Biology subjects

Rutten, T.

Publications and source records attributed to Rutten, T..

16 recordsLinked to original sources

bioRxiv2026

Spatial metabolomics links polyamine turnover and vascular lipid remodeling to barley spikelet fate

Local metabolic programs can determine whether developing organs maintain growth, differentiate, or degenerate. However, the spatial establishment of such programs during reproductive development remains poorly understood. In cereal inflorescences, this question is closely tied to grain number because the fate of initiated floral primordia is shaped by the developmental position, metabolic support, genotype, and environmental stress. To understand the metabolic logic underlying floral fate in barley (Hordeum vulgare L.), we mapped the spatial distribution of metabolites across the inflorescence in wild-type Bowman and in hvcmf4, a mutant that undergoes premature apical inflorescence degeneration. Amino acid-, carbohydrate-, and chlorophyll-associated metabolites form clear developmental gradients along the inflorescence axis. These gradients are progressively remodeled during developmental pre-anthesis tip degeneration but are both accelerated and spatially distorted in hvcmf4. Within this broader metabolic landscape, two discrete domains stand out. First, spermidine-associated domains specifically marked reproductive meristems, a pattern corroborated by the meristem-enriched expression of polyamine biosynthetic genes. This polyamine-rich meristem state declined as developmental tip degeneration proceeded and was prematurely lost in hvcmf4, where polyamine metabolism appeared to shift toward oxidative breakdown via the polyamine oxidase pathway. Second, lysophosphatidylcholine accumulated specifically at floral attachment and vascular supply zones. The developmental reduction of this bioactive lysophospholipid-associated domain in the apical regions, and its stronger disruption in hvcmf4, coincided with the reprogramming of lipid-remodeling and auxin transport-associated genes, suggesting impaired coordination of lipid signaling, auxin canalization, and vascular support. Together, our study reveals spatial polyamine and lysophospholipid domains that couple meristem maintenance with vascular support, providing a metabolic framework for the fate of developing cereal inflorescences.

plant biology↗

bioRxiv2026

Rate of meristem initiation driven by the MADS-WUS axis contributes to floral survival and inflorescence evolution in grasses

Crop domestication has repeatedly shaped inflorescence architecture to improve floral production, but mechanisms coordinating the rate of floral initiation, maturation and survival remain unclear. Combining morphometry, modelling and molecular genetic analyses, we show that floral production in the indeterminate barley (Hordeum vulgare L.) inflorescence follows an "initiate fast-die young" strategy orchestrated by a main MADS-box gene, SPIKELET INITIATION AND FERTILITY (SIF). SIF accomplishes this duality by coordinately terminating the inflorescence meristem via WUSCHEL and activating the floral meristem via APETALA1 (Vrn-H1). Hereby, the ancestral SIF "slow" allele promotes a timely commitment to floral maturation, whereas the derived "fast" allele permits more floral initiations. Postdomestication selection of SIF alleles thus enables diversified reproductive strategies in barley populations to maintain yield traits in the field. Finally, we show that a lineage-specific SIF duplication contributed to meristem fate transition and inflorescence evolution during Triticeae cold adaptation. Our results establish developmental rate as a key driver of architectural innovation and reproductive success.

plant biology↗

bioRxiv2026

Epistatic interaction of the genes Raw1 and Raw7 controls barb size and frequency in barley awn roughness

