Transcriptome Analysis Reveals Multiple Hormones, Wounding and Sugar Signaling Pathways Mediate Adventitious Root Formation in Apple Rootstock

Adventitious roots (AR) play an important role in the vegetative propagation of apple rootstocks. The potential role of hormone, wounding, and sugar signalling pathways in mediating AR formation has not been adequately explored and the whole co-expression network in AR formation has not been well established in apple. In order to identify the molecular mechanisms underlying AR formation in ‘T337’ apple rootstocks, transcriptomic changes that occur during four stages of AR formation (0, 3, 9 and 16 days) were analyzed using high-throughput sequencing. A total of 4294 differentially expressed genes were identified. Approximately 446 genes related to hormones, wounding, sugar signaling, root development, and cell cycle induction pathways were subsequently selected based on their potential to be involved in AR formation. RT-qPCR validation of 47 genes with known functions exhibited a strong positive correlation with the RNA-seq data. Interestingly, most of the candidate genes involved in AR formation that were identified by transcriptomic sequencing showed auxin-responsive expression patterns in an exogenous Indole-3-butyric acid (IBA)-treatment assay: Indicating that endogenous and exogenous auxin plays key roles in regulating AR formation via similar signalling pathways to some extent. In general, AR formation in apple rootstocks is a complex biological process which is mainly influenced by the auxin signaling pathway. In addition, multiple hormones-, wounding- and sugar-signaling pathways interact with the auxin signaling pathway and mediate AR formation in apple rootstocks.

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Faculty Opinions recommendation of Physcomitrella patens auxin-resistant mutants affect conserved elements of an auxin-signaling pathway.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.5704956.5686057 ◽

2010 ◽

Author(s):

Jiri Friml ◽

Steffen Vanneste

Keyword(s):

Signaling Pathway ◽

Physcomitrella Patens ◽

Auxin Signaling ◽

Auxin Signaling Pathway ◽

Resistant Mutants

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The OsOXO2, OsOXO3 and OsOXO4 Positively Regulate Panicle Blast Resistance in Rice

Rice ◽

10.1186/s12284-021-00494-9 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Jingfang Dong ◽

Lian Zhou ◽

Aiqing Feng ◽

Shaohong Zhang ◽

Hua Fu ◽

...

Keyword(s):

Signaling Pathways ◽

Signaling Pathway ◽

Molecular Mechanisms ◽

Blast Resistance ◽

Aba Signaling ◽

Leaf Blast ◽

Expression Levels ◽

Panicle Blast ◽

Localization Analysis ◽

Sa Signaling

Abstract Background Although panicle blast is more destructive to yield loss than leaf blast in rice, the cloned genes that function in panicle blast resistance are still very limited and the molecular mechanisms underlying panicle blast resistance remain largely unknown. Results In the present study, we have confirmed that the three Oxalate oxidase (OXO) genes, OsOXO2, OsOXO3 and OsOXO4 from a blast-resistant cultivar BC10 function in panicle blast resistance in rice. The expression of OsOXO2, OsOXO3 and OsOXO4 were induced by panicle blast inoculation. Subcellular localization analysis revealed that the three OXO proteins are all localized in the nucleus and cytoplasm. Simultaneous silencing of OsOXO2, OsOXO3 and OsOXO4 decreased rice resistance to panicle blast, whereas the OsOXO2, OsOXO3 and OsOXO4 overexpression rice plants individually showed enhanced panicle blast resistance. More H2O2 and higher expression levels of PR genes were observed in the overexpressing plants than in the control plants, while the silencing plants exhibited less H2O2 and lower expression levels of PR genes compared to the control plants. Moreover, phytohormone treatment and the phytohormone signaling related gene expression analysis showed that panicle blast resistance mediated by the three OXO genes was associated with the activation of JA and ABA signaling pathways but suppression of SA signaling pathway. Conclusion OsOXO2, OsOXO3 and OsOXO4 positively regulate panicle blast resistance in rice. The OXO genes could modulate the accumulation of H2O2 and expression levels of PR gene in plants. Moreover, the OXO genes mediated panicle blast resistance could be regulated by ABA, SA and JA, and may be associated with the activation of JA and ABA signaling pathways but suppression of the SA signaling pathway.

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Transcriptome characterization analysis and molecular profiles of obligatory diapause induction of the Chinese citrus fruit fly,Bactrocera minax(Diptera: Tephritidae)

10.1101/672642 ◽

2019 ◽

Author(s):

Zhixiong Zhou ◽

Xiaolin Dong ◽

Chuanren Li

Keyword(s):

Signaling Pathway ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Citrus Fruit ◽

Pupal Stage ◽

Fruit Fly ◽

Diapause Induction ◽

Regulation Mechanism ◽

Pupal Diapause ◽

Specific Stage

AbstractThe Chinese citrus fruit fly,Bactrocera minax, is a devastating citrus pest in China, Bhutan and India. It will enter obligatory pupal diapause in each generation at specific stage, while little is known about the course and the molecular mechanisms of diapause induction. To gain insight into possible mechanisms of obligatory pupal diapause induction, high-throughput RNA-seq data were generated from second-instar larvae (2L), third-instar larvae (3L) and pupal (P, one week after pupating). A total of 116,402 unigenes were assembled and researched against public databases, and 54,781 unigenes matched to proteins in the NCBI database using the BLAST search. Three pairwise comparisons were performed, and significantly differentially regulated transcripts were identified. Several differentially expressed genes (DEGs) expression patterns revealed that those highly or lowly expressed genes in pupal stage were predicted to be involved in diapause induction. Moreover, GO function and KEGG pathway analysis were performed on all DEGs and showed that 20-hydroxyecdysone (20E) biosynthesis, insulin signaling pathway, FoxO signaling pathway, cell cycle and metabolism pathway may be related to the obligatory diapause of the Chinese citrus fruit fly. This study provides valuable information about the Chinese citrus fruit fly transcriptome for future gene function research, and contributes to the in-depth elucidation of the molecular regulation mechanism of insect obligatory diapause induction.

