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, 18 (1), 221

Genome-wide Analysis of the Plant-Specific PLATZ Proteins in Maize and Identification of Their General Role in Interaction With RNA Polymerase III Complex

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Genome-wide Analysis of the Plant-Specific PLATZ Proteins in Maize and Identification of Their General Role in Interaction With RNA Polymerase III Complex

Jiechen Wang et al. BMC Plant Biol.

Abstract

Background: PLATZ proteins are a novel class of plant-specific zinc-dependent DNA-binding proteins that are classified as transcription factors (TFs). However, their common biochemical features and functions are poorly understood.

Result: Here, we identified and cloned 17 PLATZ genes in the maize (Zea mays) genome. All ZmPLATZs were located in nuclei, consistent with their predicted role as TFs. However, none of ZmPLATZs was found to have intrinsic activation properties in yeast. Our recent work shows that FL3 (ZmPLATZ12) interacts with RPC53 and TFC1, two critical factors in the RNA polymerase III (RNAPIII) transcription complex. Using the yeast two-hybrid assay, we determined that seven other PLATZs interacted with both RPC53 and TFC1, whereas three had no protein-protein interaction with these two factors. The other six PLATZs interacted with either RPC53 or TFC1. These findings indicate that ZmPLATZ proteins are generally involved in the modulation of RNAPIII-mediated small non-coding RNA transcription. We also identified all of the PLATZ members in rice (Oryza sativa) and Arabidopsis thaliana and constructed a Maximum likelihood phylogenetic tree for ZmPLATZs. The resulting tree included 44 members and 5 subfamilies.

Conclusions: This study provides insight into understanding of the phylogenetic relationship, protein structure, expression pattern and cellular localization of PLATZs in maize. We identified nine and thirteen ZmPLATZs that have protein-protein interaction with RPC53 and TFC1 in the current study, respectively. Overall, the characterization and functional analysis of the PLATZ family in maize will pave the way to understanding RNAPIII-mediated regulation in plant development.

Keywords: Maize; PLATZ; RNA polymerase III; RPC53; TFC1; Transcription factor.

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Figures

Fig. 1
Fig. 1
Schematic diagram of ZmPLATZs. The putative domains or motifs were identified using the Pfam and SMART databases with the default parameters. PLATZ, PLATZ domain; BBOX, B-Box-type zinc finger; SP, signal peptide; CC, coiled coil. Bar, 100 aa
Fig. 2
Fig. 2
Phylogenetic analysis of ZmPLATZs. Maximum likelihood phylogenetic tree summarizes the evolutionary relationships among ZmPLATZs. The numbers under the branches refer to the bootstrap value of the maximum likelihood phylogenetic tree. The length of the branches is proportional to the amino acid variation rates
Fig. 3
Fig. 3
Expression patterns of the ZmPLATZ genes analysed by the public RNA-seq data. The genes are located on the right, and the tissues are indicated at the bottom of each column. The colour bar represents the expression values. S0-S38: developing seed from 0 to 38 DAP (day after pollination); Em10-Em38: developing embryo from 10 to 38 DAP; En6-En38: developing endosperm from 6 to 38 DAP
Fig. 4
Fig. 4
Expression patterns of ZmPLATZ genes by RT-PCR. The gene names are placed on the left, and the examined tissues are indicated on the top of each column. The phylogenetic tree was based on the RNA-seq data (B73 genome version 3). Since ZmPLATZ16 and ZmPLATZ17 were not annotated in B73 genome version 3, they were not included in the tree. Each ZmPLATZ gene was amplified with a specific primer pair for 32 cycles. The genomic DNA bands of ZmPLATZ4 and 17 were not shown, due to their sizes being much larger than those of the cDNA bands. The GRMZM105019 gene was used as control. S1-S6: developing seed from 1 to 6 DAP; En8-En30: developing endosperm from 8 to 30 DAP; Em12-Em24: developing embryo from 12 to 24 DAP
Fig. 5
Fig. 5
Subcellular localization of ZmPLATZs. The GFP gene was fused to the C-terminal of each ZmPLATZ. The constructs were transiently expressed in N. benthamiana leaves via Agrobacteria infiltration. Scale bars = 50 μm
Fig. 6
Fig. 6
Auto-activation assay of ZmPLATZs in yeast Each ZmPLATZ and the endosperm-specific transcription factor O2 as the positive control were fused to the C-terminal of GAL4-BD. The resulting constructs pBD-PLATZs and pBD-O2 were transformed into Y2HGold and selected on the medium plates (SD/−Trp). Then, the transformed yeast colonies were grown on the selection medium plates (SD/−Trp/-His/−Ade)
Fig. 7
Fig. 7
The protein-protein interaction assay of ZmPLATZs and RPC53/TFC1 by yeast two-hybrid assay. Constructs of pAD-RPC53/TFC1 and pBD-PLATZs were transformed into Y2HGold and selected on the medium plates (SD/−Trp/−Leu). Then, the transformed yeast colonies were grown on the selection medium plates (SD/−Trp/−Leu/-His/−Ade)
Fig. 8
Fig. 8
Phylogenetic analysis of ZmPLATZs, OsPLATZs and AtPLATZs. Maximum likelihood phylogenetic tree summarizes the evolutionary relationships among PLATZs. The numbers under the branches refer to the bootstrap values of the maximum likelihood phylogenetic tree. The length of the branches is proportional to the amino acid variation rates

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