Genome-wide analysis reveals the expansion of Cytochrome P450 genes associated with xenobiotic metabolism in rice striped stem borer, Chilo suppressalis.

The Cytochrome P450 (CYP) superfamily is a large group of ancient proteins with enzymatic activities involved in various physiological processes. The rice striped stem borer, Chilo suppressalis, is an important insect pest in rice production. Here, we report the identification and characterization of 77 CYP genes from rice striped stem borer (SSB) through genome and transcriptome sequence analyses. All these CYP genes were confirmed by RT-PCR and direct sequencing. Twenty-eight CYP transcripts have full open reading frame (ORF) and four additional transcripts have a nearly full length coding region. The SSB CYP genes were classified into four clans, the mitochondrial, CYP2, CYP3, and CYP4. Phylogenetic analysis indicated that there was an apparent expansion of the CYP3 clan in insects. The CYP6AB subfamily of the CYP3 clan had nine members in SSB. Evolutionary analysis showed that this subfamily was expanded only in lepidopteran insects. In this study, we identified a new P450 subfamily, CYP321F, which is unique to SSB and located in the genome as tandem repeats. Our work provided a foundation for future studies on the functions and mechanism of P450s in the destructive rice pest.

[1]  M. Schuler.  The Role of Cytochrome P450 Monooxygenases in Plant-Insect Interactions , 1996, Plant physiology.

[2]  D W Nebert,et al.  The P450 gene superfamily: recommended nomenclature. , 1987, DNA.

[3]  May R. Berenbaum,et al.  Jasmonate and salicylate induce expression of herbivore cytochrome P450 genes , 2002, Nature.

[4]  P. Hlavica.  Insect cytochromes P450: topology of structural elements predicted to govern catalytic versatility. , 2011, Journal of inorganic biochemistry.

[5]  R. Feyereisen,et al.  4.1 – Insect Cytochrome P450 , 2005 .

[6]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[7]  D. Nelson,et al.  Cytochrome P450 nomenclature. , 1998, Methods in molecular biology.

[8]  L. Restifo,et al.  Drosophila melanogaster CYP6A8, an insect P450 that catalyzes lauric acid (omega-1)-hydroxylation. , 2004, Biochemical and biophysical research communications.

[9]  H. Sezutsu,et al.  Origins of P 450 diversity , 2012 .

[10]  J. Hemingway,et al.  Genomic analysis of detoxification genes in the mosquito Aedes aegypti. , 2008, Insect biochemistry and molecular biology.

[11]  R. Feyereisen,et al.  Evolution of insect P450. , 2006, Biochemical Society transactions.

[12]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[13]  M. Maïbèche-Coisné,et al.  Pheromone anosmia in a scarab beetle induced by in vivo inhibition of a pheromone-degrading enzyme. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[14]  R. Greenspan,et al.  Molecular analysis of flies selected for aggressive behavior , 2006, Nature Genetics.

[15]  L. Restifo,et al.  Drosophila melanogaster CYP6A8, an insect P450 that catalyzes lauric acid (ω-1)-hydroxylation , 2004 .

[16]  G. Georghiou,et al.  Overview of insecticide resistance , 1990 .

[17]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[18]  E. Kirkness,et al.  Decreased detoxification genes and genome size make the human body louse an efficient model to study xenobiotic metabolism , 2010, Insect molecular biology.

[19]  D. Nebert,et al.  Isolation and sequence of cDNA encoding a cytochrome P-450 from an insecticide-resistant strain of the house fly, Musca domestica. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Nelson,et al.  Cytochrome P450 and the individuality of species. , 1999, Archives of biochemistry and biophysics.

[21]  M. Berenbaum.  Postgenomic Chemical Ecology: From Genetic Code to Ecological Interactions , 2002, Journal of Chemical Ecology.

[22]  J. G. Scott,et al.  Cytochromes P450 and insecticide resistance. , 1999, Insect biochemistry and molecular biology.

[23]  D. Nelson,et al.  The cytochrome P450 (CYP) gene superfamily in Daphnia pulex , 2009, BMC Genomics.

[24]  Wang Hai-yan,et al.  The Research of Applying Primer Premier 5.0 to Design PCR Primer , 2004 .

[25]  M. Berenbaum,et al.  Allelic Variation in the Depressaria pastinacella CYP6AB3 Protein Enhances Metabolism of Plant Allelochemicals by Altering a Proximal Surface Residue and Potential Interactions with Cytochrome P450 Reductase* , 2007, Journal of Biological Chemistry.

[26]  Ning Ma,et al.  BLAST: a more efficient report with usability improvements , 2013, Nucleic Acids Res..

[27]  Nannan Liu,et al.  Genome Analysis of Cytochrome P450s and Their Expression Profiles in Insecticide Resistant Mosquitoes, Culex quinquefasciatus , 2011, PloS one.

[28]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[29]  Peer Bork,et al.  The Genome of the Model Beetle and Pest Tribolium Castaneum Vertebrate-specific Orthologues Insect-specific Orthologues Homology Undetectable Similarity , 2022 .

[30]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[31]  H. Sezutsu,et al.  Origins of P450 diversity , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.