Analysis of the distribution and evolution of the ATP-dependent DNA ligases of bacteria delineates a distinct phylogenetic group 'Lig E'.

Abstract:

:Prior to the discovery of a minimal ATP-dependent DNA ligase in Haemophilus influenzae, bacteria were thought to only possess a NAD-dependent ligase, which was involved in sealing of Okazaki fragments. We now know that a diverse range of bacterial species possess up to six of these accessory bacterial ATP-dependent DNA ligases (b-ADLs), which vary in size and enzymatic domain associations. Here we compare the domain structure of different types of b-ADLs and investigate their distribution among the bacterial domain to describe possible evolutionary trajectories that gave rise to the sequence and structural diversity of these enzymes. Previous biochemical and genetic analyses have delineated three main classes of these enzymes: Lig B, Lig C and Lig D, which appear to have descended from a common ancestor within the bacterial domain. In the present study, we delineate a fourth group of b-ADLs, Lig E, which possesses a number of unique features at the primary and tertiary structural levels. The biochemical characteristics, domain structure and inferred extracellular location sets this group apart from the other b-ADLs. The results presented here indicate that the Lig E type ligases were horizontally transferred into bacteria in a separate event from other b-ADLs possibly from a bacteriophage.

journal_name

Mol Microbiol

journal_title

Molecular microbiology

authors

Williamson A,Hjerde E,Kahlke T

doi

10.1111/mmi.13229

subject

Has Abstract

pub_date

2016-01-01 00:00:00

pages

274-90

issue

2

eissn

0950-382X

issn

1365-2958

journal_volume

99

pub_type

杂志文章
  • Plant defence suppression is mediated by a fungal sirtuin during rice infection by Magnaporthe oryzae.

    abstract::Crop destruction by the hemibiotrophic rice pathogen Magnaporthe oryzae requires plant defence suppression to facilitate extensive biotrophic growth in host cells before the onset of necrosis. How this is achieved at the genetic level is not well understood. Here, we report that a M. oryzae sirtuin, MoSir2, plays an e...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12743

    authors: Fernandez J,Marroquin-Guzman M,Nandakumar R,Shijo S,Cornwell KM,Li G,Wilson RA

    更新日期:2014-10-01 00:00:00

  • Glucose-induced cAMP signalling in yeast requires both a G-protein coupled receptor system for extracellular glucose detection and a separable hexose kinase-dependent sensing process.

    abstract::In Saccharomyces cerevisiae, glucose activation of cAMP synthesis requires both the presence of the G-protein-coupled receptor (GPCR) system, Gpr1-Gpa2, and uptake and phosphorylation of the sugar. In a hxt-null strain that lacks all physiologically important glucose carriers, glucose transport as well as glucose-indu...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2000.02125.x

    authors: Rolland F,De Winde JH,Lemaire K,Boles E,Thevelein JM,Winderickx J

    更新日期:2000-10-01 00:00:00

  • The Rhodobacter capsulatus hupSLC promoter: identification of cis-regulatory elements and of trans-activating factors involved in H2 activation of hupSLC transcription.

    abstract::The [NiFe]hydrogenase of the photosynthetic bacterium Rhodobacter capsulatus is encoded by the structural hupSLC operon, the expression of which is induced by H2. H2 activation was no longer observable in chromosomal hupR mutants, an indication that HupR is implicated directly in the activation by H2 of hupS gene expr...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1997.6291996.x

    authors: Toussaint B,de Sury d'Aspremont R,Delic-Attree I,Berchet V,Elsen S,Colbeau A,Dischert W,Lazzaroni Y,Vignais PM

    更新日期:1997-12-01 00:00:00

  • Dispensable nature of phosphatidylglycerol in Escherichia coli: dual roles of anionic phospholipids.

    abstract::The major anionic phospholipids of Escherichia coli, phosphatidylglycerol (PG) and cardiolipin (CL), have been considered to be indispensable for essential cellular functions, such as the initiation of DNA replication and translocation of proteins across the cytoplasmic membrane. However, we successfully constructed a...

