1
|
Adikes RC, Hallett RA, Saway BF, Kuhlman B, Slep KC. Control of microtubule dynamics using an optogenetic microtubule plus end-F-actin cross-linker. J Cell Biol 2017; 217:779-793. [PMID: 29259096 PMCID: PMC5800807 DOI: 10.1083/jcb.201705190] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 05/26/2017] [Revised: 11/07/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023] Open
Abstract
SxIP-iLID is a novel optogenetic tool designed to assess the temporal role of proteins on microtubule dynamics. The authors establish that optogenetic cross-linking of microtubule and actin networks decreases MT growth velocities and increases the cell area void of microtubules. We developed a novel optogenetic tool, SxIP–improved light-inducible dimer (iLID), to facilitate the reversible recruitment of factors to microtubule (MT) plus ends in an end-binding protein–dependent manner using blue light. We show that SxIP-iLID can track MT plus ends and recruit tgRFP-SspB upon blue light activation. We used this system to investigate the effects of cross-linking MT plus ends and F-actin in Drosophila melanogaster S2 cells to gain insight into spectraplakin function and mechanism. We show that SxIP-iLID can be used to temporally recruit an F-actin binding domain to MT plus ends and cross-link the MT and F-actin networks. Cross-linking decreases MT growth velocities and generates a peripheral MT exclusion zone. SxIP-iLID facilitates the general recruitment of specific factors to MT plus ends with temporal control enabling researchers to systematically regulate MT plus end dynamics and probe MT plus end function in many biological processes.
Collapse
Affiliation(s)
- Rebecca C Adikes
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ryan A Hallett
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Brian F Saway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kevin C Slep
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| |
Collapse
|
2
|
Zimmerman SP, Hallett RA, Bourke AM, Bear JE, Kennedy MJ, Kuhlman B. Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization. Biochemistry 2016; 55:5264-71. [PMID: 27529180 DOI: 10.1021/acs.biochem.6b00529] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inducible dimers are powerful tools for controlling biological processes through colocalizing signaling molecules. To be effective, an inducible system should have a dissociation constant in the "off" state that is greater (i.e., weaker affinity) than the concentrations of the molecules that are being controlled, and in the "on" state a dissociation constant that is less (i.e., stronger affinity) than the relevant protein concentrations. Here, we reengineer the interaction between the light inducible dimer, iLID, and its binding partner SspB, to better control proteins present at high effective concentrations (5-100 μM). iLID contains a light-oxygen-voltage (LOV) domain that undergoes a conformational change upon activation with blue light and exposes a peptide motif, ssrA, that binds to SspB. The new variant of the dimer system contains a single SspB point mutation (A58V), and displays a 42-fold change in binding affinity when activated with blue light (from 3 ± 2 μM to 125 ± 40 μM) and allows for light-activated colocalization of transmembrane proteins in neurons, where a higher affinity switch (0.8-47 μM) was less effective because more colocalization was seen in the dark. Additionally, with a point mutation in the LOV domain (N414L), we lengthened the reversion half-life of iLID. This expanded suite of light induced dimers increases the variety of cellular pathways that can be targeted with light.
Collapse
Affiliation(s)
| | | | - Ashley M Bourke
- Department of Pharmacology, University of Colorado School of Medicine , Aurora, Colorado 80045, United States
| | | | - Matthew J Kennedy
- Department of Pharmacology, University of Colorado School of Medicine , Aurora, Colorado 80045, United States
| | | |
Collapse
|
3
|
Hallett RA, Zimmerman SP, Yumerefendi H, Bear JE, Kuhlman B. Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide. ACS Synth Biol 2016; 5:53-64. [PMID: 26474029 DOI: 10.1021/acssynbio.5b00119] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-inducible dimers are powerful tools for cellular optogenetics, as they can be used to control the localization and activity of proteins with high spatial and temporal resolution. Despite the generality of the approach, application of light-inducible dimers is not always straightforward, as it is frequently necessary to test alternative dimer systems and fusion strategies before the desired biological activity is achieved. This process is further hindered by an incomplete understanding of the biophysical/biochemical mechanisms by which available dimers behave and how this correlates to in vivo function. To better inform the engineering process, we examined the biophysical and biochemical properties of three blue-light-inducible dimer variants (cryptochrome2 (CRY2)/CIB1, iLID/SspB, and LOVpep/ePDZb) and correlated these characteristics to in vivo colocalization and functional assays. We find that the switches vary dramatically in their dark and lit state binding affinities and that these affinities correlate with activity changes in a variety of in vivo assays, including transcription control, intracellular localization studies, and control of GTPase signaling. Additionally, for CRY2, we observe that light-induced changes in homo-oligomerization can have significant effects on activity that are sensitive to alternative fusion strategies.
