With no lysine kinases: the key regulatory networks and phytohormone cross talk in plant growth, development and stress response

OsWNK9 regulates cadmium concentration in brown rice by restraining cadmium transport from straw to brown rice

Selecting and breeding rice cultivars that enable strong cadmium (Cd) accumulation in rice straw but low accumulation in brown rice is a promising way to achieve Cd phytoremediation as well as to ensure the food safety of rice. Herein, we isolated a gene OsWNK9 from the quantitative trait locus associated with reducing Cd translocation from rice straw to brown rice and decreasing the Cd concentration in brown rice (BRCdC). Continuous strong expression of OsWNK9 was observed in nodes and internode and was induced after Cd supply. OsWNK9 was localized in the rice cell nucleus and participated in the regulation of Cd transport in yeast. Two independent oswnk9 rice mutants were generated via CRISPR/Cas9 gene-editing and showed significantly higher BRCdC than that of the wild type (WT). The BRCdC of knockout oswnk9 mutants was 0.227 mg kg-1and 0.238 mg kg-1, increased by 14 % and 19 % compared with that of the WT due to the lower Cd allocation in the basal stem, internode, and node III, which was unrelated to Cd uptake. Interestingly, OsWNK9 could promote iron (Fe) accumulation in rice under Cd-contaminated conditions, suggesting that OsWNK9 is an ideal gene for Cd phytoremediation and Fe biofortification in rice to support safe food production.

WNK1 Interaction with KEAP1 Promotes NRF2 Stabilization to Enhance the Oxidative Stress Response in Hepatocellular Carcinoma

Cellular oxidative stress plays a key role in the development and progression of hepatocellular carcinoma (HCC). A better understanding of the processes that regulate reactive oxygen species (ROS) homeostasis could uncover improved strategies for treating HCC. Herein, we identified protein kinase with-no-lysine kinase 1 (WNK1) as an antioxidative factor and therapeutic target in HCC. In human HCC, WNK1 expression was increased and correlated with poor patient prognosis. WNK1 knockdown significantly inhibited cell proliferation and xenograft tumor growth. Mechanistically, WNK1 competed with nuclear factor erythroid 2-related factor 2 (NRF2) for binding with the partial Kelch domain of Kelch-like ECH-associated protein 1 (KEAP1), reducing NRF2 ubiquitination and promoting NRF2 accumulation and nuclear translocation to increase antioxidant response. WNK1 silencing increased H2O2-induced apoptosis and inhibited cell growth by elevating ROS levels, which could be rescued by treatment with the antioxidant N-acetylcysteine and NRF2 activator tert-butylhydroquinone. Liver-specific WNK1 knockout mouse models of HCC substantiated that WNK1 promoted HCC development by regulating ROS levels. WNK463, an inhibitor of the WNK kinase family, suppressed HCC progression and altered the redox status. These findings suggest that WNK1 plays a critical role in HCC development and progression and that the WNK1-oxidative stress axis may be a promising therapeutic target for HCC. Significance: Inhibiting WNK1 induces NRF2 degradation and reduces the oxidative stress response to suppress hepatocellular carcinoma growth, indicating that targeting the WNK1-KEAP1-NRF2 axis is a potential strategy to treat liver cancer.

Genome-Wide Identification and Expression Pattern Analysis of the WNK Gene Family in Apple under Abiotic Stress and Colletotrichum siamense Infection

With-no-lysine kinase (WNK) is a unique serine/threonine kinase family member. WNK differs from other protein kinases by not having a standard lysine in subdomain II of the universally preserved kinase catalytic region. Conversely, the amino acid lysine located in subdomain I plays a crucial role in its phosphorylation. The WNK family has been reported to regulate Arabidopsis flowering, circadian rhythm, and abiotic stress. Eighteen members of the WNK gene family were discovered in apples in this research, and they were primarily grouped into five categories on the phylogenetic tree. Conserved domains and motifs also confirmed their identity as members of the WNK family. Promoter cis-acting element analysis indicated their potential role in responses to both abiotic stress and phytohormones. Furthermore, qRT-PCR analysis showed that the expression of MdWNK family genes was stimulated to different extents by Colletotrichum siamense, NaCl, mannitol, ABA, JA, and SA, with Colletotrichum siamense being the most prominent stimulant. MdWNK family genes were expressed across all apple tissues, with young fruits showing the greatest expression and roots showing the least expression. The research offered detailed insights into the MdWNK gene family, serving as a crucial basis for investigating the biological roles of MdWNK genes.

