De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes

Zolotarov, Yevgen; Strömvik, Martina V.

doi:10.1371/journal.pone.0129016

Cited by 29 publications

(20 citation statements)

References 130 publications

(146 reference statements)

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“…Interestingly, HvDHN5 expression was not significantly altered with elevated HvCBF14 levels. This may be related to the fact that the HvDHN5 gene belongs to the K n class of dehydrins, which respond to frost and drought, but they are not regulated by the light [37,39,52]. In the present experiment, we also observed that the HvDHN5 gene did not respond differently at different light intensities.…”

Section: The Expression Of Hvcbf14 and Its Target Genes Hvcor14b And supporting

confidence: 53%

Temperature and Light-Quality-Dependent Regulation of Freezing Tolerance in Barley

Ahres

Gierczik

Boldizsár

et al. 2020

Plants

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It is established that, besides the cold, incident light also has a crucial role in the cold acclimation process. To elucidate the interaction between these two external hardening factors, barley plantlets were grown under different light conditions with low, normal, and high light intensities at 5 and 15 °C. The expression of the HvCBF14 gene and two well-characterized members of the C-repeat binding factor (CBF)-regulon HvCOR14b and HvDHN5 were studied. In general, the expression level of the studied genes was several fold higher at 5 °C than that at 15 °C independently of the applied light intensity or the spectra. The complementary far-red (FR) illumination induced the expression of HvCBF14 and also its target gene HvCOR14b at both temperatures. However, this supplementation did not affect significantly the expression of HvDHN5. To test the physiological effects of these changes in environmental conditions, freezing tests were also performed. In all the cases, we found that the reduced R:FR ratio increased the frost tolerance of barley at every incident light intensity. These results show that the combined effects of cold, light intensity, and the modification of the R:FR light ratio can greatly influence the gene expression pattern of the plants, which can result in increased plant frost tolerance.

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Section: The Expression Of Hvcbf14 and Its Target Genes Hvcor14b And supporting

confidence: 53%

Temperature and Light-Quality-Dependent Regulation of Freezing Tolerance in Barley

Ahres

Gierczik

Boldizsár

et al. 2020

Plants

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show abstract

“…We found a number of dehydrin-like genes that were up-regulated from paradormancy to endodormancy, and these genes provide good models for how different combinations of cis -regulatory elements can lead to different patterns of gene expression. For example, Zolotarov and Stromvik (2015) identified 14 conserved motifs in 350 dehydrin promoters from 51 plant genomes, many of which were similar to motifs that were overrepresented in our differentially expressed genes, as well as in genes that have been associated with responses to cold, dehydration, ABA, and light.…”

Section: Discussionmentioning

confidence: 77%

Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus

et al. 2015

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To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin modifications as major features of dormancy transitions. Among the chromatin-associated genes, two genes similar to SPT (SUPPRESSOR OF TY) were strongly up-regulated during endodormancy. Transcription factor genes and gene sets that were atypically up-regulated during endodormancy include a gene that seems to encode a trihelix transcription factor and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses. These latter transcription factors include ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), ETHYLENE RESPONSE FACTOR (ERF), ZINC FINGER PROTEIN 10 (ZAT10), ZAT12, and WRKY DNA-binding domain proteins. Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy. We found weaker evidence for changes in genes associated with salicylic acid and jasmonic acid, and little evidence for important changes in genes associated with gibberellins, abscisic acid, and cytokinin. We identified 315 upstream sequence motifs associated with eight patterns of gene expression, including novel motifs and motifs associated with the circadian clock and responses to photoperiod, cold, dehydration, and ABA. Analogies between flowering and endodormancy suggest important roles for genes similar to SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL), DORMANCY ASSOCIATED MADS-BOX (DAM), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).

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“…Similar to our findings, Bassett et al [14] and Wisniewski et al [15] observed that no DRE elements were found in positive sense in the PpDhn2 promoter and suggested that the absence of this cis-element was related to the lack of expression in response to cold. However, other reports have confirmed the presence of one DRE/CRT element in the promoter region of the Y n SK n dehydrin class, which includes PpDhn2 [75]. In spite of this observation, it is known that Y n SK n dehydrins are not expressed in response to cold.…”

Section: Discussionmentioning

confidence: 93%

“…García-Bañuelos et al [76] concluded that MdDhn, which shows great similarity with PpDhn2, was accumulated after a period of acclimation in apple trees. Based on that, Zolotarov and Strömvik [75] affirmed that cold-induced expression of Y n SK n -type dehydrins would not be detected in some cases because of a limited time of exposure to low temperature. So that, the presence of the DRE and LTRE elements found in the anti-sense position in our individuals could have some effect in the expression of PpDhn2 in a possible response to cold.…”

Section: Discussionmentioning

confidence: 99%

Assessing Field Prunus Genotypes for Drought Responsive Potential by Carbon Isotope Discrimination and Promoter Analysis

et al. 2018

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In order to improve the effectiveness of breeding practices for Prunus rootstocks, it is essential to obtain new resistance resources, especially with regard to drought. In this study, a collection of field-grown Prunus genotypes, both wild-relative species and cultivated hybrid rootstocks, were subjected to leaf ash and carbon isotope discrimination (∆ 13 C) analyses, which are strongly correlated to water use efficiency (WUE). Almond and peach wild relative species showed the lowest ∆ 13 C ratios, and therefore, the highest WUE in comparison with hybrid genotypes. In addition, drought-related cis-regulatory elements (CREs) were identified in the promoter regions of the effector gene PpDhn2, and the transcription factor gene DREB2B, two genes involved in drought-response signaling pathways. The phylogenetic analysis of these regions revealed variability in the promoter region sequences of both genes. This finding provides evidence of genetic diversity between the peach-and almond-relative individuals. The results presented here can be used to select Prunus genotypes with the best drought resistance potential for breeding.

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De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes

Cited by 29 publications

References 130 publications

Temperature and Light-Quality-Dependent Regulation of Freezing Tolerance in Barley

Temperature and Light-Quality-Dependent Regulation of Freezing Tolerance in Barley

Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus

Assessing Field Prunus Genotypes for Drought Responsive Potential by Carbon Isotope Discrimination and Promoter Analysis

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