of rhamnose-containing compounds are in progress. In this paper, studies on the biosynthetic pathways of three rhamnose donors, i.e., deoxythymidinediphosphate-L-rhamnose (dTDP-Rha), uridine diphosphate-rhamnose (UDP-Rha), and guanosine diphosphate rhamnose (GDP-Rha), are firstly reviewed, together with the functions and crystal structures of those associated enzymes. Among them, dTDP-Rha is the most common rhamnose donor, and four enzymes, including glucose-1-phosphate thymidylyltransferase RmlA, dTDP-Glc-4,6-dehydratase RmlB, dTDP-4-keto-6-deoxy-Glc-3,5-epimerase RmlC, and dTDP-4-keto-Rha reductase RmlD, are involved in its biosynthesis. Secondly, several known rhamnosyltransferases from Geobacillus stearothermophilus, Saccharopolyspora spinosa, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Streptococcus pneumoniae are discussed. In these studies, however, the functions of rhamnosyltransferases were verified by employing gene knockout and radiolabeled substrates, which were almost impossible to obtain and characterize the products of enzymatic reactions. Finally, the application of rhamnose-containing compounds in disease treatments is briefly described.
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Affiliation(s)
- Siqiang Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Fujia Chen
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Yun Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Lizhen Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, China
| | - Hongyan Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
- Correspondence: (G.G.); (E.L.)
| | - Enzhong Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
- Correspondence: (G.G.); (E.L.)
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Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G. Structure and genetics of Escherichia coli O antigens. FEMS Microbiol Rev 2020; 44:655-683. [PMID: 31778182 PMCID: PMC7685785 DOI: 10.1093/femsre/fuz028] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and three (O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.
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Affiliation(s)
- Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Axel Furevi
- Department of Organic Chemistry, Arrhenius Laboratory, Svante Arrhenius väg 16C, Stockholm University, S-106 91 Stockholm, Sweden
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Hengchun Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Quan Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Peter R Reeves
- School of Molecular and Microbial Bioscience, University of Sydney, 2 Butilin Ave, Darlington NSW 2008, Sydney, Australia
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjing 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Svante Arrhenius väg 16C, Stockholm University, S-106 91 Stockholm, Sweden
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Li Y, Huang J, Wang X, Xu C, Han T, Guo X. Genetic Characterization of the O-Antigen and Development of a Molecular Serotyping Scheme for Enterobacter cloacae. Front Microbiol 2020; 11:727. [PMID: 32411106 PMCID: PMC7198725 DOI: 10.3389/fmicb.2020.00727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
Enterobacter cloacae is a well-characterized opportunistic pathogen that is closely associated with various nosocomial infections. The O-antigen, which is one of the most variable constituents on the cell surface, has been used widely and traditionally for serological classification of many gram-negative bacteria. E. cloacae is divided into 30 serotypes, based on its O-antigen diversity. In this study, by using genomic and comparative-genomic approaches, we analyzed the O-antigen gene clusters of 26 E. cloacae serotypes in depth. We also identified the sero-specific gene for each serotype and developed a multiplex polymerase chain reaction (PCR) method. The sensitivity of the assay was 0.1 ng for genomic DNA and 103 colony forming units for pure cultures. The assay reliability was evaluated by double-blinded testing with 81 clinical strains. Furthermore, we established a valid, genome-based tool for in silico serotyping of E. cloacae. By screening 431 E. cloacae genomes deposited in GenBank, 304 were classified into current antigenic scheme, and 112 were allocated into 55 putative novel serotypes. Our results represent the first genetic basis of the O-antigen diversity and variation of E. cloacae, providing a rationale for studying the O-antigen associated evolution and pathogenesis of this bacterium. In addition, we extended the current serotyping system for E. cloacae, which is important for detection and epidemiological surveillance purposes for this important pathogen.
