Biology subjects

Bowman, J. L.

Publications and source records attributed to Bowman, J. L..

11 recordsLinked to original sources

bioRxiv2025

Modulation of the GT Family 47 clade B gene affects arabinan deposition in elaters of Marchantia polymorpha

The plant cell wall polymer -1,5-linked arabinan is associated with important functions in plant physiology, such as cell wall flexibility and desiccation tolerance in angiosperms. However, its biosynthetic mechanism remains obscure. A putative arabinan arabinosyltransferase (AraT) is the Arabidopsis ARABINAN-DEFICIENT1 in GT family 47 clade B (GT47B), but its role is inferred by its mutant cell wall phenotypes, and not through in vitro assays. With seven other genes in the clade, investigating the function of the members in GT47B is hampered by the high genetic redundancy in Arabidopsis. Instead, we probe the function of the only two genes in GT47B in the liverwort model organism Marchantia polymorpha, named MpARAD-Like 1 (MpARADL1) and MpARADL2. Mparadl1 and Mparadl2 loss-of-function mutants and overexpression lines were generated, and their cell wall composition was probed using Comprehensive Microarray Polymer Profiling (CoMPP), glycosyl linkage analysis and immunolabelling. Interestingly, Mparadl2 mutants have much less of the 1,5--L-arabinan epitope in elaters since LM6 antibody recognition showed a notable reduction. However, 5-linked Araf levels in the Marchantia thallus tested with glycosyl linkage analysis are comparable between mutants and wild type, suggesting that there is another enzyme forming 5-Araf linkages in Marchantia. Our attempts to obtain the biochemical activity of these enzymes through the expression and purification of AtARAD1, MpARADL1 and MpARADL2 proteins in the HEK293 cell heterologous expression system were unsuccessful. Therefore, we suspect that an evolutionarily conserved, and clade-specific mechanism is required to confer solubility for purification and subsequent activity characterisation of GT47B proteins. Previous studies have shown that co-expression of protein interaction partners can enhance protein solubility in the HEK293 cell system, but co-expression of MpARADL2 with AtARAD1 and MpARADL1 did not yield soluble proteins, prompting further investigation into the protein-protein interactors of GT47B proteins.

plant biology↗

bioRxiv2025

The Building Blocks of Early Land Plants: Glycosyltransferases and Cell Wall Architecture in the model liverwort Marchantia polymorpha

The liverwort Marchantia polymorpha has emerged as an important plant model for developmental studies and may become central to elucidate the complex process of cell wall polysaccharide biosynthesis. This study comprehensively analyses the composition and structure of cell wall glycans across eight different M. polymorpha tissue types. We show that while the cell walls largely mirror known land plant cell wall composition, they also exhibit some unique characteristics. For example, -(1,5)-arabinan was prominently present in the sporophyte tissue, which may indicate a specialised role in this life stage. Furthermore, M. polymorpha cell walls displayed a remarkably low overall pectin content, yet the abundance of pectic arabinan in sporophytes hint at its putative role in the evolution and complexity of spermatophyte cell walls. Through comparative analyses of glycosyltransferase (GT) families across plant species, we found that M. polymorpha has a diversified GT repertoire compared for example, to the model plant Arabidopsis thaliana, indicating uniqueness in its cell wall biosynthesis pathways. To support research underpinning cell wall biosynthesis, we developed a Gateway compatible compendium of 93 M. polymorpha GTs, providing a valuable resource for genetic and functional studies. Our study thus works as a foundation to drive new insights into cell wall evolution, structure and function across the plant kingdom.

plant biology↗

bioRxiv2025

MarpolBase: Genome database for Marchantia polymorpha featuring high quality reference genome sequences

The liverwort Marchantia polymorpha is a key model organism for understanding land plant evolution, development, and gene regulation. To support the growing demand for high-quality genomic resources, we present MarpolBase, a comprehensive and integrated genome database that hosts newly assembled, high-accuracy reference genomes for both the male Tak-1 and female Tak-2 accessions, designated as ver. 7.1 reference genomes. These new assemblies, generated using PacBio HiFi long-read sequencing, represent nearly telomere-to-telomere chromosome-level genomes, with improvements in assembly continuity, annotation accuracy, and structural resolution--especially for repeat-rich regions and sex chromosomes. MarpolBase offers not only access to genome sequences and gene annotations but also provides a unified platform for data exploration, comparative analysis, and community-driven gene nomenclature. It includes keyword-searchable gene pages with structural and functional annotations, expression data integration, genome browser visualization, and online analytical and utility tools. By unifying genome assembly, annotation, nomenclature, and analysis tools in a single platform, MarpolBase serves as a central resource for functional genomics and evolutionary studies in M. polymorpha, and a model for future plant genome databases.

genomics↗

bioRxiv2024

The role of IAA and its transport in the complex streptophyte algae Chara braunii

