1
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Schroeder GM, Kiliushik D, Jenkins JL, Wedekind JE. Structure and function analysis of a type III preQ 1-I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence. J Biol Chem 2023; 299:105208. [PMID: 37660906 PMCID: PMC10622847 DOI: 10.1016/j.jbc.2023.105208] [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] [Received: 06/27/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023] Open
Abstract
Riboswitches are small noncoding RNAs found primarily in the 5' leader regions of bacterial messenger RNAs where they regulate expression of downstream genes in response to binding one or more cellular metabolites. Such noncoding RNAs are often regulated at the translation level, which is thought to be mediated by the accessibility of the Shine-Dalgarno sequence (SDS) ribosome-binding site. Three classes (I-III) of prequeuosine1 (preQ1)-sensing riboswitches are known that control translation. Class I is divided into three subtypes (types I-III) that have diverse mechanisms of sensing preQ1, which is involved in queuosine biosynthesis. To provide insight into translation control, we determined a 2.30 Å-resolution cocrystal structure of a class I type III preQ1-sensing riboswitch identified in Escherichia coli (Eco) by bioinformatic searches. The Eco riboswitch structure differs from previous preQ1 riboswitch structures because it has the smallest naturally occurring aptamer and the SDS directly contacts the preQ1 metabolite. We validated structural observations using surface plasmon resonance and in vivo gene-expression assays, which showed strong switching in live E. coli. Our results demonstrate that the Eco riboswitch is relatively sensitive to mutations that disrupt noncanonical interactions that form the pseudoknot. In contrast to type II preQ1 riboswitches, a kinetic analysis showed that the type III Eco riboswitch strongly prefers preQ1 over the chemically similar metabolic precursor preQ0. Our results reveal the importance of noncanonical interactions in riboswitch-driven gene regulation and the versatility of the class I preQ1 riboswitch pseudoknot as a metabolite-sensing platform that supports SDS sequestration.
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Affiliation(s)
- Griffin M Schroeder
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Daniil Kiliushik
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Joseph E Wedekind
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
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2
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Cotter M, Varghese S, Chevot F, Fergus C, Kelly VP, Connon SJ, Southern JM. Queuine Analogues Incorporating the 7-Aminomethyl-7-deazaguanine Core: Structure-Activity Relationships in the Treatment of Experimental Autoimmune Encephalomyelitis. ChemMedChem 2023; 18:e202300207. [PMID: 37350546 DOI: 10.1002/cmdc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023]
Abstract
A library of queuine analogues targeting the modification of tRNA isoacceptors for Asp, Asn, His and Tyr catalysed by queuine tRNA ribosyltransferase (QTRT, also known as TGT) was evaluated in the treatment of a chronic multiple sclerosis model: murine experimental autoimmune encephalomyelitis. Several active 7-deazaguanines emerged, together with a structure-activity relationship involving the necessity for a flexible alkyl chain of fixed length.
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Affiliation(s)
- Michelle Cotter
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Sreeja Varghese
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Franciane Chevot
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - J Mike Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
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3
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Schroeder GM, Akinyemi O, Malik J, Focht CM, Pritchett E, Baker C, McSally JP, Jenkins JL, Mathews D, Wedekind J. A riboswitch separated from its ribosome-binding site still regulates translation. Nucleic Acids Res 2023; 51:2464-2484. [PMID: 36762498 PMCID: PMC10018353 DOI: 10.1093/nar/gkad056] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/14/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10-G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch-akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold.
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Affiliation(s)
- Griffin M Schroeder
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Olayinka Akinyemi
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Department of Physics, University of Rochester, Rochester, NY 14642, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Caroline M Focht
- Department of Molecular Biophysics and Biochemistry and the Institute of Biomolecular Design and Discovery, Yale University, New Haven, CT 06516, USA
| | - Elizabeth M Pritchett
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Cameron D Baker
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - James P McSally
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Joseph E Wedekind
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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4
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Champion C, Neagoe RM, Effernberger M, Sala DT, Servant F, Christensen JE, Arnoriaga-Rodriguez M, Amar J, Lelouvier B, Loubieres P, Azalbert V, Minty M, Thomas C, Blasco-Baque V, Gamboa F, Tilg H, Cardellini M, Federici M, Fernández-Real JM, Loubes JM, Burcelin R. Human liver microbiota modeling strategy at the early onset of fibrosis. BMC Microbiol 2023; 23:34. [PMID: 36717776 PMCID: PMC9885577 DOI: 10.1186/s12866-023-02774-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Gut microbiota is involved in the development of liver diseases such as fibrosis. We and others identified that selected sets of gut bacterial DNA and bacteria translocate to tissues, notably the liver, to establish a non-infectious tissue microbiota composed of microbial DNA and a low frequency live bacteria. However, the precise set of bacterial DNA, and thereby the corresponding taxa associated with the early stages of fibrosis need to be identified. Furthermore, to overcome the impact of different group size and patient origins we adapted innovative statistical approaches. Liver samples with low liver fibrosis scores (F0, F1, F2), to study the early stages of the disease, were collected from Romania(n = 36), Austria(n = 10), Italy(n = 19), and Spain(n = 17). The 16S rRNA gene was sequenced. We considered the frequency, sparsity, unbalanced sample size between cohorts to identify taxonomic profiles and statistical differences. RESULTS Multivariate analyses, including adapted spectral clustering with L1-penalty fair-discriminant strategies, and predicted metagenomics were used to identify that 50% of liver taxa associated with the early stage fibrosis were Enterobacteriaceae, Pseudomonadaceae, Xanthobacteriaceae and Burkholderiaceae. The Flavobacteriaceae and Xanthobacteriaceae discriminated between F0 and F1. Predicted metagenomics analysis identified that the preQ0 biosynthesis and the potential pathways involving glucoryranose and glycogen degradation were negatively associated with liver fibrosis F1-F2 vs F0. CONCLUSIONS Without demonstrating causality, our results suggest first a role of bacterial translocation to the liver in the progression of fibrosis, notably at the earliest stages. Second, our statistical approach can identify microbial signatures and overcome issues regarding sample size differences, the impact of environment, and sets of analyses. TRIAL REGISTRATION TirguMECCH ROLIVER Prospective Cohort for the Identification of Liver Microbiota, registration 4065/2014. Registered 01 01 2014.
