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Pedraza-Reyes M, Abundiz-Yañez K, Rangel-Mendoza A, Martínez LE, Barajas-Ornelas RC, Cuéllar-Cruz M, Leyva-Sánchez HC, Ayala-García VM, Valenzuela-García LI, Robleto EA. Bacillus subtilis stress-associated mutagenesis and developmental DNA repair. Microbiol Mol Biol Rev 2024; 88:e0015823. [PMID: 38551349 PMCID: PMC11332352 DOI: 10.1128/mmbr.00158-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
SUMMARYThe metabolic conditions that prevail during bacterial growth have evolved with the faithful operation of repair systems that recognize and eliminate DNA lesions caused by intracellular and exogenous agents. This idea is supported by the low rate of spontaneous mutations (10-9) that occur in replicating cells, maintaining genome integrity. In contrast, when growth and/or replication cease, bacteria frequently process DNA lesions in an error-prone manner. DNA repairs provide cells with the tools needed for maintaining homeostasis during stressful conditions and depend on the developmental context in which repair events occur. Thus, different physiological scenarios can be anticipated. In nutritionally stressed bacteria, different components of the base excision repair pathway may process damaged DNA in an error-prone approach, promoting genetic variability. Interestingly, suppressing the mismatch repair machinery and activating specific DNA glycosylases promote stationary-phase mutations. Current evidence also suggests that in resting cells, coupling repair processes to actively transcribed genes may promote multiple genetic transactions that are advantageous for stressed cells. DNA repair during sporulation is of interest as a model to understand how transcriptional processes influence the formation of mutations in conditions where replication is halted. Current reports indicate that transcriptional coupling repair-dependent and -independent processes operate in differentiating cells to process spontaneous and induced DNA damage and that error-prone synthesis of DNA is involved in these events. These and other noncanonical ways of DNA repair that contribute to mutagenesis, survival, and evolution are reviewed in this manuscript.
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Affiliation(s)
- Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Karen Abundiz-Yañez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Alejandra Rangel-Mendoza
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Lissett E. Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Rocío C. Barajas-Ornelas
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Mayra Cuéllar-Cruz
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | | | | | - Luz I. Valenzuela-García
- Department of Sustainable Engineering, Advanced Materials Research Center (CIMAV), Arroyo Seco, Durango, Mexico
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Muniz Seif EJ, Icimoto MY, da Silva Junior PI. In silico bioprospecting of receptors for Doderlin: an antimicrobial peptide isolated from Lactobacillus acidophilus. In Silico Pharmacol 2023; 11:11. [PMID: 37113323 PMCID: PMC10126193 DOI: 10.1007/s40203-023-00149-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The emergence of resistant bacteria strains against traditional antibiotics and treatments increases each year. Doderlin is a cationic and amphiphilic peptide active against gram-positive, negative and yeast stains. The aim of the present work was prospect potentials receptors associated of antimicrobial activity of Doderlin using in silico bioinformatics tools. To search for potential targets of Doderlin, PharmMapper software was used. Molecular docking between Doderlin and the receptor was performed by PatchDock. Additional interaction and ligand site prediction for each receptor was performed by I-TASSER software. Those PDB Id, 1XDJ (score: 11,746), 1JMH (score: 11,046), 1YR3 (score: 10,578), 1NG3 (score: 10,082) showed highest dock score. Doderlin was found to predicted/real sites co-localize with 1XDJ and 1JMH, enzymes accountable for nitrogenic bases synthesis. The resulting receptor bioprospecting is highly correlated and suggests that Doderlin might act by interfering with DNA metabolism/production of bacteria, altering microorganism homeostasis and growth impairment. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00149-1.
