CIPK9 targets VDAC3 and modulates oxidative stress responses in Arabidopsis

Mitochondrial VOLTAGE-DEPENDENT ANION CHANNEL 3 regulates stomatal closure by abscisic acid signaling

In Arabidopsis (Arabidopsis thaliana), stomatal closure mediated by abscisic acid (ABA) is redundantly controlled by ABA receptor family proteins (PYRABACTIN RESISTANCE 1 [PYR1]/PYR1-LIKE [PYLs]) and subclass III SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASES 2 (SnRK2s). Among these proteins, the roles of PYR1, PYL2, and SnRK2.6 are more dominant. A recent discovery showed that ABA-induced accumulation of reactive oxygen species (ROS) in mitochondria promotes stomatal closure. By analyzing stomatal movements in an array of single and higher order mutants, we revealed that the mitochondrial protein VOLTAGE-DEPENDENT ANION CHANNEL 3 (VDAC3) jointly regulates ABA-mediated stomatal closure with a specialized set of PYLs and SnRK2s by affecting cellular and mitochondrial ROS accumulation. VDAC3 interacted with 9 PYLs and all 3 subclass III SnRK2s. Single mutation in VDAC3, PYLs (except PYR1 and PYL2), or SnRK2.2/2.3 had little effect on ABA-mediated stomatal closure. However, knocking out PYR1, PYL1/2/4/8, or SnRK2.2/2.3 in vdac3 mutants resulted in significantly delayed or attenuated ABA-mediated stomatal closure, despite the presence of other PYLs or SnRK2s conferring redundant functions. We found that cellular and mitochondrial accumulation of ROS induced by ABA was altered in vdac3pyl1 mutants. Moreover, H2O2 treatment restored ABA-induced stomatal closure in mutants with decreased stomatal sensitivity to ABA. Our work reveals that VDAC3 ensures redundant control of ABA-mediated stomatal closure by canonical ABA signaling components.

Voltage-dependent anion channel 3 (VDAC3) mediates P. syringae induced ABA-SA signaling crosstalk in Arabidopsis thaliana

Pathogen severely affects plant mitochondrial processes including respiration, however, the roles and mechanism of mitochondrial protein during the immune response remain largely unexplored. The interplay of plant hormone signaling during defense is an outcome of plant pathogen interaction. We recently discovered that the Arabidopsis calcineurin B-like interacting protein kinase 9 (AtCIPK9) interacts with the voltage-dependent anion channel 3 (AtVDAC3) and inhibits MV-induced oxidative damage. Here we report the characterization of AtVDAC3 in an antagonistic interaction pathway between abscisic acid (ABA) and salicylic acid (SA) signaling in Pseudomonas syringae -Arabidopsis interaction. In this study, we observed that mutants of AtVDAC3 were highly susceptible to Pseudomonas syringae infection as compared to the wild type (WT) Arabidopsis plants. Transcripts of VDAC3 and CIPK9 were inducible upon ABA application. Following pathogen exposure, expression analyses of ABA and SA biosynthesis genes indicated that the function of VDAC3 is required for isochorisimate synthase 1 (ICS1) expression but not for Nine-cis-epoxycaotenoid dioxygenase 3 (NCED3) expression. Despite the fact that vdac3 mutants had increased NCED3 expression in response to pathogen challenge, transcripts of ABA sensitive genes such as AtRD22 and AtRAB18 were downregulated even after exogenous ABA application. VDAC3 is required for ABA responsive genes expression upon exogenous ABA application. We also found that Pseudomonas syringae-induced SA signaling is downregulated in vdac3 mutants since overexpression of VDAC3 resulted in hyperaccumulation of Pathogenesis related gene1 (PR1) transcript. Interestingly, ABA application prior to P. syringae inoculation resulted in the upregulation of ABA responsive genes like Responsive to ABA18 (RAB18) and Responsive to dehydration 22 (RD22). Intriguingly, in the absence of AtVDAC3, Pst challenge can dramatically increase ABA-induced RD22 and RAB18 expression. Altogether our results reveal a novel Pathogen-SA-ABA interaction pathway in plants. Our findings show that ABA plays a significant role in modifying plant-pathogen interactions, owing to cross-talk with the biotic stress signaling pathways of ABA and SA.