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Affiliation(s)
- Camille Champion
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France ,grid.15781.3a0000 0001 0723 035XInstitut de Mathématiques de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Radu M. Neagoe
- Second Department of Surgery, Emergency Mureş County Hospital, University of Medicine Pharmacy, Science and Technology “George Emil Palade” Tîrgu Mures, Târgu Mureș, Romania
| | - Maria Effernberger
- grid.5361.10000 0000 8853 2677Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniela T. Sala
- Second Department of Surgery, Emergency Mureş County Hospital, University of Medicine Pharmacy, Science and Technology “George Emil Palade” Tîrgu Mures, Târgu Mureș, Romania
| | | | - Jeffrey E. Christensen
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France
| | - Maria Arnoriaga-Rodriguez
- grid.411295.a0000 0001 1837 4818Department of Diabetes, Endocrinology and Nutrition, University Hospital of Girona ‘Dr Josep Trueta’, Girona, Spain ,grid.429182.4Institut d’Investigacio Biomedica de Girona IdibGi, Girona, Spain ,CIBER Fisiopatologia de La Obesidad Y Nutricion, Girona, Spain
| | - Jacques Amar
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France ,grid.414295.f0000 0004 0638 3479Therapeutics Department, Rangueil Hospital, Toulouse, France
| | | | - Pascale Loubieres
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France
| | - Vincent Azalbert
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France
| | - Matthieu Minty
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France
| | - Charlotte Thomas
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France
| | - Vincent Blasco-Baque
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France
| | - Fabrice Gamboa
- grid.15781.3a0000 0001 0723 035XInstitut de Mathématiques de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Herbert Tilg
- grid.5361.10000 0000 8853 2677Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Marina Cardellini
- grid.6530.00000 0001 2300 0941Department of Systems Medicine, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Massimo Federici
- grid.6530.00000 0001 2300 0941Department of Systems Medicine, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Jose-Manuel Fernández-Real
- grid.411295.a0000 0001 1837 4818Department of Diabetes, Endocrinology and Nutrition, University Hospital of Girona ‘Dr Josep Trueta’, Girona, Spain ,grid.429182.4Institut d’Investigacio Biomedica de Girona IdibGi, Girona, Spain ,CIBER Fisiopatologia de La Obesidad Y Nutricion, Girona, Spain
| | - Jean Michel Loubes
- grid.15781.3a0000 0001 0723 035XInstitut de Mathématiques de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Rémy Burcelin
- grid.7429.80000000121866389Institut National de La Santé Et de La Recherche Médicale (INSERM), Toulouse, France ,grid.15781.3a0000 0001 0723 035XUnité Mixte de Recherche (UMR) 1297, Institut Des Maladies Métaboliques Et Cardiovasculaires (I2MC), Team 2: ‘Intestinal Risk FactorsDiabetesDyslipidemia’, Université Paul Sabatier (UPS), F-31432 Toulouse Cedex 4, France
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5
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Zhu J, Yang F, Du K, Wei ZL, Wu QF, Chen Y, Li WF, Li Q, Zhou CZ. Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer. ENVIRONMENTAL MICROBIOME 2023; 18:3. [PMID: 36639816 PMCID: PMC9837993 DOI: 10.1186/s40793-023-00461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date. RESULTS Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria. CONCLUSION In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.
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Affiliation(s)
- Jie Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Feng Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Kang Du
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Zi-Lu Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qing-Fa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Wei-Fang Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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6
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Tittle JM, Schwark DG, Biddle W, Schmitt MA, Fisk JD. Impact of queuosine modification of endogenous E. coli tRNAs on sense codon reassignment. Front Mol Biosci 2022; 9:938114. [PMID: 36120552 PMCID: PMC9471426 DOI: 10.3389/fmolb.2022.938114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
The extent to which alteration of endogenous tRNA modifications may be exploited to improve genetic code expansion efforts has not been broadly investigated. Modifications of tRNAs are strongly conserved evolutionarily, but the vast majority of E. coli tRNA modifications are not essential. We identified queuosine (Q), a non-essential, hypermodified guanosine nucleoside found in position 34 of the anticodons of four E. coli tRNAs as a modification that could potentially be utilized to improve sense codon reassignment. One suggested purpose of queuosine modification is to reduce the preference of tRNAs with guanosine (G) at position 34 of the anticodon for decoding cytosine (C) ending codons over uridine (U) ending codons. We hypothesized that introduced orthogonal translation machinery with adenine (A) at position 34 would reassign U-ending codons more effectively in queuosine-deficient E. coli. We evaluated the ability of introduced orthogonal tRNAs with AUN anticodons to reassign three of the four U-ending codons normally decoded by Q34 endogenous tRNAs: histidine CAU, asparagine AAU, and aspartic acid GAU in the presence and absence of queuosine modification. We found that sense codon reassignment efficiencies in queuosine-deficient strains are slightly improved at Asn AAU, equivalent at His CAU, and less efficient at Asp GAU codons. Utilization of orthogonal pair-directed sense codon reassignment to evaluate competition events that do not occur in the standard genetic code suggests that tRNAs with inosine (I, 6-deaminated A) at position 34 compete much more favorably against G34 tRNAs than Q34 tRNAs. Continued evaluation of sense codon reassignment following targeted alterations to endogenous tRNA modifications has the potential to shed new light on the web of interactions that combine to preserve the fidelity of the genetic code as well as identify opportunities for exploitation in systems with expanded genetic codes.
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7
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Flemmich L, Moreno S, Micura R. Synthesis of O 6-alkylated preQ 1 derivatives. Beilstein J Org Chem 2021; 17:2295-2301. [PMID: 34621392 PMCID: PMC8450960 DOI: 10.3762/bjoc.17.147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022] Open
Abstract
A naturally occurring riboswitch can utilize 7-aminomethyl-O 6-methyl-7-deazaguanine (m6preQ1) as cofactor for methyl group transfer resulting in cytosine methylation. This recently discovered riboswitch-ribozyme activity opens new avenues for the development of RNA labeling tools based on tailored O 6-alkylated preQ1 derivatives. Here, we report a robust synthesis for this class of pyrrolo[2,3-d]pyrimidines starting from readily accessible N 2-pivaloyl-protected 6-chloro-7-cyano-7-deazaguanine. Substitution of the 6-chloro atom with the alcoholate of interest proceeds straightforward. The transformation of the 7-cyano substituent into the required aminomethyl group turned out to be challenging and was solved by a hydration reaction sequence on a well-soluble dimethoxytritylated precursor via in situ oxime formation. The synthetic path now provides a solid foundation to access O 6-alkylated 7-aminomethyl-7-deazaguanines for the development of RNA labeling tools based on the preQ1 class-I riboswitch scaffold.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry, Center for molecular Biosciences Innsbruck (CMBI), Innrain 80–82, 6020 Innsbruck, Austria
| | - Sarah Moreno
- Institute of Organic Chemistry, Center for molecular Biosciences Innsbruck (CMBI), Innrain 80–82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for molecular Biosciences Innsbruck (CMBI), Innrain 80–82, 6020 Innsbruck, Austria
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8
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Kulkarni S, Rubio MAT, Hegedűsová E, Ross RL, Limbach PA, Alfonzo JD, Paris Z. Preferential import of queuosine-modified tRNAs into Trypanosoma brucei mitochondrion is critical for organellar protein synthesis. Nucleic Acids Res 2021; 49:8247-8260. [PMID: 34244755 PMCID: PMC8373054 DOI: 10.1093/nar/gkab567] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/28/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are key players in protein synthesis. To be fully active, tRNAs undergo extensive post-transcriptional modifications, including queuosine (Q), a hypermodified 7-deaza-guanosine present in the anticodon of several tRNAs in bacteria and eukarya. Here, molecular and biochemical approaches revealed that in the protozoan parasite Trypanosoma brucei, Q-containing tRNAs have a preference for the U-ending codons for asparagine, aspartate, tyrosine and histidine, analogous to what has been described in other systems. However, since a lack of tRNA genes in T. brucei mitochondria makes it essential to import a complete set from the cytoplasm, we surprisingly found that Q-modified tRNAs are preferentially imported over their unmodified counterparts. In turn, their absence from mitochondria has a pronounced effect on organellar translation and affects function. Although Q modification in T. brucei is globally important for codon selection, it is more so for mitochondrial protein synthesis. These results provide a unique example of the combined regulatory effect of codon usage and wobble modifications on protein synthesis; all driven by tRNA intracellular transport dynamics.
