Biology subjects

Brajkovic, S.

Publications and source records attributed to Brajkovic, S..

6 recordsLinked to original sources

bioRxiv2026

Brassinosteroid-regulated transcription factors confer epigenetic changes that repress plant immunity

When organisms encounter pathogens, they rapidly activate complex defense programs to ensure survival. While these immune responses are vital, they often also incur trade-offs, such as reduced growth and development and must therefore be tightly controlled 1,2. In this study, we reveal that the steroid hormones brassinosteroids (BRs) contribute to this control in Arabidopsis thaliana by repressing immunity-related genes. We provide evidence that the BR-regulated basic helix-loop-helix (bHLH) transcription factor CESTA (CES), along with its homologs BR ENHANCED EXPRESSION (BEE)1-3, mediate DNA methylation changes at transposable element (TE)-rich loci containing nucleotide-binding leucine-rich-repeat (NLR)-type receptor genes, including SUPPRESSOR OF NPR1-1 CONSTITUTIVE 1 (SNC1). These CES-induced methylation changes correlate with altered splicing of SNC1 pre-mRNA, a process that requires the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1). In support, we show that CES associates with components of the chromatin remodeling and splicing machinery. Together, our findings reveal a previously unrecognized BR-induced mechanism that modulates the epigenetic and post transcriptional regulation of immune genes, enabling plants to prioritize growth over defense. Significance statementSteroid hormones are powerful regulators of growth but also act as potent suppressors of immunity, with well-established clinical applications, for example in treating autoimmune diseases in humans. In plants, the steroid hormones brassinosteroids (BRs) exert similar effects. Here, we uncover that BR-mediated immune suppression involves DNA methylation changes and alternative splicing of a subset of immune receptor genes, that govern resistance responses mediated by the plant hormone salicylic acid. We provide evidence for a function of specific bHLH transcription factors in this process that link BR signaling to chromatin remodelling and RNA processing. Thereby our study reveals a novel mode of steroid hormone activity in immune repression, which involves epigenetic and posttranscriptional adjustment of immune receptor function.

plant biology↗

bioRxiv2025

Structural variation at lhcb6 underlies genetic variation in photosystem II maximum quantum efficiency in maize

Targeted utilization of native genetic diversity can expand the genetic basis of traits that exhibit limited genetic variation in elite breeding material and can enhance our understanding of the genotype-phenotype relationships associated with complex traits in crops. In a genome-wide association study in a European maize landrace we identified quantitative trait loci (QTL) that affected the maximum quantum efficiency of photosystem II (Fv/Fm) in field experiments. In a forward genetic approach, we focused on a QTL on chromosome 10, explaining a large proportion of the genetic variance for Fv/Fm in growth stages V4 (35%) and V6 (47%), for genetic dissection and candidate gene discovery. Integrating molecular and physiological information we show that allelic variation at the gene encoding LIGHT HARVESTING CHLOROPHYLL A/B BINDING PROTEIN6 (LHCB6), a component of the photosystem II (PSII) light-harvesting complex (LHCII) antenna, underlies the variation in Fv/Fm. We demonstrate that the allelic variation results from a hAT transposon insertion at lhcb6 and is associated with differential accumulation of the LHCII antenna components LHCB6 and LHCB3, leading to differences in non-photochemical quenching (NPQ) and plant biomass accumulation. Based on proteomic analyses we propose candidate genes that compensate the unfavorable effects caused by impaired LHCII antenna assembly. Our work provides novel insights into the function of lhcb6 in the context of LHCII antenna assembly and demonstrates the value of natural variation in landraces for the understanding and genetic improvement of complex photosynthetic processes.

genetics↗

bioRxiv2025

Multi-omics of barley Fusarium Head Blight converge on pathogen-triggered biosynthesis of aromatic amino acid derived chemical defense compounds

