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Zhang Q, Wu B, Han L, Yu D, Liang T, Wang Y, Guo T. Functional characterization of two 3-dehydroquinases of AroQ1 and AroQ2 in the shikimate pathway and expression of genes for the type III secretion system in Ralstonia solanacearum. Front Microbiol 2023; 14:1186688. [PMID: 37180250 PMCID: PMC10171560 DOI: 10.3389/fmicb.2023.1186688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 05/16/2023] Open
Abstract
The shikimate pathway is a general route for the biosynthesis of aromatic amino acids (AAAs) in many microorganisms. A 3-dehydroquinase, AroQ, controls the third step of the shikimate pathway that catalyzes the formation of 3-dehydroquinate from 3-dehydroshikimate via a trans-dehydration reaction. Ralstonia solanacearum harbors two 3-dehydroquinases, AroQ1 and AroQ2, sharing 52% similarity in amino acids. Here, we demonstrated that two 3-dehydroquinases, AroQ1 and AroQ2, are essential for the shikimate pathway in R. solanacearum. The growth of R. solanacearum was completely diminished in a nutriment-limited medium with the deletion of both aroQ1 and aroQ2, while substantially impaired in planta. The aroQ1/2 double mutant was able to replicate in planta but grew slowly, which was ~4 orders of magnitude less than the parent strain to proliferate to the maximum cell densities in tomato xylem vessels. Moreover, the aroQ1/2 double mutant failed to cause disease in tomato and tobacco plants, whereas the deletion of either aroQ1 or aroQ2 did not alter the growth of R. solanacearum or pathogenicity on host plants. Supplementary shikimic acid (SA), an important intermediate of the shikimate pathway, substantially restored the diminished or impaired growth of aroQ1/2 double mutant in a limited medium or inside host plants. The necessity of AroQ1 and AroQ2 on the pathogenicity of solanacearum toward host plants was partially due to insufficient SA inside host plants. Moreover, the deletion of both aroQ1 and aroQ2 significantly impaired the expression of genes for the type III secretion system (T3SS) both in vitro and in planta. Its involvement in the T3SS was mediated through the well-characterized PrhA signaling cascade and was independent of growth deficiency under nutrient-limited conditions. Taken together, R. solanacearum 3-dehydroquinases play important roles in bacterial growth, the expression of the T3SS, and pathogenicity in host plants. These results could extend our insights into the understanding of the biological function of AroQ and the sophisticated regulation of the T3SS in R. solanacearum.
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Affiliation(s)
- Qingshan Zhang
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Bofan Wu
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Liangliang Han
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Duan Yu
- Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Tao Liang
- Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Yan Wang
- Chongqing Academy of Agricultural Sciences, Chongqing, China
- *Correspondence: Yan Wang
| | - Tao Guo
- College of Resources and Environment, Southwest University, Chongqing, China
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Lynch JH. Revisiting the dual pathway hypothesis of Chorismate production in plants. HORTICULTURE RESEARCH 2022; 9:uhac052. [PMID: 35350169 PMCID: PMC8945279 DOI: 10.1093/hr/uhac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
The shikimate pathway, the seven enzymatic steps that synthesize chorismate from phosphoenolpyruvate and erythrose 4-phosphate, produces the last common precursor of the three aromatic amino acids. It is firmly established that all seven enzymes are present in plastids, and it is generally accepted that this organelle is likely the sole location for production of chorismate in plants. However, recently a growing body of evidence has provided support for a previous proposal that at least portions of the pathway are duplicated in the cytosol, referred to as the Dual Pathway Hypothesis. Here I revisit this obscure hypothesis by reviewing the findings that provided the original basis for its formulation as well as more recent results that provide fresh support for a possible extra-plastidial shikimate pathway duplication. Similarities between this possible intercompartmental metabolic redundancy and that of terpenoid metabolism are used to discuss potential advantages of pathway duplication, and the translational implications of the Dual Pathway Hypothesis for metabolic engineering are noted.
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Yokoyama R, de Oliveira MVV, Kleven B, Maeda HA. The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation. THE PLANT CELL 2021; 33:671-696. [PMID: 33955484 PMCID: PMC8136874 DOI: 10.1093/plcell/koaa042] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/19/2020] [Indexed: 05/22/2023]
Abstract
The plant shikimate pathway directs bulk carbon flow toward biosynthesis of aromatic amino acids (AAAs, i.e. tyrosine, phenylalanine, and tryptophan) and numerous aromatic phytochemicals. The microbial shikimate pathway is feedback inhibited by AAAs at the first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DHS). However, AAAs generally do not inhibit DHS activities from plant extracts and how plants regulate the shikimate pathway remains elusive. Here, we characterized recombinant Arabidopsis thaliana DHSs (AthDHSs) and found that tyrosine and tryptophan inhibit AthDHS2, but not AthDHS1 or AthDHS3. Mixing AthDHS2 with AthDHS1 or 3 attenuated its inhibition. The AAA and phenylpropanoid pathway intermediates chorismate and caffeate, respectively, strongly inhibited all AthDHSs, while the arogenate intermediate counteracted the AthDHS1 or 3 inhibition by chorismate. AAAs inhibited DHS activity in young seedlings, where AthDHS2 is highly expressed, but not in mature leaves, where AthDHS1 is predominantly expressed. Arabidopsis dhs1 and dhs3 knockout mutants were hypersensitive to tyrosine and tryptophan, respectively, while dhs2 was resistant to tyrosine-mediated growth inhibition. dhs1 and dhs3 also had reduced anthocyanin accumulation under high light stress. These findings reveal the highly complex regulation of the entry reaction of the plant shikimate pathway and lay the foundation for efforts to control the production of AAAs and diverse aromatic natural products in plants.
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Affiliation(s)
- Ryo Yokoyama
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Marcos V V de Oliveira
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Bailey Kleven
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin–Madison, 430 Lincoln Dr. Madison, WI 53706, USA
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Montaser R, Kelleher NL. Discovery of the Biosynthetic Machinery for Stravidins, Biotin Antimetabolites. ACS Chem Biol 2020; 15:1134-1140. [PMID: 31887014 DOI: 10.1021/acschembio.9b00890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Stravidins are peptide antibiotics produced by Streptomyces spp. Their antibacterial activity derives from an unusual amiclenomycin monomer, the warhead that inhibits biotin biosynthesis. Despite being discovered over five decades ago, stravidin biosynthesis has remained a mystery. Using our "metabologenomics" platform, we discover new stravidin analogues and identify the novel biosynthetic machinery responsible for their production. Analysis of the newly identified biosynthetic gene cluster (BGC) indicates the unusual amiclenomycin warhead is derived from chorismic acid, with initial steps similar to those involved in p-amino phenylalanine biosynthesis. However, a distinctive decarboxylation retains the nonaromatic character of a key ring and precedes a one-carbon extension to afford the warhead in its bioactive, untriggered state. Strikingly, we also identified two streptavidin genes flanking the new stravidin BGC reported here. This aligns with the known synergistic activity between the biotin-binding activity of streptavidin and the stravidins to antagonize both biotin biogenesis and bacterial growth.
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Affiliation(s)
- Rana Montaser
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
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Zhang W, Li J, Shi X, Hikichi Y, Zhang Y, Ohnishi K. Functional Characterization of Two Putative DAHP Synthases of AroG1 and AroG2 and Their Links With Type III Secretion System in Ralstonia solanacearum. Front Microbiol 2019; 10:183. [PMID: 30809210 PMCID: PMC6379268 DOI: 10.3389/fmicb.2019.00183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/23/2019] [Indexed: 11/20/2022] Open
Abstract
Type three secretion system (T3SS) is essential for Ralstonia solanacearum to cause disease in host plants and we previously screened AroG1 as a candidate with impact on the T3SS expression. Here, we focused on two putative DAHP synthases of AroG1 and AroG2, which control the first step of the shikimate pathway, a common route for biosynthesis of aromatic amino acids (AAA), to characterize their functional roles and possible links with virulence in R. solanacearum. Deletion of aroG1/2 or aroG1, but not aroG2, significantly impaired the T3SS expression both in vitro and in planta, and the impact of AroG1 on T3SS was mediated with a well-characterized PrhA signaling cascade. Virulence of the aroG1/2 or aroG1 mutants was completely diminished or significantly impaired in tomato and tobacco plants, but not the aroG2 mutants. The aroG1/2 mutants failed to grow in limited medium, but grew slowly in planta. This significantly impaired growth was also observed in the aroG1 mutants both in planta and limited medium, but not in aroG2 mutants. Complementary aroG1 significantly restored the impaired or diminished bacterial growth, T3SS expression and virulence. Supplementary AAA or shikimic acid, an important intermediate of the shikimate pathway, significantly restored diminished growth in limited medium. The promoter activity assay showed that expression of aroG1 and aroG2 was greatly increased to 10-20-folder higher levels with deletion of the other. All these results demonstrated that both AroG1 and AroG2 are involved in the shikimate pathway and cooperatively essential for AAA biosynthesis in R. solanacearum. The AroG1 plays a major role on bacterial growth, T3SS expression and pathogenicity, while the AroG2 is capable to partially carry out the function of AroG1 in the absence of AroG1.
