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Matoba Y, Oda K, Wataeda M, Kanemori H, Matsuo K. pH-dependent regulation of an acidophilic O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum. Appl Environ Microbiol 2024; 90:e0011824. [PMID: 38568076 PMCID: PMC11107162 DOI: 10.1128/aem.00118-24] [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: 01/23/2024] [Accepted: 03/16/2024] [Indexed: 05/22/2024] Open
Abstract
Bacteria have two routes for the l-methionine biosynthesis. In one route called the direct sulfuration pathway, acetylated l-homoserine is directly converted into l-homocysteine. The reaction using H2S as the second substrate is catalyzed by a pyridoxal 5'-phosphate-dependent enzyme, O-acetylhomoserine sulfhydrylase (OAHS). In the present study, we determined the enzymatic functions and the structures of OAHS from Lactobacillus plantarum (LpOAHS). The LpOAHS enzyme exhibited the highest catalytic activity under the weak acidic pH condition. In addition, crystallographic analysis revealed that the enzyme takes two distinct structures, open and closed forms. In the closed form, two acidic residues are sterically clustered. The proximity may cause the electrostatic repulsion, inhibiting the formation of the closed form under the neutral to the basic pH conditions. We concluded that the pH-dependent regulation mechanism using the two acidic residues contributes to the acidophilic feature of the enzyme. IMPORTANCE In the present study, we can elucidate the pH-dependent regulation mechanism of the acidophilic OAHS. The acidophilic feature of the enzyme is caused by the introduction of an acidic residue to the neighborhood of the key acidic residue acting as a switch for the structural interconversion. The strategy may be useful in the field of protein engineering to change the optimal pH of the enzymes. In addition, this study may be useful for the development of antibacterial drugs because the l-methionine synthesis essential for bacteria is inhibited by the OAHS inhibitors. The compounds that can inhibit the interconversion between the open and closed forms of OAHS may become antibacterial drugs.
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Affiliation(s)
- Yasuyuki Matoba
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Kosuke Oda
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Maho Wataeda
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Hina Kanemori
- Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
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2
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Yadav P, Singh R, Sur S, Bansal S, Chaudhry U, Tandon V. Moonlighting proteins: beacon of hope in era of drug resistance in bacteria. Crit Rev Microbiol 2023; 49:57-81. [PMID: 35220864 DOI: 10.1080/1040841x.2022.2036695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Moonlighting proteins (MLPs) are ubiquitous and provide a unique advantage to bacteria performing multiple functions using the same genomic content. Targeting MLPs can be considered as a futuristic approach in fighting drug resistance problem. This review follows the MLP trail from its inception to the present-day state, describing a few bacterial MLPs, viz., glyceraldehyde 3'-phosphate dehydrogenase, phosphoglucose isomerase glutamate racemase (GR), and DNA gyrase. Here, we carve out that targeting MLPs are the beacon of hope in an era of increasing drug resistance in bacteria. Evolutionary stability, structure-functional relationships, protein diversity, possible drug targets, and identification of new drugs against bacterial MLP are given due consideration. Before the final curtain calls, we provide a comprehensive list of small molecules that inhibit the biochemical activity of MLPs, which can aid the development of novel molecules to target MLPs for therapeutic applications.
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Affiliation(s)
- Pramod Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Raja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Uttar Pradesh, India
| | - Sandhya Bansal
- Norton Thoracic Institute, St. Joseph's Hospital, and Medical Center, Phoenix, AZ, USA
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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Labana P, Dornan MH, Lafrenière M, Czarny TL, Brown ED, Pezacki JP, Boddy CN. Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria. Cell Chem Biol 2021; 28:1703-1715.e11. [PMID: 34293284 DOI: 10.1016/j.chembiol.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/22/2021] [Accepted: 06/29/2021] [Indexed: 01/16/2023]
Abstract
Multi-drug-resistant bacteria present an urgent threat to modern medicine, creating a desperate need for antibiotics with new modes of action. As natural products remain an unsurpassed source for clinically viable antibiotic compounds, we investigate the mechanism of action of armeniaspirol. The armeniaspirols are a structurally unique class of Gram-positive antibiotic discovered from Streptomyces armeniacus for which resistance cannot be readily obtained. We show that armeniaspirol inhibits the ATP-dependent proteases ClpXP and ClpYQ in vitro and in the model Gram-positive Bacillus subtilis. This inhibition dysregulates the divisome and elongasome supported by an upregulation of key proteins FtsZ, DivIVA, and MreB inducing cell division arrest. The inhibition of ClpXP and ClpYQ to dysregulate cell division represents a unique antibiotic mechanism of action and armeniaspirol is the only known natural product inhibitor of the coveted anti-virulence target ClpP. Thus, armeniaspirol possesses a promising lead scaffold for antibiotic development with unique pharmacology.
