Biology subjects

Baebler, S.

Publications and source records attributed to Baebler, S..

8 recordsLinked to original sources

bioRxiv2024

Integration of multi-omics and deep phenotyping provides novel insights into multiple abiotic stress responses in potato

Potato is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, or flooding, which are severely exacerbated by climate change. Understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Desiree) under heat, drought and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress-responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising transcriptomics, proteomics, metabolomics and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analysed at the end of the stress period. Integrative analysis of multi-omics data was performed using a bioinformatic pipeline, which was established here, based on machine learning and knowledge networks. Overall, waterlogging had the most immediate and dramatic effects on potato plants, interestingly activating ABA-responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids and diverse stress induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies towards climate-adapted potato varieties. One Sentence SummaryIntegrated multi-omics analysis of high-throughput phenotyping in potato reveals distinct molecular signatures of acclimation to single and combined abiotic stresses related to climate change.

plant biology↗

bioRxiv2023

Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map (SKM, https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs describing current knowledge of biochemical, signalling, and regulatory molecular interactions in plants: a highly curated model of plant stress signalling (PSS, 543 reactions) and a large comprehensive knowledge network (CKN, 488,390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entrypoint for plant stress response investigations and the related growth tradeoffs. SKM provides interactive exploration of current knowledge. PSS is also formulated as qualitative and quantitative models for systems biology, and thus represents a starting point of a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation, design of validation experiments, or to gain new insights into experimental observations in plant biology.

plant biology↗

bioRxiv2023

Identification and characterisation of Planococcus citri cis- and trans-isoprenyl diphosphate synthase genes, supported by short- and long-read transcriptome data

Many insect species rely on diverse terpenoids for their development and interorganismal interactions. However, little is known about terpenoid biosynthesis in insects. The monoterpenoid sex pheromones of mealybugs and scale insects (Coccoidea) are particularly enigmatic, with several species producing unique structures presumed to result from the irregular coupling activity of unidentified isopentenyl diphosphate synthases (IDSs). Enzymes capable of similar transformations have previously only been described from a few plant, bacterial and archaeal species. To investigate if insect irregular monoterpenes can be biosynthesised by similar enzymes, we performed a comprehensive search for IDS coding sequences in the genome of Planococcus citri, a widespread agricultural pest. We complemented the available P. citri genome data with newly generated short- and long-read transcriptome data. The identified candidate genes had homology to both short- and long-chain IDSs and some appeared to be paralogous, indicating gene duplications and consequent IDS gene family expansion in P. citri. We tested the activity of eleven candidate gene products, confirming in vitro regular activity for five enzymes, one of which (transIDS5) also produced the irregular prenyl diphosphates, maconelliyl and lavandulyl diphosphate. Targeted mutagenesis of selected aspartates and a lysine in the active site of transIDS5 uncovered their importance for chain-length preference and irregular coupling. This work provides an important foundation for deciphering terpenoid biosynthesis in mealybugs, as well as a potential source of enzymes for the biotechnological production of sustainable insect pest management products.

biochemistry↗

bioRxiv2021

pISA-tree - a data management framework for life science research projects using a standardised directory tree

We developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality and low maintenance cost. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) based on the ISA model, in a standardised manner via consecutive batch files. Templates-based metadata is generated in parallel at each level enabling guided submission of experiment metadata. pISA-tree is complemented by two R packages, pisar and seekr. pisar facilitates integration of pISA-tree datasets into bioinformatic pipelines and generation of ISA-Tab exports. seekr enables synchronisation with the FAIRDOMHub repository. Applicability of pISA-tree was demonstrated in several national and international multi-partner projects. The system thus supports findable, accessible, interoperable and reusable (FAIR) research and is in accordance with the Open Science initiative. Source code and documentation of pISA-tree are available at https://github.com/NIB-SI/pISA-tree.

bioinformatics↗

bioRxiv2021

Chloroplast redox state changes indicate cell-to-cell signalling during the hypersensitive response