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Affiliation(s)
- Weiqi Zhang
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Jing Li
- The Ninth People's Hospital of Chongqing, Chongqing, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Yasufumi Hikichi
- Laboratory of Plant Pathology and Biotechnology, Kochi University, Kochi, Japan
| | - Yong Zhang
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Kochi, Japan
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6
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Zhao H, Gao H, Ji K, Yan B, Li Q, Mo S, Zheng M, Ou Q, Wu B, Li N, Jiang C. Isolation and biochemical characterization of a metagenome-derived 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase gene from subtropical marine mangrove wetland sediments. AMB Express 2019; 9:19. [PMID: 30715617 PMCID: PMC6362186 DOI: 10.1186/s13568-019-0742-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/23/2019] [Indexed: 11/10/2022] Open
Abstract
3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key rate-limiting enzyme in aromatic amino acid anabolism. A new Iβ-type DAHPS gene (aro1A) was identified in a metagenomic library from subtropical marine mangrove sediment. The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level. Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (β/α)8 barrel-shaped catalytic structural domain of DAHPS. The motifs and amino acid residues involved in the combination of substrates and metal ligand were highly conservative with the known DAHPS. The putative DAHPS gene was subcloned into a pET-30a(+) vector and was overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein was purified to homogeneity. The maximum activity for the recombinant Aro1A protein occurred at pH 8.0 and 40 °C. Ba2+ and Ca2+ stimulated the activity of Aro1A protein. The enzyme showed high affinity and catalytic efficiency (K m PEP = 19.58 μM, V max PEP = 29.02 μM min-1, and k cat PEP /K m PEP = 0.88 s-1 μM-1) under optimal reaction conditions. The enzymatic property of Aro1A indicates its potential in aromatic amino acid industrial production.
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Tian J, Zhu L, Wang W, Zhang L, Li Z, Zhao Q, Xing K, Feng Z, Peng X. Genomic Analysis of Microbulbifer sp. Strain A4B-17 and the Characterization of Its Metabolic Pathways for 4-Hydroxybenzoic Acid Synthesis. Front Microbiol 2019; 9:3115. [PMID: 30619190 PMCID: PMC6305291 DOI: 10.3389/fmicb.2018.03115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
The marine bacterium Microbulbifer sp. A4B-17 produces secondary metabolites such as 4-hydroxybenzoic acid (4HBA) and esters of 4HBA (parabens). 4HBA is a useful material in the synthesis of the liquid crystal. Parabens are man-made compounds that have been extensively used since the 1920s in the cosmetic, pharmaceutical, and food industries for their effective antimicrobial activity. In this study, we completed the sequencing and annotation of the A4B-17 strain genome and found all genes for glucose utilization and 4HBA biosynthesis. Strain A4B-17 uses the Embden-Meyerhof-Parnas (EMP), hexose monophosphate (HMP), and Entner-Doudoroff (ED) pathways to utilize glucose. Other sugars such as fructose, sucrose, xylose, arabinose, galactose, mannitol, and glycerol supported cell growth and 4HBA synthesis. Reverse transcriptional analysis confirmed that the key genes involved in the glucose metabolism were functional. Paraben concentrations were proportionally increased by adding alcohols to the culture medium, indicating that strain A4B-17 synthesizes the 4HBA and the alcohols separately and an esterification reaction between them is responsible for the paraben synthesis. A gene that codes for a carboxylesterase was proposed to catalyze this reaction. The temperature and NaCl concentration for optimal growth were determined to be 35°C and 22.8 g/L.
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Affiliation(s)
- Jun Tian
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Li Zhu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wenjun Wang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Liping Zhang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhi Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Qingyu Zhao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ke Xing
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhaozhong Feng
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xue Peng
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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8
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Biessy A, Filion M. Phenazines in plant-beneficialPseudomonasspp.: biosynthesis, regulation, function and genomics. Environ Microbiol 2018; 20:3905-3917. [DOI: 10.1111/1462-2920.14395] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/20/2018] [Accepted: 08/24/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Adrien Biessy
- Department of Biology; Université de Moncton; Moncton New Brunswick Canada
| | - Martin Filion
- Department of Biology; Université de Moncton; Moncton New Brunswick Canada
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9
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Pratap S, Dev A, Kumar V, Yadav R, Narwal M, Tomar S, Kumar P. Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site. Sci Rep 2017; 7:6364. [PMID: 28743924 PMCID: PMC5526877 DOI: 10.1038/s41598-017-06578-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/08/2017] [Indexed: 01/23/2023] Open
Abstract
3-deoxy-D-arabino-heptulosonate-7-phosphate-synthase (DAHPS) is the first enzyme of the shikimate pathway and is responsible for the synthesis of aromatic amino acids in microorganisms. This pathway is an attractive target for antimicrobial drugs. In Bacillus subtilis, the N-terminal domain of the bifunctional DAHPS enzyme belongs to an AroQ class of chorismate mutase and is functionally homologous to the downstream AroH class chorismate mutase. This is the first structure of chorismate mutase, AroQ (BsCM_2) enzyme from Bacillus subtilis in complex with citrate and chlorogenic acid at 1.9 Å and 1.8 Å resolution, respectively. This work provides the structural basis of ligand binding into the active site of AroQ class of chorismate mutase, while accompanied by the conformational flexibility of active site loop. Molecular dynamics results showed that helix H2′ undergoes uncoiling at the first turn and increases the mobility of loop L1′. The side chains of Arg45, Phe46, Arg52 and Lys76 undergo conformational changes, which may play an important role in DAHPS regulation by the formation of the domain-domain interface. Additionally, binding studies showed that the chlorogenic acid binds to BsCM_2 with a higher affinity than chorismate. These biochemical and structural findings could lead to the development of novel antimicrobial drugs.
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Affiliation(s)
- Shivendra Pratap
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Aditya Dev
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Vijay Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ravi Yadav
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Manju Narwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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Inhibition of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis: in silico screening and in vitro validation. Eur J Med Chem 2015; 105:182-93. [PMID: 26491981 DOI: 10.1016/j.ejmech.2015.10.014] [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: 08/28/2015] [Revised: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 11/20/2022]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, remains a serious global health threat, highlighting the urgent need for novel antituberculosis drugs. The shikimate pathway, responsible for aromatic amino acid biosynthesis, is required for the growth of Mycobacterium tuberculosis and is a potential drug target. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (mtDAH7Ps) catalyzes the first step in shikimate pathway. E-pharmacophore models for inhibitors of mtDAH7Ps - tyrosine, phenylalanine, phosphoenolpyruvate and (2S)-2,7-bis(phosphonooxy)heptanoic acid were screened against ZINC synthetic and natural compounds databases. The shortlisted compounds were subjected to induce fit docking and validated by Prime/Molecular Mechanics Generalized Born Surface Area calculation to predict ligand binding energy and ligand strain energy for ligand and receptor. The lead compounds were screened for their inhibitory activity against purified mtDAH7Ps enzyme. Lead compounds inhibited mtDAH7Ps in a concentration-dependent manner; with an IC50 value of 21 μM, 42 μM and 54 μM for α-Tocopherol, rutin and 3-Pyridine carboxyaldehyde respectively. Molecular Dynamics analysis for 50 ns of the active compounds-mtDAH7Ps complexes showed that the backbone of mtDAH7Ps was stable. These results suggest that α-tocopherol, 3 - Pyridine carboxyaldehyde and rutin could be novel drug leads to inhibit mtDAH7Ps in M. tuberculosis.
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11
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Henriquez FL, Campbell SJ, Sundararaj BK, Cano A, Muench SP, Roberts CW. The Acanthamoeba shikimate pathway has a unique molecular arrangement and is essential for aromatic amino acid biosynthesis. Protist 2014; 166:93-105. [PMID: 25576842 DOI: 10.1016/j.protis.2014.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 11/24/2022]
Abstract
The shikimate pathway is the only known biosynthetic route for de novo synthesis of aromatic compounds. It is described as an ancient eukaryotic innovation that has been retained in a subset of eukaryotes, replaced in plants through the acquisition of the chloroplast, but lost in many including humans. Herein, we demonstrate that Acanthamoeba castellanii possesses the shikimate pathway by biochemical and a combination of bioinformatics and molecular biological methods. The growth of A. castellanii (Neff strain and a recently isolated clinical specimen, both T4 genotypes) is inhibited by glyphosate [N-(phosphonomethyl) glycine], an inhibitor of EPSP synthase and the addition of phenylalanine and tryptophan, which are dependent on the shikimate pathway, rescued A. castellanii from glyphosate indicating that glyphosate was specific in action. A. castellanii has a novel complement of shikimate pathway enzymes including unique gene fusions, two Type I and one Type II DAHP synthases (for which their likely sensitivities to feedback inhibition by phenylalanine, tyrosine and tryptophan has been modelled) and a canonical chorismate synthase. The shikimate pathway in A. castellanii therefore has a novel molecular arrangement, is required for amino acid biosynthesis and represents an attractive target for antimicrobials.
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Affiliation(s)
- Fiona L Henriquez
- Institute of Biomedical Science and Environmental Health Research, School of Science, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - Sara J Campbell
- Institute of Biomedical Science and Environmental Health Research, School of Science, University of the West of Scotland, Paisley, PA1 2BE, UK; Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0NR, UK
| | - Bharath K Sundararaj
- Institute of Biomedical Science and Environmental Health Research, School of Science, University of the West of Scotland, Paisley, PA1 2BE, UK; Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0NR, UK
| | - Antonella Cano
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0NR, UK
| | - Stephen P Muench
- School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT
| | - Craig W Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0NR, UK.
