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Lyu T, Cheung KS, Deng Z, Ni L, Chen C, Wu J, Leung WK, Seto WK. Whole genome sequencing reveals novel genetic mutations of Helicobacter pylori associating with resistance to clarithromycin and levofloxacin. Helicobacter 2023:e12972. [PMID: 36965192 DOI: 10.1111/hel.12972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/16/2023] [Accepted: 03/07/2023] [Indexed: 03/27/2023]
Abstract
BACKGROUND Detection of mutations in one or a couple of genes may not provide enough data or cover all the genomic DNA variance related to antibiotic resistance of Helicobacter pylori to clarithromycin (CLA) and levofloxacin (LVX). We aimed to perform whole genome sequencing to explore novel antibiotic resistance-related genes to increase predictive accuracy for future targeted sequencing tests. METHODS Gastric mucosal biopsies were taken during upper endoscopy in 27 H. pylori-infected patients. According to culture-based antibacterial susceptibility test, H. pylori strains were divided into three groups, with nine strains in each group: CLA single-drug resistance (group C), LVX single-drug resistance (group L), and strains sensitive to all antibacterial drugs (group S). Based on whole genome sequencing with group S being the control, group C and group L group-specific single nucleotide variants and amino acid mutations were screened, and potential candidate genes related to CLA and LVX resistance were identified. RESULTS The median age of study subjects was 35 years (IQR: 31-40), and 17 (63.0%) were male. All nine CLA-resistant strains had A2143G mutations in 23S rRNA, while none of nine sensitive strains had the mutation. Six of nine strains in group L and six of nine strains in group S had 87th or 91st mutation in gyrA. After comparing sequencing data of strains among the three groups, we identified five mutated positions belonging to four genes related to CLA resistance, and 31 mutated positions belonging to 20 genes related to LVX resistance. Novel genetic mutations were detected for CLA resistance (including fliJ and clpX) and LVX resistance (including fliJ, cheA, hemE, Val360Ile, and HP0568). Missense mutations in fliJ and cheA gene were mainly involved in chemotaxis and flagellar motility to facilitate bacterial escape of antibiotics, while the functions of other novel gene mutations underpinning antibiotic resistance remain to be investigated. CONCLUSION Whole genome sequencing detected potential novel genetic mutations conferring resistance of H. pylori to CLA and LVX including fliJ and cheA. Further studies to correlate these findings with treatment outcome should be performed.
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Affiliation(s)
- Tao Lyu
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Ka Shing Cheung
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Zijie Deng
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Li Ni
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Chuan Chen
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Juan Wu
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Wai K Leung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Wai Kay Seto
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
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Bashiri G, Grove TL, Hegde SS, Lagautriere T, Gerfen GJ, Almo SC, Squire CJ, Blanchard JS, Baker EN. The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster. J Biol Chem 2019; 294:13158-13170. [PMID: 31315931 DOI: 10.1074/jbc.ra119.009498] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/15/2019] [Indexed: 01/17/2023] Open
Abstract
Iron-sulfur clusters are protein cofactors with an ancient evolutionary origin. These clusters are best known for their roles in redox proteins such as ferredoxins, but some iron-sulfur clusters have nonredox roles in the active sites of enzymes. Such clusters are often prone to oxidative degradation, making the enzymes difficult to characterize. Here we report a structural and functional characterization of dihydroxyacid dehydratase (DHAD) from Mycobacterium tuberculosis (Mtb), an essential enzyme in the biosynthesis of branched-chain amino acids. Conducting this analysis under fully anaerobic conditions, we solved the DHAD crystal structure, at 1.88 Å resolution, revealing a 2Fe-2S cluster in which one iron ligand is a potentially exchangeable water molecule or hydroxide. UV and EPR spectroscopy both suggested that the substrate binds directly to the cluster or very close to it. Kinetic analysis implicated two ionizable groups in the catalytic mechanism, which we postulate to be Ser-491 and the iron-bound water/hydroxide. Site-directed mutagenesis showed that Ser-491 is essential for activity, and substrate docking indicated that this residue is perfectly placed for proton abstraction. We found that a bound Mg2+ ion 6.5 Å from the 2Fe-2S cluster plays a key role in substrate binding. We also identified a putative entry channel that enables access to the cluster and show that Mtb-DHAD is inhibited by a recently discovered herbicide, aspterric acid, that, given the essentiality of DHAD for Mtb survival, is a potential lead compound for the design of novel anti-TB drugs.
