Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis.
Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies. In human, six distinct thiolases have been identified. Each of these thiolases is different from the other with respect to sequence, oligomeric state, substrate specificity and subcellular localization. Four sequence fingerprints, identifying catalytic loops of thiolases, have been described. In this study genome searches of two mycobacterial species (Mycobacterium tuberculosis and Mycobacterium smegmatis), were carried out, using the six human thiolase sequences as queries. Eight and thirteen different thiolase sequences were identified in M. tuberculosis and M. smegmatis, respectively. In addition, thiolase-like proteins (one encoded in the Mtb and two in the Msm genome) were found. The purpose of this study is to classify these mostly uncharacterized thiolases and thiolase-like proteins. Several other sequences obtained by searches of genome databases of bacteria, mammals and the parasitic protist family of the Trypanosomatidae were included in the analysis. Thiolase-like proteins were also found in the trypanosomatid genomes, but not in those of mammals. In order to study the phylogenetic relationships at a high confidence level, additional thiolase sequences were included such that a total of 130 thiolases and thiolase-like protein sequences were used for the multiple sequence alignment. The resulting phylogenetic tree identifies 12 classes of sequences, each possessing a characteristic set of sequence fingerprints for the catalytic loops. From this analysis it is now possible to assign the mycobacterial thiolases to corresponding homologues in other kingdoms of life. The results of this bioinformatics analysis also show interesting differences between the distributions of M. tuberculosis and M. smegmatis thiolases over the 12 different classes.
Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland.
Padmanabhan
P
Anbazhagan
Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland.
Rajesh K
RK
Harijan
Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland.
Tiila R
TR
Kiema
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
Neelanjana
N
Janardan
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
M R N
MR
Murthy
Centre for Translational and Chemical Biology, School of Biological Sciences, Michael Swann Building, The King's Buildings, University of Edinburgh, Mayfield Rd, Edinburgh EH9 3JR, UK.
Paul A M
PA
Michels
Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland.
André H
AH
Juffer
Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014, Finland. Electronic address: rik.wierenga@oulu.fi.
Rik K
RK
Wierenga
D000101:Acetyl-CoA C-Acetyltransferase / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000145:classification* / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D016680:Genome, Bacterial; D006801:Humans; D020102:Mycobacterium smegmatis / Q000201:enzymology* / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000201:enzymology* / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods
D001426:Bacterial Proteins; D000101:Acetyl-CoA C-Acetyltransferase
Classification; FadA; FadA5; Lipid metabolism; Mycobacterium; Phylogenetic analysis; Sequence fingerprint; Thiolase; Tuberculosis