1
|
Abbaali I, Truong D, Wetzel DM, Morrissette NS. Toxoplasma replication is inhibited by MMV676477 without development of resistance. Cytoskeleton (Hoboken) 2024. [PMID: 38757481 DOI: 10.1002/cm.21876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/20/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
Protozoan parasites cause life-threatening infections in both humans and animals, including agriculturally significant livestock. Available treatments are typically narrow spectrum and are complicated by drug toxicity and the development of resistant parasites. Protozoan tubulin is an attractive target for the development of broad-spectrum antimitotic agents. The Medicines for Malaria Pathogen Box compound MMV676477 was previously shown to inhibit replication of kinetoplastid parasites, such as Leishmania amazonensis and Trypanosoma brucei, and the apicomplexan parasite Plasmodium falciparum by selectively stabilizing protozoan microtubules. In this report, we show that MMV676477 inhibits intracellular growth of the human apicomplexan pathogen Toxoplasma gondii with an EC50 value of ~50 nM. MMV676477 does not stabilize vertebrate microtubules or cause other toxic effects in human fibroblasts. The availability of tools for genetic studies makes Toxoplasma a useful model for studies of the cytoskeleton. We conducted a forward genetics screen for MMV676477 resistance, anticipating that missense mutations would delineate the binding site on protozoan tubulin. Unfortunately, we were unable to use genetics to dissect target interactions because no resistant parasites emerged. This outcome suggests that future drugs based on the MMV676477 scaffold would be less likely to be undermined by the emergence of drug resistance.
Collapse
Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Dawn M Wetzel
- Department of Pediatrics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Naomi S Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| |
Collapse
|
2
|
Desroches S, Harris AR. Quantifying cytoskeletal organization from optical microscopy data. Front Cell Dev Biol 2024; 11:1327994. [PMID: 38234685 PMCID: PMC10792062 DOI: 10.3389/fcell.2023.1327994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/07/2023] [Indexed: 01/19/2024] Open
Abstract
The actin cytoskeleton plays a pivotal role in a broad range of physiological processes including directing cell shape and subcellular organization, determining cell mechanical properties, and sensing and transducing mechanical forces. The versatility of the actin cytoskeleton arises from the ability of actin filaments to assemble into higher order structures through their interaction with a vast set of regulatory proteins. Actin filaments assemble into bundles, meshes, and networks, where different combinations of these structures fulfill specific functional roles. Analyzing the organization and abundance of different actin structures from optical microscopy data provides a valuable metric for assessing cell physiological function and changes associated with disease. However, quantitative measurements of the size, abundance, orientation, and distribution of different types of actin structure remains challenging both from an experimental and image analysis perspective. In this review, we summarize image analysis methods for extracting quantitative values that can be used for characterizing the organization of actin structures and provide selected examples. We summarize the potential sample types and metric reported with different approaches as a guide for selecting an image analysis strategy.
Collapse
Affiliation(s)
- Sarah Desroches
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, Canada
- Ottawa-Carleton Institute for Biomedical Engineering Graduate Program, Ottawa, ON, Canada
| | - Andrew R. Harris
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, Canada
| |
Collapse
|
3
|
Mostert D, Grolleman J, van Turnhout MC, Groenen BGW, Conte V, Sahlgren CM, Kurniawan NA, Bouten CVC. SFAlab: image-based quantification of mechano-active ventral actin stress fibers in adherent cells. Front Cell Dev Biol 2023; 11:1267822. [PMID: 37779894 PMCID: PMC10540851 DOI: 10.3389/fcell.2023.1267822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023] Open
Abstract
Ventral actin stress fibers (SFs) are a subset of actin SFs that begin and terminate at focal adhesion (FA) complexes. Ventral SFs can transmit forces from and to the extracellular matrix and serve as a prominent mechanosensing and mechanotransduction machinery for cells. Therefore, quantitative analysis of ventral SFs can lead to deeper understanding of the dynamic mechanical interplay between cells and their extracellular matrix (mechanoreciprocity). However, the dynamic nature and organization of ventral SFs challenge their quantification, and current quantification tools mainly focus on all SFs present in cells and cannot discriminate between subsets. Here we present an image analysis-based computational toolbox, called SFAlab, to quantify the number of ventral SFs and the number of ventral SFs per FA, and provide spatial information about the locations of the identified ventral SFs. SFAlab is built as an all-in-one toolbox that besides analyzing ventral SFs also enables the identification and quantification of (the shape descriptors of) nuclei, cells, and FAs. We validated SFAlab for the quantification of ventral SFs in human fetal cardiac fibroblasts and demonstrated that SFAlab analysis i) yields accurate ventral SF detection in the presence of image imperfections often found in typical fluorescence microscopy images, and ii) is robust against user subjectivity and potential experimental artifacts. To demonstrate the usefulness of SFAlab in mechanobiology research, we modulated actin polymerization and showed that inhibition of Rho kinase led to a significant decrease in ventral SF formation and the number of ventral SFs per FA, shedding light on the importance of the RhoA pathway specifically in ventral SF formation. We present SFAlab as a powerful open source, easy to use image-based analytical tool to increase our understanding of mechanoreciprocity in adherent cells.
