Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana

Abstract Turnip crinkle virus (TCV) is a carmovirus that infects many Arabidopsis ecotypes. Most studies mainly focused on discovery of resistance genes against TCV infection and there is no Next Generation Sequencing based comparative genome wide transcriptome analysis reported. In this study, RNA-seq based transcriptome analysis revealed that 238 (155 up-regulated and 83 down-regulated) significant differentially expressed genes with at least 15-fold change were determined. Fifteen genes (including upregulated, unchanged and downregulated) were selected for RNA-seq data validation using quantitative real-time PCR, which showed consistencies between these two sets of data. GO enrichment analysis showed that numerous terms such as stress, immunity, defence and chemical stimulus were affected in TCV-infected plants. One putative plant defence related gene named WRKY61 was selected for further investigation. It showed that WRKY61 overexpression plants displayed reduced symptoms and less virus accumulation, as compared to wild type (WT) and WRKY61 deficient lines, suggesting that higher WRKY61 expression level reduced TCV viral accumulation. In conclusion, our transcriptome analysis showed that global gene expression was detected in TCV-infected Arabidopsis thaliana. WRKY61 gene was shown to be negatively correlated with TCV infection and viral symptoms, which may be connected to plant immunity pathways.

Download Full-text

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

10.1101/588780 ◽

2019 ◽

Author(s):

Emese Xochitl Szabo ◽

Philipp Reichert ◽

Marie-Kristin Lehniger ◽

Marilena Ohmer ◽

Marcella de Francisco Amorim ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcriptome Analysis ◽

Rna Processing ◽

Rna Synthesis ◽

Rna Stability ◽

Metabolic Labeling ◽

Rna Seq ◽

Genome Wide ◽

Stability Measurement ◽

Chemical Inhibition

AbstractTranscriptome analysis by RNA sequencing (RNA-seq) has become an indispensable core research tool in modern plant biology. Virtually all RNA-seq studies provide a snapshot of the steady-state transcriptome, which contains valuable information about RNA populations at a given time, but lacks information about the dynamics of RNA synthesis and degradation. Only a few specialized sequencing techniques, such as global run-on sequencing (GRO-seq), have been applied in plants and provide information about RNA synthesis rates. Here, we demonstrate that RNA labeling with a modified, non-toxic uridine analog, 5-ethynyl uridine (5-EU), in Arabidopsis thaliana seedlings provides insight into the dynamic nature of a plant transcriptome. Pulse-labeling with 5-EU allowed the detection and analysis of nascent and unstable RNAs, of RNA processing intermediates generated by splicing, and of chloroplast RNAs. We also conducted pulse-chase experiments with 5-EU, which allowed us to determine RNA stabilities without the need for chemical inhibition of transcription using compounds such as actinomycin and cordycepin. Genome-wide analysis of RNA stabilities by 5-EU pulse-chase experiments revealed that this inhibitor-free RNA stability measurement results in RNA half-lives much shorter than those reported after chemical inhibition of transcription. In summary, our results show that the Arabidopsis nascent transcriptome contains unstable RNAs and RNA processing intermediates, and suggest that half-lives of plant RNAs are largely overestimated. Our results lay the ground for an easy and affordable nascent transcriptome analysis and inhibitor-free analysis of RNA stabilities in plants.

Download Full-text

Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens

Scientific Reports ◽

10.1038/s41598-021-97306-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ludmila Mudri Hul ◽

Adriana Mércia Guaratini Ibelli ◽

Igor Ricardo Savoldi ◽

Débora Ester Petry Marcelino ◽

Lana Teixeira Fernandes ◽

...

Keyword(s):

Articular Cartilage ◽

Femoral Head ◽

Transcriptome Analysis ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Differentially Expressed ◽

