Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria

AbstractAbiotic stresses including drought, salinity, extreme temperatures, chemical toxicity and oxidative are the natural status of the environment to exert serious threats to agriculture. Abiotic stress-related microRNAs (ASmiRNAs) are a group of microRNAs (miRNAs) regulating stress responses in plants. However, the systematic investigation of ASmiRNAs is limited in Rice (O. sativa), a typical abiotic stress-resistant crop species. In the present work, we systematically investigated ASmiRNAs in silico. First, we identified 177 putative ASmiRNAs in O.sativa. Second, we found most ASmiRNAs were driven by TATA-promoter and most stress-related miRNA promoter regions contained the stress-related elements. Third, we found many ASmiRNAs families were species/family specific and a set of miRNAs might derive from genomic repeat-sequences in O. sativa. Finally, we found the ASmiRNAs in O. sativa target 289 genes with 1050 predicted target sites in which 98% sites have cleavage activity and 2% sites have translation inhibition activity. In conclusion, our findings provide an insight into both the function and evolution of ASmiRNAs and improve our understanding on the mechanism of abiotic stress resistance in O. sativa.

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Characterization of potato (Solanum tuberosum) and tomato (Solanum lycopersicum) protein phosphatases type 2A catalytic subunits and their involvement in stress responses

Planta ◽

10.1007/s00425-009-0923-5 ◽

2009 ◽

Vol 230 (1) ◽

pp. 13-25 ◽

Cited By ~ 29

Author(s):

Silvia Marina País ◽

Marina Alejandra González ◽

María Teresa Téllez-Iñón ◽

Daniela Andrea Capiati

Keyword(s):

Solanum Tuberosum ◽

Solanum Lycopersicum ◽

Stress Responses ◽

Protein Phosphatases ◽

Catalytic Subunits

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Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

International Journal of Molecular Sciences ◽

10.3390/ijms23020614 ◽

2022 ◽

Vol 23 (2) ◽

pp. 614

Author(s):

Weiqi Sun ◽

Mengdi Li ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Gene Structure ◽

Stress Responses ◽

Stress Protein ◽

Purifying Selection ◽

Cis Acting ◽

Genome Wide ◽

Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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Characterization of The Interaction Between RIN13 (RPM1-Interacting13) and Sumo Proteins in Arabidopsis Thaliana

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v9i2.9487 ◽

2017 ◽

Vol 9 (2) ◽

Author(s):

Venny Santosa ◽

Mio Nagabuchi ◽

Sachiko Okada ◽

Katsunori Tanaka

Keyword(s):

Arabidopsis Thaliana ◽

Fluorescence Microscopy ◽

Hypersensitive Response ◽

Stress Responses ◽

Molecular Interaction ◽

Nuclear Body ◽

Chromosome Organization ◽

Post Translational Modification ◽

Molecular Studies

Small Ubiquitin-related MOdifier (SUMO) proteins can be found in many organisms, including A. thaliana, which possesses 9 SUMO genes. SUMO binds to various target proteins in a reversible reaction called SUMOylation. SUMOylation participates in transcription, chromosome organization, proteins localizations and stress responses. Our study showed that RIN13 (RPM1-Interacting13/At2g20310) is a target of SUMOylation, which was initially found by interaction between this protein and AtSCE1a (E2). Recent report showed that overexpression of RIN13 enhanced the resistance to pathogen without inducing hypersensitive response. However, the molecular interaction between RIN13 and SUMO proteins and its significance have not been studied yet. Thus, our study aimed to characterize the interaction between RIN13 and SUMO proteins in A. thaliana. The result showed an isoform-specific SUMOylation between RIN13 and SUMO proteins. RIN13 is SUMOylated by SUMO1, 2, 3, and 5. Though expressed ubiquitously in A.thaliana, fluorescence microscopy showed that RIN13 localizes subcellularly in the nuclear body. Moreover, complete abolishment of SUMOylation with inactive E2 suggests the exclusion of RIN13 from nuclear body. These results showed that SUMOylation affected RIN13 localization, and indirectly influenced its interaction to other proteins and putative function. This paper presents evidence of RIN13 SUMOylation. Furthermore, RIN13 function in pathogenic resistance is shown to be supported by SUMOylation. Thus, this study enhanced the understanding of SUMO in plants and served as reference to molecular studies concerning post-translational modification of SUMO.