Collapse
Affiliation(s)
- Ryan A. Hallett
- Department of Biochemistry & Biophysics, ‡Department of Cell Biology & Physiology, §UNC Lineberger Comprehensive Cancer Center, ∥Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Seth P. Zimmerman
- Department of Biochemistry & Biophysics, ‡Department of Cell Biology & Physiology, §UNC Lineberger Comprehensive Cancer Center, ∥Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hayretin Yumerefendi
- Department of Biochemistry & Biophysics, ‡Department of Cell Biology & Physiology, §UNC Lineberger Comprehensive Cancer Center, ∥Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - James E. Bear
- Department of Biochemistry & Biophysics, ‡Department of Cell Biology & Physiology, §UNC Lineberger Comprehensive Cancer Center, ∥Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Brian Kuhlman
- Department of Biochemistry & Biophysics, ‡Department of Cell Biology & Physiology, §UNC Lineberger Comprehensive Cancer Center, ∥Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
4
|
Strande NT, Carvajal-Garcia J, Hallett RA, Waters CA, Roberts SA, Strom C, Kuhlman B, Ramsden DA. Requirements for 5'dRP/AP lyase activity in Ku. Nucleic Acids Res 2014; 42:11136-43. [PMID: 25200085 PMCID: PMC4176175 DOI: 10.1093/nar/gku796] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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] [Indexed: 11/14/2022] Open
Abstract
The non-homologous end joining (NHEJ) pathway is used in diverse species to repair chromosome breaks, and is defined in part by a requirement for Ku. We previously demonstrated mammalian Ku has intrinsic 5′ deoxyribosephosphate (5′dRP) and apurinic/apyrimidinic (AP) lyase activity, and showed this activity is important for excising abasic site damage from ends. Here we employ systematic mutagenesis to clarify the protein requirements for this activity. We identify lysine 31 in the 70 kD subunit (Ku70 K31) as the primary candidate nucleophile required for catalysis, but additional mutation of Ku70 K160 and six other lysines within Ku80 were required to eliminate all activity. Ku from Saccharomyces cerevisiae also possesses 5′dRP/AP lyase activity, and robust activity was also reliant on lysines in Ku70 analogous to K31 and K160. By comparison, these lysines are not conserved in Xenopus laevis Ku, and Ku from this species has negligible activity. A role for residues flanking Ku70 K31 in expanding the range of abasic site contexts that can be used as substrate was also identified. Our results suggest an active site well located to provide the substrate specificity required for its biological role.
Collapse
Affiliation(s)
- Natasha T Strande
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Juan Carvajal-Garcia
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryan A Hallett
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Crystal A Waters
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven A Roberts
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Christina Strom
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Brian Kuhlman
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
5
|
Lungu OI, Hallett RA, Choi EJ, Aiken MJ, Hahn KM, Kuhlman B. Designing photoswitchable peptides using the AsLOV2 domain. ACTA ACUST UNITED AC 2012; 19:507-17. [PMID: 22520757 DOI: 10.1016/j.chembiol.2012.02.006] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/12/2012] [Accepted: 02/01/2012] [Indexed: 10/28/2022]
Abstract
Photocontrol of functional peptides is a powerful tool for spatial and temporal control of cell signaling events. We show that the genetically encoded light-sensitive LOV2 domain of Avena Sativa phototropin 1 (AsLOV2) can be used to reversibly photomodulate the affinity of peptides for their binding partners. Sequence analysis and molecular modeling were used to embed two peptides into the Jα helix of the AsLOV2 domain while maintaining AsLOV2 structure in the dark but allowing for binding to effector proteins when the Jα helix unfolds in the light. Caged versions of the ipaA and SsrA peptides, LOV-ipaA and LOV-SsrA, bind their targets with 49- and 8-fold enhanced affinity in the light, respectively. These switches can be used as general tools for light-dependent colocalization, which we demonstrate with photo-activable gene transcription in yeast.
Collapse
Affiliation(s)
- Oana I Lungu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | | | | | | | | |
Collapse
|