Hypersensitive response (HR)-conferred resistance is associated with an induction of programmed cell death (PCD) and pathogen spread restriction in its proximity. While the pivotal role of salicylic acid (SA) in the restriction of pathogen spread during HR has been confirmed, the exact role of chloroplastic reactive oxygen species and the link between SA signalling and chloroplast redox state during HR remain unexplained. To unravel these relationships, we performed detailed spatiotemporal analysis of chloroplast redox response to potato virus Y (PVY) infection in resistant Ny-1-gene-bearing potato and its transgenic counterpart with impaired SA accumulation and compromised resistance. We found that the chloroplasts are highly oxidized in the cells adjacent to the cell death zone at different stages after virus inoculation in both genotypes. Moreover, we detected individual cells with moderately oxidized chloroplasts, which we call "signalling cells", in close proximity as well as farther from the cell death zone. These are relatively rare in SA-deficient plants, suggesting their role in signalling for HR-conferred resistance. This hypothesis is further supported by highly induced formation of stroma filled tubules that extend from chloroplasts (stromules) in the cells adjacent to signalling cells. Unexpectedly, the cells with the highest occurrence of stromules have chloroplasts in more reduced state than the adjacent ones. In addition, we show that stromules are induced also at the edge of PVY multiplication zone. We conclude that chloroplast redox state and stromule formation are tightly spatiotemporally regulated by SA-signalling which leads to effective HR response.

plant biology↗

bioRxiv2020

Spatial accumulation of salicylic acid is in effector-triggered immunity of potato against viruses regulated by RBOHD

While activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to restriction of pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny-1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels to reveal spatiotemporal regulation of immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes, spatiotemporal regulation is completely lost in SA-deficient line, while the others show different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during resistance response. In plants with silenced RBOHD, the functionality of resistance response is perturbed and virus spread is not arrested at the site of infection. RBOHD is required for spatial accumulation of SA, and conversely RBOHD is under transcriptional regulation of SA signaling. Using spatially resolved RNA-Seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling.

plant biology↗

bioRxiv2017

Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato

To provide means for novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modelling represents a powerful tool that can unravel properties of complex biological systems. Here, we build on a reliable Arabidopsis (Arabidopsis thaliana L.) immune signalling model, extending it with the information from diverse publically available resources. The resulting prior knowledge network (20,012 nodes, 70,091 connections) was then translated to potato (Solanum tuberosum L.) and superimposed with an ensemble network inferred from potato time-resolved transcriptomics data. We used different network modelling approaches to generate specific hypotheses of potato immune signalling mechanisms. An interesting finding was the identification of a string of molecular events, illuminating the ethylene pathway modulation of the salicylic acid pathway through NPR1 gene expression. Functional validations confirmed this modulation, thus confirming the potential of our integrative network modelling approach for unravelling molecular mechanisms in complex systems.\n\nOne-sentence summaryAnalysis of integrated prior knowledge and ensemble networks highlights a novel connection between ethylene and salicylic acid signalling modules in potato.

systems biology↗

bioRxiv2017

Tolerance To PVY Infection In Potato Is Conditioned By Perturbation Of Small RNA-Gibberellin Regulatory Network

Potato virus Y is the most economically important potato viral pathogen. We aimed at unraveling the roles of small RNAs (sRNAs) in the complex immune signaling network controlling the establishment of tolerant response of potato cv. Desiree to the virus. We constructed a sRNA regulatory network connecting sRNAs and their targets to link sRNA level responses to physiological processes. We discovered an interesting novel sRNAs-gibberellin regulatory circuit being activated as early as 3 days post inoculation before viral multiplication can be detected. Increased levels of miR167 and phasiRNA931 were reflected in decreased levels of transcripts involved in gibberellin biosynthesis. Moreover, decreased concentration of gibberellin confirmed this regulation. The functional relation between lower activity of gibberellin signaling and reduced disease severity was previously confirmed in Arabidopsis-virus interaction using knockout mutants. We further showed that this regulation is salicylic acid-dependent as the response of sRNA network was attenuated in salicylic acid-depleted transgenic counterpart NahG-Desiree expressing severe disease symptoms. Besides downregulation of gibberellin signaling, regulation of several other parts of sRNA network in tolerant Desiree revealed similarities to responses observed in mutualistic symbiotic interactions. The intertwining of different regulatory networks revealed shows how developmental signaling, disease symptom development and stress signaling can be balanced.

plant biology↗