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Moriguchi K, Zoolkefli FIRM, Abe M, Kiyokawa K, Yamamoto S, Suzuki K. Targeting Antibiotic Resistance Genes Is a Better Approach to Block Acquisition of Antibiotic Resistance Than Blocking Conjugal Transfer by Recipient Cells: A Genome-Wide Screening in Escherichia coli. Front Microbiol 2020; 10:2939. [PMID: 31969865 PMCID: PMC6960129 DOI: 10.3389/fmicb.2019.02939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 11/21/2022] Open
Abstract
The conjugal transfer is a major driving force in the spread of antibiotic resistance genes. Nevertheless, an effective approach has not yet been developed to target conjugal transfer to prevent the acquisition of antibiotic resistance by this mechanism. This study aimed to identify potential targets for plasmid transfer blockade by isolating mutants defective in the completion of the acquisition of antibiotic resistance via conjugal transfer. We performed genome-wide screening by combining an IncP1α-type broad host range plasmid conjugation system with a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection; 3884 mutants). We followed a six-step screening procedure to identify the mutants showing conjugation deficiency precisely. No mutants defective in the conjugal transfer were isolated, strongly suggesting that E. coli cannot escape from being a recipient organism for P1α plasmid transfer. However, several mutants with low viability were identified, as well as mutants defective in establishing resistance to chloramphenicol, which was used for transconjugant selection. These results suggest that developing drugs capable of inhibiting the establishment of antibiotic resistance is a better approach than attempting to prevent the conjugal transfer to block the spread of antibiotic resistance genes. Our screening system based on the IncP1α-type plasmid transfer can be extended to isolation of target genes for other drugs. This study could be the foundation for further research to understand its underlying molecular mechanism through functional analysis of the identified genes.
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Affiliation(s)
- Kazuki Moriguchi
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | | | - Masanobu Abe
- Division for Health Service Promotion, University of Tokyo, Tokyo, Japan
| | - Kazuya Kiyokawa
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Shinji Yamamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Katsunori Suzuki
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
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2
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High temperatures promote cell-to-cell plasmid transformation in Escherichia coli. Biochem Biophys Res Commun 2019; 515:196-200. [PMID: 31138439 DOI: 10.1016/j.bbrc.2019.05.134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 05/21/2019] [Indexed: 01/09/2023]
Abstract
Bacteria continuously change their genetic characteristics to adapt to the changing environment by means of horizontal gene transfer. Although three conventional mechanisms of horizontal gene transfer are well known (transformation, transduction, and conjugation), new variations of these mechanisms have also been described. We previously reported that DNase-sensitive cell-to-cell transfer of non-conjugative plasmids, termed as "cell-to-cell transformation," occurs between the cells of two Escherichia coli strains in a co-culture. In this study, to further investigate the mechanism of cell-to-cell transformation, we constructed a new experimental system for cell-to-cell transformation. By using this system, we found that high temperatures of approximately 41ºC-45 °C significantly promote cell-to-cell plasmid transformation. This transfer was much more frequent in solid-air biofilms than in liquid culture, suggesting an importance of biofilm environment. Plasmid transfer frequency reached over 10-7/cell under the optimal strain-plasmid combination and conditions tested. DNase sensitivity test and plasmid isolation from the transformants confirmed the horizontal transfer of full-length plasmids via transformation. Comparative natural transformation experiments, which used similar strains and plasmids under equivalent culture conditions, revealed that cell-to-cell transformation occurs approximately 103 times more frequently than natural transformation, indicating the uniqueness and effectiveness of the cell-to-cell transformation mechanism. As temperatures of approximately 41ºC-45 °C are common in the avian intestines and under some other environmental situations, the phenomenon demonstrated here can occur efficiently in such locations. To the best of our knowledge, this is the first study to demonstrate the enhancing effect of high temperatures on cell-to-cell plasmid transformation in E. coli.
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3
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Oerum S, Catala M, Atdjian C, Brachet F, Ponchon L, Barraud P, Iannazzo L, Droogmans L, Braud E, Ethève-Quelquejeu M, Tisné C. Bisubstrate analogues as structural tools to investigate m 6A methyltransferase active sites. RNA Biol 2019; 16:798-808. [PMID: 30879411 PMCID: PMC6546350 DOI: 10.1080/15476286.2019.1589360] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m6A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m6A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m6A RNA MTases. The same analogues cause changes in the melting temperature of the m1A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m6A RNA MTase inhibition should aim to increase selectivity, as well as affinity.