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Affiliation(s)
- Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Mark H Dornan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Matthew Lafrenière
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomasz L Czarny
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John P Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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Cheng R, Lai R, Peng C, Lopez J, Li Z, Naowarojna N, Li K, Wong C, Lee N, Whelan SA, Qiao L, Grinstaff MW, Wang J, Cui Q, Liu P. Implications for an imidazol-2-yl carbene intermediate in the rhodanase-catalyzed C-S bond formation reaction of anaerobic ergothioneine biosynthesis. ACS Catal 2021; 11:3319-3334. [PMID: 34745712 DOI: 10.1021/acscatal.0c04886] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the anaerobic ergothioneine biosynthetic pathway, a rhodanese domain containing enzyme (EanB) activates tne hercynine's sp2 ε-C-H Dona ana replaces it with a C-S bond to produce ergothioneine. The key intermediate for this trans-sulfuration reaction is the Cys412 persulfide. Substitution of the EanB-Cys412 persulfide with a Cys412 perselenide does not yield the selenium analog of ergothioneine, selenoneine. However, in deuterated buffer, the perselenide-modified EanB catalyzes the deuterium exchange between hercynine's sp2 ε-C-H bond and D2O. Results from QM/MM calculations suggest that the reaction involves a carbene intermediate and that Tyr353 plays a key role. We hypothesize that modulating the pKa of Tyr353 will affect the deuterium-exchange rate. Indeed, the 3,5-difluoro tyrosine containing EanB catalyzes the deuterium exchange reaction with k ex of ~10-fold greater than the wild-type EanB (EanBWT). With regards to potential mechanisms, these results support the involvement of a carbene intermediate in EanB-catalysis, rendering EanB as one of the few carbene-intermediate involving enzymatic systems.
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Affiliation(s)
- Ronghai Cheng
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Rui Lai
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Juan Lopez
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Zhihong Li
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Kelin Li
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Christina Wong
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Norman Lee
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Stephen A. Whelan
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Lu Qiao
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Mark W. Grinstaff
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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Methionine Limitation Impairs Pathogen Expansion and Biofilm Formation Capacity. Appl Environ Microbiol 2019; 85:AEM.00177-19. [PMID: 30824455 DOI: 10.1128/aem.00177-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/23/2019] [Indexed: 02/01/2023] Open
Abstract
Multidrug-resistant bacterial pathogens are becoming increasingly prevalent, and novel strategies to treat bacterial infections caused by these organisms are desperately needed. Bacterial central metabolism is crucial for catabolic processes and provides precursors for anabolic pathways, such as the biosynthesis of essential biomolecules like amino acids or vitamins. However, most essential pathways are not regarded as good targets for antibiotic therapy since their products might be acquired from the environment. This issue raises doubts about the essentiality of such targets during infection. A putative target in bacterial anabolism is the methionine biosynthesis pathway. In contrast to humans, almost all bacteria carry methionine biosynthesis pathways which have often been suggested as putative targets for novel anti-infectives. While the growth of methionine auxotrophic strains can be stimulated by exogenous methionine, the extracellular concentrations required by most bacterial species are unknown. Furthermore, several phenotypic characteristics of methionine auxotrophs are only partly reversed by exogenous methionine. We investigated methionine auxotrophic mutants of Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli (all differing in methionine biosynthesis enzymes) and found that each needed concentrations of exogenous methionine far exceeding that reported for human serum (∼30 µM). Accordingly, these methionine auxotrophs showed a reduced ability to proliferate in human serum. Additionally, S. aureus and P. aeruginosa methionine auxotrophs were significantly impaired in their ability to form and maintain biofilms. Altogether, our data show intrinsic defects of methionine auxotrophs. This result suggests that the pathway should be considered for further studies validating the therapeutic potential of inhibitors.IMPORTANCE New antibiotics that attack novel targets are needed to circumvent widespread resistance to conventional drugs. Bacterial anabolic pathways, such as the enzymes for biosynthesis of the essential amino acid methionine, have been proposed as potential targets. However, the eligibility of enzymes in these pathways as drug targets is unclear because metabolites might be acquired from the environment to overcome inhibition. We investigated the nutritional needs of methionine auxotrophs of the pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli We found that each auxotrophic strain retained a growth disadvantage at methionine concentrations mimicking those available in vivo and showed that biofilm biomass was strongly influenced by endogenous methionine biosynthesis. Our experiments suggest that inhibition of the methionine biosynthesis pathway has deleterious effects even in the presence of external methionine. Therefore, additional efforts to validate the effects of methionine biosynthesis inhibitors in vivo are warranted.
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Rocha JF, Pina AF, Sousa SF, Cerqueira NMFSA. PLP-dependent enzymes as important biocatalysts for the pharmaceutical, chemical and food industries: a structural and mechanistic perspective. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01210a] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PLP-dependent enzymes described on this review are attractive targets for enzyme engineering towards their application in an industrial biotechnology framework.
