Rice and Arabidopsis homologs of yeast CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 commonly interact with Polycomb complexes but exert divergent regulatory functions

Zhang, Pingxian; Zhu, Chunmei; Geng, Yuke; Wang, Yifan; Yang, Ying; Liu, Qing; Guo, Weijun; Chachar, Sadaruddin; Riaz, Adeel; Yan, Shuangyong; Yang, Liwen; Yi, Keke; Wu, Changyin; Gu, Xiaofeng

doi:10.1093/plcell/koab047

Cited by 16 publications

(13 citation statements)

References 41 publications

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“…One of the KOs is the CTF4 (chromosome transmission fidelity protein). DRW1 is the ortholog of CTF4 in rice and sustains normal cell cycle progression (Zhang et al 2021). The enrichment of this KO could be attributed to the well-developed aerenchyma in the submersed and marine life-forms.…”

Section: Kegg Orthology (Ko) Terms Related To Aquatic Environment Adaptationsmentioning

confidence: 99%

Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments

Chen

Morales‐Briones²,

Moody³

et al. 2021

Preprint

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Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times beyond. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by including 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptation, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as ((Tofieldiaceae, Araceae), core Alismatids). There is phylogenetic conflict among the backbone of the three main clades that could be due to incomplete lineage sorting and introgression. We identified 18 putative WGD events. One of them had occurred at the most recent common ancestor of core Alismatids, and four occurred at seagrass lineages. Other events are distributed in terrestrial, emergent, and submersed life-forms and seagrasses across Alismatales. We also found that lineage and life-form were each important for different evolutionary patterns for the genes related to freshwater/marine adaptation. For example, some light or ethylene-related genes were lost in the seagrass Zosteraceae, but present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments, phylogeny, and whole-genome duplication of Alismatales.

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Section: Kegg Orthology (Ko) Terms Related To Aquatic Environment Adaptationsmentioning

confidence: 99%

Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments

Chen

Morales‐Briones²,

Moody³

et al. 2021

Preprint

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“…The synthetic PRMT antibody was performed as described previously (Geng et al 2020 ; Zhang et al 2021 ). Briefly, a 15-amino acid fragment of PRMT6 (residues 105–119; TYREAIMQHQSLIEG) was synthesized by the solid-phase peptide synthesis (SPPS) method and confirmed by mass spectrometry (MS) and high-performance liquid chromatography (HPLC).…”

Section: Methodsmentioning

confidence: 99%

“…Histone protein extraction and western analysis were performed as described previously (Zhang et al 2021 ). Briefly, total histones were extracted from 10-day-old seedlings grown in LD conditions, separated on an SDS-PAGE gel, and subsequently transferred to a 0.2-μm nitrocellulose membrane (Bio-Rad).…”

Section: Methodsmentioning

confidence: 99%

PRMT6 physically associates with nuclear factor Y to regulate photoperiodic flowering in Arabidopsis

Zhang

Wang

et al. 2021

aBIOTECH

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The timing of floral transition is critical for reproductive success in flowering plants. In long-day (LD) plant Arabidopsis, the floral regulator gene FLOWERING LOCUS T (FT) is a major component of the mobile florigen. FT expression is rhythmically activated by CONSTANS (CO), and specifically accumulated at dusk of LDs. However, the underlying mechanism of adequate regulation of FT transcription in response to day-length cues to warrant flowering time still remains to be investigated. Here, we identify a homolog of human protein arginine methyltransferases 6 (HsPRMT6) in Arabidopsis, and confirm AtPRMT6 physically interacts with three positive regulators of flowering Nuclear Factors YC3 (NF-YC3), NF-YC9, and NF-YB3. Further investigations find that AtPRMT6 and its encoding protein accumulate at dusk of LDs. PRMT6-mediated H3R2me2a modification enhances the promotion of NF-YCs on FT transcription in response to inductive LD signals. Moreover, AtPRMT6 and its homologues proteins AtPRMT4a and AtPRMT4b coordinately inhibit the expression of FLOWERING LOCUS C, a suppressor of FT. Taken together, our study reveals the role of arginine methylation in photoperiodic pathway and how the PRMT6-mediating H3R2me2a system interacts with NF-CO module to dynamically control FT expression and facilitate flowering time.

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“…Taken together, these results imply that HMGB1 mediates gene expression by affecting chromatin accessibility. Notably, among the 133 genes, OsAIP1, OsIRO2, DRW1, and OsSTN8 have been reported to regulate plant growth and yield (Ogo et al, 2011;Nath et al, 2013;Shi et al, 2013;P. Zhang et al, 2021).…”

Section: Oshmgb1 Affects Chromatin Accessibilitymentioning

confidence: 99%

Rice chromatin protein OsHMGB1 is involved in phosphate homeostasis and plant growth by affecting chromatin accessibility

et al. 2023

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Summary Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we investigated the biological function and mode of action of the high‐mobility‐group box 1 protein OsHMGB1 in rice (Oryza sativa), using molecular and genetic approaches. We determined that OsHMGB1 expression is induced by Pi starvation and encodes a nucleus‐localized protein. Phenotypic analysis of Oshmgb1 mutant and OsHMGB1 overexpression transgenic plants showed that OsHMGB1 positively regulates Pi homeostasis and plant growth. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing indicated that OsHMGB1 regulates the expression of a series of phosphate starvation–responsive (PSR) genes by binding to their promoters. Furthermore, an assay for transposase‐accessible chromatin followed by sequencing revealed that OsHMGB1 is involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome‐wide chromatin accessibility and gene expression levels. Our results demonstrate that OsHMGB1 is a transcriptional facilitator that regulates the expression of a set of PSR genes to maintain Pi homeostasis in rice by increasing the chromatin accessibility, revealing a key epigenetic mechanism that fine‐tune plant acclimation responses to Pi‐limited environments.

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Rice and Arabidopsis homologs of yeast CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 commonly interact with Polycomb complexes but exert divergent regulatory functions

Cited by 16 publications

References 41 publications

Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments

Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments

PRMT6 physically associates with nuclear factor Y to regulate photoperiodic flowering in Arabidopsis

Rice chromatin protein OsHMGB1 is involved in phosphate homeostasis and plant growth by affecting chromatin accessibility

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