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Affiliation(s)
- Stephanie Oerum
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Marjorie Catala
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Franck Brachet
- Institut de Biologie Physico-Chimique, IBPC, CNRS, Paris, France
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris, France
| | - Pierre Barraud
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), Gosselies, Belgium
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Carine Tisné
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
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4
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Guerrero Montero I, Dolata KM, Schlüter R, Malherbe G, Sievers S, Zühlke D, Sura T, Dave E, Riedel K, Robinson C. Comparative proteome analysis in an Escherichia coli CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein. Microb Cell Fact 2019; 18:19. [PMID: 30696436 PMCID: PMC6350376 DOI: 10.1186/s12934-019-1071-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/23/2019] [Indexed: 01/15/2023] Open
Abstract
Background The Twin-arginine translocation (Tat) pathway of Escherichia coli has great potential for the export of biopharmaceuticals to the periplasm due to its ability to transport folded proteins, and its proofreading mechanism that allows correctly folded proteins to translocate. Coupling the Tat-dependent protein secretion with the formation of disulfide bonds in the cytoplasm of E. coli CyDisCo provides a powerful platform for the production of industrially challenging proteins. In this study, we investigated the effects on the E. coli cells of exporting a folded substrate (scFv) to the periplasm using a Tat signal peptide, and the effects of expressing an export-incompetent misfolded variant. Results Cell growth is decreased when either the correctly folded or misfolded scFv is expressed with a Tat signal peptide. However, only the production of misfolded scFv leads to cell aggregation and formation of inclusion bodies. The comprehensive proteomic analysis revealed that both conditions, recombinant protein overexpression and misfolded protein accumulation, lead to downregulation of membrane transporters responsible for protein folding and insertion into the membrane while upregulating the production of chaperones and proteases involved in removing aggregates. These conditions also differentially affect the production of transcription factors and proteins involved in DNA replication. The most distinct stress response observed was the cell aggregation caused by elevated levels of antigen 43. Finally, Tat-dependent secretion causes an increase in tatA expression only after induction of protein expression, while the subsequent post-induction analysis revealed lower tatA and tatB expression levels, which correlate with lowered TatA and TatB protein abundance. Conclusions The study identified characteristic changes occurring as a result of the production of both a folded and a misfolded protein, but also highlights an exclusive unfolded stress response. Countering and compensating for these changes may result in higher yields of pharmaceutically relevant proteins exported to the periplasm. Electronic supplementary material The online version of this article (10.1186/s12934-019-1071-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Katarzyna Magdalena Dolata
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487, Greifswald, Germany
| | - Gilles Malherbe
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.,UCB Celltech, 216 Bath Road, Slough, SL1 3WE, UK
| | - Susanne Sievers
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Thomas Sura
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Emma Dave
- UCB Celltech, 216 Bath Road, Slough, SL1 3WE, UK
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Colin Robinson
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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5
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Hasegawa H, Suzuki E, Maeda S. Horizontal Plasmid Transfer by Transformation in Escherichia coli: Environmental Factors and Possible Mechanisms. Front Microbiol 2018; 9:2365. [PMID: 30337917 PMCID: PMC6180151 DOI: 10.3389/fmicb.2018.02365] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/14/2018] [Indexed: 12/16/2022] Open
Abstract
Transformation is one mode of horizontal gene transfer (HGT) in bacteria, wherein extracellular naked DNA is taken up by cells that have developed genetic competence. Sensitivity to DNase, which degrades naked DNA, is the key to distinguishing transformation from the DNase-resistant HGT mechanisms. In general, Escherichia coli is not believed to be naturally transformable; it develops high competence only under artificial conditions, including exposure to high Ca2+ concentrations. However, E. coli can reportedly express modest competence under certain conditions that are feasible in natural environments outside laboratory. In addition, recent data suggest that environmental factors influence multiple routes of transformation. In this mini review, we (1) summarize our studies on transformation-based HGT using E. coli experimental systems and (2) discuss the possible occurrence of transformation via multiple mechanisms in the environment and its possible impact on the spread of antibiotic resistance genes.
