Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

Gomez-Porras J, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC GENOMICS. 2007;8(1): 260.Background: In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid ( ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an insilico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements ( CREs), ABRE and CE3, in thale cress ( Arabidopsis thaliana) and rice ( Oryza sativa). Results: Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element ( CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes ( ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion: Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks

In Silico analysis of the genes encoding proteins that are involved in the biosynthesis of the RMS/MAX/D pathway revealed new roles of strigolactones in plants

Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant’s response to different abiotic stresses. In the last year, investigations of the strigolactone biosynthesis pathway in two model species, Arabidopsis thaliana and Oryza sativa, resulted in great progress in understanding the functions of four enzymes that are involved in this process. We performed in silico analyses, including the identification of the cis-regulatory elements in the promoters of genes encoding proteins of the strigolactone biosynthesis pathway and the identification of the miRNAs that are able to regulate their posttranscriptional level. We also searched the databases that contain the microarray data for the genes that were analyzed from both species in order to check their expression level under different growth conditions. The results that were obtained indicate that there are universal regulations of expression of all of the genes that are involved in the strigolactone biosynthesis in Arabidopsis and rice, but on the other hand each stage of strigolactone production may be additionally regulated independently. This work indicates the presence of crosstalk between strigolactones and almost all of the other phytohormones and suggests the role of strigolactones in the response to abiotic stresses, such as wounding, cold or flooding, as well as in the response to biotic stresses

Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)

Members of the plant Heme Activator Protein (HAP) or NUCLEAR FACTOR Y (NF-Y) are trimeric transcription factor complexes composed of the NF-YA, NF-YB and NF-YC subfamilies. They bind to the CCAAT box in the promoter regions of the target genes and regulate gene expressions. Plant NF-Ys were reported to be involved in adaptation to several abiotic stresses as well as in development. In silico analysis of Sorghum bicolor genome resulted in the identification of a total of 42 NF-Y genes, among which 8 code for the SbNF-YA, 19 for SbNF-YB and 15 for the SbNF-YC subunits. Analysis was also performed to characterize gene structures, chromosomal distribution, duplication status, protein subcellular localizations, conserved motifs, ancestral protein sequences, miRNAs and phylogenetic tree construction. Phylogenetic relationships and ortholog predictions displayed that sorghum has additional NF-YB genes with unknown functions in comparison with Arabidopsis. Analysis of promoters revealed that they harbour many stress-related cis-elements like ABRE and HSE, but surprisingly, DRE and MYB elements were not detected in any of the subfamilies. SbNF-YA1, 2, and 6 were found upregulated under 200 mM salt and 200 mM mannitol stresses. While NF-YA7 appeared associated with high temperature (40˚C) stress, NF-YA8 was triggered by both cold (4˚C) and high temperature stresses. Among NF-YB genes, 7, 12, 15, and 16 were induced under multiple stress conditions such as salt, mannitol, ABA, cold and high temperatures. Likewise, NF-YC 6, 11, 12, 14, and 15 were enhanced significantly in a tissue specific manner under multiple abiotic stress conditions. Majority of the mannitol (drought)-inducible genes were also induced by salt, high temperature stresses and ABA. Few of the high temperature stress-induced genes are also induced by cold stress (NF-YA2, 4, 6, 8, NF-YB2, 7, 10, 11, 12, 14, 16, 17, NF-YC4, 6, 12, and 13) thus suggesting a cross talk among them. This work paves the way for investigating the roles of diverse sorghum NF-Y proteins during abiotic stress responses and provides an insight into the evolution of diverse NF-Y members

Genome-Wide Analysis of Two-Component Systems and Prediction of Stress-Responsive Two-Component System Members in Soybean

In plants, the two-component systems (TCSs) play important roles in regulating diverse biological processes, including responses to environmental stress stimuli. Within the soybean genome, the TCSs consist of at least 21 histidine kinases, 13 authentic and pseudo-phosphotransfers and 18 type-A, 15 type-B, 3 type-C and 11 pseudo-response regulator proteins. Structural and phylogenetic analyses of soybean TCS members with their Arabidopsis and rice counterparts revealed similar architecture of their TCSs. We identified a large number of closely homologous soybean TCS genes, which likely resulted from genome duplication. Additionally, we analysed tissue-specific expression profiles of those TCS genes, whose data are available from public resources. To predict the putative regulatory functions of soybean TCS members, with special emphasis on stress-responsive functions, we performed comparative analyses from all the TCS members of soybean, Arabidopsis and rice and coupled these data with annotations of known abiotic stress-responsive cis-elements in the promoter region of each soybean TCS gene. Our study provides insights into the architecture and a solid foundation for further functional characterization of soybean TCS elements. In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms

Promoter deletion analysis and identification of putative CIS-elements of MUTE in Arabidopsis

