The liverwort Marchantia polymorpha is a widely used model organism for studying land-plant biology, and it has also proven to be a promising testbed for bioengineering. CRISPR/Cas9 technology has become a transformative tool for precise genome modifications in M. polymorpha; however, a robust method for the simultaneous expression of multiple gRNAs, which is crucial for enhancing the versatility of CRISPR/Cas9-based genome editing, has yet to be fully developed. In this study, we introduce an adaptation from the OpenPlant kit CRISPR/Cas9 tools that facilitates expression of multiple gRNAs from a single transcript through incorporation of tRNA sequences. The ability to deliver multiple gRNAs simultaneously significantly improves the capacity and scalability of genome editing in M. polymorpha. Additionally, by combining this vector system with a simplified and optimized protocol for thallus transformation, we further streamline the generation of CRISPR/Cas9 mutants in M. polymorpha. The resulting gene-editing system offers a multipurpose, time-saving, and straightforward tool for advancing functional genomics in M. polymorpha, enabling more comprehensive genetic modifications and genome engineering.

Plant synthetic biology is a highly innovative field that aims to better understand, redesign, and reprogram plants. Progress in recent years has been driven by technical developments such as modular cloning, gene circuits, genome editing, and synthetic genomics, which have expanded the field beyond traditional single-gene strategies. However, most efforts remain focused on angiosperms, leaving much of plant diversity underexplored and limiting potential applications due to the inherent complexity of these systems. Simpler, underutilized plant systems, particularly bryophytes, provide an alternative experimental platform for rapid tool development and, more broadly, for the establishment of universal as well as synergistic bioengineering approaches across different plant lineages. This review highlights recent advances that underscore the importance of bryophytes as plant synthetic biology systems. Progress across mosses, hornworts, and liverworts is discussed, with particular emphasis on Marchantia polymorpha as a leading model.

ABSTRACT Recombinant proteins have transformative potential in biomedicine, but their production is often costly and carries contamination risks. Plants offer an attractive alternative, with low growth costs and reduced pathogen risk, yet their slow growth cycles limit their use for rapid protein engineering. Here, we establish Marchantia polymorpha , a genetically tractable liverwort with a short life cycle, as a new platform for recombinant protein production. Using stable Agrobacterium-mediated transformation, we expressed an anti-mCherry nanobody fused to the fluorescent protein mTurquoise2 with different purification tags. Expression levels reached up to ∼120 µg/g fresh weight, and nanobody functionality was validated through a microscopy-based bead-binding assay. This yield rivals that of established systems such as Nicotiana benthamiana . Our results position M. polymorpha as a scalable, safe, and efficient chassis for protein engineering, with broad potential for applications in synthetic biology. This work opens the door to exploiting liverwort biotechnology for fast, cost-effective, and biosafe production of valuable recombinant proteins. Graphical Table of Contents

Abstract Marchantia polymorpha oil bodies (OBs) are specialized cell structures housing a diverse array of C15-terpenes, called sesquiterpenes. These compounds act as herbivore repellents, yet the enzymes responsible for the biosynthesis of their precursors remain poorly characterized. We investigated the localization of isoprenoid biosynthetic enzymes using translational and transcriptional reporters, coupled with confocal microscopy. Most enzymes localized as predicted (e.g., cytosol, plastid and the endoplasmic reticulum), and OB cells were identified as the primary sites of sesquiterpene biosynthesis. To explore OBs as potential storage sites for terpenes, we attempted to produce exogenous but easily identifiable compounds in Marchantia, such as the diterpene taxadiene and the triterpene β-amyrin. Targeting to OB cells resulted in measurable amounts of these compounds, but their yields remained unaffected by the overexpression of key precursor genes, underscoring challenges in redirecting metabolic flux. To further investigate terpene accumulation in OBs, we focused on MpABCG1, an ABC transporter previously reported to localize at the OB membrane. While MpABCG1 overexpression mildly increased endogenous sesquiterpene levels, its disruption via CRISPR dramatically reduced sesquiterpene accumulation. These findings establish that MpABCG1 is necessary for sesquiterpene accumulation in OBs and add to current knowledge of terpene synthesis compartmentalisation in Marchantia polymorpha.

