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Zhao A, Varady S, O'Kelley-Bangsberg M, Deng V, Platenkamp A, Wijngaard P, Bern M, Gormley W, Kushkowski E, Thompson K, Tibbetts L, Conner AT, Noeckel D, Teran A, Ritz A, Applewhite DA. From network analysis to experimental validation: identification of regulators of non-muscle myosin II contractility using the folded-gastrulation signaling pathway. BMC Mol Cell Biol 2023; 24:32. [PMID: 37821823 PMCID: PMC10568788 DOI: 10.1186/s12860-023-00492-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023] Open
Abstract
The morphogenetic process of apical constriction, which relies on non-muscle myosin II (NMII) generated constriction of apical domains of epithelial cells, is key to the development of complex cellular patterns. Apical constriction occurs in almost all multicellular organisms, but one of the most well-characterized systems is the Folded-gastrulation (Fog)-induced apical constriction that occurs in Drosophila. The binding of Fog to its cognizant receptors Mist/Smog results in a signaling cascade that leads to the activation of NMII-generated contractility. Despite our knowledge of key molecular players involved in Fog signaling, we sought to explore whether other proteins have an undiscovered role in its regulation. We developed a computational method to predict unidentified candidate NMII regulators using a network of pairwise protein-protein interactions called an interactome. We first constructed a Drosophila interactome of over 500,000 protein-protein interactions from several databases that curate high-throughput experiments. Next, we implemented several graph-based algorithms that predicted 14 proteins potentially involved in Fog signaling. To test these candidates, we used RNAi depletion in combination with a cellular contractility assay in Drosophila S2R + cells, which respond to Fog by contracting in a stereotypical manner. Of the candidates we screened using this assay, two proteins, the serine/threonine phosphatase Flapwing and the putative guanylate kinase CG11811 were demonstrated to inhibit cellular contractility when depleted, suggestive of their roles as novel regulators of the Fog pathway.
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Affiliation(s)
- Andy Zhao
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Sophia Varady
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | | | - Vicki Deng
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Amy Platenkamp
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Petra Wijngaard
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Miriam Bern
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Wyatt Gormley
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Elaine Kushkowski
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Kat Thompson
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Logan Tibbetts
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - A Tamar Conner
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - David Noeckel
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Aidan Teran
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Anna Ritz
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA.
| | - Derek A Applewhite
- Reed College Department of Biology, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA.
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Zeng H, Zhang J, Preising GA, Rubel T, Singh P, Ritz A. Graphery: interactive tutorials for biological network algorithms. Nucleic Acids Res 2021; 49:W257-W262. [PMID: 34037782 PMCID: PMC8262715 DOI: 10.1093/nar/gkab420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 11/14/2022] Open
Abstract
Networks have been an excellent framework for modeling complex biological information, but the methodological details of network-based tools are often described for a technical audience. We have developed Graphery, an interactive tutorial webserver that illustrates foundational graph concepts frequently used in network-based methods. Each tutorial describes a graph concept along with executable Python code that can be interactively run on a graph. Users navigate each tutorial using their choice of real-world biological networks that highlight the diverse applications of network algorithms. Graphery also allows users to modify the code within each tutorial or write new programs, which all can be executed without requiring an account. Graphery accepts ideas for new tutorials and datasets that will be shaped by both computational and biological researchers, growing into a community-contributed learning platform. Graphery is available at https://graphery.reedcompbio.org/.
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Affiliation(s)
- Heyuan Zeng
- Computer Science Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA.,Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
| | - Jinbiao Zhang
- Information and Communication Technology Department, Xiamen University Malaysia, Jalan Sunsuria, Bandar Sunsuria, 43900 Sepang, Selangor Darul Ehsan, Malaysia
| | - Gabriel A Preising
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
| | - Tobias Rubel
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
| | - Pramesh Singh
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
| | - Anna Ritz
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
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Platenkamp A, Detmar E, Sepulveda L, Ritz A, Rogers SL, Applewhite DA. The Drosophila melanogaster Rab GAP RN-tre cross-talks with the Rho1 signaling pathway to regulate nonmuscle myosin II localization and function. Mol Biol Cell 2020; 31:2379-2397. [PMID: 32816624 PMCID: PMC7851959 DOI: 10.1091/mbc.e20-03-0181] [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] [Indexed: 12/04/2022] Open
Abstract
To identify novel regulators of nonmuscle myosin II (NMII) we performed an image-based RNA interference screen using stable Drosophila melanogaster S2 cells expressing the enhanced green fluorescent protein (EGFP)-tagged regulatory light chain (RLC) of NMII and mCherry-Actin. We identified the Rab-specific GTPase-activating protein (GAP) RN-tre as necessary for the assembly of NMII RLC into contractile actin networks. Depletion of RN-tre led to a punctate NMII phenotype, similar to what is observed following depletion of proteins in the Rho1 pathway. Depletion of RN-tre also led to a decrease in active Rho1 and a decrease in phosphomyosin-positive cells by immunostaining, while expression of constitutively active Rho or Rho-kinase (Rok) rescues the punctate phenotype. Functionally, RN-tre depletion led to an increase in actin retrograde flow rate and cellular contractility in S2 and S2R+ cells, respectively. Regulation of NMII by RN-tre is only partially dependent on its GAP activity as overexpression of constitutively active Rabs inactivated by RN-tre failed to alter NMII RLC localization, while a GAP-dead version of RN-tre partially restored phosphomyosin staining. Collectively, our results suggest that RN-tre plays an important regulatory role in NMII RLC distribution, phosphorylation, and function, likely through Rho1 signaling and putatively serving as a link between the secretion machinery and actomyosin contractility.
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Affiliation(s)
| | - Elizabeth Detmar
- Department of Biology & Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Liz Sepulveda
- Department of Biology, Reed College, Portland, OR 97202
| | - Anna Ritz
- Department of Biology, Reed College, Portland, OR 97202
| | - Stephen L Rogers
- Department of Biology & Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
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