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Gheorghita AA, Wozniak DJ, Parsek MR, Howell PL. Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation. FEMS Microbiol Rev 2023; 47:fuad060. [PMID: 37884397 PMCID: PMC10644985 DOI: 10.1093/femsre/fuad060] [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: 04/21/2023] [Revised: 10/04/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
The biofilm matrix is a fortress; sheltering bacteria in a protective and nourishing barrier that allows for growth and adaptation to various surroundings. A variety of different components are found within the matrix including water, lipids, proteins, extracellular DNA, RNA, membrane vesicles, phages, and exopolysaccharides. As part of its biofilm matrix, Pseudomonas aeruginosa is genetically capable of producing three chemically distinct exopolysaccharides - alginate, Pel, and Psl - each of which has a distinct role in biofilm formation and immune evasion during infection. The polymers are produced by highly conserved mechanisms of secretion, involving many proteins that span both the inner and outer bacterial membranes. Experimentally determined structures, predictive modelling of proteins whose structures are yet to be solved, and structural homology comparisons give us insight into the molecular mechanisms of these secretion systems, from polymer synthesis to modification and export. Here, we review recent advances that enhance our understanding of P. aeruginosa multiprotein exopolysaccharide biosynthetic complexes, and how the glycoside hydrolases/lyases within these systems have been commandeered for antimicrobial applications.
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Affiliation(s)
- Andreea A Gheorghita
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, 776 Biomedical Research Tower, 460 W 12th Ave, Columbus, OH 43210, United States
- Department of Microbiology, The Ohio State University College, Biological Sciences Bldg, 105, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Health Sciences Bldg, 1705 NE Pacific St, Seattle, WA 98195-7735, United States
| | - P Lynne Howell
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
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2
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Chen M, Guo Z, Sun J, Tang W, Wang M, Tang Y, Li P, Wu B, Chen Y. Insights into the biosynthesis of septacidin l-heptosamine moiety unveils a VOC family sugar epimerase. Acta Pharm Sin B 2023; 13:765-774. [PMID: 36873169 PMCID: PMC9978623 DOI: 10.1016/j.apsb.2022.05.031] [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] [Received: 03/25/2022] [Revised: 05/10/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
l-Heptopyranoses are important components of bacterial polysaccharides and biological active secondary metabolites like septacidin (SEP), which represents a group of nucleoside antibiotics with antitumor, antifungal, and pain-relief activities. However, little is known about the formation mechanisms of those l-heptose moieties. In this study, we deciphered the biosynthetic pathway of the l,l-gluco-heptosamine moiety in SEPs by functional characterizing four genes and proposed that SepI initiates the process by oxidizing the 4'-hydroxyl of l-glycero-α-d-manno-heptose moiety of SEP-328 (2) to a keto group. Subsequently, SepJ (C5 epimerase) and SepA (C3 epimerase) shape the 4'-keto-l-heptopyranose moiety by sequential epimerization reactions. At the last step, an aminotransferase SepG installs the 4'-amino group of the l,l-gluco-heptosamine moiety to generate SEP-327 (3). An interesting phenomenon is that the SEP intermediates with 4'-keto-l-heptopyranose moieties exist as special bicyclic sugars with hemiacetal-hemiketal structures. Notably, l-pyranose is usually converted from d-pyranose by bifunctional C3/C5 epimerase. SepA is an unprecedented monofunctional l-pyranose C3 epimerase. Further in silico and experimental studies revealed that it represents an overlooked metal dependent-sugar epimerase family bearing vicinal oxygen chelate (VOC) architecture.
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Affiliation(s)
- Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Laboratory of Microbial Metabolic Engineering, Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Jinyuan Sun
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
| | - Yue Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Mohideen FI, Nguyen LH, Richard JD, Ouadhi S, Kwan DH. In Vitro Reconstitution of the dTDP-l-Daunosamine Biosynthetic Pathway Provides Insights into Anthracycline Glycosylation. ACS Chem Biol 2022; 17:3331-3340. [PMID: 34751552 DOI: 10.1021/acschembio.1c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many small molecule natural products are decorated with sugar moieties that are essential for their biological activity. A considerable number of natural product glycosides and their derivatives are clinically important therapeutics. Anthracyclines like daunorubicin and doxorubicin are examples of valuable glycosylated natural products used in medicine as potent anticancer agents. The sugar moiety, l-daunosamine (a highly modified deoxyhexose), plays a key role in the bioactivity of these molecules as evidenced by semisynthetic anthracycline derivatives such as epirubicin, wherein alteration in the configuration of a single stereocenter of the sugar unit generates a chemotherapeutic drug with lower cardiotoxicity. The nucleotide activated sugar donor that provides the l-daunosamine group for attachment to the natural product scaffold in the biosynthesis of these anthracyclines is dTDP-l-daunosamine. In an in vitro system, we have reconstituted the enzymes in the daunorubicin/doxorubicin pathway involved in the biosynthesis of dTDP-l-daunosamine. Through the study of the enzymatic steps in this reconstituted pathway, we have gained several insights into the assembly of this precursor including the identification of a major bottleneck and competing reactions. We carried out kinetic analysis of the aminotransferase that catalyzes a limiting step of the pathway. Our in vitro reconstituted pathway also provided a platform to test the combinatorial enzymatic synthesis of other dTDP-activated deoxyhexoses as potential tools for "glycodiversification" of natural products. To this end, we replaced the stereospecific ketoreductase that acts in the last step of dTDP-l-daunosamine biosynthesis with an enzyme from a heterologous pathway with opposite stereospecificity and found that it is active in the in vitro pathway, demonstrating the potential for the enzymatic synthesis of nucleotide-activated sugars with regio- and stereospecific tailoring.
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Affiliation(s)
- F Ifthiha Mohideen
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6
| | - Lan Huong Nguyen
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6
| | - Joël D Richard
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
| | - Sara Ouadhi
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada, H4B 1R6
| | - David H Kwan
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, Quebec, Canada G1V 0A6.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada, H4B 1R6
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4
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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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5
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Cross AR, Roy S, Vivoli Vega M, Rejzek M, Nepogodiev SA, Cliff M, Salmon D, Isupov MN, Field RA, Prior JL, Harmer NJ. Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases. J Biol Chem 2022; 298:101903. [PMID: 35398092 PMCID: PMC9095892 DOI: 10.1016/j.jbc.2022.101903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
The sugars streptose and dihydrohydroxystreptose (DHHS) are unique to the bacteria Streptomyces griseus and Coxiella burnetii, respectively. Streptose forms the central moiety of the antibiotic streptomycin, while DHHS is found in the O-antigen of the zoonotic pathogen C. burnetii. Biosynthesis of these sugars has been proposed to follow a similar path to that of TDP-rhamnose, catalyzed by the enzymes RmlA, RmlB, RmlC, and RmlD, but the exact mechanism is unclear. Streptose and DHHS biosynthesis unusually requires a ring contraction step that could be performed by orthologs of RmlC or RmlD. Genome sequencing of S. griseus and C. burnetii has identified StrM and CBU1838 proteins as RmlC orthologs in these respective species. Here, we demonstrate that both enzymes can perform the RmlC 3'',5'' double epimerization activity necessary to support TDP-rhamnose biosynthesis in vivo. This is consistent with the ring contraction step being performed on a double epimerized substrate. We further demonstrate that proton exchange is faster at the 3''-position than the 5''-position, in contrast to a previously studied ortholog. We additionally solved the crystal structures of CBU1838 and StrM in complex with TDP and show that they form an active site highly similar to those of the previously characterized enzymes RmlC, EvaD, and ChmJ. These results support the hypothesis that streptose and DHHS are biosynthesized using the TDP pathway and that an RmlD paralog most likely performs ring contraction following double epimerization. This work will support the elucidation of the full pathways for biosynthesis of these unique sugars.
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Affiliation(s)
- Alice R Cross
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Sumita Roy
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Mirella Vivoli Vega
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Matthew Cliff
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Debbie Salmon
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom; Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Joann L Prior
- Dstl, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Exeter, United Kingdom; Department of Biosciences, University of Exeter, Exeter, United Kingdom.
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6
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Huddleston JP, Anderson TK, Girardi NM, Thoden JB, Taylor Z, Holden HM, Raushel FM. Biosynthesis of d- glycero-l- gluco-Heptose in the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry 2021; 60:1552-1563. [PMID: 33900734 DOI: 10.1021/acs.biochem.1c00183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Campylobacter jejuni is the leading cause of food poisoning in the United States and Europe. The exterior cell surface of C. jejuni is coated with a capsular polysaccharide (CPS) that is essential for the maintenance and integrity of the bacterial cell wall and evasion of the host immune response. The identity and sequences of the monosaccharide components of the CPS are quite variable and dependent on the specific strain of C. jejuni. It is currently thought that the immediate precursor for the multiple variations found in the heptose moieties of the C. jejuni CPS is GDP-d-glycero-α-d-manno-heptose. In C. jejuni NCTC 11168, the heptose moiety is d-glycero-l-gluco-heptose. It has previously been shown that Cj1427 catalyzes the oxidation of GDP-d-glycero-α-d-manno-heptose to GDP-d-glycero-4-keto-α-d-lyxo-heptose using α-ketoglutarate as a cosubstrate. Cj1430 was now demonstrated to catalyze the double epimerization of this product at C3 and C5 to form GDP-d-glycero-4-keto-β-l-xylo-heptose. Cj1428 subsequently catalyzes the stereospecific reduction of this GDP-linked heptose by NADPH to form GDP-d-glycero-β-l-gluco-heptose. The three-dimensional crystal structure of Cj1430 was determined to a resolution of 1.85 Å in the presence of bound GDP-d-glycero-β-l-gluco-heptose, a product analogue. The structure shows that it belongs to the cupin superfamily. The three-dimensional crystal structure of Cj1428 was solved in the presence of NADPH to a resolution of 1.50 Å. Its fold places it into the short-chain dehydrogenase/reductase superfamily. Typically, members in this family display a characteristic signature sequence of YXXXK, with the conserved tyrosine serving a key role in catalysis. In Cj1428, this residue is a phenylalanine.
