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Zhao M, Liu H, Liu M, Yue Z, Li C, Liu L, Li F. Metagenomics and metabolomics reveal that gut microbiome adapts to the diet transition in Hyla rabbits. Microbiol Res 2024; 283:127705. [PMID: 38554650 DOI: 10.1016/j.micres.2024.127705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/14/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
There is still a lack of longitudinal dynamic studies on the taxonomic features, functional reserves, and metabolites of the rabbit gut microbiome. An experiment was conducted to characterize the bacterial community of rabbits. By combining metagenomics and metabolomics, we have comprehensively analyzed the longitudinal dynamics of the rabbit gut microbiota and its effect on host adaptability. Our data reveal an overall increasing trend in microbial community and functional gene diversity and richness during the pre-harvest lifespan of rabbits. The introduction of solid feed is an important driving factor affecting rabbit gut microbiological compositions. Clostridium and Ruminococcus had significantly higher relative abundances in the solid feed stage. Further, the starch and fiber in solid feed promote the secretion of carbohydrate-degrading enzymes, which helps the host adapt to dietary changes. The rabbit gut microbiota can synthesize lysine, and the synthase is gradually enriched during the diet transformation. The gut microbiota of newborn rabbits has a higher abundance of lipid metabolism, which helps the host obtain more energy from breast milk lipids. The rabbit gut microbiota can also synthesize a variety of secondary bile acids after the introduction of solid feed. These findings provide a novel understanding of how the gut microbiota mediates adaptability to environment and diet in rabbits and provide multiple potential strategies for regulating intestinal health and promoting higher feed efficiency.
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Affiliation(s)
- Man Zhao
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Hongli Liu
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Mengqi Liu
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Zhengkai Yue
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Chenyang Li
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China
| | - Lei Liu
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China.
| | - Fuchang Li
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Department of Animal Science, Shandong Agricultural University, Taian, China.
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Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER. The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proc Natl Acad Sci U S A 2023; 120:e2306160120. [PMID: 38109545 PMCID: PMC10756260 DOI: 10.1073/pnas.2306160120] [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: 04/16/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.
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Affiliation(s)
| | | | - Charles Pepe-Ranney
- Soil & Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY14853
| | - Wenbo Chen
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA94025
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Nathalie H. Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
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3
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Muduli S, Karmakar S, Mishra S. The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets. Biochim Biophys Acta Gen Subj 2023; 1867:130320. [PMID: 36813209 DOI: 10.1016/j.bbagen.2023.130320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings. SCOPE OF REVIEW The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species. MAJOR CONCLUSIONS LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success. GENERAL SIGNIFICANCE This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.
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Affiliation(s)
- Sunita Muduli
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumyajit Karmakar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India.
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Role of Antimicrobial Drug in the Development of Potential Therapeutics. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2500613. [PMID: 35571735 PMCID: PMC9098294 DOI: 10.1155/2022/2500613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/17/2022]
Abstract
Population of the world run into several health-related emergencies among mankind and humans as it creates a challenge for the evolution of novel drug discoveries. One such can be the emergence of multidrug-resistant (MDR) strains in both hospital and community settings, which have been due to an inappropriate use and inadequate control of antibiotics that has led to the foremost human health concerns with a high impact on the global economy. So far, there has been application of two strategies for the development of anti-infective agents either by classical antibiotics that have been derived for their synthetic analogs with increased efficacy or screening natural compounds along with the synthetic compound libraries for the antimicrobial activities. However, need for newer treatment options for infectious diseases has led research to develop new generation of antimicrobial activity to further lessen the spread of antibiotic resistance. Currently, the principles aim to find novel mode of actions or products to target the specific sites and virulence factors in pathogens by a series of better understanding of physiology and molecular aspects of the microbial resistance, mechanism of infection process, and gene-pathogenicity relationship. The design various novel strategies tends to provide us a path for the development of various antimicrobial therapies that intends to have a broader and wider antimicrobial spectrum that helps to combat MDR strains worldwide. The development of antimicrobial peptides, metabolites derived from plants, microbes, phage-based antimicrobial agents, use of metal nanoparticles, and role of CRISPR have led to an exceptional strategies in designing and developing the next-generation antimicrobials. These novel strategies might help to combat the seriousness of the infection rates and control the health crisis system.