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Affiliation(s)
- Juliana F. Rocha
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
| | - André F. Pina
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
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Xu J, Wang F, Jakovlić I, Prisingkorn W, Li JT, Wang WM, Zhao YH. Metabolite and gene expression profiles suggest a putative mechanism through which high dietary carbohydrates reduce the content of hepatic betaine in Megalobrama amblycephala. Metabolomics 2018; 14:94. [PMID: 30830423 DOI: 10.1007/s11306-018-1389-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND High-carbohydrate diets (HCD) are favoured by the aquaculture industry for economic reasons, but they can produce negative impacts on growth and induce hepatic steatosis. We hypothesised that the mechanism behind this is the reduction of hepatic betaine content. OBJECTIVE We further explored this mechanism by supplementing betaine (1%) to the diet of a farmed fish Megalobrama amblycephala. METHODS Four diet groups were designed: control (CD, 27.11% carbohydrates), high-carbohydrate (HCD, 36.75% carbohydrates), long-term betaine (LBD, 35.64% carbohydrates) and short-term betaine diet (SBD; 12 weeks HCD + 4 weeks LBD). We analysed growth performance, body composition, liver condition, and expression of genes and profiles of metabolites associated with betaine metabolism. RESULTS HCD resulted in poorer growth and liver health (compared to CD), whereas LBD improved these parameters (compared to HCD). HCD induced the expression of genes associated with glucose, serine and cystathionine metabolisms, and (non-significantly, p = .20) a betaine-catabolizing enzyme betaine-homocysteine-methyltransferase; and decreased the content of betaine, methionine, S-adenosylhomocysteine and carnitine. Betaine supplementation (LBD) reversed these patterns, and elevated betaine-homocysteine-methyltransferase, S-adenosylmethionine and S-adenosylhomocysteine (all p ≤ .05). CONCLUSION We hypothesise that HCD reduced the content of hepatic betaine by enhancing the activity of metabolic pathways from glucose to homocysteine, reflected in increased glycolysis, serine metabolism, cystathionine metabolism and homocysteine remethylation. Long-term dietary betaine supplementation improved the negative impacts of HCD, inculding growth parameters, body composition, liver condition, and betaine metabolism. However, betaine supplementation may have caused a temporary disruption in the metabolic homeostasis.
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Affiliation(s)
- Jia Xu
- College of Fisheries Huazhong Agricultural University, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, People's Republic of China
| | - Fan Wang
- College of Fisheries Huazhong Agricultural University, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, People's Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, 430075, People's Republic of China
| | - Wassana Prisingkorn
- College of Fisheries Huazhong Agricultural University, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, People's Republic of China
| | - Jun-Tao Li
- Institute of Tropical Bioscience and Biotechnology, Haikou, 570102, People's Republic of China
| | - Wei-Min Wang
- College of Fisheries Huazhong Agricultural University, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, People's Republic of China
| | - Yu-Hua Zhao
- College of Fisheries Huazhong Agricultural University, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, People's Republic of China.
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8
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Awad R, Gans P, Reiser JB. Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri. Biochimie 2017; 137:165-173. [DOI: 10.1016/j.biochi.2017.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 02/02/2023]
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9
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Soo VWC, Yosaatmadja Y, Squire CJ, Patrick WM. Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. J Biol Chem 2016; 291:19873-87. [PMID: 27474741 PMCID: PMC5025676 DOI: 10.1074/jbc.m116.739557] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Indexed: 11/06/2022] Open
Abstract
Enzymes that utilize the cofactor pyridoxal 5′-phosphate play essential roles in amino acid metabolism in all organisms. The cofactor is used by proteins that adopt at least five different folds, which raises questions about the evolutionary processes that might explain the observed distribution of functions among folds. In this study, we show that a representative of fold type III, the Escherichia coli alanine racemase (ALR), is a promiscuous cystathionine β-lyase (CBL). Furthermore, E. coli CBL (fold type I) is a promiscuous alanine racemase. A single round of error-prone PCR and selection yielded variant ALR(Y274F), which catalyzes cystathionine β-elimination with a near-native Michaelis constant (Km = 3.3 mm) but a poor turnover number (kcat ≈10 h−1). In contrast, directed evolution also yielded CBL(P113S), which catalyzes l-alanine racemization with a poor Km (58 mm) but a high kcat (22 s−1). The structures of both variants were solved in the presence and absence of the l-alanine analogue, (R)-1-aminoethylphosphonic acid. As expected, the ALR active site was enlarged by the Y274F substitution, allowing better access for cystathionine. More surprisingly, the favorable kinetic parameters of CBL(P113S) appear to result from optimizing the pKa of Tyr-111, which acts as the catalytic acid during l-alanine racemization. Our data emphasize the short mutational routes between the functions of pyridoxal 5′-phosphate-dependent enzymes, regardless of whether or not they share the same fold. Thus, they confound the prevailing model of enzyme evolution, which predicts that overlapping patterns of promiscuity result from sharing a common multifunctional ancestor.
