Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species

Mohanty, Bijayalaxmi; Krishnan, S. P. T.; Swarup, Sanjay; Bajic, Vladimir B.

doi:10.1093/aob/mci219

Cited by 88 publications

(60 citation statements)

References 53 publications

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“…The in silico analysis reveals that the CPS promoter could play a role in such processes as response to ethylene, dark, light, auxin, and salicylic acid, but these results have not yet been validated experimentally in S. miltiorrhiza [29][30][31][33][34][35][36][37][38][39]. Also, the potential influence of such stress factors as anaerobic conditions, dehydration, pathogen infection, and protein unfolding on CPS expression should be verified and validated experimentally [40][41][42][43]. Comparison of results obtained by the in silico search to the outcome of microarray data, indicated no shared, co-regulated proteins.…”

Section: Discussionmentioning

confidence: 98%

“…1 indicated that S. miltiorrhiza CPS promoter activity could be controlled through the numerous stress factors occurring in the internal and external environment of the plant as anaerobic conditions, pathogen infection, dehydration, and protein unfolding [40][41][42][43]. …”

Section: The Structure Of Cps Promoter and 5'utr Of Cps Genementioning

confidence: 99%

“…The group of analyzed genes belongs to the seven different plant species [40]. 5'-TAACTG-3' Gel mobility experiment indicated that the consensus sequence 5'-TAACTG-3' is recognized specifically by A. thaliana MYB2 trans-factor.…”

Section: '-Aaacaaa-3'mentioning

confidence: 99%

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Isolation and characterization of a copalyl diphosphate synthase gene promoter from Salvia miltiorrhiza

et al. 2016

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The promoter, 5' UTR, and 34-nt 5' fragments of protein encoding region of the Salvia miltiorrhiza copalyl diphosphate synthase gene were cloned and characterized. No tandem repeats, miRNA binding sites, or CpNpG islands were observed in the promoter, 5' UTR, or protein encoding fragments. The entire isolated promoter and 5' UTR is 2235 bp long and contains repetitions of many cis-active elements, recognized by homologous transcription factors, found in Arabidopsis thaliana and other plant species. A pyrimidine-rich fragment with only 6 non-pyrimidine bases was localized in the 33-nt stretch from nt 2185 to 2217 in the 5' UTR. The observed cis-active sequences are potential binding sites for trans-factors that could regulate spatio-temporal CPS gene expression in response to biotic and abiotic stress conditions. Obtained results are initially verified by in silico and co-expression studies based on A. thaliana microarray data.The quantitative RT-PCR analysis confirmed that the entire 2269-bp copalyl diphosphate synthase gene fragment has the promoter activity.Quantitative RT-PCR analysis was used to study changes in CPS promoter activity occurring in response to the application of four selected biotic and abiotic regulatory factors; auxin, gibberellin, salicylic acid, and high-salt concentration.

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Section: Discussionmentioning

confidence: 98%

Section: The Structure Of Cps Promoter and 5'utr Of Cps Genementioning

confidence: 99%

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Isolation and characterization of a copalyl diphosphate synthase gene promoter from Salvia miltiorrhiza

et al. 2016

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“…Evolutionary fate of rhizome-specific genes anaerobic genes (AAACAAA; Mohanty et al, 2005) showed significantly higher abundance in S. bicolor than the other species. The promoters of S. bicolor genes were enriched relative to those of O. sativa for three additional cis-elements, À300 element (Thomas and Flavell, 1990), À10 promoter element (Thum et al, 2001) and TATA box (Grace et al, 2004).…”

Section: Evolutionary Fate Of Rhizome-specific Genesmentioning

confidence: 95%

Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

et al. 2008

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“…These include glycolytic and fermentation enzymes and other metabolic proteins as well as various signal transduction proteins, transcription factors, and other genes involved in the adaptation response to anaerobiosis (Klok et al, 2002;Branco-Price et al, 2008;Mustroph et al, 2009Mustroph et al, , 2010. These regulatory controls rely on cis-acting hypoxia regulatory elements in the promoters of hypoxia-responsive genes (Dolferus et al, 2001;Mohanty et al, 2005), posttranscriptional control by silencing RNAs (Moldovan et al, 2010;Licausi et al, 2011), mRNA sequestration in ribonucleoprotein complexes (Weber et al, 2008;Sorenson and Bailey-Serres, 2014), and the selective targeting of core hypoxia-response transcripts to polysomes (Branco-Price et al, 2008;Mustroph et al, 2009). Overall, these developmental programs prepare the plant at various fronts for a coordinated survival response to low oxygen stress.…”

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confidence: 99%

Arabidopsis CML38, a Calcium Sensor That Localizes to Ribonucleoprotein Complexes under Hypoxia Stress

et al. 2015

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During waterlogging and the associated oxygen deprivation stress, plants respond by the induction of adaptive programs, including the redirected expression of gene networks toward the synthesis of core hypoxia-response proteins. Among these core response proteins in Arabidopsis (Arabidopsis thaliana) is the calcium sensor CML38, a protein related to regulator of gene silencing calmodulin-like proteins (rgsCaMs). CML38 transcripts are up-regulated more than 300-fold in roots within 6 h of hypoxia treatment. Transfer DNA insertional mutants of CML38 show an enhanced sensitivity to hypoxia stress, with lowered survival and more severe inhibition of root and shoot growth. By using yellow fluorescent protein (YFP) translational fusions, CML38 protein was found to be localized to cytosolic granule structures similar in morphology to hypoxia-induced stress granules. Immunoprecipitation of CML38 from the roots of hypoxia-challenged transgenic plants harboring CML38pro::CML38: YFP followed by liquid chromatography-tandem mass spectrometry analysis revealed the presence of protein targets associated with messenger RNA ribonucleoprotein (mRNP) complexes including stress granules, which are known to accumulate as messenger RNA storage and triage centers during hypoxia. This finding is further supported by the colocalization of CML38 with the mRNP stress granule marker RNA Binding Protein 47 (RBP47) upon cotransfection of Nicotiana benthamiana leaves. Ruthenium Red treatment results in the loss of CML38 signal in cytosolic granules, suggesting that calcium is necessary for stress granule association. These results confirm that CML38 is a core hypoxia response calcium sensor protein and suggest that it serves as a potential calcium signaling target within stress granules and other mRNPs that accumulate during flooding stress responses.

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Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species

Abstract: It is believed that the promoter motifs identified could be functional by conferring anaerobic sensitivity to the genes that possess them. This proposal now requires experimental verification.

Cited by 88 publications

References 53 publications

Isolation and characterization of a copalyl diphosphate synthase gene promoter from Salvia miltiorrhiza

Isolation and characterization of a copalyl diphosphate synthase gene promoter from Salvia miltiorrhiza

Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype

Arabidopsis CML38, a Calcium Sensor That Localizes to Ribonucleoprotein Complexes under Hypoxia Stress

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