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Genome-Wide Identification and in Silico Analysis of Poplar Peptide Deformylases
State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
Laboratory for Chemical Defense and Microscale Analysis, P.O. Box 3, Zhijiang 443200, China
Forestry College, Beihua University, Jilin 132013, China
School of Basic Medical Sciences, Jiamusi University, Jiamusi 154000, China
Forestry Research Institution of Heilongjiang Province, Harbin 150081, China
* Author to whom correspondence should be addressed.
Received: 17 January 2012; in revised form: 12 April 2012 / Accepted: 18 April 2012 / Published: 23 April 2012
Abstract: Peptide deformylases (PDF) behave as monomeric metal cation hydrolases for the removal of the N-formyl group (Fo). This is an essential step in the N-terminal Met excision (NME) that occurs in these proteins from eukaryotic mitochondria or chloroplasts. Although PDFs have been identified and their structure and function have been characterized in several herbaceous species, it remains as yet unexplored in poplar. Here, we report on the first identification of two genes (PtrPDF1A and PtrPDF1B) respectively encoding two putative PDF polypeptides in Populus trichocarpa by genome-wide investigation. One of them (XP_002300047.1) encoded by PtrPDF1B (XM_002300011.1) was truncated, and then revised into a complete sequence based on its ESTs support with high confidence. We document that the two PDF1s of Populus are evolutionarily divergent, likely as a result of independent duplicated events. Furthermore, in silico simulations demonstrated that PtrPDF1A and PtrPDF1B should act as similar PDF catalytic activities to their corresponding PDF orthologs in Arabidopsis. This result would be value of for further assessment of their biological activities in poplar, and further experiments are now required to confirm them.
Keywords: peptide deformylase; N-terminal Met excision; in silico simulation; genome-wide investigation; phylogenetic analysis; gene duplication; ghromosome location; gene structure display
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Liu, C.-C.; Liu, B.-G.; Yang, Z.-W.; Li, C.-M.; Wang, B.-C.; Yang, C.-P. Genome-Wide Identification and in Silico Analysis of Poplar Peptide Deformylases. Int. J. Mol. Sci. 2012, 13, 5112-5124.
Liu C-C, Liu B-G, Yang Z-W, Li C-M, Wang B-C, Yang C-P. Genome-Wide Identification and in Silico Analysis of Poplar Peptide Deformylases. International Journal of Molecular Sciences. 2012; 13(4):5112-5124.
Liu, Chang-Cai; Liu, Bao-Guang; Yang, Zhi-Wei; Li, Chun-Ming; Wang, Bai-Chen; Yang, Chuan-Ping. 2012. "Genome-Wide Identification and in Silico Analysis of Poplar Peptide Deformylases." Int. J. Mol. Sci. 13, no. 4: 5112-5124.