ABSTRACTMarchantia polymorphaoil bodies (OBs) are specialised cell structures housing a diverse array of C15-terpenes, called sesquiterpenes. These compounds are known for their roles as herbivore repellents, yet the enzymes responsible for the biosynthesis of their precursors (C5 isoprenoid units) remain poorly characterized. Discrepancies remain between enzyme localizations suggested by computational predictions and those observed in earlier experimental studies, complicating our understanding of terpene biosynthesis. We investigated the localization of isoprenoid biosynthetic enzymes using translational and transcriptional reporters, coupled with confocal microscopy. Most enzymes localized as predicted (e.g., cytosol, chloroplast and the endoplasmic reticulum), and OB cells were identified as the primary sites of terpene biosynthesis.To explore OBs as potential storage sites for terpenes, we attempted to produce exogenous but easily identifiable compounds inMarchantia, such as the diterpene taxadiene and the triterpene β-amyrin. Targeting to OB cells resulted in measurable amounts of these compounds, but their yields remained unaffected by the over-expression of key precursor genes, underscoring challenges in redirecting metabolic flux.To further investigate terpene accumulation in OBs, we focused on ABCG1, an ABC transporter previously reported to localize at the OB membrane. Overexpression of ABCG1 in OB cells, alongside an exogenous sesquiterpene synthase, only increased the levels of endogenous sesquiterpenes, while CRISPR-mediated disruption of ABCG1 resulted in a dramatic reduction in sesquiterpene accumulation. These findings establish ABCG1 as a critical factor for sesquiterpene retention within OBs and provide new insights into the mechanisms governing terpene metabolism and storage inMarchantia polymorpha.

High-throughput experiments in plants are hindered by long generation times and high costs. To address these challenges, we present an optimized pipeline for Agrobacterium tumefaciens transformation and a simplified a protocol to obtain stable transgenic lines of the model liverwort Marchantia polymorpha, paving the way for efficient high-throughput experiments for plant synthetic biology and other applications. Our protocol involves a freeze-thaw Agrobacterium transformation method in six-well plates that can be adapted to robotic automation. Using the Opentrons open-source platform, we implemented a semi-automated protocol showing similar efficiency compared to manual manipulation. Additionally, we have streamlined and simplified the process of stable transformation and selection of M. polymorpha, reducing cost, time, and manual labor without compromising transformation efficiency. The addition of sucrose in the selection media significantly enhances the production of gemmae, accelerating the generation of isogenic plants. We believe these protocols have the potential to facilitate high-throughput screenings in diverse plant species and represent a significant step towards the full automation of plant transformation pipelines. This approach allows testing ~100 constructs per month, using conventional plant tissue culture facilities. We recently demonstrated the successful implementation of this protocol for screening hundreds of fluorescent reporters in Marchantia gemmae.