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Affiliation(s)
- Valerie W C Soo
- From the Institute of Natural and Mathematical Sciences, Massey University, Auckland 0632
| | - Yuliana Yosaatmadja
- the School of Biological Sciences, University of Auckland, Auckland 1142, and
| | | | - Wayne M Patrick
- the Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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10
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Inhibitors of amino acids biosynthesis as antifungal agents. Amino Acids 2014; 47:227-49. [PMID: 25408465 PMCID: PMC4302243 DOI: 10.1007/s00726-014-1873-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022]
Abstract
Fungal microorganisms, including the human pathogenic yeast and filamentous fungi, are able to synthesize all proteinogenic amino acids, including nine that are essential for humans. A number of enzymes catalyzing particular steps of human-essential amino acid biosynthesis are fungi specific. Numerous studies have shown that auxotrophic mutants of human pathogenic fungi impaired in biosynthesis of particular amino acids exhibit growth defect or at least reduced virulence under in vivo conditions. Several chemical compounds inhibiting activity of one of these enzymes exhibit good antifungal in vitro activity in minimal growth media, which is not always confirmed under in vivo conditions. This article provides a comprehensive overview of the present knowledge on pathways of amino acids biosynthesis in fungi, with a special emphasis put on enzymes catalyzing particular steps of these pathways as potential targets for antifungal chemotherapy.
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11
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Mangat CS, Bharat A, Gehrke SS, Brown ED. Rank ordering plate data facilitates data visualization and normalization in high-throughput screening. ACTA ACUST UNITED AC 2014; 19:1314-20. [PMID: 24828052 DOI: 10.1177/1087057114534298] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput screening (HTS) of chemical and microbial strain collections is an indispensable tool for modern chemical and systems biology; however, HTS data sets have inherent systematic and random error, which may lead to false-positive or false-negative results. Several methods of normalization of data exist; nevertheless, due to the limitations of each, no single method has been universally adopted. Here, we present a method of data visualization and normalization that is effective, intuitive, and easy to implement in a spreadsheet program. For each plate, the data are ordered by ascending values and a plot thereof yields a curve that is a signature of the plate data. Curve shape characteristics provide intuitive visualization of the frequency and strength of inhibitors, activators, and noise on the plate, allowing potentially problematic plates to be flagged. To reduce plate-to-plate variation, the data can be normalized by the mean of the middle 50% of ordered values, also called the interquartile mean (IQM) or the 50% trimmed mean of the plate. Positional effects due to bias in columns, rows, or wells can be corrected using the interquartile mean of each well position across all plates (IQMW) as a second level of normalization. We illustrate the utility of this method using data sets from biochemical and phenotypic screens.
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Affiliation(s)
- Chand S Mangat
- M. G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Amrita Bharat
- M. G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Sebastian S Gehrke
- M. G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Eric D Brown
- M. G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada McMaster High Throughput Screening Laboratory, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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12
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Dai R, Wilson DJ, Geders TW, Aldrich CC, Finzel BC. Inhibition of Mycobacterium tuberculosis transaminase BioA by aryl hydrazines and hydrazides. Chembiochem 2014; 15:575-86. [PMID: 24482078 PMCID: PMC4020011 DOI: 10.1002/cbic.201300748] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 01/22/2023]
Abstract
7,8-Diaminopelargonic acid synthase (BioA) of Mycobacterium tuberculosis is a recently validated target for therapeutic intervention in the treatment of tuberculosis (TB). Using biophysical fragment screening and structural characterization of compounds, we have identified a potent aryl hydrazine inhibitor of BioA that reversibly modifies the pyridoxal-5'-phosphate (PLP) cofactor, forming a stable quinonoid. Analogous hydrazides also form covalent adducts that can be observed crystallographically but are incapable of inactivating the enzyme. In the X-ray crystal structures, small molecules induce unexpected conformational remodeling in the substrate binding site. We compared these conformational changes to those induced upon binding of the substrate (7-keto-8-aminopelargonic acid), and characterized the inhibition kinetics and the X-ray crystal structures of BioA with the hydrazine compound and analogues to unveil the mechanism of this reversible covalent modification.
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Affiliation(s)
- Ran Dai
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
| | - Daniel J. Wilson
- Center for Drug Design University of Minnesota Academic Health Center, U of Minnesota, MN, 55455, United States
| | - Todd W. Geders
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
| | - Barry C. Finzel
- Department of Medicinal Chemistry University of Minnesota 308 Harvard St. SE, Minneapolis, MN 55455, United States
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13
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Jaworski AF, Aitken SM. Exploration of the six tryptophan residues of Escherichia coli cystathionine β-lyase as probes of enzyme conformational change. Arch Biochem Biophys 2013; 538:138-44. [DOI: 10.1016/j.abb.2013.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/06/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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14
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Characterization of C-S Lyase from C. diphtheriae: a possible target for new antimicrobial drugs. BIOMED RESEARCH INTERNATIONAL 2013; 2013:701536. [PMID: 24106714 PMCID: PMC3784150 DOI: 10.1155/2013/701536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/16/2013] [Indexed: 12/28/2022]
Abstract
The emergence of antibiotic resistance in microbial pathogens requires the identification of new antibacterial drugs. The biosynthesis of methionine is an attractive target because of its central importance in cellular metabolism. Moreover, most of the steps in methionine biosynthesis pathway are absent in mammals, lowering the probability of unwanted side effects. Herein, detailed biochemical characterization of one enzyme required for methionine biosynthesis, a pyridoxal-5′-phosphate (PLP-) dependent C-S lyase from Corynebacterium diphtheriae, a pathogenic bacterium that causes diphtheria, has been performed. We overexpressed the protein in E. coli and analyzed substrate specificity, pH dependence of steady state kinetic parameters, and ligand-induced spectral transitions of the protein. Structural comparison of the enzyme with cystalysin from Treponema denticola indicates a similarity in overall folding. We used site-directed mutagenesis to highlight the importance of active site residues Tyr55, Tyr114, and Arg351, analyzing the effects of amino acid replacement on catalytic properties of enzyme. Better understanding of the active site of C. diphtheriae C-S lyase and the determinants of substrate and reaction specificity from this work will facilitate the design of novel inhibitors as antibacterial therapeutics.