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Affiliation(s)
- Yayue Li
- The Third Central Hospital of Tianjin, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Junjie Huang
- Department of Vascular Surgery, Tianjin Hospital, Tianjin, China
| | - Xiaotong Wang
- Tianjin Children's Hospital, Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Cong Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Tao Han
- The Third Central Hospital of Tianjin, Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Xi Guo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
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Cao H, Wang M, Wang Q, Xu T, Du Y, Li H, Qian C, Yin Z, Wang L, Wei Y, Wu P, Guo X, Yang B, Liu B. Identifying genetic diversity of O antigens in Aeromonas hydrophila for molecular serotype detection. PLoS One 2018; 13:e0203445. [PMID: 30183757 PMCID: PMC6124807 DOI: 10.1371/journal.pone.0203445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/21/2018] [Indexed: 01/08/2023] Open
Abstract
Aeromonas hydrophila is a globally occurring, potentially virulent, gram-negative opportunistic pathogen that is known to cause water and food-borne diseases around the world. In this study, we use whole genome sequencing and in silico analyses to identify 14 putative O antigen gene clusters (OGCs) located downstream of the housekeeping genes acrB and/or oprM. We have also identified 7 novel OGCs by analyzing 15 publicly available genomes of different A. hydrophila strains. From the 14 OGCs identified initially, we have deduced that O antigen processing genes involved in the wzx/wzy pathway and the ABC transporter (wzm/wzt) pathway exhibit high molecular diversity among different A. hydrophila strains. Using these genes, we have developed a multiplexed Luminex-based array system that can identify up to 14 A. hydrophila strains. By combining our other results and including the sequences of processing genes from 13 other OGCs (7 OGCs identified from publicly available genome sequences and 6 OGCs that were previously published), we also have the data to create an array system that can identify 25 different A. hydrophila serotypes. Although clinical detection, epidemiological surveillance, and tracing of pathogenic bacteria are typically done using serotyping methods that rely on identifying bacterial surface O antigens through agglutination reactions with antisera, molecular methods such as the one we have developed may be quicker and more cost effective. Our assay shows high specificity, reproducibility, and sensitivity, being able to classify A. hydrophila strains using just 0.1 ng of genomic DNA. In conclusion, our findings indicate that a molecular serotyping system for A. hydrophila could be developed based on specific genes, providing an important molecular tool for the identification of A. hydrophila serotypes.
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Affiliation(s)
- Hengchun Cao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Min Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Qian Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Tingting Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Yuhui Du
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Huiying Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Chengqian Qian
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Zhiqiu Yin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Lu Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Yi Wei
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Pan Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Xi Guo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
| | - Bin Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
- * E-mail: (BY); (BL)
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin Economic-Technological Development Area, Tianjin, China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Economic-Technological Development Area, Tianjin, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, China
- * E-mail: (BY); (BL)
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Yu X, Torzewska A, Zhang X, Yin Z, Drzewiecka D, Cao H, Liu B, Knirel YA, Rozalski A, Wang L. Genetic diversity of the O antigens of Proteus species and the development of a suspension array for molecular serotyping. PLoS One 2017; 12:e0183267. [PMID: 28817637 PMCID: PMC5560731 DOI: 10.1371/journal.pone.0183267] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/01/2017] [Indexed: 11/18/2022] Open
Abstract
Proteus species are well-known opportunistic pathogens frequently associated with skin wound and urinary tract infections in humans and animals. O antigen diversity is important for bacteria to adapt to different hosts and environments, and has been used to identify serotypes of Proteus isolates. At present, 80 Proteus O-serotypes have been reported. Although the O antigen structures of most Proteus serotypes have been identified, the genetic features of these O antigens have not been well characterized. The O antigen gene clusters of Proteus species are located between the cpxA and secB genes. In this study, we identified 55 O antigen gene clusters of different Proteus serotypes. All clusters contain both the wzx and wzy genes and exhibit a high degree of heterogeneity. Potential functions of O antigen-related genes were proposed based on their similarity to genes in available databases. The O antigen gene clusters and structures were compared, and a number of glycosyltransferases were assigned to glycosidic linkages. In addition, an O serotype-specific suspension array was developed for detecting 31 Proteus serotypes frequently isolated from clinical specimens. To our knowledge, this is the first comprehensive report to describe the genetic features of Proteus O antigens and to develop a molecular technique to identify different Proteus serotypes.