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Song G, Chen F, Chen S, Ye S. Polysaccharides from Premna microphylla turcz ameliorate inflammation via the enhancement of intestinal resistance in host. JOURNAL OF ETHNOPHARMACOLOGY 2021; 276:114208. [PMID: 34010697 DOI: 10.1016/j.jep.2021.114208] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Premna microphylla turcz is traditionally used as a folk remedy. Its roots, stems and leaves can be invoked as medicines, which have the functions of detoxification, swelling and hemostasis. It belongs to the Premna in the Verbenaceae and is mainly distributed in the mountains of southeastern China. However, there are few reports of in-depth studies on the anti-inflammatory effects of polysaccharide, which was the main component in Premna microphylla turcz. MATERIALS AND METHODS The flies were fed with standard corn flour-yeast medium to cause inflammation by sodium lauryl sulfate (SDS). The treatment group contained Premna microphylla turcz polysaccharide (pPMTLs) extract. The survival rate was obtained by feeding a vial containing five layers of filter paper, which was infiltrated with the 5% sucrose solution contaminated with SDS or SDS polysaccharide. The microvilli and nucleus of the midgut epithelial cells of different treatments were observed by transmission electron microscope, and the expression of inflammation-related genes was detected by real-time quantitative PCR (qRT-PCR). Finally, 16S rDNA analysis was conducted on the differences in the composition of the intestinal microbes of Drosophila. RESULTS In the current study, we showed that pPMTLs significantly prolonged the life span of SDS-inflamed flies from 5 days to 6 days. And pPMTLs reduced the rupture of microvilli in the midgut and restored the nuclear structure. In addition, pPMTLs significantly improved expression level of immune-related genes in Inflammation Drosophila especially the defensin (4.32 ± 0.75 vs 9.97 ± 0.52 SDS-polysaccharide group: SDS group, p < 0.001). The analysis of intestinal microbiota showed that pPMTLs decreased the relative abundance of Raoultella while Wolbachia increased (p < 0.05). CONCLUSIONS Collectively, our results revealed the potential application of pPMTLs in enhancing inflammation defense, which would be enormous significance for the inflammation-related disorders treatment.
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Affiliation(s)
- Guanglei Song
- School of Food Science and Biotechnology, Institute of Jinhua Food Industry, Zhejiang Gongshang University, 18 Xuezheng str., Hangzhou, Zhejiang, 310018, China.
| | - Fangyuan Chen
- School of Food Science and Biotechnology, Institute of Jinhua Food Industry, Zhejiang Gongshang University, 18 Xuezheng str., Hangzhou, Zhejiang, 310018, China.
| | - Shubo Chen
- School of Food Science and Biotechnology, Institute of Jinhua Food Industry, Zhejiang Gongshang University, 18 Xuezheng str., Hangzhou, Zhejiang, 310018, China.
| | - Shuhui Ye
- School of Food Science and Biotechnology, Institute of Jinhua Food Industry, Zhejiang Gongshang University, 18 Xuezheng str., Hangzhou, Zhejiang, 310018, China.
