1
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Kim D, Cianfrocco MA, Verhey KJ, Smith GA. The HSV-1 pUL37 protein promotes cell invasion by regulating the kinesin-1 motor. Proc Natl Acad Sci U S A 2024; 121:e2401341121. [PMID: 38696466 DOI: 10.1073/pnas.2401341121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/17/2024] [Indexed: 05/04/2024] Open
Abstract
Neurotropic alphaherpesviruses, including herpes simplex virus type 1 (HSV-1), recruit microtubule motor proteins to invade cells. The incoming viral particle traffics to nuclei in a two-step process. First, the particle uses the dynein-dynactin motor to sustain transport to the centrosome. In neurons, this step is responsible for long-distance retrograde axonal transport and is an important component of the neuroinvasive property shared by these viruses. Second, a kinesin-dependent mechanism redirects the particle from the centrosome to the nucleus. We have reported that the kinesin motor used during the second step of invasion is assimilated into nascent virions during the previous round of infection. Here, we report that the HSV-1 pUL37 tegument protein suppresses the assimilated kinesin-1 motor during retrograde axonal transport. Region 2 (R2) of pUL37 was required for suppression and functioned independently of the autoinhibitory mechanism native to kinesin-1. Furthermore, the motor domain and proximal coiled coil of kinesin-1 were sufficient for HSV-1 assimilation, pUL37 suppression, and nuclear trafficking. pUL37 localized to the centrosome, the site of assimilated kinesin-1 activation during infection, when expressed in cells in the absence of other viral proteins; however, pUL37 did not suppress kinesin-1 in this context. These results indicate that the pUL37 tegument protein spatially and temporally regulates kinesin-1 via the amino-terminal motor region in the context of the incoming viral particle.
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Affiliation(s)
- DongHo Kim
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Michael A Cianfrocco
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Gregory A Smith
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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2
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Ravala SK, Adame-Garcia SR, Li S, Chen CL, Cianfrocco MA, Gutkind JS, Cash JN, Tesmer JJG. Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4. bioRxiv 2024:2023.09.15.557836. [PMID: 37745379 PMCID: PMC10515948 DOI: 10.1101/2023.09.15.557836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
PIP3-dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP3 and the heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP3, we discovered that Ins(1,3,4,5)P4 (IP4) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH-DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH-DEP1 and PH-4HB interfaces were disturbed exhibited enhanced activity during chemokine-induced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP3-containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.
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Affiliation(s)
- Sandeep K. Ravala
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sendi Rafael Adame-Garcia
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Chun-Liang Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michael A. Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - J. Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Jennifer N. Cash
- Department of Molecular and Cellular Biology, University of California-Davis, Davis, CA, 95616, USA
| | - John J. G. Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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3
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Badieyan S, Lichon D, Andreas MP, Gillies JP, Peng W, Shi J, DeSantis ME, Aiken CR, Böcking T, Giessen TW, Campbell EM, Cianfrocco MA. HIV-1 binds dynein directly to hijack microtubule transport machinery. bioRxiv 2023:2023.08.29.555335. [PMID: 37693451 PMCID: PMC10491134 DOI: 10.1101/2023.08.29.555335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dynein's tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically 'hijacks' the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.
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Affiliation(s)
| | - Drew Lichon
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael P Andreas
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John P Gillies
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Wang Peng
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Morgan E DeSantis
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Christopher R Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tobias W Giessen
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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4
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Tan Z, Yue Y, Leprevost F, Haynes S, Basrur V, Nesvizhskii AI, Verhey KJ, Cianfrocco MA. Autoinhibited kinesin-1 adopts a hierarchical folding pattern. eLife 2023; 12:RP86776. [PMID: 37910016 PMCID: PMC10619981 DOI: 10.7554/elife.86776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine crosslinking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer (kinesin-1 heavy chain [KHC]) and kinesin-1 heterotetramer (KHC bound to kinesin light chain 1 [KLC1]). Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled-coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
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Affiliation(s)
- Zhenyu Tan
- Department of Biophysics, University of MichiganAnn ArborUnited States
- Life Sciences Institute, University of MichiganAnn ArborUnited States
| | - Yang Yue
- Department of Cell & Developmental Biology, University of MichiganAnn ArborUnited States
| | - Felipe Leprevost
- Department of Pathology, University of MichiganAnn ArborUnited States
| | - Sarah Haynes
- Department of Pathology, University of MichiganAnn ArborUnited States
| | - Venkatesha Basrur
- Department of Pathology, University of MichiganAnn ArborUnited States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of MichiganAnn ArborUnited States
- Department of Computational Medicine and Bioinformatics, University of MichiganAnn ArborUnited States
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of MichiganAnn ArborUnited States
| | - Michael A Cianfrocco
- Life Sciences Institute, University of MichiganAnn ArborUnited States
- Department of Biological Chemistry, University of MichiganAnn ArborUnited States
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5
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Wilhelm CA, Mallik L, Kelly AL, Brotzman S, Mendoza J, Anders AG, Leskaj S, Castillo C, Ruotolo BT, Cianfrocco MA, Koutmos M. Bacterial RNA-free RNase P: Structural and functional characterization of multiple oligomeric forms of a minimal protein-only ribonuclease P. J Biol Chem 2023; 299:105327. [PMID: 37806495 PMCID: PMC10652100 DOI: 10.1016/j.jbc.2023.105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
tRNAs are typically transcribed with extended 5' and 3' ends that must be removed before they attain their active form. One of the first steps of tRNA processing in nearly every organism is the removal of the 5' leader sequence by ribonuclease P (RNase P). Here, we investigate a recently discovered class of RNase P enzymes, Homologs of Aquifex RNase P (HARPs). In contrast to other RNase Ps, HARPs consist only of a metallonuclease domain and lack the canonical substrate recognition domain essential in other classes of proteinaceous RNase P. We determined the cryo-EM structure of Aquifex aeolicus HARP (Aq880) and two crystal structures of Hydrogenobacter thermophilus HARP (Hth1307) to reveal that both enzymes form large ring-like assemblies: a dodecamer in Aq880 and a tetradecamer in Hth1307. In both oligomers, the enzyme active site is 42 Å away from a positively charged helical region, as seen in other protein-only RNase P enzymes, which likely serves to recognize and bind the elbow region of the pre-tRNA substrate. In addition, we use native mass spectrometry to confirm and characterize the previously unreported tetradecamer state. Notably, we find that multiple oligomeric states of Hth1307 are able to cleave pre-tRNAs. Furthermore, our single-turnover kinetic studies indicate that Hth1307 cleaves pre-tRNAs from multiple species with a preference for native substrates. These data provide a closer look at the nuanced similarities and differences in tRNA processing across disparate classes of RNase P.
