Periodic Reporting for period 4 - PLANTSTEMS (Decoding the Lateral Expansion of Plant Stems)
Período documentado: 2020-03-01 hasta 2021-08-31
In contrast to animals, in which tissue proliferation in adult individuals is often pathological and deleterious, plants have evolved an indefinite growth habit. A remarkable but under-investigated example is the thickening of plant stems and roots: It is a purely postembryonic growth process and the group of stem cells responsible – the cambium – is derived from and embedded in fully differentiated tissues. This project leveraged the unique growth mode of plants and explored the process of radial stem growth in the reference plant Arabidopsis thaliana as a paradigm for postembryonic growth and tissue remodeling. During the action, central cambium domains were functionally mapped, central cell fate regulators were identified, the role of auxin in controlling wood formation was revealed and single cell transcriptomics in the context of the cambium was established. In addition, computational modelling of cellular dynamics targeting regulatory networks and mechanical aspects of radial plant growth was developed. Thereby, an integrated and comprehensive view on one of the most productive terrestrial growth processes with regard to biomass production and long-term sequestration of carbon dioxide was generated.
As an ultimate characterization of cambium organization and representing the foundation of a large body of future work, we discovered that, in a given cell file, a single bifacial stem cell generates both xylem and phloem cell lineages (Si et al., 2019, Development). These findings settled a long-standing debate about the nature of the stem cell population driving radial plant growth. By using pulse labelling and genetically encoded lineage tracing we found that bifacial stem cells are characterized by a specific combination of gene activity and a high division rate in comparison with tissue-specific progenitors. We further revealed that a proximal domain, represents a site of xylem formation and a distal cambium domain contains cells that are determined for phloem development. Thus, we clearly mapped functional domains of the cambium and developed genetic tools for visualizing and targeting these domains in a very specific manner.
Using these tools, we provided gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues including different cambium domains (Shi et al., 2021, Plant Cell; Neumann et al., 2022, Nature Commun). By combining fluorescence-activated nucleus sorting and Laser-capture microdissection with next generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibres, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrated that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling.
In addition to these achievements, we identified functional domains of auxin signalling in the Arabidopsis cambium by local short-term modulation of auxin biosynthesis and signalling. We revealed that, while cambial stem cells do not appear to be a site of elevated auxin signalling, auxin signalling in these cells is required for cambium activity (Brackmann et al., 2018, Nature Commun). By analyzing transcriptional reporters and mutants of vasculature-associated ARFs, we identified ARF3, ARF4 and ARF5/MP as cambium regulators with different tissue-specificities as well as distinct roles in cambium regulation. In particular, we identified ARF5/MP to cell-autonomously restrict the number of stem cells by directly attenuating the activity of the stem cell-promoting WOX4 gene. Our results revealed an influence of auxin signalling on distinct cambium features by specific signalling components and allow the conceptual integration of plant stem cell systems with distinct anatomies. In fact we concluded that auxin signalling in the cambium shares features with both the situation in the root apical meristem where auxin regulates cell divisions and the shoot apical meristem where auxin, and particular ARF5/MP, is strongly correlated with cell differentiation. Thereby, we enlighten a long-observed role of auxin signalling in radial plant growth and reveal that its function is partly specific in different stem cell niches.
As a central discovery in the context of the question toward mechanisms of cambium-derived tissue formation, we identified and characterized an essential role of SUPPRESSOR OF MAX2 1-LIKE (SMXL) proteins (Wallner et al., Curr Biol, 2017; Miyashima et al., 2019, Nature; Wallner et al., 2020, PlantPhys; Cho et al., 2018; Nature Plants; Wallner et al., 2021, bioRxiv). We demonstrated that, within the SMXL gene family, specifically SMXL3, SMXL4, and SMXL5-deficiency results in strong defects in phloem formation. At the beginning of our work, the three genes formed an non-characterized subclade of the SMXL gene family which mediates hormonal strigolactone and karrikin signalling. We found that SMXL3/4/5 proteins function differently to canonical strigolactone and karrikin signalling mediators, although being functionally interchangeable with those under low strigolactone/karrikin signalling conditions. We also found that the SMXL5 protein interacts physically with the PhD finger protein OBERON3 (OBE3) forming a functional unit during phloem formation. We provided evidence that SMXL5 and OBE3 proteins interact in planta and elucidated a functional interaction between OBE3 and SMXL3/4/5 genes during phloem development using genetic means. Therefore, just like SMXL3/4/5, OBE3 is an important component during phloem initiation and differentiation. By characterizing the SMXL3/4/5-OBE3 interaction we provided also insights into the molecular network of phloem formation in plants and propose that the SMXL3/4/5-OBE3-dependent establishment of a distinct chromatin profile is an essential step during phloem specification.
