Article
You have full text access to this OnlineOpen article
Exploiting genomic patterns to discover new supramolecular protein assemblies
Article first published online: 2 DEC 2008
DOI: 10.1002/pro.1
Copyright © 2008 The Protein Society
Additional Information
How to Cite
Beeby, M., Bobik, T. A. and Yeates, T. O. (2009), Exploiting genomic patterns to discover new supramolecular protein assemblies. Protein Science, 18: 69–79. doi: 10.1002/pro.1
Publication History
- Issue published online: 16 DEC 2008
- Article first published online: 2 DEC 2008
- Manuscript Accepted: 22 SEP 2008
- Manuscript Revised: 19 SEP 2008
- Manuscript Received: 30 JUL 2008
Funded by
- BER Program, U.S. Department of Energy Office of Science
References
- 1, , , , , ( 2001) Microcompartments in prokaryotes: carboxysomes and related polyhedra. Appl Environ Microbiol 67: 5351–5361.
- 2ShivelyJM, editor. Microbiology Monographs, Vol. 2: Complex Intracellular Structures in Prokaryotes. Berlin: Springer; 2006.
- 3, , , , , , ( 2005) Protein structures forming the shell of primitive bacterial organelles. Science 309: 936–938.
- 4, , , , , , ( 2008) Atomic-level models of the bacterial carboxysome shell. Science 319: 1083–1086.
- 5, , , , ( 2008) Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 6: 681–691.
- 6, , , ( 1973) Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus. Science 182: 584–586.
- 7, ( 1989) Isolation and characterization of high CO2-requiring-mutants of the cyanobacterium Synechococcus PCC7942: two phenotypes that accumulate inorganic carbon but are apparently unable to generate CO2 within the carboxysome. Plant Physiol 91: 514–586.
- 8, , , ( 1980) Relations between D-ribulose-1,5-bisphosphate carboxylase, carboxysomes, and CO2 fixing capacity in the obligate chemolithotroph Thiobacillus neapolitanus grown under different limitations in the chemostat. Arch Microbiol 124: 185–189.
- 9, , , , ( 1999) The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B12-dependent 1, 2-propanediol degradation. J Bacteriol 181: 5967–5975.
- 10, , , ( 2002) Carboxysome genomics: a status report. Funct Plant Biol 29: 175–182.
- 11, , ( 1994) The control region of the pdu/cob regulon in Salmonella typhimurium. J Bacteriol 176: 5474–5482.
- 12, ( 2006) Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol 188: 2865–2874.
- 13( 2006) Polyhedral organelles compartmenting bacterial metabolic processes. Appl Microbiol Biotechnol 70: 517–525.
- 14, , , ( 1994) Isolation and characterization of a carboxysome shell gene from Thiobacillus neapolitanus. Mol Microbiol 12: 647–654.Direct Link:
- 15, , ( 2008) Pfam 10 years on: 10,000 families and still growing. Brief Bioinf 9: 210–219.
- 16, , . Carboxysomes and carboxysome-like inclusions. In: ShivelyJM, editor. Complex intracellular structures in prokaryotes. Berlin: Springer-Verlag; 2006. pp 141–165
- 17, , , , ( 1998) The functioning of the CO2 concentrating mechanism in several cyanobacterial strains: a review of general physiological characteristics, genes, proteins, and recent advances. Can J Bot 76: 973–1002.
- 18, , , ( 1999) The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181: 5317–5329.
- 19, , ( 1995) Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster. J Bacteriol 177: 1357–1366.
- 20, , , , , , ( 2007) The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography. J Mol Biol 372: 764–773.
- 21, , , , , , ( 2006) Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. J Mol Biol 364: 526–535.
- 22, , , , , , , ( 2007) Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol 5: e144.
- 23
- 24, , ( 1985) Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229: 1358–1365.
- 25, , , , , , , , , ( 1985) Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317: 145–153.
- 26, ( 1997) Quasi-equivalent viruses: a paradigm for protein assemblies. J Mol Biol 269: 665–675.
- 27, , , ( 2008) Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure 16: 1324–1332.
- 28, , ( 2004) Structural/functional homology between the bacterial and eukaryotic cytoskeletons. Curr Opin Cell Biol 16: 24–31.
- 29
- 30, , , ( 2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 10: 1204–1210.
- 31, ( 2007) How electron cryotomography is opening a new window onto prokaryotic ultrastructure. Curr Opin Struct Biol 17: 260–267.