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Affiliation(s)
- Sneha Kulkarni
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Mary Anne T Rubio
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Eva Hegedűsová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Robert L Ross
- Metabolomics Mass Spectrometry Core, Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Juan D Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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9
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Brenner AE, Muñoz-Leal S, Sachan M, Labruna MB, Raghavan R. Coxiella burnetii and Related Tick Endosymbionts Evolved from Pathogenic Ancestors. Genome Biol Evol 2021; 13:6278299. [PMID: 34009306 PMCID: PMC8290121 DOI: 10.1093/gbe/evab108] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Both symbiotic and pathogenic bacteria in the family Coxiellaceae cause morbidity and mortality in humans and animals. For instance, Coxiella-like endosymbionts (CLEs) improve the reproductive success of ticks—a major disease vector, while Coxiella burnetii causes human Q fever, and uncharacterized coxiellae infect both animals and humans. To better understand the evolution of pathogenesis and symbiosis in this group of intracellular bacteria, we sequenced the genome of a CLE present in the soft tick Ornithodoros amblus (CLEOA) and compared it to the genomes of other bacteria in the order Legionellales. Our analyses confirmed that CLEOA is more closely related to C. burnetii, the human pathogen, than to CLEs in hard ticks, and showed that most clades of CLEs contain both endosymbionts and pathogens, indicating that several CLE lineages have evolved independently from pathogenic Coxiella. We also determined that the last common ancestorof CLEOA and C. burnetii was equipped to infect macrophages and that even though horizontal gene transfer (HGT) contributed significantly to the evolution of C. burnetii, most acquisition events occurred primarily in ancestors predating the CLEOA–C. burnetii divergence. These discoveries clarify the evolution of C. burnetii, which previously was assumed to have emerged when an avirulent tick endosymbiont recently gained virulence factors via HGT. Finally, we identified several metabolic pathways, including heme biosynthesis, that are likely critical to the intracellular growth of the human pathogen but not the tick symbiont, and show that the use of heme analog is a promising approach to controlling C. burnetii infections.
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Affiliation(s)
- Amanda E Brenner
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, USA
| | - Sebastián Muñoz-Leal
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Ñuble, Chile
| | - Madhur Sachan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, USA
| | - Marcelo B Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, USA.,Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, USA
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10
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The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol 2021; 22:375-392. [PMID: 33658722 DOI: 10.1038/s41580-021-00342-0] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2021] [Indexed: 02/08/2023]
Abstract
Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.
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11
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Matyugina ES, Kochetkov SN, Khandazhinskaya AL. SYNTHESIS AND BIOLOGICAL ACTIVITY OF AZA- AND DEAZA-ANALOGS OF PURINE NUCLEOSIDES. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Alqasem MA, Fergus C, Southern JM, Connon SJ, Kelly VP. The eukaryotic tRNA-guanine transglycosylase enzyme inserts queuine into tRNA via a sequential bi-bi mechanism. Chem Commun (Camb) 2020; 56:3915-3918. [PMID: 32149287 DOI: 10.1039/c9cc09887a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eukaryotic tRNA-guanine transglycosylase (TGT) - an enzyme recently recognised to be of potential therapeutic importance - catalyses base-exchange of guanine for queuine at the wobble position of tRNAs associated with 4 amino acids via a distinct mechanism to that reported for its eubacterial homologue. The presence of queuine is unequivocally required as a trigger for reaction between the enzyme and tRNA and exhibits cooperativity not seen using guanine as a substrate.
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Affiliation(s)
- Mashael A Alqasem
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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13
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Jung J, Braun J, Czabany T, Nidetzky B. Unexpected NADPH Hydratase Activity in the Nitrile Reductase QueF from Escherichia coli. Chembiochem 2020; 21:1534-1543. [PMID: 31850614 PMCID: PMC7317782 DOI: 10.1002/cbic.201900679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Indexed: 11/09/2022]
Abstract
The nitrile reductase QueF catalyzes NADPH-dependent reduction of the nitrile group of preQ0 (7-cyano-7-deazaguanine) into the primary amine of preQ1 (7-aminomethyl-7-deazaguanine), a biologically unique reaction important in bacterial nucleoside biosynthesis. Here we have discovered that the QueF from Escherichia coli-its D197A and E89L variants in particular (apparent kcat ≈10-2 min-1 )-also catalyze the slow hydration of the C5=C6 double bond of the dihydronicotinamide moiety of NADPH. The enzymatically C6-hydrated NADPH is a 3.5:1 mixture of R and S forms and rearranges spontaneously through anomeric epimerization (β→α) and cyclization at the tetrahydronicotinamide C6 and the ribosyl O2. NADH and 1-methyl- or 1-benzyl-1,4-dihydronicotinamide are not substrates of the enzymatic hydration. Mutagenesis results support a QueF hydratase mechanism, in which Cys190-the essential catalytic nucleophile for nitrile reduction-acts as the general acid for protonation at the dihydronicotinamide C5 of NADPH. Thus, the NADPH hydration in the presence of QueF bears mechanistic resemblance to the C=C double bond hydration in natural hydratases.
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Affiliation(s)
- Jihye Jung
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Jan Braun
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria
| | - Tibor Czabany
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 10/12, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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14
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Ishiguro K, Arai T, Suzuki T. Depletion of S-adenosylmethionine impacts on ribosome biogenesis through hypomodification of a single rRNA methylation. Nucleic Acids Res 2019; 47:4226-4239. [PMID: 30799486 PMCID: PMC6486555 DOI: 10.1093/nar/gkz111] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 11/14/2022] Open
Abstract
S-adenosylmethionine (SAM) is an essential metabolite and a methyl group donor in all living organisms. The intracellular SAM concentration is tightly regulated, and depletion causes hypomethylation of substrates, growth defects and pathological consequences. In the emerging field of epitranscriptomics, SAM-dependent RNA methylations play a critical role in gene expression. Herein, we analyzed the methylation status of ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) in Escherichia coli Δmtn strain in which cellular SAM was down-regulated, and found hypomodification of several methylation sites, including 2′-O-methylation at position 2552 (Um2552) of 23S rRNA. We observed severe growth defect of the Δmtn strain with significant accumulation of 45S ribosomal precursor harboring 23S rRNA with hypomodified Um2552. Strikingly, the growth defect was partially restored by overexpression of rlmE encoding the SAM-dependent methyltransferase responsible for Um2552. Although SAM is involved not only in rRNA methylation but also in various cellular processes, effects on ribosome biogenesis contribute substantially to the observed defects on cell proliferation.
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Affiliation(s)
- Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taiga Arai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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15
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Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
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16
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Sekowska A, Ashida H, Danchin A. Revisiting the methionine salvage pathway and its paralogues. Microb Biotechnol 2019; 12:77-97. [PMID: 30306718 PMCID: PMC6302742 DOI: 10.1111/1751-7915.13324] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
Methionine is essential for life. Its chemistry makes it fragile in the presence of oxygen. Aerobic living organisms have selected a salvage pathway (the MSP) that uses dioxygen to regenerate methionine, associated to a ratchet-like step that prevents methionine back degradation. Here, we describe the variation on this theme, developed across the tree of life. Oxygen appeared long after life had developed on Earth. The canonical MSP evolved from ancestors that used both predecessors of ribulose bisphosphate carboxylase oxygenase (RuBisCO) and methanethiol in intermediate steps. We document how these likely promiscuous pathways were also used to metabolize the omnipresent by-products of S-adenosylmethionine radical enzymes as well as the aromatic and isoprene skeleton of quinone electron acceptors.
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Affiliation(s)
- Agnieszka Sekowska
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
| | - Hiroki Ashida
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
- Institute of Synthetic BiologyShenzhen Institutes of Advanced StudiesShenzhenChina
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17
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Jung J, Braun J, Czabany T, Nidetzky B. Interplay of nucleophilic catalysis with proton transfer in the nitrile reductase QueF from Escherichia coli. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02331j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proton relay through an active-site network of hydrogen bonds promotes enzymatic nitrile reduction to amine via a covalent thioimidate enzyme intermediate.