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Affiliation(s)
| | - Leena Mallik
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Abigail L Kelly
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Shayna Brotzman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Johnny Mendoza
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna G Anders
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Suada Leskaj
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Castillo
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA.
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6
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Tan Z, Yue Y, da Veiga Leprevost F, Haynes SE, Basrur V, Nesvizhskii AI, Verhey KJ, Cianfrocco MA. Autoinhibited kinesin-1 adopts a hierarchical folding pattern. bioRxiv 2023:2023.01.26.525761. [PMID: 36747757 PMCID: PMC9901034 DOI: 10.1101/2023.01.26.525761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine cross-linking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer [kinesin-1 heavy chain (KHC)] and kinesin-1 heterotetramer [KHC bound to kinesin light chain 1 (KLC1)]. Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
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Affiliation(s)
- Zhenyu Tan
- Department of Biophysics, University of Michigan
- Life Sciences Institute, University of Michigan
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan
| | | | | | | | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan
| | | | - Michael A. Cianfrocco
- Life Sciences Institute, University of Michigan
- Department of Biological Chemistry, University of Michigan
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7
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Gicking AM, Ma TC, Feng Q, Jiang R, Badieyan S, Cianfrocco MA, Hancock WO. Kinesin-1, -2 and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport. eLife 2022; 11:82228. [PMID: 36125250 PMCID: PMC9545524 DOI: 10.7554/elife.82228] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/19/2022] [Indexed: 12/03/2022] Open
Abstract
Bidirectional cargo transport in neurons requires competing activity of motors from the kinesin-1, -2, and -3 superfamilies against cytoplasmic dynein-1. Previous studies demonstrated that when kinesin-1 attached to dynein-dynactin-BicD2 (DDB) complex, the tethered motors move slowly with a slight plus-end bias, suggesting kinesin-1 overpowers DDB but DDB generates a substantial hindering load. Compared to kinesin-1, motors from the kinesin-2 and -3 families display a higher sensitivity to load in single-molecule assays and are thus predicted to be overpowered by dynein complexes in cargo transport. To test this prediction, we used a DNA scaffold to pair DDB with members of the kinesin-1, -2, and -3 families to recreate bidirectional transport in vitro, and tracked the motor pairs using two-channel TIRF microscopy. Unexpectedly, we find that when both kinesin and dynein are engaged and stepping on the microtubule, kinesin-1, -2, and -3 motors are able to effectively withstand hindering loads generated by DDB. Stochastic stepping simulations reveal that kinesin-2 and -3 motors compensate for their faster detachment rates under load with faster reattachment kinetics. The similar performance between the three kinesin transport families highlights how motor kinetics play critical roles in balancing forces between kinesin and dynein, and emphasizes the importance of motor regulation by cargo adaptors, regulatory proteins, and the microtubule track for tuning the speed and directionality of cargo transport in cells. Nerve cells in the human body can reach up to one meter in length. Different regions of a nerve cell require different materials to perform their roles. The motor proteins kinesins and dynein help to transport the required ‘cargo’, by moving in opposite directions along tracks called microtubules. However, many cargos have both motors attached, resulting in a tug-of-war to determine which direction and how fast the cargo will travel. In many neurodegenerative diseases, including Alzheimer’s, this cargo transport goes awry, so a better understanding of exactly how this process works may help to develop new therapies. There are three families of kinesin motors, for a total of about a dozen different kinesins that engage in this process. Motors in each of the three families have different mechanical properties. Specific cargos also tend to have specific kinesins attached to them. Here Gicking et al. hypothesized that when pulling against dynein in a tug-of-war, kinesins from the three families would behave differently. To test this hypothesis, Gicking et al. linked one kinesin to one dynein motor, one at a time in a test tube, and then observed how these two-motor complexes moved using fluorescence microscopy techniques. Unexpectedly, kinesins from the three different families competed similarly against dynein: there were no clear winners and losers. By incorporating previously published data describing the different motor behaviors, Gicking et al. developed a computational model that provided deeper insight into how this mechanical tug-of-war works. The modeling indicated that kinesins from the three families use different approaches for competing against dynein. Kinesin-1 motors tended to pull steadily against dynein, only detaching relatively rarely, but then take some time to attach back to the microtubule track. In contrast, kinesin-3 motors detached easily when they pull against dynein, but they attach back to the microtubule track quickly, taking only about a millisecond to start moving again. Kinesin-2 motors exhibited an intermediate behavior. Overall, these experiments suggest that the mechanical properties of the motor proteins are not the main factors determining the direction and speed of the cargo. In other words, the outcome of this molecular tug-of-war does not necessarily depend on which motor is stronger or faster. Rather, further mechanisms, including regulation of the adapter molecules that connect the motors to their cargo, may help to regulate which cargo go where in branched nerve cells. A better knowledge of how all these different factors work together will be important for understanding how cargo transport in nerve cells is disrupted in neurodegenerative diseases.