The TSC22D, WNK, and NRBP gene families exhibit functional buffering and evolved with Metazoa for cell volume regulation

The ability to sense and respond to osmotic fluctuations is critical for the maintenance of cellular integrity. We used gene co-essentiality analysis to identify an unappreciated relationship between TSC22D2, WNK1, and NRBP1 in regulating cell volume homeostasis. All of these genes have paralogs and are functionally buffered for osmo-sensing and cell volume control. Within seconds of hyperosmotic stress, TSC22D, WNK, and NRBP family members physically associate into biomolecular condensates, a process that is dependent on intrinsically disordered regions (IDRs). A close examination of these protein families across metazoans revealed that TSC22D genes evolved alongside a domain in NRBPs that specifically binds to TSC22D proteins, which we have termed NbrT (NRBP binding region with TSC22D), and this co-evolution is accompanied by rapid IDR length expansion in WNK-family kinases. Our study reveals that TSC22D, WNK, and NRBP genes evolved in metazoans to co-regulate rapid cell volume changes in response to osmolarity.

Drought and recovery in barley: key gene networks and retrotransposon response

Introduction

During drought, plants close their stomata at a critical soil water content (SWC), together with making diverse physiological, developmental, and biochemical responses.

Methods

Using precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673, and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought and during recovery, also examining retrotransposon BARE1expression. Transcriptional data were subjected to network analysis.

Results

The varieties differed by their critical SWC (ϴ_crit), Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether, 117 networked genes involved in ubiquitin-mediated autophagy were downregulated.

Discussion

The differential response to SWC suggests adaptation to distinct rainfall patterns. We identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated.

Cloning, homology modelling and expression analysis of Oryza sativa WNK gene family

With No Lysine kinases (WNKs) represents a gene family that encodes Ser/Thr kinases, with anomalous disposition of catalytic lysine residue in subdomain I. In plants, WNKs had been linked to circadian rhythm, photoperiodic response and abiotic stress tolerance with mechanism yet undeciphered. In the present study, full-length CDS sequences of rice WNKs (OsWNK1 to 8) were cloned from indica cultivar IR64. A total of six highly conserved kinase subdomains were identified. Comparative analysis of protein sequences from six different species of rice showed varying magnitudes of substitution (76.2 %), deletion (15.4 %), and addition (8.4 %) events. ConSurf analysis coupled with CASTp results identified functional residues that were clustered together in modelled 3-D structures. Among post-translational modifications (PTMs) studied, 87.7 % of phosphorylation sites were predicted. Mined protein-protein interactions (PPIs) depicted OsWNKs to interact notably with other OsWNK members and with key proteins like PRR95 involved in photoperiodic response and protein phosphatase like PP2C involved in ABA signalling. Gene duplication analysis revealed two paralogous duplicated gene pairs: WNK6-WNK9 and WNK7-WNK8. Oryza sativa showed maximum syntenic relationship with Sorghum bicolor among the compared species. OsWNKs showed differential transcript expression profiles on treatment with plant growth regulators indicating its versatile role in plant growth and development.

Dynamic Responses of Antioxidant and Glyoxalase Systems to Seed Aging Based on Full-Length Transcriptome in Oat (Avena sativa L.)

