Genome-Wide Identification and Evolutionary and Expression Analyses of MYB-Related Genes in Land Plants

Du, Hongwu; Wang, Yongbin; Xie, Yi; Liang, Zhe; Jiang, Sanjie; Zhang, Shuang-Shuang; Huang, Yubi; Tang, Yixiong

doi:10.1093/dnares/dst021

Cited by 126 publications

(133 citation statements)

References 43 publications

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“…Descriptions as in Table 1 Another large and diversified group of genes involved in the cold stress response comprises those related to growth regulators. Our results indicate profound changes in the metabolism of all major plant growth regulators like ethylene, brassinosteroids and jasmonate and are consistent with their proposed roles in the cold-stress response of maize (Szalai et al 2000;Janowiak et al 2002;Du et al 2013;Vardhini and Anjum 2015;Li et al 2016). The picture is much less clear regarding the metabolic pathways related to the growth stimulators auxins, cytokinins and gibberellins that appeared to be altered under severe cold in a complex and inconsistent manner.…”

Section: Severe Cold Stress Signalingsupporting

confidence: 90%

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Jończyk

Sobkowiak

Trzcińska-Danielewicz

et al. 2017

Plant Mol Biol

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numerous genes lacking circadian rhythm responded to the cold by undergoing up-or down-regulation. Notably, the transcriptome changes preceded major physiological manifestations of cold stress. In silico analysis of metabolic processes likely affected by observed gene expression changes indicated major down-regulation of photosynthesis, profound and multifarious modulation of plant hormone levels, and of chromatin structure, transcription, and translation. A role of trehalose and stachyose in cold stress signaling was also suggested. Meta-analysis of published transcriptomic data allowed discrimination between general stress response of maize and that unique to severe cold. Several cis-and trans-factors likely involved in the latter were predicted, albeit none of them seemed to have a major role. These results underscore a key role of modulation of diel gene expression in maize response to severe cold and the unique character of the cold-response of the maize circadian clock.

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Section: Severe Cold Stress Signalingsupporting

confidence: 90%

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Jończyk

Sobkowiak

Trzcińska-Danielewicz

et al. 2017

Plant Mol Biol

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“…The top HMG gene was highly expressed through the entire 192-h time course, suggesting that it regulates multiple processes. MYB-related proteins regulate seed/leaf development and circadian rhythm (46,47), and their up-and down-regulation time points were mostly synchronized with those of other photosynthesis genes (SI Appendix, Fig. S3A).…”

Section: Expression Dynamics Of Tf Gene Families During Germination Andmentioning

confidence: 99%

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

Chen²,

Chang³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up-and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development. maize transcriptomes | coexpressed genes | cis binding site M aize (Zea mays) is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, the regulatory network that controls maize leaf development is still not well understood. In fact, the number of known maize transcription factor (TF)-binding sites (TFBSs) is far smaller than that for Arabidopsis thaliana (1-3).To understand better the regulation of maize leaf development, several recent studies used next-generation sequencing (NGS) technologies to survey transcriptomic differences among maize leaf cell types and developmental stages. The first large-scale study was by Li et al. (7) investigated the transcriptomes of Kranz (i.e., the foliar leaf blade) and non-Kranz (the husk leaf sheath) maize leaves to identify cohorts of genes associated with procambium initiation and vascular patterning. Recently, Wang et al. (8) conducted comparative transcriptomic and metabolomic analyses of developing leaves in maize and rice and identified putative structural and regulatory components important for C4 and C3 photosynthesis. These studies provided insights into the regulatory mechanisms underlying the development of Kranz leaf anatomy in maize.In the present study, we obtained nine transcriptomes of the second leaf from 84-192 h post imbibition at 12-h (6:00 AM and 6:00 PM) or 24-h (6:00 PM only) intervals. Together with the 13 SignificanceMaize is a major crop and a model plant for studying C4 leaf development. However, its regulatory network of leaf ...

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“…Plant MYB transcription factors are classified into three to four groups (R2R3-R3-or 1R-and MYB-related families) that contain one to three conserved MYB DNA binding domains (a helix-turn-helix (HTH) domain) with more than 50 amino acids (Du et al 2013). In this study, we focused on one of the MYB-related genes, Ljmybr, which is expressed after M. loti infection.…”

Section: Discussionmentioning

confidence: 99%

“…Although there are many reports about R2R3-MYB proteins, little is known about MYB-related genes (Du et al 2012a;Du et al 2012b;Matus et al 2008;Stracke et al 2001). In maize and soybean, MYB-related genes have roles both in development and in stress responses (Du et al 2013). Based on the alignment of the MYB domain, MYB-related proteins have been classified into at least five groups (Du et al 2013).…”

Section: Discussionmentioning

confidence: 99%

“…In maize and soybean, MYB-related genes have roles both in development and in stress responses (Du et al 2013). Based on the alignment of the MYB domain, MYB-related proteins have been classified into at least five groups (Du et al 2013). The third helix in the MYB DNA binding domain is important for binding to target cis elements (Du et al 2013).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

A MYB-related transcription factor affects nodule formation in <i>Lotus japonicus</i>

Supriadi

Duangkhet

Thepsukhon

et al. 2016

Plant Biotechnology

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The MYB family is one of the largest groups of transcription factors in plants. Our previous microarray data revealed that a MYB-related gene (Ljmybr) was induced upon nodule formation in Lotus japonicus. As shown using real-time PCR, the expression of the Ljmybr in L. japonicus was up-regulated after M. loti infection. To determine the role of Ljmybr in the nodulation process, we created transgenic hairy roots in L. japonicus and then performed Ljmybr overexpression (MYBOX) or RNAi-mediated suppression (MYBRNAi). The results of these experiments indicated that overexpressing Ljmybr accelerated L. japonicus nodulation and increased acetylene reduction activity (ARA) in the nodules. Suppressing Ljmybr (MYBRNAi) delayed nodulation and decreased ARA compared to control suppression (GUSRNAi). Seven days post infection, the expression levels of Nin, Enod40-1 and Enod40-2 were higher in MYBOX-treated nodules and lower in MYBRNAi-treated nodules. We propose that the Ljmybr transcription factor plays a role in regulating nitrogen fixation in L. japonicus.

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Genome-Wide Identification and Evolutionary and Expression Analyses of MYB-Related Genes in Land Plants

Cited by 126 publications

References 43 publications

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

A MYB-related transcription factor affects nodule formation in <i>Lotus japonicus</i>

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