Collapse
Affiliation(s)
- Dylan Mostert
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| | - Janine Grolleman
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| | - Mark C. van Turnhout
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Bart G. W. Groenen
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Vito Conte
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| | - Cecilia M. Sahlgren
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
- Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Nicholas A. Kurniawan
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| | - Carlijn V. C. Bouten
- Department of Biomedical Engineering, Laboratory for Cell and Tissue Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| |
Collapse
|
4
|
Paranjpe I, Wang X, Anandakrishnan N, Haydak JC, Van Vleck T, DeFronzo S, Li Z, Mendoza A, Liu R, Fu J, Forrest I, Zhou W, Lee K, O'Hagan R, Dellepiane S, Menon KM, Gulamali F, Kamat S, Gusella GL, Charney AW, Hofer I, Cho JH, Do R, Glicksberg BS, He JC, Nadkarni GN, Azeloglu EU. Deep learning on electronic medical records identifies distinct subphenotypes of diabetic kidney disease driven by genetic variations in the Rho pathway. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.06.23295120. [PMID: 37732187 PMCID: PMC10508814 DOI: 10.1101/2023.09.06.23295120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Kidney disease affects 50% of all diabetic patients; however, prediction of disease progression has been challenging due to inherent disease heterogeneity. We use deep learning to identify novel genetic signatures prognostically associated with outcomes. Using autoencoders and unsupervised clustering of electronic health record data on 1,372 diabetic kidney disease patients, we establish two clusters with differential prevalence of end-stage kidney disease. Exome-wide associations identify a novel variant in ARHGEF18, a Rho guanine exchange factor specifically expressed in glomeruli. Overexpression of ARHGEF18 in human podocytes leads to impairments in focal adhesion architecture, cytoskeletal dynamics, cellular motility, and RhoA/Rac1 activation. Mutant GEF18 is resistant to ubiquitin mediated degradation leading to pathologically increased protein levels. Our findings uncover the first known disease-causing genetic variant that affects protein stability of a cytoskeletal regulator through impaired degradation, a potentially novel class of expression quantitative trait loci that can be therapeutically targeted.
Collapse
|
5
|
Shilpashree PS, Ravi T, Thanuja MY, Anupama C, Ranganath SH, Suresh KV, Srinivas SP. Grading the Severity of Damage to the Perijunctional Actomyosin Ring and Zonula Occludens-1 of the Corneal Endothelium by Ensemble Learning Methods. J Ocul Pharmacol Ther 2023. [PMID: 36930844 DOI: 10.1089/jop.2022.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Purpose: In many epithelia, including the corneal endothelium, intracellular/extracellular stresses break down the perijunctional actomyosin ring (PAMR) and zonula occludens-1 (ZO-1) at the apical junctions. This study aims to grade the severity of damage to PAMR and ZO-1 through machine learning. Methods: Immunocytochemical images of PAMR and ZO-1 were drawn from recent studies on the corneal endothelium subjected to hypothermia and oxidative stress. The images were analyzed for their morphological (e.g., Hu moments) and textural features (based on gray-level co-occurrence matrix [GLCM] and Gabor filters). The extracted features were ranked by SHapley analysis and analysis of variance. Then top features were used to grade the severity of damage using a suite of ensemble classifiers, including random forest, bagging classifier (BC), AdaBoost, extreme gradient boosting, and stacking classifier. Results: A partial set of features from GLCM, along with Hu moments and the number of hexagons, enabled the classification of damage to PAMR into Control, Mild, Moderate, and Severe with the area under the receiver operating characteristics curve (AUC) = 0.92 and F1 score = 0.77 with BC. In contrast, a bank of Gabor filters provided a partial set of features that could be combined with Hu moments, branch length, and sharpness for the classification of ZO-1 images into four levels with AUC = 0.95 and F1 score of 0.8 with BC. Conclusions: We have developed a workflow that enables the stratification of damage to PAMR and ZO-1. The approach can be applied to similar data during drug discovery or pathophysiological studies of epithelia.
