Control of rice ratooning ability by a nucleoredoxin that inhibits histidine kinase dimerization to attenuate cytokinin signaling in axillary buds

Two rice cultivars recruit different rhizospheric bacteria to promote aboveground regrowth after mechanical defoliation

Plants have evolved the ability to regrow after mechanical defoliation and environmental stresses. However, it is unclear whether and how defoliated plants exploit beneficial microbiota from the soil to promote aboveground regrowth. Here, we compared the defoliation-triggered changes in the root exudation and bacterial microbiome of two rice cultivars (Oryza sativa L ssp.), indica/xian cultivar Minghui63 and japonica/geng cultivar Nipponbare. The results show that reciprocal growth promotion existed between defoliated Minghui63 seedlings and soil bacteria. After the leaves were removed, the Minghui63 seedlings displayed approximately 1.5- and 2.1-fold higher root exudation and leaf regrowth rates, respectively, than did the Nipponbare seedlings. In field trials, Minghui63 and Nipponbare enriched taxonomically and functionally distinct bacteria in the rhizosphere and root. In particular, Minghui63 rhizosphere and root communities depleted bacteria whose functions are related to xenobiotics biodegradation and metabolism. The microbiome data implied that the bacterial family Rhodocyclaceae was specifically enriched during the regrowth of defoliated Minghui63 rice. We further isolated a Rhodocyclaceae strain, Uliginosibacterium gangwonense MDD1, from rice root. Compared with germ-free conditions, MDD1 inoculation promoted the aboveground regrowth of defoliated Minghui63 by 61% but had a weaker effect on Nipponbare plants, suggesting cultivar-specific associations between regrowth-promoting bacteria and rice. This study provides novel insight into microbiota‒root‒shoot communication, which is implicated in the belowground microbiome and aboveground regrowth in defoliated rice. These data will be helpful for microbiome engineering to increase rice resilience to defoliation and environmental stresses.IMPORTANCEAs sessile organisms, plants face a multitude of abiotic and biotic stresses which often result in defoliation. To survive, plants have evolved the ability to regrow leaves after stresses and wounding. Previous studies revealed that the rhizosphere microbiome affected plant growth and stress resilience; however, how belowground microbiota modulates the aboveground shoot regrowth is unclear. To address this question, we used rice, an important crop worldwide, to analyze the role of rhizosphere microbiota in leaf regrowth after defoliation. Our data indicate mutual growth promotion between defoliated rice and rhizosphere bacteria and such beneficial effect is cultivar specific. The microbiome analysis also led us to find a Uliginosibacterium gangwonense strain that promoted rice cv. MH63 leaf regrowth. Our findings therefore present a novel insight into plant-microbiome function and provide beneficial strains that potentially enhance rice stress resilience.

EnvZ/OmpR Controls Protein Expression and Modifications in Cronobacter sakazakii for Virulence and Environmental Resilience

Cronobacter sakazakii is a notorious foodborne opportunistic pathogen, particularly affecting vulnerable populations such as premature infants, and poses significant public health challenges. This study aimed to elucidate the role of the envZ/ompR genes in environmental tolerance, pathogenicity, and protein regulation of C. sakazakii. An envZ/ompR knockout mutant was constructed and assessed for its impact on bacterial growth, virulence, environmental tolerance, and protein regulation. Results demonstrate that deletion of envZ/ompR genes leads to reduced growth rate and attenuated virulence in animal models. Additionally, the knockout strain exhibited compromised environmental tolerance, particularly in desiccation and oxidative stress conditions, along with impaired adhesion and invasion abilities in epithelial cells. Proteomic analysis revealed significant alterations in protein expression and phosphorylation patterns, highlighting potential compensatory mechanisms triggered by gene deletion. Furthermore, investigation into protein deamidation and glucose metabolism uncovered a link between envZ/ompR deletion and energy metabolism dysregulation. Interestingly, the downregulation of MalK and GrxC proteins was identified as contributing factors to altered desiccation tolerance and disrupted redox homeostasis, respectively, providing mechanistic insights into the phenotypic changes observed. Overall, this study enhances understanding of the multifaceted roles of envZ/ompR in C. sakazakii physiology and pathogenesis, shedding light on potential targets for therapeutic intervention and food safety strategies.

Proteomic and Phosphoproteomic Analyses during Plant Regeneration Initiation in Cotton (Gossypium hirsutum L.)