    journal_title:Molecular microbiology

    pub_type: 杂志文章,评审

    doi:10.1046/j.1365-2958.2001.02320.x

    authors: Matsumoto K

    更新日期:2001-03-01 00:00:00

  • The Candida glabrata Amt1 copper-sensing transcription factor requires Swi/Snf and Gcn5 at a critical step in copper detoxification.

    abstract::The yeast Candida glabrata rapidly autoactivates transcription of the AMT1 gene in response to potentially toxic copper levels through the copper-inducible binding of the Amt1 transcription factor to a metal response element (MRE) within a positioned nucleosome. Our previous studies have characterized the role of a 16...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2001.02458.x

    authors: Koch KA,Allard S,Santoro N,Côté J,Thiele DJ

    更新日期:2001-06-01 00:00:00

  • DNA replication during endospore development in Metabacterium polyspora.

    abstract::The guinea pig intestinal symbiont Metabacterium polyspora is an uncultured, endospore-forming member of the Firmicutes. Unlike most endospore-forming bacteria, sporulation is an obligate part of the M. polyspora life cycle when it is associated with a guinea pig. Binary fission is limited to a brief period in its lif...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2008.06129.x

    authors: Ward RJ,Angert ER

    更新日期:2008-03-01 00:00:00

  • Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of the murine urinary tract.

    abstract::Although once thought to be unique to bacteria, d-amino acids are also produced by mammals. For example, d-serine is excreted in human urine at concentrations ranging from 3.0 to 40 micro g ml-1. An epidemiological survey demonstrated that urine isolates of E. coli are more likely to catabolise d-serine via expression...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2003.03543.x

    authors: Roesch PL,Redford P,Batchelet S,Moritz RL,Pellett S,Haugen BJ,Blattner FR,Welch RA

    更新日期:2003-07-01 00:00:00

  • SaPI mutations affecting replication and transfer and enabling autonomous replication in the absence of helper phage.

    abstract::The SaPIs are chromosomal islands in staphylococci and other Gram-positive bacteria that carry genes for superantigens, virulence factors, resistance and certain metabolic functions. They have intimate relationships with certain temperate phages involving phage-induced excision, replication and efficient packaging in ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2007.06027.x

    authors: Ubeda C,Maiques E,Barry P,Matthews A,Tormo MA,Lasa I,Novick RP,Penadés JR

    更新日期:2008-02-01 00:00:00

  • G1 and S phase arrest in Candida albicans induces filamentous growth via distinct mechanisms.

    abstract::Candida albicans is an opportunistic fungal pathogen. In immunocompromised individuals, it can cause bloodstream infections with high mortality rates. The ability to switch between yeast and hyphal morphologies is a critical virulence factor of C. albicans. In response to diverse environmental cues, several signaling ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.14097

    authors: Chen C,Zeng G,Wang Y

    更新日期:2018-10-01 00:00:00

  • Mapping the recognition domains of pneumococcal fibronectin-binding proteins PavA and PavB demonstrates a common pattern of molecular interactions with fibronectin type III repeats.

    abstract::Colonization of mucosal respiratory surfaces is a prerequisite for the human pathobiont Streptococcus pneumoniae (the pneumococcus) to cause severe invasive infections. The arsenal of pneumococcal adhesins interacts with a multitude of extracellular matrix proteins. A paradigm for pneumococci is their interaction with...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.13740

    authors: Kanwal S,Jensch I,Palm GJ,Brönstrup M,Rohde M,Kohler TP,Somplatzki D,Tegge W,Jenkinson HF,Hammerschmidt S

    更新日期:2017-09-01 00:00:00

  • Probing the active site of mitogillin, a fungal ribotoxin.

