Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways.

Cross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors and thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. In addition, a group of MITOGEN-ACTIVATED PROTEIN KINASES (MPKs) were identified as potential key points of cross-regulation between multiple hormones. Accordingly, the loss of function of one of these (MPK6) disrupted the global proteome, phosphoproteome and transcriptome during hormone responses. Lastly, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression.

Leaf endophytic microbiomes of different almond cultivars grafted to the same rootstock.

AIMS: We compared the bacterial endophytic communities of three genetically different almond cultivars that were all grafted on the same type of rootstock, growing side by side within a commercial orchard. METHODS AND RESULTS: We examined the diversity of leaf bacterial endophytes using cultivation-independent techniques and assessed the relative abundance of bacterial families. Two of these three cultivars were dominated by Pseudomonadaceae, while the bacterial composition of the third cultivar consisted mainly of Streptococcaceae. CONCLUSIONS: The experimental set up allowed us to analyse the impact of the shoot cultivar on endophytes, minimizing the influence of rootstock, biogeography, and cultivation status. Our data suggest that the shoot cultivar can shape the leaf endophytic community composition of almond trees. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results suggest that the shoot cultivar controls the composition of the foliar bacterial endophytic community of almonds. Overall, our results could provide a first step to develop strategies for a more sustainable almond agriculture.

Characterization of Erwinia gerundensis A4, an Almond-Derived Plant Growth-Promoting Endophyte.

The rapidly increasing global population and anthropogenic climate change have created intense pressure on agricultural systems to produce increasingly more food under steadily challenging environmental conditions. Simultaneously, industrial agriculture is negatively affecting natural and agricultural ecosystems because of intensive irrigation and fertilization to fully utilize the potential of high-yielding cultivars. Growth-promoting microbes that increase stress tolerance and crop yield could be a useful tool for helping mitigate these problems. We investigated if commercially grown almonds might be a resource for plant colonizing bacteria with growth promotional traits that could be used to foster more productive and sustainable agricultural ecosystems. We isolated an endophytic bacterium from almond leaves that promotes growth of the model plant Arabidopsis thaliana. Genome sequencing revealed a novel Erwinia gerundensis strain (A4) that exhibits the ability to increase access to plant nutrients and to produce the stress-mitigating polyamine spermidine. Because E. gerundensis is known to be able to colonize diverse plant species including cereals and fruit trees, A4 may have the potential to be applied to a wide variety of crop systems.

Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Simple methods to remove microbes from leaf surfaces.

Endophytes have been defined as microorganisms living inside plant tissues without causing negative effects on their hosts. Endophytic microbes have been extensively studied for their plant growth-promoting traits. However, analyses of endophytes require complete removal of epiphytic microorganisms. We found that the established tests to evaluate surface sterility, polymerase chain reaction, and leaf imprints, are unreliable. Therefore, we used scanning electron microscopy (SEM) as an additional assessment of epiphyte removal. We used a diverse suite of sterilization protocols to remove epiphytic microorganisms from the leaves of a gymnosperm and an angiosperm tree to test the influence of leaf morphology on the efficacy of these methods. Additionally, leaf tissue damage was also evaluated by SEM, as damaging the leaves might have an impact on endophytes and could lead to inaccurate assessment of endophytic communities. Our study indicates, that complete removal of the leaf cuticle by the sterilization technique assures loss of epiphytic microbes, and that leaves of different tree species may require different sterilization protocols. Furthermore, our study demonstrates the importance of choosing the appropriate sterilization protocol to prevent erroneous interpretation of host-endophyte interactions. Moreover, it shows the utility of SEM for evaluating the effectiveness of surface sterilization methods and their impact on leaf tissue integrity.

Integrated multi-omics framework of the plant response to jasmonic acid.

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.