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Regulation of sulphur assimilation is essential for virulence and affects iron homeostasis of the human-pathogenic mould Aspergillus fumigatus. PLoS Pathog 2013; 9:e1003573. [PMID: 24009505 PMCID: PMC3757043 DOI: 10.1371/journal.ppat.1003573] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
Sulphur is an essential element that all pathogens have to absorb from their surroundings in order to grow inside their infected host. Despite its importance, the relevance of sulphur assimilation in fungal virulence is largely unexplored. Here we report a role of the bZIP transcription factor MetR in sulphur assimilation and virulence of the human pathogen Aspergillus fumigatus. The MetR regulator is essential for growth on a variety of sulphur sources; remarkably, it is fundamental for assimilation of inorganic S-sources but dispensable for utilization of methionine. Accordingly, it strongly supports expression of genes directly related to inorganic sulphur assimilation but not of genes connected to methionine metabolism. On a broader scale, MetR orchestrates the comprehensive transcriptional adaptation to sulphur-starving conditions as demonstrated by digital gene expression analysis. Surprisingly, A. fumigatus is able to utilize volatile sulphur compounds produced by its methionine catabolism, a process that has not been described before and that is MetR-dependent. The A. fumigatus MetR transcriptional activator is important for virulence in both leukopenic mice and an alternative mini-host model of aspergillosis, as it was essential for the development of pulmonary aspergillosis and supported the systemic dissemination of the fungus. MetR action under sulphur-starving conditions is further required for proper iron regulation, which links regulation of sulphur metabolism to iron homeostasis and demonstrates an unprecedented regulatory crosstalk. Taken together, this study provides evidence that regulation of sulphur assimilation is not only crucial for A. fumigatus virulence but also affects the balance of iron in this prime opportunistic pathogen.
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Cystathionine β-Lyase-Like Protein with Pyridoxal Binding Domain Characterized in Leishmania major by Comparative Sequence Analysis and Homology Modelling. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/520435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cystathionine β-lyase-like protein (CBLP), one of the key enzymes involved in methionine biosynthesis utilising pyridoxal phosphate (PLP) as a cofactor, has recently been reported in Leishmania major. Its presence in the parasite and absence in humans warrant its full characterisation and fruition as a potent, selective, and inevitable druggable target. Due to the unavailability of X-ray 3D structure of CBLP, a homology model for this protein was developed for the first time. The model was evaluated for PLP binding site and various conserve domain residues of the protein recommended by comparative sequence analyses by different protein analysis tools. The model was validated and discovered to be robust and statistically significant. The final model was superimposed on template of Arabidopsis thaliana (PDB ID: 1IBJ) and RMSD was found to be 0.486. The PLP binding site residues of both the proteins were ensued to be highly conserved indicated by Gly71, Met72, Tyr95, Asp169, and Ser193 as well as formation of aldimine bond with Lys194. This was further verified through molecular simulation of PLP into the cofactor binding site of the modelled protein. The present study may therefore play a directing role in the designing of novel, potential, and selective antileishmanial agents.
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Sulfur-regulated control of the met-2⁺ gene of Neurospora crassa encoding cystathionine β-lyase. BMC Res Notes 2013; 6:259. [PMID: 23835025 PMCID: PMC3716945 DOI: 10.1186/1756-0500-6-259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 07/03/2013] [Indexed: 11/21/2022] Open
Abstract
Background Cystathionine β-lyase performs an essential role in the transsulfuration pathway by its primary reaction of forming homocysteine from cystathionine. Understanding how the Neurospora crassa met-2+ gene, which encodes cystathionine β-lyase, is regulated is important in determining the basis of the cellular control of transsulfuration. The aim of this study was to determine the nature of a potential regulatory connection of met-2+ to the Neurospora sulfur regulatory network. Findings The cystathionine β-lyase (met-2+) gene was cloned by the identification of a cosmid genomic clone capable of transforming a met-2 mutant to methionine prototrophy and subsequently characterized. The gene contains a single intron and encodes a protein of 457 amino acids with conserved residues predicted to be important for catalysis and pyridoxal-5′-phosphate co-factor binding. The expression of met-2+ in wild-type N. crassa increased 3.1-fold under sulfur-limiting growth conditions as compared to the transcript levels seen under high sulfur growth conditions (i.e., repressing conditions). In a Δcys-3 strain, met-2+ transcript levels were substantially reduced under either low- or high-sulfur growth conditions. In addition, the presence of CYS3 activator binding sites on the met-2+ promoter was demonstrated by gel mobility shift assays. Conclusions In this report, we demonstrate the sulfur-regulated expression of the met-2+ gene and confirm its connection to the N. crassa sulfur regulatory circuit by the reduced expression observed in a Δcys-3 mutant and the in vitro detection of CYS3 binding sites in the met-2+ promoter. The data further adds to our understanding of the regulatory dynamics of transsulfuration.