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A chemically induced proximity system engineered from the plant auxin signaling pathway

Chemical Science ◽

10.1039/c8sc02353k ◽

2018 ◽

Vol 9 (26) ◽

pp. 5822-5827 ◽

Cited By ~ 2

Author(s):

Weiye Zhao ◽

Huong Nguyen ◽

Guihua Zeng ◽

Dan Gao ◽

Hao Yan ◽

...

Keyword(s):

Signaling Pathway ◽

Auxin Signaling ◽

Auxin Signaling Pathway ◽

Chemically Induced

A new chemically induced proximity system is developed by engineering the plant auxin signaling pathway.

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Identification of Auxin Activity Like 1, a chemical with weak functions in auxin signaling pathway

Plant Molecular Biology ◽

10.1007/s11103-018-0779-9 ◽

2018 ◽

Vol 98 (3) ◽

pp. 275-287

Author(s):

Wenbo Li ◽

Haimin Li ◽

Peng Xu ◽

Zhi Xie ◽

Yajin Ye ◽

...

Keyword(s):

Signaling Pathway ◽

Auxin Signaling ◽

Auxin Activity ◽

Auxin Signaling Pathway

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Molecular Rewiring of the Jasmonate Signaling Pathway to Control Auxin-Responsive Gene Expression

Cells ◽

10.3390/cells9030641 ◽

2020 ◽

Vol 9 (3) ◽

pp. 641

Author(s):

Ning Li ◽

Linggai Cao ◽

Wenzhuo Miu ◽

Ruibin Cao ◽

Mingbo Peng ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathway ◽

Developmental Process ◽

Expression System ◽

Transient Gene Expression ◽

Transcriptional Repressor ◽

Auxin Signaling ◽

General Strategy ◽

Auxin Signaling Pathway ◽

Responsive Gene

The plant hormone jasmonic acid (JA) has an important role in many aspects of plant defense response and developmental process. JA triggers interaction between the F-box protein COI1 and the transcriptional repressors of the JAZ family that leads the later to proteasomal degradation. The Jas-motif of JAZs is critical for mediating the COI1 and JAZs interaction in the presence of JA. Here, by using the protoplast transient gene expression system we reported that the Jas-motif of JAZ1 was necessary and sufficient to target a foreign reporter protein for COI1-facilitated degradation. We fused the Jas-motif to the SHY2 transcriptional repressor of auxin signaling pathway to create a chimeric protein JaSHY. Interestingly, JaSHY retained the transcriptional repressor function while become degradable by the JA coreceptor COI1 in a JA-dependent fashion. Moreover, the JA-induced and COI1-facilitated degradation of JaSHY led to activation of a synthetic auxin-responsive promoter activity. These results showed that the modular components of JA signal transduction pathway can be artificially redirected to regulate auxin signaling pathway and control auxin-responsive gene expression. Our work provides a general strategy for using synthetic biology approaches to explore and design cell signaling networks to generate new cellular functions in plant systems.

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Signaling pathways in the coral polyp bail-out response

Coral Reefs ◽

10.1007/s00338-020-01983-x ◽

2020 ◽

Vol 39 (6) ◽

pp. 1535-1548

Author(s):

Po-Shun Chuang ◽

Satoshi Mitarai

Keyword(s):

Signaling Pathways ◽

Signaling Pathway ◽

Molecular Mechanisms ◽

Fgf Signaling ◽

Reef Restoration ◽

Qpcr Analysis ◽

Coral Polyp ◽

Bail Out ◽

Necrosis Factor ◽

Significant Activation

AbstractPolyp bail-out is a stress response exhibited by some pocilloporid corals, with mechanisms and consequences distinct from those of bleaching. Although induction of polyp bail-out has been demonstrated in the laboratory, molecular mechanisms underlying this response have rarely been discussed. We conducted genetic analyses of Pocillopora acuta during initiation of hyperosmosis-induced polyp bail-out, using both transcriptomic and qPCR techniques. Beyond upregulation of apoptosis and proteolysis, corals showed significant activation of tumor necrosis factor and fibroblast growth factor (FGF) signaling pathways during induction of polyp bail-out. In our qPCR analysis, a common upregulation profile, peaking at 43.0‰ salinity, was found in the FAS and CASP8 genes, whereas a different profile, showing significant upregulation up to 45.0‰, was displayed by matrix metalloproteinases and genes in the FGF signaling pathway. These results suggest parallel involvement of an extrinsic apoptotic signaling pathway and FGF-mediated extracellular matrix degradation in polyp bail-out. Furthermore, in the XIAP, JNK, and NFKB1 genes, we detected a third expression profile showing linear upregulation that becomes maximal at the endpoint salinity level of the experiment (46.0‰), indicating activation of anti-apoptotic and cell survival signals during polyp bail-out. Our results provide new insights into signaling pathways responsible for polyp bail-out and suggest the feasibility of inducing bail-out by specifically triggering these pathways without exerting lethal stresses on the corals, which in turn will facilitate acquisition of viable polyps for possible use in coral reef restoration.

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