Awns of wild barley (Hordeum vulgare ssp. spontaneum L.) are rough by default due to silicified upward-oriented trichomes on the awns epidermis, forming a ratcheted surface, which is advantageous for seed dispersal and burial. Cultivated barley, however, may carry smooth awns covered by smaller barbs or lacking barbs completely. The gene Raw1 on chromosome 5H is a major factor controlling barley awn roughness and was shown to encode a LONG AND BARBED AWN1 (LABA1) homolog. Here we report, by using quantitative analysis of the barb trait, map-based cloning and Cas9-mediated gene knock-out, a second gene Raw7, located on barley chromosome 7H, encoding a putative two-component response regulator. We propose that Raw7 acts downstream of Raw1 in a cytokinin signaling pathway underlying cell cycle control in epidermal barb primordia cells. Raw1 and Raw7 show epistatic interaction, suggesting that Raw1 acts as the primary driver of barb initiation, while Raw7 modulates barb size and frequency. Our findings provide the foundation to study the selection and domestication history of the awn roughness trait in barley, and thus to dissect if awn roughness is providing an advantage in cultivated barley or if the trait persisted after domestication due to linkage drag. SummaryO_LIThe presence of silicified upward-oriented trichomes or barbs arising from the epidermis of barley awns is a prominent trait. They form a ratcheted surface which is advantageous for seed dispersal and burial and defense against herbivory. C_LIO_LIPrevious work identified Raw1 on chromosome 5H as a major determinant of awn roughness in barley. Here, we identify a second awn roughness gene, Raw7 on chromosome 7H, combining quantitative phenotyping of barb traits, map-based cloning and Cas9-mediated targeted mutagenesis for functional analyses. C_LIO_LIGenetic and functional evidence suggests a complex epistatic interaction in which Raw1 primarily drives barb formation and Raw7 fine-tunes endoreduplication-dependent epidermal cell expansion and patterning in barb primordia cells. Raw1 and Raw7 likely act in a cytokinin-dependent two-component signaling pathway, where Raw1 promotes local cytokinin activation and Raw7, a type-B response regulator, mediates downstream transcriptional responses. C_LIO_LIThe proposed pathway suggests additional undetected loci may contribute to awn roughness, and emerging barley pangenome and pan-transcriptome resources provide a framework to identify and functionally validate new candidates. C_LI

plant biology↗

bioRxiv2026

Hypermorphic TaARF4 shapes wheat architecture by repressing SPL-mediated developmental timing

Integrating spatial morphogens with temporal developmental clocks is fundamental to optimizing plant architecture and crop yield, yet their molecular interface remains elusive. Here, we characterize Branched shoot 1 (Bsh1), a semi-dominant wheat mutant exhibiting non-canonical upper-aerial branching and aberrant spike development, caused by a T265I substitution in the DNA-binding domain of the auxin response factor TaARF4-A2. Unlike flanking mutations governing protein stability in basal land plants, this central substitution uniquely converts TaARF4-A2 into an auxin-insensitive hypermorphic repressor. The mutant protein disrupts auxin-cytokinin homeostasis and markedly enhances the native repression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, the core timers of developmental phase transitions. This spatial and temporal uncoupling unleashes upper axillary buds from dormancy, promoting aerial branching and diverting resources from reproductive development. Our findings demonstrate how a conserved spatial morphogen effector was evolutionarily rewired in polyploid wheat to dictate the temporal SPL clock, orchestrating species-specific shoot architectural innovation.

plant biology↗

bioRxiv2024

Structural Basis of betaKNL2 Centromeric Targeting Mechanism and Its Role in Plant-Specific Kinetochore Assembly

The kinetochore is an essential protein complex that ensures proper chromosome segregation during cell division. Kinetochore assembly is initiated by the incorporation of CENP-A/CENH3. This process depends on KNL2/M18BP1 and CENP-C proteins. In plants, two variants of KNL2, KNL2 and {beta}KNL2, are present. Both possess the conserved SANTA domain, while KNL2 additionally has the centromere-targeting CENPC-k motif. Despite lacking the CENPC-like motif, the plant-specific {beta}KNL2 localizes to centromeres and aids in CENP-A/CENH3 loading. We found that efficient centromeric targeting of {beta}KNL2 requires the SANTA domain and the C-terminal part, while nuclear targeting depends on a conserved C-terminal motif-III. Structural predictions and experimental validations reveal that {beta}KNL2 forms homodimers and interacts with centromeric DNA and KNL2. We confirm that centromeric targeting of {beta}KNL2 depends on KNL2 in a tissue-dependent manner. Our findings provide crucial insights into the unique mechanisms of plant-specific kinetochore assembly, highlighting {beta}KNL2s essential role in this process. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/605747v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@30b331org.highwire.dtl.DTLVardef@14494a3org.highwire.dtl.DTLVardef@17a6336org.highwire.dtl.DTLVardef@7ad8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Centromeric localization of KNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions

In eukaryotic organisms, proper chromosome segregation during cell division depends on the centromeric histone H3 (CENH3) variant. Our previous studies identified a plant CENH3 assembly factor, Kinetochore Null2 (KNL2), that possesses a centromere-targeting motif, CENPC-k, similar to the CENPC motif in CENP-C. Additionally, we have demonstrated that KNL2 can bind DNA in vitro, independent of its CENPC-k motif. Thus, the mechanism underlying the binding of KNL2 to centromeric DNA remains elusive. Our study shows that the CENPC-k and CENPC motifs alone are not sufficient to target the centromere in N. benthamiana and A. thaliana. In-silico analysis revealed flanking DNA-binding regions near the CENPC-k and CENPC motifs, suggesting their importance in interacting with centromeric DNA. Fusion of protein fragments containing these motifs to EYFP facilitated targeting to the centromere. Deletion of DNA-binding domains reduced the centromeric localization of KNL2-C, whereas fusion of CENPC-k to the H-NS protein from E. coli targeted it to centromeres. We conclude that targeting of KNL2 and CENP-C proteins to centromeres is dependent on the CENPC-k/CENPC motifs, and their sequence-independent DNA-binding promotes anchoring at the centromere. Understanding the targeting mechanisms of KNL2 and CENP-C may help to engineer kinetochore structure by targeting chromatin modifying proteins to centromeres.

plant biology↗

bioRxiv2024

Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. Here we genetically dissected repeated origins and losses of prickles, sharp epidermal projections, that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Strikingly, homologs promote prickle formation across angiosperms that collectively diverged over 150 million years ago. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone-activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.

evolutionary biology↗

bioRxiv2023

Anatomical insights into the vascular lay-out of the barley rachis: implications for transport and spikelet connection

Background and aimsVascular patterning is intimately related to plant form and function. However, morphologic a l studies on the vascular anatomy of cereal crops, and inflorescences in particular, are scarce despite their importance for grain yield determination. Here, using barley (Hordeum vulgare) as a model, we study the vascular anatomy of the spike-type inflorescence. Our goal is to clarify the relationship between rachis (spike axis) vasculature and spike size, the implications for transport capacity and its interaction with the spikelets. MethodsWe employed serial transversal internode sections in multiple barley lines with different spike size, and investigated the internode diameter, vascular area and vein number size along the mature barley rachis. We then modeled the vascular dynamics along the main spike axis, and analyzed their relationship with spike size. Key resultsInternode diameter and total vascular area have a clear positive correlation with spike size whereas vascular number is only weakly correlated. While the lateral periphery of the rachis contains large mature veins of constant diameter the central part is occupied by a staggered array of small immature veins. This underlines the importance of minimizing transport resistance and suggests that transport and distribution of nutrients are spatially separated. Spikelet-derived veins enter the rachis either in the central area, where they often merge with the immature rachis veins, or in the periphery where they do not merge with the large mature veins. An increase in floret fertility through the conversion of a two-rowed barley into an isogenic six-rowed line, as well a decrease in floret fertility due to enhanced pre-anthesis tip degeneration caused by the mutation tip sterile 2.b (tst2.b) significantly affected vein size, but had limited to no effects on vein number or rachis diameter. Comparative analysis of a wild barley accession suggests that the domestication of barley may have favored plants with enhanced rachis transport capacity. ConclusionsThe rachis vasculature is the result of a two-step process involving an initial lay-out followed by size adjustment according to floret fertility/spike size. The functional processes of long distance transport and local supply to spikelets are spatially separated while a vascular continuity between rachis and spikelets appears non-essential.

plant biology↗

bioRxiv2021

Dosage of duplicated and antifunctionalized homeobox proteins influences spikelet development in barley

Illuminating the mechanisms of inflorescence architecture of grain crops that feed our world may strengthen the goal towards sustainable agriculture. Lateral spikelet development of barley (Hordeum vulgare L.) is such an example of a floral architectural trait regulated by VRS1 (Vulgare Row-type Spike 1 or Six-rowed Spike 1, syn. HvHOX1). Its lateral spikelet-specific expression and the quantitative nature of suppressing spikelet development were previously shown in barley. However, the mechanistic function of this gene and its paralog HvHOX2 on spikelet development is still fragmentary.Here, we show that these duplicated transcription factors (TFs) have contrasting nucleotide diversity in various barley genotypes and several Hordeum species. Despite this difference, both proteins retain their basic properties of the homeodomain leucine zipper class I family of TFs. During spikelet development, these genes exhibit similar spatiotemporal expression patterns yet with anticyclic expression levels. A gene co-expression network analysis suggested that both have an ancestral relationship but their functions appear antagonistic to each other, i.e., HvHOX1 suppresses whereas HvHOX2 rather promotes spikelet development. Our transgenic promoter-swap analysis showed that HvHOX2 can restore suppressed lateral spikelets when expression levels are increased; however, at its low endogenous expression level, HvHOX2 appears dispensable for spikelet development. Collectively, this study proposes that the dosage of the two antagonistic TFs, HvHOX1 and HvHOX2, influence spikelet development in barley.