The role of auxin indole-3-acetic acid (IAA), a phytohormone with numerous morphogenic functions, is now well-established in land plants. Although the role of IAA and its transport in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within Streptophytes. Among streptophyte algae, Chara represents a genus with a considerable degree of complexity in body arrangement. This study investigates the auxin response and characterizes homologs of land plant PIN auxin efflux carriers in Chara braunii. Through regeneration experiments, we observed that IAA significantly promotes elongation of thallus and side branch development upon thallus tip decapitation, indicating an effect on morphogenesis. We show that IAA is actively uptaken and metabolized by thallus cells and that this process is influenced by N-1-naphthylphthalamic acid (NPA). To elucidate the underlying mechanisms, we cloned and sequenced the most expressed Chara braunii PINs, CbPINa and CbPINc. Using epitope-specific antibodies, we showed their presence in the plasma membrane (PM) of vegetative internodal cells and generative antheridial cells. Functional tests in tobacco BY-2 cells, supported by in silico docking of IAA and NPA to CbPINa and CbPINc, showed that PM-localized CbPINa interferes with auxin transport in contrast to ER-localized CbPINc. Finally, our phosphoproteome analysis indicated that IAA rapidly induces specific phosphorylation events, including RAF-like kinase phosphorylation, highlighting a potential role for IAA in fast signaling processes in Chara braunii. Altogether, we provide new insights into IAA role in Chara braunii morphogenesis and suggest that while the canonical auxin transport mechanism may not be conserved, auxin still may likely play a role in rapid signaling pathways in this close relative of land plants.

plant biology↗

bioRxiv2023

Control of cell fate specification and patterning by an ancestral microRNA

The formation of an organized body requires the establishment and maintenance of cells with structural and functional distinctive characteristics. A central question in developmental biology is how changes in the regulation of genes drive cell specification and patterning1. microRNAs (miRNAs) are small non-coding RNAs that regulate development through mRNA cleavage and/or translational repression2. In plants, miRNAs regulate key aspects including growth, development, stem cell maintenance, vegetative phase change, leaf morphogenesis, floral organ formation and flowering time3. Biogenesis of plant miRNAs depends on the activity of DICER-LIKE 1 (DCL1), an RNase type III endonuclease that processes double stranded RNA to give rise to mature miRNAs 4. The genomes of todays flora contain at least one bona fide copy of DCL1 5,6. Using Marchantia polymorpha -a model bryophyte that allows comparative approaches to infer characteristics of the ancestral land plant-, we demonstrate that MpDCL1a is required for the biogenesis of miRNAs and uncovered a central role for miR166/Homeodomain Zipper Class III-regulated auxin synthesis in the specification of cell identity, patterning, meristem function, laminar expansion and the development of the body in the last common ancestor of extant land plants.

plant biology↗

bioRxiv2023

Mapping the landscape of transcription factor promoter activity during vegetative development in Marchantia

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterising the transcriptional activity of TF genes in space and time is a critical step towards understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot-apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only [~]450 TF genes, Marchantia polymorpha is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested in planta reporter fusions for all the TF promoters in the collection and systematically analysed expression patterns in Marchantia gemmae. This allowed us to build a map of precise expression domains and identify a unique set of TFs expressed in the stem-cell zone, providing new insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that the promoter elements characterised here will be useful for cell-type specific expression, synthetic biology applications, and functional genomics.

plant biology↗

bioRxiv2022

MarpolBase Expression: A Web-based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha

The liverwort Marchantia polymorpha is equipped with a wide range of molecular and genetic tools and resources that have led to its wide use to explore the evo-devo aspects of land plants. Although its diverse transcriptome data are rapidly accumulating, there is no extensive yet user-friendly tool to exploit such a compilation of data and to summarize results with the latest annotations. Here, we have developed a web-based suite of tools, MarpolBase Expression (MBEX, https://marchantia.info/mbex/), where users can visualize gene expression profiles, identify differentially expressed genes, perform co-expression and functional enrichment analyses, and summarize their comprehensive output in various portable formats. Using oil body biogenesis as an example, we demonstrated that the results generated by MBEX were consistent with the published experimental evidence and also revealed a novel transcriptional network in this process. MBEX should facilitate the exploration and discovery of the genetic and functional networks behind various biological processes in M. polymorpha, and promote our understanding of the evolution of land plants.

plant biology↗

bioRxiv2022

Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution.

We used single-molecule nanopore tweezers (SPRNT) to resolve the millisecond single-nucleotide steps of Superfamily 1 helicase PcrA as it translocates on, or unwinds, several kb-long DNA molecules. We recorded over 2 million enzyme steps under various assisting and opposing forces in diverse ATP and ADP conditions to comprehensively explore the mechanochemistry of PcrA motion. Forces applied in SPRNT mimic forces and physical barriers PcrA experiences in vivo, such as when the helicase encounters bound proteins or duplex DNA; we show how PcrAs kinetics change with such stimuli. SPRNT allows for direct association of the underlying DNA sequence with observed enzyme kinetics. Our data reveal that the underlying DNA sequence passing through the helicase strongly influences the kinetics during translocation and unwinding. Surprisingly, unwinding kinetics are not solely dominated by the base-pairs being unwound. Instead, the sequence of the single stranded DNA on which the PcrA walks determines much of the kinetics of unwinding.

