Protein interaction networks in bacteria.

The complement of expressed cellular proteins - the proteome - is organized into functional, structured networks of protein interactions that mediate assembly of molecular machines and dynamic cellular pathways. Recent studies reveal the biological roles of protein interactions in bacteriophage T7 and Helicobacter pylori, and new methods allow to compare and to predict interaction networks in other species. Smaller scale networks provide biological insights into DNA replication and chromosome dynamics in Bacillus subtilis and Archeoglobus fulgidus, and into the assembly of multiprotein complexes such as the type IV secretion system of Agrobacterium tumefaciens, and the cell division machinery of Escherichia coli. Genome-wide interaction networks in several species are needed to obtain a biologically meaningful view of the higher order organization of the proteome in bacteria.

[1]  Daniel Auerbach,et al.  The post‐genomic era of interactive proteomics: Facts and perspectives , 2002, Proteomics.

[2]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[3]  Z. Ding,et al.  A Novel Cytology-Based, Two-Hybrid Screen for Bacteria Applied to Protein-Protein Interaction Studies of a Type IV Secretion System , 2002, Journal of bacteriology.

[4]  H. D. Ulrich,et al.  A Prokaryotic Condensin/Cohesin-Like Complex Can Actively Compact Chromosomes from a Single Position on the Nucleoid and Binds to DNA as a Ring-Like Structure , 2003, Molecular and Cellular Biology.

[5]  A. Das,et al.  The Agrobacterium T-DNA Transport Pore Proteins VirB8, VirB9, and VirB10 Interact with One Another , 2000, Journal of bacteriology.

[6]  B. Snel,et al.  Function prediction and protein networks. , 2003, Current opinion in cell biology.

[7]  P. Noirot,et al.  A new mutation delivery system for genome‐scale approaches in Bacillus subtilis , 2002, Molecular microbiology.

[8]  J. S. Parkinson,et al.  Collaborative signaling by mixed chemoreceptor teams in Escherichia coli , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[10]  G. Di Lallo,et al.  Use of a two-hybrid assay to study the assembly of a complex multicomponent protein machinery: bacterial septosome differentiation. , 2003, Microbiology.

[11]  Michael Albers,et al.  Elucidation of an Archaeal Replication Protein Network to Generate Enhanced PCR Enzymes* , 2002, The Journal of Biological Chemistry.

[12]  Alasdair C Steven,et al.  Molecular mechanisms in bacteriophage T7 procapsid assembly, maturation, and DNA containment. , 2003, Advances in protein chemistry.

[13]  Gary D Bader,et al.  A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules , 2001, Science.

[14]  C. Baron,et al.  Detergent extraction identifies different VirB protein subassemblies of the type IV secretion machinery in the membranes of Agrobacterium tumefaciens , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Brian E Snydsman,et al.  Assigning function to yeast proteins by integration of technologies. , 2003, Molecular cell.

[17]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[18]  Michael R Sawaya,et al.  Crystal Structure of T7 Gene 4 Ring Helicase Indicates a Mechanism for Sequential Hydrolysis of Nucleotides , 2000, Cell.

[19]  Gary D Bader,et al.  Analyzing yeast protein–protein interaction data obtained from different sources , 2002, Nature Biotechnology.

[20]  M. Frazier,et al.  Realizing the Potential of the Genome Revolution: The Genomes to Life Program , 2003, Science.

[21]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[22]  A. Strunnikov,et al.  Cell cycle‐dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein , 2002, The EMBO journal.

[23]  Z. Ding,et al.  VirE2, a Type IV secretion substrate, interacts with the VirD4 transfer protein at cell poles of Agrobacterium tumefaciens , 2003, Molecular microbiology.

[24]  A. Emili,et al.  Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. , 2004, Journal of proteome research.

[25]  D. Oesterhelt,et al.  Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB , 2002, Molecular microbiology.

[26]  G. Drewes,et al.  Global approaches to protein-protein interactions. , 2003, Current opinion in cell biology.

