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Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila.

Fu C, Xiong J, Miao W - BMC Genomics (2009)

Bottom Line: The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events.Evolutionary analysis including codon usage preference, site-specific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes.The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China. cjfu1981@gmail.com

ABSTRACT

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family.

Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, site-specific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes.

Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

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Phylogenetic tree of T. thermophila P450 genes with intron location analysis. Left: The NJ tree with bootstrap values. Right: Predicted P450 gene sequences were drawn as dotted lines, gene sequences with available ESTs were drawn as straight lines. A phase zero splice site lies between two codons, while a phase I splice site lies one base inside a codon in the 3' direction, and a phase II intron is two bases inside a codon in the 3' direction. Intron organization: Green, phase zero; Red, phase I; Blue, phase II. Consensus Introns that share the same aligned position are enclosed in a black square. The three largest families are enclosed in the colored squares.
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Figure 1: Phylogenetic tree of T. thermophila P450 genes with intron location analysis. Left: The NJ tree with bootstrap values. Right: Predicted P450 gene sequences were drawn as dotted lines, gene sequences with available ESTs were drawn as straight lines. A phase zero splice site lies between two codons, while a phase I splice site lies one base inside a codon in the 3' direction, and a phase II intron is two bases inside a codon in the 3' direction. Intron organization: Green, phase zero; Red, phase I; Blue, phase II. Consensus Introns that share the same aligned position are enclosed in a black square. The three largest families are enclosed in the colored squares.

Mentions: P450 genes are classified and annotated on the basis of amino acid sequence identity, phylogenetic homology and gene organization, and a four-digit naming system has been set up to meet the need of the increasing number of newly discovered P450 sequences. All the T. thermophila P450 sequences are distributed into 13 families and 21 sub-families according to the nomenclature criterion of sequence similarity (>40% as a family and >55% as a sub-family) [22], indicating P450s exist as a large gene family in this organism. The phylogenetic analysis of T. thermophila P450 genes obtained using either a neighbor-joining tree or a maximum-likelihood tree gave similar topological nodes, and bootstrap testing showed good reliability of the phylogenetic tree (Figure 1, Additional file 3).


Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila.

Fu C, Xiong J, Miao W - BMC Genomics (2009)

Phylogenetic tree of T. thermophila P450 genes with intron location analysis. Left: The NJ tree with bootstrap values. Right: Predicted P450 gene sequences were drawn as dotted lines, gene sequences with available ESTs were drawn as straight lines. A phase zero splice site lies between two codons, while a phase I splice site lies one base inside a codon in the 3' direction, and a phase II intron is two bases inside a codon in the 3' direction. Intron organization: Green, phase zero; Red, phase I; Blue, phase II. Consensus Introns that share the same aligned position are enclosed in a black square. The three largest families are enclosed in the colored squares.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2691746&req=5

Figure 1: Phylogenetic tree of T. thermophila P450 genes with intron location analysis. Left: The NJ tree with bootstrap values. Right: Predicted P450 gene sequences were drawn as dotted lines, gene sequences with available ESTs were drawn as straight lines. A phase zero splice site lies between two codons, while a phase I splice site lies one base inside a codon in the 3' direction, and a phase II intron is two bases inside a codon in the 3' direction. Intron organization: Green, phase zero; Red, phase I; Blue, phase II. Consensus Introns that share the same aligned position are enclosed in a black square. The three largest families are enclosed in the colored squares.
Mentions: P450 genes are classified and annotated on the basis of amino acid sequence identity, phylogenetic homology and gene organization, and a four-digit naming system has been set up to meet the need of the increasing number of newly discovered P450 sequences. All the T. thermophila P450 sequences are distributed into 13 families and 21 sub-families according to the nomenclature criterion of sequence similarity (>40% as a family and >55% as a sub-family) [22], indicating P450s exist as a large gene family in this organism. The phylogenetic analysis of T. thermophila P450 genes obtained using either a neighbor-joining tree or a maximum-likelihood tree gave similar topological nodes, and bootstrap testing showed good reliability of the phylogenetic tree (Figure 1, Additional file 3).

Bottom Line: The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events.Evolutionary analysis including codon usage preference, site-specific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes.The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China. cjfu1981@gmail.com

ABSTRACT

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family.

Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, site-specific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes.

Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Show MeSH
Related in: MedlinePlus