Project acronym CASINO
Project Carbohydrate signals controlling nodulation
Researcher (PI) Jens Stougaard Jensen
Host Institution (HI) AARHUS UNIVERSITET
Call Details Advanced Grant (AdG), LS3, ERC-2010-AdG_20100317
Summary Mechanisms governing interaction between multicellular organisms and microbes are central for understanding pathogenesis, symbiosis and the function of ecosystems. We propose to address these mechanisms by pioneering an interdisciplinary approach for understanding cellular signalling, response processes and organ development. The challenge is to determine factors synchronising three processes, organogenesis, infection thread formation and bacterial infection, running in parallel to build a root nodule hosting symbiotic bacteria. We aim to exploit the unique possibilities for analysing endocytosis of bacteria in model legumes and to develop genomic, genetic and biological chemistry tools to break new ground in our understanding of carbohydrates in plant development and plant-microbe interaction. Surface exposed rhizobial polysaccharides play a crucial but poorly understood role in infection thread formation and rhizobial invasion resulting in endocytosis. We will undertake an integrated functional characterisation of receptor-ligand mechanisms mediating recognition of secreted polysaccharides and subsequent signal amplification. So far progress in this field has been limited by the complex nature of carbohydrate polymers, lack of a suitable experimental model system where both partners in an interaction could be manipulated and lack of corresponding methods for carbohydrate synthesis, analysis and interaction studies. In this context our legume model system and the discovery that the legume Nod-factor receptors recognise bacterial lipochitin-oligosaccharide signals at their LysM domains provides a new opportunity. Combined with advanced bioorganic chemistry and nanobioscience approaches this proposal will engage the above mentioned limitations.
Summary
Mechanisms governing interaction between multicellular organisms and microbes are central for understanding pathogenesis, symbiosis and the function of ecosystems. We propose to address these mechanisms by pioneering an interdisciplinary approach for understanding cellular signalling, response processes and organ development. The challenge is to determine factors synchronising three processes, organogenesis, infection thread formation and bacterial infection, running in parallel to build a root nodule hosting symbiotic bacteria. We aim to exploit the unique possibilities for analysing endocytosis of bacteria in model legumes and to develop genomic, genetic and biological chemistry tools to break new ground in our understanding of carbohydrates in plant development and plant-microbe interaction. Surface exposed rhizobial polysaccharides play a crucial but poorly understood role in infection thread formation and rhizobial invasion resulting in endocytosis. We will undertake an integrated functional characterisation of receptor-ligand mechanisms mediating recognition of secreted polysaccharides and subsequent signal amplification. So far progress in this field has been limited by the complex nature of carbohydrate polymers, lack of a suitable experimental model system where both partners in an interaction could be manipulated and lack of corresponding methods for carbohydrate synthesis, analysis and interaction studies. In this context our legume model system and the discovery that the legume Nod-factor receptors recognise bacterial lipochitin-oligosaccharide signals at their LysM domains provides a new opportunity. Combined with advanced bioorganic chemistry and nanobioscience approaches this proposal will engage the above mentioned limitations.
Max ERC Funding
2 399 127 €
Duration
Start date: 2011-05-01, End date: 2016-04-30
Project acronym FlyGutHomeostasis
Project Identification of paracrine and systemic signals controlling adult stem cell activity and organ homeostasis
Researcher (PI) Ditte ANDERSEN
Host Institution (HI) KOBENHAVNS UNIVERSITET
Call Details Starting Grant (StG), LS3, ERC-2018-STG
Summary Due to its remarkable self-renewing capacity, the fly gut has recently become a prime paradigm for studying stem-cell function during adult tissue homeostasis. This capacity for self-renewal relays on the proliferative activity of the intestinal stem cells (ISC), which is tightly coupled with cell loss to maintain intestinal homeostasis. ISC proliferation is controlled by multiple local and systemic signals released from the ISC niche (enterocytes (ECs), enteroendocrine (EE) cells, enteroblasts (EBs), and visceral muscles (VMs)) and non-gastrointestinal (non-GI) organs. Despite the physiological divergence between insects and mammals, studies have shown that flies represent a model that is well suited for studying stem cell physiology during ageing, stress, and infection. As a saturating approach to identify local and systemic signals controlling intestinal homeostasis in steady-state and challenged conditions, RNAis will be used to known down all genes encoding secreted peptides specifically in ECs, EEs, or VMs and all genes encoding transmembrane and membrane-associated proteins in the VMs. The proposed screens should identify novel intra- and inter-organ circuitries allowing communication between the gut and other organs to provide organismal health. In addition, the systematic knockdown of secreted peptides from the ISC niche could identify gut-derived signals that couple changes in environmental inputs, such as nutrient availability, with systemic changes in feeding behavior, energy balance, and metabolism. Since large-scale approaches are not feasible in vertebrate models, the signals identified in the above screens could potentially reveal novel couplings contributing to mammalian GI homeostasis and disease. The final part of the proposed project aims a deciphering the molecular signals coupling epithelial fitness with ligand-independent TNFR activation to control ISC division and epithelial turnover in steady-state, challenged and pathological conditions.
