WHIRLY1 functions in the nucleus to regulate barley leaf development and associated metabolite profiles

Karpińska, Barbara; Razak, Nurhayati; James, E. K.; Morris, Jenny; Verrall, Susan; Hedley, Pete E.; Hancock, Robert D.; Foyer, Christine H.

doi:10.1042/bcj20210810

Cited by 5 publications

(4 citation statements)

References 92 publications

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“…Here, we calculated the homologous gene pairs present in the BBX genes of the three Medicago plants separately, and 106 pairs of collinear genes were calculated in MsBBXs , with five pairs of collinear genes in each of the other two plants ( Table S2 ). By calculating the Ka/Ks ratio, it was found that only two gene pairs ( MsBBX31 and MsBBX38 , and MsBBX39 and MsBBX52 ) had Ka/Ks > 1, and the rest of the gene pairs had Ka/Ks values less than 1, suggesting that these BBX genes underwent purifying selection and that the proteins were relatively conserved [ 45 , 46 ]. Furthermore, M. truncatula diverged from M. sativa spp.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of BBX Gene Family in Three Medicago Species Provides Insights into Expression Patterns under Hormonal and Salt Stresses

Wang,

Meng,

et al. 2024

IJMS

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BBX protein is a class of zinc finger transcription factors that have B-box domains at the N-terminus, and some of these proteins contain a CCT domain at the C-terminus. It plays an important role in plant growth, development, and metabolism. However, the expression pattern of BBX genes in alfalfa under hormonal and salt stresses is still unclear. In this study, we identified a total of 125 BBX gene family members by the available Medicago reference genome in diploid alfalfa (Medicago sativa spp. Caerulea), a model plant (M. truncatula), and tetraploid alfalfa (M. sativa), and divided these members into five subfamilies. We found that the conserved motifs of BBXs of the same subfamily reveal similarities. We analyzed the collinearity relationship and duplication mode of these BBX genes and found that the expression pattern of BBX genes is specific in different tissues. Analysis of the available transcriptome data suggests that some members of the BBX gene family are involved in multiple abiotic stress responses, and the highly expressed genes are often clustered together. Furthermore, we identified different expression patterns of some BBX genes under salt, ethylene, salt and ethylene, salicylic acid, and salt and salicylic acid treatments, verified by qRT-PCR, and analyzed the subcellular localization of MsBBX2, MsBBX17, and MsBBX32 using transient expression in tobacco. The results showed that BBX genes were localized in the nucleus. This study systematically analyzed the BBX gene family in Medicago plants, which provides a basis for the study of BBX gene family tolerance to abiotic stresses.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of BBX Gene Family in Three Medicago Species Provides Insights into Expression Patterns under Hormonal and Salt Stresses

Wang,

Meng,

et al. 2024

IJMS

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“…It is well known that maintaining the stable expression of genetic information DNA plays a crucial role in plant growth and development. WHY proteins are special proteins that can be located in both the nucleus and plastid 69 . WHY proteins are important in both the nucleus and plastid.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of Whirly (WHY) gene family in Medicago sativa L.

Ruan

Wang

et al. 2022

Sci Rep

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The WHY family is a group of plant-specific transcription factors, that can bind to single-stranded DNA molecules and play a variety of functions in plant nuclei and organelles, participating in the regulation of plant leaf senescence. It has been identified and analyzed in many species, however, the systematic identification and analysis of the WHY genes family have not yet been reported in alfalfa (Medicago sativa L.). Therefore, to explore the function of alfalfa the WHY genes, and 10 MsWHY genes were identified and further characterized their evolutionary relationship and expression patterns by analyzing the recently published genome of alfalfa. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the WHY gene family in alfalfa using bioinformatics methods. The results showed that 10 MsWHY genes were distributed on 10 chromosomes, and collinearity analysis showed that many MsWHYs might be derived from segmental duplications, and these genes are under purifying selection. Based on phylogenetic analyses, the WHY gene family of alfalfa can be divided into four subfamilies: I-IV subfamily, and approximately all the WHY genes within the same subfamily share similar gene structures. The 10 MsWHY gene family members contained 10 motifs, of which motif 2 and motif 4 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of the MsWHY genes. Real-time quantitative PCR demonstrated that MsWHYs gene expression is induced by drought, salt, and methyl jasmonate. The present study serves as a basic foundation for future functional studies on the alfalfa WHY family.

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“…This function is inherent to the role of WHY proteins in DNA repair mechanisms, as illustrated in Figure 4 . In the leaves of monocotyledonous species such as barley, which show a developmental gradient from base to tip, WHY1 is highly expressed in the meristematic region at the leaf base, with much lower expression levels found in the middle of the leaf or tip regions (Karpinska et al, 2022 ). The WHY1 protein is localized in the nuclei (60%) and proplastids (40%) of the cells at the base al the leaf (Karpinska et al, 2022 ).…”

Section: Why Protein Functions In Plastid Genome Repair Mechanismsmentioning

confidence: 99%

“…In the leaves of monocotyledonous species such as barley, which show a developmental gradient from base to tip, WHY1 is highly expressed in the meristematic region at the leaf base, with much lower expression levels found in the middle of the leaf or tip regions (Karpinska et al, 2022 ). The WHY1 protein is localized in the nuclei (60%) and proplastids (40%) of the cells at the base al the leaf (Karpinska et al, 2022 ). This finding suggests that WHY1 plays an important function in genome stability during DNA replication in the proliferating cells in meristems as well as in vegetative cells.…”

Section: Why Protein Functions In Plastid Genome Repair Mechanismsmentioning

confidence: 99%

WHIRLY protein functions in plants

Taylor

West

Foyer

2022

Food and Energy Security

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Environmental stresses pose a significant threat to food security. Understanding the function of proteins that regulate plant responses to biotic and abiotic stresses is therefore pivotal in developing strategies for crop improvement. The WHIRLY (WHY) family of DNA‐binding proteins are important in this regard because they fulfil a portfolio of important functions in organelles and nuclei. The WHY1 and WHY2 proteins function as transcription factors in the nucleus regulating phytohormone synthesis and associated growth and stress responses, as well as fulfilling crucial roles in DNA and RNA metabolism in plastids and mitochondria. WHY1, WHY2 (and WHY3 proteins in Arabidopsis) maintain organelle genome stability and serve as auxiliary factors for homologous recombination and double‐strand break repair. Our understanding of WHY protein functions has greatly increased in recent years, as has our knowledge of the flexibility of their localization and overlap of functions but there is no review of the topic in the literature. Our aim in this review was therefore to provide a comprehensive overview of the topic, discussing WHY protein functions in nuclei and organelles and highlighting roles in plant development and stress responses. In particular, we consider areas of uncertainty such as the flexible localization of WHY proteins in terms of retrograde signalling connecting mitochondria, plastids, and the nucleus. Moreover, we identify WHY proteins as important targets in plant breeding programmes designed to increase stress tolerance and the sustainability of crop yield in a changing climate.

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WHIRLY1 functions in the nucleus to regulate barley leaf development and associated metabolite profiles

Cited by 5 publications

References 92 publications

Genome-Wide Analysis of BBX Gene Family in Three Medicago Species Provides Insights into Expression Patterns under Hormonal and Salt Stresses

Genome-Wide Analysis of BBX Gene Family in Three Medicago Species Provides Insights into Expression Patterns under Hormonal and Salt Stresses

Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of Whirly (WHY) gene family in Medicago sativa L.

WHIRLY protein functions in plants

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