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Affiliation(s)
- Jihye Jung
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
| | - Jan Braun
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
| | - Tibor Czabany
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
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18
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Milani C, Casey E, Lugli GA, Moore R, Kaczorowska J, Feehily C, Mangifesta M, Mancabelli L, Duranti S, Turroni F, Bottacini F, Mahony J, Cotter PD, McAuliffe FM, van Sinderen D, Ventura M. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. MICROBIOME 2018; 6:145. [PMID: 30126456 PMCID: PMC6102903 DOI: 10.1186/s40168-018-0527-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/09/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a "gold standard" protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data. RESULTS Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes. CONCLUSIONS Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Eoghan Casey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Rebecca Moore
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Joanna Kaczorowska
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc, Moorepark Food Research Centre, Fermoy, Co., Cork, Cork, Ireland
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc, Moorepark Food Research Centre, Fermoy, Co., Cork, Cork, Ireland
| | - Fionnuala M McAuliffe
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe van Sinderen
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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19
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Grell TJ, Young AP, Drennan CL, Bandarian V. Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1. J Am Chem Soc 2018; 140:6842-6852. [PMID: 29792696 PMCID: PMC5994729 DOI: 10.1021/jacs.8b01493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 12/03/2022]
Abstract
TYW1 is a radical S-adenosyl-l-methionine (SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine to form the posttranscriptional modification, 4-demethylwyosine, in situ on transfer RNA (tRNA). Two mechanisms have been proposed for this transformation, with one of the possible mechanisms invoking a Schiff base intermediate formed between a conserved lysine residue and pyruvate. Utilizing a combination of mass spectrometry and X-ray crystallography, we have obtained evidence to support the formation of a Schiff base lysine adduct in TYW1. When 13C labeled pyruvate is used, the mass shift of the adduct matches that of the labeled pyruvate, indicating that pyruvate is the source of the adduct. Furthermore, a crystal structure of TYW1 provides visualization of the Schiff base lysine-pyruvate adduct, which is positioned directly adjacent to the auxiliary [4Fe-4S] cluster. The adduct coordinates the unique iron of the auxiliary cluster through the lysine nitrogen and a carboxylate oxygen, reminiscent of how the radical SAM [4Fe-4S] cluster is coordinated by SAM. The structure provides insight into the binding site for tRNA and further suggests how radical SAM chemistry can be combined with Schiff base chemistry for RNA modification.
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Affiliation(s)
- Tsehai
A. J. Grell
- Department
of Chemistry, Department of Biology, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony P. Young
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Department of Biology, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vahe Bandarian
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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20
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Jung Y, Goldman D. Role of RNA modifications in brain and behavior. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12444. [PMID: 29244246 PMCID: PMC6233296 DOI: 10.1111/gbb.12444] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Much progress in our understanding of RNA metabolism has been made since the first RNA nucleoside modification was identified in 1957. Many of these modifications are found in noncoding RNAs but recent interest has focused on coding RNAs. Here, we summarize current knowledge of cellular consequences of RNA modifications, with a special emphasis on neuropsychiatric disorders. We present evidence for the existence of an "RNA code," similar to the histone code, that fine-tunes gene expression in the nervous system by using combinations of different RNA modifications. Unlike the relatively stable genetic code, this combinatorial RNA epigenetic code, or epitranscriptome, may be dynamically reprogrammed as a cause or consequence of psychiatric disorders. We discuss potential mechanisms linking disregulation of the epitranscriptome with brain disorders and identify potential new avenues of research.
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Affiliation(s)
- Y. Jung
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - D. Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
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21
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Jung J, Nidetzky B. Evidence of a sequestered imine intermediate during reduction of nitrile to amine by the nitrile reductase QueF from Escherichia coli. J Biol Chem 2018; 293:3720-3733. [PMID: 29339556 DOI: 10.1074/jbc.m117.804583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/30/2017] [Indexed: 11/06/2022] Open
Abstract
In the biosynthesis of the tRNA-inserted nucleoside queuosine, the nitrile reductase QueF catalyzes conversion of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a biologically unique four-electron reduction of a nitrile to an amine. The QueF mechanism involves a covalent thioimide adduct between the enzyme and preQ0 that undergoes reduction to preQ1 in two NADPH-dependent steps, presumably via an imine intermediate. Protecting a labile imine from interception by water is fundamental to QueF catalysis for proper enzyme function. In the QueF from Escherichia coli, the conserved Glu89 and Phe228 residues together with a mobile structural element composing the catalytic Cys190 form a substrate-binding pocket that secludes the bound preQ0 completely from solvent. We show here that residue substitutions (E89A, E89L, and F228A) targeted at opening up the binding pocket weakened preQ0 binding at the preadduct stage by up to +10 kJ/mol and profoundly affected catalysis. Unlike wildtype enzyme, the QueF variants, including L191A and I192A, were no longer selective for preQ1 formation. The E89A, E89L, and F228A variants performed primarily (≥90%) a two-electron reduction of preQ0, releasing hydrolyzed imine (7-formyl-7-deazaguanine) as the product. The preQ0 reduction by L191A and I192A gave preQ1 and 7-formyl-7-deazaguanine at a 4:1 and 1:1 ratio, respectively. The proportion of 7-formyl-7-deazaguanine in total product increased with increasing substrate concentration, suggesting a role for preQ0 in a competitor-induced release of the imine intermediate. Collectively, these results provide direct evidence for the intermediacy of an imine in the QueF-catalyzed reaction. They reveal determinants of QueF structure required for imine sequestration and hence for a complete nitrile-to-amine conversion by this class of enzymes.
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Affiliation(s)
- Jihye Jung
- From the Austrian Centre of Industrial Biotechnology and.,the Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, A-8010 Graz, Austria
| | - Bernd Nidetzky
- From the Austrian Centre of Industrial Biotechnology and .,the Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, A-8010 Graz, Austria
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22
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Perlíková P, Hocek M. Pyrrolo[2,3-d]pyrimidine (7-deazapurine) as a privileged scaffold in design of antitumor and antiviral nucleosides. Med Res Rev 2017; 37:1429-1460. [PMID: 28834581 PMCID: PMC5656927 DOI: 10.1002/med.21465] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Accepted: 07/26/2017] [Indexed: 12/17/2022]
Abstract
7-Deazapurine (pyrrolo[2,3-d]pyrimidine) nucleosides are important analogues of biogenic purine nucleosides with diverse biological activities. Replacement of the N7 atom with a carbon atom makes the five-membered ring more electron rich and brings a possibility of attaching additional substituents at the C7 position. This often leads to derivatives with increased base-pairing in DNA or RNA or better binding to enzymes. Several types of 7-deazapurine nucleosides with potent cytostatic or cytotoxic effects have been identified. The most promising are 7-hetaryl-7-deazaadenosines, which are activated in cancer cells by phosphorylation and get incorporated both to RNA (causing inhibition of proteosynthesis) and to DNA (causing DNA damage). Mechanism of action of other types of cytostatic nucleosides, 6-hetaryl-7-deazapurine and thieno-fused deazapurine ribonucleosides, is not yet known. Many 7-deazaadenosine derivatives are potent inhibitors of adenosine kinases. Many types of sugar-modified derivatives of 7-deazapurine nucleosides are also strong antivirals. Most important are 2'-C-methylribo- or 2'-C-methyl-2'-fluororibonucleosides with anti-HCV activities (several compounds underwent clinical trials). Some underexplored areas of potential interest are also outlined.
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Affiliation(s)
- Pavla Perlíková
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesCZ‐16610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesCZ‐16610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueCZ‐12843Prague 2Czech Republic
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23
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Agris PF, Eruysal ER, Narendran A, Väre VYP, Vangaveti S, Ranganathan SV. Celebrating wobble decoding: Half a century and still much is new. RNA Biol 2017; 15:537-553. [PMID: 28812932 PMCID: PMC6103715 DOI: 10.1080/15476286.2017.1356562] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022] Open
Abstract
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.
