Research highlights
Full publication list at NCBI
Mechanisms of coat assembly and function in membrane trafficking and human disease
The goal of the Jackson lab is to understand structures and functions of important protein complexes that initiate cellular trafficking pathways. We focus on endosomal, adaptor protein 4 (AP-4), and coat protein complex I (COPI) complexes and their roles in both fundamental cell biology and human disease. Each coat functions as a “hub” to recognize cargo and to coordinate large protein networks that drive regulated formation of vesicles or tubules at precise donor membranes. We use biochemical, biophysical, and structural methods to address at the molecular level how these coats interact with protein and lipid partners to regulate coat assembly and to sort important cargoes to different destinations. We use mechanistic data to address functional relevance of coat proteins in cultured cell lines or in yeast through collaborations with other groups at Vanderbilt and other research institutes. We are working towards using this molecular knowledge to develop models of neurological disease in zebrafish, since coats are specifically linked with neurological disorders and neurodegenerative disease.
CURRENT WORK
Endosomal coat assembly. We are pursuing several projects focused on regulation of endosomal coats composed of sorting nexins and Retromer. We determined the first single particle cryoEM structures of mammalian Retromer (Kendall et al., Structure 2020; Kendall et al., JBC 2022) to reveal Retromer adopts multiple conformations in vitro. Recent work has established a full biochemical reconstitution system to test which combinations of endosomal coat proteins can remodel membranes (Chandra et al., bioRxiv 2024). This work has further revealed the role of VARP in endosomal coat assembly on membranes.
AP4 coat assembly & trafficking. We have multiple projects on the AP4 coat and how it interacts with binding partners and cargo. If you're interested in trafficking, structure, biochemistry, cell biology, or model organisms, get in touch and check out our previous work.
Tepsin binds LC3B to promote ATG9 delivery.
Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A trafficking and delivery. Mol Biol Cell. 2024 Apr 1;35(4):ar56. doi: 10.1091/mbc.E23-09-0359-T. Epub 2024 Feb 21. PubMed PMID: 38381558;
AP4 sorts ATG9A via RUSC-dependent mechanism.
Davies AK, Itzhak DN, Edgar JR, Archuleta TL, Hirst J, Jackson LP, Robinson MS, and Borner GHH. (2018). AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A. Nature Communications 9: 3958.
Structure & evolution of tepsin domains.
Archuleta TA, Frazier MN, Monken A, Kendall AK, Harp J, McCoy AJ, Creanza N, and Jackson LP. (2017). Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin. Traffic doi: 10.1111/tra.12499 [Epub ahead of print, 10 July 2017].
How AP4 interacts with a short motif found in tepsin.
Frazier MN, Davies AK, Voehler M, Kendall AK, Borner GH, Chazin WJ, Robinson MS, and Jackson LP. (2016). Molecular basis for the interaction between Adaptor Protein Complex 4 (AP4) b4 and its accessory protein, tepsin. Traffic 17: 400-415.
COPI coat regulation and cargo binding. We are interested in how COPI subcomplexes function as protein binding platforms to regulate coat assembly and disassembly. We currently have great biochemical and structural projects on the B-subcomplex. Because COPI is found in yeast, we can test our molecular data in vivo. In addition, we have a great collaboration with the Graham lab at Vanderbilt, who have identified a novel yeast cargo for COPI. We are working with them to use biochemical and biophysical methods to elucidate molecular mechanisms of cargo binding that do not involve short linear motifs.
Jackson LP. (2014) Structure and mechanism of COPI vesicle biogenesis. Curr Opin Cell Biol 29C, 67-73.
PREVIOUS WORK
Cargo recognition by the AP2 clathrin adaptor.