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Affiliation(s)
- Allison M Gicking
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Tzu-Chen Ma
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Rui Jiang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Somayesadat Badieyan
- Department of Biological Chemistry, University of Michigan-Ann Arbor, Ann Arbor, United States
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of Michigan-Ann Arbor, Ann Arbor, United States
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
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8
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Budaitis BG, Badieyan S, Yue Y, Blasius TL, Reinemann DN, Lang MJ, Cianfrocco MA, Verhey KJ. A kinesin-1 variant reveals motor-induced microtubule damage in cells. Curr Biol 2022; 32:2416-2429.e6. [PMID: 35504282 PMCID: PMC9993403 DOI: 10.1016/j.cub.2022.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/16/2022]
Abstract
Kinesins drive the transport of cellular cargoes as they walk along microtubule tracks; however, recent work has suggested that the physical act of kinesins walking along microtubules can stress the microtubule lattice. Here, we describe a kinesin-1 KIF5C mutant with an increased ability to generate damage sites in the microtubule lattice as compared with the wild-type motor. The expression of the mutant motor in cultured cells resulted in microtubule breakage and fragmentation, suggesting that kinesin-1 variants with increased damage activity would have been selected against during evolution. The increased ability to damage microtubules is not due to the enhanced motility properties of the mutant motor, as the expression of the kinesin-3 motor KIF1A, which has similar single-motor motility properties, also caused increased microtubule pausing, bending, and buckling but not breakage. In cells, motor-induced microtubule breakage could not be prevented by increased α-tubulin K40 acetylation, a post-translational modification known to increase microtubule flexibility. In vitro, lattice damage induced by wild-type KIF5C was repaired by soluble tubulin and resulted in increased rescues and overall microtubule growth, whereas lattice damage induced by the KIF5C mutant resulted in larger repair sites that made the microtubule vulnerable to breakage and fragmentation when under mechanical stress. These results demonstrate that kinesin-1 motility causes defects in and damage to the microtubule lattice in cells. While cells have the capacity to repair lattice damage, conditions that exceed this capacity result in microtubule breakage and fragmentation and may contribute to human disease.
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Affiliation(s)
- Breane G Budaitis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Somayesadat Badieyan
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - T Lynne Blasius
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana N Reinemann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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9
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Ravala SK, Li S, Chen C, Cianfrocco MA, Cash JN, Tesmer JJG. New insights into regulation of P‐Rex1 autoinhibition. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Sheng Li
- Department of MedicineUniversity of CaliforniaSan DiegoCA
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10
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Li Y, Cianfrocco MA. Cloud computing platforms to support cryo-EM structure determination. Trends Biochem Sci 2021; 47:103-105. [PMID: 34895958 DOI: 10.1016/j.tibs.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022]
Abstract
Leveraging the power of single-particle cryo-electron microscopy (cryo-EM) requires robust and accessible computational infrastructure. Here, we summarize the cloud computing landscape and picture the outlook of a hybrid cryo-EM computing workflow, and make suggestions to the community to facilitate a future for cryo-EM that integrates into cloud computing infrastructure.
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Affiliation(s)
- Yilai Li
- Life Sciences Institute & Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Michael A Cianfrocco
- Life Sciences Institute & Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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11
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Solon AL, Tan Z, Schutt KL, Jepsen L, Haynes SE, Nesvizhskii AI, Sept D, Stumpff J, Ohi R, Cianfrocco MA. Kinesin-binding protein remodels the kinesin motor to prevent microtubule binding. Sci Adv 2021; 7:eabj9812. [PMID: 34797717 PMCID: PMC8604404 DOI: 10.1126/sciadv.abj9812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
Kinesins are regulated in space and time to ensure activation only in the presence of cargo. Kinesin-binding protein (KIFBP), which is mutated in Goldberg-Shprintzen syndrome, binds to and inhibits the catalytic motor heads of 8 of 45 kinesin superfamily members, but the mechanism remains poorly defined. Here, we used cryo–electron microscopy and cross-linking mass spectrometry to determine high-resolution structures of KIFBP alone and in complex with two mitotic kinesins, revealing structural remodeling of kinesin by KIFBP. We find that KIFBP remodels kinesin motors and blocks microtubule binding (i) via allosteric changes to kinesin and (ii) by sterically blocking access to the microtubule. We identified two regions of KIFBP necessary for kinesin binding and cellular regulation during mitosis. Together, this work further elucidates the molecular mechanism of KIFBP-mediated kinesin inhibition and supports a model in which structural rearrangement of kinesin motor domains by KIFBP abrogates motor protein activity.
