scholarly journals Transposable elements contribute to activation of maize genes in response to abiotic stress

2014 ◽  
Author(s):  
Irina Makarevitch ◽  
Amanda J Waters ◽  
Patrick T West ◽  
Michelle C Stitzer ◽  
Jeffrey Ross-Ibarra ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Transposable Elements ◽  
Environmental Changes ◽  
Stress Conditions ◽  
Gene Expression Response ◽  
Regulatory Variation ◽  
Ideal System ◽  
Response To Stress ◽  
Regulated Gene Expression

Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as "junk" DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress- induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

Ubiquitin gene expression: response to environmental changes

1991 ◽  
Vol 20 (1-2) ◽  
pp. 17-23 ◽  
Author(s):  
Judith Fraser ◽  
Hue Anh Luu ◽  
Jeana Neculcea ◽  
David Y. Thomas ◽  
Reginald K. Storms
Keyword(s):  
Gene Expression ◽  
Environmental Changes ◽  
Gene Expression Response ◽  
Expression Response

scholarly journals Transcriptome-based identification and validation of optimal reference genes for quantitative real-time PCR normalization in Psathyrostachys huashanica

2020 ◽  
Author(s):  
Chuan Shen ◽  
Jingyuan Li ◽  
Caiyan Wei ◽  
Xudong Zhang ◽  
Yunfeng Wu
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Real Time ◽  
Temperature Stress ◽  
Reference Genes ◽  
18S Rrna ◽  
Stress Conditions ◽  
Psathyrostachys Huashanica ◽  
Biotic And Abiotic Stress ◽  
Ubiquitin Conjugating Enzyme

Abstract Background: P. huashanica ( Psathyrostachys huashanica ), known as an important resistance resource reservoir, is a rare and endangered plant growing suitably in Huashan mount region and would be urgently exploited in wheat genetic improvements sooner. During the utilization process, different IRGs (internal reference genes) need to be appropriately selected as standards based on biotic and abiotic stress conditions. It is crucial that Real-time RT-qPCR with combination of bioinformatics were adopted to explore the reliable IRGs from transcriptome of P . huashanica.Results: The present work reported new 3 species of IRGs, UBC2 , UBC17, 18S rRNA , which were screened from transcriptome of P. huashanica under biotic and abiotic stress conditions, using RT-qPCR and four algorithms, including geNorm, NormFinder, BestKeeper, and RefFinder, to analyse expression of sixteen candidate reference genes. These genes appear as following 18S rRNA (18S ribosomal RNA), EF1-α (eukaryotic elongation factor 1 alpha), UBC2 (ubiquitin-conjugating enzyme E2-2), UBC17 (ubiquitin-conjugating enzyme E2-17), α-TUB2A (alpha tubulin-2A), β-TUB3 (beta tubulin 3), ADF4 (Actin-depolymerising factor 4), ACTIN (actin), GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), 60SARP (60S acidic ribosomal protein), UBQ (polyubiquitin), SamDC (S-Adenosylmethionine decarboxylase), EIF4A (eukaryotic initiation factor 4A), ARF (ADP-ribosylation factor), HIS1 (histone H1), and HIS2B (histone H2B). Analysis of gene expression demonstrated that the expression of UBC2 gene was most stable under ABA hormone stress, low temperature stress and high temperature stress, similarly, UBC17 gene under IAA hormone stress, salinity stress and drought stress, both UBC17 genes and 18S rRNA genes under abiotic and biotic stress, respectively. The most stable gene was UBC2 gene in the root, UBC17 gene in stem and leaf. In this study, α-TUB2A , UBC and ACTIN genes were verified as the suitable reference genes across all tested samples. To further validate the suitability of the selected reference genes, we evaluated the relative expression of PsaCPK3 (Calcium-dependent protein kinase) and PsaHSP70-1 (heat shock protein 70-1), which are stress-related genes that may be involved in response to adversity.Conclusions: This study has identified a set of the most stable IRGs suiting for RT-qPCR detection of a few target gene expressions from P . huashanica in different experimental conditions. In addition, this study should provide the accuracy information for gene expression analysis in P . huashanica .

scholarly journals Programmed Delay of a Virulence Circuit PromotesSalmonellaPathogenicity

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Jeongjoon Choi ◽  
Heeju Kim ◽  
Yoonjee Chang ◽  
Woongjae Yoo ◽  
Dajeong Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Environmental Changes ◽  
Virulence Gene ◽  
Intracellular Pathogen ◽  
Dependent Manner ◽  
Acidic Ph ◽  
Inhibitory Protein ◽  
Virulence Gene Expression ◽  
Successful Infection ◽  
Regulated Gene Expression