Collapse
Affiliation(s)
- Palanahalli S Shilpashree
- Department of Electronics and Communication, Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Tapanmitra Ravi
- School of Optometry, Indiana University, Bloomington, Indiana, USA
| | - M Y Thanuja
- Department of Chemical Engineering, and Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Chalimeswamy Anupama
- Department of Biotechnology, Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Sudhir H Ranganath
- Department of Chemical Engineering, and Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Kaggere V Suresh
- Department of Electronics and Communication, Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | | |
Collapse
|
6
|
Østerlund I, Persson S, Nikoloski Z. Tracing and tracking filamentous structures across scales: A systematic review. Comput Struct Biotechnol J 2022; 21:452-462. [PMID: 36618983 PMCID: PMC9804014 DOI: 10.1016/j.csbj.2022.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Filamentous structures are ubiquitous in nature, are studied in diverse scientific fields, and span vastly different spatial scales. Filamentous structures in biological systems fulfill different functions and often form dynamic networks that respond to perturbations. Therefore, characterizing the properties of filamentous structures and the networks they form is important to gain better understanding of systems level functions and dynamics. Filamentous structures are captured by various imaging technologies, and analysis of the resulting imaging data addresses two problems: (i) identification (tracing) of filamentous structures in a single snapshot and (ii) characterizing the dynamics (i.e., tracking) of filamentous structures over time. Therefore, considerable research efforts have been made in developing automated methods for tracing and tracking of filamentous structures. Here, we provide a systematic review in which we present, categorize, and discuss the state-of-the-art methods for tracing and tracking of filamentous structures in sparse and dense networks. We highlight the mathematical approaches, assumptions, and constraints particular for each method, allowing us to pinpoint outstanding challenges and offer perspectives for future research aimed at gaining better understanding of filamentous structures in biological systems.
Collapse
Affiliation(s)
- Isabella Østerlund
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark,,Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Staffan Persson
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany,Corresponding author at: Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| |
Collapse
|
7
|
Simple methods for quantifying super-resolved cortical actin. Sci Rep 2022; 12:2715. [PMID: 35177729 PMCID: PMC8854627 DOI: 10.1038/s41598-022-06702-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 02/04/2022] [Indexed: 11/09/2022] Open
Abstract
Cortical actin plays a key role in cell movement and division, but has also been implicated in the organisation of cell surface receptors such as G protein-coupled receptors. The actin mesh proximal to the inner membrane forms small fenced regions, or 'corrals', in which receptors can be constrained. Quantification of the actin mesh at the nanoscale has largely been attempted in single molecule datasets and electron micrographs. This work describes the development and validation of workflows for analysis of super resolved fixed cortical actin images obtained by Super Resolved Radial Fluctuations (SRRF), Structured Illumination Microscopy (3D-SIM) and Expansion Microscopy (ExM). SRRF analysis was used to show a significant increase in corral area when treating cells with the actin disrupting agent cytochalasin D (increase of 0.31 µm2 ± 0.04 SEM), and ExM analysis allowed for the quantitation of actin filament densities. Thus, this work allows complex actin networks to be quantified from super-resolved images and is amenable to both fixed and live cell imaging.
Collapse
|
8
|
Systematic Analysis of Clemastine, a Candidate Apicomplexan Parasite-Selective Tubulin-Targeting Agent. Int J Mol Sci 2021; 23:ijms23010068. [PMID: 35008492 PMCID: PMC8744746 DOI: 10.3390/ijms23010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Apicomplexan parasites, such as Toxoplasma gondii, Plasmodium spp., Babesia spp., and Cryptosporidium spp., cause significant morbidity and mortality. Existing treatments are problematic due to toxicity and the emergence of drug-resistant parasites. Because protozoan tubulin can be selectively disrupted by small molecules to inhibit parasite growth, we assembled an in vitro testing cascade to fully delineate effects of candidate tubulin-targeting drugs on Toxoplasma gondii and vertebrate host cells. Using this analysis, we evaluated clemastine, an antihistamine that has been previously shown to inhibit Plasmodium growth by competitively binding to the CCT/TRiC tubulin chaperone as a proof-of-concept. We concurrently analyzed astemizole, a distinct antihistamine that blocks heme detoxification in Plasmodium. Both drugs have EC50 values of ~2 µM and do not demonstrate cytotoxicity or vertebrate microtubule disruption at this concentration. Parasite subpellicular microtubules are shortened by treatment with either clemastine or astemizole but not after treatment with pyrimethamine, indicating that this effect is not a general response to antiparasitic drugs. Immunoblot quantification indicates that the total α-tubulin concentration of 0.02 pg/tachyzoite does not change with clemastine treatment. In conclusion, the testing cascade allows profiling of small-molecule effects on both parasite and vertebrate cell viability and microtubule integrity.
