The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

(2021) Sergio Mascarenhas Morgado et al.   Microbial Genomics

Acidic pH Decreases the Endonuclease Activity of Initiator RepB and Increases the Stability of the Covalent RepB-DNA Intermediate while Has Only a Limited Effect on the Replication of Plasmid pMV158 in Lactococcus lactis

(2021) Rafael Valdelvira et al.   Frontiers in Molecular Biosciences

Competence pili in Streptococcus pneumoniae are highly dynamic structures that retract to promote DNA uptake

(2021) Trinh Lam et al.   MOLECULAR MICROBIOLOGY

Evolutionary mechanisms that determine which bacterial genes are carried on plasmids

(2021) Sonja Lehtinen et al.   Evolution Letters

Mechanisms of Transforming DNA Uptake to the Periplasm of Bacillus subtilis

(2021) Jeanette Hahn et al.   mBio

Translational Attenuation Mechanism of ErmB Induction by Erythromycin Is Dependent on Two Leader Peptides

(2021) Shasha Wang et al.   Frontiers in Microbiology

Be Mindful of Your Metaphors about Microbes

(2021) Jessica Maccaro   mSphere

Recognition of Streptococcal Promoters by the Pneumococcal SigA Protein

(2021) Virtu Solano-Collado et al.   Frontiers in Molecular Biosciences

Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer

(2020) Arnau Domenech et al.   Cell Host & Microbe

Bacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements

(2020) Gabriel Carvalho et al.   mBio

Grad‐seq in a Gram‐positive bacterium reveals exonucleolytic sRNA activation in competence control

(2020) Jens Hör et al.   EMBO JOURNAL

The TraK accessory factor activates substrate transfer through the pKM101 type IV secretion system independently of its role in relaxosome assembly

(2020) Yang Grace Li et al.   MOLECULAR MICROBIOLOGY

Regulation outside the box: new mechanisms for small RNAs

(2020) Kathrin S. Fröhlich et al.   MOLECULAR MICROBIOLOGY

Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes

(2020) Alberto Marin-Gonzalez et al.   NUCLEIC ACIDS RESEARCH

Translation at first sight: the influence of leading codons

(2020) Ilya A Osterman et al.   NUCLEIC ACIDS RESEARCH

Toxin-Antitoxin Gene Pairs Found in Tn3 Family Transposons Appear To Be an Integral Part of the Transposition Module

(2020) Gipsi Lima-Mendez et al.   mBio

Large-scale network analysis captures biological features of bacterial plasmids

(2020) Mislav Acman et al.   Nature Communications

Cell-Free DNA: An Underestimated Source of Antibiotic Resistance Gene Dissemination at the Interface Between Human Activities and Downstream Environments in the Context of Wastewater Reuse

(2020) Markus Woegerbauer et al.   Frontiers in Microbiology

Single‐molecule tracking reveals that the nucleoid‐associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA

(2020) Kelsey Bettridge et al.   MOLECULAR MICROBIOLOGY

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

(2020) Santiago Redondo-Salvo et al.   Nature Communications

Accelerated evolution of a minimal 63–amino acid dual transcription factor

(2020) Andreas K. Brödel et al.   Science Advances

Bacillus subtilis PcrA Couples DNA Replication, Transcription, Recombination and Segregation

(2020) María Moreno-del Alamo et al.   Frontiers in Molecular Biosciences

Efflux pumps as interventions to control infection caused by drug-resistance bacteria

(2020) Nabeela Farhat et al.   DRUG DISCOVERY TODAY

More than a feeling: microscopy approaches to understanding surface-sensing mechanisms

(2020) Katherine J. Graham et al.   JOURNAL OF BACTERIOLOGY

Friend or Foe: Interbacterial Competition in the Nasal Cavity

(2020) Britney L. Hardy et al.   JOURNAL OF BACTERIOLOGY

Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

(2020) James Robertson et al.   Microbial Genomics

Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites

(2020) Tiebin Wang et al.   NUCLEIC ACIDS RESEARCH

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering

(2020) Kassidy J Tompkins et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Regulation of Gram-Positive Conjugation

(2019) Verena Kohler et al.   Frontiers in Microbiology

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model

(2019) Bryan B. Hsu et al.   Cell Host & Microbe

The pneumococcal σX activator, ComW, is a DNA-binding protein critical for natural transformation

(2019) Nicole L. Inniss et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence

(2019) Hackwon Do et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of DNA Uptake by Naturally Competent Bacteria

