Combination of iTRAQ proteomics and RNA-seq transcriptomics reveals multiple levels of regulation in phytoplasma-infected Ziziphus jujuba Mill

Xia, Ye; Wang, Huiyu; Chen, Peng; Bing, Fu; Zhang, Mengyang; Li, Jidong; Zheng, Xianbo; Tan, Bin; Feng, Jiancan

doi:10.1038/hortres.2017.80

Cited by 61 publications

(63 citation statements)

References 41 publications

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“…They speculated that the leaf color altering was caused by expression level variations of key genes related to flavonoid biosynthesis. In addition, Xia Ye et al [46] discovered the 20 genes related to flavonoid biosynthesis in Ziziphus jujube Mill through iTRAQ proteomics and RNA-seq transcriptomics analysis. Meanwhile, the 3-ketoacyl-CoA synthase that was related to fatty acid synthesis was discovered in the DEGs of this study.…”

Section: Degs Related To Phytohormonesmentioning

confidence: 99%

Comparative Transcriptomics Analysis of Phytohormone-Related Genes and Alternative Splicing Events Related to Witches’ Broom in Paulownia

Dong

Zhang

Fan

et al. 2018

Forests

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Paulownia is a native fast-growing tree in China that has been introduced into many countries. However, it is often infected by Paulownia witches' broom (PaWB) disease, which can lead to large declines in yield. PaWB is caused by a phytoplasma that is an obligate biotrophic plant pathogen. Until now, the molecular mechanisms of interactions between the host plants and the phytoplasma have not been clear. In previous studies, it was reported that PaWB-infected Paulownia exhibited healthy morphology after being treated with methyl methane sulfonate (MMS) at the concentration of 20 mg·L −1 (for Paulownia tomentosa (PT) and Paulownia fortunei (PF) or 15 mg·L −1 (for P. tomentosa × P. fortunei) MMS. In this study, the whole transcriptome expression profile of PaWB-infected Paulownia was studied using high-throughput sequencing technology. In total, 74 significantly differentially expressed genes were detected among three species of healthy, PaWB-infected Paulownia, and the Paulownia treated with MMS. We identified and analyzed genes related to the roles of phytohormones and alternative splicing events involved in regulating plant growth. In response to phytoplasma infection, the concentrations of the plants' phytohormones were altered, leading to morphology transformation. This research will provide valuable information to detect the molecular mechanisms involved in the Paulownia response to phytoplasma infection.

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Section: Degs Related To Phytohormonesmentioning

confidence: 99%

Comparative Transcriptomics Analysis of Phytohormone-Related Genes and Alternative Splicing Events Related to Witches’ Broom in Paulownia

Dong

Zhang

Fan

et al. 2018

Forests

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“…Among these, the most significant transcript induction took place in the early stage (June or July) when the concentration of witches' broom began to increase. For example, ZjMAPKKK13, 14,15,23,34,42,44,47 and 56 were significantly induced in June or July but induction later decreased from August to September as shown in Fig. 6 (B).…”

Section: Expression Analysis Of Zjmapkkks In Witches' Broom Leavesmentioning

confidence: 83%

“…The physiological and biochemical behaviours of jujube plants infected by this phytoplasma have been widely studied [20,21,22] but the underlying molecular mechanisms remains elusive. Recently, the MAPKs have been reported in response to phytoplasma infection of Chinese jujube, with analysis of their expression levels in different phytoplasma-infected materials [23]. This study has provided valuable insights into the important roles played by MAPKs during the infection process.…”

Section: Introductionmentioning

confidence: 96%

Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)

