201
|
Vera MS, Juárez ÁB, Pizarro HN. Comparative effects of technical-grade and a commercial formulation of glyphosate on the pigment content of periphytic algae. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2014; 93:399-404. [PMID: 25129051 DOI: 10.1007/s00128-014-1355-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Abstract
We investigated the potentially different effects of one of the most commonly used glyphosate formulations in Argentina, Glifosato Atanor(®), and the technical-grade glyphosate on the pigment content, as biomass indicators of the algal fraction in a freshwater periphytic community. A laboratory bioassay was carried out in 250-ml beakers. Two treatments were used: technical-grade glyphosate acid and Glifosato Atanor(®) (isopropylamine salt of glyphosate 48 % w/v), which were at a concentration of 3 mg active ingredient per liter. Treatments and the control (without herbicide) were replicated in triplicate. The concentrations of chlorophyll a and b and carotenes were determined at 0, 2, 6, 10, 24, 48, 96 and 192 h after herbicide addition. A significant increase in pigment content was observed for both herbicides after a 2-day exposure. Moreover, the formulation had little or no effect compared to the active ingredient, suggesting that the additives of Glifosato Atanor(®) may not enhance glyphosate toxicity.
Collapse
Affiliation(s)
- María S Vera
- Departamento de Ecología, Genética y Evolución, IEGEBA UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Ciudad de Buenos Aires, Argentina,
| | | | | |
Collapse
|
202
|
Cao Y, Xu H, Xie L, Yi Y, Yu Y, Feng S, Qiao D, Cao Y. Fluorimetric analysis of the binding characteristics of 5-enolpyruvylshikimate-3-phosphate synthase with substrates in Dunaliella salina. J Basic Microbiol 2014; 54:937-44. [PMID: 24026867 DOI: 10.1002/jobm.201300324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/13/2013] [Indexed: 11/06/2022]
Abstract
A general model of the catalytic mechanism for 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) has already been proposed. But whether shikimate-3-phosphate (S3P) alone can cause EPSPs' conformation changes, and whether the binding site of phosphoenolpyruvate (PEP) and glyphosate is the same are still in debate. In this paper, DsaroA gene amplified and cloned from Dunaliella salina (our laboratory's early study) was used for DsEPSPs expression and purification. Then the DsEPSP conformation changes as it bind with different substrates were detected by fluorimetry. The results show that we obtained the DsEPSPs by prokaryotic expression and purification, and the S3P binding with DsEPSPs alone cannot cause DsEPSPs to form "close" conformation directly. However, when S3P exits, DsEPSPs did have a trend to change to the "close" conformation. Then the "close" conformation can be formed completely with the addition of phosphoenolpyruvate (PEP) or glyphosate. The inorganic phosphorus can help S3P to induce two domains of DsEPSPs to form "close" conformation. Besides, when DsEPSPs binds with S3P, in 295 nm, only the intensity of emission peak decreases, however, in 280 nm, not only the peak intensity reduces but also the blue-shift phenomenon takes place. The reason for blue-shift phenomenon was the distribution of aromatic amino acids in EPSPs. EPSPs is a good target for novel antibiotics and herbicides, because of shikimic acid pathway is only present in plants and microorganisms, completely absent in mammals, fish, birds, reptiles, and insects. The results demonstrate that the binding of substrates to EPSPs causes a conformational change from an open form to a closed form, that might be important for designing of novel antimicrobial and herbicidal agents that block closure of the enzyme.
Collapse
Affiliation(s)
- Yu Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan, P. R. China
| | | | | | | | | | | | | | | |
Collapse
|
203
|
Sammons RD, Gaines TA. Glyphosate resistance: state of knowledge. PEST MANAGEMENT SCIENCE 2014; 70:1367-77. [PMID: 25180399 PMCID: PMC4260172 DOI: 10.1002/ps.3743] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/17/2014] [Accepted: 01/25/2014] [Indexed: 05/18/2023]
Abstract
Studies of mechanisms of resistance to glyphosate have increased current understanding of herbicide resistance mechanisms. Thus far, single-codon non-synonymous mutations of EPSPS (5-enolypyruvylshikimate-3-phosphate synthase) have been rare and, relative to other herbicide mode of action target-site mutations, unconventionally weak in magnitude for resistance to glyphosate. However, it is possible that weeds will emerge with non-synonymous mutations of two codons of EPSPS to produce an enzyme endowing greater resistance to glyphosate. Today, target-gene duplication is a common glyphosate resistance mechanism and could become a fundamental process for developing any resistance trait. Based on competition and substrate selectivity studies in several species, rapid vacuole sequestration of glyphosate occurs via a transporter mechanism. Conversely, as the chloroplast requires transporters for uptake of important metabolites, transporters associated with the two plastid membranes may separately, or together, successfully block glyphosate delivery. A model based on finite glyphosate dose and limiting time required for chloroplast loading sets the stage for understanding how uniquely different mechanisms can contribute to overall glyphosate resistance.
Collapse
Affiliation(s)
| | - Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State UniversityFort Collins, CO, USA
| |
Collapse
|
204
|
Dornfeld C, Weisberg AJ, K C R, Dudareva N, Jelesko JG, Maeda HA. Phylobiochemical characterization of class-Ib aspartate/prephenate aminotransferases reveals evolution of the plant arogenate phenylalanine pathway. THE PLANT CELL 2014; 26:3101-14. [PMID: 25070637 PMCID: PMC4145135 DOI: 10.1105/tpc.114.127407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/21/2014] [Accepted: 07/03/2014] [Indexed: 05/22/2023]
Abstract
The aromatic amino acid Phe is required for protein synthesis and serves as the precursor of abundant phenylpropanoid plant natural products. While Phe is synthesized from prephenate exclusively via a phenylpyruvate intermediate in model microbes, the alternative pathway via arogenate is predominant in plant Phe biosynthesis. However, the molecular and biochemical evolution of the plant arogenate pathway is currently unknown. Here, we conducted phylogenetically informed biochemical characterization of prephenate aminotransferases (PPA-ATs) that belong to class-Ib aspartate aminotransferases (AspAT Ibs) and catalyze the first committed step of the arogenate pathway in plants. Plant PPA-ATs and succeeding arogenate dehydratases (ADTs) were found to be most closely related to homologs from Chlorobi/Bacteroidetes bacteria. The Chlorobium tepidum PPA-AT and ADT homologs indeed efficiently converted prephenate and arogenate into arogenate and Phe, respectively. A subset of AspAT Ib enzymes exhibiting PPA-AT activity was further identified from both Plantae and prokaryotes and, together with site-directed mutagenesis, showed that Thr-84 and Lys-169 play key roles in specific recognition of dicarboxylic keto (prephenate) and amino (aspartate) acid substrates. The results suggest that, along with ADT, a gene encoding prephenate-specific PPA-AT was transferred from a Chlorobi/Bacteroidetes ancestor to a eukaryotic ancestor of Plantae, allowing efficient Phe and phenylpropanoid production via arogenate in plants today.
Collapse
Affiliation(s)
- Camilla Dornfeld
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Alexandra J Weisberg
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Ritesh K C
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - John G Jelesko
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
205
|
Dai X, Zhu M, Wang YP. Circular permutation of E. coli EPSP synthase: increased inhibitor resistance, improved catalytic activity, and an indicator for protein fragment complementation. Chem Commun (Camb) 2014; 50:1830-2. [PMID: 24402609 DOI: 10.1039/c3cc48722a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We performed the first circular permutation analysis for E. coli 5-enolpyruvylshikimate-3-phosphate synthase, and identified one circular permutant with notably increased resistance to its specific inhibitor and several others with moderately improved catalytic activity. Valid circular permutation sites can be used as effective split sites of protein fragment complementation.
Collapse
Affiliation(s)
- Xiongfeng Dai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
| | | | | |
Collapse
|
206
|
Mohammed M, Ch S, Ch RV. Aniline is an inducer, and not a precursor, for indole derivatives in Rubrivivax benzoatilyticus JA2. PLoS One 2014; 9:e87503. [PMID: 24533057 PMCID: PMC3922755 DOI: 10.1371/journal.pone.0087503] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/27/2013] [Indexed: 11/19/2022] Open
Abstract
Rubrivivax benzoatilyticus JA2 and other anoxygenic photosynthetic bacteria produce indole derivatives when exposed to aniline, a xenobiotic compound. Though this phenomenon has been reported previously, the role of aniline in the production of indoles is still a biochemical riddle. The present study aims at understanding the specific role of aniline (as precursor or stimulator) in the production of indoles and elucidating the biochemical pathway of indoles in aniline-exposed cells by using stable isotope approaches. Metabolic profiling revealed tryptophan accumulation only in aniline exposed cells along with indole 3-acetic acid (IAA) and indole 3-aldehyde (IAld), the two major catabolites of tryptophan. Deuterium labelled aniline feeding studies revealed that aniline is not a precursor of indoles in strain JA2. Further, production of indoles only in aniline-exposed cells suggests that aniline is an indoles stimulator. In addition, production of indoles depended on the presence of a carbon source, and production enhanced when carbon sources were added to the culture. Isotope labelled fumarate feeding identified, fumarate as the precursor of indole, indicating de novo synthesis of indoles. Glyphosate (shikimate pathway inhibitor) inhibited the indoles production, accumulation of tryptophan, IAA and IAld indicating that indoles synthesis in strain JA2 occurs via the de novo shikimate pathway. The up-regulation of anthranilate synthase gene and induction of anthranilate synthase activity correlated well with tryptophan production in strain JA2. Induction of tryptophan aminotransferase and tryptophan 2-monooxygenase activities corroborated well with IAA levels, suggesting that tryptophan catabolism occurs simultaneously in aniline exposed cells. Our study demonstrates that aniline (stress) stimulates tryptophan/indoles synthesis via the shikimate pathway by possibly modulating the metabolic pathway.