ABSTRACTSignal transduction systems dictate various cellular behaviors in response to environmental changes. To operate cellular programs appropriately, organisms have sophisticated regulatory factors to optimize the signal response. The PhoP/PhoQ master virulence regulatory system of the intracellular pathogenSalmonella entericais activated inside acidic macrophage phagosomes. Here we report thatSalmonelladelays the activation of this system inside macrophages using an inhibitory protein, EIIANtr(a component of the nitrogen-metabolic phosphotransferase system). We establish that EIIANtrdirectly restrains PhoP binding to its target promoter, thereby negatively controlling the expression of PhoP-activated genes. PhoP furthers its activation by promoting Lon-mediated degradation of EIIANtrat acidic pH. These results suggest thatSalmonellaensures robust activation of its virulence system by suspending the activation of PhoP until a sufficient level of active PhoP is present to overcome the inhibitory effect of EIIANtr. Our findings reveal how a pathogen precisely and efficiently operates its virulence program during infection.IMPORTANCETo accomplish successful infection, pathogens must operate their virulence programs in a precise, time-sensitive, and coordinated manner. A major question is how pathogens control the timing of virulence gene expression during infection. Here we report that the intracellular pathogenSalmonellacontrols the timing and level of virulence gene expression by using an inhibitory protein, EIIANtr. A DNA binding master virulence regulator, PhoP, controls various virulence genes inside acidic phagosomes.Salmonelladecreases EIIANtramounts at acidic pH in a Lon- and PhoP-dependent manner. This, in turn, promotes expression of the PhoP-activated virulence program because EIIANtrhampers activation of PhoP-regulated genes by interfering with PhoP binding to DNA. EIIANtrenablesSalmonellato impede the activation of PhoP-regulated gene expression inside macrophages. Our findings suggest thatSalmonellaachieves programmed delay of virulence gene activation by adjusting levels of an inhibitory factor.

scholarly journals Strawberry FaNAC2 Enhances Tolerance to Abiotic Stress by Regulating Proline Metabolism

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1417
Author(s):  
Jiahui Liang ◽  
Jing Zheng ◽  
Ze Wu ◽  
Hongqing Wang
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Plant Responses ◽  
Drought Treatment ◽  
Abscisic Acid Biosynthesis ◽  
Positive Role ◽  
Transgenic Lines ◽  
Response To Stress ◽  
Simulated Drought

The quality and yields of strawberry plants are seriously affected by abiotic stress every year. NAC (NAM, ATAF, CUC) transcription factors are plant-specific, having various functions in plant development and response to stress. In our study, FaNAC2 from strawberry (Fragaria × ananassa, cultivar “Benihoppe”) was isolated and found to be a member of the ATAF sub-family, belonging to the NAC family of transcription factors. FaNAC2 was strongly expressed in the shoot apical meristem and older leaves of strawberries, and was induced by cold, high salinity, and drought stress. To investigate how FaNAC2 functions in plant responses to abiotic stress, transgenic Nicotiana benthamiana plants ectopically overexpressing FaNAC2 were generated. The transgenic plants grew better under salt and cold stress, and, during simulated drought treatment, these transgenic lines not only grew better, but also showed higher seed germination rates than wild-type plants. Gene expression analysis revealed that key genes in proline biosynthesis pathways were up-regulated in FaNAC2 overexpression lines, while its catabolic pathway genes were down-regulated and proline was accumulated more with the overexpression of FaNAC2 after stress treatments. Furthermore, the gene expression of abscisic acid biosynthesis was also promoted. Our results demonstrate that FaNAC2 plays an important positive role in response to different abiotic stresses and may be further utilized to improve the stress tolerance of strawberry plants.

scholarly journals Expression of genes for selected plant aminoacyl-tRNA synthetases in the abiotic stress

2020 ◽  
Vol 80 (1) ◽  
Author(s):  
Jurica Baranašić ◽  
Anita Mihalak ◽  
Ita Gruić-Sovulj ◽  
Nataša Bauer ◽  
Jasmina Rokov-Plavec
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Environmental Changes ◽  
Cadmium Stress ◽  
Protein Translation ◽  
Trna Synthetase ◽  
Stress Conditions ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
Global Translation

Plants, as sessile organisms, have evolved intricate mechanisms to adapt to various environmental changes and challenges. Considering that various types of stress trigger significant decrease in global translation rates we examined stress-related expression of aminoacyl-tRNA synthetases (aaRSs), enzymes that participate in the first step of protein translation. We have analyzed promoters of genes encoding cytosolic seryl-tRNA synthetase (SerRS), cytosolic aspartyl-tRNA synthetase (AspRS) and cytosolic cysteinyl-tRNA synthetase (CysRS) in Arabidopsis thaliana L., and examined SerRS, AspRS and CysRS gene expression in the seedlings exposed to different abiotic stressors. Although global translation levels are repressed by stress, our results show that plant aaRSs expression is not decreased by osmotic, salt and heavy metal/cadmium stress. Moreover, during exposure to stress conditions we detected increased AspRS and CysRS transcript levels. SerRS gene expression did not change, however participation of SerRS in stress response could be regulated at the protein level. Expression of the examined aaRS genes in stress correlated well with the length of their predicted promoters and a number of available binding sites for the stress related transcription factors. It thus appears that during the stress it is important to keep steady state levels of aaRSs for translation of specific stress related mRNAs and furthermore to rapidly continue with translation when stress conditions cease. Importantly, increased levels of plant aaRSs during stress may serve as a pool of aaRS proteins that can participate directly in stress responses through their noncanonical activities.

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