Marchantia polymorpha oil bodies (OBs) are specialised cell structures housing a diverse array of C15-terpenes, called sesquiterpenes. These compounds are known for their roles as herbivore repellents, yet the enzymes responsible for the biosynthesis of their precursors (C5 isoprenoid units) remain poorly characterized. Discrepancies remain between enzyme localizations suggested by computational predictors and those observed in earlier experimental studies, complicating our understanding of terpene biosynthesis. We investigated the localization of isoprenoid biosynthetic enzymes using translational and transcriptional reporters, coupled with confocal microscopy. Most enzymes localized as predicted (e.g., cytosol, chloroplast and the endoplasmic reticulum), and OB cells were identified as the primary sites of terpene biosynthesis. To explore OBs as potential storage sites for terpenes, we attempted to produce exogenous but easily identifiable compounds in Marchantia, such as the diterpene taxadiene and the triterpene β-amyrin. Targeting to OB cells resulted in measurable amounts of these compounds, but their yields remained unaffected by the over-expression of key precursor genes, underscoring challenges in redirecting metabolic flux. We hypothesized that precursor flux in Marchantia primarily supports the synthesis of endogenous sesquiterpenes, which are then transported into the OB lumen. To investigate this process, we focused on ABCG1, an ABC transporter previously reported to localize at the OB membrane. CRISPR-mediated disruption of ABCG1 resulted in a dramatic reduction in sesquiterpene levels, supporting its role in metabolite accumulation within OBs. Interestingly, a translational reporter of FTPSL2, a known endogenous sesquiterpene synthase in Marchantia, localized within the OB lumen, suggesting that ABCG1 may instead transport the sesquiterpene precursor farnesyl pyrophosphate (FPP). These findings identified the first potential FPP transporter, an important advancement in our understanding of terpene biosynthesis and storage in Marchantia polymorpha. ### Competing Interest Statement The authors have declared no competing interest.

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward 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 putative TF genes, Marchantia (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 reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and 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 these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.

Marchantia polymorpha has become an important model system for comparative studies and synthetic biology. The systematic characterization of genetic elements would make heterologous gene expression more predictable in this test bed for gene circuit assembly and bioproduction. Yet, the toolbox of genetic parts for Marchantia includes only a few constitutive promoters that need benchmarking to assess their utility. We compared the expression patterns of previously characterized and new constitutive promoters. We found that driving expression with the double enhancer version of the cauliflower mosaic virus 35S promoter (pro35S x 2) provided the highest yield of proteins, although it also inhibits the growth of transformants. In contrast, promoters derived from the Marchantia genes for ETHYLENE RESPONSE FACTOR 1 and the CLASS II HOMEODOMAIN-LEUCINE ZIPPER protein drove expression to higher levels across all tissues without a growth penalty and can provide intermediate levels of gene expression. In addition, we showed that the cytosol is the best subcellular compartment to target heterologous proteins for higher levels of expression without a significant growth burden. To demonstrate the potential of these promoters in Marchantia, we expressed RUBY, a polycistronic betalain synthesis cassette linked by P2A sequences, to demonstrate coordinated expression of metabolic enzymes. A heat-shock-inducible promoter was used to further mitigate growth burdens associated with high amounts of betalain accumulation. We have expanded the existing tool kit for gene expression in Marchantia and provided new resources for the Marchantia research community.

Chloroplasts develop from undifferentiated plastids in response to light. In angiosperms, after the perception of light, the Elongated Hypocotyl 5 (HY5) transcription factor initiates photomorphogenesis, and two families of transcription factors known as GOLDEN2-LIKE (GLK) and GATA are considered master regulators of chloroplast development. In addition, the MIR171-targeted SCARECROW-LIKE GRAS transcription factors also impact chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Using the model liverwort Marchantia polymorpha, we show that GLK controls chloroplast biogenesis, and HY5 shows a small conditional effect on chlorophyll content. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed that MpGLK has a broader set of targets than has been reported in angiosperms. We also identified a functional GLK homolog in green algae. In summary, our data support the hypothesis that GLK carries out a conserved role relating to chloroplast biogenesis in land plants and green algae.

Chloroplast biogenesis is dependent on master regulators from the GOLDEN2-LIKE (GLK) family of transcription factors. However, glk mutants contain residual chlorophyll, indicating that other proteins must be involved. Here, we identify MYB-related transcription factors as regulators of chloroplast biogenesis in the liverwort Marchantia polymorpha and angiosperm Arabidopsis thaliana. In both species, double-mutant alleles in MYB-related genes show very limited chloroplast development, and photosynthesis gene expression is perturbed to a greater extent than in GLK mutants. Genes encoding enzymes of chlorophyll biosynthesis are controlled by MYB-related and GLK proteins, whereas those allowing CO2 fixation, photorespiration, and photosystem assembly and repair require MYB-related proteins. Regulation between the MYB-related and GLK transcription factors appears more extensive in A. thaliana than in M. polymorpha. Thus, MYB-related and GLK genes have overlapping as well as distinct targets. We conclude that MYB-related and GLK transcription factors orchestrate chloroplast development in land plants.