- 32, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ( 2007) New developments in the InterPro database. Nucleic Acids Res 35: D224–228.
- 33, , , , ( 2007) Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells. Biochem Soc Trans 35: 508–11.
- 34, ( 1993) Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein-secretion apparatus: a general system for the formation of surface-associated protein complexes. Mol Microbiol 10: 233–43.Direct Link:
- 35
- 36, ( 1999) Characterization of a phycoerythrin without alpha-subunits from a unicellular red alga. J Biol Chem 274: 2472–82.
- 37, , ( 2007) The tad locus: postcards from the widespread colonization island. Nat Rev Microbiol 5: 363–75.
- 38, , , ( 2008) Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae. J Mol Biol 377: 91–103.
- 39, , ( 2006) The TadV protein of Actinobacillus actinomycetemcomitans is a novel aspartic acid prepilin peptidase required for maturation of the Flp1 pilin and TadE and TadF pseudopilins. J Bacteriol 188: 6899–914.
- 40( 2002) Alpha-crystallin-type heat shock proteins: socializing minichaperones in the context of a multichaperone network. Microbiol Mol Biol Rev 66: 64–93.
- 41, ( 2000) Chaperone activity and homo- and hetero-oligomer formation of bacterial small heat shock proteins. J Biol Chem 275: 37212–37218.
- 42( 1982) Phycobilisomes: structure and dynamics. Annu Rev Microbiol 36: 173–198.
- 43, , , , ( 1985) X-ray crystallographic structure of the light-harvesting biliprotein C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus and its resemblance to globin structures. J Mol Biol 184: 257–277.
- 44, , ( 2004) Type IV pilus structure and bacterial pathogenicity. Nat Rev Microbiol 2: 363–378.
- 45, , , , , , , , , ( 2006) Characterization of the pilin ortholog of the Helicobacter pylori type IV cag pathogenicity apparatus, a surface-associated protein expressed during infection. J Bacteriol 188: 5865–5877.
- 46( 1964) Starch-gel electrophoresis—application to the classification of pituitary proteins and polypeptides. Metab Clin Exp 13: 985–1002.
- 47, ( 1968) Size and charge isomer separation and estimation of molecular weights of proteins by disc gel electrophoresis. Arch Biochem Biophys 126: 155–164.
- 48, , , ( 2004) The role of the sulfur globule proteins of Allochromatium vinosum: mutagenesis of the sulfur globule protein genes and expression studies by real-time RT-PCR. Arch Microbiol 182: 165–174.
- 49, , , ( 1998) Molecular genetic evidence for extracytoplasmic localization of sulfur globules in Chromatium vinosum. Arch Microbiol 169: 434–444.
- 50, , , ( 2007) Isolated poly(3-hydroxybutyrate) (PHB) granules are complex bacterial organelles catalyzing formation of PHB from acetyl coenzyme A (CoA) and degradation of PHB to acetyl-CoA. J Bacteriol 189: 8250–8256.
- 51, , , , , , , ( 2004) The complex structure of polyhydroxybutyrate (PHB) granules: four orthologous and paralogous phasins occur in Ralstonia eutropha. Microbiology 150: 2301–2311.
- 52
- 53, , , , ( 1998) Structural characteristics of halobacterial gas vesicles. Microbiology 144 (Pt 5): 1331–1342.
- 54, ( 2004) Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. J Bacteriol 186: 3182–3186.
- 55, ( 1988) The heat-shock proteins. Annu Rev Genet 22: 631–677.
- 56, , , ( 2005) The small heat shock protein IbpA of Escherichia coli cooperates with IbpB in stabilization of thermally aggregated proteins in a disaggregation competent state. J Biol Chem 280: 12292–12298.
- 57, ( 1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23: 358–361.
- 58, , , ( 2008) Assembly reflects evolution of protein complexes. Nature 453: 1262–1265.
- 59, , ( 2006) Genome reviews: standardizing content and representation of information about complete genomes. OMICS 10: 114–118.
- 60, , , , ( 1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 96: 2896–2901.

1469-896X/asset/olbannerleft.gif?v=1&s=d218899ae53b2862ab119790ed504b8d72122fb3)
1469-896X/asset/olbannerright.gif?v=1&s=59470eb9a1d9b7b13b1be75e9445e6c46ee2214f)