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Affiliation(s)
- Elias Jorge Muniz Seif
- Postgraduate Program in Molecular Biology, Federal University of São Paulo, São Paulo, Brazil
- Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CETICS/CEPID), Butantan Institute, São Paulo, Brazil
| | | | - Pedro Ismael da Silva Junior
- Postgraduate Program in Molecular Biology, Federal University of São Paulo, São Paulo, Brazil
- Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CETICS/CEPID), Butantan Institute, São Paulo, Brazil
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3
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Martín-Galiano AJ, García E. Streptococcus pneumoniae: a Plethora of Temperate Bacteriophages With a Role in Host Genome Rearrangement. Front Cell Infect Microbiol 2021; 11:775402. [PMID: 34869076 PMCID: PMC8637289 DOI: 10.3389/fcimb.2021.775402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/29/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria. They are the most abundant biological entity on Earth (current estimates suggest there to be perhaps 1031 particles) and are found nearly everywhere. Temperate phages can integrate into the chromosome of their host, and prophages have been found in abundance in sequenced bacterial genomes. Prophages may modulate the virulence of their host in different ways, e.g., by the secretion of phage-encoded toxins or by mediating bacterial infectivity. Some 70% of Streptococcus pneumoniae (the pneumococcus)—a frequent cause of otitis media, pneumonia, bacteremia and meningitis—isolates harbor one or more prophages. In the present study, over 4000 S. pneumoniae genomes were examined for the presence of prophages, and nearly 90% were found to contain at least one prophage, either defective (47%) or present in full (43%). More than 7000 complete putative integrases, either of the tyrosine (6243) or serine (957) families, and 1210 full-sized endolysins (among them 1180 enzymes corresponding to 318 amino acid-long N-acetylmuramoyl-L-alanine amidases [LytAPPH]) were found. Based on their integration site, 26 different pneumococcal prophage groups were documented. Prophages coding for tRNAs, putative virulence factors and different methyltransferases were also detected. The members of one group of diverse prophages (PPH090) were found to integrate into the 3’ end of the host lytASpn gene encoding the major S. pneumoniae autolysin without disrupting it. The great similarity of the lytASpnand lytAPPH genes (85–92% identity) allowed them to recombine, via an apparent integrase-independent mechanism, to produce different DNA rearrangements within the pneumococcal chromosome. This study provides a complete dataset that can be used to further analyze pneumococcal prophages, their evolutionary relationships, and their role in the pathogenesis of pneumococcal disease.
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Affiliation(s)
- Antonio J Martín-Galiano
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
| | - Ernesto García
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Structural Bases for the Synergistic Inhibition of Human Thymidylate Synthase and Ovarian Cancer Cell Growth by Drug Combinations. Cancers (Basel) 2021; 13:cancers13092061. [PMID: 33923290 PMCID: PMC8123127 DOI: 10.3390/cancers13092061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Drug combinations may help overcome drug resistance, a relevant cause of failure of ovarian cancer therapy. However, designing successful combinations requires a lengthy preclinical validation process. We have analyzed combinations of 5-fluorouracil and raltitrexed, two anticancer drugs that target thymidylate synthase, a key enzyme for the nucleotide synthesis. We have observed administration sequence specific and synergistic combined effects of the two drugs against cisplatin sensitive and resistant ovarian cancer cells. However, the focus of this work was to show that a high stability of the complex of the enzyme with the two drugs, as highlighted by X-ray crystallography, and synergistic inhibition of the enzyme represent indicators, if not prerequisites, for this drug combination to be synergistically active against sensitive and resistant ovarian cancer cells. We thus propose that structural and mechanistic information acquired during the preclinical research can help predict a successful therapeutic application of a drug combination. Abstract Combining drugs represent an approach to efficiently prevent and overcome drug resistance and to reduce toxicity; yet it is a highly challenging task, particularly if combinations of inhibitors of the same enzyme target are considered. To show that crystallographic and inhibition kinetic information can provide indicators of cancer cell growth inhibition by combinations of two anti-human thymidylate synthase (hTS) drugs, we obtained the X-ray crystal structure of the hTS:raltitrexed:5-fluorodeoxyuridine monophosphate (FdUMP) complex. Its analysis showed a ternary complex with both molecules strongly bound inside the enzyme catalytic cavity. The synergistic inhibition of hTS and its mechanistic rationale were consistent with the structural analysis. When administered in combination to A2780 and A2780/CP ovarian cancer cells, the two drugs inhibited ovarian cancer cell growth additively/synergistically. Together, these results support the idea that X-ray crystallography can provide structural indicators for designing combinations of hTS (or any other target)-directed drugs to accelerate preclinical research for therapeutic application.