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Affiliation(s)
- Jamison P Huddleston
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas K Anderson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - Nicholas M Girardi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - Zane Taylor
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 553706, United States
| | - Frank M Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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7
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Wagstaff BA, Zorzoli A, Dorfmueller HC. NDP-rhamnose biosynthesis and rhamnosyltransferases: building diverse glycoconjugates in nature. Biochem J 2021; 478:685-701. [PMID: 33599745 DOI: 10.1042/bcj20200505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/17/2022]
Abstract
Rhamnose is an important 6-deoxy sugar present in many natural products, glycoproteins, and structural polysaccharides. Whilst predominantly found as the l-enantiomer, instances of d-rhamnose are also found in nature, particularly in the Pseudomonads bacteria. Interestingly, rhamnose is notably absent from humans and other animals, which poses unique opportunities for drug discovery targeted towards rhamnose utilizing enzymes from pathogenic bacteria. Whilst the biosynthesis of nucleotide-activated rhamnose (NDP-rhamnose) is well studied, the study of rhamnosyltransferases that synthesize rhamnose-containing glycoconjugates is the current focus amongst the scientific community. In this review, we describe where rhamnose has been found in nature, as well as what is known about TDP-β-l-rhamnose, UDP-β-l-rhamnose, and GDP-α-d-rhamnose biosynthesis. We then focus on examples of rhamnosyltransferases that have been characterized using both in vivo and in vitro approaches from plants and bacteria, highlighting enzymes where 3D structures have been obtained. The ongoing study of rhamnose and rhamnosyltransferases, in particular in pathogenic organisms, is important to inform future drug discovery projects and vaccine development.
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Affiliation(s)
- Ben A Wagstaff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, U.K
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Azul Zorzoli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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8
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Barnawi H, Woodward L, Fava N, Roubakha M, Shaw SD, Kubinec C, Naismith JH, Creuzenet C. Structure-function studies of the C3/C5 epimerases and C4 reductases of the Campylobacter jejuni capsular heptose modification pathways. J Biol Chem 2021; 296:100352. [PMID: 33524389 PMCID: PMC7949155 DOI: 10.1016/j.jbc.2021.100352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/14/2023] Open
Abstract
Many bacteria produce polysaccharide-based capsules that protect them from environmental insults and play a role in virulence, host invasion, and other functions. Understanding how the polysaccharide components are synthesized could provide new means to combat bacterial infections. We have previously characterized two pairs of homologous enzymes involved in the biosynthesis of capsular sugar precursors GDP-6-deoxy-D-altro-heptose and GDP-6-OMe-L-gluco-heptose in Campylobacter jejuni. However, the substrate specificity and mechanism of action of these enzymes-C3 and/or C5 epimerases DdahB and MlghB and C4 reductases DdahC and MlghC-are unknown. Here, we demonstrate that these enzymes are highly specific for heptose substrates, using mannose substrates inefficiently with the exception of MlghB. We show that DdahB and MlghB feature a jellyroll fold typical of cupins, which possess a range of activities including epimerizations, GDP occupying a similar position as in cupins. DdahC and MlghC contain a Rossman fold, a catalytic triad, and a small C-terminal domain typical of short-chain dehydratase reductase enzymes. Integrating structural information with site-directed mutagenesis allowed us to identify features unique to each enzyme and provide mechanistic insight. In the epimerases, mutagenesis of H67, D173, N121, Y134, and Y132 suggested the presence of alternative catalytic residues. We showed that the reductases could reduce GDP-4-keto-6-deoxy-mannulose without prior epimerization although DdahC preferred the pre-epimerized substrate and identified T110 and H180 as important for substrate specificity and catalytic efficacy. This information can be exploited to identify inhibitors for therapeutic applications or to tailor these enzymes to synthesize novel sugars useful as glycobiology tools.
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Affiliation(s)
- Heba Barnawi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Laura Woodward
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK
| | - Natalie Fava
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Mikhail Roubakha
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Steve D Shaw
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Chelsea Kubinec
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - James H Naismith
- Biomedical Sciences Research Complex, St Andrews University, St Andrews, UK; Rosalind Franklin Institute, Research Complex at Harwell, Harwell Campus, Didcot, UK; Division of Structural Biology, Oxford University, Oxford, UK.
| | - Carole Creuzenet
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada.
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9
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Yan Y, Yang J, Wang L, Xu D, Yu Z, Guo X, Horsman GP, Lin S, Tao M, Huang SX. Biosynthetic access to the rare antiarose sugar via an unusual reductase-epimerase. Chem Sci 2020; 11:3959-3964. [PMID: 34122866 PMCID: PMC8152690 DOI: 10.1039/c9sc05766h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Rubrolones, isatropolones, and rubterolones are recently isolated glycosylated tropolonids with notable biological activity. They share similar aglycone skeletons but differ in their sugar moieties, and rubterolones in particular have a rare deoxysugar antiarose of unknown biosynthetic provenance. During our previously reported biosynthetic elucidation of the tropolone ring and pyridine moiety, gene inactivation experiments revealed that RubS3 is involved in sugar moiety biosynthesis. Here we report the in vitro characterization of RubS3 as a bifunctional reductase/epimerase catalyzing the formation of TDP-d-antiarose by epimerization at C3 and reduction at C4 of the key intermediate TDP-4-keto-6-deoxy-d-glucose. These new findings not only explain the biosynthetic pathway of deoxysugars in rubrolone-like natural products, but also introduce RubS3 as a new family of reductase/epimerase enzymes with potential to supply the rare antiarose unit for expanding the chemical space of glycosylated natural products. Rubrolones, isarubrolones, and rubterolones are recently isolated glycosylated tropolonids with notable biological activity.![]()
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Affiliation(s)
- Yijun Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 China
| | - Jing Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 China
| | - Li Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 China
| | - Dongdong Xu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 China
| | - Zhiyin Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 China
| | - Xiaowei Guo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 China
| | - Geoff P Horsman
- Department of Chemistry & Biochemistry, Wilfrid Laurier University Waterloo ON N2L 3C5 Canada
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Sheng-Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences Kunming 650201 China
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10
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Wagstaff BA, Rejzek M, Kuhaudomlarp S, Hill L, Mascia I, Nepogodiev SA, Dorfmueller HC, Field RA. Discovery of an RmlC/D fusion protein in the microalga Prymnesium parvum and its implications for NDP-β-l-rhamnose biosynthesis in microalgae. J Biol Chem 2019; 294:9172-9185. [PMID: 31010825 PMCID: PMC6556577 DOI: 10.1074/jbc.ra118.006440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/19/2019] [Indexed: 11/06/2022] Open
Abstract
The 6-deoxy sugar l-rhamnose (l-Rha) is found widely in plant and microbial polysaccharides and natural products. The importance of this and related compounds in host-pathogen interactions often means that l-Rha plays an essential role in many organisms. l-Rha is most commonly biosynthesized as the activated sugar nucleotide uridine 5'-diphospho-β-l-rhamnose (UDP-β-l-Rha) or thymidine 5'-diphospho-β-l-rhamnose (TDP-β-l-Rha). Enzymes involved in the biosynthesis of these sugar nucleotides have been studied in some detail in bacteria and plants, but the activated form of l-Rha and the corresponding biosynthetic enzymes have yet to be explored in algae. Here, using sugar-nucleotide profiling in two representative algae, Euglena gracilis and the toxin-producing microalga Prymnesium parvum, we show that levels of UDP- and TDP-activated l-Rha differ significantly between these two algal species. Using bioinformatics and biochemical methods, we identified and characterized a fusion of the RmlC and RmlD proteins, two bacteria-like enzymes involved in TDP-β-l-Rha biosynthesis, from P. parvum Using this new sequence and also others, we explored l-Rha biosynthesis among algae, finding that although most algae contain sequences orthologous to plant-like l-Rha biosynthesis machineries, instances of the RmlC-RmlD fusion protein identified here exist across the Haptophyta and Gymnodiniaceae families of microalgae. On the basis of these findings, we propose potential routes for the evolution of nucleoside diphosphate β-l-Rha (NDP-β-l-Rha) pathways among algae.
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Affiliation(s)
- Ben A Wagstaff
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Martin Rejzek
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sakonwan Kuhaudomlarp
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.,Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Lionel Hill
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Ilaria Mascia
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sergey A Nepogodiev
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom, and
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom,
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11
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van der Beek SL, Zorzoli A, Çanak E, Chapman RN, Lucas K, Meyer BH, Evangelopoulos D, de Carvalho LPS, Boons GJ, Dorfmueller HC, van Sorge NM. Streptococcal dTDP-L-rhamnose biosynthesis enzymes: functional characterization and lead compound identification. Mol Microbiol 2019; 111:951-964. [PMID: 30600561 PMCID: PMC6487966 DOI: 10.1111/mmi.14197] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2018] [Indexed: 12/12/2022]
Abstract
Biosynthesis of the nucleotide sugar precursor dTDP‐L‐rhamnose is critical for the viability and virulence of many human pathogenic bacteria, including Streptococcus pyogenes (Group A Streptococcus; GAS), Streptococcus mutans and Mycobacterium tuberculosis. Streptococcal pathogens require dTDP‐L‐rhamnose for the production of structurally similar rhamnose polysaccharides in their cell wall. Via heterologous expression in S. mutans, we confirmed that GAS RmlB and RmlC are critical for dTDP‐L‐rhamnose biosynthesis through their action as dTDP‐glucose‐4,6‐dehydratase and dTDP‐4‐keto‐6‐deoxyglucose‐3,5‐epimerase enzymes respectively. Complementation with GAS RmlB and RmlC containing specific point mutations corroborated the conservation of previous identified catalytic residues. Bio‐layer interferometry was used to identify and confirm inhibitory lead compounds that bind to GAS dTDP‐rhamnose biosynthesis enzymes RmlB, RmlC and GacA. One of the identified compounds, Ri03, inhibited growth of GAS, other rhamnose‐dependent streptococcal pathogens as well as M. tuberculosis with an IC50 of 120–410 µM. Importantly, we confirmed that Ri03 inhibited dTDP‐L‐rhamnose formation in a concentration‐dependent manner through a biochemical assay with recombinant rhamnose biosynthesis enzymes. We therefore conclude that inhibitors of dTDP‐L‐rhamnose biosynthesis, such as Ri03, affect streptococcal and mycobacterial viability and can serve as lead compounds for the development of a new class of antibiotics that targets dTDP‐rhamnose biosynthesis in pathogenic bacteria.
