Prediction and validation of cis-regulatory elements in 5′ upstream regulatory regions of lectin receptor-like kinase gene family in rice

Abstract

Lectin receptor-like kinases (LecRLKs) play crucial roles in regulating plant growth and developmental processes in response to stress. In transcriptional gene regulation for normal cellular functions, cis-acting regulatory elements (CREs) direct the temporal and spatial gene expression with respect to environmental stimuli. A complete insightful of the transcriptional gene regulation system relies on effective functional analysis of CREs. Here, we analyzed the potential putative CREs present in the promoters of rice LecRLKs genes by using PlantCARE database. The CREs in LecRLKs promoters are associated with plant growth/development, light response, plant hormonal regulation processes, various stress responses, hormonal response like ABA, root-specific expression responsive, drought responsive, and cell and organ specific regulatory elements. The effect of methylation on these cis-regulatory elements was also analyzed. Real-time analysis of rice seedling under various stress conditions showed the expression levels of selected LecRLK genes superimposing the number of different CREs present in 5' upstream region. The overall results showed that the possible CREs function in the selective expression/regulation of LecRLKs gene family and during rice plant development under stress.

Rice lectin receptor‐like kinase provides salinity tolerance by ion homeostasis

“…The LecRLK gene from Oryza sativa with locus ID LOC_Os04g44900 has coding sequence of 2022 bp that encodes a 673 amino acids polypeptide. It comes under subfamily L‐type (Legume lectins) and shows 4‐fold upregulation under salinity stress (Passricha et al, ). The present study is designed to functionally validate the role of O sLecRLK gene in providing salinity tolerance in rice.…”

“…Real‐time PCR method was used to determine the copy number of transgene in T 0 plants by taking sucrose phosphate synthase (SPS) gene as a reference and the analysis was performed as described by Passricha et al (). Transgenic lines with single copy of transgene were further confirmed by Southern blot hybridization.…”

“…The appropriate candidate gene of LecRLK with locus ID LO-C_Os04g44900 was selected on the basis of microarray data and quantitative PCR (qPCR)-based transcript level analysis reported in Passricha, Saifi, Ansari, and Tuteja (2016). This gene was considered for further functional validation.…”

Plant Cis-regulatory elements: methods of identification and applications

“…Asian J Agric & Biol. 2020;8(2):207-222 (Ramer et al, 1992, Fukuda, 1997Passricha et al, 2016) ELI-box3 AAACCAATT ERF1 Response to fungal elicitor (Passricha et al, 2016;Wang et al, 2016) Box-WI TTGACC WRKY factors Unknown nuclear factor (Rushton et al, 1996;Passricha et al, 2016) GC CCCCCG GC-binding protein Enhancer-like element involved in anoxic specific inducibility (Olive et al, 1991;Passricha et al, 2016) GCC Box AGCCGCC Pti4 Function as an ethylene response element (Ohme-Takagi and Shinshi, 1995;Büttner and Singh, 1997;Chakravarthy et al, 2003)…”

Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta

“…This is especially brought about by TF binding to their specific cis -elements present in the 5′ flanking regions of gene(s) (Passricha et al, 2016). Moreover, the patterns of cis -elements present among the promoter and intronic regions decide the levels of gene expression (Rombauts et al, 2003; Brown et al, 2007; Zou et al, 2011; Hernandez-Garcia and Finer, 2014), and any mutation(s) occurring in this region can greatly influence the stress-responsiveness of the coded genes (Wittkopp and Kalay, 2012).…”