Exonic circular RNAs are involved in Arabidopsis immune response against bacterial and fungal pathogens by function synergistically with corresponding linear RNAs

2021 ◽  
Author(s):  
LIN WANG ◽  
Jiao Li ◽  
Baohuan Guo ◽  
Le Xu ◽  
Leyao Li ◽  
...  
Keyword(s):  
Immune Response ◽  
Pseudomonas Syringae ◽  
Stress Responses ◽  
Fungal Pathogens ◽  
Biological Function ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
The Relationship

Circular RNAs (circRNAs) are a group of covalently closed RNAs, and their biological function is largely unknown. In this study, we focused on circRNAs that are generated from exon back-splicing (exonic circRNAs). The linear RNA counterparts encode functional proteins, that we can compare and investigate the relationship between circular and linear RNAs. We compared circRNA expression profiles between untreated and Pseudomonas syringae-infected Arabidopsis, and identified and experimentally validated differentially expressed exonic circRNAs by multiple approaches. We found that exonic circRNAs are preferentially enriched in biological processes that associate with biotic and abiotic stress responses. We discovered that circR194 and circR4022 are involved in plant response against P. syringae infection, while circR11208 is involved in response against Botrytis cinerea infection. Intriguingly, our results indicate that these exonic circRNAs function synergistically with their corresponding linear RNAs. Furthermore, circR4022 and circR11208 also play substantial roles in Arabidopsis tolerance to salt stress. This study extends our understanding of the molecular functions of plant circRNAs.

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

scholarly journals The Craterostigma plantagineum protein kinase CpWAK1 interacts with pectin and integrates different environmental signals in the cell wall

Planta ◽  
2021 ◽  
Vol 253 (5) ◽  
Author(s):  
Peilei Chen ◽  
Valentino Giarola ◽  
Dorothea Bartels
Keyword(s):  
Cell Wall ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Cell Wall Protein ◽  
Biological Processes ◽  
Environmental Signals ◽  
High Affinity ◽  
Craterostigma Plantagineum ◽  
Receptor Kinases

Abstract Main conclusion The cell wall protein CpWAK1 interacts with pectin, participates in decoding cell wall signals, and induces different downstream responses. Abstract Cell wall-associated protein kinases (WAKs) are transmembrane receptor kinases. In the desiccation-tolerant resurrection plant Craterostigma plantagineum, CpWAK1 has been shown to be involved in stress responses and cell expansion by forming a complex with the C. plantagineum glycine-rich protein1 (CpGRP1). This prompted us to extend the studies of WAK genes in C. plantagineum. The phylogenetic analyses of WAKs from C. plantagineum and from other species suggest that these genes have been duplicated after species divergence. Expression profiles indicate that CpWAKs are involved in various biological processes, including dehydration-induced responses and SA- and JA-related reactions to pathogens and wounding. CpWAK1 shows a high affinity for “egg-box” pectin structures. ELISA assays revealed that the binding of CpWAKs to pectins is modulated by CpGRP1 and it depends on the apoplastic pH. The formation of CpWAK multimers is the prerequisite for the CpWAK–pectin binding. Different pectin extracts lead to opposite trends of CpWAK–pectin binding in the presence of Ca2+ at pH 8. These observations demonstrate that CpWAKs can potentially discriminate and integrate cell wall signals generated by diverse stimuli, in concert with other elements, such as CpGRP1, pHapo, Ca2+[apo], and via the formation of CpWAK multimers.

