title: Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution.
abstract: Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.
authors.affiliation: Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; King Saud University, P.O. Box 245714, Riyadh 11312, Saudi Arabia. Electronic address: monaotaibi@ksu.edu.sa.
authors.forename: Mona
authors.initials: M
authors.lastname: Alotaibi
authors.affiliation: Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
authors.forename: Ben Delos
authors.initials: BD
authors.lastname: Reyes
authors.affiliation: Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
authors.forename: Tin
authors.initials: T
authors.lastname: Le
authors.affiliation: Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
authors.forename: Phuong
authors.initials: P
authors.lastname: Luong
authors.affiliation: Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA 92182-7720, USA. Electronic address: faramarz@mail.sdsu.edu.
authors.forename: Faramarz
authors.initials: F
authors.lastname: Valafar
authors.affiliation: Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA. Electronic address: rmetzger@mail.sdsu.edu.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Metzger
authors.affiliation: Natural Selection, Inc., 6480 Weathers Place, Suite 350, San Diego, CA 92121, USA. Electronic address: gfogel@natural-selection.com.
authors.forename: Gary B
authors.initials: GB
authors.lastname: Fogel
authors.affiliation: Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; Department of Chemistry, Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA. Electronic address: dhecht@swccd.edu.
authors.forename: David
authors.initials: D
authors.lastname: Hecht
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D001407:Bacillus / Q000737:chemistry / Q000235:genetics; D001665:Binding Sites; D020134:Catalytic Domain / Q000235:genetics; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D008958:Models, Molecular; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry* / Q000378:metabolism
chemical_list: D013762:Tetrahydrofolate Dehydrogenase
keywords: DHFR; Dihydrofolate Reductase; Evolution; Horizontal Gene Transfer; Network of Coupled Protein Motion; Phylogeny; Plasmid evolution; Structure-based Alignment