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Affiliation(s)
- April L. Solon
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhenyu Tan
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Katherine L. Schutt
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Lauren Jepsen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sarah E. Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Michael A. Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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12
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Li L, Conradson DM, Bharat V, Kim MJ, Hsieh CH, Minhas PS, Papakyrikos AM, Durairaj AS, Ludlam A, Andreasson KI, Partridge L, Cianfrocco MA, Wang X. A mitochondrial membrane-bridging machinery mediates signal transduction of intramitochondrial oxidation. Nat Metab 2021; 3:1242-1258. [PMID: 34504353 PMCID: PMC8460615 DOI: 10.1038/s42255-021-00443-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Mitochondria are the main site for generating reactive oxygen species, which are key players in diverse biological processes. However, the molecular pathways of redox signal transduction from the matrix to the cytosol are poorly defined. Here we report an inside-out redox signal of mitochondria. Cysteine oxidation of MIC60, an inner mitochondrial membrane protein, triggers the formation of disulfide bonds and the physical association of MIC60 with Miro, an outer mitochondrial membrane protein. The oxidative structural change of this membrane-crossing complex ultimately elicits cellular responses that delay mitophagy, impair cellular respiration and cause oxidative stress. Blocking the MIC60-Miro interaction or reducing either protein, genetically or pharmacologically, extends lifespan and health-span of healthy fruit flies, and benefits multiple models of Parkinson's disease and Friedreich's ataxia. Our discovery provides a molecular basis for common treatment strategies against oxidative stress.
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Affiliation(s)
- Li Li
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Devon M Conradson
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Vinita Bharat
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Min Joo Kim
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Chung-Han Hsieh
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Paras S Minhas
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Neurosciences Intradepartmental Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Amanda M Papakyrikos
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
- Graduate Program in Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Anthony Ludlam
- Life Sciences Institute & Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Katrin I Andreasson
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Linda Partridge
- Institute of Healthy Ageing, Genetics, Evolution and Environment, University College London, London, UK
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Michael A Cianfrocco
- Life Sciences Institute & Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Xinnan Wang
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Maternal & Child Health Research Institute, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Kearns S, Mason FM, Rathmell WK, Park IY, Walker C, Verhey KJ, Cianfrocco MA. Molecular determinants for α-tubulin methylation by SETD2. J Biol Chem 2021; 297:100898. [PMID: 34157286 PMCID: PMC8294582 DOI: 10.1016/j.jbc.2021.100898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/28/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Post-translational modifications to tubulin are important for many microtubule-based functions inside cells. It was recently shown that methylation of tubulin by the histone methyltransferase SETD2 occurs on mitotic spindle microtubules during cell division, with its absence resulting in mitotic defects. However, the catalytic mechanism of methyl addition to tubulin is unclear. We used a truncated version of human wild type SETD2 (tSETD2) containing the catalytic SET and C-terminal Set2-Rpb1-interacting (SRI) domains to investigate the biochemical mechanism of tubulin methylation. We found that recombinant tSETD2 had a higher activity toward tubulin dimers than polymerized microtubules. Using recombinant single-isotype tubulin, we demonstrated that methylation was restricted to lysine 40 of α-tubulin. We then introduced pathogenic mutations into tSETD2 to probe the recognition of histone and tubulin substrates. A mutation in the catalytic domain (R1625C) allowed tSETD2 to bind to tubulin but not methylate it, whereas a mutation in the SRI domain (R2510H) caused loss of both tubulin binding and methylation. Further investigation of the role of the SRI domain in substrate binding found that mutations within this region had differential effects on the ability of tSETD2 to bind to tubulin versus the binding partner RNA polymerase II for methylating histones in vivo, suggesting distinct mechanisms for tubulin and histone methylation by SETD2. Finally, we found that substrate recognition also requires the negatively charged C-terminal tail of α-tubulin. Together, this study provides a framework for understanding how SETD2 serves as a dual methyltransferase for both histone and tubulin methylation.
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Affiliation(s)
- Sarah Kearns
- Program of Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank M Mason
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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14
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Spriggs CC, Badieyan S, Verhey KJ, Cianfrocco MA, Tsai B. Golgi-associated BICD adaptors couple ER membrane penetration and disassembly of a viral cargo. J Cell Biol 2021; 219:151622. [PMID: 32259203 PMCID: PMC7199864 DOI: 10.1083/jcb.201908099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/04/2019] [Accepted: 02/21/2020] [Indexed: 12/22/2022] Open
Abstract
During entry, viruses must navigate through the host endomembrane system, penetrate cellular membranes, and undergo capsid disassembly to reach an intracellular destination that supports infection. How these events are coordinated is unclear. Here, we reveal an unexpected function of a cellular motor adaptor that coordinates virus membrane penetration and disassembly. Polyomavirus SV40 traffics to the endoplasmic reticulum (ER) and penetrates a virus-induced structure in the ER membrane called “focus” to reach the cytosol, where it disassembles before nuclear entry to promote infection. We now demonstrate that the ER focus is constructed proximal to the Golgi-associated BICD2 and BICDR1 dynein motor adaptors; this juxtaposition enables the adaptors to directly bind to and disassemble SV40 upon arrival to the cytosol. Our findings demonstrate that positioning of the virus membrane penetration site couples two decisive infection events, cytosol arrival and disassembly, and suggest cargo remodeling as a novel function of dynein adaptors.
