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Table 3 Major features of the reconstructed gene set of LACA

From: Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

COG class No. of arCOGs Function Implication for LACA
J 152 Translation Complete translation system and essentially complete set of enzymes for tRNA and rRNA modification
including: 61 Ribosomal proteins  
  21 aaRS and related enzymes  
K 55 Transcription Moderately sophisticated transcription control
including: 22 Transcription regulators  
  13 RNA polymerase subunits  
L 61 Replication, recombination and repair Advanced DNA replication and repair system
including: 6 Topoisomerases  
  4 DNA polymerase subunits  
C 84 Energy production and conversion Membrane-based redox bioenergetics; partial TCA cycle
including: 13 Pyruvate oxidation  
  9 TCA cycle  
  9 NADH dehydrogenase or Na+/H+ antiporter  
  8 V-type ATPase-ATP synthase  
G 33 Carbohydrate transport and metabolism Moderately sophisticated sugar metabolism
including: 8 Glycolysis/Gluconeogenesis  
E 108 Amino acid transport and metabolism Enzymes for the biosynthesis of all amino acids
including: 72 Amino acid biosynthesis  
F 49 Nucleotide transport and metabolism Enzymes for the biosynthesis of all nucleotides
including: 29 Nucleotide biosynthesis  
  6 Nucleotide salvage  
H 67 Coenzyme transport and metabolism Enzymes for the biosynthesis of all essential cofactors
including: 60 Cofactor biosynthesis  
I 25 Lipid transport and metabolism Fully developed membrane
including: 19 Lipid biosynthesis  
M 26 Cell wall, membrane and envelope biogenesis Fully developed cell wall
P 48 Inorganic ion transport and metabolism Sophisticated ion uptake system
Q 8 Secondary metabolites biosynthesis, transport and catabolism Limited or unknown
N 5 Cell motility Limited motility and/or conjugation
O 47 Posttranslational modification, protein turnover, chaperones Sophisticated system of protein fate control
including: 2 Proteasome  
D 5 Cell cycle control Limited or unknown
T 10 Signal transduction mechanisms Limited use of bacterial type signal transduction system; original signal transduction
including: 3 Serine/threonine kinase  
U 10 Intracellular trafficking and secretion Fully developed secretion system
including: 3 Preprotein translocase  
V 20 Defense mechanisms Viruses abundant at LACA times
including: 6 CASS proteins  
R, S 183 Poorly characterized or unknown