Using these tools, we provided gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues including different cambium domains (Shi et al., 2021, Plant Cell; Neumann et al., 2022, Nature Commun). By combining fluorescence-activated nucleus sorting and Laser-capture microdissection with next generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibres, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrated that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling.
In addition to these achievements, we identified functional domains of auxin signalling in the Arabidopsis cambium by local short-term modulation of auxin biosynthesis and signalling. We revealed that, while cambial stem cells do not appear to be a site of elevated auxin signalling, auxin signalling in these cells is required for cambium activity (Brackmann et al., 2018, Nature Commun). By analyzing transcriptional reporters and mutants of vasculature-associated ARFs, we identified ARF3, ARF4 and ARF5/MP as cambium regulators with different tissue-specificities as well as distinct roles in cambium regulation. In particular, we identified ARF5/MP to cell-autonomously restrict the number of stem cells by directly attenuating the activity of the stem cell-promoting WOX4 gene. Our results revealed an influence of auxin signalling on distinct cambium features by specific signalling components and allow the conceptual integration of plant stem cell systems with distinct anatomies. In fact we concluded that auxin signalling in the cambium shares features with both the situation in the root apical meristem where auxin regulates cell divisions and the shoot apical meristem where auxin, and particular ARF5/MP, is strongly correlated with cell differentiation. Thereby, we enlighten a long-observed role of auxin signalling in radial plant growth and reveal that its function is partly specific in different stem cell niches.
As a central discovery in the context of the question toward mechanisms of cambium-derived tissue formation, we identified and characterized an essential role of SUPPRESSOR OF MAX2 1-LIKE (SMXL) proteins (Wallner et al., Curr Biol, 2017; Miyashima et al., 2019, Nature; Wallner et al., 2020, PlantPhys; Cho et al., 2018; Nature Plants; Wallner et al., 2021, bioRxiv). We demonstrated that, within the SMXL gene family, specifically SMXL3, SMXL4, and SMXL5-deficiency results in strong defects in phloem formation. At the beginning of our work, the three genes formed an non-characterized subclade of the SMXL gene family which mediates hormonal strigolactone and karrikin signalling. We found that SMXL3/4/5 proteins function differently to canonical strigolactone and karrikin signalling mediators, although being functionally interchangeable with those under low strigolactone/karrikin signalling conditions. We also found that the SMXL5 protein interacts physically with the PhD finger protein OBERON3 (OBE3) forming a functional unit during phloem formation. We provided evidence that SMXL5 and OBE3 proteins interact in planta and elucidated a functional interaction between OBE3 and SMXL3/4/5 genes during phloem development using genetic means. Therefore, just like SMXL3/4/5, OBE3 is an important component during phloem initiation and differentiation. By characterizing the SMXL3/4/5-OBE3 interaction we provided also insights into the molecular network of phloem formation in plants and propose that the SMXL3/4/5-OBE3-dependent establishment of a distinct chromatin profile is an essential step during phloem specification.
We will still harvest from three achievements made during the action in the upcoming months. This is first in the context of single nucleus RNA sequencing by which we characterized developmental trajectories in the cambium domain. Here, we expect to characterize mainly the establishment of cell identities within the xylem lineage. Second, this is in the context of cell-based computational modelling visualizing cambium activity and integrating the function of central cambium regulators and mechanical cues (e.g. Lebovak et al., 2020, bioRxiv). By manipulating cell wall properties and, thereby, mechanical profiles of individual tissues, model predictions are currently been tested. Third, we will reveal the role of stem cell-specific factors identified as described above in integrating mechano-signals originating from surrounding tissues.