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Affiliation(s)
- Chelsey C Spriggs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Somayesadat Badieyan
- Department of Biological Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Michael A Cianfrocco
- Department of Biological Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
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15
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Badieyan S, Andreas MP, Giessen TW, Cianfrocco MA. Engineered Icosahedral Protein Cage as a Flexible Model System to Study Properties of Multi-Motor Transport of Viral Cargoes. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Lu TW, Aoto PC, Weng JH, Nielsen C, Cash JN, Hall J, Zhang P, Simon SM, Cianfrocco MA, Taylor SS. Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma. PLoS Biol 2020; 18:e3001018. [PMID: 33370777 PMCID: PMC7793292 DOI: 10.1371/journal.pbio.3001018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/08/2021] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
When the J-domain of the heat shock protein DnaJB1 is fused to the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), replacing exon 1, this fusion protein, J-C subunit (J-C), becomes the driver of fibrolamellar hepatocellular carcinoma (FL-HCC). Here, we use cryo-electron microscopy (cryo-EM) to characterize J-C bound to RIIβ, the major PKA regulatory (R) subunit in liver, thus reporting the first cryo-EM structure of any PKA holoenzyme. We report several differences in both structure and dynamics that could not be captured by the conventional crystallography approaches used to obtain prior structures. Most striking is the asymmetry caused by the absence of the second cyclic nucleotide binding (CNB) domain and the J-domain in one of the RIIβ:J-C protomers. Using molecular dynamics (MD) simulations, we discovered that this asymmetry is already present in the wild-type (WT) RIIβ2C2 but had been masked in the previous crystal structure. This asymmetry may link to the intrinsic allosteric regulation of all PKA holoenzymes and could also explain why most disease mutations in PKA regulatory subunits are dominant negative. The cryo-EM structure, combined with small-angle X-ray scattering (SAXS), also allowed us to predict the general position of the Dimerization/Docking (D/D) domain, which is essential for localization and interacting with membrane-anchored A-Kinase-Anchoring Proteins (AKAPs). This position provides a multivalent mechanism for interaction of the RIIβ holoenzyme with membranes and would be perturbed in the oncogenic fusion protein. The J-domain also alters several biochemical properties of the RIIβ holoenzyme: It is easier to activate with cAMP, and the cooperativity is reduced. These results provide new insights into how the finely tuned allosteric PKA signaling network is disrupted by the oncogenic J-C subunit, ultimately leading to the development of FL-HCC.
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Affiliation(s)
- Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Phillip C. Aoto
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Cole Nielsen
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Jennifer N. Cash
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - James Hall
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Ping Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Sanford M. Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, United States of America
| | - Michael A. Cianfrocco
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
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17
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Cash JN, Kearns S, Li Y, Cianfrocco MA. High-resolution cryo-EM using beam-image shift at 200 keV. IUCrJ 2020; 7:1179-1187. [PMID: 33209328 PMCID: PMC7642776 DOI: 10.1107/s2052252520013482] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/07/2020] [Indexed: 05/26/2023]
Abstract
Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilize beam-image shift to improve throughput. Despite implementation on 300 keV cryo-EM instruments, it remains unknown how well beam-image-shift data collection affects data quality on 200 keV instruments and the extent to which aberrations can be computationally corrected. To test this, a cryo-EM data set for aldolase was collected at 200 keV using beam-image shift and analyzed. This analysis shows that the instrument beam tilt and particle motion initially limited the resolution to 4.9 Å. After particle polishing and iterative rounds of aberration correction in RELION, a 2.8 Å resolution structure could be obtained. This analysis demonstrates that software correction of microscope aberrations can provide a significant improvement in resolution at 200 keV.
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Affiliation(s)
- Jennifer N. Cash
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Kearns
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yilai Li
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael A. Cianfrocco
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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18
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Seervai RNH, Jangid RK, Karki M, Tripathi DN, Jung SY, Kearns SE, Verhey KJ, Cianfrocco MA, Millis BA, Tyska MJ, Mason FM, Rathmell WK, Park IY, Dere R, Walker CL. The Huntingtin-interacting protein SETD2/HYPB is an actin lysine methyltransferase. Sci Adv 2020; 6:6/40/eabb7854. [PMID: 33008892 PMCID: PMC7852384 DOI: 10.1126/sciadv.abb7854] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
The methyltransferase SET domain-containing 2 (SETD2) was originally identified as Huntingtin (HTT) yeast partner B. However, a SETD2 function associated with the HTT scaffolding protein has not been elucidated, and no linkage between HTT and methylation has yet been uncovered. Here, we show that SETD2 is an actin methyltransferase that trimethylates lysine-68 (ActK68me3) in cells via its interaction with HTT and the actin-binding adapter HIP1R. ActK68me3 localizes primarily to the insoluble F-actin cytoskeleton in cells and regulates actin polymerization/depolymerization dynamics. Disruption of the SETD2-HTT-HIP1R axis inhibits actin methylation, causes defects in actin polymerization, and impairs cell migration. Together, these data identify SETD2 as a previously unknown HTT effector regulating methylation and polymerization of actin filaments and provide new avenues for understanding how defects in SETD2 and HTT drive disease via aberrant cytoskeletal methylation.
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Affiliation(s)
- Riyad N H Seervai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul K Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Durga Nand Tripathi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah E Kearns
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Bryan A Millis
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Biophotonics Center, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Matthew J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Frank M Mason
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Cheryl Lyn Walker
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Li Y, Cash JN, Tesmer JJG, Cianfrocco MA. High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines. Structure 2020; 28:858-869.e3. [PMID: 32294468 PMCID: PMC7347462 DOI: 10.1016/j.str.2020.03.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022]
Abstract
Single-particle cryoelectron microscopy (cryo-EM) continues to grow into a mainstream structural biology technique. Recent developments in data collection strategies alongside new sample preparation devices herald a future where users will collect multiple datasets per microscope session. To make cryo-EM data processing more automatic and user-friendly, we have developed an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep-learning and image-analysis tools. We have verified the performance of this pipeline on a number of datasets and extended its scope to include sample screening by the user-free assessment of the qualities of a series of datasets under different conditions. We propose that our workflow provides a decision-free solution for cryo-EM, making data preprocessing more generalized and robust in the high-throughput era as well as more convenient for users from a range of backgrounds.