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Affiliation(s)
- Ghader Bashiri
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Subray S Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Thomas Lagautriere
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Gary J Gerfen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Christopher J Squire
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Edward N Baker
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
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Integrated Genomic and Proteomic Analyses of High-level Chloramphenicol Resistance in Campylobacter jejuni. Sci Rep 2017; 7:16973. [PMID: 29209085 PMCID: PMC5716995 DOI: 10.1038/s41598-017-17321-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/15/2017] [Indexed: 12/02/2022] Open
Abstract
Campylobacter jejuni is a major zoonotic pathogen, and its resistance to antibiotics is of great concern for public health. However, few studies have investigated the global changes of the entire organism with respect to antibiotic resistance. Here, we provide mechanistic insights into high-level resistance to chloramphenicol in C. jejuni, using integrated genomic and proteomic analyses. We identified 27 single nucleotide polymorphisms (SNPs) as well as an efflux pump cmeB mutation that conferred modest resistance. We determined two radical S-adenosylmethionine (SAM) enzymes, one each from an SNP gene and a differentially expressed protein. Validation of major metabolic pathways demonstrated alterations in oxidative phosphorylation and ABC transporters, suggesting energy accumulation and increase in methionine import. Collectively, our data revealed a novel rRNA methylation mechanism by a radical SAM superfamily enzyme, indicating that two resistance mechanisms existed in Campylobacter. This work provided a systems biology perspective on understanding the antibiotic resistance mechanisms in bacteria.
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 563] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Biogenesis of [Fe–S] cluster in Firmicutes: an unexploited field of investigation. Antonie Van Leeuwenhoek 2013; 104:283-300. [DOI: 10.1007/s10482-013-9966-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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Challand MR, Salvadori E, Driesener RC, Kay CWM, Roach PL, Spencer J. Cysteine methylation controls radical generation in the Cfr radical AdoMet rRNA methyltransferase. PLoS One 2013; 8:e67979. [PMID: 23861844 PMCID: PMC3702613 DOI: 10.1371/journal.pone.0067979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
The 'radical S-adenosyl-L-methionine (AdoMet)' enzyme Cfr methylates adenosine 2503 of the 23S rRNA in the peptidyltransferase centre (P-site) of the bacterial ribosome. This modification protects host bacteria, notably methicillin-resistant Staphylococcus aureus (MRSA), from numerous antibiotics, including agents (e.g. linezolid, retapamulin) that were developed to treat such organisms. Cfr contains a single [4Fe-4S] cluster that binds two separate molecules of AdoMet during the reaction cycle. These are used sequentially to first methylate a cysteine residue, Cys338; and subsequently generate an oxidative radical intermediate that facilitates methyl transfer to the unreactive C8 (and/or C2) carbon centres of adenosine 2503. How the Cfr active site, with its single [4Fe-4S] cluster, catalyses these two distinct activities that each utilise AdoMet as a substrate remains to be established. Here, we use absorbance and electron paramagnetic resonance (EPR) spectroscopy to investigate the interactions of AdoMet with the [4Fe-4S] clusters of wild-type Cfr and a Cys338 Ala mutant, which is unable to accept a methyl group. Cfr binds AdoMet with high (∼ 10 µM) affinity notwithstanding the absence of the RNA cosubstrate. In wild-type Cfr, where Cys338 is methylated, AdoMet binding leads to rapid oxidation of the [4Fe-4S] cluster and production of 5'-deoxyadenosine (DOA). In contrast, while Cys338 Ala Cfr binds AdoMet with equivalent affinity, oxidation of the [4Fe-4S] cluster is not observed. Our results indicate that the presence of a methyl group on Cfr Cys338 is a key determinant of the activity of the enzyme towards AdoMet, thus enabling a single active site to support two distinct modes of AdoMet cleavage.