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Kubota T, Tanaka Y, Takemoto N, Watanabe A, Hiraga K, Inui M, Yukawa H. Chorismate-dependent transcriptional regulation of quinate/shikimate utilization genes by LysR-type transcriptional regulator QsuR inCorynebacterium glutamicum: carbon flow control at metabolic branch point. Mol Microbiol 2014; 92:356-68. [DOI: 10.1111/mmi.12560] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Takeshi Kubota
- Research Institute of Innovative Technology for the Earth (RITE); 9-2, Kizugawadai, Kizugawa Kyoto 619-0292 Japan
| | - Yuya Tanaka
- Research Institute of Innovative Technology for the Earth (RITE); 9-2, Kizugawadai, Kizugawa Kyoto 619-0292 Japan
| | - Norihiko Takemoto
- Research Institute of Innovative Technology for the Earth (RITE); 9-2, Kizugawadai, Kizugawa Kyoto 619-0292 Japan
| | - Akira Watanabe
- Research Institute of Innovative Technology for the Earth (RITE); 9-2, Kizugawadai, Kizugawa Kyoto 619-0292 Japan
| | - Kazumi Hiraga
- Research Institute of Innovative Technology for the Earth (RITE); 9-2, Kizugawadai, Kizugawa Kyoto 619-0292 Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth (RITE); 9-2, Kizugawadai, Kizugawa Kyoto 619-0292 Japan
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth (RITE); 9-2, Kizugawadai, Kizugawa Kyoto 619-0292 Japan
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13
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Nazmi AR, Schofield LR, Dobson RC, Jameson GB, Parker EJ. Destabilization of the Homotetrameric Assembly of 3-Deoxy-d-Arabino-Heptulosonate-7-Phosphate Synthase from the Hyperthermophile Pyrococcus furiosus Enhances Enzymatic Activity. J Mol Biol 2014; 426:656-73. [DOI: 10.1016/j.jmb.2013.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/05/2013] [Accepted: 11/06/2013] [Indexed: 12/30/2022]
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14
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Cross PJ, Pietersma AL, Allison TM, Wilson-Coutts SM, Cochrane FC, Parker EJ. Neisseria meningitidis expresses a single 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase that is inhibited primarily by phenylalanine. Protein Sci 2013; 22:1087-99. [PMID: 23754471 DOI: 10.1002/pro.2293] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/26/2013] [Accepted: 05/28/2013] [Indexed: 11/12/2022]
Abstract
Neisseria meningitidis is the causative agent of meningitis and meningococcal septicemia is a major cause of disease worldwide, resulting in brain damage and hearing loss, and can be fatal in a large proportion of cases. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyzes the first reaction in the shikimate pathway leading to the biosynthesis of aromatic metabolites including the aromatic acids l-Trp, l-Phe, and l-Tyr. This pathway is absent in humans, meaning that enzymes of the pathway are considered as potential candidates for therapeutic intervention. As the entry point, feedback inhibition of DAH7PS by pathway end products is a key mechanism for the control of pathway flux. The structure of the single DAH7PS expressed by N. meningitidis was determined at 2.0 Å resolution. In contrast to the other DAH7PS enzymes, which are inhibited only by a single aromatic amino acid, the N. meningitidis DAH7PS was inhibited by all three aromatic amino acids, showing greatest sensitivity to l-Phe. An N. meningitidis enzyme variant, in which a single Ser residue at the bottom of the inhibitor-binding cavity was substituted to Gly, altered inhibitor specificity from l-Phe to l-Tyr. Comparison of the crystal structures of both unbound and Tyr-bound forms and the small angle X-ray scattering profiles reveal that N. meningtidis DAH7PS undergoes no significant conformational change on inhibitor binding. These observations are consistent with an allosteric response arising from changes in protein motion rather than conformation, and suggest ligands that modulate protein dynamics may be effective inhibitors of this enzyme.
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Affiliation(s)
- Penelope J Cross
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
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15
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Islam T, Bibi NS, Vennapusa RR, Fernandez-Lahore M. Selection of ceramic fluorapatite-binding peptides from a phage display combinatorial peptide library: optimum affinity tags for fluorapatite chromatography. J Mol Recognit 2013; 26:341-50. [DOI: 10.1002/jmr.2275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 01/12/2013] [Accepted: 02/21/2013] [Indexed: 01/26/2023]
Affiliation(s)
- Tuhidul Islam
- Department of Biochemical Engineering, School of Engineering and Science; Jacobs University Bremen, Campus Ring 1; 28759; Bremen; Germany
| | - Noor Shad Bibi
- Department of Biochemical Engineering, School of Engineering and Science; Jacobs University Bremen, Campus Ring 1; 28759; Bremen; Germany
| | - Rami Reddy Vennapusa
- Department of Biochemical Engineering, School of Engineering and Science; Jacobs University Bremen, Campus Ring 1; 28759; Bremen; Germany
| | - Marcelo Fernandez-Lahore
- Department of Biochemical Engineering, School of Engineering and Science; Jacobs University Bremen, Campus Ring 1; 28759; Bremen; Germany
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16
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Light SH, Anderson WF. The diversity of allosteric controls at the gateway to aromatic amino acid biosynthesis. Protein Sci 2013; 22:395-404. [PMID: 23400945 DOI: 10.1002/pro.2233] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 11/11/2022]
Abstract
Present within bacteria, plants, and some lower eukaryotes 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) catalyzes the first committed step in the synthesis of a number of metabolites, including the three aromatic amino acids phenylalanine, tyrosine, and tryptophan. Catalyzing the first reaction in an important biosynthetic pathway, DAHPS is situated at a critical regulatory checkpoint-at which pathway input can be efficiently modulated to respond to changes in the concentration of pathway outputs. Based on a phylogenetic classification scheme, DAHPSs have been divided into three major subtypes (Iα, Iβ, and II). These subtypes are subjected to an unusually diverse pattern of allosteric regulation, which can be used to further subdivide the enzymes. Crystal structures of most of the regulatory subclasses have been determined. When viewed collectively, these structures illustrate how distinct mechanisms of allostery are applied to a common catalytic scaffold. Here, we review structural revelations regarding DAHPS regulation and make the case that the functional difference between the three major DAHPS subtypes relates to basic distinctions in quaternary structure and mechanism of allostery.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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17
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Bhattacharya S, Kumar P. An insilico approach to structural elucidation of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Arabidopsis thaliana: hints for herbicide design. PHYTOCHEMISTRY 2012; 73:7-14. [PMID: 22000723 DOI: 10.1016/j.phytochem.2011.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 09/05/2011] [Accepted: 09/08/2011] [Indexed: 05/31/2023]
Abstract
3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS), the first enzyme of the shikimate pathway, is responsible for the synthesis of aromatic amino acids in microorganisms and plants. The pathway has been of increasing interest in the recent past as the enzymes are being targeted for antimicrobial drug and herbicide design. In the present work the three dimensional structure of the type II DAHPS present in Arabidopsis thaliana (At-DAHPS) is described and compared with type I DAHPS. The structure shows that the enzyme belongs to the (β/α)(8) TIM barrel family and that most of the active site residues are conserved in the type I DAHPS enzymes. Although the overall structures of the type I and type II enzymes are similar, there are differences in the extra barrel elements which may explain the different modes of enzyme regulation. At the N-terminus of At-DAHPS, there are three non-core helices, α0a (Ala72-Lys83), α0b (Ala94-Ala106) and α0c (Ala113-Val128), but no β(0), in contrast to the microbial type II DAHPS. Also, the (I/L)GAR motif in the type I DAHPS is substituted with xGxR in the case of type II DAHPS. Also, a motif NK(/I)PGR(/K) is present in the sequences of type II DAHPS including At-DAHPS. The elucidation of the active site architecture of At-DAHPS may provide a structural framework useful for the design of specific inhibitors towards herbicide development.
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18
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Tran D, Pietersma AL, Schofield LR, Rost M, Jameson GB, Parker EJ. Investigating the role of the hydroxyl groups of substrate erythrose 4-phosphate in the reaction catalysed by the first enzyme of the shikimate pathway. Bioorg Med Chem Lett 2011; 21:6838-41. [PMID: 21978677 DOI: 10.1016/j.bmcl.2011.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/04/2011] [Accepted: 09/06/2011] [Indexed: 11/28/2022]
Abstract
3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) synthase catalyses the first step of the shikimate pathway, which is responsible for the biosynthesis of aromatic amino acids in microorganisms and plants. This enzyme catalyses an aldol reaction between phosphoenolpyruvate and D-erythrose 4-phosphate to generate DAH7P. Both 2-deoxyerythrose 4-phosphate and 3-deoxyerythrose 4-phosphate were synthesised and tested as alternative substrates for the enzyme. Both compounds were found to be substrates for the DAH7P synthases from Escherichia coli, Pyrococcus furiosus and Mycobacterium tuberculosis, consistent with an acyclic mechanism for the enzyme for which neither C2 nor C3 hydroxyl groups are required for catalysis. The enzymes all showed greater tolerance for the loss of the C2 hydroxyl group than the C3 hydroxyl group.
