Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum

Journal of Bacteriology

Volumn 183, Issue 16, 2001, Pages 4823-4838

  Nolling J ^a   Breton, G ^a   Omelchenko, M V ^a   Makarova, K S ^a   Zeng, Q ^a   Gibson, G ^a   Hong Mei Lee, ^a   Dubois, J ^a   Qiu, D ^a   Hitti, J ^a   Aldredge, T ^a   Ayers, M ^a   Bashirzadeh, R ^a   Bochner, H ^a   Boivin, M ^a   Bross, S ^a   Bush, D ^a   Butler, C ^a   Caron, A ^a   Caruso, A ^a   Cook, R ^a   Daggett, P ^a   Deloughery, C ^a   Egan, J ^a   Ellston, D ^a   Engelstein, M ^a   Ezedi, J ^a   Gilbert, K ^a   Goyal, A ^a   Guerin, J ^a   Ho, T ^a   Holtham, K ^a   Joseph, P ^a   Keagle, P ^a   Kozlovsky, J ^a   LaPlante, M ^a   LeBlanc, G ^a   Lumm, W ^a   Majeski, A ^a   McDougall, S ^a   Mank, P ^a   Mao, J I ^a   Nocco, D ^a   Patwell, D ^a   Phillips, J ^a   Pothier, B ^a   Prabhakar, S ^a   Richterich, P ^a   Rice, P ^a   Rosetti, D ^a   Rossetti, M ^a   Rubenfield, M ^a   Sachdeva, M ^a   Snell, P ^a   Spadafora, R ^a   Spitzer, L ^a   Shimer, G ^a   Thomann, H U ^a   Vicaire, R ^a   Wall, K ^a   Wang, Y ^a   Weinstock, K ^a   Lai Peng Wong, ^a   Wonsey, A ^a   Xu, Q ^a   Zhang, L ^a   Wolf, Y I ^a   Tatusov, R L ^a   Sabathe, F ^a   Doucette Stamm, L ^a   Soucaille, P ^a   Daly, M J ^a   Bennett, G N ^a   Koonin, E V ^a   Smith, D R ^a   more..

^a GENOME THERAPEUTICS CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACILLUS SUBTILIS; CLOSTRIDIUM ACETOBUTYLICUM; COMPARATIVE STUDY; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPOROGENESIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; CHROMOSOMES, BACTERIAL; CLOSTRIDIUM; CONSERVED SEQUENCE; ENZYMES; GENES, BACTERIAL; GENOME, BACTERIAL; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; OPERON; PHYLOGENY; PLASMIDS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOLVENTS;

ARCHAEA; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); BACTERIUM SUBTILIS; CLOSTRIDIUM; CLOSTRIDIUM ACETOBUTYLICUM; CLOSTRIDIUM ACETOBUTYLICUM ATCC 824; POSIBACTERIA;

EID: 0034902930     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.183.16.4823-4838.2001     Document Type: Article

References (88)