[27]  Z. Ding,et al.  The outs and ins of bacterial type IV secretion substrates. , 2003, Trends in microbiology.

[28]  Stanley Fields,et al.  A protein linkage map of Escherichia coli bacteriophage T7 , 1996, Nature Genetics.

[29]  Pierre Legrain,et al.  Prediction, assessment and validation of protein interaction maps in bacteria. , 2002, Journal of molecular biology.

[30]  K. McKernan,et al.  Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica. , 2004, Nucleic acids research.

[31]  A. Hochschild,et al.  Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target. , 1998, Genes & development.

[32]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Beckhouse,et al.  Resistance to hydrogen peroxide in Helicobacter pylori: role of catalase (KatA) and Fur, and functional analysis of a novel gene product designated 'KatA-associated protein', KapA (HP0874). , 2002, Microbiology.

[34]  P. Legrain,et al.  Identification of the Helicobacter pylori anti‐σ28 factor , 2001, Molecular microbiology.

[35]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[36]  D. Court,et al.  High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[37]  James C. Hu,et al.  Identification and Mapping of Self-Assembling Protein Domains Encoded by the Escherichia coli K-12 Genome by Use of λ Repressor Fusions , 2004 .

[38]  J. Beckwith,et al.  Assembly of cell division proteins at the E. coli cell center. , 2002, Current opinion in microbiology.

[39]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Sebastian Maurer-Stroh,et al.  Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. , 2003, Molecular cell.

[41]  G. Sachs,et al.  Interactions among the seven Helicobacter pylori proteins encoded by the urease gene cluster. , 2003, American journal of physiology. Gastrointestinal and liver physiology.

[42]  S. Yokoyama,et al.  Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution , 2002, Nature.

[43]  D. Burns,et al.  Type IV transporters of pathogenic bacteria. , 2003, Current opinion in microbiology.

[44]  A. Barabasi,et al.  Functional and topological characterization of protein interaction networks , 2004, Proteomics.

[45]  E. Cascales,et al.  The versatile bacterial type IV secretion systems , 2003, Nature Reviews Microbiology.

[46]  E. Bouveret,et al.  New partners of acyl carrier protein detected in Escherichia coli by tandem affinity purification , 2003, FEBS letters.

[47]  T. Ellenberger,et al.  Essential Amino Acid Residues in the Single-stranded DNA-binding Protein of Bacteriophage T7 , 2002, The Journal of Biological Chemistry.

[48]  C. Richardson,et al.  Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[49]  C. Baron,et al.  Bacterial secrets of secretion: EuroConference on the biology of type IV secretion processes , 2002, Molecular microbiology.

[50]  Pierre Legrain,et al.  Biochemical Characterization of Protein Complexes from the Helicobacter pylori Protein Interaction Map , 2004, Molecular & Cellular Proteomics.

[51]  P. Christie,et al.  Agrobacterium tumefaciens VirB6 Protein Participates in Formation of VirB7 and VirB9 Complexes Required for Type IV Secretion , 2003, Journal of bacteriology.

[52]  S. Ehrlich,et al.  An expanded view of bacterial DNA replication , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[53]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[54]  William C. Ray.  MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments , 2004, Nucleic Acids Res..

[55]  P. Zambryski,et al.  Peptide linkage mapping of the Agrobacterium tumefaciens vir-encoded type IV secretion system reveals protein subassemblies , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[56]  J. Keith Joung,et al.  Activation of prokaryotic transcription through arbitrary protein–protein contacts , 1997, Nature.

[57]  E. Dervyn,et al.  The bacterial condensin/cohesin‐like protein complex acts in DNA repair and regulation of gene expression , 2004, Molecular microbiology.

[58]  Y. Ishino,et al.  Crystal structure of an archaeal DNA sliding clamp: Proliferating cell nuclear antigen from Pyrococcus furiosus , 2001, Protein science : a publication of the Protein Society.