Jackson LP*, Kelly BT*, McCoy, AJ, Gaffry, T, James LC, Collins BM, Höning S, Evans PR, Owen DJ. (2010). Cell 141, 1220-29. (*joint first authors)
Clathrin-mediated endocytosis at the plasma membrane has long served as a paradigm for understanding coated vesicle formation. However, the field lacked mechanistic information about how the clathrin adaptor complex, AP2, recognized cargo in the context of the membrane. Our structural work on AP2 in complex with cargo motifs revealed for the first time how AP2 is likely recruited to membranes: AP2 first binds a specific phosphoinositide and then undergoes a substantial conformational change to bind short amino acid motifs found in the C-termini of cargo molecules. Subsequent work by other groups showed how this conformational change is required for clathrin recruitment (Owen group, Cambridge) and is likely conserved in related coats, including AP1 (Hurley group, Berkeley) and COPI (Goldberg group, Sloan-Kettering; Briggs group, EMBL). Further work in C. elegans indicated how our ‘open AP2’ structure is relevant in vivo, because other trafficking proteins may serve as allosteric activators to drive or stabilize its conformational change (Hollopeter group, Cornell; Jorgensen group, Utah).
Dilysine motif binding by the COPI coat.
Jackson LP†, Lewis M, Kent HM, Edeling MA, Evans PR, Duden R, and Owen DJ†. (2012). Dev Cell 23, 1-8. (†corresponding authors)
Recognition of linear motifs by the clathrin coat machinery was well-understood in the field, but there were no molecular data on how the COPI coat interacted with any of its important cargoes in the retrograde pathway. Our structural work elucidated how specific COPI domains could interact with dilysine motifs found in retrograde cargoes, which in turn implied that COPI coats assemble differently from clathrin-based coats. This prediction has been subsequently supported by cryo-electron tomography on the COPI coat (Briggs & Wieland groups, EMBL).
The goal of the Jackson lab is to understand structures and functions of important protein complexes that initiate cellular trafficking pathways. We focus on endosomal, adaptor protein 4 (AP-4), and coat protein complex I (COPI) complexes and their roles in both fundamental cell biology and human disease. Each coat functions as a “hub” to recognize cargo and to coordinate large protein networks that drive regulated formation of vesicles or tubules at precise donor membranes. We use biochemical, biophysical, and structural methods to address at the molecular level how these coats interact with protein and lipid partners to regulate coat assembly and to sort important cargoes to different destinations. We use mechanistic data to address functional relevance of coat proteins in cultured cell lines or in yeast through collaborations with other groups at Vanderbilt and other research institutes. We are working towards using this molecular knowledge to develop models of neurological disease in zebrafish, since coats are specifically linked with neurological disorders and neurodegenerative disease.
CURRENT WORK
Endosomal coat assembly. We are pursuing several projects focused on regulation of endosomal coats composed of sorting nexins and Retromer. We determined the first single particle cryoEM structures of mammalian Retromer (Kendall et al., Structure 2020; Kendall et al., JBC 2022) to reveal Retromer adopts multiple conformations in vitro. Recent work has established a full biochemical reconstitution system to test which combinations of endosomal coat proteins can remodel membranes (Chandra et al., bioRxiv 2024). This work has further revealed the role of VARP in endosomal coat assembly on membranes.
AP4 coat assembly & trafficking. We have multiple projects on the AP4 coat and how it interacts with binding partners and cargo. If you're interested in trafficking, structure, biochemistry, cell biology, or model organisms, get in touch and check out our previous work.
Tepsin binds LC3B to promote ATG9 delivery.
Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A trafficking and delivery. Mol Biol Cell. 2024 Apr 1;35(4):ar56. doi: 10.1091/mbc.E23-09-0359-T. Epub 2024 Feb 21. PubMed PMID: 38381558;
AP4 sorts ATG9A via RUSC-dependent mechanism.
Davies AK, Itzhak DN, Edgar JR, Archuleta TL, Hirst J, Jackson LP, Robinson MS, and Borner GHH. (2018). AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A. Nature Communications 9: 3958.
Structure & evolution of tepsin domains.
Archuleta TA, Frazier MN, Monken A, Kendall AK, Harp J, McCoy AJ, Creanza N, and Jackson LP. (2017). Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin. Traffic doi: 10.1111/tra.12499 [Epub ahead of print, 10 July 2017].
How AP4 interacts with a short motif found in tepsin.
Frazier MN, Davies AK, Voehler M, Kendall AK, Borner GH, Chazin WJ, Robinson MS, and Jackson LP. (2016). Molecular basis for the interaction between Adaptor Protein Complex 4 (AP4) b4 and its accessory protein, tepsin. Traffic 17: 400-415.
