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.
Highlights
In all organisms, the protein synthesis machinery requires newly synthesized peptides to start systematically with methionine (Met) [1]
To calibrate our identification of the two peptide deformylase (PDF) genes from JGI poplar database, their encoding proteins were further compared by a BLASTP search against NCBI Reference sequence (RefSeq) database, which provides a non-redundant and validated collection of sequences representing genomic data, transcripts and proteins [16,17]
Phylogenetic analysis demonstrates that PDFs are grouped as type 1 (PDF1) of Populus is encoded by evolutionarily divergent genes, which is consistent with previous reports in Arabidopsis and rice (PDF1A and PDF1B; Figure 3a) [2]
Summary
The protein synthesis machinery requires newly synthesized peptides to start systematically with methionine (Met) [1]. Together with the release of complete genome sequences for different organisms, have led to the identification of PDFs in eukaryotes; two PDFs have been identified in Arabidopsis [8,9], three in rice [10] and one in humans [11]. Since these PDFs do not contain the two insertions typical of PDF2 molecules, all eukaryotic PDFs are grouped as type 1 (PDF1). This result would be valuable towards further assessment of their functional roles in poplar
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