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6
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Hall CJ, Lee M, Boarder MP, Mangion AM, Gendall AR, Panjikar S, Perugini MA, Soares da Costa TP. Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms. FEBS J 2021; 288:4973-4986. [PMID: 33586321 DOI: 10.1111/febs.15766] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/16/2021] [Accepted: 02/12/2021] [Indexed: 12/31/2022]
Abstract
Lysine biosynthesis in plants occurs via the diaminopimelate pathway. The first committed and rate-limiting step of this pathway is catalysed by dihydrodipicolinate synthase (DHDPS), which is allosterically regulated by the end product, l-lysine (lysine). Given that lysine is a common nutritionally limiting amino acid in cereal crops, there has been much interest in probing the regulation of DHDPS. Interestingly, knockouts in Arabidopsis thaliana of each isoform (AtDHDPS1 and AtDHDPS2) result in different phenotypes, despite the enzymes sharing > 85% protein sequence identity. Accordingly, in this study, we compared the catalytic activity, lysine-mediated inhibition and structures of both A. thaliana DHDPS isoforms. We found that although the recombinantly produced enzymes have similar kinetic properties, AtDHDPS1 is 10-fold more sensitive to lysine. We subsequently used X-ray crystallography to probe for structural differences between the apo- and lysine-bound isoforms that could account for the differential allosteric inhibition. Despite no significant changes in the overall structures of the active or allosteric sites, we noted differences in the rotamer conformation of a key allosteric site residue (Trp116) and proposed that this could result in differences in lysine dissociation. Microscale thermophoresis studies supported our hypothesis, with AtDHDPS1 having a ~ 6-fold tighter lysine dissociation constant compared to AtDHDPS2, which agrees with the lower half minimal inhibitory concentration for lysine observed. Thus, we highlight that subtle differences in protein structures, which could not have been predicted from the primary sequences, can have profound effects on the allostery of a key enzyme involved in lysine biosynthesis in plants. DATABASES: Structures described are available in the Protein Data Bank under the accession numbers 6VVH and 6VVI.
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Affiliation(s)
- Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Matthew P Boarder
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Alexandra M Mangion
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, Australia.,Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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7
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Marjanovic A, Ramírez-Palacios CJ, Masman MF, Drenth J, Otzen M, Marrink SJ, Janssen DB. Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase. Protein Eng Des Sel 2021; 34:gzab016. [PMID: 34258615 PMCID: PMC8277567 DOI: 10.1093/protein/gzab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/03/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Diaminopimelate decarboxylases (DAPDCs) are highly selective enzymes that catalyze the common final step in different lysine biosynthetic pathways, i.e. the conversion of meso-diaminopimelate (DAP) to L-lysine. We examined the modification of the substrate specificity of the thermostable decarboxylase from Thermotoga maritima with the aim to introduce activity with 2-aminopimelic acid (2-APA) since its decarboxylation leads to 6-aminocaproic acid (6-ACA), a building block for the synthesis of nylon-6. Structure-based mutagenesis of the distal carboxylate binding site resulted in a set of enzyme variants with new activities toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily acted as a 2-APA decarboxylase. We next used computational modeling to explain the observed shift in catalytic activities of the mutants. The results suggest that predictive computational protocols can support the redesign of the catalytic properties of this class of decarboxylating PLP-dependent enzymes.