Stomata are found on the surfaces of land plants and are crucial for regulating gas exchange between plants and the atmosphere. These structures are composed of a pore that is surrounded by two specialized guard cells. The critical importance of stomata in providing CO2 uptake while controlling the release of water has made them a prime target for improvement of plant productivity and water use efficiency. In Arabidopsis, the production of a mature stomata requires the expression of the basic helix-loop-helix (bHLH) master regulatory gene, MUTE. The function of MUTE and its expression pattern have been characterized. In this study, promoter deletion analysis of MUTE was performed to identify specific regions that control the spatiotemporal expression of MUTE. Expression vectors with truncated promoter segments driving the expression of GFP (Green Fluorescent Protein) were transformed into Arabidopsis. A region of 110-bp was identified as required for MUTE expression. This 110-bp region was further analyzed for putative cis-elements using publicly available databases. Seven possible CREs (CIS-Regulatory Elements) were identified which are known binding sites for transcription factors involved in development, dehydration, light regulation, and stomatal pore physiology. Three of these putative elements were chosen for targeted mutagenesis to produce GFP expression vectors for future molecular characterization in A.thaliana. This work provides novel insight into the regulatory mechanism driving MUTE expression and offers new tools for identifying key regulatory elements in the future

ANALYSIS OF THE CIS-REGULATORY ELEMENT LEXICON IN UPSTREAM GENE PROMOTERS OF ARABIDOPSIS THALIANA AND ORYZA SATIVA

AN ABSTRACT OF THE DISSERTATION OF BELAN M. KHALIL, for the Doctor of Philosophy degree in Plant Biology, presented July 11, 2018, at Southern Illinois University Carbondale. TITLE: ANALYSIS OF THE CIS-REGULATORY ELEMENT LEXICON IN UPSTREAM GENE PROMOTERS OF ARABIDOPSIS THALIANA AND ORYZA SATIVA. MAJOR PROFESSOR: Dr Matt Geisler Gene expression in plants is partly regulated through an interaction of trans-acting factors with the promoter regions of the gene. Trans-acting factor binding sites consist of short nucleotide sequences most often present in the upstream promoter region. These binding sites, the cis-regulatory elements (CREs), vary in structure, complexity and function. In binding to trans-acting factors, CREs connect genes to signalling and regulatory pathways that affect plant growth, development, and response to the environment. As words in a language, CREs and thus promoters can be analyzed by looking for spelling (patterns of nucleotides) associated with meaning (functions). Considering CREs as words in a language, this kind of analysis provides a great opportunity for comprehensive understanding of promoter language. Identification and characterization of CREs are challenging either experimentally or bioinformatically, and has previously been accomplished by discovering degenerate words, with ambiguous nucleotides. This kind of result implicitly makes a hypothesis that binding of a specific trans-acting factor is somewhat promiscuous (or sloppy) and that all words represented by a degenerate pattern are equally good at binding. In this study, we unpack the “degeneracy hypothesis” by systematically considering each combination of letters independently for CRE function. Our results demonstrate that not all degenerate combinations of published CREs have the same effect on gene expression. A systematic search and comparison of all 65,536 possible 8 bp CRE words were searched in the 500 bp and 1000 bp upstream promoters of all genes in Arabidopsis thaliana and Oryza sativa, respectively. The function of each CRE was evaluated by statistically comparing the presence or absence of the element in the promoter with that genes response (induction or suppression) to stimuli in 1691 public availability transcriptomes of differential gene expression data. Arabidopsis, a model dicot plant had a much larger number of such data sets, than rice, however rice was chosen as a comparison as it had the largest number of datasets for a monocot, the most distantly related plant group with sufficient data available. A comprehensive list of 8 bp words associated with differential gene expression, linguistically known as lexicon, was retrieved for both species by establishing that the presence of a CRE significantly increased the likelihood for differential expression by at least one stimulus. The lexicons were composed of 641 and 856 CREs respectively in Arabidopsis and rice, and there were only 78 shared CREs between the two lexicons. The CRE lexicon was then characterized for their strength and breadth of response, occurrence frequency, sequence complexity, and sequence conservation between two species. In Arabidopsis, evening element (EE) showed the strongest response to a cold stress transcriptome (p-value 10-99). In rice, the element AAACCCTA showed strongest response to a tissue specific transcriptome (p-value 10-79). The breadth of response varied between the two species due to number of transcriptomes used in the study. The element AAACCCTA and GCGGCGGA significantly correlated to 197 and 58 transcriptomes in both Arabidopsis and rice, respectively. On the other side of the breadth scale there were also many CREs with very restricted response. There were 291 and 258 CREs in Arabidopsis and rice, respectively, significantly correlated to a single stimulus. Occurrence frequency revealed that the most abundant CREs in Arabidopsis and rice genes were TATA box and TATA box like CREs. The structure of the CREs in the lexicon was also varied. CREs were distributed on seven levels of complexity. Level one comprised CREs having 8 copies of the same nucleotide, level seven comprised CREs having two copies of the same nucleotide. In Arabidopsis, out of 641 CREs, 314 were of level 6 complexity, which means having 3 copies of the same nucleotide. In rice, the majority of the lexicon, 263 CREs were of level 5 complexity, which means having 4 copies of the same nucleotide. Each CRE of the lexicon was correlated to at least one experimental condition in the differential gene expression data, but many were correlated to multiple and often related conditions such as drought, temperature and salinity. Therefore, each CRE was assigned a “meaning”, i.e. the associated stimuli, thus providing a sort of CRE function dictionary in addition to the lexicon itself. Many CREs possessed different meanings (termed homographs in language), and in many cases the meanings of different CREs overlapped like language synonyms. Sharing meanings (synonyms) was often among CREs with strong sequence similarity (homonyms or homophones), however, not in all cases. Analyzed as a linguistic aspect, CRE homonymity and synonymity was applied to explore the hypothesis “all CRE synonyms are also homonyms and all CRE homonyms are also synonyms.” To the end a single CRE was compared to all possible CREs with only one letter mismatch in their sequences are considered as homonyms. The CREs meaning was converted to a matrix of stimuli to generate clusters of synonyms that were analyzed for similarity of spelling (sequence). This analysis showed that not all homonyms are synonyms, however most synonyms are homonyms. Furthermore, despite a search of all one letter mismatches among homonyms, many of the functional homonyms shared smaller 4-5bp core sequence and only varied at the flanks. Synonyms being homonyms in the language of promoters raises a question, how did this evolve? Duplication of transcription factors in the genome generated transcription factor families where each family member shares the same core domain, usually a DNA recognition site. We here propose that CREs also duplicate during gene duplication process building CRE families in parallel. Members of CRE families may show different connectivity and affinity to individual members of transcription factors in a transcription factor family. In environmental sensors and developmental decision panel, this association of two families of interaction factors is called dense overlapping region (or DOR) and is a highly overrepresented network topology in biological systems. This also explains the degeneracy of initially discovered CREs. The fact is only a portion of nucleotide combinations implied by a degenerate CRE is bioactive, it represents an overlap of different members of a CRE family which is part of the process of family expansion and diversification and done as compensatory mutations as the family of transcription factors expanded and diversified. We also extensively studied CREs involved abiotic stress and identifies shared elements among abiotic stresses as well as abiotic stress specific CREs. Furthermore, CREs follow a time-sensitive response rule, which means some CREs participates in gene expression regulation only at a certain period during the course of exposure to the abiotic stress