Identification of Ubiquitin Ligase From Grapevine Ring C3H2C3E3 and Characterization of Drought Resistance Function of VyRCHC114

2020 ◽  
Author(s):  
Yihe Yu ◽  
Shengdi Yang ◽  
Lu Bian ◽  
Keke Yu ◽  
Xiangxuan Meng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Ubiquitin Ligase ◽  
Stress Responses ◽  
Phylogenetic Trees ◽  
Expression Profiles ◽  
E3 Ubiquitin Ligase ◽  
Pcr Analysis ◽  
Biotic And Abiotic Stress ◽  
Element Analysis

Abstract Background: RING is one of the largest E3 ubiquitin ligase families and C3H2C3 type is the largest subfamily of RING, playing an important role in plants’ development and growth and their biotic and abiotic stress responses. Results: A total of 143 RING C3H2C3-type genes (RCHCs) were discovered from the grapevine genome and separated into groups (I-XI) according to their phylogenetic analysis, with these genes named according to their positions on chromosomes. Gene replication analysis showed that tandem duplications play a predominant role in the expansion of VyRCHCs family together. Structural analysis showed that most VyRCHCs(67.13%) had no more than 2 introns, while genes clustered together based on phylogenetic trees had similar motifs and evolutionarily conserved structures. Cis-acting element analysis showed the diversity of VyRCHCs regulation. The expression profiles of eight DEGs in RNA-Seq after drought stress were similar to those in qRT-PCR analysis. The in vitro ubiquitin experiment showed that VyRCHC114 had E3 ubiquitin ligase activity, overexpression of VyRCHC114 in Arabidopsis improved drought tolerance, moreover, the transgenic plant survival rate increased by 30%, accompanied by changing of electrolyte leakage, chlorophyll content and the activities of SOD, POD, APX and CAT were changed. AtCOR15a, AtRD29A, AtERD15 and AtP5CS1 were expressed quantitatively, the results showed that they participated in the drought stress response may be regulated by the expression of VyRCHC114.Conclusions: Valuable new information on the evolution of grapevine RCHCs and its relevance for studying the functional characteristics of grapevine VyRCHC114 genes under drought stress emerged from this research.

scholarly journals Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katie Emelianova ◽  
Andrea Martínez Martínez ◽  
Lucia Campos-Dominguez ◽  
Catherine Kidner
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Genome Size ◽  
Stress Responses ◽  
Chalcone Synthase ◽  
Expression Profiles ◽  
Rna Seq ◽  
Biotic And Abiotic Stress ◽  
Chalcone Synthase Gene ◽  
Study Species

AbstractBegonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.

scholarly journals Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress

2019 ◽  
Vol 20 (22) ◽  
pp. 5676 ◽  
Author(s):  
Haifeng Yan ◽  
Mingzhi Li ◽  
Yuping Xiong ◽  
Jianming Wu ◽  
Jaime A. Teixeira da Silva ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Sequences ◽  
Santalum Album ◽  
Biotic And Abiotic Stress ◽  
Functional Identification ◽  
Wrky Protein

WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.

scholarly journals The RsmA RNA-Binding Proteins in Pseudomonas syringae Exhibit Distinct and Overlapping Roles in Modulating Virulence and Survival Under Different Nutritional Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Jun Liu ◽  
Menghao Yu ◽  
Yixin Ge ◽  
Yanli Tian ◽  
Baishi Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pseudomonas Syringae ◽  
Stress Responses ◽  
Capsular Polysaccharide ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Transcriptomic Analysis ◽  
Phosphate Metabolism ◽  
Nutritional Conditions