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Affiliation(s)
- Antonija Marjanovic
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Carlos J Ramírez-Palacios
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Marcelo F Masman
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Van’t Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jeroen Drenth
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marleen Otzen
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert-Jan Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotechnology and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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8
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Weatherhead AW, Crowther JM, Horne CR, Meng Y, Coombes D, Currie MJ, Watkin SAJ, Adams LE, Parthasarathy A, Dobson RCJ, Hudson AO. Structure-Function Studies of the Antibiotic Target l,l-Diaminopimelate Aminotransferase from Verrucomicrobium spinosum Reveal an Unusual Oligomeric Structure. Biochemistry 2020; 59:2274-2288. [PMID: 32478518 DOI: 10.1021/acs.biochem.0c00185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While humans lack the biosynthetic pathways for meso-diaminopimelate and l-lysine, they are essential for bacterial survival and are therefore attractive targets for antibiotics. It was recently discovered that members of the Chlamydia family utilize a rare aminotransferase route of the l-lysine biosynthetic pathway, thus offering a new enzymatic drug target. Here we characterize diaminopimelate aminotransferase from Verrucomicrobium spinosum (VsDapL), a nonpathogenic model bacterium for Chlamydia trachomatis. Complementation experiments verify that the V. spinosum dapL gene encodes a bona fide diaminopimelate aminotransferase, because the gene rescues an Escherichia coli strain that is auxotrophic for meso-diaminopimelate. Kinetic studies show that VsDapL follows a Michaelis-Menten mechanism, with a KMapp of 4.0 mM toward its substrate l,l-diaminopimelate. The kcat (0.46 s-1) and the kcat/KM (115 s-1 M-1) are somewhat lower than values for other diaminopimelate aminotransferases. Moreover, whereas other studied DapL orthologs are dimeric, sedimentation velocity experiments demonstrate that VsDapL exists in a monomer-dimer self-association, with a KD2-1 of 7.4 μM. The 2.25 Å resolution crystal structure presents the canonical dimer of chalice-shaped monomers, and small-angle X-ray scattering experiments confirm the dimer in solution. Sequence and structural alignments reveal that active site residues important for activity are conserved in VsDapL, despite the lower activity compared to those of other DapL homologues. Although the dimer interface buries 18% of the total surface area, several loops that contribute to the interface and active site, notably the L1, L2, and L5 loops, are highly mobile, perhaps explaining the unstable dimer and lower catalytic activity. Our kinetic, biophysical, and structural characterization can be used to inform the development of antibiotics.
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Affiliation(s)
- Anthony W Weatherhead
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Jennifer M Crowther
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Yanxiang Meng
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Serena A J Watkin
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Lily E Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623-5603, United States
| | - Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623-5603, United States
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand.,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623-5603, United States
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Adams LE, Rynkiewicz P, Babbitt GA, Mortensen JS, North RA, Dobson RCJ, Hudson AO. Comparative Molecular Dynamics Simulations Provide Insight Into Antibiotic Interactions: A Case Study Using the Enzyme L,L-Diaminopimelate Aminotransferase (DapL). Front Mol Biosci 2020; 7:46. [PMID: 32274387 PMCID: PMC7113581 DOI: 10.3389/fmolb.2020.00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/04/2020] [Indexed: 12/03/2022] Open
Abstract
The L,L-diaminopimelate aminotransferase (DapL) pathway, a recently discovered variant of the lysine biosynthetic pathway, is an attractive pipeline to identify targets for the development of novel antibiotic compounds. DapL is a homodimer that catalyzes the conversion of tetrahydrodipicolinate to L,L-diaminopimelate in a single transamination reaction. The penultimate and ultimate products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are key components of the Gram-negative and Gram-positive bacterial peptidoglycan cell wall. Humans are not able to synthesize lysine, and DapL has been identified in 13% of bacteria whose genomes have been sequenced and annotated to date, thus it is an attractive target for the development of narrow spectrum antibiotics through the prevention of both lysine biosynthesis and peptidoglycan crosslinking. To address the common lack of structural information when conducting compound screening experiments and provide support for the use of modeled structures, our analyses utilized inferred structures from related homologous enzymes. Using a comprehensive and comparative molecular dynamics (MD) software package-DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations) 2.0, we investigated the binding dynamics of four previously identified antagonistic ligands of DapL from Verrucomicrobium spinosum, a non-pathogenic relative of Chlamydia trachomatis. Here, we present putative docking positions of the four ligands and provide confirmatory comparative molecular dynamics simulations supporting the conformations. The simulations performed in this study can be applied to evaluate putative targets to predict compound effectiveness prior to in vivo and in vitro experimentation. Moreover, this approach has the potential to streamline the process of antibiotic development.
