Genome-Wide Identification and in Silico Analysis of Poplar Peptide Deformylases

International Journal of Molecular Sciences

Chang-Cai Liu³  Bao-Guang Liu¹  Zhi-Wei Yang²  Chun-Ming Li⁴  Bai-Chen Wang³ 

[1] Forestry College, Beihua University, Jilin 132013, China; E-Mail:;School of Basic Medical Sciences, Jiamusi University, Jiamusi 154000, China; E-Mail:;State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; E-Mail:;Forestry Research Institution of Heilongjiang Province, Harbin 150081, China; E-Mail:

关键词: peptide deformylase;    N-terminal Met excision;    in silico simulation;    genome-wide investigation;    phylogenetic analysis;    gene duplication;    ghromosome location;    gene structure display;   

DOI  :  10.3390/ijms13045112

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.