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Affiliation(s)
- Paul F. Agris
- The RNA Institute, State University of New York, Albany, NY, USA
- Department of Biology, State University of New York, Albany, NY, USA
- Department of Chemistry, State University of New York, Albany, NY, USA
| | - Emily R. Eruysal
- Department of Biology, State University of New York, Albany, NY, USA
| | - Amithi Narendran
- Department of Biology, State University of New York, Albany, NY, USA
| | - Ville Y. P. Väre
- Department of Biology, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, State University of New York, Albany, NY, USA
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24
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Kandlinger F, Plach MG, Merkl R. AGeNNT: annotation of enzyme families by means of refined neighborhood networks. BMC Bioinformatics 2017; 18:274. [PMID: 28545394 PMCID: PMC5445326 DOI: 10.1186/s12859-017-1689-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/16/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Large enzyme families may contain functionally diverse members that give rise to clusters in a sequence similarity network (SSN). In prokaryotes, the genome neighborhood of a gene-product is indicative of its function and thus, a genome neighborhood network (GNN) deduced for an SSN provides strong clues to the specific function of enzymes constituting the different clusters. The Enzyme Function Initiative ( http://enzymefunction.org/ ) offers services that compute SSNs and GNNs. RESULTS We have implemented AGeNNT that utilizes these services, albeit with datasets purged with respect to unspecific protein functions and overrepresented species. AGeNNT generates refined GNNs (rGNNs) that consist of cluster-nodes representing the sequences under study and Pfam-nodes representing enzyme functions encoded in the respective neighborhoods. For cluster-nodes, AGeNNT summarizes the phylogenetic relationships of the contributing species and a statistic indicates how unique nodes and GNs are within this rGNN. Pfam-nodes are annotated with additional features like GO terms describing protein function. For edges, the coverage is given, which is the relative number of neighborhoods containing the considered enzyme function (Pfam-node). AGeNNT is available at https://github.com/kandlinf/agennt . CONCLUSIONS An rGNN is easier to interpret than a conventional GNN, which commonly contains proteins without enzymatic function and overly specific neighborhoods due to phylogenetic bias. The implemented filter routines and the statistic allow the user to identify those neighborhoods that are most indicative of a specific metabolic capacity. Thus, AGeNNT facilitates to distinguish and annotate functionally different members of enzyme families.
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Affiliation(s)
- Florian Kandlinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
- Faculty of Mathematics and Computer Science, University of Hagen, D-58084 Hagen, Germany
| | - Maximilian G. Plach
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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25
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Bednářová A, Hanna M, Durham I, VanCleave T, England A, Chaudhuri A, Krishnan N. Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. Front Mol Neurosci 2017; 10:135. [PMID: 28536502 PMCID: PMC5422465 DOI: 10.3389/fnmol.2017.00135] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are key molecules participating in protein synthesis. To augment their functionality they undergo extensive post-transcriptional modifications and, as such, are subject to regulation at multiple levels including transcription, transcript processing, localization and ribonucleoside base modification. Post-transcriptional enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and influences specific anticodon-codon interactions and regulates translation, its efficiency and fidelity. This phenomenon of nucleoside modification is most remarkable and results in a rich structural diversity of tRNA of which over 100 modified nucleosides have been characterized. Most often these hypermodified nucleosides are found in the wobble position of tRNAs, where they play a direct role in codon recognition as well as in maintaining translational efficiency and fidelity, etc. Several recent studies have pointed to a link between defects in tRNA modifications and human diseases including neurological disorders. Therefore, defects in tRNA modifications in humans need intensive characterization at the enzymatic and mechanistic level in order to pave the way to understand how lack of such modifications are associated with neurological disorders with the ultimate goal of gaining insights into therapeutic interventions.
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Affiliation(s)
- Andrea Bednářová
- Department of Biochemistry and Physiology, Institute of Entomology, Biology Centre, Academy of SciencesČeské Budějovice, Czechia.,Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Marley Hanna
- Molecular Biosciences Program, Arkansas State UniversityJonesboro, AR, USA
| | - Isabella Durham
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State UniversityMississippi State, MS, USA
| | - Tara VanCleave
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Alexis England
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | | | - Natraj Krishnan
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
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26
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Mohammad A, Bon Ramos A, Lee BWK, Cohen SW, Kiani MK, Iwata-Reuyl D, Stec B, Swairjo MA. Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide. Biomolecules 2017; 7:biom7010030. [PMID: 28300774 PMCID: PMC5372742 DOI: 10.3390/biom7010030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 01/07/2023] Open
Abstract
QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ₀) to 7-aminomethyl-7-deazaguanine (preQ₁) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF-catalyzed reaction includes formation of a covalent thioimide intermediate with a conserved active site cysteine that is prone to oxidation in vivo. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide formed between the catalytic Cys55 and a conserved Cys99 located near the active site. This structure is more symmetric than the substrate-bound structure and exhibits major rearrangement of the loops responsible for substrate binding. Mutation of Cys99 to Ala/Ser does not compromise enzyme activity, indicating that the disulfide does not play a catalytic role. Peroxide-induced inactivation of the wild-type enzyme is reversible with thioredoxin, while such inactivation of the Cys99Ala/Ser mutants is irreversible, consistent with protection of Cys55 from irreversible oxidation by disulfide formation with Cys99. Conservation of the cysteine pair, and the reported in vivo interaction of QueF with the thioredoxin-like hydroperoxide reductase AhpC in Escherichia coli suggest that regulation by the thioredoxin disulfide-thiol exchange system may constitute a general mechanism for protection of QueF from oxidative stress in vivo.
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Affiliation(s)
- Adeba Mohammad
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second Street, Pomona, CA 91766, USA.
| | - Adriana Bon Ramos
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA.
| | - Bobby W K Lee
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA.
| | - Spencer W Cohen
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA.
| | - Maryam K Kiani
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second Street, Pomona, CA 91766, USA.
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA.
| | - Boguslaw Stec
- Department of Chemistry and Biochemistry, San Diego State University 5500 Campanile Drive, San Diego, CA 92182, USA.
| | - Manal A Swairjo
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second Street, Pomona, CA 91766, USA.
- Department of Chemistry and Biochemistry, San Diego State University 5500 Campanile Drive, San Diego, CA 92182, USA.
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27
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Jung J, Czabany T, Wilding B, Klempier N, Nidetzky B. Kinetic Analysis and Probing with Substrate Analogues of the Reaction Pathway of the Nitrile Reductase QueF from Escherichia coli. J Biol Chem 2016; 291:25411-25426. [PMID: 27754868 DOI: 10.1074/jbc.m116.747014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/01/2016] [Indexed: 11/06/2022] Open
Abstract
The enzyme QueF catalyzes a four-electron reduction of a nitrile group into an amine, the only reaction of this kind known in biology. In nature, QueF converts 7-cyano-7-deazaguanine (preQ0) into 7-aminomethyl-7-deazaguanine (preQ1) for the biosynthesis of the tRNA-inserted nucleoside queuosine. The proposed QueF mechanism involves a covalent thioimide adduct between preQ0 and a cysteine nucleophile in the enzyme, and this adduct is subsequently converted into preQ1 in two NADPH-dependent reduction steps. Here, we show that the Escherichia coli QueF binds preQ0 in a strongly exothermic process (ΔH = -80.3 kJ/mol; -TΔS = 37.9 kJ/mol, Kd = 39 nm) whereby the thioimide adduct is formed with half-of-the-sites reactivity in the homodimeric enzyme. Both steps of preQ0 reduction involve transfer of the 4-pro-R-hydrogen from NADPH. They proceed about 4-7-fold more slowly than trapping of the enzyme-bound preQ0 as covalent thioimide (1.63 s-1) and are thus mainly rate-limiting for the enzyme's kcat (=0.12 s-1). Kinetic studies combined with simulation reveal a large primary deuterium kinetic isotope effect of 3.3 on the covalent thioimide reduction and a smaller kinetic isotope effect of 1.8 on the imine reduction to preQ1 7-Formyl-7-deazaguanine, a carbonyl analogue of the imine intermediate, was synthesized chemically and is shown to be recognized by QueF as weak ligand for binding (ΔH = -2.3 kJ/mol; -TΔS = -19.5 kJ/mol) but not as substrate for reduction or oxidation. A model of QueF substrate recognition and a catalytic pathway for the enzyme are proposed based on these data.