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Affiliation(s)
- Yilai Li
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer N Cash
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - John J G Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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20
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Abstract
Cryo-electron microscopy (cryo-EM) has enjoyed explosive recent growth due to revolutionary advances in hardware and software, resulting in a steady stream of long-awaited, high-resolution structures with unprecedented atomic detail. With this comes an increased number of microscopes, cryo-EM facilities, and scientists eager to leverage the ability to determine protein structures without crystallization. However, numerous pitfalls and considerations beset the path toward high-resolution structures and are not necessarily obvious from literature surveys. Here, we detail the most common misconceptions when initiating a cryo-EM project and common technical hurdles, as well as their solutions, and we conclude with a vision for the future of this exciting field.
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Affiliation(s)
- Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics,Cornell University, Ithaca, New York 14850, United States
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21
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Eberhardt EL, Ludlam AV, Tan Z, Cianfrocco MA. Miro: A molecular switch at the center of mitochondrial regulation. Protein Sci 2020; 29:1269-1284. [PMID: 32056317 DOI: 10.1002/pro.3839] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/24/2022]
Abstract
The orchestration of mitochondria within the cell represents a critical aspect of cell biology. At the center of this process is the outer mitochondrial membrane protein, Miro. Miro coordinates diverse cellular processes by regulating connections between organelles and the cytoskeleton that range from mediating contacts between the endoplasmic reticulum and mitochondria to the regulation of both actin and microtubule motor proteins. Recently, a number of cell biological, biochemical, and protein structure studies have helped to characterize the myriad roles played by Miro. In addition to answering questions regarding Miro's function, these studies have opened the door to new avenues in the study of Miro in the cell. This review will focus on summarizing recent findings for Miro's structure, function, and activity while highlighting key questions that remain unanswered.
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Affiliation(s)
- Emily L Eberhardt
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan
| | - Anthony V Ludlam
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Zhenyu Tan
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Michael A Cianfrocco
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan
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22
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Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US. Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nat Commun 2019; 10:5540. [PMID: 31804488 PMCID: PMC6895043 DOI: 10.1038/s41467-019-13550-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity. MLL family histone methyltransferases deposit histone H3 Lys4 mono-/di-/tri-methylation and regulate gene expression in mammals. Here the authors report the single-particle cryo-EM structure of the NCP-bound human MLL1 core complex, shedding light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.
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Affiliation(s)
- Sang Ho Park
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Alex Ayoub
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Young-Tae Lee
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Hanseong Kim
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Wei Zheng
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Biao Zhang
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Liang Sha
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Sojin An
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yang Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yali Dou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA. .,Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.
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Cash JN, Urata S, Li S, Ravala SK, Avramova LV, Shost MD, Gutkind JS, Tesmer JJG, Cianfrocco MA. Cryo-electron microscopy structure and analysis of the P-Rex1-Gβγ signaling scaffold. Sci Adv 2019; 5:eaax8855. [PMID: 31663027 PMCID: PMC6795519 DOI: 10.1126/sciadv.aax8855] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/22/2019] [Indexed: 05/29/2023]
Abstract
PIP3-dependent Rac exchanger 1 (P-Rex1) is activated downstream of G protein-coupled receptors to promote neutrophil migration and metastasis. The structure of more than half of the enzyme and its regulatory G protein binding site are unknown. Our 3.2 Å cryo-EM structure of the P-Rex1-Gβγ complex reveals that the carboxyl-terminal half of P-Rex1 adopts a complex fold most similar to those of Legionella phosphoinositide phosphatases. Although catalytically inert, the domain coalesces with a DEP domain and two PDZ domains to form an extensive docking site for Gβγ. Hydrogen-deuterium exchange mass spectrometry suggests that Gβγ binding induces allosteric changes in P-Rex1, but functional assays indicate that membrane localization is also required for full activation. Thus, a multidomain assembly is key to the regulation of P-Rex1 by Gβγ and the formation of a membrane-localized scaffold optimized for recruitment of other signaling proteins such as PKA and PTEN.
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Affiliation(s)
- Jennifer N. Cash
- Department of Biological Chemistry & Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Sarah Urata
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Sandeep K. Ravala
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Larisa V. Avramova
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Michael D. Shost
- Department of Biological Chemistry & Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - J. Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, San Diego, CA, USA
| | - John J. G. Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Michael A. Cianfrocco
- Department of Biological Chemistry & Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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Cianfrocco MA. Cloud computing tools for training the next generation of cryo-EM structural biologists. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319097939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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25
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Cianfrocco MA, Lahiri I, DiMaio F, Leschziner AE. cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud. J Struct Biol 2018; 203:230-235. [PMID: 29864529 PMCID: PMC6091888 DOI: 10.1016/j.jsb.2018.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/14/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools ("cryoem-cloud-tools") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ∼55 h on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud.
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Affiliation(s)
- Michael A Cianfrocco
- Department of Cellular & Molecular Medicine, University of California - San Diego, La Jolla, CA, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States.
| | - Indrajit Lahiri
- Department of Cellular & Molecular Medicine, University of California - San Diego, La Jolla, CA, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, United States; Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Andres E Leschziner
- Department of Cellular & Molecular Medicine, University of California - San Diego, La Jolla, CA, United States; Section of Molecular Biology, Division of Biology, University of California - San Diego, La Jolla, CA, United States
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Htet ZM, DeSantis ME, Cianfrocco MA, Tran PT, Leschziner AE, Reck-Peterson SL. Two Opposing Modes of Cytoplasmic Dynein Regulation by Lis1. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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27
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Baldwin PR, Tan YZ, Eng ET, Rice WJ, Noble AJ, Negro CJ, Cianfrocco MA, Potter CS, Carragher B. Big data in cryoEM: automated collection, processing and accessibility of EM data. Curr Opin Microbiol 2017; 43:1-8. [PMID: 29100109 DOI: 10.1016/j.mib.2017.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/27/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022]
Abstract
The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing.