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Affiliation(s)
- Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Patrick Rynkiewicz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Jamie S. Mortensen
- Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, United States
| | - Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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10
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Parthasarathy A, Adams LE, Savka FC, Hudson AO. The Arabidopsis thaliana gene annotated by the locus tag At3g08860 encodes alanine aminotransferase. PLANT DIRECT 2019; 3:e00171. [PMID: 31549019 PMCID: PMC6750192 DOI: 10.1002/pld3.171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/18/2019] [Accepted: 08/30/2019] [Indexed: 05/22/2023]
Abstract
The aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes, eight of which are suggested to be alanine aminotransferases. One of the putative alanine aminotransferases genes, At3g08860, was attributed the function of alanine:glyoxylate aminotransferase/β-alanine:pyruvate aminotransferase based on the analysis of gene expression networks and homology to other β-alanine aminotransferases in plants. It was earlier demonstrated that At3g08860 is specifically upregulated in response to osmotic stress, but not other stresses (β-alanine is an osmoprotectant in plants). Furthermore, it was shown that the expression of At3g08860 is highly coordinated with the genes of the uracil degradation pathway leading to the non-proteinogenic amino acid β-alanine. These evidence were suggestive of the involvement of At3g08860 in β-alanine metabolism. However, direct experimental evidence for the function of At3g08860 was lacking, and therefore, the goal of this study was to elucidate the function of the uncharacterized aminotransferase annotated by the locus tag At3g08860. The cDNA of At3g08860 was demonstrated to functionally complement two E. coli mutants auxotrophic for the amino acids, L-alanine (proteinogenic) and β-alanine (non-proteinogenic). Enzyme activity using purified recombinant At3g08860 further demonstrated that the enzyme is endowed with L-alanine:glyoxylate aminotransferase activity.
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Affiliation(s)
| | - Lily E. Adams
- The Thomas H. Gosnell School of Life SciencesRochester Institute of TechnologyRochesterNYUSA
| | - Francisco C. Savka
- The Thomas H. Gosnell School of Life SciencesRochester Institute of TechnologyRochesterNYUSA
| | - André O. Hudson
- The Thomas H. Gosnell School of Life SciencesRochester Institute of TechnologyRochesterNYUSA
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Opoku-Temeng C, Onyedibe KI, Aryal UK, Sintim HO. Proteomic analysis of bacterial response to a 4-hydroxybenzylidene indolinone compound, which re-sensitizes bacteria to traditional antibiotics. J Proteomics 2019; 202:103368. [PMID: 31028946 DOI: 10.1016/j.jprot.2019.04.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/21/2019] [Accepted: 04/23/2019] [Indexed: 02/07/2023]
Abstract
Halogenated 4-hydroxybenzylidene indolinones have been shown to re-sensitize methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE) to methicillin and vancomycin respectively. The mechanism of antibiotic re-sensitization was however not previously studied. Here, we probe the scope of antibiotic re-sensitization and present the global proteomics analysis of S. aureus treated with GW5074, a 4-hydroxybenzylidene indolinone compound. With a minimum inhibitory concentration (MIC) of 8 μg/mL against S. aureus, GW5074 synergized with beta-lactam antibiotics like ampicillin, carbenicillin and cloxacillin, the DNA synthesis inhibitor, ciprofloxacin, the protein synthesis inhibitor, gentamicin and the folate acid synthesis inhibitor, trimethoprim. Global proteomics analysis revealed that GW5074 treatment resulted in significant downregulation of enzymes involved in the purine biosynthesis. S. aureus proteins involved in amino acid metabolism and peptide transport were also observed to be downregulated. Interestingly, anti-virulence targets such as AgrC (a quorum sensing-related histidine kinase), AgrA (a quorum sensing-related response regulator) as well as downstream targets, such as hemolysins, lipases and proteases in S. aureus were also downregulated by GW5074. We observed that the peptidoglycan hydrolase, SceD was significantly upregulated. The activity of GW5074 on S. aureus suggests that the compound primes bacteria for the antibacterial action of ineffective antibiotics. SIGNIFICANCE: Antibiotic resistance continues to present significant challenges to the treatment of bacterial infections. Given that antibiotic resistance is a natural phenomenon and that it has become increasingly difficult to discover novel antibiotics, efforts to improve the activity of existing agents are worth pursuing. A few small molecules that re-sensitize resistant bacteria to traditional antibiotics have been described but the molecular details that underpin how these compounds work to re-sensitize bacteria remain largely unknown. In this report, global label-free quantitative proteomics was used to identify changes in the proteome that occurs when GW5074, a compound that re-sensitize MRSA to methicillin, is administered to S. aureus. The identification of pathways that are impacted by GW5074 could help identify novel targets for antibiotic re-sensitization.