Economic Losses ◽

Rna Seq ◽

Cellular Activation ◽

Bone Anomalies

AbstractLocomotor problems are among one of the main concerns in the current poultry industry, causing major economic losses and affecting animal welfare. The most common bone anomalies in the femur are dyschondroplasia, femoral head separation (FHS), and bacterial chondronecrosis with osteomyelitis (BCO), also known as femoral head necrosis (FHN). The present study aimed to identify differentially expressed (DE) genes in the articular cartilage (AC) of normal and FHS-affected broilers by RNA-Seq analysis. In the transcriptome analysis, 12,169 genes were expressed in the femur AC. Of those, 107 genes were DE (FDR < 0.05) between normal and affected chickens, of which 9 were downregulated and 98 were upregulated in the affected broilers. In the gene-set enrichment analysis using the DE genes, 79 biological processes (BP) were identified and were grouped into 12 superclusters. The main BP found were involved in the response to biotic stimulus, gas transport, cellular activation, carbohydrate-derived catabolism, multi-organism regulation, immune system, muscle contraction, multi-organism process, cytolysis, leukocytes and cell adhesion. In this study, the first transcriptome analysis of the broilers femur articular cartilage was performed, and a set of candidate genes (AvBD1, AvBD2, ANK1, EPX, ADA, RHAG) that could trigger changes in the broiler´s femoral growth plate was identified. Moreover, these results could be helpful to better understand FHN in chickens and possibly in humans.

Download Full-text

Diverse Responses Are Involved in the Defence of Arabidopsis thaliana against Turnip Crinkle Virus

Zeitschrift für Naturforschung C ◽

10.1515/znc-2013-3-411 ◽

2013 ◽

Vol 68 (3-4) ◽

pp. 148-154 ◽

Cited By ~ 3

Author(s):

Hui Yang ◽

Shu Yuan ◽

Yi Luo ◽

Ji Huang ◽

Yang-Er Chen ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Plant Hormones ◽

Plant Defence ◽

Mitogen Activated Protein Kinase ◽

Turnip Crinkle Virus ◽

Wild Type ◽

Antagonistic Action ◽

Pathogenesis Related ◽

Mitogen Activated Protein ◽

Plant Pathogen Interactions

Plant hormones play pivotal roles as signals of plant-pathogen interactions. Here, we report that exogenous application of salicylic acid (SA), jasmonic acid (JA), ethephon (ETH), and abscisic acid (ABA) can reduce Turnip crinkle virus (TCV) accumulation in systemic leaves of Arabidopsis thaliana during early infection. SA and ABA are more efficient and confer a longer-lasting resistance against TCV than JA and ETH, and the plant hormones interact in effecting the plant defence. Synergistic actions of SA and JA, and SA and ET, and an antagonistic action of SA and ABA have been observed in the Arabidopsis-TCV interaction. ABA can down-regulate the expression of the pathogenesis-related genes PR1 and PDF1.2, and compared to the wild type, it drastically reduces TCV accumulation in NahG transgenic plants and the eds5-p1 mutant, both of which do not accumulate SA. This indicates that SA signaling negatively regulates the ABA-mediated defence. ABA-induced resistance against TCV is independent of SA. We also found that mitogen-activated protein kinase 5 (MPK5) may be involved in ABA-mediated defence. These results indicate that Arabidopsis can activate distinct signals to inhibit virus accumulation. Cooperative or antagonistic crosstalk between them is pivotal for establishing disease resistance. These results show potential to enhance the plant defence against viruses by manipulating diverse hormones.

Download Full-text

MiMIF-2 Effector of Meloidogyne incognita Exhibited Enzyme Activities and Potential Roles in Plant Salicylic Acid Synthesis

International Journal of Molecular Sciences ◽

10.3390/ijms21103507 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3507

Author(s):

Jianlong Zhao ◽

Zhenchuan Mao ◽

Qinghua Sun ◽

Qian Liu ◽

Heng Jian ◽

...

Keyword(s):

Salicylic Acid ◽

Transcriptome Analysis ◽

Meloidogyne Incognita ◽

Plant Immunity ◽

Acid Synthesis ◽

Host Immunity ◽

Parasitic Nematodes ◽

Marker Genes ◽

Rna Seq ◽

Shock Proteins

Plant-parasitic nematodes secrete a series of effectors to promote parasitism by modulating host immunity, but the detailed molecular mechanism is ambiguous. Animal parasites secrete macrophage migration inhibitory factor (MIF)-like proteins for evasion of host immune systems, in which their biochemical activities play essential roles. Previous research demonstrated that MiMIF-2 effector was secreted by Meloidogyne incognita and modulated host immunity by interacting with annexins. In this study, we show that MiMIF-2 had tautomerase activity and protected nematodes against H2O2 damage. MiMIF-2 expression not only decreased the amount of H2O2 generation during nematode infection in Arabidopsis, but also suppressed Bax-induced cell death by inhibiting reactive oxygen species burst in Nicotiana benthamiana. Further, RNA-seq transcriptome analysis and RT-qPCR showed that the expression of some heat-shock proteins was down regulated in MiMIF-2 transgenic Arabidopsis. After treatment with flg22, RNA-seq transcriptome analysis indicated that the differentially expressed genes in MiMIF-2 expressing Arabidopsis were pointed to plant hormone signal transduction, compound metabolism and plant defense. RT-qPCR and metabolomic results confirmed that salicylic acid (SA) related marker genes and SA content were significantly decreased. Our results provide a comprehensive understanding of how MiMIF-2 modulates plant immunity and broaden knowledge of the intricate relationship between M. incognita and host plants.

