Characterization of TPP-binding proteins in Methanococci archaeal species

Acetolactate synthase (ALS) is a highly conserved protein family responsible for producing branched chain amino acids. In Methanocaldococcus jannaschii, two ALS proteins, MJ0277 and MJ0663 exist though variations in features between them are noted. Researchers are quick to examine MJ0277 homologs due to their increased function and close relationship, but few have characterized MJ0663 homologs. This study identified homologs for both MJ0277 and MJ0663 in all 15 Methanococci species with fully sequenced genomes. EggNOG database does not define four of the MJ0663 homologs, JH146_1236, WP_004591614, WP_018154400, and EHP89635. BLASTP comparisons suggest these four proteins had around 30% identity to MJ0277 homologs, close to the identity similarities between other MJ0663 homologs to the MJ0277 homologous group. ExPASY physiochemical characterization shows a statistically significant difference in molecular weight and grand average hydropathy between homologous groups. CDD-BLAST showed distinct domains between homologous groups. MJ0277 homologs had TPP_AHAS and PRL06276 while MJ0663 homologs had TPP_enzymes super family and IlvB domains instead. Multiple sequence alignment using PROMALS3D showed the MJ0277 homologs a tighter group than MJ0663 and its homologs. PHYLIP showed these homologous groups as evolutionarily distinct yet equal distance from bacterial ALS proteins of established structure. The four proteins EggNOG did not define had the same features as other MJ0663 homologs. This indicates that JH146_1236, WP_004591614, WP_018154400, and EHP89635, should be included in EggNOG database cluster arCOG02000 with the other MJ0663 homologs.