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Affiliation(s)
- Philip R Baldwin
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - William J Rice
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Alex J Noble
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Carl J Negro
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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DeSantis ME, Cianfrocco MA, Htet ZM, Tran PT, Reck-Peterson SL, Leschziner AE. Lis1 Has Two Opposing Modes of Regulating Cytoplasmic Dynein. Cell 2017; 170:1197-1208.e12. [PMID: 28886386 DOI: 10.1016/j.cell.2017.08.037] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/08/2017] [Accepted: 08/21/2017] [Indexed: 11/28/2022]
Abstract
Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a conserved regulator of dynein, binds to its motor domain and induces a tight microtubule-binding state in dynein. The work we present here-a combination of biochemistry, single-molecule assays, and cryoelectron microscopy-led to the surprising discovery that Lis1 has two opposing modes of regulating dynein, being capable of inducing both low and high affinity for the microtubule. We show that these opposing modes depend on the stoichiometry of Lis1 binding to dynein and that this stoichiometry is regulated by the nucleotide state of dynein's AAA3 domain. The low-affinity state requires Lis1 to also bind to dynein at a novel conserved site, mutation of which disrupts Lis1's function in vivo. We propose a new model for the regulation of dynein by Lis1.
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Affiliation(s)
- Morgan E DeSantis
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zaw Min Htet
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biophysics Graduate Program, Harvard University, Boston, MA 92105, USA
| | - Phuoc Tien Tran
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Section of Cellular and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA.
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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Cui J, Zhu Q, Zhang H, Cianfrocco MA, Leschziner AE, Dixon JE, Xiao J. Structure of Fam20A reveals a pseudokinase featuring a unique disulfide pattern and inverted ATP-binding. eLife 2017; 6. [PMID: 28432788 PMCID: PMC5413348 DOI: 10.7554/elife.23990] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/20/2017] [Indexed: 12/19/2022] Open
Abstract
Mutations in FAM20A cause tooth enamel defects known as Amelogenesis Imperfecta (AI) and renal calcification. We previously showed that Fam20A is a secretory pathway pseudokinase and allosterically activates the physiological casein kinase Fam20C to phosphorylate secreted proteins important for biomineralization (Cui et al., 2015). Here we report the nucleotide-free and ATP-bound structures of Fam20A. Fam20A exhibits a distinct disulfide bond pattern mediated by a unique insertion region. Loss of this insertion due to abnormal mRNA splicing interferes with the structure and function of Fam20A, resulting in AI. Fam20A binds ATP in the absence of divalent cations, and strikingly, ATP is bound in an inverted orientation compared to other kinases. Fam20A forms a dimer in the crystal, and residues in the dimer interface are critical for Fam20C activation. Together, these results provide structural insights into the function of Fam20A and shed light on the mechanism by which Fam20A mutations cause disease. DOI:http://dx.doi.org/10.7554/eLife.23990.001
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Affiliation(s)
- Jixin Cui
- Department of Pharmacology, University of California, San Diego, United States
| | - Qinyu Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Hui Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, United States
| | - Junyu Xiao
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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30
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Cianfrocco MA, DeSantis ME, Htet ZM, Tran PT, Leschziner AE, Reck-Peterson SL. Lis1 has Two Distinct Modes of Regulating Dynein's Mechanochemical Cycle. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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31
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Ciferri C, Chandramouli S, Leitner A, Donnarumma D, Cianfrocco MA, Gerrein R, Friedrich K, Aggarwal Y, Palladino G, Aebersold R, Norais N, Settembre EC, Carfi A. Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies. PLoS Pathog 2015; 11:e1005230. [PMID: 26485028 PMCID: PMC4617720 DOI: 10.1371/journal.ppat.1005230] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/24/2015] [Indexed: 12/05/2022] Open
Abstract
Human Cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and in fetuses following congenital infection. The glycoprotein complexes gH/gL/gO and gH/gL/UL128/UL130/UL131A (Pentamer) are required for HCMV entry in fibroblasts and endothelial/epithelial cells, respectively, and are targeted by potently neutralizing antibodies in the infected host. Using purified soluble forms of gH/gL/gO and Pentamer as well as a panel of naturally elicited human monoclonal antibodies, we determined the location of key neutralizing epitopes on the gH/gL/gO and Pentamer surfaces. Mass Spectrometry (MS) coupled to Chemical Crosslinking or to Hydrogen Deuterium Exchange was used to define residues that are either in proximity or part of neutralizing epitopes on the glycoprotein complexes. We also determined the molecular architecture of the gH/gL/gO- and Pentamer-antibody complexes by Electron Microscopy (EM) and 3D reconstructions. The EM analysis revealed that the Pentamer specific neutralizing antibodies bind to two opposite surfaces of the complex, suggesting that they may neutralize infection by different mechanisms. Together, our data identify the location of neutralizing antibodies binding sites on the gH/gL/gO and Pentamer complexes and provide a framework for the development of antibodies and vaccines against HCMV. Human Cytomegalovirus (HCMV) is a double stranded DNA, enveloped virus infecting >60% of the population worldwide. Typically asymptomatic in healthy adults, HCMV infection causes morbidity and mortality in immunocompromised patients and is the most common viral cause of birth defects in industrialized countries. Despite more than 30 years of research, however, no vaccine against HCMV is available. HCMV utilizes two distinct glycoprotein complexes, gH/gL/gO and gH/gL/UL128/UL130/UL131A (Pentamer), to enter fibroblast and endothelial/epithelial cells, respectively and both are neutralizing antibodies targets. We used orthogonal techniques to study the interaction between gH/gL/gO or Pentamer and a panel of naturally occurring human neutralizing antibodies. The results of this analysis identify three neutralizing epitopes in gH, which are conserved in both glycoproteins complexes, and a different subset of five neutralizing sites in the UL128/Ul130/Ul131A (ULs) portion of the Pentamer. Moreover, EM analysis defines two distinct surfaces targeted by neutralizing antibodies on the ULs suggesting different neutralization mechanisms. Our results reveal regions of the gH/gL/gO and Pentamer complexes important for eliciting strong neutralizing responses in humans and for function in viral entry. Together our data will guide the development of therapeutic monoclonal antibodies and vaccines against HCMV.