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Affiliation(s)
- Samantha L van der Beek
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Azul Zorzoli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Ebru Çanak
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Robert N Chapman
- Department of Chemistry, Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, USA
| | - Kieron Lucas
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Benjamin H Meyer
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Dimitrios Evangelopoulos
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
| | - Luiz Pedro S de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
| | - Geert-Jan Boons
- Department of Chemistry, Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, USA.,Department of Medical Chemistry and Chemical Biology, Utrecht Institute Pharmaceutical Science, University Utrecht, Utrecht, 3508 TB, The Netherlands
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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12
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Liu B, Hou Y, Wang X, Ma X, Fang S, Huang T, Chen Y, Bai Z, Lin S, Zhang R, Hu K. Structural basis of the mechanism of β-methyl epimerization by enzyme MarH. Org Biomol Chem 2019; 17:9605-9614. [PMID: 31681917 DOI: 10.1039/c9ob01996k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Structures of free MarH and MarH in complex with l-Trp, the analogue of substrate, were determined and the mechanism of MarH-catalyzed stereospecific β-methyl epimerization was proposed.
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13
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Dhaked DK, Bala Divya M, Guruprasad L. A structural and functional perspective on the enzymes of Mycobacterium tuberculosis involved in the L-rhamnose biosynthesis pathway. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 145:52-64. [PMID: 30550737 DOI: 10.1016/j.pbiomolbio.2018.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/12/2018] [Accepted: 12/06/2018] [Indexed: 11/19/2022]
Abstract
Tuberculosis is one of the leading causes of death from bacterial infections. The multi-drug resistant strain has warranted the development of new drug molecules which can inhibit the growth of Mycobacterium tuberculosis (M.tb). Most of the known drugs inhibit the enzymes in the cell wall biosynthesis pathway. One such pathway is L-rhamnose, which involves four druggable enzymes RmlA, B, C and D. The 3D structure analyses of these protein models (RmlA, B and D) and crystal structure (RmlC) has been carried out. Multiple sequence alignments of homologs from distant species of 32 taxa and analyses of available structures were performed in order to study the conservation of sequence and structural motifs, and catalytically important residues. Based on these results and reported mechanism in other organisms, we have predicted putative catalytic mechanism of M.tb enzymes involved in the L-rhamnose biosynthesis pathway.
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Affiliation(s)
- Devendra K Dhaked
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - M Bala Divya
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Lalitha Guruprasad
- School of Chemistry, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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14
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Poosarla VG, Wood TL, Zhu L, Miller DS, Yin B, Wood TK. Dispersal and inhibitory roles of mannose, 2-deoxy-d-glucose and N-acetylgalactosaminidase on the biofilm of Desulfovibrio vulgaris. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:779-787. [PMID: 28925553 DOI: 10.1111/1758-2229.12595] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
Biofilms of sulfate-reducing bacteria (SRB) are often the major cause of microbiologically influenced corrosion. The representative SRB Desulfovibrio vulgaris has previously been shown to have a biofilm that consists primarily of protein. In this study, by utilizing lectin staining, we identified that the biofilm of D. vulgaris also consists of the matrix components mannose, fucose and N-acetylgalactosamine (GalNAc), with mannose predominating. Based on these results, we found that the addition of mannose and the nonmetabolizable mannose analog 2-deoxy-d-glucose inhibits the biofilm formation of D. vulgaris as well as that of D. desulfuricans; both compounds also dispersed the SRB biofilms. In addition, the enzyme N-acetylgalactosaminidase, which degrades GalNAc, was effective in dispersing D. vulgaris biofilms. Therefore, by determining composition of the SRB biofilm, effective biofilm control methods may be devised.
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Affiliation(s)
- Venkata G Poosarla
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Thammajun L Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Lei Zhu
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Daniel S Miller
- Dow Microbial Control, Dow Chemical Company, Collegeville, PA 19426, USA
| | - Bei Yin
- Dow Microbial Control, Dow Chemical Company, Collegeville, PA 19426, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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15
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Shornikov A, Tran H, Macias J, Halavaty AS, Minasov G, Anderson WF, Kuhn ML. Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC). Acta Crystallogr F Struct Biol Commun 2017; 73:664-671. [PMID: 29199987 PMCID: PMC5713671 DOI: 10.1107/s2053230x17015849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022] Open
Abstract
The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 Å resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.
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Affiliation(s)
| | - Ha Tran
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Jennifer Macias
- Department of Chemistry and Biochemistry, San Francisco State University, USA
| | - Andrei S. Halavaty
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - George Minasov
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Wayne F. Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, USA
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16
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Michailidou F, Chung C, Brown MJB, Bent AF, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2017; 56:12492-12497. [PMID: 28786545 PMCID: PMC5656905 DOI: 10.1002/anie.201705639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/28/2017] [Indexed: 01/27/2023]
Abstract
The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3'-deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine-5'-aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3'-deoxy pacidamycin moiety with the synthetic anti-retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.
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Affiliation(s)
- Freideriki Michailidou
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
- GSKStevenageSG1 2NYUK
| | | | | | - Andrew F. Bent
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - James H. Naismith
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | | | | | - Sunil V. Sharma
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Rebecca J. M. Goss
- School of ChemistryUniversity of St AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
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17
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Michailidou F, Chung C, Brown MJB, Bent AF, Naismith JH, Leavens WJ, Lynn SM, Sharma SV, Goss RJM. Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Freideriki Michailidou
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
- GSK Stevenage SG1 2NY UK
| | | | | | - Andrew F. Bent
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - James H. Naismith
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | | | | | - Sunil V. Sharma
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
| | - Rebecca J. M. Goss
- School of Chemistry University of St Andrews North Haugh St Andrews Fife KY16 9ST UK
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18
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Ishigaki Y, Akanuma G, Yoshida M, Horinouchi S, Kosono S, Ohnishi Y. Protein acetylation involved in streptomycin biosynthesis in Streptomyces griseus. J Proteomics 2016; 155:63-72. [PMID: 28034645 DOI: 10.1016/j.jprot.2016.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/03/2016] [Accepted: 12/16/2016] [Indexed: 12/25/2022]
Abstract
Protein acetylation, the reversible addition of an acetyl group to lysine residues, is a protein post-translational modification ubiquitous in living cells. Although the involvement of protein acetylation in the regulation of primary metabolism has been revealed, the function of protein acetylation is largely unknown in secondary metabolism. Here, we characterized protein acetylation in Streptomyces griseus, a streptomycin producer. Protein acetylation was induced in the stationary and sporulation phases in liquid and solid cultures, respectively, in S. griseus. By comprehensive acetylome analysis, we identified 134 acetylated proteins with 162 specific acetylated sites. Acetylation was found in proteins related to primary metabolism and translation, as in other bacteria. However, StrM, a deoxysugar epimerase involved in streptomycin biosynthesis, was identified as a highly acetylated protein by 2-DE-based proteomic analysis. The Lys70 residue, which is critical for the enzymatic activity of StrM, was the major acetylation site. Thus, acetylation of Lys70 was presumed to abolish enzymatic activity of StrM. In accordance with this notion, an S. griseus mutant producing the acetylation-mimic K70Q StrM hardly produced streptomycin, though the K70Q mutation apparently decreased the stability of StrM. A putative lysine acetyltransferase (KAT) SGR1683 in S. griseus, as well as the Escherichia coli KAT YfiQ, acetylated Lys70 of StrM in vitro. Furthermore, absolute quantification analysis estimated that 13% of StrM molecules were acetylated in mycelium grown in solid culture for 3days. These results indicate that StrM acetylation is of biological significance. We propose that StrM acetylation functions as a limiter of streptomycin biosynthesis in S. griseus. BIOLOGICAL SIGNIFICANCE Protein acetylation has been extensively studied not only in eukaryotes, but also in prokaryotes. The acetylome has been analyzed in more than 14 bacterial species. Here, by comprehensive acetylome analysis, we showed that acetylation was found in proteins related to primary metabolism and translation in Streptomyces griseus, similarly to other bacteria. However, five proteins involved in secondary metabolism were also identified as acetylated proteins; these proteins are enzymes in the biosynthesis of streptomycin (StrB1 and StrS), grixazone (GriF), a nonribosomal peptide (NRPS1-2), and a siderophore (AlcC). Additionally, StrM in streptomycin biosynthesis was identified as a highly acetylated protein by 2-DE-based proteomic analysis; approximately 13% of StrM molecules were acetylated. The acetylation occurs at Lys70 to abolish the enzymatic activity of StrM, suggesting that StrM acetylation functions as a limiter of streptomycin biosynthesis in S. griseus. This is the first detailed analysis of protein acetylation of an enzyme involved in secondary metabolism.