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Affiliation(s)
| | | | - Sumio Maeda
- Graduate School of Humanities and Sciences, Nara Women’s University, Nara, Japan
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6
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Sun D. Pull in and Push Out: Mechanisms of Horizontal Gene Transfer in Bacteria. Front Microbiol 2018; 9:2154. [PMID: 30237794 PMCID: PMC6135910 DOI: 10.3389/fmicb.2018.02154] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/22/2018] [Indexed: 01/06/2023] Open
Abstract
Horizontal gene transfer (HGT) plays an important role in bacterial evolution. It is well accepted that DNA is pulled/pushed into recipient cells by conserved membrane-associated DNA transport systems, which allow the entry of only single-stranded DNA (ssDNA). However, recent studies have uncovered a new type of natural bacterial transformation in which double-stranded DNA (dsDNA) is taken up into the cytoplasm, thus complementing the existing methods of DNA transfer among bacteria. Regulated by the stationary-phase regulators RpoS and cAMP receptor protein (CRP), Escherichia coli establishes competence for natural transformation with dsDNA, which occurs in agar plates. To pass across the outer membrane, a putative channel, which may compete for the substrate with the porin OmpA, may mediate the transfer of exogenous dsDNA into the cell. To pass across the inner membrane, dsDNA may be bound to the periplasmic protein YdcS, which delivers it into the inner membrane channel formed by YdcV. The discovery of cell-to-cell contact-dependent plasmid transformation implies the presence of additional mechanism(s) of transformation. This review will summarize the current knowledge about mechanisms of HGT with an emphasis on recent progresses regarding non-canonical mechanisms of natural transformation. Fully understanding the mechanisms of HGT will provide a foundation for monitoring and controlling multidrug resistance.
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Affiliation(s)
- Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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7
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Sugiura C, Miyaue S, Shibata Y, Matsumoto A, Maeda S. Bacteriophage P1 vir-induced cell-to-cell plasmid transformation in Escherichia coli. AIMS Microbiol 2017; 3:784-797. [PMID: 31294189 PMCID: PMC6604958 DOI: 10.3934/microbiol.2017.4.784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/28/2017] [Indexed: 01/14/2023] Open
Abstract
Bacteria undergo horizontal gene transfer via various mechanisms. We recently reported that cell-to-cell transfer of nonconjugative plasmids occurs between strains of Escherichia coli in co-cultures, and that a specific strain (CAG18439) causes frequent plasmid transfer involving a DNase-sensitive mechanism, which we termed "cell-to-cell transformation". Here we found that CAG18439 is a type of P1 bacteriophage lysogen that continuously releases phages. We tested the ability of P1vir bacteriophage to induce horizontal plasmid transfer and demonstrated that such a horizontal plasmid transfer was caused by adding culture supernatants of P1vir-infected cells harboring plasmids to other plasmid-free cells. This plasmid transfer system also reproduced the major features of plasmid transfer involving CAG18439, suggesting that P1vir-induced plasmid transfer is equivalent or very similar to plasmid transfer involving CAG18439. We further revealed that approximately two-thirds of the P1vir-induced plasmid transfer was DNase-sensitive, but that complete abolition of plasmid transfer was observed when proteins were denatured or removed, despite the presence or absence of DNase. Therefore, we concluded that P1vir-induced plasmid transfer is largely due to the occurrence of cell-to-cell transformation, which involves the assistance of some proteinaceous factor, and partly due to the occurrence of plasmid transduction, which is mediated by phage virions. This is the first demonstration of the P1-phage-induced cell-to-cell transformation.
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Affiliation(s)
- Chiaki Sugiura
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara 630-8506, Japan
| | - Saki Miyaue
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara 630-8506, Japan
| | - Yuka Shibata
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara 630-8506, Japan
| | - Akiko Matsumoto
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara 630-8506, Japan
| | - Sumio Maeda
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara 630-8506, Japan
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8
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Matsumoto A, Sekoguchi A, Imai J, Kondo K, Shibata Y, Maeda S. Natural Escherichia coli strains undergo cell-to-cell plasmid transformation. Biochem Biophys Res Commun 2016; 481:59-62. [PMID: 27833021 DOI: 10.1016/j.bbrc.2016.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/05/2016] [Indexed: 01/16/2023]
Abstract
Horizontal gene transfer is a strong tool that allows bacteria to adapt to various environments. Although three conventional mechanisms of horizontal gene transfer (transformation, transduction, and conjugation) are well known, new variations of these mechanisms have also been observed. We recently reported that DNase-sensitive cell-to-cell transfer of nonconjugative plasmids occurs between laboratory strains of Escherichia coli in co-culture. We termed this phenomenon "cell-to-cell transformation." In this report, we found that several combinations of Escherichia coli collection of reference (ECOR) strains, which were co-cultured in liquid media, resulted in DNase-sensitive cell-to-cell transfer of antibiotic resistance genes. Plasmid isolation of these new transformants demonstrated cell-to-cell plasmid transfer between the ECOR strains. Natural transformation experiments, using a combination of purified plasmid DNA and the same ECOR strains, revealed that cell-to-cell transformation occurs much more frequently than natural transformation under the same culture conditions. Thus, cell-to-cell transformation is both unique and effective. In conclusion, this study is the first to demonstrate cell-to-cell plasmid transformation in natural E. coli strains.