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Affiliation(s)
- Clement Opoku-Temeng
- Graduate Program in Biochemistry, University of Maryland, College Park, MD 20742, USA; Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Kenneth Ikenna Onyedibe
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Herman O Sintim
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.
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12
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Sadhasivam A, Vetrivel U. Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach. J Cell Biochem 2019; 120:2271-2288. [PMID: 30302805 DOI: 10.1002/jcb.27553] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/02/2018] [Indexed: 01/24/2023]
Abstract
Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria, which is a major causative of infectious blindness and sexually transmitted diseases. A surge in multidrug resistance among chlamydial species has posed a challenge to adopt alternative drug targeting strategies. Recently, in C.t, L,L-diaminopimelate aminotransferase (CtDAP-AT) is proven to be a potential drug target due its essential role in cell survival and host nonspecificity. Hence, in this study, a multilevel precision-based virtual screening of CtDAP-AT was performed to identify potential inhibitors, wherein, an integrative stringent scoring and filtration were performed by coupling, glide docking score, binding free energy, ADMET (absorption, distribution, metabolism, and excretion, toxicity) prediction, density functional theory (quantum mechanics), and molecular dynamics simulation (molecular mechanics). On cumulative analysis, NSC_5485 (1,3-bis((7-chloro-4-quinolinyl)amino)-2-propanol) was found to be the most potential lead, as it showed higher order significance in terms of binding affinity, bonded interactions, favorable ADMET, chemical reactivity, and greater stabilization during complex formation. This is the first report on prioritization of small molecules from National Cancer Institute (NCI) and Maybridge data sets (341 519 compounds) towards targeting CtDAP-AT. Thus, the proposed compound shall aid in effective combating of a broad spectrum of C.t infections as it surpassed all the levels of prioritization.
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Affiliation(s)
- Anupriya Sadhasivam
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, SankaraNethralaya, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, SankaraNethralaya, Chennai, Tamil Nadu, India
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13
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Mantravadi PK, Kalesh KA, Dobson RCJ, Hudson AO, Parthasarathy A. The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies. Antibiotics (Basel) 2019; 8:E8. [PMID: 30682820 PMCID: PMC6466574 DOI: 10.3390/antibiotics8010008] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/17/2019] [Accepted: 01/20/2019] [Indexed: 12/11/2022] Open
Abstract
Pathogenic antibiotic resistant bacteria pose one of the most important health challenges of the 21st century. The overuse and abuse of antibiotics coupled with the natural evolutionary processes of bacteria has led to this crisis. Only incremental advances in antibiotic development have occurred over the last 30 years. Novel classes of molecules, such as engineered antibodies, antibiotic enhancers, siderophore conjugates, engineered phages, photo-switchable antibiotics, and genome editing facilitated by the CRISPR/Cas system, are providing new avenues to facilitate the development of antimicrobial therapies. The informatics revolution is transforming research and development efforts to discover novel antibiotics. The explosion of nanotechnology and micro-engineering is driving the invention of antimicrobial materials, enabling the cultivation of "uncultivable" microbes and creating specific and rapid diagnostic technologies. Finally, a revival in the ecological aspects of microbial disease management, the growth of prebiotics, and integrated management based on the "One Health" model, provide additional avenues to manage this health crisis. These, and future scientific and technological developments, must be coupled and aligned with sound policy and public awareness to address the risks posed by rising antibiotic resistance.