Download Full-text

Antidepressant Mechanism Research of Acupuncture: Insights from a Genome-Wide Transcriptome Analysis of Frontal Cortex in Rats with Chronic Restraint Stress

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2017/1676808 ◽

2017 ◽

Vol 2017 ◽

pp. 1-13 ◽

Cited By ~ 9

Author(s):

Yu Wang ◽

Huili Jiang ◽

Hong Meng ◽

Jing Li ◽

XinJing Yang ◽

...

Keyword(s):

Frontal Cortex ◽

Signaling Pathway ◽

Restraint Stress ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Chronic Restraint Stress ◽

Rna Seq ◽

Toll Like Receptor ◽

Genome Wide ◽

Receptor Signaling Pathway

Major depressive disorder (MDD) is a chronic disease that adversely affects mood and cognition. In this study, we randomly divided the rats into control group (C), model group (M), fluoxetine group (F), and acupuncture group (A), used open-field test to ascertain whether acupuncture affects chronic restraint stress (CRS) induced depression-like behaviors of rats, and explored the antidepressant mechanism of acupuncture at the molecular level of transcriptome in the frontal cortex of CRS rats by RNA-sequencing (RNA-seq). According to differentially expressed genes (DEG) analysis, we identified 134, 46, and 89 response genes differentially expressed in C versus M, F versus M, and A versus M, respectively. Through Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we identified the gene sets involved in extracellular space, inflammatory response, Toll-like receptor signaling pathway, chemokine signaling pathway, and TNF signaling pathway. In this study, RNA-seq technology was used to investigate the frontal cortex genome-wide transcriptomes in depression rats under CRS, which suggested that the antidepressant effect of acupuncture is effective and has a multitarget characteristic, which may be related to amino acid metabolism and inflammatory pathways, especially the Toll-like receptor signaling pathway, TNF signaling pathway, and NF-kappa B signaling pathway.

Download Full-text

Single-stranded oligodeoxynucleotides induce plant defence in Arabidopsis thaliana

Annals of Botany ◽

10.1093/aob/mcaa061 ◽

2020 ◽

Vol 126 (3) ◽

pp. 413-422

Author(s):

Laila Toum ◽

Gabriela Conti ◽

Francesca Coppola Guerriero ◽

Valeria P Conforte ◽

Franco A Garolla ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Nadph Oxidase ◽

Pseudomonas Syringae ◽

Plant Immunity ◽

Stomatal Closure ◽

Plant Defence ◽

Oxidase Inhibitor ◽

Bacterial Toxin ◽

Dependent Manner ◽

Concentration Dependent Manner

Abstract Background and Aims Single-stranded DNA oligodeoxynucleotides (ssODNs) have been shown to elicit immune responses in mammals. In plants, RNA and genomic DNA can activate immunity, although the exact mechanism through which they are sensed is not clear. The aim of this work was to study the possible effect of ssODNs on plant immunity. Key Results The ssODNs IMT504 and 2006 increased protection against the pathogens Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea but not against tobacco mosaic virus-Cg when infiltrated in Arabidopsis thaliana. In addition, ssODNs inhibited root growth and promoted stomatal closure in a concentration-dependent manner, with half-maximal effective concentrations between 0.79 and 2.06 µm. Promotion of stomatal closure by ssODNs was reduced by DNase I treatment. It was also diminished by the NADPH oxidase inhibitor diphenyleneiodonium and by coronatine, a bacterial toxin that inhibits NADPH oxidase-dependent reactive oxygen species (ROS) synthesis in guard cells. In addition it was found that ssODN-mediated stomatal closure was impaired in bak1-5, bak1-5/bkk1, mpk3 and npr1-3 mutants. ssODNs also induced early expression of MPK3, WRKY33, PROPEP1 and FRK1 genes involved in plant defence, an effect that was reduced in bak1-5 and bak1-5/bkk1 mutants. Conclusions ssODNs are capable of inducing protection against pathogens through the activation of defence genes and promotion of stomatal closure through a mechanism similar to that of other elicitors of plant immunity, which involves the BAK1 co-receptor, and ROS synthesis.