Collapse
Affiliation(s)
- Mujahid Mohammed
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sasikala Ch
- Bacterial Discovery Laboratory, Centre for Environment, IST, J NT University Hyderabad, Kukatpally, Hyderabad, India
| | - Ramana V. Ch
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
- * E-mail:
| |
Collapse
|
207
|
Garg B, Vaid N, Tuteja N. In-silico analysis and expression profiling implicate diverse role of EPSPS family genes in regulating developmental and metabolic processes. BMC Res Notes 2014; 7:58. [PMID: 24450620 PMCID: PMC3903108 DOI: 10.1186/1756-0500-7-58] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/16/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The EPSPS, EC 2.5.1.19 (5-enolpyruvylshikimate -3-phosphate synthase) is considered as one of the crucial enzyme in the shikimate pathway for the biosynthesis of essential aromatic amino acids and secondary metabolites in plants, fungi along with microorganisms. It is also proved as a specific target of broad spectrum herbicide glyphosate. RESULTS On the basis of structure analysis, this EPSPS gene family comprises the presence of EPSPS I domain, which is highly conserved among different plant species. Here, we followed an in-silico approach to identify and characterize the EPSPS genes from different plant species. On the basis of their phylogeny and sequence conservation, we divided them in to two groups. Moreover, the interacting partners and co-expression data of the gene revealed the importance of this gene family in maintaining cellular and metabolic functions in the cell. The present study also highlighted the highest accumulation of EPSPS transcript in mature leaves followed by young leaves, shoot and roots of tobacco. In order to gain the more knowledge about gene family, we searched for the previously reported motifs and studied its structural importance on the basis of homology modelling. CONCLUSIONS The results presented here is a first detailed in-silico study to explore the role of EPSPS gene in forefront of different plant species. The results revealed a great deal for the diversification and conservation of EPSPS gene family across different plant species. Moreover, some of the EPSPS from different plant species may have a common evolutionary origin and may contain same conserved motifs with related and important molecular function. Most importantly, overall analysis of EPSPS gene elucidated its pivotal role in immense function within the plant, both in regulating plant growth as well its development throughout the life cycle of plant. Since EPSPS is a direct target of herbicide glyphosate, understanding its mechanism for regulating developmental and cellular processes in different plant species would be a great revolution for developing glyphosate resistant crops.
Collapse
Affiliation(s)
- Bharti Garg
- International Centre Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Neha Vaid
- International Centre Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Narendra Tuteja
- International Centre Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| |
Collapse
|
208
|
Uren Webster TM, Laing LV, Florance H, Santos EM. Effects of glyphosate and its formulation, roundup, on reproduction in zebrafish (Danio rerio). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:1271-9. [PMID: 24364672 DOI: 10.1021/es404258h] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Roundup and its active ingredient glyphosate are among the most widely used herbicides worldwide and may contaminate surface waters. Research suggests both Roundup and glyphosate induce oxidative stress in fish and may also cause reproductive toxicity in mammalian systems. We aimed to investigate the reproductive effects of Roundup and glyphosate in fish and the potential associated mechanisms of toxicity. To do this, we conducted a 21-day exposure of breeding zebrafish (Danio rerio) to 0.01, 0.5, and 10 mg/L (glyphosate acid equivalent) Roundup and 10 mg/L glyphosate. 10 mg/L glyphosate reduced egg production but not fertilization rate in breeding colonies. Both 10 mg/L Roundup and glyphosate increased early stage embryo mortalities and premature hatching. However, exposure during embryogenesis alone did not increase embryo mortality, suggesting that this effect was caused primarily by exposure during gametogenesis. Transcript profiling of the gonads revealed 10 mg/L Roundup and glyphosate induced changes in the expression of cyp19a1 and esr1 in the ovary and hsd3b2, cat, and sod1 in the testis. Our results demonstrate that these chemicals cause reproductive toxicity in zebrafish, although only at high concentrations unlikely to occur in the environment, and likely mechanisms of toxicity include disruption of the steroidogenic biosynthesis pathway and oxidative stress.
Collapse
Affiliation(s)
- Tamsyn M Uren Webster
- Biosciences, College of Life & Environmental Sciences, University of Exeter , Geoffrey Pope Building, Exeter, EX4 4QD, United Kingdom
| | | | | | | |
Collapse
|
209
|
Huang ZF, Zhang CX, Huang HJ, Wei SH, Liu Y, Cui HL, Chen JC, Yang L, Chen JY. Molecular cloning and characterization of 5-enolpyruvylshikimate-3-phosphate synthase gene from Convolvulus arvensis L. Mol Biol Rep 2014; 41:2077-84. [PMID: 24413996 DOI: 10.1007/s11033-014-3056-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 01/04/2014] [Indexed: 11/27/2022]
Abstract
5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS), the target enzyme for glyphosate inhibition, catalyzes an essential step in the shikimate pathway for aromatic amino acid biosynthesis. The full-length cDNA of 1,751 nucleotides (CaEPSPS, Genbank accession number: EU698030) from Convolvulus arvensis was cloned and characterized. The CaEPSPS encodes a polypeptide of 520 amino acids with a calculated molecular weight of 55.5 kDa and an isoelectric point of 7.05. The results of homology analysis revealed that CaEPSPS showed highly homologous with EPSPS proteins from other plant species. Tissue expression pattern analysis indicated that CaEPSPS was constitutively expressed in stems, leaves and roots, with lower expression in roots. CaEPSPS expression level could increase significantly with glyphosate treatment, and reached its maximum at 24 h after glyphosate application. We fused CaEPSPS to the CaMV 35S promoter and introduced the chimeric gene into Arabidopsis. The resultant expression of CaEPSPS in transgenic Arabidopsis plants exhibited enhanced tolerance to glyphosate in comparison with control.
Collapse
Affiliation(s)
- Zhao-Feng Huang
- Institute of Plant Protection, Key Laboratory of Weed and Rodent Biology and Management, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | | | | | | | | | | | | | | | | |
Collapse
|
210
|
Żmieńko A, Samelak A, Kozłowski P, Figlerowicz M. Copy number polymorphism in plant genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1-18. [PMID: 23989647 PMCID: PMC4544587 DOI: 10.1007/s00122-013-2177-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/12/2013] [Indexed: 05/18/2023]
Abstract
Copy number variants (CNVs) are genomic rearrangements resulting from gains or losses of DNA segments. Typically, the term refers to rearrangements of sequences larger than 1 kb. This type of polymorphism has recently been shown to be a key contributor to intra-species genetic variation, along with single-nucleotide polymorphisms and short insertion-deletion polymorphisms. Over the last decade, a growing number of studies have highlighted the importance of copy number variation (CNV) as a factor affecting human phenotype and individual CNVs have been linked to risks for severe diseases. In plants, the exploration of the extent and role of CNV is still just beginning. Initial genomic analyses indicate that CNVs are prevalent in plants and have greatly affected plant genome evolution. Many CNV events have been observed in outcrossing and autogamous species. CNVs are usually found on all chromosomes, with CNV hotspots interspersed with regions of very low genetic variation. Although CNV is mainly associated with intergenic regions, many CNVs encompass protein-coding genes. The collected data suggest that CNV mainly affects the members of large families of functionally redundant genes. Thus, the effects of individual CNV events on phenotype are usually modest. Nevertheless, there are many cases in which CNVs for specific genes have been linked to important traits such as flowering time, plant height and resistance to biotic and abiotic stress. Recent reports suggest that CNVs may form rapidly in response to stress.
Collapse
Affiliation(s)
- Agnieszka Żmieńko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, Poland
| | - Anna Samelak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Piotr Kozłowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| |
Collapse
|
211
|
Zhan T, Zhang K, Chen Y, Lin Y, Wu G, Zhang L, Yao P, Shao Z, Liu Z. Improving glyphosate oxidation activity of glycine oxidase from Bacillus cereus by directed evolution. PLoS One 2013; 8:e79175. [PMID: 24223901 PMCID: PMC3818420 DOI: 10.1371/journal.pone.0079175] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/20/2013] [Indexed: 11/18/2022] Open
Abstract
Glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (GO) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the C-N bond in glyphosate. Here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of Bacillus cereus (BceGO), we used a bacteriophage T7 lysis-based method for high-throughput screening of oxidase activity and engineered the gene encoding BceGO by directed evolution. Six mutants exhibiting enhanced activity toward glyphosate were screened from two rounds of error-prone PCR combined with site directed mutagenesis, and the beneficial mutations of the six evolved variants were recombined by DNA shuffling. Four recombinants were generated and, when compared with the wild-type BceGO, the most active mutant B3S1 showed the highest activity, exhibiting a 160-fold increase in substrate affinity, a 326-fold enhancement in catalytic efficiency against glyphosate, with little difference between their pH and temperature stabilities. The role of these mutations was explored through structure modeling and molecular docking, revealing that the Arg(51) mutation is near the active site and could be an important residue contributing to the stabilization of glyphosate binding, while the role of the remaining mutations is unclear. These results provide insight into the application of directed evolution in optimizing glycine oxidase function and have laid a foundation for the development of glyphosate-tolerant crops.