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Affiliation(s)
| | | | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800 Christchurch, New Zealand.
| | - André O Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA.
| | - Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA.
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14
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Gupta R, Hogan CJ, Perugini MA, Soares da Costa TP. Characterization of recombinant dihydrodipicolinate synthase from the bread wheat Triticum aestivum. PLANTA 2018; 248:381-391. [PMID: 29744651 DOI: 10.1007/s00425-018-2894-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/14/2018] [Indexed: 06/08/2023]
Abstract
Recombinant wheat DHDPS was produced for the first time in milligram quantities and shown to be an enzymatically active tetramer in solution using analytical ultracentrifugation and small angle X-ray scattering. Wheat is an important cereal crop with an extensive role in global food supply. Given our rapidly growing population, strategies to increase the nutritional value and production of bread wheat are of major significance in agricultural science to satisfy our dietary requirements. Lysine is one of the most limiting essential amino acids in wheat, thus, a thorough understanding of lysine biosynthesis is of upmost importance to improve its nutritional value. Dihydrodipicolinate synthase (DHDPS; EC 4.3.3.7) catalyzes the first committed step in the lysine biosynthesis pathway of plants. Here, we report for the first time the expression and purification of recombinant DHDPS from the bread wheat Triticum aestivum (Ta-DHDPS). The optimized protocol yielded 36 mg of > 98% pure recombinant Ta-DHDPS per liter of culture. Enzyme kinetic studies demonstrate that the recombinant Ta-DHDPS has a KM (pyruvate) of 0.45 mM, KM (l-aspartate-4-semialdehyde) of 0.07 mM, kcat of 56 s-1, and is inhibited by lysine (IC 50 LYS of 0.033 mM), which agree well with previous studies using labor-intensive purification from wheat suspension cultures. We subsequently employed circular dichroism spectroscopy, analytical ultracentrifugation and small angle X-ray scattering to show that the recombinant enzyme is folded with 60% α/β structure and exists as a 7.5 S tetrameric species with a Rg of 33 Å and Dmax of 118 Å. This study is the first to report the biophysical properties of the recombinant Ta-DHDPS in aqueous solution and offers an excellent platform for future studies aimed at improving nutritional value and primary production of bread wheat.
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Affiliation(s)
- Ruchi Gupta
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Campbell J Hogan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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15
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Cala AR, Nadeau MT, Abendroth J, Staker BL, Reers AR, Weatherhead AW, Dobson RCJ, Myler PJ, Hudson AO. The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:885-891. [PMID: 27917836 PMCID: PMC5137465 DOI: 10.1107/s2053230x16018525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/19/2016] [Indexed: 11/10/2022] Open
Abstract
In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space group P4322, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. Rr.i.m. was 0.11, Rwork was 0.177 and Rfree was 0.208. The three-dimensional structural features of the enzymes show that DapB from B. henselae is a tetramer consisting of four identical polypeptides. In addition, the substrate NADP+ was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.
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Affiliation(s)
- Ali R. Cala
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Maria T. Nadeau
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Jan Abendroth
- Beryllium Discovery Inc., Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Alexandra R. Reers
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Anthony W. Weatherhead
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
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16
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Naqvi KF, Staker BL, Dobson RCJ, Serbzhinskiy D, Sankaran B, Myler PJ, Hudson AO. Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:2-9. [PMID: 26750477 PMCID: PMC4708043 DOI: 10.1107/s2053230x15023213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%(w/v) PEG 4000, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.10 Å resolution. They belonged to space group P212121, with unit-cell parameters a = 79.96, b = 106.33, c = 136.25 Å. The final R values were Rr.i.m. = 0.098, Rwork = 0.183, Rfree = 0.233.
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Affiliation(s)
- Kubra F. Naqvi
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Dmitry Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Ernest Orlando Lawrence Berkeley National Laboratory, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
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