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Yoshikawa T, Aoyama T, Sakamaki K, Oshima T, Lin J, Zhang S, Sapari NS, Soong R, Tan I, Chan XB, Bottomley D, Hewitt LC, Arai T, Teh BT, Epstein D, Ogata T, Kameda Y, Miyagi Y, Tsuburaya A, Morita S, Grabsch HI, Tan P. Comprehensive biomarker analyses identifies HER2, EGFR, MET RNA expression and thymidylate synthase 5'UTR SNP as predictors of benefit from S-1 adjuvant chemotherapy in Japanese patients with stage II/III gastric cancer. J Cancer 2019; 10:5130-5138. [PMID: 31602266 PMCID: PMC6775596 DOI: 10.7150/jca.34741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/25/2019] [Indexed: 12/14/2022] Open
Abstract
Purpose: A comprehensive molecular analysis was conducted to identify prognostic and predictive markers for adjuvant S-1 chemotherapy in stage II/III Japanese gastric cancer (GC) patients and to evaluate their potential suitability for alternative cytotoxic or targeted drugs. Experimental Design: We investigated genetic polymorphisms of enzymes potentially involved in 5-fluoruracil (5-FU) metabolism as well as platinum resistance, previously identified genomic subtypes potentially predicting 5-FU benefit, and mRNA expression levels of receptor tyrosine kinases and KRAS as potential treatment targets in a single institution cohort of 252 stage II/III GC patients treated with or without S-1 after D2 gastrectomy. Results: 88% and 62% GC had a potentially 5-FU sensitive phenotype by SNP analyses of TS 3'UTR, and TS 5'UTR, respectively. 24%, 46%, 40%, 5%, and 44% GC had a potentially platinum sensitive phenotype by SNP analyses of GSTP1, ERCC1 rs11615, ERCC1 rs3212986, ERCC2, and XRCC1, respectively. High HER2, EGFR, FGFR2, or MET mRNA expression was observed in 49%, 66%, 72%, and 54% GC, respectively. High HER2 expression was the only significant prognosticator (HR=3.912, 95%CI: 1.706-8.973, p=0.0005). High HER2 (p=0.031), low EGFR (p=0.124), high MET (p=0.165) RNA expression, and TS 5'UTR subtype 2R/2R, 2R/3C, or 3C (p=0.058) were significant independent predictors for S-1 resistance. Conclusions: The present study suggests that platinum-based or RTK targeted agents could be alternative treatment options for a substantial subgroup of Japanese GC patients currently treated with S-1. HER2, EGFR, MET, and TS 5'UTR SNP appear to be promising predictive markers for S-1 resistance warranting validation in an independent GC series.
