Genome-wide in silico identification of membrane-bound transcription factors in plant species.

Shixiang Yao,Lili Deng,Kaifang Zeng

doi:10.7717/peerj.4051

Abstract

Membrane-bound transcription factors (MTFs) are located in cellular membranes due to their transmembrane domains. In plants, proteolytic processing is considered to be the main mechanism for MTF activation, which ensures the liberation of MTFs from membranes and further their translocation into the nucleus to regulate gene expression; this process skips both the transcriptional and translational stages, and thus it guarantees the prompt responses of plants to various stimuli. Currently, information concerning plant MTFs is limited to model organisms, including Arabidopsis thaliana and Oryza sativa, and little is known in other plant species at the genome level. In the present study, seven membrane topology predictors widely used by the research community were employed to establish a reliable workflow for MTF identification. Genome-wide in silico analysis of MTFs was then performed in 14 plant species spanning the chlorophytes, bryophytes, gymnosperms, monocots and eudicots. A total of 1,089 MTFs have been identified from a total of 25,850 transcription factors in these 14 plant species. These MTFs belong to 52 gene family, and the top six most abundant families are the NAC (128), SBP (77), C2H2 (70), bZIP (67), MYB-related (65) and bHLH (63) families. The MTFs have transmembrane spans ranging from one to thirteen, and 71.5% and 21.1% of the MTFs have one and two transmembrane motifs, respectively. Most of the MTFs in this study have transmembrane motifs located in either N- or C-terminal regions, indicating that proteolytic cleavage could be a conserved mechanism for MTF activation. Additionally, approximately half of the MTFs in the genome of either Arabidopsis thaliana or Gossypium raimondii could be potentially regulated by alternative splicing, indicating that alternative splicing is another conserved activation mechanism for MTFs. The present study performed systematic analyses of MTFs in plant lineages at the genome level, and provides invaluable information for the research community.

Highlights

Transcription factors play a primary regulatory role in gene transcription and ensure normal growth of plants and promote their adaptation to environmental stress (Li et al, 2011)
To perform genome-wide analyses of the Membranebound transcription factors (MTFs) in the different plant species, seven tools that are widely used to predict transmembrane segments were selected in present study: TMHMM 2.0 (Krogh et al, 2001), HMMTOP (Tusnady & Simon, 2001), PHOBIUS (Kall, Krogh & Sonnhammer, 2004), S-TMHMM (Viklund & Elofsson, 2004), TOPPRED (Vonheijne, 1992), SCAMPI-single (Bernsel et al, 2008) and MEMSAT 1.0 (Jones, Taylor & Thorton, 1994)
Their methods are based on different algorithms such as the hidden Markov model (HMM), the artificial neural network (ANN) and hydrophobicity (Table 2)

Summary

Introduction

Transcription factors play a primary regulatory role in gene transcription and ensure normal growth of plants and promote their adaptation to environmental stress (Li et al, 2011). A small proportion of transcription factors containing transmembrane (TM) motifs are translated in the cytoplasm and rapidly anchored to cellular membranes including plasma, mitochondrial, endoplasmic reticulum (ER) membranes, rather than being translocated to the nucleus (Kim et al, 2010). In response to environmental stimuli and physiological signals, the MTFs can be cleaved near the TM region by a specific protease, and the transcription factor can be released from the membrane and translocated into the nucleus to exert its functions (Che et al, 2010). The proteolytic processing-dependent activation of MTFs skips both transcriptional and translational steps, and it ensures the prompt response of plants to exogenous and endogenous signals

Methods

Results

Conclusion