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Affiliation(s)
- Xiang Yu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Agnieszka Torzewska
- Department of Immunobiology of Bacteria, Department of General Microbiology Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Xinjie Zhang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Zhiqiu Yin
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Dominika Drzewiecka
- Department of Immunobiology of Bacteria, Department of General Microbiology Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Hengchun Cao
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Yuriy A. Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Antoni Rozalski
- Department of Immunobiology of Bacteria, Department of General Microbiology Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Lei Wang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
- * E-mail:
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Structure and genetics of the O-antigen of Cronobacter sakazakii G2726 (serotype O3) closely related to the O-antigen of C. muytjensii 3270. Carbohydr Res 2012; 355:50-5. [DOI: 10.1016/j.carres.2012.02.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/24/2012] [Accepted: 02/27/2012] [Indexed: 11/23/2022]
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7
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Genetic analysis of the Cronobacter sakazakii O4 to O7 O-antigen gene clusters and development of a PCR assay for identification of all C. sakazakii O serotypes. Appl Environ Microbiol 2012; 78:3966-74. [PMID: 22447597 DOI: 10.1128/aem.07825-11] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative bacterium Cronobacter sakazakii is an emerging food-borne pathogen that causes severe invasive infections in neonates. Variation in the O-antigen lipopolysaccharide in the outer membrane provides the basis for Gram-negative bacteria serotyping. The O-antigen serotyping scheme for C. sakazakii, which includes seven serotypes (O1 to O7), has been recently established, and the O-antigen gene clusters and specific primers for three C. sakazakii serotypes (O1, O2, and O3) have been characterized. In this study, the C. sakazakii O4, O5, O6, and O7 O-antigen gene clusters were sequenced, and gene functions were predicted on the basis of homology. C. sakazakii O4 shared a similar O-antigen gene cluster with Escherichia coli O103. The general features and anomalies of all seven C. sakazakii O-antigen gene clusters were evaluated and the relationship between O-antigen structures and their gene clusters were investigated. Serotype-specific genes for O4 to O7 were identified, and a molecular serotyping method for all C. sakazakii O serotypes, a multiplex PCR assay, was developed by screening against 136 strains of C. sakazakii and closely related species. The sensitivity of PCR-based serotyping method was determined to be 0.01 ng of genomic DNA and 10(3) CFU of each strain/ml. This study completes the elucidation of C. sakazakii O-antigen genetics and provides a molecular method suitable for the identification of C. sakazakii O1 to O7 strains.
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Shashkov AS, Arbatsky NP, Knirel YA. Structures and genetics of Kdo-containing O-antigens of Cronobacter sakazakii G2706 and G2704, the reference strains of serotypes O5 and O6. Carbohydr Res 2011; 346:1924-9. [DOI: 10.1016/j.carres.2011.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/11/2011] [Accepted: 05/12/2011] [Indexed: 01/28/2023]
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9
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Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves PR, Wang L. Structure and genetics ofShigellaO antigens. FEMS Microbiol Rev 2008; 32:627-53. [DOI: 10.1111/j.1574-6976.2008.00114.x] [Citation(s) in RCA: 241] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Molecular analysis of the Enterobacter sakazakii O-antigen gene locus. Appl Environ Microbiol 2008; 74:3783-94. [PMID: 18441119 DOI: 10.1128/aem.02302-07] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleotide polymorphism associated with the O-antigen-encoding locus, rfb, in Enterobacter sakazakii was determined by PCR-restriction fragment length polymorphism analysis. Based on the analysis of these DNA profiles, 12 unique banding patterns were detected among a collection of 62 strains from diverse origins. Two common profiles were identified and were designated serotypes O:1 and O:2. DNA sequencing of the 12,500-bp region flanked by galF and gnd identified 11 open reading frames, all with the same transcriptional direction. Analysis of the proximal region of both sequences demonstrated remarkable heterogeneity. A PCR assay targeting genes specific for the two prominent serotypes was developed and applied for the identification of these strains recovered from food, environmental, and clinical samples.
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11
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The Aeromonas hydrophila wb*O34 gene cluster: genetics and temperature regulation. J Bacteriol 2008; 190:4198-209. [PMID: 18408022 DOI: 10.1128/jb.00153-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Aeromonas hydrophila wb*(O34) gene cluster of strain AH-3 (serotype O34) was cloned and sequenced. This cluster contains genes necessary for the production of O34-antigen lipopolysaccharide (LPS) in A. hydrophila. We determined, using either mutation or sequence homology, roles for the majority of genes in the cluster by using the chemical O34-antigen LPS structure obtained for strain AH-3. The O34-antigen LPS export system has been shown to be a Wzy-dependent pathway typical of heteropolysaccharide pathways. Furthermore, the production of A. hydrophila O34-antigen LPS in Escherichia coli K-12 strains is dependent on incorporation of the Gne enzyme (UDP-N-acetylgalactosamine 4-epimerase) necessary for the formation of UDP-galactosamine in these strains. By using rapid amplification of cDNA ends we were able to identify a transcription start site upstream of the terminal wzz gene, which showed differential transcription depending on the growth temperature of the strain. The Wzz protein is able to regulate the O34-antigen LPS chain length. The differential expression of this protein at different temperatures, which was substantially greater at 20 degrees C than at 37 degrees C, explains the previously observed differential production of O34-antigen LPS and its correlation with the virulence of A. hydrophila serotype O34 strains.