Download Full-text

Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

BMC Genomics ◽

10.1186/s12864-018-5039-5 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 12

Author(s):

Lyudmila V. Dergunova ◽

Ivan B. Filippenkov ◽

Vasily V. Stavchansky ◽

Alina E. Denisova ◽

Vadim V. Yuzhakov ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Rat Model ◽

Transcriptome Analysis ◽

Differentially Expressed ◽

Rna Seq ◽

Genome Wide

Download Full-text

Author Correction: Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana

Scientific Reports ◽

10.1038/s41598-020-75427-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ruimin Gao ◽

Peng Liu ◽

Yuhan Yong ◽

Sek-Man Wong

Keyword(s):

Arabidopsis Thaliana ◽

Symptom Severity ◽

Transcriptomic Analysis ◽

Turnip Crinkle Virus ◽

Genome Wide

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Download Full-text

Transcriptome analysis of the regulation of natamycin biosynthesis in Streptomyces natalensis HW-2 by fungal elicitor

10.21203/rs.2.18475/v1 ◽

2019 ◽

Author(s):

Dahong Wang ◽

Wenhao Shen ◽

Jiangfeng Yuan ◽

Lanlan Wei ◽

Ying Zhang

Keyword(s):

Gene Expression ◽

Transcriptome Analysis ◽

Tricarboxylic Acid Cycle ◽

Enrichment Analysis ◽

Pentose Phosphate ◽

Fungal Elicitor ◽

Natural Food ◽

Rna Seq ◽

Expression Levels ◽

Streptomyces Natalensis

Abstract Background Natamycin is a polyene macrolide polyketide antibiotics and used in 150 countries as a natural food preservative. Streptomyces natalensis is an important producer. Elicitation had been approved to be an effective method to improve the biosynthesis of secondary metabolites. Fungal elicitor from Penicillium chrysogenum AS 3.5163 showed inductive effect on the biosynthesis of natamycin in S. natalensis HW-2 fermentation. However, regarding the global gene expression of natamycin in response to fungal elicitor is not still reported. Results RNA-Seq analysis showed that there were 1265 differential expression genes (DEGs) at 40 h and 2196 DEGs at 80 h. The fungal elicitor had stronger effects on the transcription level of S. natalensis HW-2 at 80 h than that at 40 h. Gene Ontology (GO) enrichment analysis of DEGs showed significant enrichment in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the fungal elicitor mainly affected the expression levels of some genes about cellular process, metabolism and genetic information, especially in pentose phosphate pathway (PPP), glycolytic pathway (EMP) and tricarboxylic acid cycle (TCA). KEGG pathway showed that fungal elicitor had a greater influence on the metabolism of branched-chain amino acids (BCAAs). Among them, 23 DEGs associated with BCAAs metabolism were up-regulated or down-regulated. The supplementation experiment with BCAAs confirmed that 0.2 g/L of L-Ile and 0.5 g/L of L-Val increased natamycin yield by 17.6% and 37.8%, respectively. Fungal elicitor also up-regulated the transcriptional levels of most of the enzymes associated with the biosynthesis of natamycin and two important transcription regulators ( pimR and pimM ). To confirm the accuracy of RNA-Seq, the results of qPCR showed that these gene expression levels were in agreement with the transcription changes by RNA-Seq. Conclusion In this study, the change of transcriptional levels in S. natalensis HW-2 under treated with the fungal elicitor was firstly reported. The major finding of our comparative transcriptome analysis is that the fungal elicitor improves the supply of precursor, and alters the expression of natamycin related genes and regulator of secondary metabolism. From our results, we conclude that regulatory alterations are important factors for the enhancement of natamycin.

Download Full-text

Regulation of global transcription inE. coliby Rsd and 6S RNA

10.1101/058339 ◽

2016 ◽

Cited By ~ 1

Author(s):

Avantika Lal ◽

Sandeep Krishna ◽

Aswin Sai Narain Seshasayee

Keyword(s):

Rna Polymerase ◽

Sigma Factor ◽

Global Gene Expression ◽

Rna Seq ◽

Genome Wide ◽

A Genome ◽

6S Rna ◽

Wide Scale ◽

Five Phases ◽

First Time

ABSTRACTInEscherichia coli, the sigma factor σ70directs RNA polymerase to transcribe growth-related genes, while σ38directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ70, and the non-coding 6S RNA which binds to the RNA polymerase- σ70holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show for the first time that Rsd and 6S RNA facilitate σ38activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.

Download Full-text