COPI coat regulation and cargo binding. We are interested in how COPI subcomplexes function as protein binding platforms to regulate coat assembly and disassembly. We currently have great biochemical and structural projects on the B-subcomplex. Because COPI is found in yeast, we can test our molecular data in vivo. In addition, we have a great collaboration with the Graham lab at Vanderbilt, who have identified a novel yeast cargo for COPI. We are working with them to use biochemical and biophysical methods to elucidate molecular mechanisms of cargo binding that do not involve short linear motifs.
Jackson LP. (2014) Structure and mechanism of COPI vesicle biogenesis. Curr Opin Cell Biol 29C, 67-73.
PREVIOUS WORK
Cargo recognition by the AP2 clathrin adaptor.
Jackson LP*, Kelly BT*, McCoy, AJ, Gaffry, T, James LC, Collins BM, Höning S, Evans PR, Owen DJ. (2010). Cell 141, 1220-29. (*joint first authors)
Clathrin-mediated endocytosis at the plasma membrane has long served as a paradigm for understanding coated vesicle formation. However, the field lacked mechanistic information about how the clathrin adaptor complex, AP2, recognized cargo in the context of the membrane. Our structural work on AP2 in complex with cargo motifs revealed for the first time how AP2 is likely recruited to membranes: AP2 first binds a specific phosphoinositide and then undergoes a substantial conformational change to bind short amino acid motifs found in the C-termini of cargo molecules. Subsequent work by other groups showed how this conformational change is required for clathrin recruitment (Owen group, Cambridge) and is likely conserved in related coats, including AP1 (Hurley group, Berkeley) and COPI (Goldberg group, Sloan-Kettering; Briggs group, EMBL). Further work in C. elegans indicated how our ‘open AP2’ structure is relevant in vivo, because other trafficking proteins may serve as allosteric activators to drive or stabilize its conformational change (Hollopeter group, Cornell; Jorgensen group, Utah).
Dilysine motif binding by the COPI coat.
Jackson LP†, Lewis M, Kent HM, Edeling MA, Evans PR, Duden R, and Owen DJ†. (2012). Dev Cell 23, 1-8. (†corresponding authors)
Recognition of linear motifs by the clathrin coat machinery was well-understood in the field, but there were no molecular data on how the COPI coat interacted with any of its important cargoes in the retrograde pathway. Our structural work elucidated how specific COPI domains could interact with dilysine motifs found in retrograde cargoes, which in turn implied that COPI coats assemble differently from clathrin-based coats. This prediction has been subsequently supported by cryo-electron tomography on the COPI coat (Briggs & Wieland groups, EMBL).
GRADUATE HIGHLIGHTS
SNAREs as cargo.
Pryor PR, Jackson LP, Gray SR, Edeling MA, Thompson A, Sanderson CM, Evans PR, Owen DJ, Luzio JP. (2008). Cell 134, 817-27.
SNARE proteins mediate fusion events between vesicles and their target membranes and thus must be included in all outgoing vesicles to ensure fusion. How then are SNARE proteins sorted as cargo back to their steady-state destination following a fusion event? During my graduate studies, my biochemical data and X-ray crystal structure of the lysosomal SNARE protein, VAMP7, with Hrb provided one of the first two mechanistic examples of how coats package SNAREs into forming vesicles in a non-competitive way. Instead of linear motifs, SNAREs can use highly specific folded structural domains to interact with a single adaptor protein; loss of important residues in the binding interface has important implications for mis-sorting.
SNAREs as cargo.
Pryor PR, Jackson LP, Gray SR, Edeling MA, Thompson A, Sanderson CM, Evans PR, Owen DJ, Luzio JP. (2008). Cell 134, 817-27.
SNARE proteins mediate fusion events between vesicles and their target membranes and thus must be included in all outgoing vesicles to ensure fusion. How then are SNARE proteins sorted as cargo back to their steady-state destination following a fusion event? During my graduate studies, my biochemical data and X-ray crystal structure of the lysosomal SNARE protein, VAMP7, with Hrb provided one of the first two mechanistic examples of how coats package SNAREs into forming vesicles in a non-competitive way. Instead of linear motifs, SNAREs can use highly specific folded structural domains to interact with a single adaptor protein; loss of important residues in the binding interface has important implications for mis-sorting.