Summary
Due to its remarkable self-renewing capacity, the fly gut has recently become a prime paradigm for studying stem-cell function during adult tissue homeostasis. This capacity for self-renewal relays on the proliferative activity of the intestinal stem cells (ISC), which is tightly coupled with cell loss to maintain intestinal homeostasis. ISC proliferation is controlled by multiple local and systemic signals released from the ISC niche (enterocytes (ECs), enteroendocrine (EE) cells, enteroblasts (EBs), and visceral muscles (VMs)) and non-gastrointestinal (non-GI) organs. Despite the physiological divergence between insects and mammals, studies have shown that flies represent a model that is well suited for studying stem cell physiology during ageing, stress, and infection. As a saturating approach to identify local and systemic signals controlling intestinal homeostasis in steady-state and challenged conditions, RNAis will be used to known down all genes encoding secreted peptides specifically in ECs, EEs, or VMs and all genes encoding transmembrane and membrane-associated proteins in the VMs. The proposed screens should identify novel intra- and inter-organ circuitries allowing communication between the gut and other organs to provide organismal health. In addition, the systematic knockdown of secreted peptides from the ISC niche could identify gut-derived signals that couple changes in environmental inputs, such as nutrient availability, with systemic changes in feeding behavior, energy balance, and metabolism. Since large-scale approaches are not feasible in vertebrate models, the signals identified in the above screens could potentially reveal novel couplings contributing to mammalian GI homeostasis and disease. The final part of the proposed project aims a deciphering the molecular signals coupling epithelial fitness with ligand-independent TNFR activation to control ISC division and epithelial turnover in steady-state, challenged and pathological conditions.
Max ERC Funding
1 498 964 €
Duration
Start date: 2019-02-01, End date: 2024-01-31
Project acronym REPLICONSTRAINTS
Project Dissecting the constraints that define the eukaryotic DNA replication program
Researcher (PI) Luis Ignacio Toledo Lazaro
Host Institution (HI) KOBENHAVNS UNIVERSITET
Call Details Starting Grant (StG), LS3, ERC-2015-STG
Summary DNA replication is essential for the perpetuation of life and, yet, it is also a major source of genomic instability that can lead to cancer and other human diseases. Despite the vast efforts invested in establishing the origins of genomic instability, the mechanisms that coordinate faithful genome duplication while ensuring its integrity remain unknown.
This dilemma is molecularly best exemplified by single stranded DNA (ssDNA), which inevitably results from unwinding the double helix due to replication fork progression, but is at the same time a vulnerable intermediate that can lead to severe genomic lesions. Thus, maintaining an appropriate balance of ssDNA is a paramount challenge for replicating cells. My own work has significantly contributed to this concept by showing that eukaryotic cells have limited resources to guard its ssDNA, and that exhaustion of these resources (due to increased overall levels of ssDNA) causes a lethal fragmentation of the genome termed ‘replication catastrophe’ (RC). To prevent this terminal scenario, ssDNA levels and DNA replication activity must be constrained by yet uncharacterized mechanisms. In eukaryotes, where DNA is simultaneously replicated at multiple sites throughout the genome, this represents a particularly challenging task. Understanding how this is molecularly accomplished could transform our view of the very principles of DNA replication regulation, and also reveal potential therapeutic avenues to exploit RC in the treatment for cancer.
With the present proposal I will address this challenge by investigating how ssDNA maintenance is enrooted in the regulatory principles of DNA replication. I will dissect the mechanisms that, globally and locally, constrain replication activity to prevent genomic instability. By using novel and innovative analytical tools, I aim to provide an unmatched picture of the DNA replication apparatus and to identify novel anticancer strategies based on provoking RC selectively in tumor cells.
Summary
DNA replication is essential for the perpetuation of life and, yet, it is also a major source of genomic instability that can lead to cancer and other human diseases. Despite the vast efforts invested in establishing the origins of genomic instability, the mechanisms that coordinate faithful genome duplication while ensuring its integrity remain unknown.