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12
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Barry CE, Crick DC, McNeil MR. Targeting the formation of the cell wall core of M. tuberculosis. Infect Disord Drug Targets 2007; 7:182-202. [PMID: 17970228 PMCID: PMC4747060 DOI: 10.2174/187152607781001808] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mycobacteria have a unique cell wall, which is rich in drug targets. The cell wall core consists of a peptidoglycan layer, a mycolic acid layer, and an arabinogalactan polysaccharide connecting them. The detailed structure of the cell wall core is largely, although not completely, understood and will be presented. The biosynthetic pathways of all three components reveal significant drug targets that are the basis of present drugs and/or have potential for new drugs. These pathways will be reviewed and include enzymes involved in polyisoprene biosynthesis, soluble arabinogalactan precursor production, arabinogalactan polymerization, fatty acid synthesis, mycolate maturation, and soluble peptidoglycan precursor formation. Information relevant to targeting all these enzymes will be presented in tabular form. Selected enzymes will then be discussed in more detail. It is thus hoped this chapter will aid in the selection of targets for new drugs to combat tuberculosis.
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Affiliation(s)
- Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Host Defense, NIAID, NIH, Twinbrook 2, Room 239, 12441 Parklawn Drive, Rockville, MD 20852
| | - Dean C. Crick
- Mycobacterial Research Laboratories, Dept. of Microbiology, Immunology, and Pathology, 1682 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1682
| | - Michael R. McNeil
- Mycobacterial Research Laboratories, Dept. of Microbiology, Immunology, and Pathology, 1682 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1682
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13
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Abstract
The rapid progress in structural and molecular biology over the past fifteen years has allowed chemists to access the structures of enzymes, of their complexes and of mutants. This wealth of structural information has led to a surge in the interest in enzymes as elegant chemical catalysts. Enzymology is a distinguished field and has been making vital contributions to medicine and basic science long before structural biology. This review for the Colworth Medal Lecture discusses work from the author's laboratory. This work has been carried out in collaboration with many other laboratories. The work has mapped out the chemical mechanisms and structures of interesting novel enzymes. The review tries to highlight the interesting chemical aspects of the mechanisms involved and how structural analysis has provided a detailed insight. The review focuses on carbohydrate-processing pathways in bacteria, and includes some recent data on an integral membrane protein.
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Affiliation(s)
- J H Naismith
- Centre for Biomolecular Sciences, The University, St Andrews, KY16 9ST, UK.
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14
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Samuel G, Reeves P. Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Carbohydr Res 2004; 338:2503-19. [PMID: 14670712 DOI: 10.1016/j.carres.2003.07.009] [Citation(s) in RCA: 344] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The O-antigen is an important component of the outer membrane of Gram-negative bacteria. It is a repeat unit polysaccharide and consists of a number of repeats of an oligosaccharide, the O-unit, which generally has between two and six sugar residues. O-Antigens are extremely variable, the variation lying in the nature, order and linkage of the different sugars within the polysaccharide. The genes involved in O-antigen biosynthesis are generally found on the chromosome as an O-antigen gene cluster, and the structural variation of O-antigens is mirrored by genetic variation seen in these clusters. The genes within the cluster fall into three major groups. The first group is involved in nucleotide sugar biosynthesis. These genes are often found together in the cluster and have a high level of identity. The genes coding for a significant number of nucleotide sugar biosynthesis pathways have been identified and these pathways seem to be conserved in different O-antigen clusters and across a wide range of species. The second group, the glycosyl transferases, is involved in sugar transfer. They are often dispersed throughout the cluster and have low levels of similarity. The third group is the O-antigen processing genes. This review is a summary of the current knowledge on these three groups of genes that comprise the O-antigen gene clusters, focusing on the most extensively studied E. coli and S. enterica gene clusters.
