Growth-limiting drought stress induces time-of-day dependent transcriptome and physiological responses in hybrid poplar

Drought stress negatively impacts the health of long-lived trees. Understanding the genetic mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. We aimed to determine how hybrid poplars respond to prolonged and uniform exposure to drought; how responses to moderate and more severe growth-limiting drought stresses differed; and, how drought responses change throughout the day. We established hybrid poplar trees (Populus x 'Okanese') from unrooted stem cutting with abundant soil moisture for six weeks. We then withheld water to establish well-watered, moderate, and severe growth-limiting drought conditions. These conditions were maintained for three weeks during which growth was monitored. We then measured photosynthetic rates and transcriptomes of leaves that had developed during the drought treatments at two times of day. The moderate and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates, and global transcriptome profiles. Notably, the time of day of sampling produced the strongest signal in the transcriptome data. The moderate drought treatment elicited global transcriptome changes that were intermediate to the severe and well-watered treatments in the early evening, but did not elicit a strong drought response in the morning, emphasizing the complex nature of drought regulation in long-lived trees.

Much more than a toxin: hydrogen cyanide is a volatile modulator of bacterial behaviour

Bacteria communicate with each other and with other organisms in a chemical language comprising both diffusible and volatile molecules, and volatiles have recently gained increasing interest as mediators of bacterial interactions. One of the first volatile compounds discovered to play a role in biotic interactions is hydrogen cyanide (HCN), a well-known toxin, which irreversibly binds to the key respiratory enzyme cytochrome C oxidase. The main ecological function of this molecule was so far thought to lie in the inhibition of competing microorganisms. Here we show that HCN is much more than a respiratory toxin and should be considered a major regulator of bacterial behaviour rather than a solely defensive secondary metabolite. Cyanogenesis occurs in both environmental and clinical Pseudomonas strains. Using cyanide-deficient mutants in two Pseudomonas strains, we demonstrate that HCN functions as an intracellular and extracellular volatile signalling molecule, which leads to global transcriptome reprogramming affecting growth, motility, and biofilm formation, as well as the production of other secondary metabolites such as siderophores and phenazines. Our data suggest that bacteria are not only using endogenous HCN to control their own cellular functions, but are also able to remotely influence the behaviour of other bacteria sharing the same environment.

PIF4 and PIF4-Interacting Proteins: At the Nexus of Plant Light, Temperature and Hormone Signal Integrations

Basic helix-loop-helix (bHLH) family transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is necessary for plant adaption to light or high ambient temperature. PIF4 directly associates with plenty of its target genes and modulates the global transcriptome to induce or reduce gene expression levels. However, PIF4 activity is tightly controlled by its interacting proteins. Until now, twenty-five individual proteins have been reported to physically interact with PIF4. These PIF4-interacting proteins act together with PIF4 and form a unique nexus for plant adaption to light or temperature change. In this review, we will discuss the different categories of PIF4-interacting proteins, including photoreceptors, circadian clock regulators, hormone signaling components, and transcription factors. These distinct PIF4-interacting proteins either integrate light and/or temperature cues with endogenous hormone signaling, or control PIF4 abundances and transcriptional activities. Taken together, PIF4 and PIF4-interacting proteins play major roles for exogenous and endogenous signal integrations, and therefore establish a robust network for plants to cope with their surrounding environmental alterations.

An atlas of the Norway spruce needle seasonal transcriptome

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 to June 30), cell walls, organelles etc. were formed, and this developmental program heavily influenced the transcriptome, explained by over represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July-August), autumn (September-October), winter (November-February) and spring (March-April), where over represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

Global transcriptome landscape of the rabbit protozoan parasite Eimeria stiedae

Background Coccidiosis caused by Eimeria stiedae is a widespread and economically significant disease of rabbits. The lack of studies on the life-cycle development and host interactions of E. stiedae at the molecular level has hampered our understanding of its pathogenesis. Methods In this study, we present a comprehensive transcriptome landscape of E. stiedae to illustrate its dynamic development from unsporulated oocysts to sporulated oocysts, merozoites, and gametocytes, and to identify genes related to parasite-host interactions during parasitism using combined PacBio single-molecule real-time and Illumina RNA sequencing followed by bioinformatics analysis and qRT-PCR validation. Results In total, 12,582 non-redundant full-length transcripts were generated with an average length of 1808 bp from the life-cycle stages of E. stiedae. Pairwise comparisons between stages revealed 8775 differentially expressed genes (DEGs) showing highly significant description changes, which compiled a snapshot of the mechanisms underlining asexual and sexual biology of E. stiedae including oocyst sporulation between unsporulated and sporulated oocysts; merozoite replication between sporulated oocysts and merozoites; and gametophyte development and gamete generation between merozoites and gametocytes. Further, 248 DEGs were grouped into nine series clusters and five groups by expression patterns, and showed that parasite–host interaction-related genes predominated in merozoites and gametocytes and were mostly involved in steroid biosynthesis and lipid metabolism and carboxylic acid. Additionally, co-expression analyses identified genes associated with development and host invasion in unsporulated and sporulated oocysts and immune interactions during gametocyte parasitism. Conclusions This is the first study, to our knowledge, to use the global transcriptome profiles to decipher molecular changes across the E. stiedae life cycle, and these results not only provide important information for the molecular characterization of E. stiedae, but also offer valuable resources to study other apicomplexan parasites with veterinary and public significance. Graphic Abstract