(2019) David Dubnau et al.   Annual Review of Genetics

Alternative ORFs and small ORFs: shedding light on the dark proteome

(2019) Mona Wu Orr et al.   NUCLEIC ACIDS RESEARCH

Ring-shaped replicative helicase encircles double-stranded DNA during unwinding

(2019) Sihwa Joo et al.   NUCLEIC ACIDS RESEARCH

The torpedo effect in Bacillus subtilis : RN ase J1 resolves stalled transcription complexes

(2019) Michaela Šiková et al.   EMBO JOURNAL

Dynamics of DNA nicking and unwinding by the RepC–PcrA complex

(2019) Carolina Carrasco et al.   NUCLEIC ACIDS RESEARCH

Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

(2019) Virginie Libante et al.   Pathogens

The first high frequency of recombination-like conjugal transfer from an integrated origin of transfer sequence in Bacillus subtilis 168

(2018) Mitsuhiro Itaya et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Hunting for Treasure Chests in Microbial Defense Islands

(2018) Eugene V. Koonin   MOLECULAR CELL

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

HU of Streptococcus pneumoniae Is Essential for the Preservation of DNA Supercoiling

(2018) María-José Ferrándiz et al.   Frontiers in Microbiology

Mobile Genetic Elements Associated with Antimicrobial Resistance

(2018) Sally R. Partridge et al.   CLINICAL MICROBIOLOGY REVIEWS

Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs

(2018) Radoslaw Pluta et al.   Wiley Interdisciplinary Reviews-RNA

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Antibiotic-Induced Cell Chaining Triggers Pneumococcal Competence by Reshaping Quorum Sensing to Autocrine-Like Signaling

(2018) Arnau Domenech et al.   Cell Reports

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Interbacterial predation as a strategy for DNA acquisition in naturally competent bacteria

(2017) Jan-Willem Veening et al.   NATURE REVIEWS MICROBIOLOGY

Classification and function of small open reading frames

(2017) Juan-Pablo Couso et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Crosstalk between vertical and horizontal gene transfer: plasmid replication control by a conjugative relaxase

(2017) Fabián Lorenzo-Díaz et al.   NUCLEIC ACIDS RESEARCH

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance

(2017) Radoslaw Pluta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcriptome of Streptococcus pneumoniae Induced by Local and Global Changes in Supercoiling

(2017) Adela G. de la Campa et al.   Frontiers in Microbiology

Molecular Mechanisms That Contribute to Horizontal Transfer of Plasmids by the Bacteriophage SPP1

(2017) Ana Valero-Rello et al.   Frontiers in Microbiology

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

(2017) Alex Orlek et al.   Frontiers in Microbiology

The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems

(2017) et al.   Genes

AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks

(2016) Val F. Lanza et al.   BIOINFORMATICS

Autonomous Replication of the Conjugative Transposon Tn 916

(2016) Laurel D. Wright et al.   JOURNAL OF BACTERIOLOGY

Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules

(2016) Cesar L. Pastrana et al.   NUCLEIC ACIDS RESEARCH

Structures of replication initiation proteins from staphylococcal antibiotic resistance plasmids reveal protein asymmetry and flexibility are necessary for replication

(2016) Stephen B. Carr et al.   NUCLEIC ACIDS RESEARCH

Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158

(2016) D. Roeland Boer et al.   Scientific Reports

Streptococcal group B integrative and mobilizable element IMESag-rpsIencodes a functional relaxase involved in its transfer

(2016) Fabian Lorenzo-Diaz et al.   Open Biology

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

(2016) Nicholas J. Croucher et al.   PLOS BIOLOGY

The Streptococcus pneumoniae pezAT Toxin–Antitoxin System Reduces β-Lactam Resistance and Genetic Competence

(2016) Wai T. Chan et al.   Frontiers in Microbiology

Distribution and diversity of ribosome binding sites in prokaryotic genomes

(2015) Damilola Omotajo et al.   BMC GENOMICS

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

In vitrobiofilm development ofStreptococcus pneumoniaeand formation of choline-binding protein-DNA complexes

(2015) Mirian Domenech et al.   Environmental Microbiology Reports

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

The 5′-tail of antisense RNAII of pMV158 plays a critical role in binding to the target mRNA and in translation inhibition of repB

(2015) Celeste López-Aguilar et al.   Frontiers in Genetics

The antibiotic resistome: what's new?