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Affiliation(s)
- Jihye Jung
- From the Austrian Centre of Industrial Biotechnology, Petersgasse 14.,the Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWIGraz, Petersgasse 12/1, and
| | - Tibor Czabany
- the Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWIGraz, Petersgasse 12/1, and
| | - Birgit Wilding
- From the Austrian Centre of Industrial Biotechnology, Petersgasse 14.,the Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Norbert Klempier
- the Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Bernd Nidetzky
- From the Austrian Centre of Industrial Biotechnology, Petersgasse 14, .,the Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWIGraz, Petersgasse 12/1, and
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28
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Antibacterial Activity of Juglone against Staphylococcus aureus: From Apparent to Proteomic. Int J Mol Sci 2016; 17:ijms17060965. [PMID: 27322260 PMCID: PMC4926497 DOI: 10.3390/ijms17060965] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/07/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
The proportion of foodborne disease caused by pathogenic microorganisms is rising worldwide, with staphylococcal food poisoning being one of the main causes of this increase. Juglone is a plant-derived 1,4-naphthoquinone with confirmed antibacterial and antitumor activities. However, the specific mechanism underlying its antibacterial activity against Staphylococcus aureus remains unclear. To elucidate the mechanism underlying its antibacterial activity, isobaric tags for relative and absolute quantitation methods of quantitative proteomics were applied for analysis of the 53 proteins that were differentially expressed after treatment with juglone. Combined with verification experiments, such as detection of changes in DNA and RNA content and quantification of oxidative damage, our results suggested that juglone effectively increased the protein expression of oxidoreductase and created a peroxidative environment within the cell, significantly reducing cell wall formation and increasing membrane permeability. We hypothesize that juglone binds to DNA and reduces DNA transcription and replication directly. This is the first study to adopt a proteomic approach to investigate the antibacterial mechanism of juglone.
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29
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Perche-Letuvée P, Molle T, Forouhar F, Mulliez E, Atta M. Wybutosine biosynthesis: structural and mechanistic overview. RNA Biol 2015; 11:1508-18. [PMID: 25629788 DOI: 10.4161/15476286.2014.992271] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Over the last 10 years, significant progress has been made in understanding the genetics, enzymology and structural components of the wybutosine (yW) biosynthetic pathway. These studies have played a key role in expanding our understanding of yW biosynthesis and have revealed unexpected evolutionary ties, which are presently being unraveled. The enzymes catalyzing the 5 steps of this pathway, from genetically encoded guanosine to wybutosine base, provide an ensemble of amazing reaction mechanisms that are to be discussed in this review article.
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30
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Abstract
This review focuses on the steps unique to methionine biosynthesis, namely the conversion of homoserine to methionine. The past decade has provided a wealth of information concerning the details of methionine metabolism and the review focuses on providing a comprehensive overview of the field, emphasizing more recent findings. Details of methionine biosynthesis are addressed along with key cellular aspects, including regulation, uptake, utilization, AdoMet, the methyl cycle, and growing evidence that inhibition of methionine biosynthesis occurs under stressful cellular conditions. The first unique step in methionine biosynthesis is catalyzed by the metA gene product, homoserine transsuccinylase (HTS, or homoserine O-succinyltransferase). Recent experiments suggest that transcription of these genes is indeed regulated by MetJ, although the repressor-binding sites have not yet been verified. Methionine also serves as the precursor of S-adenosylmethionine, which is an essential molecule employed in numerous biological processes. S-adenosylhomocysteine is produced as a consequence of the numerous AdoMet-dependent methyl transfer reactions that occur within the cell. In E. coli and Salmonella, this molecule is recycled in two discrete steps to complete the methyl cycle. Cultures challenged by oxidative stress appear to experience a growth limitation that depends on methionine levels. E. coli that are deficient for the manganese and iron superoxide dismutases (the sodA and sodB gene products, respectively) require the addition of methionine or cysteine for aerobic growth. Modulation of methionine levels in response to stressful conditions further increases the complexity of its regulation.
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31
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Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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32
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Abstract
Carbon–sulfur biological chemistry encompasses a fascinating area of biochemistry and medicinal chemistry and includes the roles that methionine and S-adenosyl-l-methionine play in cells as well as the chemistry of intracellular thiols such as glutathione. This article, based on the 2014 Bernard Belleau Award lecture, provides an overview of some of the key investigations that were undertaken in this area from a bioorganic perspective. The research has ameliorated our fundamental knowledge of several of the enzymes utilizing these sulfur-containing molecules, has led to the development of several novel 19F biophysical probes, and has explored some of the medicinal chemistry associated with these processes.
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Affiliation(s)
- John F. Honek
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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33
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Qiu H, Price DC, Yang EC, Yoon HS, Bhattacharya D. Evidence of ancient genome reduction in red algae (Rhodophyta). JOURNAL OF PHYCOLOGY 2015; 51:624-36. [PMID: 26986787 DOI: 10.1111/jpy.12294] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/30/2015] [Indexed: 05/27/2023]
Abstract
Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.
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Affiliation(s)
- Huan Qiu
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Dana C Price
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Eun Chan Yang
- Marine Ecosystem Research Division, Korea Institute of Ocean Sciences & Technology, 787 Haeanro, Ansan, 426-744, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
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34
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Sawhney B, Chopra K, Misra R, Ranjan A. Identification of Plasmodium falciparum apicoplast-targeted tRNA-guanine transglycosylase and its potential inhibitors using comparative genomics, molecular modelling, docking and simulation studies. J Biomol Struct Dyn 2015; 33:2404-20. [PMID: 25869381 DOI: 10.1080/07391102.2015.1040074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
tRNA modifications play an important role in the proper folding of tRNA and thereby determine its functionality as an adaptor molecule. Notwithstanding the centrality of this basic process in translation, a major gap in the genomics of Plasmodium falciparum is unambiguous identification of enzymes catalysing the various tRNA modifications. In this study, tRNA-modifying enzymes of P. falciparum were annotated using homology-based approach. Based on the presence of these identified enzymes, the modifications were compared with those of prokaryotic and eukaryotic organisms. Through sequence comparison and phylogenetic analysis, we have identified P. falciparum apicoplast tRNA-guanine 34 transglycosylase (TGT, EC: 2.4.2.29), which shows evidence of its prokaryotic origin. The docking analysis of the modelled TGT structures revealed that binding of quinazolinone derivatives is more favourable with P. falciparum apicoplast TGT as compared to human TGT. Molecular dynamic simulation and molecular mechanics/generalized Born surface area analysis of the complex confirmed the greater binding affinity of the ligand in the binding pocket of P. falciparum TGT protein. Further, evolutionary patterning analysis identified the amino acids of P. falciparum apicoplast TGT that are under purifying selection pressure and hence can be good inhibitor-targeting sites. Based on these computational studies, we suggest that P. falciparum apicoplast tRNA-guanine 34 transglycosylase can be a promising drug target.
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Affiliation(s)
- Bhavik Sawhney
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,b Graduate School , Manipal University , Manipal, Karnataka 576104 , India
| | - Kriti Chopra
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,c Department of Biotechnology and Bioinformatics, School of Life Sciences , University of Hyderabad , Gachibowli, Hyderabad , Telangana 500046 , India.,d National Centre for Cell Science, NCCS Complex , University of Pune Campus , Ganeshkhind, Pune , Maharashtra 411007 , India
| | - Rohan Misra
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India.,b Graduate School , Manipal University , Manipal, Karnataka 576104 , India
| | - Akash Ranjan
- a Computational and Functional Genomics Group , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500001 , India
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35
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Wu MC, Lowe PT, Robinson CJ, Vincent HA, Dixon N, Leigh J, Micklefield J. Rational Re-engineering of a Transcriptional Silencing PreQ1 Riboswitch. J Am Chem Soc 2015; 137:9015-21. [PMID: 26106809 DOI: 10.1021/jacs.5b03405] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Re-engineered riboswitches that no longer respond to cellular metabolites, but that instead can be controlled by synthetic molecules, are potentially useful gene regulatory tools for use in synthetic biology and biotechnology fields. Previously, extensive genetic selection and screening approaches were employed to re-engineer a natural adenine riboswitch to create orthogonal ON-switches, enabling translational control of target gene expression in response to synthetic ligands. Here, we describe how a rational targeted approach was used to re-engineer the PreQ1 riboswitch from Bacillus subtilis into an orthogonal OFF-switch. In this case, the evaluation of just six synthetic compounds with seven riboswitch mutants led to the identification of an orthogonal riboswitch-ligand pairing that effectively repressed the transcription of selected genes in B. subtilis. The streamlining of the re-engineering approach, and its extension to a second class of riboswitches, provides a methodological platform for the creation of new orthogonal regulatory components for biotechnological applications including gene functional analysis and antimicrobial target validation and screening.