Fusarium Head Blight (FHB) is a devastating fungal disease of small grain cereals like wheat and barley, causing substantial yield and quality losses each year worldwide. FHB is caused by Fusarium species that produce mycotoxins such as deoxynivalenol (DON) that impairs protein biosynthesis. Although defense responses in barley to Fusarium infection have been described at the transcriptional level, it remains unclear to what extent these responses are translated into functional changes at the protein and metabolite levels. In this study, we employed comprehensive transcriptomics, proteomics, and metabolomics to dissect the defense responses of barley heads during infection with Fusarium culmorum. Our integrated analyses revealed a set of significantly regulated gene-protein pairs linked to biosynthetic pathways that consistently correspond to upregulated defense-related metabolites. These include tryptophan-derived stress metabolites such as tryptamine and serotonin, as well as barley-specific hydroxycinnamylamides, including conjugates from the trypthophan metabolism, hordatines, and their biosynthetic precursors. Integrating data across multiple omics layers identifies the upregulation of aromatic amino acid derived secondary metabolism as the most consistent barley response to FHB infection across diverse barley varieties that share barley-typical type II resistance to fungal spreading in the head rachis.

plant biology↗

bioRxiv2024

Embracing native diversity to enhance maximum quantum efficiency of photosystem II in maize (Zea mays L.)

Sustainability of maize cultivation would benefit tremendously from early sowing but is hampered by low temperatures during early development in temperate climate. We show that allelic variation of subunit M of NADH-dehydrogenase-like (NDH) complex (ndhm1), discovered in a European maize landrace affects several quantitative traits relevant during early development in cold climates through NDH-mediated cyclic electron transport (CET) around photosystem I, a process crucial for photosynthesis. Starting from a genome-wide association study (GWAS) for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm) we capitalized on large phenotypic effects of a hAT transposon insertion in ndhm1 on quantitative traits early plant height (EPH), Fv/Fm, chlorophyll content and cold tolerance caused by reduced protein levels of NDHM and associated NDH components. Analysis of the native allelic series of ndhm1 revealed a rare allele of ndhm1 which is associated with small albeit significant effects on maximum potential quantum yield of photosystem II in dark- and light adapted leaves (Fv/Fm, {Phi}PSII) and early plant height compared to common alleles. Our work showcases the extraction of novel, favorable alleles from locally adapted landraces, offering an efficient strategy for broadening the genetic variation of elite germplasm by breeding or genome editing.

plant biology↗

bioRxiv2024

KIPK and KIPK-LIKE1 suppress overbending during negative hypocotyl gravitropic growth

Plants use environmental cues, such as the direction of gravity or the direction, quantity and quality of light, to orientate organ and plant growth. During germination of angiosperm seeds in the soil, hypocotyl elongation is directed by negative gravitropism responses such that the seedling can reach the light for photosynthesis and autotrophic growth. Hypocotyl elongation in the soil, however, also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of hypocotyl bending, in that KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector after obstacle avoidance. At the same time, we find that the highly homologous KIPKL2 (KIPK-LIKE2) must be functionally distinct. We further find that KIPK, and likely also KIPKL1, phosphorylate BRXL2 (BREVIS RADIX LIKE2) and ARKs (ARMADILLO REPEAT KINESINs), that mutants of both KIPK phosphorylation substrates share the overbending phenotype with kipk kipkl1 mutants, and that KIPK and KIPKL1 act synergistically with the ARK-regulatory NEK6 (NIMA-RELATED PROTEIN KINASE6). We propose that KIPK and KIPKL1 regulate ARK kinesins and thereby cortical microtubules for efficient gravitropic hypocotyl bending.

plant biology↗

bioRxiv2023

Fully Automated Sequential Immunofluorescence (seqIF) for Hyperplex Spatial Proteomics

Tissues are complex environments where different cell types are in constant interaction with each other and with non-cellular components. Preserving the spatial context during proteomics analyses of tissue samples has become an important objective for different applications, one of the most important being the investigation of the tumor microenvironment. Here, we describe a multiplexed protein biomarker detection method on the COMET instrument, coined sequential ImmunoFluorescence (seqIF). The fully automated method uses successive applications of antibody incubation and elution, and in-situ imaging enabled by an integrated microscope and a microfluidic chip that provides optimized optical access to the sample. We show seqIF data on different sample types such as tumor and healthy tissue, including 40-plex on a single tissue section that is obtained in less than 24 hours, using off-the-shelf antibodies. We also present extensive characterization of the developed method, including elution efficiency, epitope stability, repeatability and reproducibility, signal uniformity, and dynamic range, in addition to marker and panel optimization strategies. The streamlined workflow using off-the-shelf antibodies, data quality enabling quantitative downstream analysis, and ease of reaching hyperplex levels make seqIF suitable for immune-oncology research and other disciplines requiring spatial analysis, paving the way for its adoption in clinical settings.

cancer biology↗