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Affiliation(s)
- David Tran
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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19
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Zhou L, Wu J, Vijayalakshmi J, Shumilin IA, Bauerle R, Kretsinger RH, Woodard RW. Structure and characterization of the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix. Bioorg Chem 2011; 40:79-86. [PMID: 22035970 DOI: 10.1016/j.bioorg.2011.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/07/2011] [Accepted: 09/08/2011] [Indexed: 11/18/2022]
Abstract
The first enzyme in the shikimic acid biosynthetic pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), varies significantly in size and complexity in the bacteria and plants that express it. The DAH7PS from the archaebacterium Aeropyrum pernix (DAH7PS(Ap)) is among the smallest and least complex of the DAH7PS enzymes, leading to the hypothesis that DAH7PS(Ap) would not be subject to feedback regulation by shikimic acid pathway products. We overexpressed DAH7PS(Ap) in Escherichia coli, purified it, and characterized its enzymatic activity. We then solved its X-ray crystal structure with a divalent manganese ion and phosphoenolpyruvate bound (PDB ID: 1VS1). DAH7PS(Ap) is a homodimeric metalloenzyme in solution. Its enzymatic activity increases dramatically above 60 °C, with optimum activity at 95 °C. Its pH optimum at 60 °C is 5.7. DAH7PS(Ap) follows Michaelis-Menten kinetics at 60 °C, with a K(M) for erythrose 4-phosphate of 280 μM, a K(M) for phosphoenolpyruvate of 891 μM, and a k(cat) of 1.0 s(-1). None of the downstream products of the shikimate biosynthetic pathway we tested inhibited the activity of DAH7PS(Ap). The structure of DAH7PS(Ap) is similar to the structures of DAH7PS from Thermatoga maritima (PDB ID: 3PG8) and Pyrococcus furiosus (PDB ID: 1ZCO), and is consistent with its designation as an unregulated DAH7PS.
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Affiliation(s)
- Lily Zhou
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States.
| | - Jing Wu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States.
| | - J Vijayalakshmi
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States
| | - Igor A Shumilin
- Department of Biology, University of Virginia, Charlottesville, VA 22903, United States.
| | - Ronald Bauerle
- Department of Biology, University of Virginia, Charlottesville, VA 22903, United States.
| | - Robert H Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA 22903, United States.
| | - Ronald W Woodard
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States.
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20
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Allison TM, Hutton RD, Cochrane FC, Yeoman JA, Jameson GB, Parker EJ. Targeting the Role of a Key Conserved Motif for Substrate Selection and Catalysis by 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase. Biochemistry 2011; 50:3686-95. [DOI: 10.1021/bi200251f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Timothy M. Allison
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Richard D. Hutton
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Fiona C. Cochrane
- The Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Jeffrey A. Yeoman
- The Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Geoffrey B. Jameson
- The Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Emily J. Parker
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
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21
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Cross PJ, Dobson RCJ, Patchett ML, Parker EJ. Tyrosine latching of a regulatory gate affords allosteric control of aromatic amino acid biosynthesis. J Biol Chem 2011; 286:10216-24. [PMID: 21282100 DOI: 10.1074/jbc.m110.209924] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The first step of the shikimate pathway for aromatic amino acid biosynthesis is catalyzed by 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Thermotoga maritima DAH7PS (TmaDAH7PS) is tetrameric, with monomer units comprised of a core catalytic (β/α)(8) barrel and an N-terminal domain. This enzyme is inhibited strongly by tyrosine and to a lesser extent by the presence of phenylalanine. A truncated mutant of TmaDAH7PS lacking the N-terminal domain was catalytically more active and completely insensitive to tyrosine and phenylalanine, consistent with a role for this domain in allosteric inhibition. The structure of this protein was determined to 2.0 Å. In contrast to the wild-type enzyme, this enzyme is dimeric. Wild-type TmaDAH7PS was co-crystallized with tyrosine, and the structure of this complex was determined to a resolution of 2.35 Å. Tyrosine was found to bind at the interface between two regulatory N-terminal domains, formed from diagonally located monomers of the tetramer, revealing a major reorganization of the regulatory domain with respect to the barrel relative to unliganded enzyme. This significant conformational rearrangement observed in the crystal structures was also clearly evident from small angle X-ray scattering measurements recorded in the presence and absence of tyrosine. The closed conformation adopted by the protein on tyrosine binding impedes substrate entry into the neighboring barrel, revealing an unusual tyrosine-controlled gating mechanism for allosteric control of this enzyme.
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Affiliation(s)
- Penelope J Cross
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8040, New Zealand
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22
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Webby CJ, Jiao W, Hutton RD, Blackmore NJ, Baker HM, Baker EN, Jameson GB, Parker EJ. Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis. J Biol Chem 2010; 285:30567-76. [PMID: 20667835 DOI: 10.1074/jbc.m110.111856] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The shikimate pathway, responsible for aromatic amino acid biosynthesis, is required for the growth of Mycobacterium tuberculosis and is a potential drug target. The first reaction is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Feedback regulation of DAH7PS activity by aromatic amino acids controls shikimate pathway flux. Whereas Mycobacterium tuberculosis DAH7PS (MtuDAH7PS) is not inhibited by the addition of Phe, Tyr, or Trp alone, combinations cause significant loss of enzyme activity. In the presence of 200 μm Phe, only 2.4 μm Trp is required to reduce enzymic activity to 50%. Reaction kinetics were analyzed in the presence of inhibitory concentrations of Trp/Phe or Trp/Tyr. In the absence of inhibitors, the enzyme follows Michaelis-Menten kinetics with respect to substrate erythrose 4-phosphate (E4P), whereas the addition of inhibitor combinations caused significant homotropic cooperativity with respect to E4P, with Hill coefficients of 3.3 (Trp/Phe) and 2.8 (Trp/Tyr). Structures of MtuDAH7PS/Trp/Phe, MtuDAH7PS/Trp, and MtuDAH7PS/Phe complexes were determined. The MtuDAH7PS/Trp/Phe homotetramer binds four Trp and six Phe molecules. Binding sites for both aromatic amino acids are formed by accessory elements to the core DAH7PS (β/α)(8) barrel that are unique to the type II DAH7PS family and contribute to the tight dimer and tetramer interfaces. A comparison of the liganded and unliganded MtuDAH7PS structures reveals changes in the interface areas associated with inhibitor binding and a small displacement of the E4P binding loop. These studies uncover a previously unrecognized mode of control for the branched pathways of aromatic amino acid biosynthesis involving synergistic inhibition by specific pairs of pathway end products.
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Affiliation(s)
- Celia J Webby
- From the Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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23
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Tapas S, Kumar Patel G, Dhindwal S, Tomar S. In Silico sequence analysis and molecular modeling of the three-dimensional structure of DAHP synthase from Pseudomonas fragi. J Mol Model 2010; 17:621-31. [DOI: 10.1007/s00894-010-0764-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Accepted: 05/18/2010] [Indexed: 11/30/2022]
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24
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Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. Microbiol Mol Biol Rev 2010; 73:594-651. [PMID: 19946135 DOI: 10.1128/mmbr.00024-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspartokinase (Ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. Lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ASK network or from alternative pathways. Ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. Two subhomology divisions, ASK(alpha) and ASK(beta), have been recognized. The ASK(alpha) subhomology division is the most ancient, being widely distributed throughout the Archaea and Eukarya and in some Bacteria. Within an indel region of about 75 amino acids near the N terminus, ASK(beta) sequences differ from ASK(alpha) sequences by the possession of a proposed ancient deletion. ASK(beta) sequences are present in most Bacteria and usually exhibit an in-frame internal translational start site that can generate a small Ask subunit that is identical to the C-terminal portion of the larger subunit of a heterodimeric unit. Particularly novel are ask genes embedded in gene contexts that imply specialization for ectoine (osmotic agent) or aromatic amino acids. The cohesion group approach is well suited for the easy recognition of relatively recent lateral gene transfer (LGT) events, and many examples of these are described. Given the current density of genome representation for Proteobacteria, it is possible to reconstruct more ancient landmark LGT events. Thus, a plausible scenario in which the three well-studied and iconic Ask homologs of Escherichia coli are not within the vertical genealogy of Gammaproteobacteria, but rather originated via LGT from a Bacteroidetes donor, is supported.
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25
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Planchon S, Desvaux M, Chafsey I, Chambon C, Leroy S, Hébraud M, Talon R. Comparative subproteome analyses of planktonic and sessile Staphylococcus xylosus C2a: new insight in cell physiology of a coagulase-negative Staphylococcus in biofilm. J Proteome Res 2009; 8:1797-809. [PMID: 19253936 DOI: 10.1021/pr8004056] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Staphylococcus xylosus is a Gram-positive bacterium found on the skin of mammals and frequently isolated from food plants and fermented cheese or meat. To gain further insight in protein determinants involved in biofilm formation by this coagulase-negative Staphylococcus, a comparative proteomic analysis between planktonic and sessile cells was performed. With the use of a protocol previously developed, protein patterns of the cytoplasmic and cell envelope fractions were compared by 2-DE. Following protein identification by MALDI-TOF mass spectrometry and bioinformatic analyses, this study revealed differences in expression levels of 89 distinct proteins with 55 up-expressed and 34 down-expressed proteins in biofilm compared to planktonic cells. Most proteins differentially expressed were related to nitrogen and carbon metabolisms. Besides amino acid biosynthesis and protein translation, protein determinants related to protein secretion were up-expressed in biofilm, suggesting a more active protein trafficking in sessile cells. While up-expression of several enzymes involved in pentose phosphate and glycolytic pathways was observed in biofilm, connections with unexpected metabolic routes were further unravelled. Indeed, this proteomic analysis allowed identifying novel proteins that could be involved in a previously uncovered exopolysaccharide biosynthetic pathway in S. xylosus as well as several enzymes related to polyketide biosynthesis. This findings are particularly relevant considering exopolysaccharide production in S. xylosus is ica-independent contrary to coagulase-negative model strain Staphylococcus epidermidis RP62A.