Regulation of plant stress response by dehydration responsive element binding (DREB) transcription factors

Plant growth and productivity are greatly affected by environmental stresses such as dehydration, high salinity, low temperature and biotic pathogen infection. Plant adaptation to these environmental stresses is controlled by cascades of molecular networks. The dehydration responsive element binding (DREB) transcription factors, which specifically interact with C-repeat/DRE (A/GCCGAC), play an important role in plant environmental stress tolerance by controlling the expression of many stress related genes. This review specifically focused on the structure characteristics of DREB proteins and their roles in regulating abiotic and biotic stress tolerance in plants. The DREB proteins are also involved in phytohormones signaling pathway such as abscisic acid, salicylic acid, jasmonate acid, ethylene and gibberellic acid. In addition, this review summarized the progress of the genetic engineering of DREB transcription factors in the main crops and model plants.Keywords: Abscisic acid, biotic stress, DREB transcription factor, environmental stress, signaling pathway, transgenic cro

Methylome and epialleles in rice epilines selected for energy use efficiency

Epigenetics offers important opportunities in breeding to improve the potential yield in a wide variety of crops. Starting from a pure breeder seed lot of a rice (Oryza sativa ssp. indica) inbred population, repeated testing for improved cellular respiration rates and energy use efficiency (EUE) over three generations identified performant epilines with distinct epigenetic signatures and with improved seed yield in field trials. Epiline DNA methylomes were characterized by genome-wide bisulfite sequencing to discern cytosine methylation changes in relation to transcriptome and phenotype. Regional methylation changes were dispersed over the epiline genomes. A number of upstream-associated differentially methylated regions (DMRs) correlated with differentially expressed genes (DEGs) with a role in particular molecular functions like transmembrane transport and protein kinase activity. Targeted bisulfite sequencing confirmed epiline DMRs that anti-correlated with DEGs, identifying putative epialleles that were susceptible for cytosine methylation changes that might affect gene expression and contribute to the phenotype. Chromatin immunoprecipitation sequencing revealed the extensive enrichment of gene-associated histone H3 lysine-4 trimethylation (H3K4me3), which correlated with gene activation and reduced cytosine methylation. Our data indicate that seed formation is prone to epigenetic changes that might be used as a resource in crop improvement