Liu

Wang

Xue

et al. 2019

Preprint

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KEYWORDSChinese jujube, MAPKKKs, Jujube witches' broom, Phytoplasma, Expression profiles salinity, cold and pathogen attack [1][2][3]. The conserved serine/threonine MAPKKKs can be activated by plasma membrane receptors, these in turn phosphorylate the MAPKKs, which then activate the MAPKs by sequential phosphorylation. Finally, the MAPKs regulate other kinases or related transcription factors in response to various stresses [4, 5]. Each MAPK cascade family consists of a number of members, the number of members varies significantly between families. For example, the MAPKKKs family comprises a greater number of members and shows more complex sequence diversity than the other two families. The members belonging to the MAPKKKs family can be classified into the subfamilies Raf, ZIK and MEKK, according to their characteristic sequence motifs [6]. A structural diversity is found among MAPKKKs in each subfamily. The Raf subfamily has a C-terminal kinase domain and a long N-terminal regulatory domain, while ZIK proteins have only an N-terminal kinase domains and the MEKK subfamily has fewer conserved kinase domains. In addition, a long N-terminal regulatory domain forms the backbone for the Raf and ZIK subfamilies [1, 6]. The MAPK cascades have been implicated in signal transduction in distinct innate immunity [7, 8]. In Arabidopsis, the MEKK1-MKK4/5-MPK3/6-WRKY22/WRKY29/FRK1 cascade is involved in innate immunity signalling transduction and the MEKK1-MKK1/MKK2-MPK4 kinase cascade can negatively activate MEKK2 which further leads to a SUMM2-mediated immune responses [9, 10]. In tobacco, NPK1-MEK1-Ntf6 can regulate WRKY/MYB transcription factors to participate in the tobacco mosaic virus infection pathway [11]. In addition, the MAPKKKα-MKK2/MKK4-MPK2/MPK3 cascades take part in the Pto-mediated effect or triggered immunity (ETI) pathway by regulating the transcription factor TGA in tomato [12]. Hence, the MAPKs pathway is indeed involved in response to pathogen attack and may also play essential roles in the response to phytoplasma infection in Chinese jujube. The MAPKKKs family has now been characterised in the plant kingdom. A total of 80 MAPKKKs were first identified in Arabidopsis in 2002 [6, 13]. Since then, an array of different MAPKKKs have been identified from in a range of plant species including rice (75 members), Zea mays (71 members), Vitis vinifera (45 members), Malus domestica (72 members) and Musa nana (77 members) [14-17].However, little is known about the biological information and function of the MAPKKK gene family in Chinese jujube, even though detailed information for ZjMAPKKs and ZjMAPKs has previously been ZjMAPKKKs subfamily was used to find the highest number of conserved domains [30]. Sequence alignment, phylogenetic and gene duplication analysisAll the protein sequences of ZjMAPKKKs were aligned by ClusterX software using the default parameter values. The alignments of the protein sequences of 56 ZjMAPKKKs and 80 AtMAPKKKs were then subjected to phylogenetic analysis using MEGA 6.06 alignment expl...

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“…Moreover, ZjMKK2 could activate ZjMPK2 and thus play essential roles in the JWB defence response [23]. Ye et al [22] have shown that after phytoplasma infection, MAPKs can also be activated and that the transcription factor WRKY33 is regulated. Taken together, these results indicate the likely ZjMAPKKKs that mediate ZjMKK2-ZjMPK2 to WRKY transcription factors in response to phytoplasma infection, which will need to be resolved in future studies.…”

Section: Discussionmentioning

confidence: 99%

“…The physiological and biochemical behaviours of jujube plants infected by this phytoplasma have been widely studied [19][20][21], but the underlying molecular mechanisms have not been elucidated. Recently, MAPKs have been reported in response to phytoplasma infection of Chinese jujube with analysis of their expression levels in different phytoplasma-infected materials [22]. This study has provided valuable insights into the important roles played by MAPKs during the infection process.…”

Section: Introductionmentioning

confidence: 93%

Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)

et al. 2020

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Background: Mitogen-activated protein kinase (MAPK) cascades play vital roles in signal transduction in response to a wide range of biotic and abiotic stresses. In a previous study, we identified ten ZjMAPKs and five ZjMAPKKs in the Chinese jujube genome. We found that some members of ZjMAPKs and ZjMAPKKs may play key roles in the plant's response to phytoplasma infection. However, how these ZjMAPKKs are modulated by ZjMAPKKKs during the response process has not been elucidated. Little information is available regarding MAPKKKs in Chinese jujube.Results: A total of 56 ZjMAPKKKs were identified in the jujube genome. All of these kinases contain the key S-TKc (serine/threonine protein kinase) domain, which is distributed among all 12 chromosomes. Phylogenetic analyses show that these ZjMAPKKKs can be classified into two subfamilies. Specifically, 41 ZjMAPKKKs belong to the Raf subfamily, and 15 belong to the MEKK subfamily. In addition, the ZjMAPKKKs in each subfamily share the same conserved motifs and gene structures. Only one pair of ZjMAPKKKs (15/16, on chromosome 5) was found to be tandemly duplicated. Using qPCR, the expression profiles of these MAPKKKs were investigated in response to infection with phytoplasma. In the three main infected tissues (witches' broom leaves, phyllody leaves, and apparently normal leaves), ZjMAPKKK26 and − 45 were significantly upregulated, and ZjMAPKKK3, − 43 and − 50 were significantly downregulated. ZjMAPKKK4, − 10, − 25 and − 44 were significantly and highly induced in sterile cultivated tissues infected by phytoplasma, while ZjMAPKKK6, − 7, − 17, − 18, − 30, − 34, − 35, − 37, − 40, − 41, − 43, − 46, − 52 and − 53 were significantly downregulated.Conclusions: For the first time, we present an identification and classification analysis of ZjMAPKKKs. Some ZjMAPKKK genes may play key roles in the response to phytoplasma infection. This study provides an initial understanding of the mechanisms through which ZjMAPKKKs are involved in the response of Chinese jujube to phytoplasma infection.

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Combination of iTRAQ proteomics and RNA-seq transcriptomics reveals multiple levels of regulation in phytoplasma-infected Ziziphus jujuba Mill

Cited by 61 publications

References 41 publications

Comparative Transcriptomics Analysis of Phytohormone-Related Genes and Alternative Splicing Events Related to Witches’ Broom in Paulownia

Comparative Transcriptomics Analysis of Phytohormone-Related Genes and Alternative Splicing Events Related to Witches’ Broom in Paulownia

Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)

Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)

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