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Affiliation(s)
- Akiko Matsumoto
- Graduate School of Humanities and Sciences, Nara Women's University, 630-8506 Kitauoya-nishimachi, Nara, Japan
| | - Ayuka Sekoguchi
- Graduate School of Humanities and Sciences, Nara Women's University, 630-8506 Kitauoya-nishimachi, Nara, Japan
| | - Junko Imai
- Faculty of Human Life and Environment, Nara Women's University, 630-8506 Kitauoya-nishimachi, Nara, Japan
| | - Kumiko Kondo
- Graduate School of Humanities and Sciences, Nara Women's University, 630-8506 Kitauoya-nishimachi, Nara, Japan
| | - Yuka Shibata
- Graduate School of Humanities and Sciences, Nara Women's University, 630-8506 Kitauoya-nishimachi, Nara, Japan
| | - Sumio Maeda
- Graduate School of Humanities and Sciences, Nara Women's University, 630-8506 Kitauoya-nishimachi, Nara, Japan; Faculty of Human Life and Environment, Nara Women's University, 630-8506 Kitauoya-nishimachi, Nara, Japan.
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9
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Militello KT, Chang MM, Simon RD, Lazatin JC. Blue genes: An integrative laboratory to differentiate genetic transformation from gene mutation for underclassmen. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:55-62. [PMID: 26525488 DOI: 10.1002/bmb.20923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/25/2015] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
The ability of students to understand the relationship between genotype and phenotype, and the mechanisms by which genotypes and phenotypes can change is essential for students studying genetics. To this end, we have developed a four-week laboratory called Blue Genes, which is designed to help novice students discriminate between two mechanisms by which the genetic material can be altered: genetic transformation and gene mutation. In the first week of the laboratory, students incubate a plasmid DNA with calcium chloride-treated Escherichia coli JM109 cells and observe a phenotype change from ampicillin sensitive to ampicillin resistant and from white color to blue color on plates containing 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) and isopropyl β-D-thiogalactopyranoside (IPTG). Over the course of the next three weeks, students use a battery of approaches including plasmid DNA isolation experiments, restriction maps, and PCR to differentiate between mutation and transformation. The students ultimately come to the conclusion that the changes in phenotypes are due to genetic transformation and not mutation based on the evidence generated over the four-week period. Pre-laboratory tests and post-laboratory tests indicate that this set of exercises is successful in helping students differentiate between transformation and mutation. The laboratory is designed for underclassmen and is a good prerequisite for an apprentice-based research opportunity, although it is not designed as a class based research experience. Potential modifications and future directions of the laboratory based upon student experiences and assessment are presented.
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Affiliation(s)
- Kevin T Militello
- Biology Department, State University of New York at Geneseo, Geneseo, New York, 14454
| | - Ming-Mei Chang
- Biology Department, State University of New York at Geneseo, Geneseo, New York, 14454
| | - Robert D Simon
- Biology Department, State University of New York at Geneseo, Geneseo, New York, 14454
| | - Justine C Lazatin
- Biology Department, State University of New York at Geneseo, Geneseo, New York, 14454
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10
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Punekar AS, Liljeruhm J, Shepherd TR, Forster AC, Selmer M. Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ. Nucleic Acids Res 2013; 41:9537-48. [PMID: 23945937 PMCID: PMC3814359 DOI: 10.1093/nar/gkt719] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
RlmJ catalyzes the m6A2030 methylation of 23S rRNA during ribosome biogenesis in Escherichia coli. Here, we present crystal structures of RlmJ in apo form, in complex with the cofactor S-adenosyl-methionine and in complex with S-adenosyl-homocysteine plus the substrate analogue adenosine monophosphate (AMP). RlmJ displays a variant of the Rossmann-like methyltransferase (MTase) fold with an inserted helical subdomain. Binding of cofactor and substrate induces a large shift of the N-terminal motif X tail to make it cover the cofactor binding site and trigger active-site changes in motifs IV and VIII. Adenosine monophosphate binds in a partly accommodated state with the target N6 atom 7 Å away from the sulphur of AdoHcy. The active site of RlmJ with motif IV sequence 164DPPY167 is more similar to DNA m6A MTases than to RNA m62A MTases, and structural comparison suggests that RlmJ binds its substrate base similarly to DNA MTases T4Dam and M.TaqI. RlmJ methylates in vitro transcribed 23S rRNA, as well as a minimal substrate corresponding to helix 72, demonstrating independence of previous modifications and tertiary interactions in the RNA substrate. RlmJ displays specificity for adenosine, and mutagenesis experiments demonstrate the critical roles of residues Y4, H6, K18 and D164 in methyl transfer.
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Affiliation(s)
- Avinash S Punekar
- Department of Cell and Molecular Biology, Uppsala University, PO Box 596, SE 751 24 Uppsala, Sweden
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