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Affiliation(s)
- Ming-Cheng Wu
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Phillip T Lowe
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Helen A Vincent
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Neil Dixon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - James Leigh
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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36
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Ribeiro AJM, Yang L, Ramos MJ, Fernandes PA, Liang ZX, Hirao H. Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00528] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- António J. M. Ribeiro
- UCIBIO,
REQUIMTE, Departamento de Quı́mica e Bioquı́mica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo
Alegre s/n, 4169-007 Porto, Portugal
| | - Lifeng Yang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Maria J. Ramos
- UCIBIO,
REQUIMTE, Departamento de Quı́mica e Bioquı́mica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo
Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO,
REQUIMTE, Departamento de Quı́mica e Bioquı́mica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo
Alegre s/n, 4169-007 Porto, Portugal
| | - Zhao-Xun Liang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Hajime Hirao
- Division
of Chemistry and Biological Chemistry, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
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37
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Fergus C, Barnes D, Alqasem MA, Kelly VP. The queuine micronutrient: charting a course from microbe to man. Nutrients 2015; 7:2897-929. [PMID: 25884661 PMCID: PMC4425180 DOI: 10.3390/nu7042897] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/25/2015] [Indexed: 12/24/2022] Open
Abstract
Micronutrients from the diet and gut microbiota are essential to human health and wellbeing. Arguably, among the most intriguing and enigmatic of these micronutrients is queuine, an elaborate 7-deazaguanine derivative made exclusively by eubacteria and salvaged by animal, plant and fungal species. In eubacteria and eukaryotes, queuine is found as the sugar nucleotide queuosine within the anticodon loop of transfer RNA isoacceptors for the amino acids tyrosine, asparagine, aspartic acid and histidine. The physiological requirement for the ancient queuine molecule and queuosine modified transfer RNA has been the subject of varied scientific interrogations for over four decades, establishing relationships to development, proliferation, metabolism, cancer, and tyrosine biosynthesis in eukaryotes and to invasion and proliferation in pathogenic bacteria, in addition to ribosomal frameshifting in viruses. These varied effects may be rationalized by an important, if ill-defined, contribution to protein translation or may manifest from other presently unidentified mechanisms. This article will examine the current understanding of queuine uptake, tRNA incorporation and salvage by eukaryotic organisms and consider some of the physiological consequence arising from deficiency in this elusive and lesser-recognized micronutrient.
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Affiliation(s)
- Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Dominic Barnes
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Mashael A Alqasem
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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38
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Barandun LJ, Ehrmann FR, Zimmerli D, Immekus F, Giroud M, Grünenfelder C, Schweizer WB, Bernet B, Betz M, Heine A, Klebe G, Diederich F. Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appendedlin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT). Chemistry 2014; 21:126-35. [DOI: 10.1002/chem.201405764] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 11/09/2022]
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Boschi-Muller S, Motorin Y. Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modification. BIOCHEMISTRY (MOSCOW) 2014; 78:1392-404. [PMID: 24490730 DOI: 10.1134/s0006297913130026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Modified nucleotides are universally conserved in all living kingdoms and are present in almost all types of cellular RNAs, including tRNA, rRNA, sn(sno)RNA, and mRNA and in recently discovered regulatory RNAs. Altogether, over 110 chemically distinct RNA modifications have been characterized and localized in RNA by various analytical methods. However, this impressive list of known modified nucleotides is certainly incomplete, mainly due to difficulties in identification and characterization of these particular residues in low abundance cellular RNAs. In DNA, modified residues are formed by both enzymatic reactions (like DNA methylations, for example) and by spontaneous chemical reactions resulting from oxidative damage. In contrast, all modified residues characterized in cellular RNA molecules are formed by specific action of dedicated RNA-modification enzymes, which recognize their RNA substrate with high specificity. These RNA-modification enzymes display a great diversity in terms of the chemical reaction and use various low molecular weight cofactors (or co-substrates) in enzymatic catalysis. Depending on the nature of the target base and of the co-substrate, precise chemical mechanisms are used for appropriate activation of the base and the co-substrate in the enzyme active site. In this review, we give an extended summary of the enzymatic mechanisms involved in formation of different methylated nucleotides in RNA, as well as pseudouridine residues, which are almost universally conserved in all living organisms. Other interesting mechanisms include thiolation of uridine residues by ThiI and the reaction of guanine exchange catalyzed by TGT. The latter implies the reversible cleavage of the N-glycosidic bond in order to replace the initially encoded guanine by an aza-guanosine base. Despite the extensive studies of RNA modification and RNA-modification machinery during the last 20 years, our knowledge on the exact chemical steps involved in catalysis of RNA modification remains very limited. Recent discoveries of radical mechanisms involved in base methylation clearly demonstrate that numerous possibilities are used in Nature for these difficult reactions. Future studies are certainly required for better understanding of the enzymatic mechanisms of RNA modification, and this knowledge is crucial not only for basic research, but also for development of new therapeutic molecules.
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Affiliation(s)
- S Boschi-Muller
- Université de Lorraine, Laboratoire IMoPA, UMR 7365 CNRS-UL, Faculté de Médecine de Nancy, BP 184, Vandoeuvre les Nancy, 54505, France.
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Levic J, Micura R. Syntheses of (15)N-labeled pre-queuosine nucleobase derivatives. Beilstein J Org Chem 2014; 10:1914-8. [PMID: 25246950 PMCID: PMC4168690 DOI: 10.3762/bjoc.10.199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/14/2014] [Indexed: 01/21/2023] Open
Abstract
Pre-queuosine or queuine (preQ1) is a guanine derivative that is involved in the biosynthetic pathway of the hypermodified tRNA nucleoside queuosine (Que). The core structure of preQ1 is represented by 7-(aminomethyl)-7-deazaguanine (preQ1 base). Here, we report the synthesis of three preQ1 base derivatives with complementary (15)N-labeling patterns, utilizing [(15)N]-KCN, [(15)N]-phthalimide, and [(15)N3]-guanidine as cost-affordable (15)N sources. Such derivatives are required to explore the binding process of the preQ1 base to RNA targets using advanced NMR spectroscopic methods. PreQ1 base specifically binds to bacterial mRNA domains and thereby regulates genes that are required for queuosine biosynthesis.
