A Dashiff

AA Medina

AC Wilson

AI Severin

AV Afinogenova

BS Goldman

C Lambert

CM Litwin

D Kadouri

Daniel E Kadouri

DR Yoder-Himes

E Jurkevitch

E Waters

EE Ishiguro

ET Lally

G Rocap

GM Garrity

GP Dubey

H Chen

H Huber

H Schmidt

HF Oliver

HM Oh

J Frey

J Sommerville

JE Berleman

JJ Germida

JJ Tudor

JS Mattick

K Rutherford

KJ Evans

KJ Livak

KK Mahmoud

LE Casida

M Sandkvist

M Wu

Martin Wu

N Sharon

NA Chemeris

O Gal-Mor

P Graumann

P Horvath

RA Wozniak

RE Sockett

RF Gordon

RJ Seidler

RS Stephens

S Beck

S Bhakdi

S Guindon

S Kurtz

S Rendulic

S Shigenobu

SG Andersson

SJ Giovannoni

U Nagalakshmi

V Burrus

VA Lambina

W Jiang

WC Lathe

Y Davidov

Zhang Wang

ZM Ruggeri

BMC Genomics

English

PubMed

Springer - Publisher Connector

Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13

Abstract
          
            Background
            Although bacterial predators play important roles in the dynamics of natural microbial communities, little is known about the molecular mechanism of bacterial predation and the evolution of diverse predatory lifestyles.
          
          
            Results
            We determined the complete genome sequence of Micavibrio aeruginosavorus ARL-13, an obligate bacterial predator that feeds by "leeching" externally to its prey. Despite being an obligate predator depending on prey for replication, M. aeruginosavorus encodes almost all major metabolic pathways. However, our genome analysis suggests that there are multiple amino acids that it can neither make nor import directly from the environment, thus providing a simple explanation for its strict dependence on prey. Remarkably, despite apparent genome reduction, there is a massive expansion of genomic islands of foreign origin. At least nine genomic islands encode many genes that are likely important for Micavibrio-prey interaction such as hemolysin-related proteins. RNA-Seq analysis shows substantial transcriptome differences between the attack phase, when M. aeruginosavorus seeks its prey, and the attachment phase, when it feeds and multiplies. Housekeeping genes as well as genes involved in protein secretion were all dramatically up-regulated in the attachment phase. In contrast, genes involved in chemotaxis and flagellum biosynthesis were highly expressed in the attack phase but were shut down in the attachment phase. Our transcriptomic analysis identified additional genes likely important in Micavibrio predation, including porins, pilins and many hypothetical genes.
          
          
            Conclusions
            The findings from our phylogenomic and transcriptomic analyses shed new light on the biology and evolution of the epibiotic predatory lifestyle of M. aeruginosavorus. The analysis reported here and the availability of the complete genome sequence should catalyze future studies of this organism.
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Crossref

Activities of cold-shock domain proteins in translation control. Bioessays

Afinogennova AV: Role of carbohydrate receptors in the interaction of Micavibrio admirandus and host-bacterium. Zentbl Mikrobiol

Afinogenova AV, Kulaev IS: Isolation and some physicochemical properties of lytic proteinase of the parasitic bacterium Micavibrio admirandus. Biokhimiya

Afinogenova AV, Romai Penabad S, Konovalova SM, Pushkareva AP: Micavibrio admirandus gen. et sp. nov. Mikrobiologiia

al: Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature

Andreev LV: New species of exoparasitic bacteria of the genus Micavibrio infecting gram-positive bacteria. Mikrobiologiia

Artemis: sequence visualization and annotation. Bioinformatics

Bacterial Predators of Micrococcus luteus in Soil. Appl Environ Microbiol

Barrangou R: CRISPR/Cas, the immune system of bacteria and archaea. Science

BB: Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell Microbiol

Ben-Yehuda S: Intercellular nanotubes mediate bacterial communication. Cell

Biology of type II secretion. Mol Microbiol

Calderwood SB: Role of iron in regulation of virulence genes. Clin Microbiol Rev

CG: The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature

Cho JC: Complete genome sequence of “Candidatus Puniceispirillum marinum“ IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria.

CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone.

Davidov Y: Phylogenetic Diversity and Evolution of Predatory Prokaryotes. Microbiology Monographs

DE: A New Method for Isolating Host-Independent Variants of Bdellovibrio bacteriovorus Using E. coli Auxotrophs. Open Microbiol J

Deciphering the hunting strategy of a bacterial wolfpack. FEMS Microbiol Rev

Development of a novel system for isolating genes involved in predator-prey interactions using host independent derivatives of Bdellovibrio bacteriovorus 109J. BMC Microbiol

DL: Heat shock-induced axenic growth of Bdellovibrio bacteriovorus.

E: A new alpha-proteobacterial clade of Bdellovibrio-like predators: implications for the mitochondrial endosymbiotic theory. Environ Microbiol

E: Characterization of outer membrane protein fractions of Bdellovibrionales.

Eisen JA: A simple, fast, and accurate method of phylogenomic inference. Genome Biol

Ensifer adhaerens gen. nov., sp. nov.: a bacerial predator of bacteria in soil.

Ensifer adhaerens Predatory Activity Against Other Bacteria in Soil, as Monitored by Indirect Phage Analysis. Appl Environ Microbiol

et al: A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science

et al: Evolution of sensory complexity recorded in a myxobacterial genome. Proc Natl Acad Sci USA

et al: Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science

et al: Genome streamlining in a cosmopolitan oceanic bacterium. Science

et al: Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola. Insect Mol Biol

et al: The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA

Evolution of tuf genes: ancient duplication, differential loss and gene conversion.

FASTX-Toolkit: FASTQ/A short-reads pre-processing tools.

Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol

Genetics and phylogeny of RTX cytolysins. In The comprehensive sourcebook of bacterial protein toxins.. 3 edition. Edited by: Alouf JE, Popoff MR.

H: Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp.

HN: Prey bacteria shape the community structure of their predators.

IB: Escherichia coli hemolysin may damage target cell membranes by generating transmembrane pores. Infect Immun

Inhibition of Predation by Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus via Host Cell Metabolic Activity in the Presence of Carbohydrates. Appl Environ Microbiol

KJ: Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.

Koval SF: Characterization of type IV pili in the life cycle of the predator bacterium Bdellovibrio.

Lambina VA: Analysis of the interpopulational interactions in a 2-component bacterial system of Micavibrio admirandus - Escherichia coli. Nauchnye Doki Vyss Shkoly Biol Nauki

Lis H: Lectins as cell recognition molecules. Science

Mapping and Assembly with Qualities.

Marahiel MA: A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures. Mol Microbiol

Minimum nutritional requirements for growth of hostindependent derivatives of Bdellovibrio bacteriovorus strain 109 Davis.

MP: Isolation and characterization of host-independent Bdellovibrios.

O’Toole GA: Vulnerability of pathogenic biofilms to Micavibrio aeruginosavorus. Appl Environ Microbiol

Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev

Predation of human pathogens by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus.

Predatory lifestyle of Bdellovibrio bacteriovorus. Annu Rev Microbiol

Predatory prokaryotes: biology, ecology, and evolution

Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods

Sockett L: A predatory patchwork: membrane and surface structures of Bdellovibrio bacteriovorus. Adv Microb Physiol

Sockett RE: Predation by Bdellovibrio bacteriovorus HD100 requires type IV pili.

Sorek R: Mapping the Burkholderia cenocepacia niche response via highthroughput sequencing. Proc Natl Acad Sci USA

Stetter KO: A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature

TG: Taxonomic outline of the prokaryotes. Bergey’s manual of systematic bacteriology. Second edition.

The transcriptional landscape of the yeast genome defined by RNA sequencing. Science

The Vmatch large scale sequence analysis software.

Translocation of an outer membrane protein into prey cytoplasmic membranes by bdellovibrios.

Type IV pili and twitching motility. Annu Rev Microbiol

Waldor MK: Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol

Waldor MK: Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol

https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-12-453?site=bmcgenomics.biomedcentral.com

Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13

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