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Affiliation(s)
- Takaki Yoshikawa
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan.,Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Toru Aoyama
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Kentaro Sakamaki
- Department of Biostatistics and Epidemiology, Yokohama City University, Yokohama, Japan
| | - Takasi Oshima
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Joyce Lin
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Shenli Zhang
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore
| | - Nur Sabrina Sapari
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Iain Tan
- Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Xiu Bin Chan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Dan Bottomley
- Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Lindsay C Hewitt
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, NL
| | - Tomio Arai
- Department of Pathology, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore
| | - David Epstein
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore
| | - Takashi Ogata
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Yoichi Kameda
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Akira Tsuburaya
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Satoshi Morita
- Department of Biomedical Statistics and Bioinformatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Heike I Grabsch
- Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.,Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, NL
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
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Structural Comparison of Enterococcus faecalis and Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities. Molecules 2019; 24:molecules24071257. [PMID: 30935102 PMCID: PMC6479881 DOI: 10.3390/molecules24071257] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/22/2019] [Accepted: 03/28/2019] [Indexed: 12/17/2022] Open
Abstract
Thymidylate synthase (TS) is an enzyme of paramount importance as it provides the only de novo source of deoxy-thymidine monophosphate (dTMP). dTMP, essential for DNA synthesis, is produced by the TS-catalyzed reductive methylation of 2′-deoxyuridine-5′-monophosphate (dUMP) using N5,N10-methylenetetrahydrofolate (mTHF) as a cofactor. TS is ubiquitous and a validated drug target. TS enzymes from different organisms differ in sequence and structure, but are all obligate homodimers. The structural and mechanistic differences between the human and bacterial enzymes are exploitable to obtain selective inhibitors of bacterial TSs that can enrich the currently available therapeutic tools against bacterial infections. Enterococcus faecalis is a pathogen fully dependent on TS for dTMP synthesis. In this study, we present four new crystal structures of Enterococcus faecalis and human TSs in complex with either the substrate dUMP or the inhibitor FdUMP. The results provide new clues about the half-site reactivity of Enterococcus faecalis TS and the mechanisms underlying the conformational changes occurring in the two enzymes. We also identify relevant differences in cofactor and inhibitor binding between Enterococcus faecalis and human TS that can guide the design of selective inhibitors against bacterial TSs.
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Fahim AM, Shalaby MA. Synthesis, biological evaluation, molecular docking and DFT calculations of novel benzenesulfonamide derivatives. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.087] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Lopez-Zavala AA, Guevara-Hernandez E, Vazquez-Lujan LH, Sanchez-Paz A, Garcia-Orozco KD, Contreras-Vergara CA, Lopez-Leal G, Arvizu-Flores AA, Ochoa-Leyva A, Sotelo-Mundo RR. A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites. PeerJ 2018; 6:e5023. [PMID: 29922516 PMCID: PMC6005164 DOI: 10.7717/peerj.5023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022] Open
Abstract
Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA, which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the Km for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The Km for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.,Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Eduardo Guevara-Hernandez
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Luz H Vazquez-Lujan
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Arturo Sanchez-Paz
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biologicas del Noroeste, Hermosillo, Sonora, Mexico
| | - Karina D Garcia-Orozco
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Carmen A Contreras-Vergara
- Laboratorio de Genetica de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Gamaliel Lopez-Leal
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rogerio R Sotelo-Mundo
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
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Implementation of a loss-of-function system to determine growth and stress-associated mutagenesis in Bacillus subtilis. PLoS One 2017; 12:e0179625. [PMID: 28700593 PMCID: PMC5507404 DOI: 10.1371/journal.pone.0179625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/01/2017] [Indexed: 11/19/2022] Open
Abstract
A forward mutagenesis system based on the acquisition of mutations that inactivate the thymidylate synthase gene (TMS) and confer a trimethoprim resistant (Tmpr) phenotype was developed and utilized to study transcription-mediated mutagenesis (TMM). In addition to thyA, Bacillus subtilis possesses thyB, whose expression occurs under conditions of cell stress; therefore, we generated a thyB- thyA+ mutant strain. Tmpr colonies of this strain were produced with a spontaneous mutation frequency of ~1.4 × 10-9. Genetic disruption of the canonical mismatch (MMR) and guanine oxidized (GO) repair pathways increased the Tmpr frequency of mutation by ~2-3 orders of magnitude. A wide spectrum of base substitutions as well as insertion and deletions in the ORF of thyA were found to confer a Tmpr phenotype. Stationary-phase-associated mutagenesis (SPM) assays revealed that colonies with a Tmpr phenotype, accumulated over a period of ten days with a frequency of ~ 60 ×10-7. The Tmpr system was further modified to study TMM by constructing a ΔthyA ΔthyB strain carrying an IPTG-inducible Pspac-thyA cassette. In conditions of transcriptional induction of thyA, the generation of Tmpr colonies increased ~3-fold compared to conditions of transcriptional repression. Further, the Mfd and GreA factors were necessary for the generation of Tmpr colonies in the presence of IPTG in B. subtilis. Because GreA and Mfd facilitate transcription-coupled repair, our results suggest that TMM is a mechanim to produce genetic diversity in highly transcribed regions in growth-limited B. subtilis cells.
