Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides.
Analysis of the genome of Bacillus halodurans strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the comEB gene and the dcdB gene, encoding dCMP deaminase and the bifunctional dCTP deaminase:dUTPase (DCD:DUT), respectively, were both shown to be expressed in B. halodurans, and both genes were subject to repression by the nucleosides thymidine and deoxycytidine. The latter nucleoside presumably exerts its repression after deamination by cytidine deaminase. Both comEB and dcdB were cloned, overexpressed in Escherichia coli, and purified to homogeneity. Both enzymes were active and displayed the expected regulatory properties: activation by dCTP for dCMP deaminase and dTTP inhibition for both enzymes. Structurally, the B. halodurans enzyme resembled the Mycobacterium tuberculosis enzyme the most. An investigation of sequenced genomes from other species of the genus Bacillus revealed that not only the genome of B. halodurans but also the genomes of Bacillus pseudofirmus, Bacillus thuringiensis, Bacillus hemicellulosilyticus, Bacillus marmarensis, Bacillus cereus, and Bacillus megaterium encode both the dCMP deaminase and the DCD:DUT enzymes. In addition, eight dcdB homologs from Bacillus species within the genus for which the whole genome has not yet been sequenced were registered in the NCBI Entrez database.
Department of Chemistry, Technical University of Denmark, Lyngby, Denmark.
Christian Berg
CB
Oehlenschlæger
Department of Chemistry, Technical University of Denmark, Lyngby, Denmark.
Monika Nøhr
MN
Løvgreen
Metabolic Signaling and Regulation Group, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
Eva
E
Reinauer
Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Copenhagen, Denmark.
Emilia
E
Lehtinen
Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Copenhagen, Denmark.
Marie-Louise Lindberg
ML
Pind
Department of Chemistry, Technical University of Denmark, Lyngby, Denmark ph@kemi.dtu.dk willemoes@bio.ku.dk.
Pernille
P
Harris
Metabolic Signaling and Regulation Group, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
Jan
J
Martinussen
Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Copenhagen, Denmark ph@kemi.dtu.dk willemoes@bio.ku.dk.
Martin
M
Willemoës
D000595:Amino Acid Sequence; D001407:Bacillus / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D053898:Biosynthetic Pathways; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000378:metabolism*; D003844:DCMP Deaminase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D003854:Deoxyribonucleotides / Q000378:metabolism*; D003856:Deoxyuracil Nucleotides / Q000096:biosynthesis*; D007700:Kinetics; D008969:Molecular Sequence Data; D009709:Nucleotide Deaminases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
D001426:Bacterial Proteins; D003854:Deoxyribonucleotides; D003856:Deoxyuracil Nucleotides; D003596:Cytosine; C007267:2'-deoxyuridylic acid; D009709:Nucleotide Deaminases; D003844:DCMP Deaminase; C019988:dCTP deaminase