    abstract::Fungal ribotoxins, such as mitogillin and the related Aspergillus toxins restrictocin and alpha-sarcin, are highly specific ribonucleases, which inactivate the ribosome enzymatically by cleaving the eukaryotic 28S RNA of the large ribosomal subunit at a single phosphodiester bond. The site of cleavage occurs between G...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1998.00987.x

    authors: Kao R,Shea JE,Davies J,Holden DW

    更新日期:1998-08-01 00:00:00

  • The pAM beta 1 CopF repressor regulates plasmid copy number by controlling transcription of the repE gene.

    abstract::pAM beta 1 is a low-copy-number, promiscuous plasmid from Gram-positive bacteria that replicates by a unidirectional theta-type mode. Its replication is initiated by an original mechanism, involving the positive rate-limiting RepE protein. Here we show that the pAM beta 1-encoded CopF protein is involved in negative r...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1994.tb02181.x

    authors: Le Chatelier E,Ehrlich SD,Jannière L

    更新日期:1994-11-01 00:00:00

  • Genetic and functional analysis of the phosphorylcholine moiety of commensal Neisseria lipopolysaccharide.

    abstract::Phosphorylcholine (ChoP) is a common surface feature of many mucosal organisms, including Neisseria spp., in which it is present exclusively on pili of pathogenic Neisseria and on the lipopolysaccharide (LPS) of commensal Neisseria (Cn). Its presence in Cn has been confirmed by nuclear magnetic resonance. It appears t...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2002.02755.x

    authors: Serino L,Virji M

    更新日期:2002-01-01 00:00:00

  • Identification and functional analysis of the Rz/Rz1-like accessory lysis genes in the membrane-containing bacteriophage PRD1.

    abstract::Bacteriophage PRD1 is a tailless membrane-containing double-stranded (ds) DNA virus infecting a variety of Gram-negative bacteria. In order to affect cell lysis, like most dsDNA phages, PRD1 uses the holin-endolysin system. In this study, we identified two accessory lysis genes, XXXVI and XXXVII, coding for proteins P...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2008.06165.x

    authors: Krupovic M,Cvirkaite-Krupovic V,Bamford DH

    更新日期:2008-04-01 00:00:00

  • The Intimin periplasmic domain mediates dimerisation and binding to peptidoglycan.

    abstract::Intimin and Invasin are prototypical inverse (Type Ve) autotransporters and important virulence factors of enteropathogenic Escherichia coli and Yersinia spp. respectively. In addition to a C-terminal extracellular domain and a β-barrel transmembrane domain, both proteins also contain a short N-terminal periplasmic do...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12840

    authors: Leo JC,Oberhettinger P,Chaubey M,Schütz M,Kühner D,Bertsche U,Schwarz H,Götz F,Autenrieth IB,Coles M,Linke D

    更新日期:2015-01-01 00:00:00

  • Initiation of chromosome replication after induction of DnaA protein synthesis in a dnaA(nuII) rnh mutant of Escherichia coli.

    abstract::The kinetics of initiation of chromosome replication after induction of DnaA protein synthesis was studied in a dnaA(nuII) rnh mutant of Escherichia coli. DnaA protein synthesis was induced to different extents using the wild-type dnaA gene controlled by a lac promoter. Initiation of chromosome replication from oriC, ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1995.tb02229.x

    authors: Hansen FG,Atlung T

    更新日期:1995-01-01 00:00:00

  • Cloning and characterization of three genes (SUT1-3) encoding glucose transporters of the yeast Pichia stipitis.

    abstract::We have identified and characterized three genes, SUT1, SUT2 and SUT3, that encode glucose transporters of the yeast Pichia stipitis. When expressed in a Saccharomyces cerevisiae hxt null mutant strain that is unable to take up monosaccharides, all three proteins restored growth on glucose. Sequencing of the genes rev...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1999.01224.x

    authors: Weierstall T,Hollenberg CP,Boles E

    更新日期:1999-02-01 00:00:00

  • Genetic linkage analyses redefine the roles of PfCRT and PfMDR1 in drug accumulation and susceptibility in Plasmodium falciparum.