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Choi YM, Yeo HK, Park YW, Lee JY. Structural Analysis of Thymidylate Synthase from Kaposi's Sarcoma-Associated Herpesvirus with the Anticancer Drug Raltitrexed. PLoS One 2016; 11:e0168019. [PMID: 27936107 PMCID: PMC5148040 DOI: 10.1371/journal.pone.0168019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/25/2016] [Indexed: 01/07/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a highly infectious human herpesvirus that causes Kaposi's sarcoma. KSHV encodes functional thymidylate synthase, which is a target for anticancer drugs such as raltitrexed or 5-fluorouracil. Thymidylate synthase catalyzes the conversion of 2'-deoxyuridine-5'-monophosphate (dUMP) to thymidine-5'-monophosphate (dTMP) using 5,10-methylenetetrahydrofolate (mTHF) as a co-substrate. The crystal structures of thymidylate synthase from KSHV (apo), complexes with dUMP (binary), and complexes with both dUMP and raltitrexed (ternary) were determined at 1.7 Å, 2.0 Å, and 2.4 Å, respectively. While the ternary complex structures of human thymidylate synthase and E. coli thymidylate synthase had a closed conformation, the ternary complex structure of KSHV thymidylate synthase was observed in an open conformation, similar to that of rat thymidylate synthase. The complex structures of KSHV thymidylate synthase did not have a covalent bond between the sulfhydryl group of Cys219 and C6 atom of dUMP, unlike the human thymidylate synthase. The catalytic Cys residue demonstrated a dual conformation in the apo structure, and its sulfhydryl group was oriented toward the C6 atom of dUMP with no covalent bond upon ligand binding in the complex structures. These structural data provide the potential use of antifolates such as raltitrexed as a viral induced anticancer drug and structural basis to design drugs for targeting the thymidylate synthase of KSHV.
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Affiliation(s)
- Yong Mi Choi
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Hyun Ku Yeo
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Young Woo Park
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Jae Young Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
- * E-mail:
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Abeysinghe T, Hong B, Wang Z, Kohen A. Preserved hydride transfer mechanism in evolutionarily divergent thymidylate synthases. CURRENT TOPICS IN BIOCHEMICAL RESEARCH 2016; 17:19-30. [PMID: 28018055 PMCID: PMC5172458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Thymidylate synthase (TSase) catalyzes a hydride transfer in the last step of the de novo biosynthesis of the DNA nucleotide thymine. We compared two isozymes, namely, TSase from Escherichia coli (ecTSase) and TSase from Bacillus subtilis (bsTSase) that represent a case of divergent evolution. Interestingly, a highly conserved histidine (H147 of ecTSase) was proposed to serve a critical role in catalysis, but in bsTSase it is naturally substituted by valine (Val). Yet, bsTSase is more active than ecTSase, and the intrinsic kinetic isotope effects (KIEs) of both are temperature-independent, suggesting a similarly well-organized transition state (TS) for the catalyzed hydride transfer. To examine the role of that histidine (His) in TSase catalysis, we examined the kinetics of H147V ecTSase, which "bridges" between these two TSases. In contrast to both wild-type TSases, the single mutation results in deficient catalysis. The mutation leads to intrinsic KIEs that are temperature-dependent, indicating a substantial imperfection in its TS. The findings reveal two important features: a direct role of H147 in the hydride transfer step catalyzed by the ecTSase and the evolutionary compensation for its deficiency in bsTSase via extensive polymorphism across the protein. Very different active site residues are observed for these evolutionarily divergent isozymes, which result in a well-organized TS for both. It is suggested that evolutionary pressure compensated for the H to V substitution at the active site of bsTSase by polymorphism leading to a well-organized TS in both enzymes.
