Comparative genomics and bioenergetics

Biochimica et Biophysica Acta - Bioenergetics

Volumn 1506, Issue 3, 2001, Pages 147-162

  Castresana, Jose ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Aerobic respiration; Anaerobic respiration; Genomics; Last universal ancestor; Molecular evolution; Photosynthesis

Indexed keywords

ENZYME; RIBOSOME RNA;

ARCHAEBACTERIUM; BACTERIUM; BIOENERGY; BREATHING; COMPARATIVE STUDY; DATA BASE; ENERGY CONSERVATION; ENERGY METABOLISM; EUKARYOTE EVOLUTION; EVOLUTION; GENE MAPPING; GENE SEQUENCE; GENOME ANALYSIS; GRAM NEGATIVE BACTERIUM; MITOCHONDRION; MULTIGENE FAMILY; PHOTOSYNTHESIS; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FAMILY; RESPIRATORY SYSTEM; REVIEW;

ARCHAEA; BACTERIA; ENERGY METABOLISM; EVOLUTION, MOLECULAR; GENOMICS; PHOTOSYNTHESIS; PHYLOGENY;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA; PROTEOBACTERIA;

EID: 0035519262     PISSN: 00052728     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0005-2728(01)00227-4     Document Type: Review

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5. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions
6. The complete genome sequence of Escherichia coli K-12
7. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
8. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
9. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
10. Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: Functional analysis and comparative genomics
11. The complete genome sequence of the gastric pathogen Helicobacter pylori
12. The genome sequence of Rickettsia prowazekii and the origin of mitochondria
13. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
14. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus
15. Complete genome sequence of Treponema pallidum, the syphilis spirochete
16. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3
17. Genome sequence of an obligate intracellular pathogen of humans Chlamydia trachomatis
18. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori
19. Comparative genomes of Chlamydia pneumoniae and C. trachomatis
20. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1
21. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima
22. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1
23. The complete sequence of the mucosal pathogen Ureaplasma urealyticum
24. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
25. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti
26. Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium
27. Genome sequence of Halobacterium species NRC-1
28. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491
29. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences
30. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
31. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum
32. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
33. Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA
34. The genome sequence of the plant pathogen Xylella fastidiosa
35. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen
36. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis
37. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58
38. Massive gene decay in the leprosy bacillus
39. Complete genomic sequence of Pasteurella multocida, Pm70
40. Genome sequence of enterohaemorrhagic Escherichia coli O157H7
41. A genomic perspective on protein families
42. Reconstruction of amino acid biosynthesis pathways from the complete genome sequence
43. Pathway alignment: Application to the comparative analysis of glycolytic enzymes
44. Variation and evolution of the citric-acid cycle: A genomic perspective
45. Monitoring gene expression using DNA microarrays
46. Analysis of the microbial proteome
47. Novel forms of anaerobic respiration of environmental relevance
48. Carbon cycling: The prokaryotic contribution
49. Microbial nitrogen cycles: Physiology, genomics and applications
50. Earth science and evolution genomics and the geosciences
51. KEGG: Kyoto encyclopedia of genes and genomes
52. The COG database: New developments in phylogenetic classification of proteins from complete genomes
53. Basic local alignment search tool
54. The RDP-II (Ribosomal Database Project)
55. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
56. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
57. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
58. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
59. Mitochondrial origins
60. The endosymbiont hypothesis revisited
61. Evolution of organellar genomes
62. Bacterial evolution
63. Ribosomal DNA: Molecular evolution and phylogenetic inference
64. Ribosomal RNA: A key to phylogeny
65. The European small subunit ribosomal RNA database
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69. Where is the root of the universal tree of life?
70. The root of the tree of life in the light of the covarion model
71. The rooting of the universal tree of life is not reliable
