Biology subjects

Hake, S.

Publications and source records attributed to Hake, S..

7 recordsLinked to original sources

bioRxiv2023

Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants

A major challenge in plant biology is to understand how the plant hormone auxin regulates diverse transcriptional responses throughout development, in different environments, and in different species. The answer may lie in the specific complement of auxin signaling components in each cell. The balance between activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) is particularly important. It is unclear how this balance is achieved. Through comparative analysis of novel, dominant mutants in maize and the moss Physcomitrium patens, we have discovered a [~]500-million-year-old mechanism of class-B ARF protein level regulation, important in determining cell fate decisions across land plants. Thus, our results add a key piece to the puzzle of how auxin regulates plant development.

plant biology↗

bioRxiv2023

Regulatory variation controlling architectural pleiotropy in maize

An early event in plant organogenesis is establishment of a boundary between the meristem and differentiating lateral organ. In maize (Zea mays), evidence suggests a common gene network functions at boundaries of distinct organs and contributes to pleiotropy between leaf angle and tassel branch number, two agronomic traits. To uncover regulatory variation at the nexus of these two traits, we used regulatory network topologies derived from specific developmental contexts to guide multivariate genome-wide association analyses. In addition to defining network plasticity around core pleiotropic loci, we identified new transcription factors that contribute to phenotypic variation in canopy architecture, and structural variation that contributes to cis-regulatory control of pleiotropy between tassel branching and leaf angle across maize diversity. Results demonstrate the power of informing statistical genetics with context-specific developmental networks to pinpoint pleiotropic loci and their cis-regulatory components, which can be used to fine-tune plant architecture for crop improvement.

plant biology↗

bioRxiv2022

Liguleless narrow and narrow odd dwarf act in overlapping pathways to regulate maize development & physiology

narrow odd dwarf (nod) and Liguleless narrow (Lgn) are pleiotropic maize mutants that both encode plasma membrane proteins, cause similar developmental patterning defects, and constitutively induce stress signaling pathways. To investigate how these mutants coordinate maize development and physiology, we screened for protein interactors of NOD by affinity purification. LGN was identified by this screen as a strong candidate interactor, and we confirmed the NOD-LGN molecular interaction through orthogonal experiments. We further demonstrated that LGN, a receptor-like kinase, can phosphorylate NOD in vitro, hinting that they could act in intersecting signal transduction pathways. To test this hypothesis, we generated Lgn-R;nod mutants in two backgrounds (B73 and A619) and found that these mutations enhance each other, causing more severe developmental defects than either single mutation on its own, with phenotypes including very narrow leaves, increased tillering, and failure of the main shoot. Transcriptomic and metabolomic analyses of the single and double mutants in the two genetic backgrounds revealed widespread induction of pathogen defense genes and a shift in resource allocation away from primary metabolism in favor of specialized metabolism. These effects were similar in each single mutant and heightened in the double mutant, leading us to conclude that NOD and LGN act cumulatively in overlapping signaling pathways to coordinate growth-defense tradeoffs in maize.

plant biology↗

bioRxiv2020

Degradation of mixed-linkage (1,3;1,4)-β-D-glucan in maize is mediated by the CAL1 licheninase

The presence of mixed-linkage (1,3;1,4)-{beta}-D-glucan (MLG) in plant cell walls is a key feature of grass species such as cereals - the main source of calorie intake for humans and cattle. Accumulation of this polysaccharide involves the coordinated regulation of biosynthetic and metabolic machineries. While several components of the MLG biosynthesis machinery have been identified in diverse plant species, degradation of MLG is poorly understood. A large-scale forward genetic maize screen for mutants with altered cell wall polysaccharide structural properties resulted in the identification of candy-leaf1 (cal1). Cell walls of CAL1-deficient plants contain higher amounts of MLG in several tissues, including adult leaves and senesced organs, where only trace amounts of MLG are usually detected. In addition, cal1 plants exhibit increased saccharification yields upon enzymatic digestion. Stacking cal1 with lignin-deficient mutations results in synergistic saccharification increases. Identification of the causative mutation revealed that CAL1 encodes a GH17 licheninase. Maize plants overexpressing CAL1 exhibit a 90% reduction in MLG content, indicating that CAL1 is not only required, but its expression sufficient to degrade MLG. CAL1 specifically hydrolyzes (1,3;1,4)-{beta}-D-Glucans in vitro, and the single CAL1E262K amino acid substitution is able to block all detectable activity. Time profiling experiments indicate that wall MLG content is modulated during day/night cycles inversely correlating with CAL1 transcript accumulation. This cycling is absent in the cal1 mutant, suggesting that the mechanism involved requires MLG degradation that may in turn regulate CAL1 gene expression. One sentence summary Mixed-linkage glucan is degraded by the CAL1 licheninase in maize