Seed aging is a major challenge for food security, agronomic production, and germplasm conservation, and reactive oxygen species (ROS) and methylglyoxal (MG) are highly involved in the aging process. However, the regulatory mechanisms controlling the abundance of ROS and MG are not well characterized. To characterize dynamic response of antioxidant and glyoxalase systems during seed aging, oat (Avena sativa L.) aged seeds with a range of germination percentages were used to explore physiological parameters, biochemical parameters and relevant gene expression. A reference transcriptome based on PacBio sequencing generated 67,184 non-redundant full-length transcripts, with 59,050 annotated. Subsequently, eleven seed samples were used to investigate the dynamic response of respiration, ROS and MG accumulation, antioxidant enzymes and glyoxalase activity, and associated genes expression. The 48 indicators with high correlation coefficients were divided into six major response patterns, and were used for placing eleven seed samples into four groups, i.e., non-aged (Group N), higher vigor (Group H), medium vigor (Group M), and lower vigor (Group L). Finally, we proposed a putative model for aging response and self-detoxification mechanisms based on the four groups representing different aging levels. In addition, the outcomes of the study suggested the dysfunction of antioxidant and glyoxalase system, and the accumulation of ROS and MG definitely contribute to oat seed aging.

Abscisic Acid: Role in Fruit Development and Ripening

Abscisic acid (ABA) is a plant growth regulator known for its functions, especially in seed maturation, seed dormancy, adaptive responses to biotic and abiotic stresses, and leaf and bud abscission. ABA activity is governed by multiple regulatory pathways that control ABA biosynthesis, signal transduction, and transport. The transport of the ABA signaling molecule occurs from the shoot (site of synthesis) to the fruit (site of action), where ABA receptors decode information as fruit maturation begins and is significantly promoted. The maximum amount of ABA is exported by the phloem from developing fruits during seed formation and initiation of fruit expansion. In the later stages of fruit ripening, ABA export from the phloem decreases significantly, leading to an accumulation of ABA in ripening fruit. Fruit growth, ripening, and senescence are under the control of ABA, and the mechanisms governing these processes are still unfolding. During the fruit ripening phase, interactions between ABA and ethylene are found in both climacteric and non-climacteric fruits. It is clear that ABA regulates ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism controlling the interaction between ABA and ethylene has not yet been discovered. The effects of ABA and ethylene on fruit ripening are synergistic, and the interaction of ABA with other plant hormones is an essential determinant of fruit growth and ripening. Reaction and biosynthetic mechanisms, signal transduction, and recognition of ABA receptors in fruits need to be elucidated by a more thorough study to understand the role of ABA in fruit ripening. Genetic modifications of ABA signaling can be used in commercial applications to increase fruit yield and quality. This review discusses the mechanism of ABA biosynthesis, its translocation, and signaling pathways, as well as the recent findings on ABA function in fruit development and ripening.

Comparative Transcriptomic Analysis of Root Cadmium Responses in Two Chinese Rice Cultivars Yuzhenxiang and Xiangwanxian 12

Cadmium (Cd) pollution in paddy soil is an increasingly serious issue in rice production. It has been reported that there is a higher or lower grain Cd accumulation in the rice cultivars Yuzhenxiang (YZX) or Xiangwanxian 12 (XWX), respectively. To better manage the Cd pollution problem, the genes that might play vital roles in governing the difference in root Cd responses between these two rice cultivars were examined. In this study, the results of RNA sequencing (RNA-seq) showed that there were 341 and 161 differentially expressed genes in the roots of YZX and XWX after Cd exposure, respectively. Among these genes, 7 genes, such as Os06g0196300 (OsJ_019618), Os07g0570700 (OsJ_24808), ADI1, GDCSH, HSFB2C, PEX11-4, and CLPB1, possessed higher degree nodes with each other, through interaction analysis by the STRING (search tool for the retrieval of interacting genes/proteins) software, suggesting that they might play vital roles in Cd response. Based on GO enrichment analysis, 41 differently expressed genes after Cd treatment in YZX or XWX were identified to be related to Cd response. Through comparative transcriptomic analysis, 257 genes might be associated with the root Cd response difference between YZX and XWX. Furthermore, we supposed that ADI1, CFBP1, PEX11-4, OsJ_019618, OsJ_24808, GDCSH, CLPB1, LAC6, and WNK3 might be implicated in Cd response based on the combined analysis of RT-qPCR, interaction, and GO annotation analysis. In conclusion, the numerous genes that might be related to Cd stress response and root Cd response difference between YZX and XWX at the booting stage may be of benefit for the development of rice varieties with low Cd consumption.