Collapse
Affiliation(s)
- Tao Zhan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Kai Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yangyan Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yongjun Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, College of Life Science, Tarim University, Alar, Xinjiang, P. R. China
| | - Pei Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, P. R. China
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| |
Collapse
|
212
|
Blanco B, Prado V, Lence E, Otero JM, Garcia-Doval C, van Raaij MJ, Llamas-Saiz AL, Lamb H, Hawkins AR, González-Bello C. Mycobacterium tuberculosis shikimate kinase inhibitors: design and simulation studies of the catalytic turnover. J Am Chem Soc 2013; 135:12366-76. [PMID: 23889343 DOI: 10.1021/ja405853p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shikimate kinase (SK) is an essential enzyme in several pathogenic bacteria and does not have any counterpart in human cells, thus making it an attractive target for the development of new antibiotics. The key interactions of the substrate and product binding and the enzyme movements that are essential for catalytic turnover of the Mycobacterium tuberculosis shikimate kinase enzyme (Mt-SK) have been investigated by structural and computational studies. Based on these studies several substrate analogs were designed and assayed. The crystal structure of Mt-SK in complex with ADP and one of the most potent inhibitors has been solved at 2.15 Å. These studies reveal that the fixation of the diaxial conformation of the C4 and C5 hydroxyl groups recognized by the enzyme or the replacement of the C3 hydroxyl group in the natural substrate by an amino group is a promising strategy for inhibition because it causes a dramatic reduction of the flexibility of the LID and shikimic acid binding domains. Molecular dynamics simulation studies showed that the product is expelled from the active site by three arginines (Arg117, Arg136, and Arg58). This finding represents a previously unknown key role of these conserved residues. These studies highlight the key role of the shikimic acid binding domain in the catalysis and provide guidance for future inhibitor designs.
Collapse
Affiliation(s)
- Beatriz Blanco
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
213
|
Ding X, Yang KL. Development of an oligopeptide functionalized surface plasmon resonance biosensor for online detection of glyphosate. Anal Chem 2013; 85:5727-33. [PMID: 23675691 DOI: 10.1021/ac400273g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a surface plasmon resonance (SPR) biosensor for online detection of glyphosate. The surface of the sensing element is decorated with an oligopeptide, TPFDLRPSSDTR, which is identified by using phage display library. This oligopeptide shows high binding specificity for glyphosate (KD = 8.6 μM), probably because of the presence of R and D in the oligopeptide. To detect glyphosate in buffer solution, an SPR gold sensor chip is modified by using the oligopeptide with a surface density of 0.6 1/nm(2). The sensitivity of this oligopeptide-functionalized SPR biosensor is 1.02 RU/μM whereas the limit of detection (LOD) is 0.58 μM. This oligopeptide functionalized SPR biosensor also shows good specificity against other analytes such as glycine, thiacloprid, and imidacloprid.
Collapse
Affiliation(s)
- Xiaokang Ding
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117576
| | | |
Collapse
|
214
|
Noge K, Tamogami S. Herbivore-induced phenylacetonitrile is biosynthesized from de novo-synthesized L-phenylalanine in the giant knotweed, Fallopia sachalinensis. FEBS Lett 2013; 587:1811-7. [PMID: 23673319 DOI: 10.1016/j.febslet.2013.04.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 04/27/2013] [Accepted: 04/29/2013] [Indexed: 11/16/2022]
Abstract
Plants emit a series of characteristic volatile blends when damaged by insect feeding. Phenylacetonitrile is one of the volatiles from the leaves of the giant knotweed, Fallopia sachalinensis, infested by the Japanese beetle, Popillia japonica, or treated with exogenous airborne methyl jasmonate (MeJA). We examined the precursor of the nitrile and its origin in this system. L-Phenylalanine was determined to be a precursor of the nitrile in F. sachalinensis leaves, and the phenylalanine was also induced by beetle feeding and MeJA treatment. We also found that exogenous MeJA enhanced the biosynthesis of several amino acids in F. sachalinensis leaves.
Collapse
Affiliation(s)
- Koji Noge
- Department of Biological Production, Akita Prefectural University, Akita 010-0195, Japan.
| | | |
Collapse
|
215
|
Caetano MS, Freitas MP, da Cunha EFF, Ramalho TC. Construction and assessment of reaction models of Class I EPSP synthase. Part II: investigation of the EPSP ketal. J Biomol Struct Dyn 2013; 31:393-402. [PMID: 22877309 DOI: 10.1080/07391102.2012.703066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Although the proposed mechanisms are reasonable, there are still many questions about the 5-enolpyruvyl shikimate-3-phosphate (EPSP) synthase mechanism that are difficult to answer by experimental means alone. EPSP synthase is a key enzyme in the shikimic acid pathway, which is found only in plants and some micro-organisms and is also molecular target of glyphosate, active component of one of the top-selling herbicides. In the study of reaction mechanism of EPSP synthase, in addition to inorganic phosphate and EPSP products, after long time at equilibrium, it was shown that a side product is formed, the EPSP ketal. In this line, studies using density functional theory (DFT) techniques were performed to investigate the reaction mechanism of formation of EPSP and the corresponding ketal. Our findings indicate some key amino acid residues in the EPSP synthase mechanism and a possible route for the formation of the EPSP ketal.
Collapse
|
216
|
Tian YS, Xu J, Han J, Zhao W, Fu XY, Peng RH, Yao QH. Complementary screening, identification and application of a novel class II 5-enopyruvylshikimate-3-phosphate synthase from Bacillus cereus. World J Microbiol Biotechnol 2013; 29:549-57. [PMID: 23161452 DOI: 10.1007/s11274-012-1209-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/03/2012] [Indexed: 11/25/2022]
Abstract
A novel aroA gene encoding 5-enolpyruvylshikimate-3-phosphate synthase from Bacillus cereus was identified and overexpressed by genomic library construction and complementary screening. The enzyme was then purified to homogeneity. We also transformed the aroA ( B. cereus ) gene into Arabidopsis thaliana by a floral dip method, and demonstrated that transgenic A. thaliana plants exhibited significant glyphosate resistance compared with the wild type. These results strongly suggested that the strategy was highly efficient and advantageous for rapidly cloning aroA genes from microorganisms in natural environments.
Collapse
Affiliation(s)
- Yong-Sheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
217
|
Zhou CY, Tian YS, Xu ZS, Zhao W, Chen C, Bao WH, Bian L, Cai R, Wu AZ. Identification of a new gene encoding 5-enolpyruvylshikimate-3-phosphate synthase using genomic library construction strategy. Mol Biol Rep 2012; 39:10939-47. [PMID: 23090479 DOI: 10.1007/s11033-012-1994-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 10/01/2012] [Indexed: 11/28/2022]
Abstract
Applying the genomic library construction strategy and colony screening, a new aroA gene encoding 5-enolpyruvylshikimate-3-phosphate synthase has been identified, cloned and overexpressed in Escherichia coli, and the enzyme was purified to homogeneity. Kinetic analysis of the AroA( P.fluorescens ) indicated that the full-length enzyme exhibits 10-fold increased IC50 and an approximately 38-fold increased K ( i ) for glyphosate compared to those of the AroA( E.coli ), while retaining high affinity for the substrate phosphoenolpyruvate. Furthermore, we have transformed the new aroA ( P.fluorescens ) gene into Arabidopsis thaliana via a floral dip method, and demonstrated that transgenic A. thaliana plants exhibit significant glyphosate resistance when compared with the wild type.
Collapse
Affiliation(s)
- Chang-Yan Zhou
- College of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | | | | | | | | | | | | | | |
Collapse
|
218
|
Peng RH, Tian YS, Xiong AS, Zhao W, Fu XY, Han HJ, Chen C, Jin XF, Yao QH. A novel 5-enolpyruvylshikimate-3-phosphate synthase from Rahnella aquatilis with significantly reduced glyphosate sensitivity. PLoS One 2012; 7:e39579. [PMID: 22870190 PMCID: PMC3411725 DOI: 10.1371/journal.pone.0039579] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 05/23/2012] [Indexed: 11/19/2022] Open
Abstract
The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19) is a key enzyme in the shikimate pathway for the production of aromatic amino acids and chorismate-derived secondary metabolites in plants, fungi, and microorganisms. It is also the target of the broad-spectrum herbicide glyphosate. Natural glyphosate resistance is generally thought to occur within microorganisms in a strong selective pressure condition. Rahnella aquatilis strain GR20, an antagonist against pathogenic agrobacterial strains of grape crown gall, was isolated from the rhizosphere of grape in glyphosate-contaminated vineyards. A novel gene encoding EPSPS was identified from the isolated bacterium by complementation of an Escherichia coli auxotrophic aroA mutant. The EPSPS, named AroA(R. aquatilis), was expressed and purified from E. coli, and key kinetic values were determined. The full-length enzyme exhibited higher tolerance to glyphosate than the E. coli EPSPS (AroA(E. coli)), while retaining high affinity for the substrate phosphoenolpyruvate. Transgenic plants of AroA(R. aquatilis) were also observed to be more resistant to glyphosate at a concentration of 5 mM than that of AroA(E. coli). To probe the sites contributing to increased tolerance to glyphosate, mutant R. aquatilis EPSPS enzymes were produced with the c-strand of subdomain 3 and the f-strand of subdomain 5 (Thr38Lys, Arg40Val, Arg222Gln, Ser224Val, Ile225Val, and Gln226Lys) substituted by the corresponding region of the E. coli EPSPS. The mutant enzyme exhibited greater sensitivity to glyphosate than the wild type R. aquatilis EPSPS with little change of affinity for its first substrate, shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP). The effect of the residues on subdomain 5 on glyphosate resistance was more obvious.