This dilemma is molecularly best exemplified by single stranded DNA (ssDNA), which inevitably results from unwinding the double helix due to replication fork progression, but is at the same time a vulnerable intermediate that can lead to severe genomic lesions. Thus, maintaining an appropriate balance of ssDNA is a paramount challenge for replicating cells. My own work has significantly contributed to this concept by showing that eukaryotic cells have limited resources to guard its ssDNA, and that exhaustion of these resources (due to increased overall levels of ssDNA) causes a lethal fragmentation of the genome termed ‘replication catastrophe’ (RC). To prevent this terminal scenario, ssDNA levels and DNA replication activity must be constrained by yet uncharacterized mechanisms. In eukaryotes, where DNA is simultaneously replicated at multiple sites throughout the genome, this represents a particularly challenging task. Understanding how this is molecularly accomplished could transform our view of the very principles of DNA replication regulation, and also reveal potential therapeutic avenues to exploit RC in the treatment for cancer.
With the present proposal I will address this challenge by investigating how ssDNA maintenance is enrooted in the regulatory principles of DNA replication. I will dissect the mechanisms that, globally and locally, constrain replication activity to prevent genomic instability. By using novel and innovative analytical tools, I aim to provide an unmatched picture of the DNA replication apparatus and to identify novel anticancer strategies based on provoking RC selectively in tumor cells.
Max ERC Funding
1 498 899 €
Duration
Start date: 2016-08-01, End date: 2021-07-31
Project acronym RINFEC
Project The Roots of Infection
Researcher (PI) Jens Stougaard
Host Institution (HI) AARHUS UNIVERSITET
Call Details Advanced Grant (AdG), LS3, ERC-2018-ADG
Summary Plant roots and soil microbes have been associated since the emergence of plants on land. Nevertheless the mechanisms that have coevolved to control these commensal and mutualistic associations are currently unknown. RINFEC will identify both plant and bacterial genes involved in root colonization by commensal and mutualistic bacteria with an approach that would be transformative in the field. The ambitious challenge is to identify and functionally characterize the central genes controlling root cells competence for infection. RINFEC´s central hypothesis is that key components of ancient pathways for bacterial colonization of the root surface (rhizosphere) and root interior (endosphere) were adapted during evolution of mechanism(s) controlling colonization of legume roots by symbiotic rhizobia. RINFEC will uncover the genetics and biochemistry of these shared mechanisms by characterizing a novel, unexplored intercellular infection mode observed for certain rhizobia that act as endophytes in non-legume plants and are able to infect the model legume Lotus japonicus. The unique biological feature exploited in RINFEC is the capacity of Lotus to support either intercellular entry (conserved mode) or legume specific infection thread entry, dependent on the rhizobia encountered. This allows comparative investigations of these two infection modes in simple binary interactions with the same host. Given the exceptional ability of different rhizobia for intercellular endophytic colonization of non-legume roots this provides an unprecedented platform to identify mechanisms by which plants selectively enable a subset of bacteria to infect roots. RINFEC will build on my considerable expertise with Lotus and pioneers novel plant and bacterial genetic methods, cell-layer transcriptomics, phospho-proteomics and advanced biochemistry to break new ground in understanding infection and soil microbe influences on plant performance under environmental stress conditions.
Summary
Plant roots and soil microbes have been associated since the emergence of plants on land. Nevertheless the mechanisms that have coevolved to control these commensal and mutualistic associations are currently unknown. RINFEC will identify both plant and bacterial genes involved in root colonization by commensal and mutualistic bacteria with an approach that would be transformative in the field. The ambitious challenge is to identify and functionally characterize the central genes controlling root cells competence for infection. RINFEC´s central hypothesis is that key components of ancient pathways for bacterial colonization of the root surface (rhizosphere) and root interior (endosphere) were adapted during evolution of mechanism(s) controlling colonization of legume roots by symbiotic rhizobia. RINFEC will uncover the genetics and biochemistry of these shared mechanisms by characterizing a novel, unexplored intercellular infection mode observed for certain rhizobia that act as endophytes in non-legume plants and are able to infect the model legume Lotus japonicus. The unique biological feature exploited in RINFEC is the capacity of Lotus to support either intercellular entry (conserved mode) or legume specific infection thread entry, dependent on the rhizobia encountered. This allows comparative investigations of these two infection modes in simple binary interactions with the same host. Given the exceptional ability of different rhizobia for intercellular endophytic colonization of non-legume roots this provides an unprecedented platform to identify mechanisms by which plants selectively enable a subset of bacteria to infect roots. RINFEC will build on my considerable expertise with Lotus and pioneers novel plant and bacterial genetic methods, cell-layer transcriptomics, phospho-proteomics and advanced biochemistry to break new ground in understanding infection and soil microbe influences on plant performance under environmental stress conditions.
Max ERC Funding
2 499 999 €
Duration
Start date: 2019-10-01, End date: 2024-09-30