Collapse
|
9
|
Hauke L, Narasimhan S, Primeßnig A, Kaverina I, Rehfeldt F. A Focal Adhesion Filament Cross-correlation Kit for fast, automated segmentation and correlation of focal adhesions and actin stress fibers in cells. PLoS One 2021; 16:e0250749. [PMID: 34506490 PMCID: PMC8432882 DOI: 10.1371/journal.pone.0250749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
Focal adhesions (FAs) and associated actin stress fibers (SFs) form a complex mechanical system that mediates bidirectional interactions between cells and their environment. This linked network is essential for mechanosensing, force production and force transduction, thus directly governing cellular processes like polarization, migration and extracellular matrix remodeling. We introduce a tool for fast and robust coupled analysis of both FAs and SFs named the Focal Adhesion Filament Cross-correlation Kit (FAFCK). Our software can detect and record location, axes lengths, area, orientation, and aspect ratio of focal adhesion structures as well as the location, length, width and orientation of actin stress fibers. This enables users to automate analysis of the correlation of FAs and SFs and study the stress fiber system in a higher degree, pivotal to accurately evaluate transmission of mechanocellular forces between a cell and its surroundings. The FAFCK is particularly suited for unbiased and systematic quantitative analysis of FAs and SFs necessary for novel approaches of traction force microscopy that uses the additional data from the cellular side to calculate the stress distribution in the substrate. For validation and comparison with other tools, we provide datasets of cells of varying quality that are labelled by a human expert. Datasets and FAFCK are freely available as open source under the GNU General Public License.
Collapse
Affiliation(s)
- Lara Hauke
- Third Institute of Physics—Biophysics, Georg-August-University Göttingen, Göttingen, Germany
| | - Shwetha Narasimhan
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States of America
| | - Andreas Primeßnig
- Third Institute of Physics—Biophysics, Georg-August-University Göttingen, Göttingen, Germany
| | - Irina Kaverina
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States of America
- * E-mail: (IK); (FR)
| | - Florian Rehfeldt
- Third Institute of Physics—Biophysics, Georg-August-University Göttingen, Göttingen, Germany
- Experimental Physics I, University of Bayreuth, Bayreuth, Germany
- * E-mail: (IK); (FR)
| |
Collapse
|
10
|
Xia S, Lim YB, Zhang Z, Wang Y, Zhang S, Lim CT, Yim EKF, Kanchanawong P. Nanoscale Architecture of the Cortical Actin Cytoskeleton in Embryonic Stem Cells. Cell Rep 2020; 28:1251-1267.e7. [PMID: 31365868 DOI: 10.1016/j.celrep.2019.06.089] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/24/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
Mechanical cues influence pluripotent stem cell differentiation, but the underlying mechanisms are not well understood. Mouse embryonic stem cells (mESCs) exhibit unusual cytomechanical properties, including low cell stiffness and attenuated responses to substrate rigidity, but the underlying structural basis remains obscure. Using super-resolution microscopy to investigate the actin cytoskeleton in mESCs, we observed that the actin cortex consists of a distinctively sparse and isotropic network. Surprisingly, the architecture and mechanics of the mESC actin cortex appear to be largely myosin II-independent. The network density can be modulated by perturbing Arp2/3 and formin, whereas capping protein (CP) negatively regulates cell stiffness. Transient Arp2/3-containing aster-like structures are implicated in the organization and mechanical homeostasis of the cortical network. By generating a low-density network that physically excludes myosin II, the interplay between Arp2/3, formin, and CP governs the nanoscale architecture of the actin cortex and prescribes the cytomechanical properties of mESCs.