Collapse
Affiliation(s)
- Ri-He Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Yong-Sheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Ai-Sheng Xiong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Wei Zhao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Xiao-Yan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Hong-Juan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Chen Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Xiao-Fen Jin
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Quan-Hong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| |
Collapse
|
219
|
Lou M, Burger SK, Gilpin ME, Gawuga V, Capretta A, Berti PJ. Transition State Analysis of Enolpyruvylshikimate 3-Phosphate (EPSP) Synthase (AroA)-Catalyzed EPSP Hydrolysis. J Am Chem Soc 2012; 134:12958-69. [PMID: 22765279 DOI: 10.1021/ja304339h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meiyan Lou
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Steven K. Burger
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Meghann E. Gilpin
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Vivian Gawuga
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Alfredo Capretta
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul J. Berti
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| |
Collapse
|
220
|
Oberdorfer G, Binter A, Ginj C, Macheroux P, Gruber K. Structural and functional characterization of NikO, an enolpyruvyl transferase essential in nikkomycin biosynthesis. J Biol Chem 2012; 287:31427-36. [PMID: 22810238 DOI: 10.1074/jbc.m112.352096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nikkomycins are peptide-nucleoside compounds with fungicidal, acaricidal, and insecticidal properties because of their strong inhibition of chitin synthase. Thus, they are potential antibiotics especially for the treatment of immunosuppressed patients, for those undergoing chemotherapy, or after organ transplants. Although their chemical structure has been known for more than 30 years, only little is known about their complex biosynthesis. The genes encoding for proteins involved in the biosynthesis of the nucleoside moiety of nikkomycins are co-transcribed in the same operon, comprising the genes nikIJKLMNO. The gene product NikO was shown to belong to the family of enolpyruvyl transferases and to catalyze the transfer of an enolpyruvyl moiety from phosphoenolpyruvate to the 3'-hydroxyl group of UMP. Here, we report activity and inhibition studies of the wild-type enzyme and the variants C130A and D342A. The x-ray crystal structure revealed differences between NikO and its homologs. Furthermore, our studies led to conclusions concerning substrate binding and preference as well as to conclusions about inhibition/alkylation by the antibiotic fosfomycin.
Collapse
Affiliation(s)
- Gustav Oberdorfer
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
| | | | | | | | | |
Collapse
|
221
|
Harris WR, Sammons RD, Grabiak RC, Mehrsheikh A, Bleeke MS. Computer simulation of the interactions of glyphosate with metal ions in phloem. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:6077-87. [PMID: 22651133 DOI: 10.1021/jf3004288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Essential nutrients such as trace metal ions, amino acids, and sugars are transported in the phloem from leaves to other parts of the plant. The major chelating agents in phloem include nicotianamine, histidine, cysteine, glutamic acid, and citrate. A computer model for the speciation of metal ions in phloem has been used to assess the degree to which the widely used herbicide glyphosate binds to Fe(3+), Fe(2+), Cu(2+), Zn(2+), Mn(2+), Ca(2+), and Mg(2+) in this fluid over the pH range of 8 to 6.5. The calculations show that glyphosate is largely unable to compete effectively with the biological chelating agents in phloem. At a typical phloem pH of 8, 1.5 mM glyphosate binds 8.4% of the total Fe(3+), 3.4% of the total Mn(2+), and 2.3% of the total Mg(2+) but has almost no effect on the speciation of Ca(2+), Cu(2+), Zn(2+), and Fe(2+). As the pH decreases to 6.5, there are some major shifts of the metal ions among the biological chelators, but only modest increases in glyphosate binding to 6% for Fe(2+) and 2% for Zn(2+). The calculations also indicate that over 90% of the glyphosate in phloem is not bound to any metal ion and that none of the metal-glyphosate complexes exceed their solubility limits.
Collapse
Affiliation(s)
- Wesley R Harris
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, MO 63121, United States
| | | | | | | | | |
Collapse
|
222
|
Cao G, Liu Y, Zhang S, Yang X, Chen R, Zhang Y, Lu W, Liu Y, Wang J, Lin M, Wang G. A novel 5-enolpyruvylshikimate-3-phosphate synthase shows high glyphosate tolerance in Escherichia coli and tobacco plants. PLoS One 2012; 7:e38718. [PMID: 22715408 PMCID: PMC3371024 DOI: 10.1371/journal.pone.0038718] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 05/09/2012] [Indexed: 11/19/2022] Open
Abstract
A key enzyme in the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the primary target of the broad-spectrum herbicide glyphosate. Identification of new aroA genes coding for EPSPS with a high level of glyphosate tolerance is essential for the development of glyphosate-tolerant crops. In the present study, the glyphosate tolerance of five bacterial aroA genes was evaluated in the E. coli aroA-defective strain ER2799 and in transgenic tobacco plants. All five aroA genes could complement the aroA-defective strain ER2799, and AM79 aroA showed the highest glyphosate tolerance. Although glyphosate treatment inhibited the growth of both WT and transgenic tobacco plants, transgenic plants expressing AM79 aroA tolerated higher concentration of glyphosate and had a higher fresh weight and survival rate than plants expressing other aroA genes. When treated with high concentration of glyphosate, lower shikimate content was detected in the leaves of transgenic plants expressing AM79 aroA than transgenic plants expressing other aroA genes. These results suggest that AM79 aroA could be a good candidate for the development of transgenic glyphosate-tolerant crops.
Collapse
Affiliation(s)
- Gaoyi Cao
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengxue Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuewen Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rongrong Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuwen Zhang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
223
|
Mazzei P, Piccolo A. Quantitative evaluation of noncovalent interactions between glyphosate and dissolved humic substances by NMR spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:5939-46. [PMID: 22591574 DOI: 10.1021/es300265a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Interactions of glyphosate (N-phosphonomethylglycine) herbicide (GLY) with soluble fulvic acids (FAs) and humic acids (HAs) at pH 5.2 and 7 were studied by (1)H and (31)P NMR spectroscopy. Increasing concentrations of soluble humic matter determined broadening and chemical shift drifts of proton and phosphorus GLY signals, thereby indicating the occurrence of weak interactions between GLY and humic superstructures. Binding was larger for FAs and pH 5.2 than for HAs and pH 7, thus suggesting formation of hydrogen bonds between GLY carboxyl and phosphonate groups and protonated oxygen functions in humic matter. Changes in relaxation and correlation times of (1)H and (31)P signals and saturation transfer difference NMR experiments confirmed the noncovalent nature of GLY-humic interactions. Diffusion-ordered NMR spectra allowed calculation of the glyphosate fraction bound to humic superstructures and association constants (K(a)) and Gibbs free energies of transfer for GLY-humic complex formation at both pH values. These values showed that noncovalent interactions occurred most effectively with FAs and at pH 5.2. Our findings indicated that glyphosate may spontaneously and significantly bind to soluble humic matter by noncovalent interactions at slightly acidic pH and, thus, potentially pollute natural water bodies by moving through soil profiles in complexes with dissolved humus.
Collapse
Affiliation(s)
- Pierluigi Mazzei
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare (CERMANU), Università di Napoli Federico II, Via Università 100, 80055 Portici, Italy
| | | |
Collapse
|
224
|
Cheng WC, Chen YF, Wang HJ, Hsu KC, Lin SC, Chen TJ, Yang JM, Wang WC. Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism. PLoS One 2012; 7:e33481. [PMID: 22438938 PMCID: PMC3306394 DOI: 10.1371/journal.pone.0033481] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 02/14/2012] [Indexed: 12/13/2022] Open
Abstract
Shikimate kinase (SK), which catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP, is the enzyme in the fifth step of the shikimate pathway for biosynthesis of aromatic amino acids. This pathway is present in bacteria, fungi, and plants but absent in mammals and therefore represents an attractive target pathway for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here we investigated the detailed structure–activity relationship of SK from Helicobacter pylori (HpSK). Site-directed mutagenesis and isothermal titration calorimetry studies revealed critical conserved residues (D33, F48, R57, R116, and R132) that interact with shikimate and are therefore involved in catalysis. Crystal structures of HpSK·SO4, R57A, and HpSK•shikimate-3-phosphate•ADP show a characteristic three-layer architecture and a conformationally elastic region consisting of F48, R57, R116, and R132, occupied by shikimate. The structure of the inhibitor complex, E114A•162535, was also determined, which revealed a dramatic shift in the elastic LID region and resulted in conformational locking into a distinctive form. These results reveal considerable insight into the active-site chemistry of SKs and a selective inhibitor-induced-fit mechanism.