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Affiliation(s)
- Claudio Ciferri
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
- * E-mail: (CC); (AC)
| | - Sumana Chandramouli
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
| | - Alexander Leitner
- ETH Zürich, Department of Biology, Institute of Molecular Systems Biology, Zürich, Switzerland
| | | | - Michael A. Cianfrocco
- Harvard University, Department of Molecular and Cellular Biology, Cambridge, Massachusetts, United States of America
- Harvard Medical School, Department of Cell Biology, Boston, Massachusetts, United States of America
| | - Rachel Gerrein
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
| | - Kristian Friedrich
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
| | - Yukti Aggarwal
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
| | - Giuseppe Palladino
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
| | - Ruedi Aebersold
- ETH Zürich, Department of Biology, Institute of Molecular Systems Biology, Zürich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | | | - Ethan C. Settembre
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
| | - Andrea Carfi
- Novartis Vaccines (a GSK company), Cambridge, Massachusetts, United States of America
- * E-mail: (CC); (AC)
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Abstract
Until recently, dynein was the least understood of the cytoskeletal motors. However, a wealth of new structural, mechanistic, and cell biological data is shedding light on how this complicated minus-end-directed, microtubule-based motor works. Cytoplasmic dynein-1 performs a wide array of functions in most eukaryotes, both in interphase, in which it transports organelles, proteins, mRNAs, and viruses, and in mitosis and meiosis. Mutations in dynein or its regulators are linked to neurodevelopmental and neurodegenerative diseases. Here, we begin by providing a synthesis of recent data to describe the current model of dynein's mechanochemical cycle. Next, we discuss regulators of dynein, with particular focus on those that directly interact with the motor to modulate its recruitment to microtubules, initiate cargo transport, or activate minus-end-directed motility.
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Affiliation(s)
- Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Morgan E DeSantis
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
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Cianfrocco MA, Leschziner AE. Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud. eLife 2015; 4:e06664. [PMID: 25955969 PMCID: PMC4440898 DOI: 10.7554/elife.06664] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/01/2015] [Indexed: 01/27/2023] Open
Abstract
The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16-480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.
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Affiliation(s)
- Michael A Cianfrocco
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Andres E Leschziner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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Affiliation(s)
- Michael A Cianfrocco
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Andres E Leschziner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
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Abstract
Recent structural and biochemical studies of human TFIID have significantly increased our understanding of the mechanisms underlying the recruitment of TFIID to promoter DNA and its role in transcription initiation. Structural studies using cryo-EM revealed that modular interactions underlie TFIID’s ability to bind simultaneously multiple promoter motifs and to define a DNA state that will facilitate transcription initiation. Here we propose a general model of promoter binding by TFIID, where co-activators, activators, and histone modifications promote and/or stabilize a conformational state of TFIID that results in core promoter engagement. Within this high affinity conformation, we propose that TFIID’s extensive interaction with promoter DNA leads to topological changes in the DNA that facilitate the eventual loading of RNAP II. While more work is required to dissect the individual contributions of activators and repressors to TFIID’s DNA binding, the recent cryo-EM studies provide a physical framework to guide future structural, biophysical, and biochemical experiments.
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Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, Nogales E. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell 2013; 152:120-31. [PMID: 23332750 DOI: 10.1016/j.cell.2012.12.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/20/2012] [Accepted: 11/28/2012] [Indexed: 12/23/2022]
Abstract
A mechanistic description of metazoan transcription is essential for understanding the molecular processes that govern cellular decisions. To provide structural insights into the DNA recognition step of transcription initiation, we used single-particle electron microscopy (EM) to visualize human TFIID with promoter DNA. This analysis revealed that TFIID coexists in two predominant and distinct structural states that differ by a 100 Å translocation of TFIID's lobe A. The transition between these structural states is modulated by TFIIA, as the presence of TFIIA and promoter DNA facilitates the formation of a rearranged state of TFIID that enables promoter recognition and binding. DNA labeling and footprinting, together with cryo-EM studies, were used to map the locations of TATA, Initiator (Inr), motif ten element (MTE), and downstream core promoter element (DPE) promoter motifs within the TFIID-TFIIA-DNA structure. The existence of two structurally and functionally distinct forms of TFIID suggests that the different conformers may serve as specific targets for the action of regulatory factors.
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Affiliation(s)
- Michael A Cianfrocco
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
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