72. The winds of (evolutionary) change: Breathing new life into microbiology
73. A phylogenetic analysis of Aquifex pyrophilus
74. Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: Phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences
75. Structural features of cytochrome oxidase
76. The happy family of cytochrome oxidases
77. The superfamily of heme-copper respiratory oxidases
78. Evolution of cytochrome oxidase
79. Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen
80. Evolution of energetic metabolism: The respiration-early hypothesis
81. An archaebacterial terminal oxidase combines core structures of two mitochondrial respiratory complexes
82. A second terminal oxidase in Sulfolobus acidocaldarius
83. Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis
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85. Cytochrome bd terminal oxidase
86. Sequence analysis of cytochrome bd oxidase suggests a revised topology for subunit I
87. Gene structure and quinol oxidase activity of a cytochrome bd-type oxidase from Bacillus stearothermophilus
88. The denitrifying prokaryotes
89. Cell biology and molecular basis of denitrification
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91. Functional, biochemical and genetic diversity of prokaryotic nitrate reductases
92. Nitric oxide reductases in bacteria
93. Adenylylsulphate reductase from the sulphate-reducing archaeon Archaeoglobus fulgidus: Cloning and characterization of the genes and comparison of the enzyme with other iron-sulphur flavoproteins
94. Towards the phylogeny of APS reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes
95. Cloning and nucleotide sequence of the psrA gene of Wolinella succinogenes polysulphide reductase
96. Respiratory chains in the last common ancestor of living organisms
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100. Methanogenesis: Genes, genomes, and who's on first?
101. Biochemistry of methanogenesis: A tribute to Marjory Stephenson
102. Photosynthetic reaction centres: Variations on a common structural theme?
103. The origin and evolution of oxygenic photosynthesis
104. Metabolism of hyperthermophiles
105. Metabolic pathways in Paracoccus denitrificans and closely related bacteria in relation to the phylogeny of prokaryotes
106. About the last common ancestor, the universal life-tree and lateral gene transfer: A reappraisal
107. Reductive evolution of resident genomes
108. Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis
109. Functions of the gene products of Escherichia coli
110. Systems for categorizing functions of gene products
111. Archaea and the prokaryote-to-eukaryote transition
112. Evolution by acquisition: The case for horizontal gene transfers
113. Horizontal gene transfer: Evidence and possible consequences
114. Lateral genomics
115. Reverse gyrase from hyperthermophiles: Probable transfer of a thermoadaptation trait from archaea to bacteria
116. Lateral gene transfer and the nature of bacterial innovation
117. Archaeal and bacterial hyperthermophiles: Horizontal gene exchange or common ancestry?
118. Something for everyone: Horizontal gene transfer in evolution
119. Microbial genes in the human genome: Lateral transfer or gene loss?
120. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates
121. Molecular evidence for an ancient duplication of the entire yeast genome
122. The evolutionary fate and consequences of duplicate genes
123. Yesterday's polyploids and the mystery of diploidization
124. The nature of the last universal ancestor and the root of the tree of life, still open questions
125. The universal ancestor
126. Universal protein families and the functional content of the last universal common ancestor
127. The nature of the last universal common ancestor
128. The nature of the universal ancestor and the evolution of the proteome
129. Reconstruction of ancient molecular phylogeny
130. New archaebacterial genes coding for redox proteins: Implications for the evolution of aerobic metabolism
131. Earth's early atmosphere: Constraints and opportunities for early evolution
132. Environmental oxygen conditions during the origin and early evolution of life
133. Respiratory chains of archaea and extremophiles
134. Generation of proton-motive force by an archaeal terminal quinol oxidase from Sulfolobus acidocaldarius
135. Energy-transducing properties of primary proton pumps reconstituted into archaeal bipolar lipid vesicles
136. Cytochrome oxidase evolved by tinkering with denitrification enzymes
137. The heme-copper oxidase family consists of three distinct types of terminal oxidases and is related to nitric oxide reductase
138. The heme-copper oxidases of Thermus thermophilus catalyze the reduction of nitric oxide: Evolutionary implications
139. Mitochondrial evolution
140. The dual origin of the yeast mitochondrial proteome
141. Origin and evolution of the mitochondrial proteome