The post-transcriptional regulator RsmA globally controls gene expression in bacteria. Previous studies showed that RsmA2 and RsmA3 played critical roles in regulating type III secretion system (T3SS), motility, syringafactin, and alginate productions in Pseudomonas syringae pv. tomato strain DC3000 (PstDC3000). In this study, we investigated global gene expression profiles of the wild-type PstDC3000, the rsmA3 mutant, and the rsmA2/A3 double mutant in the hrp-inducing minimum medium (HMM) and King’s B (KB) medium. By comparing the rsmA2/A3 and rsmA3 mutants to PstDC3000, a total of 1358 and 1074 differentially expressed genes (DEGs) in HMM, and 870 and 1463 DEGs in KB were uncovered, respectively. When comparing the rsmA2/A3 mutant with the rsmA3 mutant, 277 and 741 DEGs in HMM and KB, respectively, were revealed. Transcriptomic analysis revealed that the rsmY, rsmZ, and rsmX1-5 non-coding small RNAs (ncsRNAs) were positively affected by RsmA2 and RsmA3, while RsmA3 positively regulates the expression of the rsmA2 gene and negatively regulates both rsmA1 and rsmA5 gene expression. Comparative transcriptomic analysis showed that RsmA2 and RsmA3 synergistically influenced the expression of genes involved in T3SS and alginate biosynthesis in HMM and chemotaxis in KB. RsmA2 and RsmA3 inversely affected genes involved in syringafactin production in HMM and ribosomal protein biosynthesis in KB. In addition, RsmA2 played a major role in influencing genes involved in sarcosine and thiamine biosynthesis in HMM and in mannitol and phosphate metabolism in KB. On the other hand, genes involved in fatty acid metabolism, cellulose biosynthesis, signal transduction, and stress responses were mainly impacted by RsmA3 in both HMM and KB; whereas RsmA3 played a major role in controlling genes involved in c-di-GMP, phosphate metabolism, chemotaxis, and capsular polysaccharide in HMM. Furthermore, regulation of syringafactin production and oxidative stress by RsmA2 and RsmA3 was experimentally verified. Our results suggested the potential interplay among the RsmA proteins, which exhibit distinct and overlapping roles in modulating virulence and survival in P. syringae under different nutritional conditions.

scholarly journals CircRNA Expression Profile in Lung Cancer Complicated with Chronic Obstructive Pulmonary Disease Patients

2020 ◽  
Author(s):  
Fuqiang Wen ◽  
Xiaoou Li ◽  
Yongchun Shen ◽  
Jiahan Cheng ◽  
Jun Chen ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Chronic Obstructive Pulmonary Disease ◽  
Pulmonary Disease ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Chronic Obstructive ◽  
Biological Processes ◽  
Obstructive Pulmonary Disease ◽  
Copd Patients ◽  
Diagnosis Of Lung Cancer

Abstract Background: Lung cancer complicated with chronic obstructive pulmonary disease (COPD) are major causes of mortality worldwide, and the incidence of lung cancer and COPD increasing significantly. Circular RNAs (circRNAs), have been reported to participate in various biological processes, whereas the role of circRNAs in lung cancer complicated with COPD remains unclear. We aims to identify differentially expressed circRNAs (DEcircRNAs) between lung cancer complicated with COPD and lung cancer without COPD. Method: The circRNAs expression profiles were identified using a high-throughput circRNA microarray in cancer adjacent tissues from 6 lung cancer without COPD patients and 8 lung cancer complicated with COPD patients. Bioinformatic analyses were conducted to identify the functions of DEcircRNAs. Result: A total of 115 up- and 128 down-regulated circRNAs were screened in lung cancer complicated with COPD patients compared with lung cancer without COPD patients. The myD88-dependent toll-like receptor signaling pathway and positive regulation of nitric oxide biosynthetic process ranked the top 2 enriched biological processes in Gene Ontology analysis. Signaling transduction and infectious diseases were the most significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways in both up- and down-regulated circRNAs. Compared with lung cancer without COPD, circRNAs are dysregulated in the adjacent tissues of lung cancer with COPD. Conclusion: The DEcircRNAs might act as potential targets for the diagnosis of lung cancer with COPD.