Collapse
Affiliation(s)
- Wen-Chi Cheng
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Yen-Fu Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hung-Jung Wang
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Kai-Cheng Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shuang-Chih Lin
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Tzu-Jung Chen
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Jinn-Moon Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- * E-mail: (J-MY); (W-CW)
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (J-MY); (W-CW)
| |
Collapse
|
225
|
Shaner DL, Lindenmeyer RB, Ostlie MH. What have the mechanisms of resistance to glyphosate taught us? PEST MANAGEMENT SCIENCE 2012; 68:3-9. [PMID: 21842528 DOI: 10.1002/ps.2261] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 06/24/2011] [Accepted: 06/24/2011] [Indexed: 05/26/2023]
Abstract
The intensive use of glyphosate alone to manage weeds has selected populations that are glyphosate resistant. The three mechanisms of glyphosate resistance that have been elucidated are (1) target-site mutations, (2) gene amplification and (3) altered translocation due to sequestration. What have we learned from the selection of these mechanisms, and how can we apply those lessons to future herbicide-resistant crops and new mechanisms of action? First, the diversity of glyphosate resistance mechanisms has helped further our understanding of the mechanism of action of glyphosate and advanced our knowledge of plant physiology. Second, the relatively rapid evolution of glyphosate-resistant weed populations provides further evidence that no herbicide is invulnerable to resistance. Third, as new herbicide-resistant crops are developed and new mechanisms of action are discovered, the weed science community needs to ensure that we apply the lessons we have learned on resistance management from the experience with glyphosate. Every new weed management system must be evaluated during development for its potential to select for resistance, and stewardship programs should be in place when the new program is introduced.
Collapse
Affiliation(s)
- Dale L Shaner
- Water Management Research, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, USA.
| | | | | |
Collapse
|
226
|
Rojano-Delgado AM, Cruz-Hipolito H, De Prado R, Luque de Castro MD, Franco AR. Limited uptake, translocation and enhanced metabolic degradation contribute to glyphosate tolerance in Mucuna pruriens var. utilis plants. PHYTOCHEMISTRY 2012; 73:34-41. [PMID: 22015254 DOI: 10.1016/j.phytochem.2011.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 09/08/2011] [Accepted: 09/13/2011] [Indexed: 05/26/2023]
Abstract
Velvet bean (Mucuna pruriens, Fabaceae) plants exhibits an innate, very high resistance (i.e., tolerance) to glyphosate similar to that of plants which have acquired resistance to this herbicide as a trait. We analyzed the uptake of [(14)C]-glyphosate by leaves and its translocation to meristematic tissues, and used scanning electron micrographs to further analyze the cuticle and 3D capillary electrophoresis to investigate a putative metabolism capable of degrading the herbicide. Velvet bean exhibited limited uptake of glyphosate and impaired translocation of the compound to meristematic tissues. Also, for the first time in a higher plant, two concurrent pathways capable of degrading glyphosate to AMPA, Pi, glyoxylate, sarcosine and formaldehyde as end products were identified. Based on the results, the innate tolerance of velvet bean to glyphosate is possibly a result of the combined action of the previous three traits, namely: limited uptake, impaired translocation and enhanced degradation.
Collapse
Affiliation(s)
- Antonia María Rojano-Delgado
- Departamento de Química Agrícola, Edificio Marie Curie, Campus de Rabanales, Universidad de Córdoba, E-14071 Córdoba, Spain
| | | | | | | | | |
Collapse
|
227
|
Tian YS, Xu J, Xiong AS, Zhao W, Gao F, Fu XY, Peng RH, Yao QH. Functional characterization of Class II 5-enopyruvylshikimate-3-phosphate synthase from Halothermothrix orenii H168 in Escherichia coli and transgenic Arabidopsis. Appl Microbiol Biotechnol 2012; 93:241-50. [PMID: 21720820 DOI: 10.1007/s00253-011-3443-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 06/11/2011] [Accepted: 06/13/2011] [Indexed: 10/18/2022]
Abstract
Although a large number of AroA enzymes (5-enopyruvylshikimate-3-phosphate synthase [EPSPS]) have been identified, cloned and tested for glyphosate resistance, only AroA variants derived from Agrobacterium tumefaciens strain CP4 have been successfully used commercially. We have now used a polymerase chain reaction (PCR)-based two-step DNA synthesis (PTDS) method to synthesize an aroA gene (aroA(H. orenii)) from Halothermothrix orenii H168 encoding a new EPSPS similar to AroA(A. tumefaciens CP4.) AroA(H. orenii) was then expressed in Escherichia coli and key kinetic values of the purified enzyme were determined. Kinetic analysis of AroA(H. orenii) indicated that the full-length enzyme exhibited increased tolerance to glyphosate compared with E. coli AroA(E. coli) while retaining a high affinity for the substrate phosphoenolpyruvate. Transgenic Arabidopsis plants containing aroA(H. orenii) were resistant to 15 mM glyphosate. Site-directed mutagenesis showed that residues Thr355Ser affected the affinity of AroA(H. orenii) for glyphosate, providing further evidence that specific amino acid residues are responsible for differences in enzymatic behavior among different AroA enzymes.
Collapse
Affiliation(s)
- Yong-Sheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai, China
| | | | | | | | | | | | | | | |
Collapse
|
228
|
Maeda H, Dudareva N. The shikimate pathway and aromatic amino Acid biosynthesis in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:73-105. [PMID: 22554242 DOI: 10.1146/annurev-arplant-042811-105439] [Citation(s) in RCA: 722] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
L-tryptophan, L-phenylalanine, and L-tyrosine are aromatic amino acids (AAAs) that are used for the synthesis of proteins and that in plants also serve as precursors of numerous natural products, such as pigments, alkaloids, hormones, and cell wall components. All three AAAs are derived from the shikimate pathway, to which ≥30% of photosynthetically fixed carbon is directed in vascular plants. Because their biosynthetic pathways have been lost in animal lineages, the AAAs are essential components of the diets of humans, and the enzymes required for their synthesis have been targeted for the development of herbicides. This review highlights recent molecular identification of enzymes of the pathway and summarizes the pathway organization and the transcriptional/posttranscriptional regulation of the AAA biosynthetic network. It also identifies the current limited knowledge of the subcellular compartmentalization and the metabolite transport involved in the plant AAA pathways and discusses metabolic engineering efforts aimed at improving production of the AAA-derived plant natural products.
Collapse
Affiliation(s)
- Hiroshi Maeda
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907-2010, USA.
| | | |
Collapse
|
229
|
Tian YS, Xu J, Xiong AS, Zhao W, Fu XY, Peng RH, Yao QH. Improvement of glyphosate resistance through concurrent mutations in three amino acids of the Ochrobactrum 5-enopyruvylshikimate-3-phosphate synthase. Appl Environ Microbiol 2011; 77:8409-14. [PMID: 21948846 PMCID: PMC3233053 DOI: 10.1128/aem.05271-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 09/19/2011] [Indexed: 11/20/2022] Open
Abstract
A mutant of 5-enopyruvylshikimate-3-phosphate synthase from Ochrobactrum anthropi was identified after four rounds of DNA shuffling and screening. Its ability to restore the growth of the mutant ER2799 cell on an M9 minimal medium containing 300 mM glyphosate led to its identification. The mutant had mutations in seven amino acids: E145G, N163H, N267S, P318R, M377V, M425T, and P438L. Among these mutations, N267S, P318R, and M425T have never been previously reported as important residues for glyphosate resistance. However, in the present study they were found by site-directed mutagenesis to collectively contribute to the improvement of glyphosate tolerance. Kinetic analyses of these three mutants demonstrated that the effectiveness of these three individual amino acid alterations on glyphosate tolerance was in the order P318R > M425T > N267S. The results of the kinetic analyses combined with a three-dimensional structure modeling of the location of P318R and M425T demonstrate that the lower hemisphere's upper surface is possibly another important region for glyphosate resistance. Furthermore, the transgenic Arabidopsis was obtained to confirm the potential of the mutant in developing glyphosate-resistant crops.
Collapse
Affiliation(s)
| | | | - Ai-Sheng Xiong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, People's Republic of China
| | - Wei Zhao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, People's Republic of China
| | - Xiao-Yan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, People's Republic of China
| | - Ri-He Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, People's Republic of China
| | - Quan-Hong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, People's Republic of China
| |
Collapse
|
230
|
Kumari S, van der Hoorn RAL. A structural biology perspective on bioactive small molecules and their plant targets. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:480-8. [PMID: 21803639 DOI: 10.1016/j.pbi.2011.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/01/2011] [Accepted: 06/14/2011] [Indexed: 05/08/2023]
Abstract
Structural biology efforts in recent years have generated numerous co-crystal structures of bioactive small molecules interacting with their plant targets. These studies include the targets of various phytohormones, pathogen-derived effectors, herbicides and other bioactive compounds. Here we discuss that this collection of structures contains excellent examples of nine collective observations: molecular glues, allostery, inhibitors, molecular mimicry, promiscuous binding sites, unexpected electron densities, natural selection at atomic resolution, and applications in structure-guided mutagenesis and small molecule design.