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Affiliation(s)
- Yuji Ishigaki
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Genki Akanuma
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Minoru Yoshida
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Sueharu Horinouchi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Saori Kosono
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Biological Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
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19
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Yin S, Liu M, Kong JQ. Functional analyses of OcRhS1 and OcUER1 involved in UDP-L-rhamnose biosynthesis in Ornithogalum caudatum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:536-548. [PMID: 27835851 DOI: 10.1016/j.plaphy.2016.10.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/31/2016] [Accepted: 10/31/2016] [Indexed: 05/27/2023]
Abstract
UDP-L-rhamnose (UDP-Rha) is an important sugar donor for the synthesis of rhamnose-containing compounds in plants. However, only a few enzymes and their encoding genes involved in UDP-Rha biosynthesis are available in plants. Here, two genes encoding rhamnose synthase (RhS) and bi-functional UDP-4-keto-6-deoxy-D-glucose (UDP-4K6DG) 3, 5-epimerase/UDP-4-keto-L-rhamnose (UDP-4KR) 4-keto-reductase (UER) were isolated from Ornithogalum caudatum based on the RNA-Seq data. The OcRhS1 gene has an ORF (open reading frame) of 2019 bp encoding a tri-functional RhS enzyme. In vitro enzymatic assays revealed OcRhS1 can really convert UDP-D-glucose (UDP-Glc) into UDP-Rha via three consecutive reactions. Biochemical evidences indicated that the recombinant OcRhS1 was active in the pH range of 5-11 and over the temperature range of 0-60 °C. The Km value of OcRhS1 for UDP-Glc was determined to be 1.52 × 10-4 M. OcRhS1 is a multi-domain protein with two sets of cofactor-binding motifs. The cofactors dependent properties of OcRhS1 were thus characterized in this research. Moreover, the N-terminal portion of OcRhS1 (OcRhS1-N) was observed to metabolize UDP-Glc to form intermediate UDP-4K6DG. OcUER1 contains an ORF of 906 bp encoding a polypeptide of 301 aa. OcUER1 shared high similarity with the carboxy-terminal domain of OcRhS1 (OcRhS1-C), suggesting its intrinsic ability of converting UDP-4K6DG into UDP-Rha. It was thus reasonably inferred that UDP-Glc could be bio-transformed into UDP-Rha under the collaborating action of OcRhS1-N and OcUER1. The subsequently biochemical assay verified this notion. Importantly, expression profiles of OcRhS1 and OcUER1 revealed their possible involvement in the biosynthesis of rhamnose-containing polysaccharides in O. caudatum.
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Affiliation(s)
- Sen Yin
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products), Beijing, 100050, China
| | - Ming Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products), Beijing, 100050, China
| | - Jian-Qiang Kong
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products), Beijing, 100050, China.
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20
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Yan Y, Yang J, Yu Z, Yu M, Ma YT, Wang L, Su C, Luo J, Horsman GP, Huang SX. Non-enzymatic pyridine ring formation in the biosynthesis of the rubrolone tropolone alkaloids. Nat Commun 2016; 7:13083. [PMID: 27713400 PMCID: PMC5059770 DOI: 10.1038/ncomms13083] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/01/2016] [Indexed: 11/16/2022] Open
Abstract
The pyridine ring is a potent pharmacophore in alkaloid natural products. Nonetheless, its biosynthetic pathways are poorly understood. Rubrolones A and B are tropolone alkaloid natural products possessing a unique tetra-substituted pyridine moiety. Here, we report the gene cluster and propose a biosynthetic pathway for rubrolones, identifying a key intermediate that accumulates upon inactivation of sugar biosynthetic genes. Critically, this intermediate was converted to the aglycones of rubrolones by non-enzymatic condensation and cyclization with either ammonia or anthranilic acid to generate the respective pyridine rings. We propose that this non-enzymatic reaction occurs via hydrolysis of the key intermediate, which possesses a 1,5-dione moiety as an amine acceptor capable of cyclization. This study suggests that 1,5-dione moieties may represent a general strategy for pyridine ring biosynthesis, and more broadly highlights the utility of non-enzymatic diversification for exploring and expanding natural product chemical space.
The biosynthesis of pyridine rings is still poorly understood. Here the authors propose a biosynthetic pathway for pyridine-containing rubrolones, which is characterized by a non-enzymatic condensation and cyclization of the pyridine moiety.
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Affiliation(s)
- Yijun Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jing Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhiyin Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mingming Yu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ya-Tuan Ma
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Li Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Can Su
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jianying Luo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Geoffrey P Horsman
- Department of Chemistry &Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Sheng-Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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McDaniel C, Su S, Panmanee W, Lau GW, Browne T, Cox K, Paul AT, Ko SHB, Mortensen JE, Lam JS, Muruve DA, Hassett DJ. A Putative ABC Transporter Permease Is Necessary for Resistance to Acidified Nitrite and EDTA in Pseudomonas aeruginosa under Aerobic and Anaerobic Planktonic and Biofilm Conditions. Front Microbiol 2016; 7:291. [PMID: 27064218 PMCID: PMC4817314 DOI: 10.3389/fmicb.2016.00291] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/23/2016] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa (PA) is an important airway pathogen of cystic fibrosis and chronic obstructive disease patients. Multiply drug resistant PA is becoming increasing prevalent and new strategies are needed to combat such insidious organisms. We have previously shown that a mucoid, mucA22 mutant PA is exquisitely sensitive to acidified nitrite (A-NO2−, pH 6.5) at concentrations that are well tolerated in humans. Here, we used a transposon mutagenesis approach to identify PA mutants that are hypersensitive to A-NO2−. Among greater than 10,000 mutants screened, we focused on PA4455, in which the transposon was found to disrupt the production of a putative cytoplasmic membrane-spanning ABC transporter permease. The PA4455 mutant was not only highly sensitive to A-NO2−, but also the membrane perturbing agent, EDTA and the antibiotics doxycycline, tigecycline, colistin, and chloramphenicol, respectively. Treatment of bacteria with A-NO2− plus EDTA, however, had the most dramatic and synergistic effect, with virtually all bacteria killed by 10 mM A-NO2−, and EDTA (1 mM, aerobic, anaerobic). Most importantly, the PA4455 mutant was also sensitive to A-NO2− in biofilms. A-NO2− sensitivity and an anaerobic growth defect was also noted in two mutants (rmlC and wbpM) that are defective in B-band LPS synthesis, potentially indicating a membrane defect in the PA4455 mutant. Finally, this study describes a gene, PA4455, that when mutated, allows for dramatic sensitivity to the potential therapeutic agent, A-NO2− as well as EDTA. Furthermore, the synergy between the two compounds could offer future benefits against antibiotic resistant PA strains.
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Affiliation(s)
- Cameron McDaniel
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Shengchang Su
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Warunya Panmanee
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Gee W Lau
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Tristan Browne
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Kevin Cox
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Andrew T Paul
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Seung-Hyun B Ko
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Joel E Mortensen
- Diagnostic and Infectious Diseases Testing Laboratory, Cincinnati Children's Hospital Medical Center Cincinnati, OH, USA
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Daniel A Muruve
- Department of Medicine, University of Calgary Calgary, AB, Canada
| | - Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of MedicineCincinnati, OH, USA; Department of Research Services, Cincinnati Veteran's Association Medical CenterCincinnati, OH, USA
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22
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Mistou MY, Sutcliffe IC, van Sorge NM. Bacterial glycobiology: rhamnose-containing cell wall polysaccharides in Gram-positive bacteria. FEMS Microbiol Rev 2016; 40:464-79. [PMID: 26975195 PMCID: PMC4931226 DOI: 10.1093/femsre/fuw006] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
The composition of the Gram-positive cell wall is typically described as containing peptidoglycan, proteins and essential secondary cell wall structures called teichoic acids, which comprise approximately half of the cell wall mass. The cell walls of many species within the genera Streptococcus, Enterococcus and Lactococcus contain large amounts of the sugar rhamnose, which is incorporated in cell wall-anchored polysaccharides (CWP) that possibly function as homologues of well-studied wall teichoic acids (WTA). The presence and chemical structure of many rhamnose-containing cell wall polysaccharides (RhaCWP) has sometimes been known for decades. In contrast to WTA, insight into the biosynthesis and functional role of RhaCWP has been lacking. Recent studies in human streptococcal and enterococcal pathogens have highlighted critical roles for these complex polysaccharides in bacterial cell wall architecture and pathogenesis. In this review, we provide an overview of the RhaCWP with regards to their biosynthesis, genetics and biological function in species most relevant to human health. We also briefly discuss how increased knowledge in this field can provide interesting leads for new therapeutic compounds and improve biotechnological applications. This review summarizes new insights into the genetics and function of rhamnose-containing cell wall polysaccharides expressed by lactic acid bacteria, which includes medically important pathogens, and discusses perspectives on possible future therapeutic and biotechnological applications.
