Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids

Matsuda, Ayako; Kurono, Naomi; Kawano, Chinatsu; Shirota, Kozue; Hirabayashi, Akiko; Horino, Mutsumi; Etchuya, Rika; Sobue, Rina; Sasaki, Yumi; Miyaue, Saki; Sekoguchi, Ayuka; Sugiura, Chiaki; Shibata, Yuka; Ito, Miki; Ando, Tsuyako; Maeda, Sumio

doi:10.1016/j.bbrc.2012.10.098

Cited by 16 publications

(25 citation statements)

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“…RlmJ was found to contain a sequence motif characteristic for m 6 A MTases acting on DNA (9) and has also been implicated in the ability of bacteria to use DNA as nutrient (9) and in repression of plasmid uptake (10), but these processes are poorly understood. The knockout of rlmJ does not affect the growth rate (2) but lowers the competitive fitness at long-term growth in stationary phase (9) and provides a small growth advantage under anaerobic conditions (2).…”

Section: Introductionmentioning

confidence: 99%

Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ

Punekar

Liljeruhm

Shepherd

et al. 2013

Nucleic Acids Research

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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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Section: Introductionmentioning

confidence: 99%

Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ

Punekar

Liljeruhm

Shepherd

et al. 2013

Nucleic Acids Research

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“…Theoretically, these mutants could be isolated from both the conjugation and transformation mutant screens, as they showed a severe growth deficiency. In fact, rnt and priA mutants were isolated in a genome-wide screening of the cell-tocell transfer of non-conjugative plasmids (Matsuda et al, 2012). Drugs that inhibit the products of the rnt, priA, and dnaT genes may, therefore, be potential new antibiotics, although they will not repress conjugation.…”

Section: Discussionmentioning

confidence: 99%

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

Moriguchi¹,

Zoolkefli²,

Abe³

et al. 2020

Front. Microbiol.

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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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“…By changing the rate with which fresh medium is added to the bioreactor, the growth rate of the microorganism can be controlled (Novick and Szilard 1950). Recently, it has been observed that, under specific conditions, cells may take up plasmids from the surrounding environment, but this phenomenon seems to be too rare to explain the maintenance of plasmids in nature (Maeda et al 2006;Kurono et al 2012;Matsuda et al 2012; Perez-Mendoza and de la Cruz 2009). However, not all conjugative plasmids seem to transfer to other cells with enough speed (Dionisio et al 2002;Gordon 1992).…”

Section: What Do We Know About Maintenancementioning

confidence: 99%

Reticulate Evolution

Gontier¹

2015

Interdisciplinary Evolution Research

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The time when only biologists studied evolution has long since passed. Accepting evolution requires us to come to terms with the fact that everything that exists must be the outcome of evolutionary processes. Today, a wide variety of academic disciplines are therefore confronted with evolutionary problems, ranging from physics and medicine, to linguistics, anthropology and sociology. Solving evolutionary problems also necessitates an inter-and transdisciplinary approach, which is why the Modern Synthesis is currently extended to include drift theory, symbiogenesis, lateral gene transfer, hybridization, epigenetics and punctuated equilibria theory.The series Interdisciplinary Evolution Research aims to provide a scholarly platform for the growing demand to examine specific evolutionary problems from the perspectives of multiple disciplines. It does not adhere to one specific academic field, one specific school of thought, or one specific evolutionary theory. Rather, books in the series thematically analyze how a variety of evolutionary fields and evolutionary theories provide insights into specific, well-defined evolutionary problems of life and the socio-cultural domain.Editors-in-chief of the series are Nathalie Gontier and Olga Pombo. The Series is edited from within the Applied Evolutionary Epistemology Lab, more information on the lab is available at http://appeel.fc.ul.pt. This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made.Printed on acid-free paper Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com) v Although originally a systematic term associated with speciation by hybridization, this book exemplifies "reticulate evolution" as it occurs by mechanisms and processes of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. These phenomena are currently taking up a prominent role in the evolutionary sciences. Almost on a daily basis, new and fascinat...

show abstract

Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids

Cited by 16 publications

References 31 publications

Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ

Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ

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

Reticulate Evolution

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