Photosynthesis regulation, cell membrane stabilization and methylglyoxal detoxification seems major altered pathways under cold stress as revealed by integrated multi-omics meta-analysis

Climate change has altered cold weather patterns, resulting in irregular cold weather conditions, and changing the global plant distribution pattern affecting plant development processes resulting in severe yield losses. Although molecular mechanisms and interconnections are quite well studied, a cumulative understanding of plant responses to cold stress (CS) is still lacking. Through meta-analysis, integration of data at the multi-omics level and its correlation with known physiological changes to map and understand the global changes in response to CS was made. Meta-analysis was conducted using the metafor R package program based on physiological parameters like relative electrolytic leakage, malondialdehyde, soluble sugar, proline and antioxidant enzymes activity. Proline and soluble sugars showed the highest (> 1.5 mean fold) change over control thus qualifying as global markers for studying CS. Surprisingly most up-regulated (> 15-fold) DEGs corresponded with the dehydrin family and glyoxalase superfamily proteins. Functional annotations of DEGs corresponded with photosynthesis and glycolysis pathway. Proteins responsible for cell signalling and increased soluble sugars were common in all the datasets studied thus correlating with the transcriptome and proteomic data. Proline and soluble sugars were positively regulated in all the metabolomics datasets. This study supported the earlier known players like proline and soluble sugars. Surprisingly, a new player glyoxalase seems to be contributing in CS.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01367-9.

Population Structure, Genetic Diversity and Candidate Genes for the Adaptation to Environmental Stress in Picea koraiensis

Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.

Identification, expression, and association analysis of calcineurin B-like protein–interacting protein kinase genes in peanut

Plants usually respond to the external environment by initiating a series of signal transduction processes mediated by protein kinases, especially calcineurin B-like protein–interacting protein kinases (CIPKs). In this study, 54 CIPKs were identified in the peanut genome, of which 26 were from cultivated species (named AhCIPKs) and 28 from two diploid progenitors (Arachis duranensis—AdCIPKs and Arachis ipaensis—AiCIPKs). Evolution analysis revealed that the 54 CIPKs were composed of two different evolutionary branches. The CIPK members were unevenly distributed at different chromosomes. Synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CIPK. Comparative genomics analysis showed that there was only one common collinear CIPK pairs among peanut, Arabidopsis, rice, grape, and soybean. The prediction results of cis-acting elements showed that AhCIPKs, AdCIPKs, and AiCIPKs contained different proportions of transcription factor binding motifs involved in regulating plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCIPKs had tissue-specific expression patterns. Furthermore, association analysis identified one polymorphic site in AdCIPK12 (AhCIPK11), which was significantly associated with pod length, seed length, hundred seed weight, and shoot root ratio. Our results provide valuable information of CIPKs in peanut and facilitate better understanding of their biological functions.

Nitrate transporter NRT1.1 and anion channel SLAH3 form a functional unit to regulate nitrate-dependent alleviation of ammonium toxicity

Ammonium (NH₄ ⁺ ) and nitrate (NO₃ ^- ) are major inorganic nitrogen (N) sources for plants. When serving as the sole or dominant N supply, NH₄ ⁺ often causes root inhibition and shoot chlorosis in plants, known as ammonium toxicity. NO₃ ^- usually causes no toxicity and can mitigate ammonium toxicity even at low concentrations, referred to as nitrate-dependent alleviation of ammonium toxicity. Our previous studies indicated a NO₃ ^- efflux channel SLAH3 is involved in this process. However, whether additional components contribute to NO₃ ^- -mediated NH₄ ⁺ detoxification is unknown. Previously, mutations in NO₃ ^- transporter NRT1.1 were shown to cause enhanced resistance to high concentrations of NH₄ ⁺ . Whereas, in this study, we found when the high-NH₄ ⁺ medium was supplemented with low concentrations of NO₃ ^- , nrt1.1 mutant plants showed hyper-sensitive phenotype instead. Furthermore, mutation in NRT1.1 caused enhanced medium acidification under high-NH₄ ⁺ /low-NO₃ ^- condition, suggesting NRT1.1 regulates ammonium toxicity by facilitating H⁺ uptake. Moreover, NRT1.1 was shown to interact with SLAH3 to form a transporter-channel complex. Interestingly, SLAH3 appeared to affect NO₃ ^- influx while NRT1.1 influenced NO₃ ^- efflux, suggesting NRT1.1 and SLAH3 regulate each other at protein and/or gene expression levels. Our study thus revealed NRT1.1 and SLAH3 form a functional unit to regulate nitrate-dependent alleviation of ammonium toxicity through regulating NO₃ ^- transport and balancing rhizosphere acidification.