Somatic embryogenesis (SE) is a biotechnological tool used to generate new individuals and is the preferred method for rapid plant regeneration. However, the molecular basis underlying somatic cell regeneration through SE is not yet fully understood, particularly regarding interactions between the proteome and post-translational modifications. Here, we performed association analysis of high-throughput proteomics and phosphoproteomics in three representative samples (non-embryogenic calli, NEC; primary embryogenic calli, PEC; globular embryos, GE) during the initiation of plant regeneration in cotton, a pioneer crop for genetic biotechnology applications. Our results showed that protein accumulation is positively regulated by phosphorylation during SE, as revealed by correlation analyses. Of the 1418 proteins that were differentially accumulated in the proteome and the 1106 phosphoproteins that were differentially regulated in the phosphoproteome, 115 proteins with 229 phosphorylation sites overlapped (co-differential). Furthermore, seven dynamic trajectory patterns of differentially accumulated proteins (DAPs) and the correlated differentially regulated phosphoproteins (DRPPs) pairs with enrichment features were observed. During the initiation of plant regeneration, functional enrichment analysis revealed that the overlapping proteins (DAPs-DRPPs) were considerably enriched in cellular nitrogen metabolism, spliceosome formation, and reproductive structure development. Moreover, 198 DRPPs (387 phosphorylation sites) were specifically regulated at the phosphorylation level and showed four patterns of stage-enriched phosphorylation susceptibility. Furthermore, enrichment annotation analysis revealed that these phosphoproteins were significantly enriched in endosomal transport and nucleus organization processes. During embryogenic differentiation, we identified five DAPs-DRPPs with significantly enriched characteristic patterns. These proteins may play essential roles in transcriptional regulation and signaling events that initiate plant regeneration through protein accumulation and/or phosphorylation modification. This study enriched the understanding of key proteins and their correlated phosphorylation patterns during plant regeneration, and also provided a reference for improving plant regeneration efficiency.

Organelle Ca2+/CAM1-SELTP confers somatic cell embryogenic competence acquisition and transformation in plant regeneration

Somatic cell totipotency in plant regeneration represents the forefront of the compelling scientific puzzles and one of the most challenging problems in biology. How somatic embryogenic competence is achieved in regeneration remains elusive. Here, we discover uncharacterized organelle-based embryogenic differentiation processes of intracellular acquisition and intercellular transformation, and demonstrate the underlying regulatory system of somatic embryogenesis-associated lipid transfer protein (SELTP) and its interactor calmodulin1 (CAM1) in cotton as the pioneer crop for biotechnology application. The synergistic CAM1 and SELTP exhibit consistent dynamical amyloplast-plasmodesmata (PD) localization patterns but show opposite functional effects. CAM1 inhibits the effect of SELTP to regulate embryogenic differentiation for plant regeneration. It is noteworthy that callus grafting assay reflects intercellular trafficking of CAM1 through PD for embryogenic transformation. This work originally provides insight into the mechanisms responsible for embryogenic competence acquisition and transformation mediated by the Ca2+/CAM1-SELTP regulatory pathway, suggesting a principle for plant regeneration and cell/genetic engineering.

Comparative Transcriptome Analysis Reveals Inhibitory Roles of Strigolactone in Axillary Bud Outgrowth in Ratoon Rice

Axillary bud outgrowth, a key factor in ratoon rice yield formation, is regulated by several phytohormone signals. The regulatory mechanism of key genes underlying ratoon buds in response to phytohormones in ratoon rice has been less reported. In this study, GR24 (a strigolactone analogue) was used to analyze the ratooning characteristics in rice cultivar Huanghuazhan (HHZ). Results show that the elongation of the axillary buds in the first seasonal rice was significantly inhibited and the ratoon rate was reduced at most by up to 40% with GR24 treatment. Compared with the control, a significant reduction in the content of auxin and cytokinin in the second bud from the upper spike could be detected after GR24 treatment, especially 3 days after treatment. Transcriptome analysis suggested that there were at least 742 and 2877 differentially expressed genes (DEGs) within 6 h of GR24 treatment and 12 h of GR24 treatment, respectively. Further bioinformatics analysis revealed that GR24 treatment had a significant effect on the homeostasis and signal transduction of cytokinin and auxin. It is noteworthy that the gene expression levels of OsCKX1, OsCKX2, OsGH3.6, and OsGH3.8, which are involved in cytokinin or auxin metabolism, were enhanced by the 12 h GR24 treatment. Taken overall, this study showed the gene regulatory network of auxin and cytokinin homeostasis to be regulated by strigolactone in the axillary bud outgrowth of ratoon rice, which highlights the importance of these biological pathways in the regulation of axillary bud outgrowth in ratoon rice and would provide theoretical support for the molecular breeding of ratoon rice.