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Affiliation(s)
- Stella Planchon
- INRA, UR454 Microbiologie, F-63122 Saint-Genès Champanelle, France
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26
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Li PP, Liu YJ, Liu SJ. Genetic and biochemical identification of the chorismate mutase from Corynebacterium glutamicum. Microbiology (Reading) 2009; 155:3382-3391. [DOI: 10.1099/mic.0.029819-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chorismate mutase (CM) catalyses the rearrangement of chorismate to prephenate and is also the first and the key enzyme that diverges the shikimate pathway to either tryptophan (Trp) or phenylalanine (Phe) and tyrosine (Tyr). Corynebacterium glutamicum is one of the most important amino acid producers for the fermentation industry and has been widely investigated. However, the gene(s) encoding CM has not been experimentally identified in C. glutamicum. In this study, the ncgl0819 gene, which was annotated as ‘conserved hypothetical protein’ in the C. glutamicum genome, was genetically characterized to be essential for growth in minimal medium, and a mutant deleted of ncgl0819 was a Phe and Tyr auxotroph. Genetic cloning and expression of ncgl0819 in Escherichia coli resulted in the formation of a new protein (NCgl0819) having CM activity. It was concluded that ncgl0819 encoded the CM of C. glutamicum (CM0819). CM0819 was demonstrated to be a homodimer and is a new member of the monofunctional CMs of the AroQ structural class. The CM0819 activity was not affected by Phe, Tyr or Trp. Two 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthases (DS0950 and DS2098, formerly NCgl0950 and NCgl2098) had been previously identified from C. glutamicum. CM0819 significantly stimulated DAHP synthase (DS2098) activity. Physical interaction between CM0819 and DS2098 was observed. When CM0819 was present, DS2098 activity was subject to allosteric inhibition by chorismate and prephenate. Conserved hypothetical proteins homologous to CM0819 were identified in all known Corynebacterium genomes, suggesting a universal occurrence of CM0819-like CMs in the genus Corynebacterium.
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Affiliation(s)
- Pan-Pan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ya-Jun Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- Environmental Microbiology and Biotechnology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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27
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Sasso S, Okvist M, Roderer K, Gamper M, Codoni G, Krengel U, Kast P. Structure and function of a complex between chorismate mutase and DAHP synthase: efficiency boost for the junior partner. EMBO J 2009; 28:2128-42. [PMID: 19556970 DOI: 10.1038/emboj.2009.165] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 05/26/2009] [Indexed: 11/09/2022] Open
Abstract
Chorismate mutase catalyzes a key step in the shikimate biosynthetic pathway towards phenylalanine and tyrosine. Curiously, the intracellular chorismate mutase of Mycobacterium tuberculosis (MtCM; Rv0948c) has poor activity and lacks prominent active-site residues. However, its catalytic efficiency increases >100-fold on addition of DAHP synthase (MtDS; Rv2178c), another shikimate-pathway enzyme. The 2.35 A crystal structure of the MtCM-MtDS complex bound to a transition-state analogue shows a central core formed by four MtDS subunits sandwiched between two MtCM dimers. Structural comparisons imply catalytic activation to be a consequence of the repositioning of MtCM active-site residues on binding to MtDS. The mutagenesis of the C-terminal extrusion of MtCM establishes conserved residues as part of the activation machinery. The chorismate-mutase activity of the complex, but not of MtCM alone, is inhibited synergistically by phenylalanine and tyrosine. The complex formation thus endows the shikimate pathway of M. tuberculosis with an important regulatory feature. Experimental evidence suggests that such non-covalent enzyme complexes comprising an AroQ(delta) subclass chorismate mutase like MtCM are abundant in the bacterial order Actinomycetales.
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Affiliation(s)
- Severin Sasso
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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28
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Cochrane FC, Cookson TVM, Jameson GB, Parker EJ. Reversing evolution: re-establishing obligate metal ion dependence in a metal-independent KDO8P synthase. J Mol Biol 2009; 390:646-61. [PMID: 19447118 DOI: 10.1016/j.jmb.2009.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 05/08/2009] [Accepted: 05/11/2009] [Indexed: 10/20/2022]
Abstract
Two distinct groups of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS), a key enzyme of cell-wall biosynthesis, differ by their requirement for a divalent metal ion for enzymatic activity. The unique difference between these groups is the replacement of the metal-binding Cys by Asn. Substitution of just this Asn for a Cys in metal-independent KDO8PS does not create the obligate metal-ion dependency of natural metal-dependent enzymes. We describe how three or four mutations of the metal-independent KDO8PS from Neisseria meningitidis produce a fully functional, obligately metal-dependent KDO8PS. For the substitutions Asn23Cys, Asp247Glu (this Asp binds to the metal ion in all metal-dependent KDO8PS) and Pro249Ala, and for double and triple combinations, mutant enzymes that contained Cys in place of Asn showed an increase in activity in the presence of divalent metal ions. However, combining these mutations with substitution by Ser of the Cys residue in the conserved (246)CysAspGlyPro(249) motif of metal-independent KDO8PS created enzymes with obligate metal dependency. The quadruple mutant (Asn23Cys/Cys246Ser/Asp247Glu/Pro249Ala) showed comparable activity to wild-type enzymes only in the presence of metal ions, with maximum activity with Cd(2+), the metal ion that is strongly inhibitory at micromolar concentrations for the wild-type enzyme. In the absence of metal ions, activity was barely detectable for this quadruple mutant or for triple mutants bearing both Cys246Ser and Asn23Cys mutations. The structures of NmeKDO8PS and its Asn23Cys/Asp247Glu/Pro249Ala and quadruple mutants at pH 4.6 were characterized at resolutions better than 1.85 A. Aged crystals of the Asn23Cys/Asp247Glu/Pro249Ala mutant featured a Cys23-Cys246 disulfide linkage, explaining the spectral bleaching observed when this mutant was incubated with Cu(2+). Such bleaching was not observed for the quadruple mutant. Reverse evolution to a fully functional obligately metal-dependent KDO8PS has been achieved with just three directed mutations for enzymes that have, at best, 47% identity between metal-dependent and metal-independent pairs.
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Affiliation(s)
- Fiona C Cochrane
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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29
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Corynebacterium glutamicum contains 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases that display novel biochemical features. Appl Environ Microbiol 2008; 74:5497-503. [PMID: 18621870 DOI: 10.1128/aem.00262-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase (EC 2.5.1.54) catalyzes the first step of the shikimate pathway that finally leads to the biosynthesis of aromatic amino acids phenylalanine (Phe), tryptophan (Trp), and tyrosine (Tyr). In Corynebacterium glutamicum ATCC 13032, two chromosomal genes, NCgl0950 (aroF) and NCgl2098 (aroG), were located that encode two putative DAHP synthases. The deletion of NCgl2098 resulted in the loss of the ability of C. glutamicum RES167 (a restriction-deficient strain derived from C. glutamicum ATCC 13032) to grow in mineral medium; however, the deletion of NCgl0950 did not result in any observable phenotypic alteration. Analysis of DAHP synthase activities in the wild type and mutants of C. glutamicum RES167 indicated that NCgl2098, rather than NCgl0950, was involved in the biosynthesis of aromatic amino acids. Cloning and expression in Escherichia coli showed that both NCgl0950 and NCgl2098 encoded active DAHP synthases. Both the NCgl0950 and NCgl2098 DAHP synthases were purified from recombinant E. coli cells and characterized. The NCgl0950 DAHP synthase was sensitive to feedback inhibition by Tyr and, to a much lesser extent, by Phe and Trp. The NCgl2098 DAHP synthase was slightly sensitive to feedback inhibition by Trp, but not sensitive to Tyr and Phe, findings that were in contrast to the properties of previously known DAHP synthases from C. glutamicum subsp. flavum. Both Co2+ and Mn2+ significantly stimulated the NCgl0950 DAHP synthase's activity, whereas Mn2+ was much more stimulatory than Co2+ to the NCgl2098 DAHP synthase's activity.
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Richards TA, Dacks JB, Campbell SA, Blanchard JL, Foster PG, McLeod R, Roberts CW. Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. EUKARYOTIC CELL 2006; 5:1517-31. [PMID: 16963634 PMCID: PMC1563581 DOI: 10.1128/ec.00106-06] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been an important process in eukaryote genome evolution.