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Affiliation(s)
- Thelma Abeysinghe
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Baoyu Hong
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Genentech, South San Francisco, CA 94080, USA
| | - Zhen Wang
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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Pozzi C, Ferrari S, Cortesi D, Luciani R, Stroud RM, Catalano A, Costi MP, Mangani S. The structure of Enterococcus faecalis thymidylate synthase provides clues about folate bacterial metabolism. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1232-41. [PMID: 22948925 PMCID: PMC10316677 DOI: 10.1107/s0907444912026236] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/10/2012] [Indexed: 11/11/2022]
Abstract
Drug resistance to therapeutic antibiotics poses a challenge to the identification of novel targets and drugs for the treatment of infectious diseases. Infections caused by Enterococcus faecalis are a major health problem. Thymidylate synthase (TS) from E. faecalis is a potential target for antibacterial therapy. The X-ray crystallographic structure of E. faecalis thymidylate synthase (EfTS), which was obtained as a native binary complex composed of EfTS and 5-formyltetrahydrofolate (5-FTHF), has been determined. The structure provides evidence that EfTS is a half-of-the-sites reactive enzyme, as 5-FTHF is bound to two of the four independent subunits present in the crystal asymmetric unit. 5-FTHF is a metabolite of the one-carbon transfer reaction catalysed by 5-formyltetrahydrofolate cyclo-ligase. Kinetic studies show that 5-FTHF is a weak inhibitor of EfTS, suggesting that the EfTS-5-FTHF complex may function as a source of folates and/or may regulate one-carbon metabolism. The structure represents the first example of endogenous 5-FTHF bound to a protein involved in folate metabolism.
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Affiliation(s)
- Cecilia Pozzi
- Dipartimento di Chimica, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefania Ferrari
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Debora Cortesi
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Rosaria Luciani
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Robert M. Stroud
- Department of Biochemistry and Biophysiscs, University of California, San Francisco, S-412C Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517, USA
| | - Alessia Catalano
- Dipartimento Farmaco-Chimico, University of Bari ‘Aldo Moro’, Via E. Orabona 4, 70125 Bari, Italy
| | - Maria Paola Costi
- Dipartimento di Scienze Farmaceutiche, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy
| | - Stefano Mangani
- Dipartimento di Chimica, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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Biochemical characterization of two thymidylate synthases in Corynebacterium glutamicum NCHU 87078. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1751-9. [PMID: 20595007 DOI: 10.1016/j.bbapap.2010.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 05/06/2010] [Accepted: 05/17/2010] [Indexed: 11/23/2022]
Abstract
The genome of Corynebacterium glutamicum NCHU 87078 contains two putative thymidylate synthase genes, designated CgthyA and CgthyX. These two genes were expressed in Escherichia coli NovaBlue and the expressed His(6)-tagged enzymes were purified by nickel-chelate chromatography. The purified CgThyA had a specific activity of 414 mU mg(-)(1) protein, whereas thymidylate synthase activity for CgThyX could not be detected in a functional complementation assay using a 10-day incubation period. Gel filtration chromatography and chemical cross-linking experiments showed that CgThyX may exist as a dimer in solution, unlike a typical ThyX protein with homotetrameric structure for catalytic activity. Spectroscopic analysis indicated that purified CgThyX lacked the cofactor FAD. The 2.3A resolution crystal structure of CgThyX-FAD demonstrated a loose tetramer, in which FAD is chelated between the subunits via a manner distinct from that of other flavin-dependent thymidylate synthases. Structure-based mutational studies have identified a non-conserved segment (residues 70-73) of CgThyX protein with crucial role in binding to FAD. Taken together, our biochemical and structural analyses highlight unique features of the C. glutamicum ThyX that distinguish this enzyme from ThyX proteins from other organisms. Our results also suggest that thymidylate synthesis in C. glutamicum requires ThyA but not ThyX.