plant biology↗

bioRxiv2021

The barley mutant multiflorus2.b reveals quantitative genetic variation for new spikelet architecture

Understanding the genetic basis of yield forming factors in small grain cereals is of extreme importance, especially in the wake of stagnation of further yield gains in these crops. One such yield forming factor in these cereals is the number of grain-bearing florets produced per spikelet. Wildtype barley (Hordeum vulgare L.) spikelets are determinate structures, the spikelet axis (rachilla) degenerates after producing single floret. In contrast, the rachilla of wheat (Triticum ssp.) spikelets, which are indeterminate, elongates to produce up to 12 florets. In our study, we characterized the barley spikelet determinacy mutant multiflorus2.b (mul2.b) that produced up to three fertile florets on elongated rachillae of lateral spikelets. Apart from the lateral spikelet indeterminacy (LS-IN), we also characterized the supernumerary spikelet phenotype in the central spikelets (CS-SS) of mul2.b. Through our phenotypic and genetic analyses, we identified two major QTLs on chromosomes 2H and 6H, and two minor QTLs on 3H for the LS-IN phenotype. For, the CS-SS phenotype we identified one major QTL on 6H, and a minor QTL on 5H chromosomes. Notably, the 6H QTLs for CS-SS and LS-IN phenotypes co-located with each other, potentially indicating that a single genetic factor might regulate both phenotypes. Thus, our in-depth phenotyping combined with genetic analyses revealed the quantitative nature of the LS-IN and CS-SS phenotypes in mul2.b, paving the way for cloning the genes underlying these QTLs in the future. Key messageSpikelet indeterminacy and supernumerary spikelet phenotypes in barley multiflorus2.b mutant show polygenic inheritance. Genetic analysis of multiflorus2.b revealed major QTLs for spikelet determinacy and supernumerary spikelet phenotypes on 2H and 6H chromosomes.

plant biology↗

bioRxiv2020

Application of aptamers improves CRISPR-based live imaging of plant telomeres

Development of live imaging techniques for providing information how chromatin is organized in living cells is pivotal to decipher the regulation of biological processes. Here, we demonstrate the improvement of a live imaging technique based on CRISPR/Cas9. In this approach, the sgRNA scaffold is fused to RNA aptamers including MS2 and PP7. When the dead Cas9 (dCas9) is co-expressed with chimeric sgRNA, the aptamer-binding proteins fused to fluorescent protein (MCP-FP and PCP-FP) are recruited to the targeted sequence. Compared to previous work with dCas9:GFP, we show that the quality of telomere labelling was improved in transiently transformed Nicotiana benthamiana using aptamer-based CRISPR-imaging constructs. Labelling is influenced by the copy number of aptamers and less by the promoter types. The same constructs were not applicable for labelling of repeats in stably transformed plants and roots. The constant interaction of the RNP complex with its target DNA might interfere with cellular processes. HighlightAptamer-based CRISPR imaging: an opportunity for improving live-cell imaging in plants

cell biology↗

bioRxiv2020

COMPOSITUM 1 (COM1) contributes to the architectural simplification of barley inflorescence via cell wall-mediated and meristem identity signals

Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. We identified the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressed in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in Triticeae (barley) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts revealed barley COM1 regulates cell growth, affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity partially independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae.

plant biology↗

bioRxiv2020

Providing an additional electron sink by the introduction of cyanobacterial flavodiirons enhances the growth of Arabidopsis thaliana in varying light

The ability of plants to maintain photosynthesis in a dynamically changing environment is of central importance for their growth. As their photosynthetic machinery typically cannot adapt rapidly to fluctuations in the intensity of radiation, the level of photosynthetic efficiency is not always optimal. Cyanobacteria, algae, non-vascular plants (mosses and liverworts) and gymnosperms all produce flavodiirons (Flvs), a class of proteins not represented in the angiosperms; these proteins act to mitigate the photoinhibition of photosystem I. Here, genes specifying two cyanobacterial Flvs have been expressed in the chloroplasts of Arabidopsis thaliana in an attempt to improve the robustness of Photosystem I (PSI). The expression of Flv1 and Flv3 together shown to enhance the efficiency of the utilization of light and to boost the plants capacity to accumulate biomass. Based on an assessment of the chlorophyll fluorescence in the transgenic plants, the implication was that photosynthetic activity (including electron transport flow and non-photochemical quenching during a dark-to-light transition) was initiated earlier in the transgenic than in wild type plants. The improved photosynthetic performance of the transgenics was accompanied by an increased production of ATP, an acceleration of carbohydrate metabolism and a more pronounced partitioning of sucrose into starch. The indications are that Flvs are able to establish an efficient electron sink downstream of PSI, thereby ensuring that the photosynthetic electron transport chain remains in a more oxidized state. The expression of Flvs in a plant acts to both protect photosynthesis and to control the ATP/NADPH ratio; together, their presence is beneficial for the plants growth potential.

