A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility

(2019) Rémi Denise et al.   PLOS BIOLOGY

Gram-negative synthase-dependent exopolysaccharide biosynthetic machines

(2018) Kristin E Low et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly-β(1,6)-N-acetylglucosamine and can disrupt bacterial biofilms

(2018) Dustin J. Little et al.   PLoS Pathogens

PelA and PelB proteins form a modification and secretion complex essential for Pel polysaccharide-dependent biofilm formation inPseudomonas aeruginosa

(2017) Lindsey S. Marmont et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insights into the structure and assembly of a bacterial cellulose secretion system

(2017) Petya Violinova Krasteva et al.   Nature Communications

Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host

(2017) Maite Echeverz et al.   PLoS Genetics

Structural Basis for Translocation of a Biofilm-supporting Exopolysaccharide across the Bacterial Outer Membrane

(2016) Yan Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BcsZ inhibits biofilm phenotypes and promotes virulence by blocking cellulose production in Salmonella enterica serovar Typhimurium

(2016) Irfan Ahmad et al.   Microbial Cell Factories

Cellulose production, activated by cyclic di-GMP through BcsA and BcsZ, is a virulence factor and an essential determinant of the three-dimensional architectures of biofilms formed by Erwinia amylovora Ea1189

(2016) Luisa F. Castiblanco et al.   MOLECULAR PLANT PATHOLOGY

Observing cellulose biosynthesis and membrane translocation in crystallo

(2016) Jacob L. W. Morgan et al.   NATURE

Sporulation, bacterial cell envelopes and the origin of life

(2016) Elitza I. Tocheva et al.   NATURE REVIEWS MICROBIOLOGY

Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation

(2016) Ivan Junier et al.   PLoS One

Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07

(2016) Kaihua Ji et al.   Scientific Reports

Operon Gene Order Is Optimized for Ordered Protein Complex Assembly

(2016) Jonathan N. Wells et al.   Cell Reports

Characterization of a biofilm-formingShigella flexneriphenotype due to deficiency in Hep biosynthesis

(2016) Dan Xu et al.   PeerJ

Structure of the Cellulose Synthase Complex of Gluconacetobacter hansenii at 23.4 Å Resolution

(2016) Juan Du et al.   PLoS One

Flocculation-Related Gene Identification by Whole-Genome Sequencing of Thauera aminoaromatica MZ1T Floc-Defective Mutants

(2015) P. Prombutara et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

An event-driven approach for studying gene block evolution in bacteria

(2015) David C. Ream et al.   BIOINFORMATICS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2015) T. Tatusova et al.   NUCLEIC ACIDS RESEARCH

Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions

(2015) Ute Römling et al.   TRENDS IN MICROBIOLOGY

Enzymatic modifications of exopolysaccharides enhance bacterial persistence

(2015) Gregory B. Whitfield et al.   Frontiers in Microbiology

A different path: Revealing the function of staphylococcal proteins in biofilm formation

(2014) Kate E. Atkin et al.   FEBS LETTERS

Structural Basis for the De-N-acetylation of Poly-β-1,6-N-acetyl-d-glucosamine in Gram-positive Bacteria

(2014) Dustin J. Little et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

(2014) Adrian M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Automated analysis of phylogenetic clusters

(2013) Manon Ragonnet-Cronin et al.   BMC BIOINFORMATICS

Top-Down Clustering for Protein Subfamily Identification

(2013) Eduardo P. Costa et al.   Evolutionary Bioinformatics

DOOR 2.0: presenting operons and their functions through dynamic and integrated views

(2013) Xizeng Mao et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The Structure- and Metal-dependent Activity ofEscherichia coliPgaB Provides Insight into the Partial De-N-acetylation of Poly-β-1,6-N-acetyl-d-glucosamine

(2012) Dustin J. Little et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystallographic snapshot of cellulose synthesis and membrane translocation

(2012) Jacob L. W. Morgan et al.   NATURE

Synthase-dependent exopolysaccharide secretion in Gram-negative bacteria

(2012) J.C. Whitney et al.   TRENDS IN MICROBIOLOGY

Integrated Bioinformatic and Targeted Deletion Analyses of the SRS Gene Superfamily Identify SRS29C as a Negative Regulator of Toxoplasma Virulence

(2012) J. D. Wasmuth et al.   mBio

Complete genome sequence of Thauera aminoaromatica strain MZ1T

(2012) Ke Jiang et al.   Standards in Genomic Sciences

The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems

(2012) Sophie S. Abby et al.   PLoS Genetics

The Dickeya dadantii biofilm matrix consists of cellulose nanofibres, and is an emergent property dependent upon the type III secretion system and the cellulose synthesis operon

(2011) C. E. Jahn et al.   MICROBIOLOGY-SGM

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Biosynthesis of the Pseudomonas aeruginosa Extracellular Polysaccharides, Alginate, Pel, and Psl

(2011) Michael J. Franklin et al.   Frontiers in Microbiology

Gene duplications in prokaryotes can be associated with environmental adaptation

(2010) Marit S Bratlie et al.   BMC GENOMICS

A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407

(2010) L. C. Crossman et al.   JOURNAL OF BACTERIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Threshold Bootstrap Clustering: A New Approach to Find Families or Transmission Clusters within Molecular Quasispecies

(2010) Mattia C. F. Prosperi et al.   PLoS One

Structure of bacterial cellulose synthase subunit D octamer with four inner passageways

(2010) S.-Q. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting gene clusters under evolutionary constraint in a large number of genomes

(2009) Xu Ling et al.   BIOINFORMATICS

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

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

Evolution by leaps: gene duplication in bacteria

(2009) Margrethe H Serres et al.   Biology Direct

Contribution of Gene Amplification to Evolution of Increased Antibiotic Resistance in Salmonella typhimurium

(2009) Song Sun et al.   GENETICS

Pivotal Roles of the Outer Membrane Polysaccharide Export and Polysaccharide Copolymerase Protein Families in Export of Extracellular Polysaccharides in Gram-Negative Bacteria

(2009) L. Cuthbertson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bacterial gene amplification: implications for the evolution of antibiotic resistance

(2009) Linus Sandegren et al.   NATURE REVIEWS MICROBIOLOGY

Persistence drives gene clustering in bacterial genomes

(2008) Gang Fang et al.   BMC GENOMICS

A Staphylococcal GGDEF Domain Protein Regulates Biofilm Formation Independently of Cyclic Dimeric GMP

(2008) L. M. Holland et al.   JOURNAL OF BACTERIOLOGY

Roles of pgaABCD Genes in Synthesis, Modification, and Export of the Escherichia coli Biofilm Adhesin Poly- -1,6-N-Acetyl-D-Glucosamine

(2008) Y. Itoh et al.   JOURNAL OF BACTERIOLOGY