Land plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, with Anthoceros agrestis being developed as a hornwort model system. Availability of a high-quality genome assembly and a recently developed genetic transformation technique makes A. agrestis an attractive model species for hornworts. Here we describe an updated and optimized transformation protocol for A. agrestis, which can be successfully used to genetically modify one more strain of A. agrestis and three more hornwort species, Anthoceros punctatus, Leiosporoceros dussii, and Phaeoceros carolinianus. The new transformation method is less laborious, faster, and results in the generation of greatly increased numbers of transformants compared with the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localization signal peptides for hornworts providing new tools to better understand the hornwort cell biology.

Chloroplast biogenesis is dependent on master regulators from the GOLDEN2-LIKE (GLK) family of transcription factors, but glk mutants contain residual chlorophyll and therefore other proteins must also be involved. Here we identify MYB-related transcription factors as regulators of chloroplast biogenesis in the liverwort Marchantia polymorpha and angiosperm Arabidopsis thaliana . In both species, double mutant alleles in MYB-Related genes show very limited chloroplast development, and photosynthesis gene expression is perturbed to a greater extent than in mutants of GLK. In M. polymorpha MYB-related genes act upstream of GLK, while in A. thaliana this relationship has been rewired. In both species, genes encoding enzymes of chlorophyll biosynthesis are controlled by MYB-related and GLK proteins whilst those allowing CO2 fixation, photorespiration and photosystem assembly and repair require the MYB-related proteins. Thus, MYB-related and GLK genes have overlapping as well as distinct targets. We conclude that together MYB-related and GLK transcription factors orchestrate chloroplast development in land plants.### Competing Interest StatementThe authors have declared no competing interest.

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Photosynthesis in eukaryotic cells takes place in chloroplasts that develop from undifferentiated plastids in response to light. In angiosperms, after perception of light de-repression allows Elongated Hypocotyl 5 (HY5) transcription factor to initiate photomorphogenesis, and two families of transcription factors known as Golden2-like (GLK) and GATA are considered master regulators of chloroplast development. The MIR171-targeted SCARECROW-LIKE (SCL) GRAS transcription factors also impact on chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Here we report in the model liverwort Marchantia polymorpha that GLK controls chloroplast biogenesis and HY5 shows a small conditional effect on chlorophyll content. In contrast, GATA and SCL have no detectable roles in this fundamental process. ChIP-SEQ and RNA-SEQ revealed that MpGLK regulates many photosynthetic and chloroplast development-related genes, but also has a broader set of targets than previously reported in angiosperms. This implies GLK carries out a conserved role relating to chloroplast biogenesis in land plants but also supports extensive divergence between its targets in M. polymorpha and flowering plants. The data support the hypothesis that regulation of chloroplast biogenesis in M. polymorpha is streamlined compared with angiosperms and allows us to present a core regulatory network for chloroplast biogenesis in land plants.### Competing Interest StatementThe authors have declared no competing interest.

AbstractChloroplast biogenesis is dependent on master regulators from the GOLDEN2-LIKE (GLK) family of transcription factors, butglkmutants contain residual chlorophyll and therefore other proteins must also be involved. Here we identify MYB-related transcription factors as regulators of chloroplast biogenesis in the liverwortMarchantia polymorphaand angiospermArabidopsis thaliana. In both species, double mutant alleles in MYB-Related genes show very limited chloroplast development, and photosynthesis gene expression is perturbed to a greater extent than in mutants of GLK. InM. polymorphaMYB-related genes act upstream of GLK, while inA. thalianathis relationship has been rewired. In both species, genes encoding enzymes of chlorophyll biosynthesis are controlled by MYB-related and GLK proteins whilst those allowing CO2fixation, photorespiration and photosystem assembly and repair require the MYB-related proteins. Thus,MYB-relatedand GLK genes have overlapping as well as distinct targets. We conclude that together MYB-related and GLK transcription factors orchestrate chloroplast development in land plants.