biochemistry↗

bioRxiv2019

Leaf Variegation and Impaired Chloroplast Development Caused by a Truncated CCT Domain gene in albostrians Barley

Chloroplasts fuel plant development and growth by converting solar into chemical energy. They mature from proplastids through the concerted action of genes in both the organellar and the nuclear genome. Defects in such genes impair chloroplast development and may lead to pigment-deficient seedlings or seedlings with variegated leaves. Such mutants are instrumental as tools for dissecting genetic factors underlying the mechanisms involved in chloroplast biogenesis. Characterization of the green-white variegated albostrians mutant of barley has greatly broadened the field of chloroplast biology including the discovery of retrograde signaling. Here, we report the identification of the ALBOSTRIANS gene HvAST by positional cloning as well as its functional validation based on independently induced mutants by TILLING and RNA-guided Cas9 endonuclease mediated gene editing. The phenotypes of the independent HvAST mutants imply residual activity of HvAST in the original albostrians allele conferring an imperfect penetrance of the variegated phenotype even at homozygous state of the mutation. HvAST is a homolog of the Arabidopsis thaliana CCT Motif transcription factor gene AtCIA2, which was reported to be involved in the expression of nuclear genes essential for chloroplast biogenesis. Interestingly, in barley we localized HvAST to the chloroplast indicating novel without any clear evidence of nuclear localization. One-sentence summaryLeaf variegation in the barley mutant albostrians is caused by mutation of a single CCT-domain containing gene with residual activity, which is directed to the chloroplast.

genetics↗

bioRxiv2017

The partial duplication of an E3-ligase gene in Triticeaespecies mediates resistance to powdery mildew fungi

In plant-pathogen interactions, components of the plant ubiquitination machinery are preferred targets of pathogen-encoded effectors suppressing defense responses or co-opting host cellular functions for accommodation. Here, we employed transient and stable gene silencing-and over-expression systems in Hordeum vulgare (barley) to study the function of HvARM1 (for H. vulgare Armadillo 1), a partial gene duplicate of the U-box/armadillo-repeat E3 ligase HvPUB15 (for H. vulgare Plant U-Box 15). The partial ARM1 gene was derived from an ancient gene-duplication event in a common ancestor of the Triticeae tribe of grasses comprising the major crop species H. vulgare, Triticum aestivum and Secale cereale. The barley gene HvARM1 contributed to quantitative host as well as nonhost resistance to the biotrophic powdery mildew fungus Blumeria graminis, and allelic variants were found to be associated with powdery mildew-disease severity. Both HvPUB15 and HvARM1 proteins interacted in yeast and plant cells with the susceptibility-related, plastid-localized barley homologs of THF1 (for Thylakoid formation 1) and of ClpS1 (for Clp-protease adaptor S1) of Arabidopsis thaliana. The results suggest a neo-functionalization HvARM1 to increase resistance against powdery mildew and provide a link to plastid function in susceptibility to biotrophic pathogen attack.

plant biology↗

bioRxiv2017

Neural Networks for Efficient Bayesian Decoding of Natural Images from Retinal Neurons

Decoding sensory stimuli from neural signals can be used to reveal how we sense our physical environment, and is valuable for the design of brain-machine interfaces. However, existing linear techniques for neural decoding may not fully reveal or exploit the fidelity of the neural signal. Here we develop a new approximate Bayesian method for decoding natural images from the spiking activity of populations of retinal ganglion cells (RGCs). We sidestep known computational challenges with Bayesian inference by exploiting artificial neural networks developed for computer vision, enabling fast nonlinear decoding that incorporates natural scene statistics implicitly. We use a decoder architecture that first linearly reconstructs an image from RGC spikes, then applies a convolutional autoencoder to enhance the image. The resulting decoder, trained on natural images and simulated neural responses, significantly outperforms linear decoding, as well as simple point-wise nonlinear decoding. These results provide a tool for the assessment and optimization of retinal prosthesis technologies, and reveal that the retina may provide a more accurate representation of the visual scene than previously appreciated.

neuroscience↗