Expression profile associated with CD274 (PD-L1) expression in cervical cancer.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e17005-e17005
Author(s):  
Edgar Roman Bassaure ◽  
Jaime Berumen Campos ◽  
Ingrid Yasbeth Medina
Keyword(s):  
Cervical Cancer ◽  
Immune Response ◽  
Expression Profiles ◽  
Mrna Level ◽  
Treatment Strategies ◽  
High Expression ◽  
Control Group ◽  
Biological Processes ◽  
New Treatment ◽  
Low Expression

e17005 Background: In Mexico, cervical cancer (CaCU) is the second leading cause of death in women. New treatment strategies are now emerging specifically the pathway of PD-1. We evaluated the frequency of PD-L1 expression at mRNA level and analyzed the expression profiles associated with different levels of CD274 expression. Methods: We analyzed the mRNA of 17 controls and 59 cervical cancer tumors by an expression microarray that allows the analysis of 22,607 human genes. Tumors were classified based on the mRNA expression of CD274. The deregulated genes in each group of tumors were compared against the control group using a T-test and Fold Change value. Functional analysis was using the DAVID tool. Correlation gene analysis was performed using the Pearson test. Results: The 59 cervical cancer tumors were classified in 3 groups: CD274-, CD274 low expression and CD274 high expression. The 71.2% of the tumors of CaCU have CD274 expression, 20 tumors with low expression and 22 tumors with high expression. 786 altered genes in the CD274- group, 1759 in the group of low expression and 2465 in the group of high expression were found. We found 19 altered biological processes in the CD274- group, being the most significant, cell cycle, DNA replication and DNA repair. In the tumors CD274 low were found 20 biological processes altered and were similar to those identified in the CD274- tumors. In the group CD274 high, 28 altered biological processes were found, interestingly 5 biological processes associated with innate immune response and antigenic processing. We found 24 genes correlated with the CD274 expression related to the immune response. Conclusions: The frequency of CD274 expression in cervical cancer is similar to that found in other tumors, it would be interesting explore the correlation between mRNA and protein. The number of altered genes is higher in the group of high expression of CD274. In the CD274 high group genes associated with processes related to the immune response are altered. The genes that correlate with the expression of CD274 are mostly associated with the immune system, these results suggest that overexpression of CD274 is accompanied by other immune processes.

scholarly journals Phenotypic Analyses of Arabidopsis T-DNA Insertion Lines and Expression Profiling Reveal That Multiple L-Type Lectin Receptor Kinases Are Involved in Plant Immunity

2014 ◽  
Vol 27 (12) ◽  
pp. 1390-1402 ◽  
Author(s):  
Yan Wang ◽  
Klaas Bouwmeester ◽  
Patrick Beseh ◽  
Weixing Shan ◽  
Francine Govers
Keyword(s):  
Abiotic Stress ◽  
Pseudomonas Syringae ◽  
Plant Development ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Alternaria Brassicicola ◽  
Lectin Receptor ◽  
Receptor Kinases ◽  
Dna Insertion

L-type lectin receptor kinases (LecRK) are membrane-spanning receptor-like kinases with putative roles in biotic and abiotic stress responses and in plant development. In Arabidopsis, 45 LecRK were identified but their functions are largely unknown. Here, a systematic functional analysis was carried out by evaluating phenotypic changes of Arabidopsis LecRK T-DNA insertion lines in plant development and upon exposure to various external stimuli. None of the LecRK T-DNA insertion lines showed clear developmental changes, either under normal conditions or upon abiotic stress treatment. However, many of the T-DNA insertion lines showed altered resistance to Phytophthora brassicae, Phytophthora capsici, Pseudomonas syringae, or Alternaria brassicicola. One mutant defective in LecRK-V.5 expression was compromised in resistance to two Phytophthora spp. but showed enhanced resistance to Pseudomonas syringae. LecRK-V.5 overexpression confirmed its dual role in resistance and susceptibility depending on the pathogen. Combined analysis of these phenotypic data and LecRK expression profiles retrieved from public datasets revealed that LecRK which are hardly induced upon infection or even suppressed are also involved in pathogen resistance. Computed coexpression analysis revealed that LecRK with similar function displayed diverse expression patterns. Because LecRK are widespread in plants, the results presented here provide invaluable information for exploring the potential of LecRK as novel sources of resistance in crops.

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