Current Research
Root architecture impacts the efficient uptake of nutrients, minerals and water from the soil. A greater understanding of the molecular and cellular mechanisms that control root architectural traits like lateral root development (Swarup et al 2008, Nature cell Biology, 10, 946-954) are likely to identify key regulators that may provide the tools to design novel strategies for future crop improvement programmes. My group is working on various aspects of root development programmes as summarised below- My work on AXR4 ((Dharamsiri and Swarup et al, 2006, Science, 318, 1218-1220) has identified a novel class of endoplasmic reticulum protein in plants that regulate targeting of multi membrane spanning proteins. Such proteins form a very important class of proteins that regulate many important physiological and biochemical processes and can have profound impact on plant growth and development. One of the key focus of my research group is to identify and characterise novel ER accessory proteins. This would be of considerable agronomic interest, given the importance of resource use efficiency to sustainable farming practices.
Plant hormone auxin is crucial for plant growth and development. We mapped the tissues required for auxin transport and auxin response during root gravitropism (Swarup et al, 2005, Nature Cell Biology, 7, 1057-1065). This study revealed that epidermis is the primary site for auxin action during root gravitropism. Using an inducible version of a strong auxin repressor protein axr3, we are fine mapping kinetics of gravitropic response in Arabidopsis roots.
The establishment and maintenance of membrane polarity is crucial during plant and animal development, helping specify cell fate, and to underpin numerous transport functions. For example, the polar targeting of auxin influx and efflux carriers at the apical and basal ends of the root cells, respectively, ensures the polar transport of the plant hormone auxin (Swarup and Bennett 2009, Annual Plant Reviews, 37, 167-174). My group is investigating mechanisms of polar membrane targeting as well as cell type specific targeting.
For further details, see below-
A global investigation of role of vesicular trafficking network in regulating lateral root development in Arabidopsis. Lateral roots originate from cells deep within a root. These cells undergo a series of divisions to form a new root which must emerge via the outer cell layers into the soil environment. During lateral root development transport network of the cell (vesicular trafficking network) must play a key role to maintain the supply of plasma-membrane materials and cell wall components during the formation of this new organ. Despite the importance of vesicular trafficking in lateral root formation, there is poor understanding of the key molecular players regulating lateral root development. A detailed expression profiling of lateral root development (Ute and Bennett 2010) reveals that several genes encoding components of the intracellular vesicular trafficking network show significant changes in gene expression during lateral root development and are currently being investigated for their role in regulating lateral root development. In addition, several unknown genes are also differentially regulated and characterisation of these genes is likely to identify novel regulators of lateral root development. Identification and characterisation of ER accessory proteins in Arabidopsis. We have recently discovered a novel class of ER proteins in plants that facilitate the assembly of polytopic membrane proteins in the ER. AXR4 represents one such ER protein that regulates the trafficking of the auxin influx carrier, AUX1 (Dharamsiri and Swarup et al, 2006, Science, 318, 1218-1220). AUX1 is a polytopic membrane protein which is localised to the plasma membrane (PM) and plays a key role in root gravitropic responses (Swarup et al, 2005, Nature cell Biology, 7, 1057-1065). In the absence of AXR4, AUX1 mainly accumulates in the endoplasmic reticulum (ER). Currently, we are investigating whether AXR4 interacts with AUX1 and are also identifying functionally critical domains in AXR4. Besides, my group is also involved in identifying other novel ER accessory proteins in Arabidopsis that can regulate trafficking of polytopic membrane proteins. Polytopic membrane proteins form a very important class of proteins that regulate many important physiological and biochemical processes and can have profound impact on plant growth and development. Identification and characterisation of their cognate ER accessory proteins would be of considerable agronomic interest, given the importance of resource use efficiency to sustainable farming practices. We have obtained knock outs in many putative novel ER proteins and work is currently underway to characterise these mutants. One of my candidate genes is of particular interest to us because there are evidences in animal systems that this class of proteins may have a role in protein trafficking. This gene belongs to a small multi gene family and my group is currently establishing the developmental role of these proteins in Arabidopsis. Investigating mechanisms of cell type specific targeting. The establishment and maintenance of membrane polarity is crucial during plant and animal development, helping specify cell fate, and to underpin numerous transport functions. For example, the polar targeting of auxin influx and efflux carriers at the apical and basal ends of the root cells, respectively, ensures the polar transport of the plant hormone auxin (Swarup and Bennett 2009, Annual Plant Reviews, 37, 167-174). Membrane polarity at the single cell level often contributes to multicellular plant development. For example, basal targeting of the auxin efflux carrier PIN1 is required for establishment of apical basal polarity in Arabidopsis embryos, whilst trafficking of the COBRA protein to the lateral face of root cells is required for root expansion. Polar membrane targeting of other PM proteins such as receptors, transporters and ion channels are also likely to have important developmental or regulatory consequences. Advancement in the in situ localisation (French et al, 2008. Nature Protocols, 3, 619-628) of proteins in the last decade has not only identified many marker proteins that are polarly localised but has also revealed that several membrane proteins show cell type specific localisation. In Arabidopsis roots for example, targeting of auxin transporters AUX1, LAX2 and LAX3 is cell type dependent. In the protophloem cells, AUX1 is localised on the apical face of the cells but in contrast, is localised symmetrically in columella and lateral root cap cells (Swarup et al, 2001, Genes and Development, 15, 2648-2653.) On the other hand, LAX3 is targeted to the plasma membrane in the cortical and epidermal cells but not in the mature vascular cells (Swarup et al 2008, Nature cell Biology, 10, 946-954). Ectopic expression of LAX2 and LAX3 revealed even more interesting patterns of localisation indicating complex regulatory mechanism(s). Using a variety of molecular, genetic and bioinormatic approaches, my group is probing molecular mechanisms regulating polar as well as cell type specific targeting. Fine mapping of gravitropic response in Arabidopsis root apex. Plant hormone auxin is crucial for plant growth and development. In roots, auxin plays a key role in root gravitropism (differential growth). In an earlier study, we mapped the tissues required for auxin transport and auxin response during root gravitropism (Swarup et al, 2005, Nature Cell Biology, 7, 1057-1065). This study revealed that epidermis is the primary site for auxin action during root gravitropism. Using an inducible version of a strong auxin repressor protein axr3, we are fine mapping kinetics of gravitropic response in Arabidopsis roots.