plant biology↗

bioRxiv2020

The Hoja loca1 Mutant and AUX/1 IAA Function in Maize

Plant architecture is determined by the iterative building of phytomer units, each containing a portion of stem, an organ and an axillary meristem. Each phytomer can follow different developmental paths underpinning the complexity, and plasticity, of plant form. Auxin plays a central role in the coordination of phytomer development, regulating organ initiation and patterning across all axes. This diversity in auxin function results from changes in the activities and expression of auxin signaling components, including the AUX/IAA repressors. Higher land plants have multigene AUX/IAA families, which leads to functional redundancy. Dominant mutations, which prevent AUX/IAA degradation in response to auxin, have highlighted the importance of these proteins in fine-tuning organ development. Here we report a new dominant AUX/IAA mutant in maize, Hoja loca1 (Oja). Oja has a mutation in the degron motif of ZmIAA28 and specifically affects aerial organ initiation and leaf medio-lateral patterning, but phytomer initiation remains unchanged. Mutant phenotypes are variable and transcriptional profiling of individual meristems identified clusters of genes that may underpin the phenotypic differences. The unique phenotype of Oja provides evidence of species-specific sub-functionalization of the AUX/IAAs, and illustrates the crucial role of auxin signaling in the tight coordination of phytomer unit development.

plant biology↗

bioRxiv2019

Phosphorylation of the ancestral histone variant H3.3 amplifies stimulation-induced transcription

Complex organisms are able to rapidly induce select genes among thousands in response to diverse environmental cues. This occurs in the context of large genomes condensed with histone proteins into chromatin. The macrophage response to pathogen sensing, for example, rapidly engages highly conserved signaling pathways and transcription factors (TFs) for coordination of inflammatory gene induction1-3. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a feature of inflammatory genes and, in general, dynamically regulated chromatin and transcription4-7. However, little is known of how chromatin is regulated at rapidly induced genes and what features of H3.3, conserved from yeast to human, might enable rapid and high-level transcription. The amino-terminus of H3.3 contains a unique serine residue as compared with alanine residues found in \"canonical\" H3.1/2. We find that this H3.3-specific serine residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along the gene bodies of rapidly induced response genes in mouse macrophages responding to pathogen sensing. Further, this selective mark of stimulation-responsive genes directly engages histone methyltransferase (HMT) SETD2, a component of the active transcription machinery. Our structure-function studies reveal that a conserved positively charged cleft in SETD2 contacts H3.3S31ph and specifies preferential methylation of H3.3S31ph nucleosomes. We propose that features of H3.3 at stimulation induced genes, including H3.3S31ph, afford preferential access to the transcription apparatus. Our results provide insight into the function of ancestral histone variant H3.3 and the dedicated epigenetic mechanisms that enable rapid gene induction, with implications for understanding and treating inflammation.

biochemistry↗

bioRxiv2019

Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development

Assembling meaningful comparisons between species is a major limitation in studying the evolution of organismal form. To understand development in maize and sorghum, closely-related species with architecturally distinct inflorescences, we collected RNAseq profiles encompassing inflorescence body plan specification in both species. We reconstructed molecular ontogenies from 40 B73 maize tassels and 47 BTx623 sorghum panicles and separated them into transcriptional stages. To discover new markers of inflorescence development, we used random forest machine learning to determine stage by RNAseq. We used two descriptions of transcriptional conservation to identify hourglass-like developmental stages. Despite short evolutionary ancestry of 12 million years, we found maize and sorghum inflorescences are most different during their hourglass-like stages of development, following an inverse-hourglass model of development. We discuss if agricultural selection may account for the rapid divergence signatures in these species and the observed separation of evolutionary pressure and developmental reprogramming.\n\nHighlightsO_LITranscript dynamics identify maize tassel and sorghum panicle developmental stages\nC_LIO_LIRandom forest predicts developmental age by gene expression, providing molecular markers and an in silico staging application\nC_LIO_LIMaize and sorghum inflorescences are most similar when committing stem cells to a determinant fate\nC_LIO_LIExpression conservation identifies hourglass-like stage, but transcriptomes diverge, similar to inverse hourglass observations in cross-phyla animal embryo comparisons\nC_LI

plant biology↗