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Affiliation(s)
- Michel-Yves Mistou
- Laboratory for Food Safety, Université Paris-Est, ANSES, F-94701 Maisons-Alfort, France
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Nina M van Sorge
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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23
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Widderich N, Czech L, Elling FJ, Könneke M, Stöveken N, Pittelkow M, Riclea R, Dickschat JS, Heider J, Bremer E. Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environ Microbiol 2016; 18:1227-48. [PMID: 26636559 DOI: 10.1111/1462-2920.13156] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/19/2015] [Accepted: 11/27/2015] [Indexed: 11/29/2022]
Abstract
Ectoine and hydroxyectoine are compatible solutes widely synthesized by members of the Bacteria to cope with high osmolarity surroundings. Inspection of 557 archaeal genomes revealed that only 12 strains affiliated with the Nitrosopumilus, Methanothrix or Methanobacterium genera harbour ectoine/hydroxyectoine gene clusters. Phylogenetic considerations suggest that these Archaea have acquired these genes through horizontal gene transfer events. Using the Thaumarchaeon 'Candidatus Nitrosopumilus maritimus' as an example, we demonstrate that the transcription of its ectABCD genes is osmotically induced and functional since it leads to the production of both ectoine and hydroxyectoine. The ectoine synthase and the ectoine hydroxylase were biochemically characterized, and their properties resemble those of their counterparts from Bacteria. Transcriptional analysis of osmotically stressed 'Ca. N. maritimus' cells demonstrated that they possess an ectoine/hydroxyectoine gene cluster (hyp-ectABCD-mscS) different from those recognized previously since it contains a gene for an MscS-type mechanosensitive channel. Complementation experiments with an Escherichia coli mutant lacking all known mechanosensitive channel proteins demonstrated that the (Nm)MscS protein is functional. Hence, 'Ca. N. maritimus' cells cope with high salinity not only through enhanced synthesis of osmostress-protective ectoines but they already prepare themselves simultaneously for an eventually occurring osmotic down-shock by enhancing the production of a safety-valve (NmMscS).
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Affiliation(s)
- Nils Widderich
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Laura Czech
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, D-28334, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, D-28334, Bremen, Germany
| | - Nadine Stöveken
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Marco Pittelkow
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Ramona Riclea
- Kekulé-Institut for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, Gerhard-Domagk Str. 1, D-53121, Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-University Bonn, Gerhard-Domagk Str. 1, D-53121, Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Johann Heider
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Erhard Bremer
- Laboratory for Molecular Microbiology, Department of Biology, Philipps-University, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
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24
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Van Overtveldt S, Verhaeghe T, Joosten HJ, van den Bergh T, Beerens K, Desmet T. A structural classification of carbohydrate epimerases: From mechanistic insights to practical applications. Biotechnol Adv 2015; 33:1814-28. [DOI: 10.1016/j.biotechadv.2015.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/15/2015] [Accepted: 10/22/2015] [Indexed: 12/26/2022]
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25
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Salinger AJ, Brown HA, Thoden JB, Holden HM. Biochemical studies on WbcA, a sugar epimerase from Yersinia enterocolitica. Protein Sci 2015; 24:1633-9. [PMID: 26174084 DOI: 10.1002/pro.2747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 11/08/2022]
Abstract
Yersinia enterocolitica is a Gram-negative bacterium that causes yersiniosis, a zoonotic disease affecting the gastrointestinal tract of humans, cattle, and pigs, among others. The lipopolysaccharide of Y. enterocolitica O:8 contains an unusual sugar, 6-deoxy-d-gulose, which requires four enzymes for its biosynthesis. Here, we describe a combined structural and functional investigation of WbcA, which catalyzes the third step in the pathway, namely an epimerization about the C-3' carbon of a CDP-linked sugar. The structure of WbcA was determined to 1.75-Å resolution, and the model was refined to an overall R-factor of 19.5%. The fold of WbcA places it into the well-defined cupin superfamily of sugar epimerases. Typically, these enzymes contain both a conserved histidine and a tyrosine residue that play key roles in catalysis. On the basis of amino acid sequence alignments, it was anticipated that the "conserved" tyrosine had been replaced with a cysteine residue in WbcA (Cys 133), and indeed this was the case. However, what was not anticipated was the fact that another tyrosine residue (Tyr 50) situated on a neighboring β-strand moved into the active site. Site-directed mutant proteins were subsequently constructed and their kinetic properties analyzed to address the roles of Cys 133 and Tyr 50 in WbcA catalysis. This study emphasizes the continuing need to experimentally verify assumptions that are based solely on bioinformatics approaches.
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Affiliation(s)
- Ari J Salinger
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - Haley A Brown
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706
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26
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Han X, Qian L, Zhang L, Liu X. Structural and biochemical insights into nucleotide-rhamnose synthase/epimerase-reductase from Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1476-86. [PMID: 26116145 DOI: 10.1016/j.bbapap.2015.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/03/2015] [Accepted: 06/20/2015] [Indexed: 11/26/2022]
Abstract
L-Rhamnose (Rha) is synthesized via a similar enzymatic pathway in bacteria, plants and fungi. In plants, nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER) catalyzes the final step in the conversion of dTDP/UDP-α-D-Glc to dTDP/UDP-β-L-Rha in an NAD(P)H dependent manner. Currently, only biochemical evidence for the function of NRS/ER has been described. In this study, a crystal structure for Arabidopsis thaliana NRS/ER was determined, which is the first report of a eukaryotic rhamnose synthase with both epimerase and reductase activities. NRS/ER functions as a metal ion independent homodimer that forms through hydrophobic interactions via a four-helix bundle. Each monomer exhibits α/β folding that can be divided into two regions, nucleotide cofactor binding domain and sugar substrate binding domain. The affinities of ligands with NRS/ER were measured using isothermal titration calorimetry, which showed that NRS/ER has a preference for dTDP over UDP, while the cofactor binding site has a similar affinity for NADH and NADPH. Structural analysis coupled to site-directed mutagenesis suggested C115 and K183 as the acid/base pair responsible for epimerization, while T113, Y144 and K148 are the conserved residues in reduction. These findings shed light on the molecular mechanism of NRS/ER and were helpful to explore other eukaryotic enzymes involved in L-Rha synthesis.
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Affiliation(s)
- Xiaodong Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China; Food and Pharmaceutical Engineering Institute, Shanxi University of Traditional Chinese Medicine, Taiyuan 030024, China.
| | - Lei Qian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin 300192, China.
| | - Lianwen Zhang
- College of Pharmacy, Collaborative Innovation Center for Biotherapy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China.
| | - Xinqi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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27
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Virtual screening for the identification of novel inhibitors of Mycobacterium tuberculosis cell wall synthesis: inhibitors targeting RmlB and RmlC. Comput Biol Med 2015; 58:110-7. [PMID: 25637777 DOI: 10.1016/j.compbiomed.2014.12.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 11/20/2022]
Abstract
BACKGROUND Tuberculosis remains one of the deadliest infectious diseases in humans. It has caused more than 100 million deaths since its discovery in 1882. Currently, more than 5 million people are infected with TB bacterium each year. The cell wall of Mycobacterium tuberculosis plays an important role in maintaining the ability of mycobacteria to survive in a hostile environment. Therefore, we report a virtual screening (VS) study aiming to identify novel inhibitors that simultaneously target RmlB and RmlC, which are two essential enzymes for the synthesis of the cell wall of M. tuberculosis. METHODS A hybrid VS method that combines drug-likeness prediction, pharmacophore modeling and molecular docking studies was used to indentify inhibitors targeting RmlB and RmlC. RESULTS The pharmacophore models HypoB and HypoC of RmlB inhibitors and RmlC inhibitors, respectively, were developed based on ligands complexing with their corresponding receptors. In total, 20 compounds with good absorption, distribution, metabolism, excretion, and toxicity properties were carefully selected using the hybird VS method. DISCUSSION We have established a hybrid VS method to discover novel inhibitors with new scaffolds. The molecular interactions of the selected potential inhibitors with the active-site residues are discussed in detail. These compounds will be further evaluated using biological activity assays and deserve consideration for further structure-activity relationship studies.
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28
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Barketi-Klai A, Monot M, Hoys S, Lambert-Bordes S, Kuehne SA, Minton N, Collignon A, Dupuy B, Kansau I. The flagellin FliC of Clostridium difficile is responsible for pleiotropic gene regulation during in vivo infection. PLoS One 2014; 9:e96876. [PMID: 24841151 PMCID: PMC4026244 DOI: 10.1371/journal.pone.0096876] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/12/2014] [Indexed: 01/09/2023] Open
Abstract
Clostridium difficile is the main agent responsible for hospital acquired antibiotic associated diarrhoea. In recent years, epidemic strains have emerged causing more severe infections. Whilst C. difficile has two major virulence factors, toxins TcdA and TcdB, it is generally accepted that other virulence components of the bacterium contribute to disease. Previously, it has been suggested that flagella expression from pathogenic bacteria might be implicated in virulence. In a recent study, we observed an increased mortality in a gnotobiotic mouse model when animals were colonized with an isogenic fliC mutant constructed in the PCR-ribotype 027 (B1/NAP1) strain R20291, while animals survived when colonized by the parental strain or after colonization by other high-toxin-producing C. difficile strains. To understand the reasons for this increased virulence, we compared the global gene expression profiles between the fliC-R20291 mutant and its parental strain using an in vitro and in vivo transcriptomic approach. The latter made use of the gnotobiotic mouse model. Interestingly, in the fliC mutant, we observed considerable up-regulation of genes involved in mobility, membrane transport systems (PTS, ABC transporters), carbon metabolism, known virulence factors and sporulation. A smaller but significant up-regulation of genes involved in cell growth, fermentation, metabolism, stress and antibiotic resistance was also apparent. All of these genes may be associated with the increased virulence of the fliC-R20921 mutant. We confirmed that the fliC mutation is solely responsible for the observed changes in gene expression in the mutant strain since expression profiles were restored to that of the wild-type strain in the fliC-complemented strain. Thus, the absence of FliC is directly or indirectly involved in the high mortality observed in the fliC mutant infected animals. Therefore, we provide the first evidence that when the major structural component of the flagellum is neutralized, deregulation of gene expression can occur during infection.