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Lee BC, Park K, Kim D. Analysis of the residue-residue coevolution network and the functionally important residues in proteins. Proteins 2008; 72:863-72. [PMID: 18275083 DOI: 10.1002/prot.21972] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
It is a common belief that some residues of a protein are more important than others. In some cases, point mutations of some residues make butterfly effect on the protein structure and function, but in other cases they do not. In addition, the residues important for the protein function tend to be not only conserved but also coevolved with other interacting residues in a protein. Motivated by these observations, the authors propose that there is a network composed of the residues, the residue-residue coevolution network (RRCN), where nodes are residues and links are set when the coevolutionary interaction strengths between residues are sufficiently large. The authors build the RRCN for the 44 diverse protein families. The interaction strengths are calculated by using McBASC algorithm. After constructing the RRCN, the authors identify residues that have high degree of connectivity (hub nodes), and residues that play a central role in network flow of information (C(I) nodes). The authors show that these residues are likely to be functionally important residues. Moreover, the C(I) nodes appear to be more relevant to the function than the hub nodes. Unlike other similar methods, the method described in this study is solely based on sequences. Therefore, the method can be applied to the function annotation of a wider range of proteins.
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Affiliation(s)
- Byung-Chul Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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Edgell DR, Stanger MJ, Belfort M. Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene. J Mol Biol 2004; 343:1231-41. [PMID: 15491609 DOI: 10.1016/j.jmb.2004.09.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 08/25/2004] [Accepted: 09/02/2004] [Indexed: 12/01/2022]
Abstract
To maximize spread of their host intron or intein, many homing endonucleases recognize nucleotides that code for important and conserved amino acid residues of the target gene. Here, we examine the cleavage requirements for I-TevI, which binds a stretch of thymidylate synthase (TS) DNA that codes for functionally critical residues in the TS active site. Using an in vitro selection scheme, we identified two base-pairs in the I-TevI cleavage site region as important for cleavage efficiency. These were confirmed by comparison of I-TevI cleavage efficiencies on mutant and on wild-type substrates. We also showed that nicking of the bottom strand by I-TevI is not affected by mutation of residues surrounding the bottom-strand cleavage site, unlike other homing endonucleases. One of these two base-pairs is universally conserved in all TS sequences, and is identical with a previously identified cleavage determinant of I-BmoI, a related GIY-YIG endonuclease that binds a homologous stretch of TS-encoding DNA. The other base-pair is conserved only in a subset of TS genes that includes the I-TevI, but not the I-BmoI, target sequence. Both the I-TevI and I-BmoI cleavage site requirements correspond to functionally critical residues involved in an extensive hydrogen bond network within the TS active site. Remarkably, these cleavage requirements correlate with TS phylogeny in bacteria, suggesting that each endonuclease has individually adapted to efficiently cleave distinct TS substrates.
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Affiliation(s)
- David R Edgell
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health, PO Box 22002, Albany, NY 12201-2002, USA.
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Birdsall DL, Finer-Moore J, Stroud RM. The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity. Protein Eng Des Sel 2003; 16:229-40. [PMID: 12702803 DOI: 10.1093/proeng/gzg020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cysteine is the only variant of D169, a cofactor-binding residue in thymidylate synthase, that shows in vivo activity. The 2.4 A crystal structure of Escherichia coli thymidylate synthase D169C in a complex with dUMP and the antifolate CB3717 shows it to be an asymmetric dimer, with only one active site covalently bonded to dUMP. At the active site with covalently bound substrate, C169 S gamma adopts the roles of both carboxyl oxygens of D169, making a 3.6 A S...H[bond]N hydrogen bond to 3-NH of CB3717 and a 3.4 A water-mediated hydrogen bond to H212. Analogous hydrogen bonds formed during the enzyme reaction are important for cofactor binding and are postulated to contribute to catalysis. The C169 side chain is likely to be ionized, making it a better hydrogen bond acceptor than a neutral sulfhydryl group. At the second active site, C169 S gamma makes a shorter (3 A) hydrogen bond to the 3-NH of CB3717, CB3717 is approximately 1.5 A out of its binding site and there is no covalent bond between dUMP and the catalytic cysteine. Changes to partitioning among productive and non-productive conformations of reaction intermediates may contribute as much, if not more, to the diminished activity of this mutant than reduced stabilization of transition states.