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Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability. PLoS One 2013; 8:e61528. [PMID: 23626695 PMCID: PMC3634020 DOI: 10.1371/journal.pone.0061528] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/12/2013] [Indexed: 12/04/2022] Open
Abstract
The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111T. The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.
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Paritala H, Carroll KS. New targets and inhibitors of mycobacterial sulfur metabolism. Infect Disord Drug Targets 2013; 13:85-115. [PMID: 23808874 PMCID: PMC4332622 DOI: 10.2174/18715265113139990022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022]
Abstract
The identification of new antibacterial targets is urgently needed to address multidrug resistant and latent tuberculosis infection. Sulfur metabolic pathways are essential for survival and the expression of virulence in many pathogenic bacteria, including Mycobacterium tuberculosis. In addition, microbial sulfur metabolic pathways are largely absent in humans and therefore, represent unique targets for therapeutic intervention. In this review, we summarize our current understanding of the enzymes associated with the production of sulfated and reduced sulfur-containing metabolites in Mycobacteria. Small molecule inhibitors of these catalysts represent valuable chemical tools that can be used to investigate the role of sulfur metabolism throughout the Mycobacterial lifecycle and may also represent new leads for drug development. In this light, we also summarize recent progress made in the development of inhibitors of sulfur metabolism enzymes.
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Affiliation(s)
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, 33458, USA
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20
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Ihnatko R, Shaw E, Toman R. Proteome of Coxiella burnetii. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 984:105-30. [DOI: 10.1007/978-94-007-4315-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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Lodha PH, Aitken SM. Characterization of the Side-Chain Hydroxyl Moieties of Residues Y56, Y111, Y238, Y338, and S339 as Determinants of Specificity in E. coli Cystathionine β-Lyase. Biochemistry 2011; 50:9876-85. [DOI: 10.1021/bi201090n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pratik H. Lodha
- Department of Biology, Carleton University, Ottawa, Canada K1S 5B6
| | - Susan M. Aitken
- Department of Biology, Carleton University, Ottawa, Canada K1S 5B6
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Yin J, Garen CR, Bateman K, Yu M, Alipio Lyon EZ, Habel J, Kim H, Hung LW, Kim CY, James MNG. Expression, purification and preliminary crystallographic analysis of O-acetylhomoserine sulfhydrylase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:959-63. [PMID: 21821905 PMCID: PMC3151138 DOI: 10.1107/s1744309111017611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/10/2011] [Indexed: 11/11/2022]
Abstract
The gene product of the open reading frame Rv3340 from Mycobacterium tuberculosis is annotated as encoding a probable O-acetylhomoserine (OAH) sulfhydrylase (MetC), an enzyme that catalyzes the last step in the biosynthesis of methionine, which is an essential amino acid in bacteria and plants. Following overexpression in Escherichia coli, the M. tuberculosis MetC enzyme was purified and crystallized using the hanging-drop vapor-diffusion method. Native diffraction data were collected from crystals belonging to space group P2(1) and were processed to a resolution of 2.1 Å.
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Affiliation(s)
- Jiang Yin
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Katherine Bateman
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Minmin Yu
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Emily Z. Alipio Lyon
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeff Habel
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Heungbok Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Li-wei Hung
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Chang-Yub Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Holt S, Cordente AG, Williams SJ, Capone DL, Jitjaroen W, Menz IR, Curtin C, Anderson PA. Engineering Saccharomyces cerevisiae to release 3-Mercaptohexan-1-ol during fermentation through overexpression of an S. cerevisiae Gene, STR3, for improvement of wine aroma. Appl Environ Microbiol 2011; 77:3626-32. [PMID: 21478306 PMCID: PMC3127618 DOI: 10.1128/aem.03009-10] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/26/2011] [Indexed: 11/20/2022] Open
Abstract
Sulfur-containing aroma compounds are key contributors to the flavor of a diverse range of foods and beverages. The tropical fruit characters of Vitis vinifera L. cv. Sauvignon blanc wines are attributed to the presence of the aromatic thiols 3-mercaptohexan-1-ol (3MH), 3-mercaptohexan-1-ol-acetate, and 4-mercapto-4-methylpentan-2-one (4MMP). These volatile thiols are found in small amounts in grape juice and are formed from nonvolatile cysteinylated precursors during fermentation. In this study, we overexpressed a Saccharomyces cerevisiae gene, STR3, which led to an increase in 3MH release during fermentation of a V. vinifera L. cv. Sauvignon blanc juice. Characterization of the enzymatic properties of Str3p confirmed it to be a pyridoxal-5'-phosphate-dependent cystathionine β-lyase, and we demonstrated that this enzyme was able to cleave the cysteinylated precursors of 3MH and 4MMP to release the free thiols. These data provide direct evidence for a yeast enzyme able to release aromatic thiols in vitro that can be applied in the development of self-cloned yeast to enhance wine flavor.