(2014) Julie Ann Perry et al.   CURRENT OPINION IN MICROBIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

(2014) Julien Guglielmini et al.   NUCLEIC ACIDS RESEARCH

Bringing them together: Plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective

(2014) Fabián Lorenzo-Díaz et al.   PLASMID

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Breaking and joining single-stranded DNA: the HUH endonuclease superfamily

(2013) Michael Chandler et al.   NATURE REVIEWS MICROBIOLOGY

Regulation of plant translation by upstream open reading frames

(2013) Albrecht G. von Arnim et al.   PLANT SCIENCE

Probing the sequence and structure of in vitro synthesized antisense and target RNAs from the replication control system of plasmid pMV158

(2013) Celeste López-Aguilar et al.   PLASMID

Translation initiation of the replication initiator repB gene of promiscuous plasmid pMV158 is led by an extended non-SD sequence

(2013) Celeste López-Aguilar et al.   PLASMID

Nicking activity of the pMV158 MobM relaxase on cognate and heterologous origins of transfer

(2013) Cris Fernández-López et al.   PLASMID

The Conserved C-Terminus of the PcrA/UvrD Helicase Interacts Directly with RNA Polymerase

(2013) Emma J. Gwynn et al.   PLoS One

Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus

(2013) J. S. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plasmids as models for studying macromolecular interactions: the pMV158 paradigm

(2013) Manuel Espinosa   RESEARCH IN MICROBIOLOGY

A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element

(2013) Jacob Thomas et al.   PLoS Genetics

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?

(2012) Xavier Charpentier et al.   CURRENT OPINION IN MICROBIOLOGY

Conjugative DNA transfer inStreptomycesby TraB: is one protein enough?

(2012) Lina Thoma et al.   FEMS MICROBIOLOGY LETTERS

Autoregulation of the Synthesis of the MobM Relaxase Encoded by the Promiscuous Plasmid pMV158

(2012) F. Lorenzo-Diaz et al.   JOURNAL OF BACTERIOLOGY

Toxin-Antitoxin Genes of the Gram-Positive Pathogen Streptococcus pneumoniae: So Few and Yet So Many

(2012) Wai Ting Chan et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Welcome to the plasmidome

(2012) Alan Walker   NATURE REVIEWS MICROBIOLOGY

Fitness of the pMV158 replicon in Streptococcus pneumoniae

(2012) Ana María Hernández-Arriaga et al.   PLASMID

The MobM relaxase domain of plasmid pMV158: thermal stability and activity upon Mn2+ and specific DNA binding

(2011) Fabián Lorenzo-Díaz et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Novel plasmid-based genetic tools for the study of promoters and terminators in Streptococcus pneumoniae and Enterococcus faecalis

(2010) Sofía Ruiz-Cruz et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Nucleases: diversity of structure, function and mechanism

(2010) Wei Yang   QUARTERLY REVIEWS OF BIOPHYSICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

(2009) D Roeland Boer et al.   EMBO JOURNAL

Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes

(2009) Ana M. Hernández-Arriaga et al.   NUCLEIC ACIDS RESEARCH

The unique structure of A-tracts and intrinsic DNA bending

(2009) Tali E. Haran et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity of Streptococcus agalactiae

(2008) M. Brochet et al.   JOURNAL OF BACTERIOLOGY

Analysis of ColE1 MbeC Unveils an Extended Ribbon-Helix-Helix Family of Nicking Accessory Proteins

(2008) A. Varsaki et al.   JOURNAL OF BACTERIOLOGY

Precise Determination, Cross-Recognition, and Functional Analysis of the Double-Strand Origins of the Rolling-Circle Replication Plasmids in Haloarchaea

(2008) L. Zhou et al.   JOURNAL OF BACTERIOLOGY

Lagging-Strand DNA Replication Origins Are Required for Conjugal Transfer of the Promiscuous Plasmid pMV158

(2008) Fabián Lorenzo-Díaz et al.   JOURNAL OF BACTERIOLOGY

Chromosomal Toxin-Antitoxin Systems May Act as Antiaddiction Modules

(2008) M. Saavedra De Bast et al.   JOURNAL OF BACTERIOLOGY

Analysis of RNA polymerase-promoter complex formation

(2008) Wilma Ross et al.   METHODS

The functional response of upstream DNA to dynamic supercoiling in vivo

(2008) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Large-scale filter mating assay for intra- and inter-specific conjugal transfer of the promiscuous plasmid pMV158 in Gram-positive bacteria

(2008) Fabián Lorenzo-Díaz et al.   PLASMID