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Affiliation(s)
- Martin R. Challand
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
| | - Enrico Salvadori
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | | | - Christopher W. M. Kay
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - Peter L. Roach
- Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Medical Sciences Building, Bristol, United Kingdom
- * E-mail: (CWMK); (PLR); (JS)
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Abstract
The success of linezolid stimulated significant efforts to discover new agents in the oxazolidinone class. Over a dozen oxazolidinones have reached the clinic, but many were discontinued due to lack of differentiated potency, inadequate pharmacokinetics, and safety risks that included myelosuppression. Four oxazolidinones are currently undergoing clinical evaluation. The Trius Therapeutics compound tedizolid phosphate (formerly known as torezolid phosphate, TR-701, DA-7218), the most advanced, is in phase 3 clinical trials for acute bacterial skin and skin structure infections. Rib-X completed two phase 2 studies for radezolid (Rx-01_667, RX-1741) in uncomplicated skin and skin structure infections and community-acquired pneumonia. Pfizer and AstraZeneca have each identified antitubercular compounds that have completed phase 1 studies: sutezolid (PNU-100480, PF-02341272) and AZD5847 (AZD2563), respectively. The oxazolidinones share a relatively low frequency of resistance largely due to the requirement of mutations in 23S ribosomal RNA genes. However, maintaining potency against strains carrying the mobile cfr gene poses a challenge for the oxazolidinone class, as well as other 50S ribosome inhibitors that target the peptidyl transferase center.
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Affiliation(s)
- Karen Joy Shaw
- Trius Therapeutics, Inc., Department of Biology, San Diego, California 92121, USA.
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Lanz ND, Grove TL, Gogonea CB, Lee KH, Krebs C, Booker SJ. RlmN and AtsB as Models for the Overproduction and Characterization of Radical SAM Proteins. Methods Enzymol 2012; 516:125-52. [DOI: 10.1016/b978-0-12-394291-3.00030-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Grove TL, Radle MI, Krebs C, Booker SJ. Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation. J Am Chem Soc 2011; 133:19586-9. [PMID: 21916495 PMCID: PMC3596424 DOI: 10.1021/ja207327v] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The radical SAM (RS) proteins RlmN and Cfr catalyze methylation of carbons 2 and 8, respectively, of adenosine 2503 in 23S rRNA. Both reactions are similar in scope, entailing the synthesis of a methyl group partially derived from S-adenosylmethionine (SAM) onto electrophilic sp(2)-hybridized carbon atoms via the intermediacy of a protein S-methylcysteinyl (mCys) residue. Both proteins contain five conserved Cys residues, each required for turnover. Three cysteines lie in a canonical RS CxxxCxxC motif and coordinate a [4Fe-4S]-cluster cofactor; the remaining two are at opposite ends of the polypeptide. Here we show that each protein contains only the one "radical SAM" [4Fe-4S] cluster and the two remaining conserved cysteines do not coordinate additional iron-containing species. In addition, we show that, while wild-type RlmN bears the C355 mCys residue in its as-isolated state, RlmN that is either engineered to lack the [4Fe-4S] cluster by substitution of the coordinating cysteines or isolated from Escherichia coli cultured under iron-limiting conditions does not bear a C355 mCys residue. Reconstitution of the [4Fe-4S] cluster on wild-type apo RlmN followed by addition of SAM results in rapid production of S-adenosylhomocysteine (SAH) and the mCys residue, while treatment of apo RlmN with SAM affords no observable reaction. These results indicate that in Cfr and RlmN, SAM bound to the unique iron of the [4Fe-4S] cluster displays two reactivities. It serves to methylate C355 of RlmN (C338 of Cfr), or to generate the 5'-deoxyadenosyl 5'-radical, required for substrate-dependent methyl synthase activity.
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Affiliation(s)
- Tyler L. Grove
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Matthew I. Radle
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
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Grove TL, Benner JS, Radle MI, Ahlum JH, Landgraf BJ, Krebs C, Booker SJ. A radically different mechanism for S-adenosylmethionine-dependent methyltransferases. Science 2011; 332:604-7. [PMID: 21415317 DOI: 10.1126/science.1200877] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Methylation of small molecules and macromolecules is crucial in metabolism, cell signaling, and epigenetic programming and is most often achieved by S-adenosylmethionine (SAM)-dependent methyltransferases. Most employ an S(N)2 mechanism to methylate nucleophilic sites on their substrates, but recently, radical SAM enzymes have been identified that methylate carbon atoms that are not inherently nucleophilic via the intermediacy of a 5'-deoxyadenosyl 5'-radical. We have determined the mechanisms of two such reactions targeting the sp(2)-hybridized carbons at positions 2 and 8 of adenosine 2503 in 23S ribosomal RNA, catalyzed by RlmN and Cfr, respectively. In neither case is a methyl group transferred directly from SAM to the RNA; rather, both reactions proceed by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.
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Affiliation(s)
- Tyler L Grove
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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