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Affiliation(s)
- Sylvester Holt
- University of Copenhagen, Copenhagen, Denmark
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | | | - Simon J. Williams
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | | | | | - Ian R. Menz
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Chris Curtin
- The Australian Wine Research Institute, Adelaide, SA, Australia
| | - Peter A. Anderson
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
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De Pascale G, Griffiths EJ, Shakya T, Nazi I, Wright GD. Identification and Characterization of New Inhibitors of Fungal Homoserine Kinase. Chembiochem 2011; 12:1179-82. [DOI: 10.1002/cbic.201100121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Indexed: 11/09/2022]
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25
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De Pascale G, Nazi I, Harrison PHM, Wright GD. β-Lactone natural products and derivatives inactivate homoserine transacetylase, a target for antimicrobial agents. J Antibiot (Tokyo) 2011; 64:483-7. [DOI: 10.1038/ja.2011.37] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Aitken SM, Lodha PH, Morneau DJK. The enzymes of the transsulfuration pathways: active-site characterizations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1511-7. [PMID: 21435402 DOI: 10.1016/j.bbapap.2011.03.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 03/03/2011] [Accepted: 03/09/2011] [Indexed: 11/19/2022]
Abstract
The diversity of reactions catalyzed by enzymes reliant on pyridoxal 5'-phosphate (PLP) demonstrates the catalytic versatility of this cofactor and the plasticity of the protein scaffolds of the major fold types of PLP-dependent enzymes. The enzymes of the transsulfuration (cystathionine γ-synthase and cystathionine β-lyase) and reverse transsulfuration (cystathionine β-synthase and cystathionine γ-lyase) pathways interconvert l-cysteine and l-homocysteine, the immediate precursor of l-methionine, in plants/bacteria and yeast/animals, respectively. These enzymes provide a useful model system for investigation of the mechanisms of substrate and reaction specificity in PLP-dependent enzymes as they catalyze distinct side chain rearrangements of similar amino acid substrates. Exploration of the underlying factors that enable enzymes to control the substrate and reaction specificity of this cofactor will enable the engineering of these properties and the development of therapeutics and antimicrobial compounds. Recent studies probing the role of active-site residues, of the enzymes of the transsulfuration pathways, as determinants of substrate and reaction specificity are the subject of this review. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Susan M Aitken
- Department of Biology, Carleton University, Ottowa, Canada.
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27
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Lodha PH, Jaworski AF, Aitken SM. Characterization of site-directed mutants of residues R58, R59, D116, W340 and R372 in the active site of E. coli cystathionine beta-lyase. Protein Sci 2010; 19:383-91. [PMID: 20014435 DOI: 10.1002/pro.308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cystathionine beta-lyase (CBL) catalyzes the hydrolysis of L-cystathionine (L-Cth) to produce L-homocysteine, pyruvate, and ammonia. A series of active-site mutants of Escherichia coli CBL (eCBL) was constructed to investigate the roles of residues R58, R59, D116, W340, and R372 in catalysis and inhibition by aminoethoxyvinylglycine (AVG). The effects of these mutations on the k(cat)/K(m) (L-Cth) for the beta-elimination reaction range from a reduction of only 3-fold for D116A and D116N to 6 orders of magnitude for the R372L and R372A mutants. The order of importance of these residues for the hydrolysis of L-Cth is: R372 >> R58 > W340 approximately R59 > D116. Comparison of the kinetic parameters for L-Cth hydrolysis with those for inhibition of eCBL by AVG demonstrates that residue R58 tethers the distal carboxylate group of the substrate and confirms that residues W340 and R372 interact with the alpha-carboxylate moiety. The increase in the pK(a) of the acidic limb and decrease in the pK(a) of the basic limb of the k(cat)/K(m) (L-Cth) versus pH profiles of the R58K and R58A mutants, respectively, support a role for this residue in modulating the pK(a) of an active-site residue.
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Affiliation(s)
- Pratik H Lodha
- Department of Biology, Carleton University, Ottawa K1S 5B6, Canada
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28
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Lodha PH, Shadnia H, Woodhouse CM, Wright JS, Aitken SM. Investigation of residues Lys112, Glu136, His138, Gly247, Tyr248, and Asp249 in the active site of yeast cystathionine β-synthase. Biochem Cell Biol 2009; 87:531-40. [DOI: 10.1139/o09-003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cystathionine β-synthase (CBS), the first enzyme of the reverse transsulfuration pathway, catalyzes the pyridoxal 5′-phosphate–dependent condensation of l-serine and l-homocysteine to form l-cystathionine (l-Cth). A model of the l-Cth complex of the truncated form of yeast CBS (ytCBS), comprising the catalytic core, was constructed to identify residues involved in the binding of l-homocysteine and the distal portion of l-Cth. Residue K112 was selected for site-directed mutagenesis based on the results of the in silico docking of l-Cth to the modeled structure of ytCBS. Residues E136, H138, Y248, and D249 of ytCBS were also targeted as they correspond to identical polar residues lining the mouth of the active site in the structure of human CBS. A series of 8 site-directed mutants was constructed, and their order of impact on the ability of ytCBS to catalyze the β-replacement reaction is G247S ≈ K112Q > K112L ≈ K112R >> Y248F > D249A ≈ H138F > E136A. The β-replacement activity of G247S, which corresponds to the homocystinuria-associated G307S mutant of human CBS, is undetectable. The Kml-Ser of the K112L and K112R mutants is increased by 50- and 90-fold, respectively, while Kml-Hcys increases by only 2- and 4-fold, respectively. The Kml-Hcys of H138F and Y248F is increased by 8- and 18-fold, respectively. These results indicate that, while the targeted residues are not direct determinants of l-Hcys binding, G307, Y248, and K112 play essential roles in the maintenance of appropriate active-site conformation.