Collapse
Affiliation(s)
- Selva Kumari
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | | |
Collapse
|
231
|
Peek J, Lee J, Hu S, Senisterra G, Christendat D. Structural and Mechanistic Analysis of a Novel Class of Shikimate Dehydrogenases: Evidence for a Conserved Catalytic Mechanism in the Shikimate Dehydrogenase Family. Biochemistry 2011; 50:8616-27. [DOI: 10.1021/bi200586y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James Peek
- Department of Cell
and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - John Lee
- Department of Cell
and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Shi Hu
- Department of Cell
and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Guillermo Senisterra
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Dinesh Christendat
- Department of Cell
and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| |
Collapse
|
232
|
Pollegioni L, Schonbrunn E, Siehl D. Molecular basis of glyphosate resistance-different approaches through protein engineering. FEBS J 2011; 278:2753-66. [PMID: 21668647 PMCID: PMC3145815 DOI: 10.1111/j.1742-4658.2011.08214.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glyphosate (N-phosphonomethyl-glycine) is the most widely used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. The extraordinary success of this simple, small molecule is mainly attributable to the high specificity of glyphosate for the plant enzyme enolpyruvyl shikimate-3-phosphate synthase in the shikimate pathway, leading to the biosynthesis of aromatic amino acids. Starting in 1996, transgenic glyphosate-resistant plants were introduced, thus allowing application of the herbicide to the crop (post-emergence) to remove emerged weeds without crop damage. This review focuses on mechanisms of resistance to glyphosate as obtained through natural diversity, the gene-shuffling approach to molecular evolution, and a rational, structure-based approach to protein engineering. In addition, we offer a rationale for the means by which the modifications made have had their intended effect.
Collapse
Affiliation(s)
- Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze Molecolari, Università degli Studi dell'Insubria, Varese, Italy.
| | | | | |
Collapse
|
233
|
Reichau S, Jiao W, Walker SR, Hutton RD, Baker EN, Parker EJ. Potent inhibitors of a shikimate pathway enzyme from Mycobacterium tuberculosis: combining mechanism- and modeling-based design. J Biol Chem 2011; 286:16197-207. [PMID: 21454647 PMCID: PMC3093739 DOI: 10.1074/jbc.m110.211649] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/07/2011] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis remains a serious global health threat, with the emergence of multidrug-resistant strains highlighting the urgent need for novel antituberculosis drugs. The enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyzes the first step of the shikimate pathway for the biosynthesis of aromatic compounds. This pathway has been shown to be essential in Mycobacterium tuberculosis, the pathogen responsible for tuberculosis. DAH7PS catalyzes a condensation reaction between P-enolpyruvate and erythrose 4-phosphate to give 3-deoxy-D-arabino-heptulosonate 7-phosphate. The enzyme reaction mechanism is proposed to include a tetrahedral intermediate, which is formed by attack of an active site water on the central carbon of P-enolpyruvate during the course of the reaction. Molecular modeling of this intermediate into the active site reported in this study shows a configurational preference consistent with water attack from the re face of P-enolpyruvate. Based on this model, we designed and synthesized an inhibitor of DAH7PS that mimics this reaction intermediate. Both enantiomers of this intermediate mimic were potent inhibitors of M. tuberculosis DAH7PS, with inhibitory constants in the nanomolar range. The crystal structure of the DAH7PS-inhibitor complex was solved to 2.35 Å. Both the position of the inhibitor and the conformational changes of active site residues observed in this structure correspond closely to the predictions from the intermediate modeling. This structure also identifies a water molecule that is located in the appropriate position to attack the re face of P-enolpyruvate during the course of the reaction, allowing the catalytic mechanism for this enzyme to be clearly defined.
Collapse
Affiliation(s)
- Sebastian Reichau
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Wanting Jiao
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Scott R. Walker
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Richard D. Hutton
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| | - Edward N. Baker
- the Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Emily J. Parker
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8140 and
| |
Collapse
|
234
|
Zelaya IA, Anderson JAH, Owen MDK, Landes RD. Evaluation of spectrophotometric and HPLC methods for shikimic acid determination in plants: models in glyphosate-resistant and -susceptible crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:2202-12. [PMID: 21338087 DOI: 10.1021/jf1043426] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Endogenous shikimic acid determinations are routinely used to assess the efficacy of glyphosate in plants. Numerous analytical methods exist in the public domain for the detection of shikimic acid, yet the most commonly cited comprise spectrophotometric and high-pressure liquid chromatography (HPLC) methods. This paper compares an HPLC and two spectrophotometric methods (Spec 1 and Spec 2) and assesses the effectiveness in the detection of shikimic acid in the tissues of glyphosate-treated plants. Furthermore, the study evaluates the versatility of two acid-based shikimic acid extraction methods and assesses the longevity of plant extract samples under different storage conditions. Finally, Spec 1 and Spec 2 are further characterized with respect to (1) the capacity to discern between shikimic acid and chemically related alicyclic hydroxy acids, (2) the stability of the chromophore (t1/2), (3) the detection limits, and (4) the cost and simplicity of undertaking the analytical procedure. Overall, spectrophotometric methods were more cost-effective and simpler to execute yet provided a narrower detection limit compared to HPLC. All three methods were specific to shikimic acid and detected the compound in the tissues of glyphosate-susceptible crops, increasing exponentially in concentration within 24 h of glyphosate application and plateauing at approximately 72 h. Spec 1 estimated more shikimic acid in identical plant extract samples compared to Spec 2 and, likewise, HPLC detection was more effective than spectrophotometric determinations. Given the unprecedented global adoption of glyphosate-resistant crops and concomitant use of glyphosate, an effective and accurate assessment of glyphosate efficacy is important. Endogenous shikimic acid determinations are instrumental in corroborating the efficacy of glyphosate and therefore have numerous applications in herbicide research and related areas of science as well as resolving many commercial issues as a consequence of glyphosate utilization.
Collapse
Affiliation(s)
- Ian A Zelaya
- Department of Agronomy, Iowa State University, Ames, Iowa 50011-1011, USA.
| | | | | | | |
Collapse
|
235
|
Haghani K, Khajeh K, Salmanian AH, Ranjbar B, Bakhtiyari S. Acid-Induced Formation of Molten Globule States in the Wild Type Escherichia coli 5-Enolpyruvylshikimate 3-Phosphate Synthase and its Three Mutated Forms: G96A, A183T and G96A/A183T. Protein J 2011; 30:132-7. [DOI: 10.1007/s10930-011-9308-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
236
|
Alternative split sites for fragment complementation, and glyphosate function as extra ligand and stabilizer for the AroA enzyme complexes. CHINESE SCIENCE BULLETIN-CHINESE 2011. [DOI: 10.1007/s11434-010-4323-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
237
|
Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MNG, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) 2011; 91:155-72. [PMID: 21247804 DOI: 10.1016/j.tube.2010.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/19/2010] [Accepted: 11/26/2010] [Indexed: 01/03/2023]
Abstract
The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately lead to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design.
Collapse
Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
238
|
Tian YS, Xiong AS, Xu J, Zhao W, Gao F, Fu XY, Xu H, Zheng JL, Peng RH, Yao QH. Isolation from Ochrobactrum anthropi of a novel class II 5-enopyruvylshikimate-3-phosphate synthase with high tolerance to glyphosate. Appl Environ Microbiol 2010; 76:6001-5. [PMID: 20601515 PMCID: PMC2935038 DOI: 10.1128/aem.00770-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 06/19/2010] [Indexed: 11/20/2022] Open
Abstract
Applying the genomic library construction process and colony screening, a novel aroA gene encoding 5-enopyruvylshikimate-3-phosphate synthase from Ochrobactrum anthropi was identified, cloned, and overexpressed, and the enzyme was purified to homogeneity. Furthermore, site-directed mutagenesis was employed to assess the role of single amino acid residues in glyphosate resistance.
Collapse
Affiliation(s)
- Yong-Sheng Tian
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Ai-Sheng Xiong
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Jing Xu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Wei Zhao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Feng Gao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Xiao-Yan Fu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Hu Xu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Jian-Li Zheng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Ri-He Peng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| | - Quan-Hong Yao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai 201106, China
| |
Collapse
|
239
|
Zhong R, Thompson J, Ottesen E, Lamppa GK. A forward genetic screen to explore chloroplast protein import in vivo identifies Moco sulfurase, pivotal for ABA and IAA biosynthesis and purine turnover. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:44-59. [PMID: 20374530 DOI: 10.1111/j.1365-313x.2010.04220.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A genetic screen in Arabidopsis was developed to explore the regulation of chloroplast protein import in vivo using two independent reporters representing housekeeping and photosynthetic pre-proteins. We first used 5-enolpyruvylshikimate 3-phosphate synthase (EPSP synthase*), a key enzyme in the shikimic acid pathway, with a mutation that confers tolerance to the herbicide glyphosate. Because the EPSP synthase* pre-protein must be imported for its function, the loss of glyphosate tolerance provided an initial indication of an import deficiency. Second, the fate of GFP fused to a ferredoxin transit peptide (FD5-GFP) was determined. A class of altered chloroplast import (aci) mutants showed both glyphosate sensitivity and FD5-GFP mislocalized to nuclei. aci2-1 was selected for further study. Yellow fluorescent protein (YFP) fused to the transit peptide of EPSP synthase* or the small subunit of Rubisco was not imported into chloroplasts, but also localized to nuclei during protoplast transient expression. Isolated aci2-1 chloroplasts showed a 50% reduction in pre-protein import efficiency in an in vitro assay. Mutants did not grow photoautotrophically on media without sucrose and were small and dark green in soil. aci2-1 and two alleles code for Moco-sulfurase, which activates the aldehyde oxidases required for the biosynthesis of the plant hormones abscisic acid (ABA) and indole-acetic acid (IAA) and controls purine nucleotide (ATP and GTP) turnover and nitrogen recycling via xanthine dehydrogenase. These enzyme activities were not detected in aci2-1. ABA, IAA and/or purine turnover may play previously unrecognized roles in the regulation of chloroplast protein import in response to developmental, metabolic and environmental cues.