    abstract::Resistance to quinoline antimalarial drugs has emerged in different parts of the world and involves sets of discrete mutational changes in pfcrt and pfmdr1 in the human malaria parasite Plasmodium falciparum. To better understand how the different polymorphic haplotypes of pfmdr1 and pfcrt contribute to drug resistanc...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2011.07855.x

    authors: Sanchez CP,Mayer S,Nurhasanah A,Stein WD,Lanzer M

    更新日期:2011-11-01 00:00:00

  • Differential transcriptome profiling identifies Plasmodium genes encoding pre-erythrocytic stage-specific proteins.

    abstract::Invasive sporozoite and merozoite stages of malaria parasites that infect mammals enter and subsequently reside in hepatocytes and red blood cells respectively. Each invasive stage may exhibit unique adaptations that allow it to interact with and survive in its distinct host cell environment, and these adaptations are...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2003.03909.x

    authors: Kaiser K,Matuschewski K,Camargo N,Ross J,Kappe SH

    更新日期:2004-03-01 00:00:00

  • DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli.

    abstract::In contrast to many type II restriction enzymes, dimeric proteins that cleave DNA at individual recognition sites 4-6 bp long, the SfiI endonuclease is a tetrameric protein that binds to two copies of an elongated sequence before cutting the DNA at both sites. The mode of action of the SfiI endonuclease thus seems mor...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1999.01266.x

    authors: Bilcock DT,Halford SE

    更新日期:1999-02-01 00:00:00

  • Liver-specific protein 2: a Plasmodium protein exported to the hepatocyte cytoplasm and required for merozoite formation.

    abstract::The liver stage is the first stage of the malaria parasite that replicates in the vertebrate host. However, little is known about the interplay between the parasite liver stage and its host cell, the hepatocyte. In this study, we identified an exported protein that has a critical role in parasite development in host h...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/mmi.12083

    authors: Orito Y,Ishino T,Iwanaga S,Kaneko I,Kato T,Menard R,Chinzei Y,Yuda M

    更新日期:2013-01-01 00:00:00

  • Suppression of a nuclear frameshift mutation by a mitochondrial tRNA in the yeast Kluyveromyces lactis.

    abstract::A fragment of mitochondrial DNA containing the Kluyveromyces lactis gene for valine-tRNA (tRNAVAL) was isolated as a multicopy suppressor of a respiratory-deficient mutant of this yeast. The mutant produced a truncated Cox14p because of a +1 frameshift mutation in COX14, a nuclear gene encoding a protein imported into...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2002.03147.x

    authors: Fiori A,Francisci S,Falcone C

    更新日期:2002-10-01 00:00:00

  • Amplified expression of a transcriptional pattern formed during development of Anabaena.

    abstract::The cyanobacterium Anabaena responds to nitrogen deprivation by producing heterocysts, cells specialized for nitrogen fixation, at well-spaced intervals along its filaments. The gene hepA, required for heterocyst maturation, is expressed in response to nitrogen deprivation, prior to visible differentiation. A spatial ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1993.tb01135.x

    authors: Wolk CP,Elhai J,Kuritz T,Holland D

    更新日期:1993-02-01 00:00:00

  • Gene expression in mycobacteria: transcriptional fusions based on xylE and analysis of the promoter region of the response regulator mtrA from Mycobacterium tuberculosis.

    abstract::Understanding promoter regulation and signal-transduction systems in pathogenic mycobacteria is critical for uncovering the processes that govern interactions of these bacteria with the human host. In order to develop additional genetic tools for analysis of mycobacterial promoters, the xyIE gene from Pseudomonas was ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.1994.tb00496.x

    authors: Curcic R,Dhandayuthapani S,Deretic V

    更新日期:1994-09-01 00:00:00

  • The penicillin sensory transducer, BlaR, involved in the inducibility of beta-lactamase synthesis in Bacillus licheniformis is embedded in the plasma membrane via a four-alpha-helix bundle.