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Affiliation(s)
- David L Birdsall
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143-0448, USA
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Almog R, Waddling CA, Maley F, Maley GF, Van Roey P. Crystal structure of a deletion mutant of human thymidylate synthase Delta (7-29) and its ternary complex with Tomudex and dUMP. Protein Sci 2001; 10:988-96. [PMID: 11316879 PMCID: PMC2374201 DOI: 10.1110/ps.47601] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The crystal structures of a deletion mutant of human thymidylate synthase (TS) and its ternary complex with dUMP and Tomudex have been determined at 2.0 A and 2.5 A resolution, respectively. The mutant TS, which lacks 23 residues near the amino terminus, is as active as the wild-type enzyme. The ternary complex is observed in the open conformation, similar to that of the free enzyme and to that of the ternary complex of rat TS with the same ligands. This is in contrast to Escherichia coli TS, where the ternary complex with Tomudex and dUMP is observed in the closed conformation. While the ligands interact with each other in identical fashion regardless of the enzyme conformation, they are displaced by about 1.0 A away from the catalytic cysteine in the open conformation. As a result, the covalent bond between the catalytic cysteine sulfhydryl and the base of dUMP, which is the first step in the reaction mechanism of TS and is observed in all ternary complexes of the E. coli enzyme, is not formed. This displacement results from differences in the interactions between Tomudex and the protein that are caused by differences in the environment of the glutamyl tail of the Tomudex molecule. Despite the absence of the closed conformation, Tomudex inhibits human TS ten-fold more strongly than E. coli TS. These results suggest that formation of a covalent bond between the catalytic cysteine and the substrate dUMP is not required for effective inhibition of human TS by cofactor analogs and could have implications for drug design by eliminating this as a condition for lead compounds.
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Affiliation(s)
- R Almog
- Division of Molecular Medicine, Wadsworth Center, Albany, New York 12201, USA
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Changchien LM, Garibian A, Frasca V, Lobo A, Maley GF, Maley F. High-level expression of Escherichia coli and Bacillus subtilis thymidylate synthases. Protein Expr Purif 2000; 19:265-70. [PMID: 10873540 DOI: 10.1006/prep.2000.1245] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Procedures are described for the preparation of highly purified thymidylate synthases from Escherichia coli and Bacillus subtilis. The yields in each case are quite high with about 350 mg of pure protein obtained from 1 liter of cells. Basically all that is required to obtain pure enzyme is an induction step from a high-expression vector, followed by a DE-52 column elution. Both enzymes appeared to be fairly stable in that incubation at 43 degrees C for 10 min resulted in the loss of 50% of the E. coli thymidylate synthase activity, while 50 degrees C for 10 min was required to obtain the same effect with the B. subtilis enzyme. In the presence of the substrate, dUMP, each protein was stabilized further by 6 to 7 degrees C, which was increased to 9 to 10 degrees C on addition of dihydrofolate. It was shown also that the E. coli thymidylate synthase could be maintained at 4 degrees C for at least 4 months with little or no loss in activity provided that mercaptoethanol was not present. The presence of the latter led to a progressive loss in activity until little activity could be detected after 18 weeks, which was due, in part, to the formation of a disulfide bond with the active site cysteine. Addition of dithiothreitol restored the enzyme activity to its original state.
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Affiliation(s)
- L M Changchien
- New York State Department of Health, Wadsworth Center, Empire State Plaza, Albany, New York, 12201-0509, USA
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