Collapse
Affiliation(s)
- Rong Zhong
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
240
|
Brocker C, Lassen N, Estey T, Pappa A, Cantore M, Orlova VV, Chavakis T, Kavanagh KL, Oppermann U, Vasiliou V. Aldehyde dehydrogenase 7A1 (ALDH7A1) is a novel enzyme involved in cellular defense against hyperosmotic stress. J Biol Chem 2010; 285:18452-63. [PMID: 20207735 DOI: 10.1074/jbc.m109.077925] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Mammalian ALDH7A1 is homologous to plant ALDH7B1, an enzyme that protects against various forms of stress, such as salinity, dehydration, and osmotic stress. It is known that mutations in the human ALDH7A1 gene cause pyridoxine-dependent and folic acid-responsive seizures. Herein, we show for the first time that human ALDH7A1 protects against hyperosmotic stress by generating osmolytes and metabolizing toxic aldehydes. Human ALDH7A1 expression in Chinese hamster ovary cells attenuated osmotic stress-induced apoptosis caused by increased extracellular concentrations of sucrose or sodium chloride. Purified recombinant ALDH7A1 efficiently metabolized a number of aldehyde substrates, including the osmolyte precursor, betaine aldehyde, lipid peroxidation-derived aldehydes, and the intermediate lysine degradation product, alpha-aminoadipic semialdehyde. The crystal structure for ALDH7A1 supports the enzyme's substrate specificities. Tissue distribution studies in mice showed the highest expression of ALDH7A1 protein in liver, kidney, and brain, followed by pancreas and testes. ALDH7A1 protein was found in the cytosol, nucleus, and mitochondria, making it unique among the aldehyde dehydrogenase enzymes. Analysis of human and mouse cDNA sequences revealed mitochondrial and cytosolic transcripts that are differentially expressed in a tissue-specific manner in mice. In conclusion, ALDH7A1 is a novel aldehyde dehydrogenase expressed in multiple subcellular compartments that protects against hyperosmotic stress by generating osmolytes and metabolizing toxic aldehydes.
Collapse
Affiliation(s)
- Chad Brocker
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado 80045, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
241
|
Abstract
Modern herbicides make major contributions to global food production by easily removing weeds and substituting for destructive soil cultivation. However, persistent herbicide selection of huge weed numbers across vast areas can result in the rapid evolution of herbicide resistance. Herbicides target specific enzymes, and mutations are selected that confer resistance-endowing amino acid substitutions, decreasing herbicide binding. Where herbicides bind within an enzyme catalytic site very few mutations give resistance while conserving enzyme functionality. Where herbicides bind away from a catalytic site many resistance-endowing mutations may evolve. Increasingly, resistance evolves due to mechanisms limiting herbicide reaching target sites. Especially threatening are herbicide-degrading cytochrome P450 enzymes able to detoxify existing, new, and even herbicides yet to be discovered. Global weed species are accumulating resistance mechanisms, displaying multiple resistance across many herbicides and posing a great challenge to herbicide sustainability in world agriculture. Fascinating genetic issues associated with resistance evolution remain to be investigated, especially the possibility of herbicide stress unleashing epigenetic gene expression. Understanding resistance and building sustainable solutions to herbicide resistance evolution are necessary and worthy challenges.
Collapse
Affiliation(s)
- Stephen B Powles
- Western Australian Herbicide Resistance Initiative, School of Plant Biology, University of Western Australia, Crawley, WA, Australia.
| | | |
Collapse
|
242
|
Roos G, Geerlings P, Messens J. Enzymatic catalysis: the emerging role of conceptual density functional theory. J Phys Chem B 2009; 113:13465-75. [PMID: 19754087 DOI: 10.1021/jp9034584] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Experimentalists and quantum chemists are living in a different world. A wealth of theoretical enzymology-related publications is hardly known by experimentalists, and vice versa. Our aim is to bring both worlds together and to show the powerful possibilities of a multidisciplinary approach to study subtle details of complicated enzymatic processes to a broad readership. MD simulations and QM/MM approaches often focus on the calculation of reaction paths based on activation energies, which is a time-consuming task. A valuable alternative is the reactivity descriptors founded in conceptual DFT like softness, electrophilicity, and the Fukui function, which describe the kinetic aspects of a reaction in terms of the response to perturbations in N and/or upsilon(r), typical for a chemical reaction, of the reagents in the ground state. As such, the relative energies at the beginning of the reaction predict a sequence of activation energies only based on the properties of the reactants (Figure 5 ). In 2003, Geerlings et al. published a key review giving a detailed description of the principles and concepts of conceptual DFT and highlighting its success to study generalized acid/base reactions including addition, substitution, and elimination reactions. Since the time that this review appeared, conceptual DFT has proven its strength in literally hundreds of papers with application to organic and inorganic reactions. Its role in unravelling enzymatic reaction mechanisms, in handling experimentally difficult accessible biochemical problems, and in the interpretation of biochemical experimental observations is emerging and very promising.
Collapse
Affiliation(s)
- Goedele Roos
- Department of Molecular and Cellular Interactions, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
| | | | | |
Collapse
|
243
|
Ramalho TC, Caetano MS, da Cunha EFF, Souza TCS, Rocha MVJ. Construction and assessment of reaction models of class I EPSP synthase: molecular docking and density functional theoretical calculations. J Biomol Struct Dyn 2009; 27:195-207. [PMID: 19583445 DOI: 10.1080/07391102.2009.10507309] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The high frequency of contamination by herbicides suggests the need for more active and selective herbicides. Glyphosate is the active component of one of the top-selling herbicides, which is also a potent EPSP synthase inhibitor. That is a key enzyme in the shikimic acid pathway, which is found only in plants and some microorganisms. Thus, EPSP synthase is regarded as a prime target for herbicides. In this line, molecular modeling studies using molecular dynamics simulations and DFT techniques were performed to understand the interaction of glyphosate and its analogs with the wild type enzyme and Gly96Ala mutant EPSP synthase. In addition, we investigated the reaction mechanism of the natural substrate. Our findings indicate some key points to the design of new selective glyphosate derivates.
Collapse
Affiliation(s)
- Teodorico C Ramalho
- Departamento de Química, Universidade Federal de Lavras, 37200-000 Lavras-MG, Brazil.
| | | | | | | | | |
Collapse
|
244
|
Berti PJ, Chindemi P. Catalytic residues and an electrostatic sandwich that promote enolpyruvyl shikimate 3-phosphate synthase (AroA) catalysis. Biochemistry 2009; 48:3699-707. [PMID: 19271774 DOI: 10.1021/bi802251s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enolpyruvylshikimate 3-phosphate synthase (EPSP synthase, AroA) catalyzes the sixth step in aromatic amino acid biosynthesis. It forms EPSP from shikimate 3-phosphate (S3P) and phosphoenolpyruvate (PEP) in an addition/elimination reaction that proceeds through a tetrahedral intermediate. In spite of numerous mechanistic studies, the catalytic roles of specific amino acid residues remain an open question. Recent experimental evidence for cationic intermediates or cationic transition states, and a consideration of the catalytic imperative, have guided this study on the catalytic roles of Lys22 (K22), Asp313 (D313), and Glu341 (E341). Steady-state and pre-steady-state kinetics and protein stability studies showed that mutations of D313 and E341 caused k(cat) to decrease up to 30,000-fold and 76,000-fold, respectively, while the effects on K(M) were modest, never more than 40-fold. Thus, both are identified as catalytic residues. In an active site that is overwhelmingly positively charged, the D313 and E341 side chains are positioned to form an "electrostatic sandwich" around the positive charge at C2 in cationic intermediates/transition states, stabilizing them and thereby promoting catalysis. Mutation of K22 showed large effects on K(M,S3P) (100-fold), K(M,PEP) (>760-fold), and up to 120-fold on k(cat). Thus, K22 had roles in both substrate-binding and transition-state stabilization. These results support the identification of E341 and K22 as general acid/base catalytic residues.
Collapse
Affiliation(s)
- Paul J Berti
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada.
| | | |
Collapse
|
245
|
Funke T, Yang Y, Han H, Healy-Fried M, Olesen S, Becker A, Schönbrunn E. Structural basis of glyphosate resistance resulting from the double mutation Thr97 -> Ile and Pro101 -> Ser in 5-enolpyruvylshikimate-3-phosphate synthase from Escherichia coli. J Biol Chem 2009; 284:9854-60. [PMID: 19211556 PMCID: PMC2665107 DOI: 10.1074/jbc.m809771200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 02/11/2009] [Indexed: 11/06/2022] Open
Abstract
The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the target of the broad spectrum herbicide glyphosate. The genetic engineering of EPSPS led to the introduction of glyphosate-resistant crops worldwide. The genetically engineered corn lines NK603 and GA21 carry distinct EPSPS enzymes. CP4 EPSPS, expressed in NK603 corn and transgenic soybean, cotton, and canola, belongs to class II EPSPS, glyphosate-insensitive variants of this enzyme isolated from certain Gram-positive bacteria. GA21 corn, on the other hand, was created by point mutations of class I EPSPS, such as the enzymes from Zea mays or Escherichia coli, which are sensitive to low glyphosate concentrations. The structural basis of the glyphosate resistance resulting from these point mutations has remained obscure. We studied the kinetic and structural effects of the T97I/P101S double mutation, the molecular basis for GA21 corn, using EPSPS from E. coli. The T97I/P101S enzyme is essentially insensitive to glyphosate (K(i) = 2.4 mm) but maintains high affinity for the substrate phosphoenolpyruvate (PEP) (K(m) = 0.1 mm). The crystal structure at 1.7-A resolution revealed that the dual mutation causes a shift of residue Gly(96) toward the glyphosate binding site, impairing efficient binding of glyphosate, while the side chain of Ile(97) points away from the substrate binding site, facilitating PEP utilization. The single site T97I mutation renders the enzyme sensitive to glyphosate and causes a substantial decrease in the affinity for PEP. Thus, only the concomitant mutations of Thr(97) and Pro(101) induce the conformational changes necessary to produce catalytically efficient, glyphosate-resistant class I EPSPS.
