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Microbiology and Molecular Biology Reviews, December 2009, p. 594-651, Vol. 73, No. 4
1092-2172/09/$08.00+0     doi:10.1128/MMBR.00024-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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

Chien-Chi Lo,1 Carol A. Bonner,2 Gary Xie,1 Mark D'Souza,2 and Roy A. Jensen2*

Los Alamos National Laboratory, Bioscience Division, MS M888, Los Alamos, New Mexico 87545,1 Computation Institute, University of Chicago, Chicago, Illinois 606372

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, ASK{alpha} and ASKβ, have been recognized. The ASK{alpha} 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 ASK{alpha} 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.

* Corresponding author. Mailing address: Emerson Hall, University of Florida, P.O. Box 14425, Gainesville, FL 32604. Phone: (352) 475-3019. Fax: (352) 846-3631. E-mail: rjensen{at}ufl.edu

Microbiology and Molecular Biology Reviews, December 2009, p. 594-651, Vol. 73, No. 4
1092-2172/09/$08.00+0     doi:10.1128/MMBR.00024-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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