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Affiliation(s)
- Pratik H. Lodha
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Hooman Shadnia
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Colleen M. Woodhouse
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - James S. Wright
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Susan M. Aitken
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
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29
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Farsi A, Lodha PH, Skanes JE, Los H, Kalidindi N, Aitken SM. Interconversion of a pair of active-site residues in Escherichia coli cystathionine γ-synthase, E. coli cystathionine β-lyase, and Saccharomyces cerevisiae cystathionine γ-lyase and development of tools for the investigation of their mechanisms and reaction specificity. Biochem Cell Biol 2009; 87:445-57. [DOI: 10.1139/o08-144] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cystathionine γ-synthase (CGS) and cystathionine β-lyase (CBL), which comprise the transsulfuration pathway of bacteria and plants, and cystathionine γ-lyase (CGL), the second enzyme of the fungal and animal reverse transsulfuration pathway, share ∼30% sequence identity and are almost indistinguishable in overall structure. One difference between the active site of Escherichia coli CBL and those of E. coli CGS and Saccharomyces cerevisiae CGL is the replacement of a pair of aromatic residues, F55 and Y338, of the former by acidic residues in CGS (D45 and E325) and CGL (E48 and E333). A series of interconverting, site-directed mutants of these 2 residues was constructed in CBL (F55D, Y338E, F55D/Y338E), CGS (D45F, E325Y and D45F/E325Y) and CGL (E48A,D and E333A,D,Y) to probe the role of these residues as determinants of reaction specificity. Mutation of either position results in a reduction in catalytic efficiency, as exemplified by the 160-fold reduction in the kcat/Kml-Cys of eCGS-D45F and the 2850- and 30-fold reductions in the kcat/Kml-Cth of the eCBL-Y338E and the yCGL-E333A,Y mutants, respectively. However, the in vivo reaction specificity of the mutants was not altered, compared with the corresponding wild-type enzymes. The ΔmetB and ΔmetC strains, the optimized CBL and CGL assay conditions, and the efficient expression and affinity purification systems described provide the necessary tools to enable the continued exploration of the determinants of reaction specificity in the enzymes of the transsulfuration pathways.
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Affiliation(s)
- Ali Farsi
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Pratik H. Lodha
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | | | - Heidi Los
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Navya Kalidindi
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Susan M. Aitken
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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Dolle RE, Bourdonnec BL, Goodman AJ, Morales GA, Thomas CJ, Zhang W. Comprehensive Survey of Chemical Libraries for Drug Discovery and Chemical Biology: 2007. ACTA ACUST UNITED AC 2008; 10:753-802. [PMID: 18991466 DOI: 10.1021/cc800119z] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Roland E. Dolle
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Bertrand Le Bourdonnec
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Allan J. Goodman
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Guillermo A. Morales
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Craig J. Thomas
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Wei Zhang
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
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Discovery and characterization of QPT-1, the progenitor of a new class of bacterial topoisomerase inhibitors. Antimicrob Agents Chemother 2008; 52:2806-12. [PMID: 18519725 DOI: 10.1128/aac.00247-08] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
QPT-1 was discovered in a compound library by high-throughput screening and triage for substances with whole-cell antibacterial activity. This totally synthetic compound is an unusual barbituric acid derivative whose activity resides in the (-)-enantiomer. QPT-1 had activity against a broad spectrum of pathogenic, antibiotic-resistant bacteria, was nontoxic to eukaryotic cells, and showed oral efficacy in a murine infection model, all before any medicinal chemistry optimization. Biochemical and genetic characterization showed that the QPT-1 targets the beta subunit of bacterial type II topoisomerases via a mechanism of inhibition distinct from the mechanisms of fluoroquinolones and novobiocin. Given these attributes, this compound represents a promising new class of antibacterial agents. The success of this reverse genomics effort demonstrates the utility of exploring strategies that are alternatives to target-based screens in antibacterial drug discovery.
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A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: Crystal structure and site-directed mutagenesis studies. Biochim Biophys Acta Gen Subj 2008; 1780:809-18. [DOI: 10.1016/j.bbagen.2008.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/29/2008] [Accepted: 01/30/2008] [Indexed: 11/23/2022]
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