1. Iterated profile searches with PSI-BLAST - A tool for discovery in protein databases
2. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
3. Expression of heat shock genes in Clostridium acetobutylicum
4. Cellulosomes - Structure and ultrastructure
5. Molecular biology and genetics of substrate utilization in Clostridia
6. Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay
7. Isolation and characterization of mutants of Clostridium acetobutylicum ATCC 824 deficient in acetoacetyl-coenzyme A:acetate/butyrate:coenzyme A-transferase (EC 2.8.3.9) and other solvent pathway enzymes
8. Physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome
9. The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to degeneration of the strain
10. Solvent forming genes in Clostridia
11. DNA uptake in bacteria
12. New insights and novel developments in Clostridial acetone/ butanol/isopropanol fermentation
13. Solventogenic enzymes of Clostridium acetobutylicum: Catalytic properties, genetic organization, and transcriptional regulation
14. Base-calling automated sequencer traces using phred. I. Accuracy assessment
15. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
16. Identification of a gene in Staphylococcus xylosus encoding a novel glucose uptake protein
17. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
18. The minimal gene complement of Mycoplasma genitalium
19. Butanol fermentation process
20. Regulation of metabolic shifts in Clostridium acetobutylicum ATCC 824
21. Regulation of Clostridium acetobutylicum metabolism as revealed by mixed-substrate steady-state continuous cultures: Role of NADH/NAD ratio and ATP pool
22. Regulation of solvent production in Clostridium acetobutylicum
23. The internal pH of Clostridium acetobutylicum and its effect on the shift from acid to solvent formation
24. Genetic manipulation of acid formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824
25. From complete genomes to measures of substitution rate variability within and between proteins
26. The sigma factors of Bacillus subtilis
27. Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: Need for new phenomenological models for solventogenesis and butanol inhibition?
28. Using CLUSTAL for multiple sequence alignments
29. Variation and evolution of the citric-acid cycle: A genomic perspective
30. Multiple histidine kinases regulate entry into stationary phase and sporulation in Bacillus subtilis
31. Taxonomic relationships among strains of Clostridium acetobutylicum and other phenotypically similar organisms
32. Origins and relationships of industrial solvent-producing clostridial strains
33. Acetone-butanol fermentation revisited
34. Acetone-butanol fermentation by mutants selected for resistance to acetate and butyrate halogen analogs
35. Cloning and DNA sequencing of the genes encoding Clostridium josui scaffolding protein CipA and cellulase Ce1D and identification of their gene products as major components of the cellulosome
36. KEGG: Kyoto encyclopedia of genes and genomes
37. Taxonomy and phylogeny of industrial solven-producing clostridia
38. Structure of the cell-adhesion fragment of intimin from enteropathogenic Escherichia coli
39. The anchorage function of CipA (Ce1L), a scaffolding protein of the Clostridium thermocellum cellulosome
40. The complete genome sequence of the gram-positive bacterium Bacillus subtilis
41. Xylanolytic activity of Clostridium acetobutylicum
42. Purification of characterization of two endoxylanases from Clostridium acetobutylicum ATCC 824
43. Novel families of putative protein kinases in bacteria and archaea: Evolution of the "eukaryotic" protein kinase superfamily
44. Asymmetric substitution patterns in the two DNA strands of bacteria
45. Structure of the In1B leucine-rich repeats, a domain that triggers host cell invasion by the bacterial pathogen L. monocytogenes
46. Analysis of Tn916-induced mutants of Clostridium acetobutylicum altered in solventogenesis and sporulation
47. Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824
48. Genetic and metabolic engineering of Clostridium acetobutylicum ATCC 824
49. Vector systems for the genetic analysis of Clostridium acetobutylicum
50. Vectors for use in Clostridium acetobutylicum
51. Physiology of carbohydrate to solvent conversion by Clostridia
52. History and future potential for the Clostridia in bio/technology
53. Regulation of the sol locus genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 by a putative transcriptional repressor
54. WIT: Integrated system for high-throughout genome sequence analysis and metabolic reconstruction
55. Molecular regulation and metabolic engineering of solvent production by Clostridium acetobutylicum
56. Study of the NADH and NADPH-ferredoxin oxidoreductase activities in Clostridium acetobutylicum
57. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
58. Production of acetone butanol ethanol (ABE) by a hyper-producing mutant strain of Clostridium beijerinckii BA101 and recovery by pervaporation
59. Spo0A directly controls the switch from acid to solvent production in solvent-forming Clostridia
60. Novel phosphotransferase system genes revealed by genome analysis - The complete complement of PTS proteins encoded within the genome of Bacillus subtilis
61. Biochemistry and regulation of acid and solvent formation in Clostridia
62. Catabolite repression and inducer control in Gram-positive bacteria
63. IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
64. SMART: A web-based tool for the study of genetically mobile domains
65. SMART, a simple modular architecture research tool: Identification of signaling domains
66. Terminal-sequence analysis of bacterial ribosomal RNA. Correlation between the 3′-terminal-polypyrimidine sequence of 16-S RNA and translational specificity of the ribosome
67. The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides
68. Isolation of spontaneous butanol-resistant mutants of Clostridium acetobutylicum
69. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics
70. Butanol tolerance and autobacteriocin production by Clostridium acetobutylicum
71. Phylogenetic basis for a taxonomic dissection of the genus Clostridium
72. Phylogenetic relationships
73. Identification of three oligosaccharide binding sites in ricin
74. Molecular genetics of sporulation in Bacillus subtilis
75. Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum
76. A large gene cluster for the clostridium cellulovorans cellulosome
77. The COG database: A tool for genome-scale analysis of protein functions and evolution
78. Stress and growth-phase associated proteins of Clostridium acetobutylicum
79. Regulation of carbon and electron flow in Clostridium acetobutylicum grown in chemostat culture at neutral pH on mixtures of glucose and glycerol
80. SEALS: A system for easy analysis of lots of sequences
81. A comparative study of six different strains of the organism commonly concerned in large-scale production of butyl alcohol and acetone by the biological process
82. Targeted integration of genes into the Clostridium acetobutylicum chromosome
83. Evolution of aminoacyl-tRNA synthetases - Analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
84. The genetic engineering of microbial solvent production
85. Non-globular domains in protein sequences: Automated segmentation using complexity measures