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Affiliation(s)
- Amira Barketi-Klai
- Faculté de Pharmacie, EA4043, Université Paris Sud, Châtenay-Malabry, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Sandra Hoys
- Faculté de Pharmacie, EA4043, Université Paris Sud, Châtenay-Malabry, France
| | | | - Sarah A. Kuehne
- Clostridia Research Group, Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nigel Minton
- Clostridia Research Group, Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Anne Collignon
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
| | - Imad Kansau
- Faculté de Pharmacie, EA4043, Université Paris Sud, Châtenay-Malabry, France
- * E-mail:
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29
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Zou Y, Fang Q, Yin H, Liang Z, Kong D, Bai L, Deng Z, Lin S. Stereospecific biosynthesis of β-methyltryptophan from (L)-tryptophan features a stereochemical switch. Angew Chem Int Ed Engl 2013; 52:12951-5. [PMID: 24166888 DOI: 10.1002/anie.201306255] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/04/2013] [Indexed: 11/10/2022]
Abstract
Make the switch: The three-enzyme cassette MarG/H/I is responsible for stereospecific biosynthesis of β-methyltryptophan from L-tryptophan (1). MarG/I convert 1 into (2S,3R)-β-methyltryptophan, while MarG/I combined with MarH convert 1 into (2S,3S)-β-methyltryptophan. MarH serves as a stereochemical switch by catalyzing the stereoinversion of the β-stereocenter.
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Affiliation(s)
- Yi Zou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240 (P.R. China)
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30
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Zou Y, Fang Q, Yin H, Liang Z, Kong D, Bai L, Deng Z, Lin S. Stereospecific Biosynthesis of β-Methyltryptophan fromL-Tryptophan Features a Stereochemical Switch. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Uberto R, Moomaw EW. Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PLoS One 2013; 8:e74477. [PMID: 24040257 PMCID: PMC3765361 DOI: 10.1371/journal.pone.0074477] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/01/2013] [Indexed: 12/11/2022] Open
Abstract
The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional clustering. Networks based only on cupin domains and networks based on the whole proteins provide complementary information. Domain-clustering supports phylogenetic conclusions that the N- and C-terminal domains of bicupin proteins evolved independently. Interestingly, although many functionally similar enzymatic cupin members bind the same active site metal ion, the structure and sequence clustering does not correlate with the identity of the bound metal. It is anticipated that the application of PSNs to this superfamily will inform experimental work and influence the functional annotation of databases.
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Affiliation(s)
- Richard Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Ellen W. Moomaw
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
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32
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McCallum M, Shaw GS, Creuzenet C. Comparison of predicted epimerases and reductases of the Campylobacter jejuni D-altro- and L-gluco-heptose synthesis pathways. J Biol Chem 2013; 288:19569-80. [PMID: 23689373 DOI: 10.1074/jbc.m113.468066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uniquely modified heptoses found in surface carbohydrates of bacterial pathogens are potential therapeutic targets against such pathogens. Our recent biochemical characterization of the GDP-6-deoxy-D-manno- and GDP-6-deoxy-D-altro-heptose biosynthesis pathways has provided the foundation for elucidation of the more complex L-gluco-heptose synthesis pathway of Campylobacter jejuni strain NCTC 11168. In this work we use GDP-4-keto,6-deoxy-D-lyxo-heptose as a surrogate substrate to characterize three enzymes predicted to be involved in this pathway: WcaGNCTC (also known as Cj1427), MlghB (Cj1430), and MlghC (Cj1428). We compare them with homologues involved in d-altro-heptose production: WcaG81176 (formerly WcaG), DdahB (Cjj1430), and DdahC (Cjj1427). We show that despite high levels of similarity, the enzymes have pathway-specific catalytic activities and substrate specificities. MlghB forms three products via C3 and C5 epimerization activities, whereas its DdahB homologue only had C3 epimerase activity along its cognate pathway. MlghC is specific for the double C3/C5 epimer generated by MlghB and produces L-gluco-heptose via stereospecific C4 reductase activity. In contrast, its homologue DdahC only uses the C3 epimer to yield d-altro-heptose via C4 reduction. Finally, we show that WcaGNCTC is not necessary for L-gluco-heptose synthesis and does not affect its production by MlghB and MlghC, in contrast to its homologue WcaG81176, that has regulatory activity on d-altro-heptose synthesis. These studies expand our fundamental understanding of heptose modification, provide new glycobiology tools to synthesize novel heptose derivatives with biomedical applications, and provide a foundation for the structure function analysis of these enzymes.
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Affiliation(s)
- Matthew McCallum
- Department of Microbiology and Immunology, Infectious Diseases Research Group, University of Western Ontario, London, Ontario N6A 5C1, Canada
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33
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Kim MO, Nichols SE, Wang Y, McCammon JA. Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. J Comput Aided Mol Des 2013; 27:235-46. [PMID: 23579613 PMCID: PMC3639364 DOI: 10.1007/s10822-013-9643-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/02/2013] [Indexed: 11/12/2022]
Abstract
While it is well established that protonation and tautomeric states of ligands can significantly affect the results of virtual screening, such effects of ionizable residues of protein receptors are less well understood. In this study, we focus on histidine protonation and rotameric states and their impact on virtual screening of Mycobacterium tuberculosis enzyme RmlC. Depending on the net charge and the location of proton(s), a histidine can adopt three states: HIP (+1 charged, both δ- and ε-nitrogens protonated), HID (neutral, δ-nitrogen protonated), and HIE (neutral, ε-nitrogen protonated). Due to common ambiguities in X-ray crystal structures, a histidine may also be resolved as three additional states with its imidazole ring flipped. Here, we systematically investigate the predictive power of 36 receptor models with different protonation and rotameric states of two histidines in the RmlC active site by using results from a previous high-throughput screening. By measuring enrichment factors and area under the receiver operating characteristic curves, we show that virtual screening results vary depending on hydrogen bonding networks provided by the histidines, even in the cases where the ligand does not obviously interact with the side chain. Our results also suggest that, even with the help of widely used pKa prediction software, assigning histidine protonation and rotameric states for virtual screening can still be challenging and requires further examination and systematic characterization of the receptor-ligand complex.
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Affiliation(s)
- Meekyum Olivia Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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Detection and characterization of megasatellites in orthologous and nonorthologous genes of 21 fungal genomes. EUKARYOTIC CELL 2013; 12:794-803. [PMID: 23543670 DOI: 10.1128/ec.00001-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Megasatellites are large DNA tandem repeats, originally described in Candida glabrata, in protein-coding genes. Most of the genes in which megasatellites are found are of unknown function. In this work, we extended the search for megasatellites to 20 additional completely sequenced fungal genomes and extracted 216 megasatellites in 203 out of 142,121 genes, corresponding to the most exhaustive description of such genetic elements available today. We show that half of the megasatellites detected encode threonine-rich peptides predicted to be intrinsically disordered, suggesting that they may interact with several partners or serve as flexible linkers. Megasatellite motifs were clustered into several families. Their distribution in fungal genes shows that different motifs are found in orthologous genes and similar motifs are found in unrelated genes, suggesting that megasatellite formation or spreading does not necessarily track the evolution of their host genes. Altogether, these results suggest that megasatellites are created and lost during evolution of fungal genomes, probably sharing similar functions, although their primary sequences are not necessarily conserved.
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Kubiak RL, Phillips RK, Zmudka MW, Ahn MR, Maka EM, Pyeatt GL, Roggensack SJ, Holden HM. Structural and functional studies on a 3'-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose. Biochemistry 2012; 51:9375-83. [PMID: 23116432 DOI: 10.1021/bi3012737] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unusual deoxy sugars are often attached to natural products such as antibiotics, antifungals, and chemotherapeutic agents. One such sugar is mycinose, which has been found on the antibiotics chalcomycin and tylosin. An intermediate in the biosynthesis of mycinose is dTDP-6-deoxy-D-allose. Four enzymes are required for the production of dTDP-6-deoxy-D-allose in Streptomyces bikiniensis, a soil-dwelling microbe first isolated from the Bikini and Rongelap atolls. Here we describe a combined structural and functional study of the enzyme ChmJ, which reportedly catalyzes the third step in the pathway leading to dTDP-6-deoxy-D-allose formation. Specifically, it has been proposed that ChmJ is a 3'-epimerase that converts dTDP-4-keto-6-deoxyglucose to dTDP-4-keto-6-deoxyallose. This activity, however, has never been verified in vitro. As reported here, we demonstrate using (1)H nuclear magnetic resonance that ChmJ, indeed, functions as a 3'-epimerase. In addition, we determined the structure of ChmJ complexed with dTDP-quinovose to 2.0 Å resolution. The structure of ChmJ shows that it belongs to the well-characterized "cupin" superfamily. Two active site residues, His 60 and Tyr 130, were subsequently targeted for study via site-directed mutagenesis and kinetic analyses, and the three-dimensional architecture of the H60N/Y130F mutant protein was determined to 1.6 Å resolution. Finally, the structure of the apoenzyme was determined to 2.2 Å resolution. It has been previously suggested that the position of a conserved tyrosine, Tyr 130 in the case of ChmJ, determines whether an enzyme in this superfamily functions as a mono- or diepimerase. Our results indicate that the orientation of the tyrosine residue in ChmJ is a function of the ligand occupying the active site cleft.