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Affiliation(s)
- Thomas A Richards
- Deparment of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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Porat I, Sieprawska-Lupa M, Teng Q, Bohanon FJ, White RH, Whitman WB. Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Mol Microbiol 2006; 62:1117-31. [PMID: 17010158 DOI: 10.1111/j.1365-2958.2006.05426.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methanococcus maripaludis is a strictly anaerobic, methane-producing archaeon and facultative autotroph capable of biosynthesizing all the amino acids and vitamins required for growth. In this work, the novel 6-deoxy-5-ketofructose-1-phosphate (DKFP) pathway for the biosynthesis of aromatic amino acids (AroAAs) and p-aminobenzoic acid (PABA) was demonstrated in M. maripaludis. Moreover, PABA was shown to be derived from an early intermediate in AroAA biosynthesis and not from chorismate. Following metabolic labelling with [U-(13)C]-acetate, the expected enrichments for phenylalanine and arylamine derived from PABA were observed. DKFP pathway activity was reduced following growth with aryl acids, an alternative source of the AroAAs. Lastly, a deletion mutant of aroA', which encodes the first step in the DKFP pathway, required AroAAs and PABA for growth. Complementation of the mutants by an aroA' expression vector restored the wild-type phenotype. In contrast, a deletion of aroB', which encodes the second step in the DKFP pathway, did not require AroAAs or PABA for growth. Presumably, methanococci contain an alternative activity for this step. These results identify the initial reactions of a new pathway for the biosynthesis of PABA in methanococci.
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Affiliation(s)
- Iris Porat
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Wu J, Sheflyan G, Woodard R. Bacillus subtilis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase revisited: resolution of two long-standing enigmas. Biochem J 2006; 390:583-90. [PMID: 15869469 PMCID: PMC1198938 DOI: 10.1042/bj20050294] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mono/bifunctional and metallo/non-metallo properties of Bacillus subtilis DAHPS (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase) have been controversial for several decades. The present study investigated the DAHPSs from both the B. subtilis parent Marburg strain and the derivative strain 168 in detail and clarified the above two long-standing questions. The DAHPSs from the parent and the derivative 168 strains have identical sequence and are both bifunctional enzymes with a CM (chorismate mutase) activity and a DAHPS activity. The parent strain expresses a second independent monofunctional CM, encoded by aroH, that is highly active, while the 168 strain expresses an aroH containing a single residue mutation (A112V) that is significantly less active thus leading to previous confusion regarding the mono/bifunctionality of DAHPS. Metal analysis showed that B. subtilis DAHPS as isolated contained iron and zinc and is inactivated by dipicolinic acid; the inactive apoenzyme can be reactivated by bivalent metal ions, indicating that the enzyme is a metalloenzyme. The enzyme-bound metal is insensitive to EDTA treatment, leading to the previous conclusion that this DAHPS does not require a metal. The enzyme displays a homotetrameric structure in solution and appears to follow Michaelis-Menten kinetics with K(m)(PEP)=139+/-11.4 microM for phosphoenolpyruvate, K(m)(E4P)=1760+/-110 microM for D-erythrose 4-phosphate, kcat=4.6+/-0.1 s(-1) for DAHPS activity and K(m)(chorismate)=850+/-97 microM, kcat=0.41+/-0.01 s(-1) for CM activity. B. subtilis DAHPS is inhibited by the Shikimate pathway intermediates prephenate and chorismate.
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Affiliation(s)
- Jing Wu
- Department of Medicinal Chemistry and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, U.S.A
| | - Galina Ya. Sheflyan
- Department of Medicinal Chemistry and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, U.S.A
| | - Ronald W. Woodard
- Department of Medicinal Chemistry and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, U.S.A
- To whom correspondence should be addressed, at College of Pharmacy, 428 Church St., Ann Arbor, MI 48109-1065, U.S.A. (email )
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Wu J, Woodard RW. New insights into the evolutionary links relating to the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase subfamilies. J Biol Chem 2005; 281:4042-8. [PMID: 16339761 DOI: 10.1074/jbc.m512223200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial 3-deoxy-d-arabino-heptulosonate 7-phosphate synthases (DAHPSs) have been divided into either of two classes (Class I/Class II) or subfamilies (AroAI(alpha)/AroAI(beta)). Our investigation into the biochemical properties of the unique bifunctional DAHPS from Bacillus subtilis provides new insight into the evolutionary link among DAHPS subfamilies. In the present study, the DAHPS (aroA) and chorismate mutase (aroQ) activities of B. subtilis DAHPS are separated by domain truncation. Detailed enzymatic studies with the full-length wild-type protein and the truncated domains led to our hypothesis that the aroQ domain was fused to the N terminus of aroA in B. subtilis during evolution for the purpose of feedback regulation and not for the creation of a bona fide bifunctional enzyme. In addition, examination of aroA and aroQ fusion proteins from Porphyromonas gingivalis, in which the aroQ domain is fused to the C terminus of aroA, further supports the hypothesis. These results, along with sequence structure analysis of the DAHPS families suggest that "feedback regulation" may indeed be the evolutionary link between the two classes/subfamilies. It is likely that DAHPSs evolved from a primitive unregulated member of the AroAI(beta) subfamily. During evolution, some members of the AroAI(beta) subfamily remained unregulated, whereas other members acquired an extra domain for feedback regulation. The AroAI(alpha) subfamilies, however, evolved in a more complex manner to acquire insertions/extensions in the (beta/alpha)(8) barrel to function as regulatory elements.
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Affiliation(s)
- Jing Wu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, 48109-1065, USA
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Webby C, Patchett M, Parker E. Characterization of a recombinant type II 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Helicobacter pylori. Biochem J 2005; 390:223-30. [PMID: 15853768 PMCID: PMC1184578 DOI: 10.1042/bj20050259] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DAH7P (3-Deoxy-D-arabino-heptulosonate 7-phosphate) synthase catalyses the condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) as the first committed step in the biosynthesis of aromatic compounds in plants and micro-organisms. Previous work has identified two families of DAH7P synthases based on sequence similarity and molecular mass, with the majority of the mechanistic and structural studies being carried out on the type I paralogues from Escherichia coli. Whereas a number of organisms possess genes encoding both type I and type II DAH7P synthases, the pathogen Helicobacter pylori has only a single, type II, enzyme. Recombinant DAH7P synthase from H. pylori was partially solubilized by co-expression with chaperonins GroEL/GroES in E. coli, and purified to homogeneity. The enzyme reaction follows an ordered sequential mechanism with the following kinetic parameters: K(m) (PEP), 3 microM; K(m) (E4P), 6 microM; and kcat, 3.3 s(-1). The enzyme reaction involves interaction of the si face of PEP with the re face of E4P. H. pylori DAH7P synthase is not inhibited by phenylalanine, tyrosine, tryptophan or chorismate. EDTA inactivates the enzyme, and activity is restored by a range of bivalent metal ions, including (in order of decreasing effectiveness) Co2+, Mn2+, Ca2+, Mg2+, Cu2+ and Zn2+. Analysis of type II DAH7P synthase sequences reveals several highly conserved motifs, and comparison with the type I enzymes suggests that catalysis by these two enzyme types occurs on a similar active-site scaffold and that the two DAH7P synthase families may indeed be distantly related.
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Affiliation(s)
- Celia J. Webby
- *Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Mark L. Patchett
- †Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
| | - Emily J. Parker
- *Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- To whom correspondence should be sent, at the following address: Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand (email )
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Webby CJ, Baker HM, Lott JS, Baker EN, Parker EJ. The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes. J Mol Biol 2005; 354:927-39. [PMID: 16288916 DOI: 10.1016/j.jmb.2005.09.093] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/28/2005] [Accepted: 09/29/2005] [Indexed: 11/28/2022]
Abstract
The shikimate pathway, responsible for the biosynthesis of aromatic compounds, is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The first step of this pathway is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). The DAH7PSs have been classified into two apparently unrelated types and, whereas structural data have been obtained for the type I DAH7PSs, no structural information is available for their type II counterparts. The type II DAH7PS from M.tuberculosis has been expressed in Escherichia coli, purified, functionally characterized and crystallized. It is found to be metal ion-dependent and subject to feedback inhibition by phenylalanine, tryptophan, tyrosine and chorismate, with a significant synergistic effect when tryptophan is used in combination with phenylalanine. The crystal structure of M.tuberculosis DAH7PS has been determined by single-wavelength anomalous diffraction and refined at 2.3A in complex with substrate phosphoenolpyruvate and Mn(2+). The structure reveals a tightly associated dimer of (beta/alpha)(8) TIM barrels. The monomer fold, the arrangement of key residues in the active site, and the binding modes of PEP and Mn(2+), all match those of the type I enzymes, and indicate a common ancestry for the type I and type II DAH7PSs, despite their minimal sequence identity. In contrast, the structural elements that decorate the core (beta/alpha)(8) fold differ from those in the type I enzymes, consistent with their different regulatory and oligomeric properties.