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Affiliation(s)
- Jasmin Levic
- Institute of Organic Chemistry, University of Innsbruck and Center for Molecular Biosciences Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, University of Innsbruck and Center for Molecular Biosciences Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
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41
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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Eichhorn CD, Kang M, Feigon J. Structure and function of preQ 1 riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:939-950. [PMID: 24798077 DOI: 10.1016/j.bbagrm.2014.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/22/2014] [Accepted: 04/25/2014] [Indexed: 12/17/2022]
Abstract
PreQ1 riboswitches help regulate the biosynthesis and transport of preQ1 (7-aminomethyl-7-deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of preQ1 riboswitches have been identified (preQ1-I and preQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon preQ1 binding, each of which has distinct unusual features and modes of preQ1 recognition. These features include an unusually long loop 2 in preQ1-I pseudoknots and an embedded hairpin in loop 3 in preQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, dynamics, and applications to biotechnology of preQ1 riboswitches. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Mijeong Kang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
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43
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Björk GR, Hagervall TG. Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus 2014; 6. [PMID: 26442937 DOI: 10.1128/ecosalplus.esp-0007-2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 06/05/2023]
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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Affiliation(s)
- Glenn R Björk
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Tord G Hagervall
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
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44
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Liberman JA, Bogue JT, Jenkins JL, Salim M, Wedekind JE. ITC analysis of ligand binding to preQ₁ riboswitches. Methods Enzymol 2014; 549:435-50. [PMID: 25432759 DOI: 10.1016/b978-0-12-801122-5.00018-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Riboswitches regulate genes by binding to small-molecule effectors. Isothermal titration calorimetry (ITC) provides a label-free method to quantify the equilibrium association constant, K(A), of a riboswitch interaction with its cognate ligand. In addition to probing affinity and specific chemical contributions that contribute to binding, ITC can be used to measure the thermodynamic parameters of an interaction (ΔG, ΔH, and ΔS), in addition to the binding stoichiometry (N). Here, we describe methods developed to measure the binding affinity of various preQ1 riboswitch classes for the pyrrolopyrimidine effector, preQ1. Example isotherms are provided along with a review of various preQ1-II (class 2) riboswitch mutants that were interrogated by ITC to quantify the energetic contributions of specific interactions visualized in the crystal structure. Protocols for ITC are provided in sufficient detail that the reader can reproduce experiments independently, or develop derivative methods suitable for analyzing novel riboswitch-ligand binding interactions.
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Affiliation(s)
- Joseph A Liberman
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jarrod T Bogue
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jermaine L Jenkins
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Structural Biology & Biophysics Facility, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mohammad Salim
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Structural Biology & Biophysics Facility, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
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45
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Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. ACTA ACUST UNITED AC 2013; 21:174-85. [PMID: 24315934 DOI: 10.1016/j.chembiol.2013.10.015] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 12/15/2022]
Abstract
Nature combines existing biochemical building blocks, at times with subtlety of purpose. RNA modifications are a prime example of this, where standard RNA nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. The result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. Here, we highlight several modifications that, because of their chemical intricacy, rely on seemingly unrelated pathways to provide cofactors for their synthesis. Besides their immediate role in affecting RNA function, modifications may act as sensors and transducers of information that connect a cell's metabolic state to its translational output, carefully orchestrating a delicate balance between metabolic rate and protein synthesis at a system's level.
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46
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Barandun LJ, Immekus F, Kohler PC, Ritschel T, Heine A, Orlando P, Klebe G, Diederich F. High-affinity inhibitors ofZymomonas mobilistRNA–guanine transglycosylase through convergent optimization. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1798-807. [DOI: 10.1107/s0907444913014509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/26/2013] [Indexed: 11/11/2022]
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Yu CH, Luo J, Iwata-Reuyl D, Olsthoorn RCL. Exploiting preQ(1) riboswitches to regulate ribosomal frameshifting. ACS Chem Biol 2013; 8:733-40. [PMID: 23327288 DOI: 10.1021/cb300629b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Knowing the molecular details of the interaction between riboswitch aptamers and their corresponding metabolites is important to understand gene expression. Here we report on a novel in vitro assay to study preQ(1) riboswitch aptamers upon binding of 7-aminomethyl-7-deazaguanine (preQ(1)). The assay is based on the ability of the preQ(1) aptamer to fold, upon ligand binding, into a pseudoknotted structure that is capable of stimulating -1 ribosomal frameshifting (-1 FS). Aptamers from three different species were found to induce between 7% and 20% of -1 FS in response to increasing preQ(1) levels, whereas preQ(1) analogues were 100-1000-fold less efficient. In depth mutational analysis of the Fusobacterium nucleatum aptamer recapitulates most of the structural details previously identified for preQ(1) aptamers from other bacteria by crystallography and/or NMR spectroscopy. In addition to providing insight into the role of individual nucleotides of the preQ(1) riboswitch aptamer in ligand binding, the presented system provides a valuable tool to screen small molecules against bacterial riboswitches in a eukaryotic background.
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Affiliation(s)
| | | | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, Oregon 97201,
United States
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48
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Gerber HD, Klebe G. Concise and efficient syntheses of preQ1 base, Q base, and (ent)-Q base. Org Biomol Chem 2013; 10:8660-8. [PMID: 23032613 DOI: 10.1039/c2ob26387d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To thoroughly study the functional role of prokaryotic t-RNA-guanine-transglycosylases which are essential in the pathogenesis of shigellosis, novel efficient, high-yielding synthetic approaches for preQ(1) base, Q base, as well as for (ent)-Q base mainly employing cheap and readily available starting materials have been developed. Q base as well as (ent)-Q base are accessible starting from preQ(1) base via nucleophilic substitution reactions with appropriately decorated halocyclopentenyl synthons, prior to that prepared from naturally occurring carbohydrates.
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Affiliation(s)
- Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie der Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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49
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Marchetti M, Capela D, Poincloux R, Benmeradi N, Auriac MC, Le Ru A, Maridonneau-Parini I, Batut J, Masson-Boivin C. Queuosine biosynthesis is required for sinorhizobium meliloti-induced cytoskeletal modifications on HeLa Cells and symbiosis with Medicago truncatula. PLoS One 2013; 8:e56043. [PMID: 23409119 PMCID: PMC3568095 DOI: 10.1371/journal.pone.0056043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 01/08/2013] [Indexed: 11/18/2022] Open
Abstract
Rhizobia are symbiotic soil bacteria able to intracellularly colonize legume nodule cells and form nitrogen-fixing symbiosomes therein. How the plant cell cytoskeleton reorganizes in response to rhizobium colonization has remained poorly understood especially because of the lack of an in vitro infection assay. Here, we report on the use of the heterologous HeLa cell model to experimentally tackle this question. We observed that the model rhizobium Sinorhizobium meliloti, and other rhizobia as well, were able to trigger a major reorganization of actin cytoskeleton of cultured HeLa cells in vitro. Cell deformation was associated with an inhibition of the three major small RhoGTPases Cdc42, RhoA and Rac1. Bacterial entry, cytoskeleton rearrangements and modulation of RhoGTPase activity required an intact S. meliloti biosynthetic pathway for queuosine, a hypermodifed nucleoside regulating protein translation through tRNA, and possibly mRNA, modification. We showed that an intact bacterial queuosine biosynthetic pathway was also required for effective nitrogen-fixing symbiosis of S. meliloti with its host plant Medicago truncatula, thus indicating that one or several key symbiotic functions of S. meliloti are under queuosine control. We discuss whether the symbiotic defect of que mutants may originate, at least in part, from an altered capacity to modify plant cell actin cytoskeleton.
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Affiliation(s)
- Marta Marchetti
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Delphine Capela
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Renaud Poincloux
- CNRS-IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS (Université Paul Sabatier), IPBS, Toulouse, France
| | - Nacer Benmeradi
- Institut de Biologie Cellulaire et de Génétique IBCG CNRS, Toulouse, France
| | - Marie-Christine Auriac
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Aurélie Le Ru
- Plateforme de Microscopie FRBT - Centre de Biologie du Développement, Toulouse, France
| | - Isabelle Maridonneau-Parini
- CNRS-IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS (Université Paul Sabatier), IPBS, Toulouse, France
| | - Jacques Batut
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
- * E-mail:
| | - Catherine Masson-Boivin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
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50
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El Yacoubi B, Bailly M, de Crécy-Lagard V. Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs. Annu Rev Genet 2012; 46:69-95. [DOI: 10.1146/annurev-genet-110711-155641] [Citation(s) in RCA: 380] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Marc Bailly
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
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