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Affiliation(s)
- Rachel L Kubiak
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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Singh B, Oh TJ, Sohng JK. Exploration of two epimerase homologs in Streptomyces peucetius ATCC 27952. Appl Microbiol Biotechnol 2012; 97:2493-502. [DOI: 10.1007/s00253-012-4327-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/03/2012] [Accepted: 07/18/2012] [Indexed: 11/28/2022]
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McCallum M, Shaw SD, Shaw GS, Creuzenet C. Complete 6-deoxy-D-altro-heptose biosynthesis pathway from Campylobacter jejuni: more complex than anticipated. J Biol Chem 2012; 287:29776-88. [PMID: 22787156 DOI: 10.1074/jbc.m112.390492] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Campylobacter jejuni capsule is important for colonization and virulence in various infection models. In most strains, the capsule includes a modified heptose whose biological role and biosynthetic pathway are unknown. To decipher the biosynthesis pathway for the 6-deoxy-D-altro-heptose of strain 81-176, we previously showed that the 4,6-dehydratase WcbK and the reductase WcaG generated GDP-6-deoxy-D-manno-heptose, but the C3 epimerase necessary to form GDP-6-deoxy-D-altro-heptose was not identified. Herein, we characterized the putative C3/C5 epimerase Cjj1430 and C3/C5 epimerase/C4 reductase Cjj1427 from the capsular cluster. We demonstrate that GDP-6-deoxy-D-altro-heptose biosynthesis is more complex than anticipated and requires the sequential action of WcbK, Cjj1430, and Cjj1427. We show that Cjj1430 serves as C3 epimerase devoid of C5 epimerization activity and that Cjj1427 has no epimerization activity and only serves as a reductase to produce GDP-6-deoxy-D-altro-heptose. Cjj1430 and Cjj1427 are the only members of the C3/C5 epimerases and C3/C5 epimerase/C4 reductase families shown to have activity on a heptose substrate and to exhibit only one of their two to three potential activities, respectively. Furthermore, we show that although the reductase WcaG is not part of the main pathway, its presence and its product affect the outcome of the pathway in a complex regulatory loop involving Cjj1427. This work provides the grounds for the elucidation of similar pathways found in other C. jejuni strains and other pathogens. It provides new molecular tools for the synthesis of carbohydrate antigens useful for vaccination and for the screening of enzymatic inhibitors that may have antibacterial effects.
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Affiliation(s)
- Matthew McCallum
- Department of Microbiology and Immunology, Infectious Diseases Research Group, University of Western Ontario, London, Ontario N6A 5C1, Canada
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains. Biochem J 2012; 443:671-80. [PMID: 22320426 DOI: 10.1042/bj20112049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CP (capsular polysaccharide) is an important virulence factor during infections by the bacterium Staphylococcus aureus. The enzyme CapF is an attractive therapeutic candidate belonging to the biosynthetic route of CP of pathogenic strains of S. aureus. In the present study, we report two independent crystal structures of CapF in an open form of the apoenzyme. CapF is a homodimer displaying a characteristic dumb-bell-shaped architecture composed of two domains. The N-terminal domain (residues 1-252) adopts a Rossmann fold belonging to the short-chain dehydrogenase/reductase family of proteins. The C-terminal domain (residues 252-369) displays a standard cupin fold with a Zn2+ ion bound deep in the binding pocket of the β-barrel. Functional and thermodynamic analyses indicated that each domain catalyses separate enzymatic reactions. The cupin domain is necessary for the C3-epimerization of UDP-4-hexulose. Meanwhile, the N-terminal domain catalyses the NADPH-dependent reduction of the intermediate species generated by the cupin domain. Analysis by ITC (isothermal titration calorimetry) revealed a fascinating thermodynamic switch governing the attachment and release of the coenzyme NADPH during each catalytic cycle. These observations suggested that the binding of coenzyme to CapF facilitates a disorder-to-order transition in the catalytic loop of the reductase (N-terminal) domain. We anticipate that the present study will improve the general understanding of the synthesis of CP in S. aureus and will aid in the design of new therapeutic agents against this pathogenic bacterium.
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Kocincova D, Lam JS. Structural diversity of the core oligosaccharide domain of Pseudomonas aeruginosa lipopolysaccharide. BIOCHEMISTRY (MOSCOW) 2011; 76:755-60. [DOI: 10.1134/s0006297911070054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Martinez V, Ingwers M, Smith J, Glushka J, Yang T, Bar-Peled M. Biosynthesis of UDP-4-keto-6-deoxyglucose and UDP-rhamnose in pathogenic fungi Magnaporthe grisea and Botryotinia fuckeliana. J Biol Chem 2011; 287:879-92. [PMID: 22102281 DOI: 10.1074/jbc.m111.287367] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is increasing evidence that in several fungi, rhamnose-containing glycans are involved in processes that affect host-pathogen interactions, including adhesion, recognition, virulence, and biofilm formation. Nevertheless, little is known about the pathways for the synthesis of these glycans. We show that rhamnose is present in glycans isolated from the rice pathogen Magnaporthe grisea and from the plant pathogen Botryotinia fuckeliana. We also provide evidence that these fungi produce UDP-rhamnose. This is in contrast to bacteria where dTDP-rhamnose is the activated form of this sugar. In bacteria, formation of dTDP-rhamnose requires three enzymes. Here, we demonstrate that in fungi only two genes are required for UDP-Rha synthesis. The first gene encodes a UDP-glucose-4,6-dehydratase that converts UDP-glucose to UDP-4-keto-6-deoxyglucose. The product was shown by time-resolved (1)H NMR spectroscopy to exist in solution predominantly as a hydrated form along with minor amounts of a keto form. The second gene encodes a bifunctional UDP-4-keto-6-deoxyglucose-3,5-epimerase/-4-reductase that converts UDP-4-keto-6-deoxyglucose to UDP-rhamnose. Sugar composition analysis and gene expression studies at different stages of growth indicate that the synthesis of rhamnose-containing glycans is under tissue-specific regulation. Together, our results provide new insight into the formation of rhamnose-containing glycans during the fungal life cycle. The role of these glycans in the interactions between fungal pathogens and their hosts is discussed. Knowledge of the metabolic pathways involved in the formation of rhamnose-containing glycans may facilitate the development of drugs to combat fungal diseases in humans, as to the best of our knowledge mammals do not make these types of glycans.
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Affiliation(s)
- Viviana Martinez
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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Iyer LM, Abhiman S, de Souza RF, Aravind L. Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. Nucleic Acids Res 2010; 38:5261-79. [PMID: 20423905 PMCID: PMC2938197 DOI: 10.1093/nar/gkq265] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Unlike classical 2-oxoglutarate and iron-dependent dioxygenases, which include several nucleic acid modifiers, the structurally similar jumonji-related dioxygenase superfamily was only known to catalyze peptide modifications. Using comparative genomics methods, we predict that a family of jumonji-related enzymes catalyzes wybutosine hydroxylation/peroxidation at position 37 of eukaryotic tRNAPhe. Identification of this enzyme raised questions regarding the emergence of protein- and nucleic acid-modifying activities among jumonji-related domains. We addressed these with a natural classification of DSBH domains and reconstructed the precursor of the dioxygenases as a sugar-binding domain. This precursor gave rise to sugar epimerases and metal-binding sugar isomerases. The sugar isomerase active site was exapted for catalysis of oxygenation, with a radiation of these enzymes in bacteria, probably due to impetus from the primary oxygenation event in Earth’s history. 2-Oxoglutarate-dependent versions appear to have further expanded with rise of the tricarboxylic acid cycle. We identify previously under-appreciated aspects of their active site and multiple independent innovations of 2-oxoacid-binding basic residues among these superfamilies. We show that double-stranded β-helix dioxygenases diversified extensively in biosynthesis and modification of halogenated siderophores, antibiotics, peptide secondary metabolites and glycine-rich collagen-like proteins in bacteria. Jumonji-related domains diversified into three distinct lineages in bacterial secondary metabolism systems and these were precursors of the three major clades of eukaryotic enzymes. The specificity of wybutosine hydroxylase/peroxidase probably relates to the structural similarity of the modified moiety to the ancestral amino acid substrate of this superfamily.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Sivendran S, Jones V, Sun D, Wang Y, Grzegorzewicz AE, Scherman MS, Napper AD, McCammon JA, Lee RE, Diamond SL, McNeil M. Identification of triazinoindol-benzimidazolones as nanomolar inhibitors of the Mycobacterium tuberculosis enzyme TDP-6-deoxy-d-xylo-4-hexopyranosid-4-ulose 3,5-epimerase (RmlC). Bioorg Med Chem 2010; 18:896-908. [PMID: 19969466 PMCID: PMC2818544 DOI: 10.1016/j.bmc.2009.11.033] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 11/12/2009] [Accepted: 11/14/2009] [Indexed: 11/23/2022]
Abstract
High-throughput screening of 201,368 compounds revealed that 1-(3-(5-ethyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one (SID 7975595) inhibited RmlC a TB cell wall biosynthetic enzyme. SID 7975595 acts as a competitive inhibitor of the enzyme's substrate and inhibits RmlC as a fast-on rate, fully reversible inhibitor. An analog of SID 7975595 had a K(i) of 62nM. Computer modeling showed that the binding of the tethered two-ringed system into the active site occurred at the thymidine binding region for one ring system and the sugar region for the other ring system.
