Cohesion Group Approach for Evolutionary Analysis of Aspartokinase, an Enzyme That Feeds a Branched Network of Many Biochemical Pathways

Abstract

SUMMARY Aspartokinase (Ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. Lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ASK network or from alternative pathways. Ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. Two subhomology divisions, ASKα and ASKβ, have been recognized. The ASKα subhomology division is the most ancient, being widely distributed throughout the Archaea and Eukarya and in some Bacteria. Within an indel region of about 75 amino acids near the N terminus, ASKβ sequences differ from ASKα sequences by the possession of a proposed ancient deletion. ASKβ sequences are present in most Bacteria and usually exhibit an in-frame internal translational start site that can generate a small Ask subunit that is identical to the C-terminal portion of the larger subunit of a heterodimeric unit. Particularly novel are ask genes embedded in gene contexts that imply specialization for ectoine (osmotic agent) or aromatic amino acids. The cohesion group approach is well suited for the easy recognition of relatively recent lateral gene transfer (LGT) events, and many examples of these are described. Given the current density of genome representation for Proteobacteria, it is possible to reconstruct more ancient landmark LGT events. Thus, a plausible scenario in which the three well-studied and iconic Ask homologs of Escherichia coli are not within the vertical genealogy of Gammaproteobacteria, but rather originated via LGT from a Bacteroidetes donor, is supported.

The AlternativeTranslational Profile That Underlies the Immune-Evasive State of Persistence in Chlamydiaceae Exploits Differential Tryptophan Contents of the Protein Repertoire

“…It seems clear that up-Trp selection occurred in the Chlamydiaceae. Eight aspartokinases in CG-09 are fused to DAP decarboxylase, the last enzyme of lysine biosynthesis, and have been proposed to have originated from the Bacteroidetes lineage (74). The E. coli enzyme belongs to CG-21, a group which has only a slightly higher Trp content than the average of all the genomes included.…”

“…Entries in either table highlighted with horizontal green bars show proteins having local concentrations of Trp residues, i.e., locations where at least three amino acid residues in a scanning window of six residues are Trp. Table S3 is a version of the sortable, dynamic table used for the previous analysis of aspartokinase (74), but it is expanded to contain Trp content data. Two additional tables ( Table S4 and Table S5) are not specifically referred to in this paper, but they may be a resource of interest for some readers.…”

Genetic and Biochemical Aspects of Ectoine Biosynthesis in Moderately Halophilic and Halotolerant Methylotrophic Bacteria

“…Other described species of the genus are non-halophilic. It could be proposed that the ect-operon ubiquity in ancient prokaryotic world that was largely marine, followed by loss in lineages that became adapted to a terrestrial environment (Lo et al, 2009). It is also possible that an ancestor, terrestrial species of Methylobacter adapted to marine ecosystem by acquiring ectoine biosynthesis genes from phylogenetically distant species.…”

“…It should be mentioned that in gram-positive bacteria ectoine is not the sole osmoprotectant and other organic compatible solutes belonging to the glutamate family amino acids, glutamate, glutamine and/or proline contribute to osmotic balance (Kuhlmann and Bremer, 2002;Lo et al, 2009;Saum and Muller, 2007;2008a;2008b). (underlined) and those from other bacteria possessing ect genes.…”

“…It may explain the absence of the ask homologues in the ectgene cluster of gram-positive bacteria. Remarkably, the halophilic Firmicutes typically possess multiple ask homologues not linked to the ect-genes (Lo et al, 2009).…”