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Affiliation(s)
- Celia J Webby
- Centre of Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Webby CJ, Lott JS, Baker HM, Baker EN, Parker EJ. Crystallization and preliminary X-ray crystallographic analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:403-6. [PMID: 16511053 PMCID: PMC1952427 DOI: 10.1107/s1744309105007931] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Accepted: 03/14/2005] [Indexed: 11/10/2022]
Abstract
The enzymes of the shikimate pathway are attractive targets for new-generation antimicrobial agents. The first step of this pathway is catalysed by 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAH7P) synthase and involves the condensation of phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) to form DAH7P. DAH7P synthases have been classified into two apparently evolutionarily unrelated types and whereas structural data have been obtained for the type I DAH7P synthases, no structural information is available for their type II counterparts. The type II DAH7P synthase from Mycobacterium tuberculosis was co-expressed as native and selenomethionine-substituted protein with the Escherichia coli chaperonins GroEL and GroES in E. coli, purified and crystallized. Native crystals of M. tuberculosis DAH7P synthase belong to space group P3(1)21 or P3(2)21 and diffract to 2.5 A, with unit-cell parameters a = b = 203.61, c = 66.39 A. There are either two or three molecules in the asymmetric unit. Multiwavelength anomalous diffraction (MAD) phasing using selenomethionine-substituted protein is currently under way.
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Affiliation(s)
- Celia J Webby
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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37
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Schofield LR, Patchett ML, Parker EJ. Expression, purification, and characterization of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Pyrococcus furiosus. Protein Expr Purif 2004; 34:17-27. [PMID: 14766297 DOI: 10.1016/j.pep.2003.11.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2003] [Revised: 11/06/2003] [Indexed: 11/25/2022]
Abstract
The enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyzes the condensation reaction between phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P). DAH7PS from the hyperthermophile Pyrococcus furiosus has been expressed in Escherichia coli. The expressed protein was insoluble but was partially solubilized as a dimer by the inclusion of 200 mM KCl in the cell lysis buffer. An effective two step purification procedure has been developed. The first step resulted in a high degree of purification and involved lysis by sonication at approximately 40 degrees C followed by a heat treatment at 70 degrees C. A continuous assay measuring the loss of PEP at 232 nm at elevated temperatures was also developed. Temperature, pH, and divalent metal ions all had an effect on the extinction coefficient of PEP. Purified recombinant P. furiosus DAH7PS is a dimer with a subunit Mr of 29,226 (determined by ESMS), shows resistance to denaturation by SDS, has activity over a broad pH range, and has an activation energy of 88 kJmol-1. The kinetic parameters are Km (PEP) 120 microM, Km (E4P) 28 microM, and kcat 1.5s-1, at 60 degrees C and pH 6.8. DAH7PS is not inhibited by phenylalanine, tyrosine, or tryptophan. EDTA inactivates the enzyme and enzyme activity is restored by a wide range of divalent metal ions including (in order of decreasing effectiveness): Zn2+, Cd2+, Mn2+, Co2+, Ni2+, Ca2+, Hg2+, and Cu2+. This detailed characterization of the DAH7PS from P. furiosus raises the possibility that the subfamily Ibeta DAH7PS enzymes are metal ion dependent, contrary to previous predictions.
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Affiliation(s)
- Linley R Schofield
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Shumilin IA, Bauerle R, Wu J, Woodard RW, Kretsinger RH. Crystal Structure of the Reaction Complex of 3-Deoxy- d - arabino -heptulosonate-7-phosphate Synthase from Thermotoga maritima Refines the Catalytic Mechanism and Indicates a New Mechanism of Allosteric Regulation. J Mol Biol 2004; 341:455-66. [PMID: 15276836 DOI: 10.1016/j.jmb.2004.05.077] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Revised: 04/16/2004] [Accepted: 05/27/2004] [Indexed: 10/26/2022]
Abstract
3-Deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHPS) catalyzes the first reaction of the aromatic biosynthetic pathway in bacteria, fungi, and plants, the condensation of phosphoenolpyruvate (PEP) and d-erythrose-4-phosphate (E4P) with the formation of DAHP. Crystals of DAHPS from Thermotoga maritima (DAHPS(Tm)) were grown in the presence of PEP and metal cofactor, Cd(2+), and then soaked with E4P at 4 degrees C where the catalytic activity of the enzyme is negligible. The crystal structure of the "frozen" reaction complex was determined at 2.2A resolution. The subunit of the DAHPS(Tm) homotetramer consists of an N-terminal ferredoxin-like (FL) domain and a (beta/alpha)(8)-barrel domain. The active site located at the C-end of the barrel contains Cd(2+), PEP, and E4P, the latter bound in a non-productive conformation. The productive conformation of E4P is suggested and a catalytic mechanism of DAHPS is proposed. The active site of DAHPS(Tm) is nearly identical to the active sites of the other two known DAHPS structures from Escherichia coli (DAHPS(Ec)) and Saccharomyces cerevisiae (DAHPS(Sc)). However, the secondary, tertiary, and quaternary structures of DAHPS(Tm) are more similar to the functionally related enzyme, 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDOPS) from E.coli and Aquiflex aeolicus, than to DAHPS(Ec) and DAHPS(Sc). Although DAHPS(Tm) is feedback-regulated by tyrosine and phenylalanine, it lacks the extra barrel segments that are required for feedback inhibition in DAHPS(Ec) and DAHPS(Sc). A sequence similarity search revealed that DAHPSs of phylogenetic family Ibeta possess a FL domain like DAHPS(Tm) while those of family Ialpha have extra barrel segments similar to those of DAHPS(Ec) and DAHPS(Sc). This indicates that the mechanism of feedback regulation in DAHPS(Tm) and other family Ibeta enzymes is different from that of family Ialpha enzymes, most likely being mediated by the FL domain.
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Affiliation(s)
- Igor A Shumilin
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
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Kloosterman H, Hessels GI, Vrijbloed JW, Euverink GJ, Dijkhuizen L. (De)regulation of key enzyme steps in the shikimate pathway and phenylalanine-specific pathway of the actinomycete Amycolatopsis methanolica. MICROBIOLOGY-SGM 2004; 149:3321-3330. [PMID: 14600244 DOI: 10.1099/mic.0.26494-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prephenate dehydratase (PDT), chorismate mutase (CM) and 3-deoxy-D-arabino-7-heptulosonate 7-phosphate (DAHP) synthase are key regulatory enzymes in aromatic amino acid biosynthesis in the actinomycete Amycolatopsis methanolica. Deregulated, feedback-control-resistant mutants were isolated by incubation of A. methanolica on glucose mineral agar containing the toxic analogue p-fluoro-DL-phenylalanine (pFPhe). Several of these mutants had completely lost PDT sensitivity to Phe inhibition and Tyr activation. Mutant characterization yielded new information about PDT amino acid residues involved in Phe and Tyr effector binding sites. A. methanolica wild-type cells grown on glucose mineral medium normally possess a bifunctional CM/DAHP synthase protein complex (with DS1, a plant-type DAHP synthase). The CM activity of this protein complex is feedback-inhibited by Tyr and Phe, while DS1 activity is mainly inhibited by Trp. Isolation of pFPhe-resistant mutants yielded two feedback-inhibition-resistant CM mutants. These were characterized as regulatory mutants, derepressed in (a) synthesis of CM, now occurring as an abundant, feedback-inhibition-resistant, separate protein, and (b) synthesis of an alternative DAHP synthase (DS2, an E. coli-type DAHP synthase), only inhibited by Tyr and Trp. DS1 and DS2 thus are well integrated in A. methanolica primary metabolism: DS1 and CM form a protein complex, which stimulates CM activity and renders it sensitive to feedback inhibition by Phe and Tyr. Synthesis of CM and DS2 proteins appears to be controlled co-ordinately, sensitive to Phe-mediated feedback repression.
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Affiliation(s)
- H Kloosterman
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands
| | - G I Hessels
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands
| | - J W Vrijbloed
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands
| | - G J Euverink
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands
| | - L Dijkhuizen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands
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Campbell SA, Richards TA, Mui EJ, Samuel BU, Coggins JR, McLeod R, Roberts CW. A complete shikimate pathway in Toxoplasma gondii: an ancient eukaryotic innovation. Int J Parasitol 2004; 34:5-13. [PMID: 14711585 DOI: 10.1016/j.ijpara.2003.10.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The shikimate pathway is essential for survival of the apicomplexan parasites Plasmodium falciparum, Toxoplasma gondii and Cryptosporidium parvum. As it is absent in mammals it is a promising therapeutic target. Herein, we describe the genes encoding the shikimate pathway enzymes in T. gondii. The molecular arrangement and phylogeny of the proteins suggests homology with the eukaryotic fungal enzymes, including a pentafunctional AROM. Current rooting of the eukaryotic evolutionary tree infers that the fungi and apicomplexan lineages diverged deeply, suggesting that the arom is an ancient supergene present in early eukaryotes and subsequently lost or replaced in a number of lineages.
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Affiliation(s)
- S A Campbell
- Department of Immunology, Strathclyde Institute for Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow, Scotland G4 ONR, UK
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Xie G, Keyhani NO, Bonner CA, Jensen RA. Ancient origin of the tryptophan operon and the dynamics of evolutionary change. Microbiol Mol Biol Rev 2003; 67:303-42, table of contents. [PMID: 12966138 PMCID: PMC193870 DOI: 10.1128/mmbr.67.3.303-342.2003] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting features that can be distinguished. As additional genomes are thoroughly analyzed, an increasingly refined resolution of the sequential evolutionary steps is clearly possible. These comparisons suggest that present-day trp operons that possess finely tuned regulatory features are under strong positive selection and are able to resist the disruptive evolutionary events that may be experienced by simpler, poorly regulated operons.