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Affiliation(s)
- Gabrielle Samuel
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia
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15
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Amann S, Dräger G, Rupprath C, Kirschning A, Elling L. (Chemo)enzymatic synthesis of dTDP-activated 2,6-dideoxysugars as building blocks of polyketide antibiotics. Carbohydr Res 2001; 335:23-32. [PMID: 11553351 DOI: 10.1016/s0008-6215(01)00195-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The flexible substrate spectrum of the recombinant enzymes from the biosynthetic pathway of dTDP-beta-L-rhamnose in Salmonella enterica, serovar typhimurium (LT2), was exploited for the chemoenzymatic synthesis of deoxythymidine diphosphate- (dTDP-) activated 2,6-dideoxyhexoses. The enzymatic synthesis strategy yielded dTDP-2-deoxy-alpha-D-glucose and dTDP-2,6-dideoxy-4-keto-alpha-D-glucose (13) in a 40-60 mg scale. The nucleotide deoxysugar 13 was further used for the enzymatic synthesis of dTDP-2,6-dideoxy-beta-L-arabino-hexose (dTDP-beta-L-olivose) (15) in a 30-mg scale. The chemical reduction of 13 gave dTDP-2,6-dideoxy-alpha-D-arabino-hexose (dTDP-alpha-D-olivose) (1) as the main isomer after product isolation in a 10-mg scale. With 13 as an important key intermediate, the in vitro characterization of enzymes involved in the biosynthesis of dTDP-activated 2,6-dideoxy-, 2,3,6-trideoxy-D- and L-hexoses can now be addressed. Most importantly, compounds 1 and 15 are donor substrates for the in vitro characterization of glycosyltransferases involved in the biosynthesis of polyketides and other antibiotic/antitumor drugs. Their synthetic access may contribute to the evaluation of the glycosylation potential of bacterial glycosyltransferases to generate hybrid antibiotics.
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Affiliation(s)
- S Amann
- Institute of Enzyme Technology, Heinrich-Heine-University, Düsseldorf Research Center Jülich, D-52426 Jülich, Germany
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16
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Ma Y, Stern RJ, Scherman MS, Vissa VD, Yan W, Jones VC, Zhang F, Franzblau SG, Lewis WH, McNeil MR. Drug targeting Mycobacterium tuberculosis cell wall synthesis: genetics of dTDP-rhamnose synthetic enzymes and development of a microtiter plate-based screen for inhibitors of conversion of dTDP-glucose to dTDP-rhamnose. Antimicrob Agents Chemother 2001; 45:1407-16. [PMID: 11302803 PMCID: PMC90481 DOI: 10.1128/aac.45.5.1407-1416.2001] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An L-rhamnosyl residue plays an essential structural role in the cell wall of Mycobacterium tuberculosis. Therefore, the four enzymes (RmlA to RmlD) that form dTDP-rhamnose from dTTP and glucose-1-phosphate are important targets for the development of new tuberculosis therapeutics. M. tuberculosis genes encoding RmlA, RmlC, and RmlD have been identified and expressed in Escherichia coli. It is shown here that genes for only one isotype each of RmlA to RmlD are present in the M. tuberculosis genome. The gene for RmlB is Rv3464. Rv3264c was shown to encode ManB, not a second isotype of RmlA. Using recombinant RmlB, -C, and -D enzymes, a microtiter plate assay was developed to screen for inhibitors of the formation of dTDP-rhamnose. The three enzymes were incubated with dTDP-glucose and NADPH to form dTDP-rhamnose and NADP(+) with a concomitant decrease in optical density at 340 nm (OD(340)). Inhibitor candidates were monitored for their ability to lower the rate of OD(340) change. To test the robustness and practicality of the assay, a chemical library of 8,000 compounds was screened. Eleven inhibitors active at 10 microM were identified; four of these showed activities against whole M. tuberculosis cells, with MICs from 128 to 16 microg/ml. A rhodanine structural motif was present in three of the enzyme inhibitors, and two of these showed activity against whole M. tuberculosis cells. The enzyme assay was used to screen 60 Peruvian plant extracts known to inhibit the growth of M. tuberculosis in culture; two extracts were active inhibitors in the enzyme assay at concentrations of less than 2 microg/ml.