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Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress

10.21203/rs.3.rs-36113/v3 ◽

2020 ◽

Author(s):

Yanan Song ◽

Hongli Cui ◽

Ying Shi ◽

Jinai Xue ◽

Chunli Ji ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Stress Resistance ◽

Segmental Duplication ◽

Functional Characterization ◽

High Stress ◽

Camelina Sativa ◽

Genome Wide ◽

Large Expansion

Abstract Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina.Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress.Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.

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Characterization of a c-Rel Inhibitor That Mediates Anticancer Properties in Hematologic Malignancies by Blocking NF-κB–Controlled Oxidative Stress Responses

Cancer Research ◽

10.1158/0008-5472.can-14-2814 ◽

2016 ◽

Vol 76 (2) ◽

pp. 377-389 ◽

Cited By ~ 21

Author(s):

Yusuke Shono ◽

Andrea Z. Tuckett ◽

Hsiou-Chi Liou ◽

Ekaterina Doubrovina ◽

Enrico Derenzini ◽

...

Keyword(s):

Oxidative Stress ◽

Stress Responses ◽

Hematologic Malignancies ◽

Anticancer Properties ◽

Oxidative Stress Responses

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sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs

mSphere ◽

10.1128/msphere.00561-18 ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 4

Author(s):

Alisa M. King ◽

Carin K. Vanderpool ◽

Patrick H. Degnan

Keyword(s):

Experimental Data ◽

Stress Responses ◽

Small Rnas ◽

Metabolic Regulation ◽

Functional Characterization ◽

Target Prediction ◽

Structure Stability ◽

Accurate Identification ◽

Mrna Targets

Small RNAs (sRNAs) regulate gene expression in diverse bacteria by interacting with mRNAs to change their structure, stability, or translation. Hundreds of sRNAs have been identified in bacteria, but characterization of their regulatory functions is limited by difficulty with sensitive and accurate identification of mRNA targets. Thus, new robust methods of bacterial sRNA target identification are in demand. Here, we describe our small RNA target prediction organizing tool (SPOT), which streamlines the process of sRNA target prediction by providing a single pipeline that combines available computational prediction tools with customizable results filtering based on experimental data. SPOT allows the user to rapidly produce a prioritized list of predicted sRNA-target mRNA interactions that serves as a basis for further experimental characterization. This tool will facilitate elucidation of sRNA regulons in bacteria, allowing new discoveries regarding the roles of sRNAs in bacterial stress responses and metabolic regulation.

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A typical RNA-binding protein gene (AccRBM11) in Apis cerana cerana: characterization of AccRBM11 and its possible involvement in development and stress responses

Cell Stress and Chaperones ◽

10.1007/s12192-016-0725-1 ◽

2016 ◽

Vol 21 (6) ◽

pp. 1005-1019 ◽

Cited By ~ 9

Author(s):

Guilin Li ◽

Haihong Jia ◽

Hongfang Wang ◽

Yan Yan ◽

Xingqi Guo ◽

...

Keyword(s):

Stress Responses ◽

Rna Binding ◽

Protein Gene ◽

Binding Protein ◽

Apis Cerana ◽

Rna Binding Protein ◽

Apis Cerana Cerana ◽

Binding Protein Gene

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Characterization of Somatic Embryogenesis Receptor-Like Kinase 4 as a Negative Regulator of Leaf Senescence in Arabidopsis

Cells ◽

10.3390/cells8010050 ◽

2019 ◽

Vol 8 (1) ◽

pp. 50 ◽

Cited By ~ 6

Author(s):

Xiaoxu Li ◽

Salman Ahmad ◽

Akhtar Ali ◽

Cun Guo ◽

Hong Li ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Leaf Senescence ◽

Stress Responses ◽

Negative Regulator ◽

Knockout Mutant ◽

Surface Receptors ◽

Extracellular Signals ◽

Early Leaf Senescence

Leaf senescence is a genetically controlled process that involves the perception of extracellular signals and signal transduction. The receptor-like protein kinases (RLKs) are known to act as an important class of cell surface receptors and are involved in multiple biological processes such as development and stress responses. The functions of a number of RLK members have been characterized in Arabidopsis and other plant species, but only a limited number of RLK proteins have been reported to be associated with leaf senescence. In the present study, we have characterized the role of the somatic embryogenesis receptor kinase 4 (SERK4) gene in leaf senescence. The expression of SERK4 was up-regulated during leaf senescence and by several abiotic stress treatments in Arabidopsis. The serk4-1 knockout mutant was found to display a significant early leaf senescence phenotype. Furthermore, the results of overexpression analysis and complementary analysis supported the idea that SERK4 acts as a negative regulator in the process of leaf senescence.

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