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

Liu, Chang-Cai; Liu, Baoguang; Yang, Zhiwei; Li, Chunming; Wang, Baichen; Yang, Chuanping

doi:10.3390/ijms13045112

Cited by 5 publications

(4 citation statements)

References 29 publications

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“…[ 12 ]. The tandem gene duplication in poplar was determined according to the criteria that five or fewer gene loci occurred within a range of 100 kb distance [ 17 , 18 , 30 – 32 ].…”

Section: Methodsmentioning

confidence: 99%

In Silico Identification and Characterization of N-Terminal Acetyltransferase Genes of Poplar (Populus trichocarpa)

Zhu

Wang

et al. 2014

IJMS

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N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A–F), being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.

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“…[ 12 ]. The tandem gene duplication in poplar was determined according to the criteria that five or fewer gene loci occurred within a range of 100 kb distance [ 17 , 18 , 30 – 32 ].…”

Section: Methodsmentioning

confidence: 99%

In Silico Identification and Characterization of N-Terminal Acetyltransferase Genes of Poplar (Populus trichocarpa)

Zhu

Wang

et al. 2014

IJMS

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“…Human genes of peptide deformylase ( def ) have been cloned and expressed, and the resulting human peptide deformylase (HsPDF) has been studied extensively [1,11,12,13]. HsPDF distributes over the mitochondrion in human cells, and also functions similarly to the PDF in pathogenic microorganisms, which catalyzes the deformylation of polypeptides [14,15,16,17]. Inhibition of HsPDF results in mitochondrial membrane depolarization and promotes cell death [13,18].…”

Section: Introductionmentioning

confidence: 99%

Structure-Based Drug Design of Small Molecule Peptide Deformylase Inhibitors to Treat Cancer

et al. 2016

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Human peptide deformylase (HsPDF) is an important target for anticancer drug discovery. In view of the limited HsPDF, inhibitors were reported, and high-throughput virtual screening (HTVS) studies based on HsPDF for developing new PDF inhibitors remain to be reported. We reported here on diverse small molecule inhibitors with excellent anticancer activities designed based on HTVS and molecular docking studies using the crystal structure of HsPDF. The compound M7594_0037 exhibited potent anticancer activities against HeLa, A549 and MCF-7 cell lines with IC 50s of 35.26, 29.63 and 24.63 µM, respectively. Molecular docking studies suggested that M7594_0037 and its three derivatives could interact with HsPDF by several conserved hydrogen bonds. Moreover, the pharmacokinetic and toxicity properties of M7594_0037 and its derivatives were predicted using the OSIRIS property explorer. Thus, M7594_0037 and its derivatives might represent a promising scaffold for the further development of novel anticancer drugs.

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“…Therefore, NME of the nuclear-encoded proteins requires only methionine aminopeptidase (MAP; EC 3.4.11.18) activity, which proteolytically removes the N-terminal Met [4], [6]. NME of the plastid-encoded proteins requires MAP activity and peptide deformylase (PDF) activity [7]. The latter enzymatic activity is required for the removal of the Fo groups, thereby unmasking the amino group of the first Met and allowing the subsequent action of MAP [1], [5], [8].…”

Section: Introductionmentioning

confidence: 99%

Identification and Analysis of the Acetylated Status of Poplar Proteins Reveals Analogous N-Terminal Protein Processing Mechanisms with Other Eukaryotes

et al. 2013

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BackgroundThe N-terminal protein processing mechanism (NPM) including N-terminal Met excision (NME) and N-terminal acetylation (Nα-acetylation) represents a common protein co-translational process of some eukaryotes. However, this NPM occurred in woody plants yet remains unknown.Methodology/Principal FindingsTo reveal the NPM in poplar, we investigated the Nα-acetylation status of poplar proteins during dormancy by combining tandem mass spectrometry with TiO2 enrichment of acetylated peptides. We identified 58 N-terminally acetylated (Nα-acetylated) proteins. Most proteins (47, >81%) are subjected to Nα-acetylation following the N-terminal removal of Met, indicating that Nα-acetylation and NME represent a common NPM of poplar proteins. Furthermore, we confirm that poplar shares the analogous NME and Nα-acetylation (NPM) to other eukaryotes according to analysis of N-terminal features of these acetylated proteins combined with genome-wide identification of the involving methionine aminopeptidases (MAPs) and N-terminal acetyltransferase (Nat) enzymes in poplar. The Nα-acetylated reactions and the involving enzymes of these poplar proteins are also identified based on those of yeast and human, as well as the subcellular location information of these poplar proteins.Conclusions/SignificanceThis study represents the first extensive investigation of Nα-acetylation events in woody plants, the results of which will provide useful resources for future unraveling the regulatory mechanisms of Nα-acetylation of proteins in poplar.

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

Cited by 5 publications

References 29 publications

In Silico Identification and Characterization of N-Terminal Acetyltransferase Genes of Poplar (Populus trichocarpa)

In Silico Identification and Characterization of N-Terminal Acetyltransferase Genes of Poplar (Populus trichocarpa)

Structure-Based Drug Design of Small Molecule Peptide Deformylase Inhibitors to Treat Cancer

Identification and Analysis of the Acetylated Status of Poplar Proteins Reveals Analogous N-Terminal Protein Processing Mechanisms with Other Eukaryotes

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