biophysics↗

bioRxiv2020

Gamete-specific expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha

Eukaryotic life cycles alternate between haploid and diploid phases and in phylogenetically diverse unicellular eukaryotes, expression of paralogous homeodomain genes in the two gametes directs the haploid-to-diploid transition. In the unicellular Chlorophyte alga Chlamydomonas KNOX and BELL TALE-homeodomain genes mediate the transition. Here we demonstrate that in the liverwort Marchantia polymorpha paternal (sperm) expression three of the five phylogenetically diverse BELL genes, MpBELL234, and maternal (egg) expression of MpKNOX1 mediate the haploid-to-diploid transition. Loss-of-function alleles of either result in zygotic or early embryonic arrest. In land plants both the haploid gametophyte and diploid sporophyte are complex multicellular organisms. Expression of MpKNOX1 and two other paralogs, MpBELL1 and MpKNOX2, during sporophyte development is consistent with a later role in patterning the sporophyte. These results indicate that the ancestral mechanism to activate diploid gene expression was retained in early diverging land plants and subsequently co-opted during evolution of the diploid sporophyte body.

developmental biology↗

bioRxiv2020

Oil body formation in Marchantia polymorpha is controlled by MpC1HDZ and serves as a defense against arthropod herbivores

The origin of a terrestrial flora in the Ordovician required adaptation to novel biotic and abiotic stressors. Oil bodies, a synapomorphy of liverworts, accumulate secondary metabolites, but their function and development are poorly understood. Oil bodies of Marchantia polymorpha develop within specialized cells as one single large organelle. Here, we show that a CLASS I HOMEODOMAIN LEUCINE-ZIPPER (C1HDZ) transcription factor controls the differentiation of oil body cells in two different ecotypes of the liverwort M. polymorpha, a model genetic system for early divergent land plants. In flowering plants, these transcription factors primarily modulate responses to abiotic stresss including drought. However, loss-of-function alleles of the single ortholog gene, MpC1HDZ, in M. polymorpha did not exhibit phenotypes associated with abiotic stress. Rather Mpc1hdz mutant plants were more susceptible to herbivory and total plant extracts of the mutant exhibited reduced antibacterial activity. Transcriptomic analysis of the mutant revealed a reduction in expression of genes related to secondary metabolism that was accompanied by a specific depletion of oil body terpenoid compounds. Through time lapse imaging we observed that MpC1HDZ expression maxima precede oil body formation indicating that MpC1HDZ mediates differentiation of oil body cells. Our results indicate that M. polymorpha oil bodies, and MpC1HDZ, are critical for defense against herbivory but not for abiotic stress-tolerance. Thus, C1HDZ genes were co-opted to regulate separate responses to biotic and abiotic stressors in two distinct land plant lineages.

plant biology↗

bioRxiv2017

Marchantia liverworts as a proxy to plants basal microbiomes.

Microbiomes influence plant development, establishment, nutrient acquisition, pathogen defense, and the myriad of roles that ultimately impacts plant health. Plants microbiome are shaped through interactions between the microbes (ranging from cooperative functions to chemical warfare) and a selection process entailed by the host plants that distinguishes between pathogens, commensals, symbionts and transient bacteria. The soil is a primary source for microbes colonizing plants, along with other environmental sources including rain and interactions with other organisms. In this work, we explore the microbiomes through massive sequencing of the 16S rRNA gene in the eldest terrestrial plants: Marchantia liverworts. We compared microbiomes from M. polymorpha, and M. paleacea plants collected in the wild and their soils, all together luckily in the same geographical location (sympatric) thus reducing geographic effects; and also from plants grown in vitro and established from gemmae obtained from the same population of wild plants. Qualitative and quantitative microbiome analysis allowed us to identify microbes conserved in both native and in vitro Marchantia species. While M. polymorpha native plants microbiomes richness is reduced about M. paleacea, containing almost half of the Operative Taxonomic Units (OTUs) observed in M. paleacea, M. polymorpha grown in vitro exhibits larger OTUs. This diversity differences might be the result of impairment to recognize their microbial partners and being an open niche for opportunistic bacteria. The main OTUs in Marchantia microbiomes were assigned to the genera: Methylobacterium, Rhizobium, Paenibacillus, Lysobacter, Pirellula, Steroidobacter, and Bryobacter. The assigned genera correspond to bacteria capable of plant-growth promotion, complex exudates degradation, nitrogen fixation, methylotrophs, and disease-suppressive bacteria, all hosted in the relatively simple anatomy of the plant that provides refuge on their surfaces, rhizoids, and multiple gas chambers that work as specialized niches for different bacterial groups. Marchantia is a promising model to study not only long-term relationships between plants and their microbes but also the transgenerational impact of microbiomes because of Marchantia long 450 million years under climate change conditions testing microbiome configurations.

microbiology↗