Collapse
Affiliation(s)
- Shumin Xia
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Ying Bena Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Zhen Zhang
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yilin Wang
- Department of Biology, South University of Science and Technology of China, Shenzhen 518055, China
| | - Shan Zhang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore; Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
| | - Evelyn K F Yim
- Department of Chemical Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.
| |
Collapse
|
11
|
Nowak J, Gennermann K, Persson S, Nikoloski Z. CytoSeg 2.0: automated extraction of actin filaments. Bioinformatics 2020; 36:2950-2951. [PMID: 31971582 PMCID: PMC7203740 DOI: 10.1093/bioinformatics/btaa035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 12/23/2019] [Accepted: 01/19/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Actin filaments (AFs) are dynamic structures that substantially change their organization over time. The dynamic behavior and the relatively low signal-to-noise ratio during live-cell imaging have rendered the quantification of the actin organization a difficult task. RESULTS We developed an automated image-based framework that extracts AFs from fluorescence microscopy images and represents them as networks, which are automatically analyzed to identify and compare biologically relevant features. Although the source code is freely available, we have now implemented the framework into a graphical user interface that can be installed as a Fiji plugin, thus enabling easy access by the research community. AVAILABILITY AND IMPLEMENTATION CytoSeg 2.0 is open-source software under the GPL and is available on Github: https://github.com/jnowak90/CytoSeg2.0. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jacqueline Nowak
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia.,Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Kristin Gennermann
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| |
Collapse
|
12
|
Krueger D, Quinkler T, Mortensen SA, Sachse C, De Renzis S. Cross-linker-mediated regulation of actin network organization controls tissue morphogenesis. J Cell Biol 2019; 218:2743-2761. [PMID: 31253650 PMCID: PMC6683744 DOI: 10.1083/jcb.201811127] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/29/2019] [Accepted: 06/04/2019] [Indexed: 11/22/2022] Open
Abstract
Spatio-temporal organization of actomyosin contraction during epithelial morphogenesis in Drosophila is regulated by the developmental modulation of actin cross-linking through induction of Bottleneck. Bottleneck protein restrains contractility by promoting actin bundling, functioning in a similar way to Filamin and in an opposite way to Fimbrin. Contraction of cortical actomyosin networks driven by myosin activation controls cell shape changes and tissue morphogenesis during animal development. In vitro studies suggest that contractility also depends on the geometrical organization of actin filaments. Here we analyze the function of actomyosin network topology in vivo using optogenetic stimulation of myosin-II in Drosophila embryos. We show that early during cellularization, hexagonally arrayed actomyosin fibers are resilient to myosin-II activation. Actomyosin fibers then acquire a ring-like conformation and become contractile and sensitive to myosin-II. This transition is controlled by Bottleneck, a Drosophila unique protein expressed for only a short time during early cellularization, which we show regulates actin bundling. In addition, it requires two opposing actin cross-linkers, Filamin and Fimbrin. Filamin acts synergistically with Bottleneck to facilitate hexagonal patterning, while Fimbrin controls remodeling of the hexagonal network into contractile rings. Thus, actin cross-linking regulates the spatio-temporal organization of actomyosin contraction in vivo, which is critical for tissue morphogenesis.
Collapse
Affiliation(s)
- Daniel Krueger
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Collaboration for joint PhD degree between European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Theresa Quinkler
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Simon Arnold Mortensen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Ernst-Ruska Center for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Jülich, Germany
| | - Stefano De Renzis
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| |
Collapse
|
13
|
Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. PLoS Biol 2019; 17:e2006540. [PMID: 30897078 PMCID: PMC6445471 DOI: 10.1371/journal.pbio.2006540] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/02/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022] Open
Abstract
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates. While the impact of localization and recruitment on kinase-substrate targeting can be readily assessed, evaluating the relative importance of direct phosphorylation site interactions remains challenging. In this study, we examine the STE20 family of protein serine-threonine kinases to investigate basic mechanisms of substrate targeting. We used peptide arrays to define the phosphorylation site specificity for the majority of STE20 kinases and categorized them into four distinct groups. Using structure-guided mutagenesis, we identified key specificity-determining residues within the kinase catalytic cleft, including an unappreciated role for the kinase β3-αC loop region in controlling specificity. Exchanging key residues between the STE20 kinases p21-activated kinase 4 (PAK4) and Mammalian sterile 20 kinase 4 (MST4) largely interconverted their phosphorylation site preferences. In cells, a reprogrammed PAK4 mutant, engineered to recognize MST substrates, failed to phosphorylate PAK4 substrates or to mediate remodeling of the actin cytoskeleton. In contrast, this mutant could rescue signaling through the Hippo pathway in cells lacking multiple MST kinases. These observations formally demonstrate the importance of catalytic site specificity for directing protein kinase signal transduction pathways. Our findings further suggest that phosphorylation site specificity is both necessary and sufficient to mediate distinct signaling outputs of STE20 kinases and imply broad applicability to other kinase signaling systems.
Collapse
Affiliation(s)
- Chad J. Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bert van de Kooij
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Byung Hak Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oriana S. Fisher
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Natasha L. Pirman
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Michael B. Yaffe
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|