Protocols are described for the induction of strong, consistent serum and mucosal antibody responses to Vibrio cholerae O1 or O139 lipopolysaccharide (LPS) following intranasal or oral immunization of adult mice with viable or formalin-killed bacteria. A simplified two-dose schedule for intranasal immunization has been identified, whereby viable bacteria elicit strong serum responses and, most importantly, also induce significant, sustained intestinal IgA responses. Using higher doses of bacteria it was also possible to generate consistently high intestinal and serum anti-LPS responses by the oral route. The efficacy of these immunization schedules was not dependent on co-administration of adjuvant. Gut responses were estimated using two sampling techniques involving the collection of fresh faecal pellets or the preparation of intestinal tissue extracts. The significant correlation between these estimates validates the more convenient approach of measuring intestinal responses using faecal pellet extracts, which allows repeated sampling from the same animals. V. cholerae O1 and O139 were similarly immunogenic by either mucosal route. More intensive immunization schedules for administration of formalin-killed bacteria have also been defined. Using these regimes it was possible to generate serum and gut antibody responses comparable to those elicited by viable V. cholerae. The established immunization protocols will allow evaluation of the systemic and mucosal immunogenicity of new vaccine formulations.

AbstractLand plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, withAnthoceros agrestisbeing developed as a hornwort model system. Availability of a high quality genome assembly and a recently developed genetic transformation technique makesA. agrestisan attractive model species for hornworts. Here we describe an updated and optimised transformation protocol forA. agrestiswhich can be successfully used to genetically modify one more strain ofA. agrestisand three more hornwort species,Anthoceros punctatus, Leiosporoceros dussiandPhaeoceros carolinianus.The new transformation method is less laborious, faster and results in the generation of greatly increased numbers of transformants compared to the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localisation signal peptides for hornworts providing new tools to better understand hornwort cell biology.

The first plastid evolved from an endosymbiotic cyanobacterium in the common ancestor of the Archaeplastida. The transformative steps from cyanobacterium to organelle included the transfer of control over developmental processes, a necessity for the host to orchestrate, for example, the fission of the organelle. The plastids of almost all embryophytes divide independently from nuclear division, leading to cells housing multiple plastids. Hornworts, however, are monoplastidic (or near-monoplastidic), and their photosynthetic organelles are a curious exception among embryophytes for reasons such as the occasional presence of pyrenoids. In this study, we screened genomic and transcriptomic data of eleven hornworts for components of plastid developmental pathways. We found intriguing differences among hornworts and specifically highlight that pathway components involved in regulating plastid development and biogenesis were differentially lost in this group of bryophytes. Our results also confirmed that hornworts underwent significant instances of gene loss, underpinning that the gene content of this group is significantly lower than other bryophytes and tracheophytes. In combination with ancestral state reconstruction, our data suggest that hornworts have reverted back to a monoplastidic phenotype due to the combined loss of two plastid division-associated genes, namely, ARC3 and FtsZ2.

A detailed protocol for the protoplast transformation of hornwort tissue is not yet available, limiting molecular biological investigations of these plants and comparative analyses with other bryophytes, which display a gametophyte-dominant life cycle and are critical to understanding the evolution of key land plant traits. We describe a detailed protocol to isolate and transiently transform protoplasts of the model hornwort Anthoceros agrestis . The digestion of liquid cultures with Driselase yields a high number of viable protoplasts suitable for polyethylene glycol (PEG)-mediated transformation. We also report early signs of protoplast regeneration, such as chloroplast division and cell wall reconstitution. This protocol represents a straightforward method for isolating and transforming A. agrestis protoplasts that is less laborious than previously described approaches. In combination with the recently developed stable genome transformation technique, this work further expands the prospects of functional studies in this model hornwort.