In silico identification of cis-regulatory elements of phosphate transporter genes in rice (Oryza sativa L.)

Hatorangan, Marcelinus Rocky; Sentausa, Erwin; Wijaya, Grace Yasmein

doi:10.1007/s12892-008-0054-8

Cited by 14 publications

(5 citation statements)

References 27 publications

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“…The RAV1 protein contains Ap2-like and B3-like domains [ 43 ]. AP2 is a member of the transcription factor family unique to plants and is a key regulator of several developmental processes in the plant life cycle including floral organ identity determination [ 44 ].…”

Section: Resultsmentioning

confidence: 99%

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Putative cis-regulatory elements in genes highly expressed in rice sperm cells

et al. 2011

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BackgroundThe male germ line in flowering plants is initiated within developing pollen grains via asymmetric division. The smaller cell then becomes totally encased within a much larger vegetative cell, forming a unique "cell within a cell structure". The generative cell subsequently divides to give rise to two non-motile diminutive sperm cells, which take part in double fertilization and lead to the seed set. Sperm cells are difficult to investigate because of their presence within the confines of the larger vegetative cell. However, recently developed techniques for the isolation of rice sperm cells and the fully annotated rice genome sequence have allowed for the characterization of the transcriptional repertoire of sperm cells. Microarray gene expression data has identified a subset of rice genes that show unique or highly preferential expression in sperm cells. This information has led to the identification of cis-regulatory elements (CREs), which are conserved in sperm-expressed genes and are putatively associated with the control of cell-specific expression.FindingsWe aimed to identify the CREs associated with rice sperm cell-specific gene expression data using in silico prediction tools. We analyzed 1-kb upstream regions of the top 40 sperm cell co-expressed genes for over-represented conserved and novel motifs. Analysis of upstream regions with the SIGNALSCAN program with the PLACE database, MEME and the Mclip tool helped to find combinatorial sets of known transcriptional factor-binding sites along with two novel motifs putatively associated with the co-expression of sperm cell-specific genes.ConclusionsOur data shows the occurrence of novel motifs, which are putative CREs and are likely targets of transcriptional factors regulating sperm cell gene expression. These motifs can be used to design the experimental verification of regulatory elements and the identification of transcriptional factors that regulate sperm cell-specific gene expression.

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Section: Resultsmentioning

confidence: 99%

“…Some reports about CRE and promoter duplications indicate that the duplication numbers of CREs might participate in leveling the mRNA concentration or gene expression [ 44 ]. Thus, these investigations may reveal some clues about synchronous expression of this subset of genes in sperm cells.…”

Section: Resultsmentioning

confidence: 99%

Putative cis-regulatory elements in genes highly expressed in rice sperm cells

et al. 2011

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“…Further motifs in MC1 are related to organ specificity (ROOTMOTIFTAPOX1 [66]) and hormone regulation (ARR1AT, WRKY71OS) [67], [68]. ARR1AT is a binding element [69], [70] for ARR1 , which is a cytokinin response transcriptional activator [67], [68]. WRKY71OS, a binding element for WRKY71 , encodes a transcriptional repressor of gibberillic acid signaling [71] and is induced by cold, salt and dehydration stress in Musa spp.…”

Section: Discussionmentioning

confidence: 99%

The Nitrate Transporter (NRT) Gene Family in Poplar

et al. 2013

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Nitrate is an important nutrient required for plant growth. It also acts as a signal regulating plant development. Nitrate is actively taken up and transported by nitrate transporters (NRT), which form a large family with many members and distinct functions. In contrast to Arabidopsis and rice there is little information about the NRT family in woody plants such as Populus. In this study, a comprehensive analysis of the Populus NRT family was performed. Sixty-eight PtNRT1/PTR, 6 PtNRT2, and 5 PtNRT3 genes were identified in the P. trichocarpa genome. Phylogenetic analysis confirmed that the genes of the NRT family are divided into three clades: NRT1/PTR with four subclades, NRT2, and NRT3. Topological analysis indicated that all members of PtNRT1/PTR and PtNRT2 have 8 to 12 trans-membrane domains, whereas the PtNRT3 proteins have no or up to two trans-membrane domains. Four PtNRT3 members were predicted as secreted proteins. Microarray analyses revealed tissue-specific expression patterns of PtNRT genes with distinct clusters of NRTs for roots, for the elongation zone of the apical stem segment and the developing xylem and a further cluster for leaves, bark and wood. A comparison of different poplar species (P. trichocarpa, P. tremula, P. euphratica, P. fremontii x P. angustifolia, and P. x canescens) showed that the tissue-specific patterns of the NRT genes varied to some extent with species. Bioinformatic analysis of putative cis-regulatory elements in the promoter regions of PtNRT family retrieved motifs suggesting the regulation of the NRT genes by N metabolism, by energy and carbon metabolism, and by phytohormones and stress. Multivariate analysis suggested that the combination and abundance of motifs in distinct promoters may lead to tissue-specificity. Our genome wide analysis of the PtNRT genes provides a valuable basis for functional analysis towards understanding the role of nitrate transporters for tree growth.

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“…3). All of these transcription factors are known to be involved in abiotic stress response and are influenced by phytohormones such as auxin, ABA, and gibberellins (Hatorangan et al 2009;Chen et al 2012;Zou et al 2008;Castela ´n-mun ˜oz et al 2019). However, experimental validation through CHIP-seq analysis will be needed to establish the mechanistic details of these in silico study based observations.…”

Section: Cep Gene Promoters Show An Abundance Of Multiple Stress-responsive Caresmentioning

confidence: 99%

C-terminally encoded peptides (CEPs) are potential mediators of abiotic stress response in plants

Aggarwal

Kumar

Jain

et al. 2020

Physiol Mol Biol Plants

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Intracellular signaling is a critical determinant of the normal growth and development of plants. Signaling peptides, also known as peptide hormones, along with classical phytohormones, are the significant players of plant intracellular signaling. C-terminally encoded peptide (CEP), a 15-amino acid post-translationally peptide identified in Arabidopsis, plays a pivotal role in lateral root formation, nodulation, and act as long-distance root to shoot signaling molecule in N-starvation conditions. Expression of CEP gene members in Arabidopsis is perturbed by nitrogen starvation; however, not much is known regarding their role in other abiotic stress conditions. To gain a comprehensive insight into CEP biology, we identified CEP genes across diverse plant genera (Glycine max, Sorghum bicolor, Brassica rapa, Zea mays, and Oryza sativa) using bioinformatics tools. In silico promoter analysis revealed that CEP gene promoters show an abundance of abiotic stress-responsive elements suggesting a possible role of CEPs in abiotic stress signaling. Spatial and temporal expression patterns of CEP via RNA seq and microarray revealed that various CEP genes are transcriptionally regulated in response to abiotic stresses. Validation of rice CEP genes expression by qRT-PCR showed that OsCEP1, OsCEP8, OsCEP9, and OsCEP10 were highly upregulated in response to different abiotic stress conditions. Our findings suggest these CEP genes might be important mediators of the abiotic stress response and warrant further overexpression/knockout studies to delineate their precise role in abiotic stress response.

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In silico identification of cis-regulatory elements of phosphate transporter genes in rice (Oryza sativa L.)

Cited by 14 publications

References 27 publications

Putative cis-regulatory elements in genes highly expressed in rice sperm cells

Putative cis-regulatory elements in genes highly expressed in rice sperm cells

The Nitrate Transporter (NRT) Gene Family in Poplar

C-terminally encoded peptides (CEPs) are potential mediators of abiotic stress response in plants

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