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Mol. Cells 2011; 31(1): 55-64

Published online November 25, 2010

https://doi.org/10.1007/s10059-011-0001-2

© The Korean Society for Molecular and Cellular Biology

Phylogenetic and Expression Analysis of RNA-binding Proteins with Triple RNA Recognition Motifs in Plants

Lila Peal1, Niranjani Jambunathan1,2, and Ramamurthy Mahalingam1,*

1Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, USA, 2Present Address: Monsanto, Saint Louis, USA

Correspondence to : *Correspondence: ramamurthy.mahalingam@okstate.edu

Received: August 11, 2010; Revised: September 17, 2010; Accepted: September 29, 2010

Abstract

The superfamily of RNA binding proteins (RBPs) is vastly expanded in plants compared to other eukaryotes. A sub-family of RBPs that contain three RNA recognition motifs (RRMs) from the Arabidopsis (24), rice (19) and poplar (37) genomes was analyzed in this study. Phylogenetic analysis with full-length protein sequences of 80 RBPs identified nine clades. The largest clade, comprising 23 members, showed high homology to human RBPs involved in oxidative signaling. Digital northern analysis revealed that Arabidopsis RBPs are transcriptionally responsive to biotic, abiotic and hormonal treatments. Northern blot analysis of eight Arabidopsis RBPs belonging to the tobacco RBP45/47 family showed that these genes respond to ozone stress. AtRBP45b, which shows closest homology to the yeast oxidative stress regulatory protein, CSX1, was expressed in multiple tissues. Two novel splice variant forms of AtRBP45b were identified by 3’RACE analysis. Based on RT-PCR, splice variant AtRBP45b-SV1 was observed only in response to mechanical wounding caused by pathogen or chemical infiltrations and was not detecta-ble in response to salt or temperature stress. Electropho-retic mobility shift assay demonstrated that recombinant full-length and splice variant forms of AtRBP45b bound synthetic RNA. Identifying in vivo RNA targets of AtRBP45b will aid in determining the precise functional role of these proteins during oxidative signaling.

Keywords AtRBP45, electrophoretic mobility shift assay, oxidative signaling, RNA binding proteins, splice variant, stress

Article

Research Article

Mol. Cells 2011; 31(1): 55-64

Published online January 31, 2011 https://doi.org/10.1007/s10059-011-0001-2

Copyright © The Korean Society for Molecular and Cellular Biology.

Phylogenetic and Expression Analysis of RNA-binding Proteins with Triple RNA Recognition Motifs in Plants

Lila Peal1, Niranjani Jambunathan1,2, and Ramamurthy Mahalingam1,*

1Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, USA, 2Present Address: Monsanto, Saint Louis, USA

Correspondence to:*Correspondence: ramamurthy.mahalingam@okstate.edu

Received: August 11, 2010; Revised: September 17, 2010; Accepted: September 29, 2010

Abstract

The superfamily of RNA binding proteins (RBPs) is vastly expanded in plants compared to other eukaryotes. A sub-family of RBPs that contain three RNA recognition motifs (RRMs) from the Arabidopsis (24), rice (19) and poplar (37) genomes was analyzed in this study. Phylogenetic analysis with full-length protein sequences of 80 RBPs identified nine clades. The largest clade, comprising 23 members, showed high homology to human RBPs involved in oxidative signaling. Digital northern analysis revealed that Arabidopsis RBPs are transcriptionally responsive to biotic, abiotic and hormonal treatments. Northern blot analysis of eight Arabidopsis RBPs belonging to the tobacco RBP45/47 family showed that these genes respond to ozone stress. AtRBP45b, which shows closest homology to the yeast oxidative stress regulatory protein, CSX1, was expressed in multiple tissues. Two novel splice variant forms of AtRBP45b were identified by 3’RACE analysis. Based on RT-PCR, splice variant AtRBP45b-SV1 was observed only in response to mechanical wounding caused by pathogen or chemical infiltrations and was not detecta-ble in response to salt or temperature stress. Electropho-retic mobility shift assay demonstrated that recombinant full-length and splice variant forms of AtRBP45b bound synthetic RNA. Identifying in vivo RNA targets of AtRBP45b will aid in determining the precise functional role of these proteins during oxidative signaling.

Keywords: AtRBP45, electrophoretic mobility shift assay, oxidative signaling, RNA binding proteins, splice variant, stress

Mol. Cells
Nov 30, 2023 Vol.46 No.11, pp. 655~725
COVER PICTURE
Kim et al. (pp. 710-724) demonstrated that a pathogen-derived Ralstonia pseudosolanacearum type III effector RipL delays flowering time and enhances susceptibility to bacterial infection in Arabidopsis thaliana. Shown is the RipL-expressing Arabidopsis plant, which displays general dampening of the transcriptional program during pathogen infection, grown in long-day conditions.

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