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Affiliation(s)
- Y Ma
- Department of Microbiology, Colorado State University, Fort Collins, Colorado 80523, USA
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17
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Rahim R, Burrows LL, Monteiro MA, Perry MB, Lam JS. Involvement of the rml locus in core oligosaccharide and O polysaccharide assembly in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 11):2803-2814. [PMID: 11065359 DOI: 10.1099/00221287-146-11-2803] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
L-Rhamnose (L-Rha) is a component of the lipopolysaccharide (LPS) core, several O antigen polysaccharides, and the cell surface surfactant rhamnolipid of Pseudomonas aeruginosa. In this study, four contiguous genes (rmlBDAC) responsible for the synthesis of dTDP-L-Rha in P. aeruginosa have been cloned and characterized. Non-polar chromosomal rmlC mutants were generated in P. aeruginosa strains PAO1 (serotype O5) and PAK (serotype O6) and LPS extracted from the mutants was analysed by SDS-PAGE and Western immunoblotting. rmlC mutants of both serotype O5 and serotype O6 synthesized a truncated core region which was unable to act as an attachment point for either A-band or B-band O antigen. A rmd rmlC PAO1 double mutant (deficient in biosynthesis of both D-Rha and L-Rha) was constructed to facilitate structural analysis of the mutant core region. This strain has an incomplete core oligosaccharide region and does not produce A-band O antigen. These results provide the genetic and structural evidence that L-Rha is the receptor on the P. aeruginosa LPS core for the attachment of O polysaccharides. This is the first report of a genetically defined mutation that affects the synthesis of a single sugar in the core oligosaccharide region of P. aeruginosa LPS, and provides further insight into the mechanisms of LPS biosynthesis and assembly in this bacterium.
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Affiliation(s)
- Rahim Rahim
- Canadian Bacterial Diseases Network, Networks of Centers of Excellence, Heritage Medical Research Building, Hospital Drive, Calgary, Alberta, Canada T2N 4N12
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada, N1G 2W11
| | - Lori L Burrows
- Center for Infection and Biomaterials Research, NU13-143, Toronto General Hospital, Toronto, Ontario, Canada M5G 2C43
| | - Mario A Monteiro
- Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada K1A OR64
- Canadian Bacterial Diseases Network, Networks of Centers of Excellence, Heritage Medical Research Building, Hospital Drive, Calgary, Alberta, Canada T2N 4N12
| | - Malcolm B Perry
- Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada K1A OR64
- Canadian Bacterial Diseases Network, Networks of Centers of Excellence, Heritage Medical Research Building, Hospital Drive, Calgary, Alberta, Canada T2N 4N12
| | - Joseph S Lam
- Canadian Bacterial Diseases Network, Networks of Centers of Excellence, Heritage Medical Research Building, Hospital Drive, Calgary, Alberta, Canada T2N 4N12
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada, N1G 2W11
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18
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Graninger M, Nidetzky B, Heinrichs DE, Whitfield C, Messner P. Characterization of dTDP-4-dehydrorhamnose 3,5-epimerase and dTDP-4-dehydrorhamnose reductase, required for dTDP-L-rhamnose biosynthesis in Salmonella enterica serovar Typhimurium LT2. J Biol Chem 1999; 274:25069-77. [PMID: 10455186 DOI: 10.1074/jbc.274.35.25069] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The thymidine diphosphate-L-rhamnose biosynthesis pathway is required for assembly of surface glycoconjugates in a growing list of bacterial pathogens, making this pathway a potential therapeutic target. However, the terminal reactions have not been characterized. To complete assignment of the reactions, the four enzymes (RmlABCD) that constitute the pathway in Salmonella enterica serovar Typhimurium LT2 were overexpressed. The purified RmlC and D enzymes together catalyze the terminal two steps involving NAD(P)H-dependent formation of dTDP-L-rhamnose from dTDP-6-deoxy-D-xylo-4-hexulose. RmlC was assigned as the thymidine diphosphate-4-dehydrorhamnose 3,5-epimerase by showing its activity to be NAD(P)H-independent. Spectrofluorometric and radiolabeling experiments were used to demonstrate the ability of RmlC to catalyze the formation of dTDP-6-deoxy-L-lyxo-4-hexulose from dTDP-6-deoxy-D-xylo-4-hexulose. Under reaction conditions, RmlC converted approximately 3% of its substrate to product. RmlD was unequivocally identified as the thymidine diphosphate-4-dehydrorhamnose reductase. The reductase property of RmlD was shown by equilibrium analysis and its ability to enable efficient biosynthesis of dTDP-L-rhamnose, even in the presence of low amounts of dTDP-6-deoxy-L-lyxo-4-hexulose. Comparison of 23 known and predicted RmlD sequences identified several conserved amino acid residues, especially the serine-tyrosine-lysine catalytic triad, characteristic for members of the reductase/epimerase/dehydrogenase protein superfamily. In conclusion, RmlD is a novel member of this protein superfamily.
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Affiliation(s)
- M Graninger
- Zentrum für Ultrastrukturforschung und Ludwig Boltzmann-Institut für Molekulare Nanotechnologie, Universität für Bodenkultur Wien, A-1180 Wien, Austria
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