    abstract::Prediction studies, conformational analyses and membrane-topology mapping lead to the conclusion that the penicillin sensory transducer, BlaR, involved in the inducibility of beta-lactamase synthesis in Bacillus licheniformis, is embedded in the plasma membrane bilayer via four transmembrane segments TM1-TM4 that form...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1997.2761642.x

    authors: Hardt K,Joris B,Lepage S,Brasseur R,Lampen JO,Frère JM,Fink AL,Ghuysen JM

    更新日期:1997-03-01 00:00:00

  • Patatin-like phospholipases in microbial infections with emerging roles in fatty acid metabolism and immune regulation by Apicomplexa.

    abstract::Emerging lipidomic technologies have enabled researchers to dissect the complex roles of phospholipases in lipid metabolism, cellular signaling and immune regulation. Host phospholipase products are involved in stimulating and resolving the inflammatory response to pathogens. While many pathogen-derived phospholipases...

    journal_title:Molecular microbiology

    pub_type: 杂志文章,评审

    doi:10.1111/mmi.13871

    authors: Wilson SK,Knoll LJ

    更新日期:2018-01-01 00:00:00

  • Inactivation of the replication-termination system affects the replication mode and causes unstable maintenance of plasmid R1.

    abstract::Two so-called Ter sites, which bind the Escherichia coli Tus protein, are located near the replication origin of plasmid R1. Inactivation of the tus gene caused a large decrease in the stability of maintenance of the R1 mini-derivative pOU47 despite the presence of a functional partition system on the plasmid. Deletio...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.1997.3791747.x

    authors: Krabbe M,Zabielski J,Bernander R,Nordström K

    更新日期:1997-05-01 00:00:00

  • Septal and lateral wall localization of PBP5, the major D,D-carboxypeptidase of Escherichia coli, requires substrate recognition and membrane attachment.

    abstract::The distribution of PBP5, the major D,D-carboxypeptidase in Escherichia coli, was mapped by immunolabelling and by visualization of GFP fusion proteins in wild-type cells and in mutants lacking one or more D,D-carboxypeptidases. In addition to being scattered around the lateral envelope, PBP5 was also concentrated at ...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2010.07205.x

    authors: Potluri L,Karczmarek A,Verheul J,Piette A,Wilkin JM,Werth N,Banzhaf M,Vollmer W,Young KD,Nguyen-Distèche M,den Blaauwen T

    更新日期:2010-07-01 00:00:00

  • Cytoplasmic membrane protonmotive force energizes periplasmic interactions between ExbD and TonB.

    abstract::The TonB system of Escherichia coli (TonB/ExbB/ExbD) transduces the protonmotive force (pmf) of the cytoplasmic membrane to drive active transport by high-affinity outer membrane transporters. In this study, chromosomally encoded ExbD formed formaldehyde-linked complexes with TonB, ExbB and itself (homodimers) in vivo...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1111/j.1365-2958.2009.06785.x

    authors: Ollis AA,Manning M,Held KG,Postle K

    更新日期:2009-08-01 00:00:00

  • Characterization of integration host factor (IHF) binding upstream of the cysteine-rich protein operon (omcAB) promoter of Chlamydia trachomatis LGV serovar L2.

    abstract::Chlamydiae are bacterial parasites that carry out a distinct developmental cycle within host cells; however, the mechanisms by which these organisms regulate stage-specific gene expression are not known. We identified a DNA element located between nucleotide (nt) -135 and -90 upstream from the transcription start poin...

    journal_title:Molecular microbiology

    pub_type: 杂志文章

    doi:10.1046/j.1365-2958.2001.02531.x

    authors: Zhong J,Douglas AL,Hatch TP

    更新日期:2001-07-01 00:00:00