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Affiliation(s)
- Gary Xie
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA
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Wu J, Howe DL, Woodard RW. Thermotoga maritima 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase: the ancestral eubacterial DAHP synthase? J Biol Chem 2003; 278:27525-31. [PMID: 12743122 DOI: 10.1074/jbc.m304631200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gene encoding the 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase from the thermophilic microorganism Thermotoga maritima was cloned, and the enzyme was overexpressed in Escherichia coli. The purified DAHP synthase displays a homotetrameric structure and exhibits maximal activity at 90 degrees C. The enzyme is extremely thermostable, with 50% of its initial activity retained after incubation for approximately 5 h at 80 degrees C, 21 h at 70 degrees C, and 86 h at 60 degrees C. The enzyme appears to follow Michaelis-Menten kinetics with Km for phosphoenolpyruvate = 9.5-13 microm, Km for d-erythrose 4-phosphate = 57.3-350.1 microm, and kcat = 2.3-7.6 s-1 between 50 degrees C and 70 degrees C. Metal analysis indicates that DAHP synthase as isolated contains Zn2+, and the enzyme is inactivated by treatment with EDTA. The apo-enzyme is partially reactivated by a variety of divalent metals including Zn2+, Cd2+, Mn2+, Cu2+, Co2+, and Ni2+. These observations suggest that T. maritima DAHP synthase is a metalloenzyme. The activity of T. maritima DAHP synthase is inhibited by two of the three aromatic amino acids (l-Phe and l-Tyr) formed in the Shikimate pathway. This report is the first description of a thermophilic eubacterial DAHP synthase.
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Affiliation(s)
- Jing Wu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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Gaille C, Reimmann C, Haas D. Isochorismate synthase (PchA), the first and rate-limiting enzyme in salicylate biosynthesis of Pseudomonas aeruginosa. J Biol Chem 2003; 278:16893-8. [PMID: 12624097 DOI: 10.1074/jbc.m212324200] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Pseudomonas aeruginosa the extracellular metabolite and siderophore pyochelin is synthesized from two major precursors, chorismate and l-cysteine via salicylate as an intermediate. The regulatory role of isochorismate synthase, the first enzyme in the pyochelin biosynthetic pathway, was studied. This enzyme is encoded by pchA, the last gene in the pchDCBA operon. The PchA protein was purified to apparent electrophoretic homogeneity from a PchA-overexpressing P. aeruginosa strain. The native enzyme was a 52-kDa monomer in solution, and its activity strictly depended on Mg(2+). At pH 7.0, the optimum, a K(m) = 4.5 microm and a k(cat) = 43.1 min(-1) were determined for chorismate. No feedback inhibitors or other allosteric effectors were found. The intracellular PchA concentration critically determined the rate of salicylate formation both in vitro and in vivo. In cultures grown in iron-limiting media to high cell densities, overexpression of the pchA gene resulted in overproduction of salicylate as well as in enhanced pyochelin formation. From this work and earlier studies, it is proposed that one important factor influencing the flux through the pyochelin biosynthetic pathway is the PchA concentration, which is determined at a transcriptional level, with pyochelin acting as a positive signal and iron as a negative signal.
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Affiliation(s)
- Catherine Gaille
- Institut de Microbiologie Fondamentale, Université de Lausanne, CH-1015 Lausanne, Switzerland
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Xie G, Bonner CA, Brettin T, Gottardo R, Keyhani NO, Jensen RA. Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria. Genome Biol 2003; 4:R14. [PMID: 12620124 PMCID: PMC151304 DOI: 10.1186/gb-2003-4-2-r14] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2002] [Revised: 11/04/2002] [Accepted: 11/26/2002] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. A seven-gene cluster in Xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-CoA synthetase, and trpR. A second gene block, present in the Anabaena/Nostoc lineage, but not in other cyanobacteria, contains a near-complete tryptophan operon nested within an apparent supraoperon containing other aromatic-pathway genes. RESULTS The gene block in X. fastidiosa exhibits a sharply delineated low-GC content. This, as well as bias of codon usage and 3:1 dinucleotide analysis, strongly implicates lateral gene transfer (LGT). In contrast, parametric studies and protein tree phylogenies did not support the origination of the Anabaena/Nostoc gene block by LGT. CONCLUSIONS Judging from the apparent minimal amelioration, the low-GC gene block in X. fastidiosa probably originated by LGT at a relatively recent time. The surprising inability to pinpoint a donor lineage still leaves room for alternative, albeit less likely, explanations other than LGT. On the other hand, the large Anabaena/Nostoc gene block does not seem to have arisen by LGT. We suggest that the contemporary Anabaena/Nostoc array of divergent paralogs represents an ancient ancestral state of paralog divergence, with extensive streamlining by gene loss occurring in the lineage of descent representing other (unicellular) cyanobacteria.
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Affiliation(s)
- Gary Xie
- Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Carol A Bonner
- Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA
| | - Tom Brettin
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Raphael Gottardo
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Nemat O Keyhani
- Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA
| | - Roy A Jensen
- Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL 32611, USA
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
- Department of Chemistry, City College of New York, New York, NY 10031, USA
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Jensen RA, Xie G, Calhoun DH, Bonner CA. The correct phylogenetic relationship of KdsA (3-deoxy-d-manno-octulosonate 8-phosphate synthase) with one of two independently evolved classes of AroA (3-deoxy-d-arabino-heptulosonate 7-phosphate synthase). J Mol Evol 2002; 54:416-23. [PMID: 11847568 DOI: 10.1007/s00239-001-0031-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2001] [Accepted: 09/27/2001] [Indexed: 11/26/2022]
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Xie G, Forst C, Bonner C, Jensen RA. Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants. Genome Biol 2002; 3:RESEARCH0004. [PMID: 11806827 PMCID: PMC150451 DOI: 10.1186/gb-2001-3-1-research0004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2001] [Revised: 10/30/2001] [Accepted: 10/30/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tryptophan synthase consists of two subunits, alpha and beta. Two distinct subgroups of beta chain exist. The major group (TrpEb_1) includes the well-studied beta chain of Salmonella typhimurium. The minor group of beta chain (TrpEb_2) is most frequently found in the Archaea. Most of the amino-acid residues important for catalysis are highly conserved between both TrpE subfamilies. RESULTS Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the alpha chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. In those prokaryotes where two trpEb genes coexist, one is usually trpEb_1 and is adjacent to trpEa, whereas the second is trpEb_2 and is usually unlinked with other tryptophan-pathway genes. CONCLUSIONS TrpEb_1 is nearly always partnered with TrpEa in the tryptophan synthase reaction. However, by default at least six lineages of the Archaea are likely to use TrpEb_2 as the functional beta chain, as TrpEb_1 is absent. The six lineages show a distinctive divergence within the overall TrpEa phylogenetic tree, consistent with the lack of selection for amino-acid residues in TrpEa that are otherwise conserved for interfacing with TrpEb_1. We suggest that the standalone function of TrpEb_2 might be to catalyze the serine deaminase reaction, an established catalytic capability of tryptophan synthase beta chains. A coincident finding of interest is that the Archaea seem to use the citramalate pathway, rather than threonine deaminase (IlvA), to initiate the pathway of isoleucine biosynthesis.
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Affiliation(s)
- Gary Xie
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.
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Calhoun DH, Bonner CA, Gu W, Xie G, Jensen RA. The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa. Genome Biol 2001; 2:RESEARCH0030. [PMID: 11532214 PMCID: PMC55327 DOI: 10.1186/gb-2001-2-8-research0030] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Revised: 05/21/2001] [Accepted: 06/13/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chorismate mutases of the AroQ homology class are widespread in the Bacteria and the Archaea. Many of these exist as domains that are fused with other aromatic-pathway catalytic domains. Among the monofunctional AroQ proteins, that from Erwinia herbicola was previously shown to have a cleavable signal peptide and located in the periplasmic compartment. Whether or not this might be unique to E. herbicola was unknown. RESULTS The gene coding for the AroQ protein was cloned from Salmonella typhimurium, and the AroQ protein purified from both S. typhimurium and Pseudomonas aeruginosa was shown to have a periplasmic location. The periplasmic chorismate mutases (denoted *AroQ) are shown to be a distinct subclass of AroQ, being about twice the size of cytoplasmic AroQ proteins. The increased size is due to a carboxy-terminal extension of unknown function. In addition, a so-far novel aromatic aminotransferase was shown to be present in the periplasm of P. aeruginosa. CONCLUSIONS Our analysis has detected a number of additional *aroQ genes. The joint presence of *AroQ, cyclohexadienyl dehydratase and aromatic aminotransferase in the periplasmic compartment of P. aeruginosa comprises a complete chorismate-to-phenylalanine pathway and accounts for the "hidden overflow pathway" to phenylalanine described previously.
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Affiliation(s)
- David H Calhoun
- Department of Chemistry, City College of New York, New York, NY 10031, USA
| | - Carol A Bonner
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
| | - Wei Gu
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
| | - Gary Xie
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Roy A Jensen
- Department of Chemistry, City College of New York, New York, NY 10031, USA
- Department of Microbiology and Cell Science, Gainesville, FL 32611, USA
- BioScience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
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