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Affiliation(s)
- Sharmila Sivendran
- Penn Center for Molecular Discovery, Department of Chemical and Biomolecular Engineering Institute for Medicine and Engineering, 1024 Vagelos Research Laboratories, University of Pennsylvania, Philadelphia, PA 19104 U.S.A
| | - Victoria Jones
- Colorado State University, Department of Microbiology, Immunology and Pathology, 1682 Campus Delivery Ft. Collins, CO 80523-1682 U.S.A
| | - Dianqing Sun
- Dept. of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN U.S.A
| | - Yi Wang
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Dr La Jolla, CA 92093 U.S.A
| | - Anna E. Grzegorzewicz
- Colorado State University, Department of Microbiology, Immunology and Pathology, 1682 Campus Delivery Ft. Collins, CO 80523-1682 U.S.A
| | - Michael S. Scherman
- Colorado State University, Department of Microbiology, Immunology and Pathology, 1682 Campus Delivery Ft. Collins, CO 80523-1682 U.S.A
| | - Andrew D. Napper
- Penn Center for Molecular Discovery, Department of Chemical and Biomolecular Engineering Institute for Medicine and Engineering, 1024 Vagelos Research Laboratories, University of Pennsylvania, Philadelphia, PA 19104 U.S.A
| | - J. Andrew McCammon
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Dr La Jolla, CA 92093 U.S.A
| | - Richard E. Lee
- Dept. of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN U.S.A
| | - Scott L. Diamond
- Penn Center for Molecular Discovery, Department of Chemical and Biomolecular Engineering Institute for Medicine and Engineering, 1024 Vagelos Research Laboratories, University of Pennsylvania, Philadelphia, PA 19104 U.S.A
| | - Michael McNeil
- Colorado State University, Department of Microbiology, Immunology and Pathology, 1682 Campus Delivery Ft. Collins, CO 80523-1682 U.S.A
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Ito S. Catalysis, Structures, and Applications of Carbohydrate Epimerases. J Appl Glycosci (1999) 2010. [DOI: 10.5458/jag.57.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, Lawley TD, Sebaihia M, Quail MA, Rose G, Gerding DN, Gibert M, Popoff MR, Parkhill J, Dougan G, Wren BW. Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol 2009; 10:R102. [PMID: 19781061 PMCID: PMC2768977 DOI: 10.1186/gb-2009-10-9-r102] [Citation(s) in RCA: 352] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 06/29/2009] [Accepted: 09/25/2009] [Indexed: 11/10/2022] Open
Abstract
A genome comparison of non-epidemic and epidemic strains of Clostridium difficile reveals gene gains that could explain how a hypervirulent strain has emerged Background The continued rise of Clostridium difficile infections worldwide has been accompanied by the rapid emergence of a highly virulent clone designated PCR-ribotype 027. To understand more about the evolution of this virulent clone, we made a three-way genomic and phenotypic comparison of an 'historic' non-epidemic 027 C. difficile (CD196), a recent epidemic and hypervirulent 027 (R20291) and a previously sequenced PCR-ribotype 012 strain (630). Results Although the genomes are highly conserved, the 027 genomes have 234 additional genes compared to 630, which may contribute to the distinct phenotypic differences we observe between these strains relating to motility, antibiotic resistance and toxicity. The epidemic 027 strain has five unique genetic regions, absent from both the non-epidemic 027 and strain 630, which include a novel phage island, a two component regulatory system and transcriptional regulators. Conclusions A comparison of a series of 027 isolates showed that some of these genes appeared to have been gained by 027 strains over the past two decades. This study provides genetic markers for the identification of 027 strains and offers a unique opportunity to explain the recent emergence of a hypervirulent bacterium.
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Affiliation(s)
- Richard A Stabler
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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King JD, Kocíncová D, Westman EL, Lam JS. Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa. Innate Immun 2009; 15:261-312. [PMID: 19710102 DOI: 10.1177/1753425909106436] [Citation(s) in RCA: 225] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa causes serious nosocomial infections, and an important virulence factor produced by this organism is lipopolysaccharide (LPS). This review summarizes knowledge about biosynthesis of all three structural domains of LPS - lipid A, core oligosaccharide, and O polysaccharides. In addition, based on similarities with other bacterial species, this review proposes new hypothetical pathways for unstudied steps in the biosynthesis of P. aeruginosa LPS. Lipid A biosynthesis is discussed in relation to Escherichia coli and Salmonella, and the biosyntheses of core sugar precursors and core oligosaccharide are summarised. Pseudomonas aeruginosa attaches a Common Polysaccharide Antigen and O-Specific Antigen polysaccharides to lipid A-core. Both forms of O polysaccharide are discussed with respect to their independent synthesis mechanisms. Recent advances in understanding O-polysaccharide biosynthesis since the last major review on this subject, published nearly a decade ago, are highlighted. Since P. aeruginosa O polysaccharides contain unusual sugars, sugar-nucleotide biosynthesis pathways are reviewed in detail. Knowledge derived from detailed studies in the O5, O6 and O11 serotypes is applied to predict biosynthesis pathways of sugars in poorly-studied serotypes, especially O1, O4, and O13/O14. Although further work is required, a full understanding of LPS biosynthesis in P. aeruginosa is almost within reach.
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Affiliation(s)
- Jerry D King
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Ito S. Features and applications of microbial sugar epimerases. Appl Microbiol Biotechnol 2009; 84:1053-60. [PMID: 19697019 DOI: 10.1007/s00253-009-2179-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
Abstract
Sugar (carbohydrate) epimerases catalyze the reversible conversion of a sugar epimer into its counterpart form. More than 20 types of sugar epimerase have been reported to date, and their biological properties, catalytic mechanisms, and 3D structures are very diverse among them. Recently, microbial sugar epimerases have been characterized in detail. This review surveys the catalytic aspects of microbial epimerases, which are relevant for production of bioactive mono- and oligosaccharides.
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Affiliation(s)
- Susumu Ito
- Department of Bioscience and Biotechnology, University of the Ryukyus, Nishihara-cho, Okinawa, Japan.
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Byrd MS, Sadovskaya I, Vinogradov E, Lu H, Sprinkle AB, Richardson SH, Ma L, Ralston B, Parsek MR, Anderson EM, Lam JS, Wozniak DJ. Genetic and biochemical analyses of the Pseudomonas aeruginosa Psl exopolysaccharide reveal overlapping roles for polysaccharide synthesis enzymes in Psl and LPS production. Mol Microbiol 2009; 73:622-38. [PMID: 19659934 DOI: 10.1111/j.1365-2958.2009.06795.x] [Citation(s) in RCA: 254] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Exopolysaccharides contribute significantly to attachment and biofilm formation in the opportunisitc pathogen Pseudomonas aeruginosa. The Psl polysaccharide, which is synthesized by the polysaccharide synthesis locus (psl), is required for biofilm formation in non-mucoid strains that do not rely on alginate as the principal biofilm polysaccharide. In-frame deletion and complementation studies of individual psl genes revealed that 11 psl genes, pslACDEFGHIJKL, are required for Psl production and surface attachment. We also present the first structural analysis of the psl-dependent polysaccharide, which consists of a repeating pentasaccharide containing d-mannose, d-glucose and l-rhamnose: [See text]. In addition, we identified the sugar nucleotide precursors involved in Psl generation and demonstrated the requirement for GDP-d-mannose, UDP-d-glucose and dTDP-l-rhamnose in Psl production and surface attachment. Finally, genetic analyses revealed that wbpW restored Psl production in a pslB mutant and pslB promoted A-band LPS synthesis in a wbpW mutant, indicating functional redundancy and overlapping roles for these two enzymes. The structural and genetic data presented here provide a basis for further investigation of the Psl proteins and potential roles for Psl in the biology and pathogenesis of P. aeruginosa.
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Affiliation(s)
- Matthew S Byrd
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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Agarwal G, Rajavel M, Gopal B, Srinivasan N. Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PLoS One 2009; 4:e5736. [PMID: 19478949 PMCID: PMC2684688 DOI: 10.1371/journal.pone.0005736] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 04/27/2009] [Indexed: 01/22/2023] Open
Abstract
Background The members of cupin superfamily exhibit large variations in their sequences, functions, organization of domains, quaternary associations and the nature of bound metal ion, despite having a conserved β-barrel structural scaffold. Here, an attempt has been made to understand structure-function relationships among the members of this diverse superfamily and identify the principles governing functional diversity. The cupin superfamily also contains proteins for which the structures are available through world-wide structural genomics initiatives but characterized as “hypothetical”. We have explored the feasibility of obtaining clues to functions of such proteins by means of comparative analysis with cupins of known structure and function. Methodology/Principal Findings A 3-D structure-based phylogenetic approach was undertaken. Interestingly, a dendrogram generated solely on the basis of structural dissimilarity measure at the level of domain folds was found to cluster functionally similar members. This clustering also reflects an independent evolution of the two domains in bicupins. Close examination of structural superposition of members across various functional clusters reveals structural variations in regions that not only form the active site pocket but are also involved in interaction with another domain in the same polypeptide or in the oligomer. Conclusions/Significance Structure-based phylogeny of cupins can influence identification of functions of proteins of yet unknown function with cupin fold. This approach can be extended to other proteins with a common fold that show high evolutionary divergence. This approach is expected to have an influence on the function annotation in structural genomics initiatives.
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Affiliation(s)
- Garima Agarwal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Caravano A, Field RA, Percy JM, Rinaudo G, Roig R, Singh K. Developing an asymmetric, stereodivergent route to selected 6-deoxy-6-fluoro-hexoses. Org Biomol Chem 2009; 7:996-1008. [PMID: 19225683 DOI: 10.1039/b815342f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Free radical bromination and nucleophilic fluorination allows the conversion of methyl sorbate into the 6-fluoro analogue which undergoes sequential asymmetric dihydroxylation reactions. A range of 6-deoxy-6-fluorosugars were prepared by using different combinations of ligands. While the enantiomeric excesses obtained were comparable to those from other 6-substituted sorbates, the regioselectivity of dihydroxylation was moderate, with both 2,3- and 4,5-diols being obtained. A successful temporary persilylation strategy was evolved to convert the products of dihydroxylation rapidly to the fluorosugars 6-deoxy-6-fluoro-L-idose, 6-fluoro-L-fucose and 6-deoxy-6-fluoro-D-galactose, which were obtained in overall yields of 4%, 6% and 8% from methyl 6-fluoro-hexa-2E,4E-dienoate .
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Affiliation(s)
- Audrey Caravano
- Department of Chemistry, University of Leicester, University Road, Leicester LE17RH, UK
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