Collapse
Affiliation(s)
- Todd Funke
- Drug Discovery Department, Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | | | | | | | | | | | | |
Collapse
|
246
|
Ahsan N, Lee DG, Lee KW, Alam I, Lee SH, Bahk JD, Lee BH. Glyphosate-induced oxidative stress in rice leaves revealed by proteomic approach. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:1062-70. [PMID: 18755596 DOI: 10.1016/j.plaphy.2008.07.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Accepted: 07/10/2008] [Indexed: 05/19/2023]
Abstract
Glyphosate is one of the most widely used herbicides in cereal-growing regions worldwide. In the present work, the protein expression profile of rice leaves exposed to glyphosate was analyzed in order to investigate the alternative effects of glyphosate on plants. Two-week-old rice leaves were subjected to glyphosate or a reactive oxygen species (ROS) inducing herbicide paraquat, and total soluble proteins were extracted and analyzed by two-dimensional gel electrophoresis (2-DE) coupled with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) analysis. A total of 25 differentially expressed proteins were identified from the glyphosate treated sample, wherein 18 proteins were up-regulated and 7 proteins were down-regulated. These proteins had shown a parallel expression pattern in response to paraquat. Results from the 2-DE analysis, combined with immunoblotting, clearly revealed that ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit was significantly decreased by the treatment of both herbicides. An increased accumulation of antioxidant enzymes including ascorbate peroxidase, glutathione S-transferase, thioredoxin h-type, nucleoside diphosphate kinase 1, peroxiredoxin and a superoxide dismutase [Cu-Zn] chloroplast precursor in the glyphosate-treated sample suggests that a glyphosate treatment possibly generates oxidative stress in plants. Moreover, a gene expression analysis of five antioxidant enzymes by Northern blot confirmed their mRNA levels in the rice leaves. A histo-cytochemical investigation with DAB (3,3-diaminobenzidine) to localize H(2)O(2) and increases of the thiobarbituric acid reactive substances (TBARS) concentration revealed that the glyphosate application generates ROS, which resulted in the peroxidation and destruction of lipids in the rice leaves.
Collapse
Affiliation(s)
- Nagib Ahsan
- Division of Applied Life Sciences (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
247
|
Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP. J Mol Model 2008; 15:147-55. [PMID: 19043750 DOI: 10.1007/s00894-008-0403-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 09/16/2008] [Indexed: 02/06/2023]
Abstract
Bacillus anthracis has been employed as an agent of bioterrorism, with high mortality, despite anti-microbial treatment, which strongly indicates the need of new drugs to treat anthrax. Shikimate pathway is a seven step biosynthetic route which generates chorismic acid from phosphoenol pyruvate and erythrose-4-phosphate. Chorismic acid is the major branch point in the synthesis of aromatic amino acids, ubiquinone, and secondary metabolites. The shikimate pathway is essential for many pathological organisms, whereas it is absent in mammals. Therefore, these enzymes are potential targets for the development of nontoxic antimicrobial agents and herbicides and have been submitted to intensive structural studies. The forth enzyme of this pathway is responsible for the conversion of dehydroshikimate to shikimate in the presence of NADP. In order to pave the way for structural and functional efforts toward development of new antimicrobials we describe the molecular modeling of shikimate dehydrogenase from Bacillus anthracis complexed with the cofactor NADP. This study was able to identify the main residues of the NADP binding site responsible for ligand affinities. This structural study can be used in the design of more specific drugs against infectious diseases.
Collapse
|
248
|
Abstract
This chapter describes in detail the genes and proteins of Escherichia coli involved in the biosynthesis and transport of the three aromatic amino acids tyrosine, phenylalanine, and tryptophan. It provides a historical perspective on the elaboration of the various reactions of the common pathway converting erythrose-4-phosphate and phosphoenolpyruvate to chorismate and those of the three terminal pathways converting chorismate to phenylalanine, tyrosine, and tryptophan. The regulation of key reactions by feedback inhibition, attenuation, repression, and activation are also discussed. Two regulatory proteins, TrpR (108 amino acids) and TyrR (513 amino acids), play a major role in transcriptional regulation. The TrpR protein functions only as a dimer which, in the presence of tryptophan, represses the expression of trp operon plus four other genes (the TrpR regulon). The TyrR protein, which can function both as a dimer and as a hexamer, regulates the expression of nine genes constituting the TyrR regulon. TyrR can bind each of the three aromatic amino acids and ATP and under their influence can act as a repressor or activator of gene expression. The various domains of this protein involved in binding the aromatic amino acids and ATP, recognizing DNA binding sites, interacting with the alpha subunit of RNA polymerase, and changing from a monomer to a dimer or a hexamer are all described. There is also an analysis of the various strategies which allow TyrR in conjunction with particular amino acids to differentially affect the expression of individual genes of the TyrR regulon.
Collapse
|
249
|
Haghani K, Salmanian AH, Ranjbar B, Zakikhan-Alang K, Khajeh K. Comparative studies of wild type Escherichia coli 5-enolpyruvylshikimate 3-phosphate synthase with three glyphosate-insensitive mutated forms: activity, stability and structural characterization. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:1167-75. [PMID: 18567546 DOI: 10.1016/j.bbapap.2007.07.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 07/22/2007] [Accepted: 07/23/2007] [Indexed: 10/22/2022]
Abstract
5-Enolpyruvylshikimate 3-phosphate (EPSP) synthase is an essential enzyme of the shikimate pathway and is the target for the herbicide, glyphosate. Several glyphosate-insensitive forms of Escherichia coli EPSP synthase had been reported in the literatures. In the present study the function and structure of wild type enzyme and three different mutated variants (G96A, A183T and G96A/A183T) were compared. Results showed that G96A and G96A/A183T variants are insensitive to glyphosate but display a 31- and 8-fold lower affinity for phosphoenolpyruvate (PEP) as substrate, respectively. In addition, chemical stability of the enzyme variants against Gdn-HCl revealed more stability of the wild type and G96A variant when compared to the G96A/A183T and A183T variants. Comparison of the enzymes containing Ala183Thr replacement with the wild type showed a lower resistance to digestion by the proteases. Moreover, with respect to fluorescence quenching by acrylamide, A183T and G96A/A183T variants were characterized by a higher structural flexibility and more exposure of tryptophan residues to the solvent. In addition, based on the results of circular dichroism and intrinsic fluorescence studies, these two variants represent a significant decrease of secondary structures and changes in the tertiary structure as compared to the wild type and the G96A variant.
Collapse
Affiliation(s)
- Karimeh Haghani
- Department of Biochemistry and Biophysics, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | | | | | | | | |
Collapse
|
250
|
Marques MR, Vaso A, Neto JR, Fossey MA, Oliveira JS, Basso LA, dos Santos DS, de Azevedo Junior WF, Palma MS. Dynamics of glyphosate-induced conformational changes of Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) determined by hydrogen-deuterium exchange and electrospray mass spectrometry. Biochemistry 2008; 47:7509-22. [PMID: 18558720 DOI: 10.1021/bi800134y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation in the absence of substrates and/or inhibitors and in a closed conformation when bound to the substrate and/or inhibitor. In the present report, the H/D exchange properties of EPSPS from Mycobacterium tuberculosis ( Mt) were investigated for both enzyme conformations using ESI mass spectrometry and circular dichroism (CD). When the conformational changes identified by H/D exchanges were mapped on the 3-D structure, it was observed that the apoenzyme underwent extensive conformational changes due to glyphosate complexation, characterized by an increase in the content of alpha-helices from 40% to 57%, while the beta-sheet content decreased from 30% to 23%. These results indicate that the enzyme underwent a series of rearrangements of its secondary structure that were accompanied by a large decrease in solvent access to many different regions of the protein. This was attributed to the compaction of 71% of alpha-helices and 57% of beta-sheets as a consequence of glyphosate binding to the enzyme. Apparently, MtEPSPS undergoes a series of inhibitor-induced conformational changes, which seem to have caused synergistic effects in preventing solvent access to the core of molecule, especially in the cleft region. This may be part of the mechanism of inhibition of the enzyme, which is required to prevent the hydration of the substrate binding site and also to induce the cleft closure to avoid entrance of the substrates.
Collapse
Affiliation(s)
- Maurício R Marques
- Laboratory of Structural Biology and Zoochemistry, CEIS/Department of Biology, Institute of Biosciences, UNESP, Rio Claro, SP 13506-900, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|