Deciphering evolutionary dynamics of WRKY genes in Arachis species

Chen, Mingwei; Li, Meiran; Zhao, Longgang; Song, Hui

doi:10.1186/s12864-023-09149-z

Cited by 9 publications

(7 citation statements)

References 49 publications

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“…Environmental selection eliminates unfavorable genes in plants and preserves favorable genes, so the analysis of environmental selection can better understand the replacement of gene bases in plants during the process of adapting to environmental changes, and thus understand the stability of plant genes [ 38 , 39 ]. Most genes in plants undergo environmental selection during their evolutionary process.…”

Section: Discussionmentioning

confidence: 99%

Evolution of the WRKY Family in Angiosperms and Functional Diversity under Environmental Stress

Wu,

Yang,

et al. 2024

IJMS

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The transcription factor is an essential factor for regulating the responses of plants to external stimuli. The WRKY protein is a superfamily of plant transcription factors involved in response to various stresses (e.g., cold, heat, salt, drought, ions, pathogens, and insects). During angiosperm evolution, the number and function of WRKY transcription factors constantly change. After suffering from long-term environmental battering, plants of different evolutionary statuses ultimately retained different numbers of WRKY family members. The WRKY family of proteins is generally divided into three large categories of angiosperms, owing to their conserved domain and three-dimensional structures. The WRKY transcription factors mediate plant adaptation to various environments via participating in various biological pathways, such as ROS (reactive oxygen species) and hormone signaling pathways, further regulating plant enzyme systems, stomatal closure, and leaf shrinkage physiological responses. This article analyzed the evolution of the WRKY family in angiosperms and its functions in responding to various external environments, especially the function and evolution in Magnoliaceae plants. It helps to gain a deeper understanding of the evolution and functional diversity of the WRKY family and provides theoretical and experimental references for studying the molecular mechanisms of environmental stress.

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Section: Discussionmentioning

confidence: 99%

Evolution of the WRKY Family in Angiosperms and Functional Diversity under Environmental Stress

Wu,

Yang,

et al. 2024

IJMS

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“…WRKY TFs have been identified in various Arachis species [ 5 , 21 ]. A. duranensis , A. ipaensis , A. monticola , and A. hypogaea cv.…”

Section: Methodsmentioning

confidence: 99%

“…A. duranensis , A. ipaensis , A. monticola , and A. hypogaea cv. Tifrunner have 16 WRKY TFs, which are AtWRKY12 and AtWRKY75 homologs and are involved in regulating flowering time [ 5 , 21 , 22 ]. The 16 WRKY TFs in the four Arachis species were retrieved from PeanutBase database based on previous studies [ 5 , 21 , 22 ].…”

Section: Methodsmentioning

confidence: 99%

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WRKY transcription factors modulate flowering time in four Arachis species: a bioinformatics analysis

Fang,

Liu,

et al. 2024

BMC Plant Biol

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Background WRKY proteins are important transcription factors (TFs) in plants, involved in growth and development and responses to environmental changes. Although WRKY TFs have been studied at the genome level in Arachis genus, including oil crop and turfgrass, their regulatory networks in controlling flowering time remain unclear. The aim of this study was to predict the molecular mechanisms of WRKY TFs regulation flowering time in Arachis genus at the genome level using bioinformatics approaches. Results The flowering-time genes of Arachis genus were retrieved from the flowering-time gene database. The regulatory networks between WRKY TFs and downstream genes in Arachis genus were predicted using bioinformatics tools. The results showed that WRKY TFs were involved in aging, autonomous, circadian clock, hormone, photoperiod, sugar, temperature, and vernalization pathways to modulate flowering time in Arachis duranensis, Arachis ipaensis, Arachis monticola, and Arachis hypogaea cv. Tifrunner. The WRKY TF binding sites in homologous flowering-time genes exhibited asymmetric evolutionary pattern, indicating that the WRKY TFs interact with other transcription factors to modulate flowering time in the four Arachis species. Protein interaction network analysis showed that WRKY TFs interacted with FRUITFULL and APETALA2 to modulate flowering time in the four Arachis species. WRKY TFs implicated in regulating flowering time had low expression levels, whereas their interaction proteins had varying expression patterns in 22 tissues of A. hypogaea cv. Tifrunner. These results indicate that WRKY TFs exhibit antagonistic or synergistic interactions with the associated proteins. Conclusions This study reveals complex regulatory networks through which WRKY TFs modulate flowering time in the four Arachis species using bioinformatics approaches.

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“…and HLA-HD v1.3 for MHC-II (HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1 and HLA-DRB1), following previously published recommendations 21 . Both tools were ran using default parameters.…”

Section: Mhc Genotypingmentioning

confidence: 99%

MHC class I and class II genotypes are independent predictors of anti-PD1 immunotherapy response in melanoma

Eynden,

Claeys

2023

Preprint

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Immune checkpoint blockade is a highly successful anti-cancer immunotherapy. Both CTLA4 and PD1 checkpoint blockers are clinically available for melanoma treatment, with anti-PD1 therapy reaching response rates of 35-40%. These responses, which are mediated via neoantigen presentation by the polymorphic MHC complex, are hard to predict and the tumor mutation burden is currently the best available biomarker. Here we demonstrate that the germline MHC class I (MHC-I) and class II (MHC-II) genotypes are TMB-independent predictors of anti-PD1 immunotherapy responses in melanoma. Opposite responses were found for both classes, with strong MHC-I and MHC-II binding genotypes predicting good and bad responses, respectively. Interestingly, MHC-II binding genotypes were mainly associated with treatment response failure in a subgroup of anti-CTLA4 pretreated patients. As MHC genotyping does not require tumor material and/or advanced sequencing, it has clinical potential as a non-invasive and tumor-independent biomarker to guide anti-cancer immunotherapy in melanoma.

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Deciphering evolutionary dynamics of WRKY genes in Arachis species

Cited by 9 publications

References 49 publications

Evolution of the WRKY Family in Angiosperms and Functional Diversity under Environmental Stress

Evolution of the WRKY Family in Angiosperms and Functional Diversity under Environmental Stress

WRKY transcription factors modulate flowering time in four Arachis species: a bioinformatics analysis

MHC class I and class II genotypes are independent predictors of anti-PD1 immunotherapy response in melanoma

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