Interaction network containing conserved and essential protein complexes in Escherichia coli

Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (∼ 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.

[1]  W. Broughton,et al.  Control of leghaemoglobin synthesis in snake beans. , 1971, The Biochemical journal.

[2]  P. Lerouge,et al.  Sulphated lipo-oligosaccharide signals of Rhizobium meliloti elicit root nodule organogenesis in alfalfa , 1991, Nature.

[3]  J. Downie,et al.  Resistance to nodulation of cv. Afghanistan peas is overcome by nodX, which mediates an O‐acetylation of the Rhizobium leguminosarum lipo‐oligosaccharide nodulation factor , 1993, Molecular microbiology.

[4]  M. O’Donnell,et al.  Assembly of a Chromosomal Replication Machine: Two DNA Polymerases, a Clamp Loader, and Sliding Clamps in One Holoenzyme Particle. , 1995, The Journal of Biological Chemistry.

[5]  M. O’Donnell,et al.  Assembly of a Chromosomal Replication Machine: Two DNA Polymerases, a Clamp Loader, and Sliding Clamps in One Holoenzyme Particle. , 1995, The Journal of Biological Chemistry.

[6]  D. Ehrhardt,et al.  Calcium Spiking in Plant Root Hairs Responding to Rhizobium Nodulation Signals , 1996, Cell.

[7]  F. Neidhart.  Escherichia coli and Salmonella. , 1996 .

[8]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[9]  W. Webb,et al.  Exchange of protein molecules through connections between higher plant plastids. , 1997, Science.

[10]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[11]  T. Thykjær,et al.  Symbiotic mutants deficient in nodule establishment identified after T-DNA transformation of Lotus japonicus , 1998, Molecular and General Genetics MGG.

[12]  F. Dazzo,et al.  Nodule Organogenesis and Symbiotic Mutants of the Model Legume Lotus japonicus , 1998 .

[13]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[14]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[15]  S. Kawasaki,et al.  Genome Analysis of Lotus japonicus , 2000, Journal of Plant Research.

[16]  J. Feijó,et al.  Ion changes in legume root hairs responding to Nod factors. , 2000, Plant physiology.

[17]  L. Schauser,et al.  The Lotus japonicus LjSym4 gene is required for the successful symbiotic infection of root epidermal cells. , 2000, Molecular plant-microbe interactions : MPMI.

[18]  D. Court,et al.  An efficient recombination system for chromosome engineering in Escherichia coli. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[19]  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.

[20]  S. Akao,et al.  Isolation of two different phenotypes of mycorrhizal mutants in the model legume plant Lotus japonicus after EMS-treatment. , 2000, Plant & cell physiology.

[21]  M. Kawaguchi,et al.  Providing the basis for genomics in Lotus japonicus: the accessions Miyakojima and Gifu are appropriate crossing partners for genetic analyses , 2001, Molecular Genetics and Genomics.

[22]  Ian M. Donaldson,et al.  BIND: the Biomolecular Interaction Network Database , 2001, Nucleic Acids Res..

[23]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[24]  H. Kouchi,et al.  Responses of a model legume Lotus japonicus to lipochitin oligosaccharide nodulation factors purified from Mesorhizobium loti JRL501. , 2001, Molecular plant-microbe interactions : MPMI.

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

[26]  G. Oldroyd.  Dissecting Symbiosis: Developments in Nod Factor Signal Transduction , 2001 .

[27]  Monica Riley,et al.  A functional update of the Escherichia coli K-12 genome , 2001, Genome Biology.

[28]  M Taketa,et al.  Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[29]  M. Parniske,et al.  Dual requirement of the LjSym4 gene for mycorrhizal development in epidermal and cortical cells of Lotus japonicus roots. , 2002, The New phytologist.

[30]  M. Parniske,et al.  Evolution of signal transduction in intracellular symbiosis. , 2002, Trends in plant science.

[31]  H. Nakayama.  RecQ family helicases: roles as tumor suppressor proteins , 2002, Oncogene.

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

[33]  S. Tabata,et al.  Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-mb regions of the genome. , 2002, DNA research : an international journal for rapid publication of reports on genes and genomes.

[34]  H. Bussey,et al.  Comprehensive essential gene identification as a platform for novel anti-infective drug discovery. , 2002, Current pharmaceutical design.

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

[36]  S. Akao,et al.  Root, root hair, and symbiotic mutants of the model legume Lotus japonicus. , 2002, Molecular plant-microbe interactions : MPMI.

[37]  Eugene V Koonin,et al.  No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly , 2003, BMC Evolutionary Biology.

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

[39]  Joel P. Brockman,et al.  RecQ Helicase Stimulates Both DNA Catenation and Changes in DNA Topology by Topoisomerase III* , 2003, Journal of Biological Chemistry.

[40]  Z N Oltvai,et al.  Evolutionary conservation of motif constituents in the yeast protein interaction network , 2003, Nature Genetics.

[41]  Dennis P Wall,et al.  A simple dependence between protein evolution rate and the number of protein-protein interactions , 2003, BMC Evolutionary Biology.

[42]  S. Long,et al.  Rhizobium-lnduced calcium spiking in Lotus japonicus. , 2003, Molecular plant-microbe interactions : MPMI.

[43]  S. Tabata,et al.  Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases , 2003, Nature.

[44]  Edward M Marcotte,et al.  Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages , 2003, Nature Biotechnology.

[45]  Martin Parniske,et al.  A TILLING Reverse Genetics Tool and a Web-Accessible Collection of Mutants of the Legume Lotus japonicus 1 , 2003, Plant Physiology.

[46]  Sophia Tsoka,et al.  The phylogenetic extent of metabolic enzymes and pathways. , 2003, Genome research.

[47]  Simon Kasif,et al.  Identification of functional links between genes using phylogenetic profiles , 2003, Bioinform..

[48]  Ute Curth,et al.  DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery. , 2003, Nucleic acids research.

[49]  Christian von Mering,et al.  STRING: a database of predicted functional associations between proteins , 2003, Nucleic Acids Res..

[50]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[51]  Matteo Pellegrini,et al.  Prolinks: a database of protein functional linkages derived from coevolution , 2004, Genome Biology.

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

[53]  T. Hughes,et al.  High-definition macromolecular composition of yeast RNA-processing complexes. , 2004, Molecular cell.

[54]  B. Roe,et al.  Medicago truncatula DMI1 Required for Bacterial and Fungal Symbioses in Legumes , 2004, Science.

[55]  M. Gerstein,et al.  Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. , 2004, Genome research.

[56]  Maureen R. Hanson,et al.  Plastids and stromules interact with the nucleus and cell membrane in vascular plants , 2004, Plant Cell Reports.