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Locke TM, Fields R, Gizinski H, Otto GM, Shechner DM, Berg MD, Villen J, Sancak Y, Schweppe D. High-Throughput Identification of Calcium Regulated Proteins Across Diverse Proteomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.575273. [PMID: 38293219 PMCID: PMC10827220 DOI: 10.1101/2024.01.18.575273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Calcium ions play important roles in nearly every biological process, yet whole-proteome analysis of calcium effectors has been hindered by lack of high-throughput, unbiased, and quantitative methods to identify proteins-calcium engagement. To address this, we adapted protein thermostability assays in the budding yeast, human cells, and mouse mitochondria. Based on calcium-dependent thermostability, we identified 2884 putative calcium-regulated proteins across human, mouse, and yeast proteomes. These data revealed calcium engagement of novel signaling hubs and cellular processes, including metabolic enzymes and the spliceosome. Cross-species comparison of calcium-protein engagement and mutagenesis experiments identified residue-specific cation engagement, even within well-known EF-hand domains. Additionally, we found that the dienoyl-CoA reductase DECR1 binds calcium at physiologically-relevant concentrations with substrate-specific affinity, suggesting direct calcium regulation of mitochondrial fatty acid oxidation. These unbiased, proteomic analyses of calcium effectors establish a key resource to dissect cation engagement and its mechanistic effects across multiple species and diverse biological processes.
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Affiliation(s)
- Timothy M Locke
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Hayden Gizinski
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - George M Otto
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - David M Shechner
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Matthew D Berg
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Judit Villen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Yasemin Sancak
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Devin Schweppe
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
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Varabyou A, Erdogdu B, Salzberg SL, Pertea M. Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage. NATURE COMPUTATIONAL SCIENCE 2023; 3:700-708. [PMID: 38098813 PMCID: PMC10718564 DOI: 10.1038/s43588-023-00496-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 12/17/2023]
Abstract
ORFanage is a system designed to assign open reading frames (ORFs) to known and novel gene transcripts while maximizing similarity to annotated proteins. The primary intended use of ORFanage is the identification of ORFs in the assembled results of RNA sequencing experiments, a capability that most transcriptome assembly methods do not have. Our experiments demonstrate how ORFanage can be used to find novel protein variants in RNA-seq datasets, and to improve the annotations of ORFs in tens of thousands of transcript models in the human annotation databases. Through its implementation of a highly accurate and efficient pseudo-alignment algorithm, ORFanage is substantially faster than other ORF annotation methods, enabling its application to very large datasets. When used to analyze transcriptome assemblies, ORFanage can aid in the separation of signal from transcriptional noise and the identification of likely functional transcript variants, ultimately advancing our understanding of biology and medicine.
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Affiliation(s)
- Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Beril Erdogdu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
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Varabyou A, Erdogdu B, Salzberg SL, Pertea M. Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533704. [PMID: 36993373 PMCID: PMC10055401 DOI: 10.1101/2023.03.23.533704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
ORFanage is a system designed to assign open reading frames (ORFs) to both known and novel gene transcripts while maximizing similarity to annotated proteins. The primary intended use of ORFanage is the identification of ORFs in the assembled results of RNA sequencing (RNA-seq) experiments, a capability that most transcriptome assembly methods do not have. Our experiments demonstrate how ORFanage can be used to find novel protein variants in RNA-seq datasets, and to improve the annotations of ORFs in tens of thousands of transcript models in the RefSeq and GENCODE human annotation databases. Through its implementation of a highly accurate and efficient pseudo-alignment algorithm, ORFanage is substantially faster than other ORF annotation methods, enabling its application to very large datasets. When used to analyze transcriptome assemblies, ORFanage can aid in the separation of signal from transcriptional noise and the identification of likely functional transcript variants, ultimately advancing our understanding of biology and medicine.
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Affiliation(s)
- Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Beril Erdogdu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
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Grewal T, Enrich C, Rentero C, Buechler C. Annexins in Adipose Tissue: Novel Players in Obesity. Int J Mol Sci 2019; 20:ijms20143449. [PMID: 31337068 PMCID: PMC6678658 DOI: 10.3390/ijms20143449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Obesity and the associated comorbidities are a growing health threat worldwide. Adipose tissue dysfunction, impaired adipokine activity, and inflammation are central to metabolic diseases related to obesity. In particular, the excess storage of lipids in adipose tissues disturbs cellular homeostasis. Amongst others, organelle function and cell signaling, often related to the altered composition of specialized membrane microdomains (lipid rafts), are affected. Within this context, the conserved family of annexins are well known to associate with membranes in a calcium (Ca2+)- and phospholipid-dependent manner in order to regulate membrane-related events, such as trafficking in endo- and exocytosis and membrane microdomain organization. These multiple activities of annexins are facilitated through their diverse interactions with a plethora of lipids and proteins, often in different cellular locations and with consequences for the activity of receptors, transporters, metabolic enzymes, and signaling complexes. While increasing evidence points at the function of annexins in lipid homeostasis and cell metabolism in various cells and organs, their role in adipose tissue, obesity and related metabolic diseases is still not well understood. Annexin A1 (AnxA1) is a potent pro-resolving mediator affecting the regulation of body weight and metabolic health. Relevant for glucose metabolism and fatty acid uptake in adipose tissue, several studies suggest AnxA2 to contribute to coordinate glucose transporter type 4 (GLUT4) translocation and to associate with the fatty acid transporter CD36. On the other hand, AnxA6 has been linked to the control of adipocyte lipolysis and adiponectin release. In addition, several other annexins are expressed in fat tissues, yet their roles in adipocytes are less well examined. The current review article summarizes studies on the expression of annexins in adipocytes and in obesity. Research efforts investigating the potential role of annexins in fat tissue relevant to health and metabolic disease are discussed.
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Affiliation(s)
- Thomas Grewal
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Carlos Enrich
- Department of Biomedicine, Unit of Cell Biology, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Carles Rentero
- Department of Biomedicine, Unit of Cell Biology, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
- Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Christa Buechler
- Department of Internal Medicine I, Regensburg University Hospital, 93053 Regensburg, Germany.
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McCulloch KM, Yamakawa I, Shifrin DA, McConnell RE, Foegeding NJ, Singh PK, Mao S, Tyska MJ, Iverson TM. An alternative N-terminal fold of the intestine-specific annexin A13a induces dimerization and regulates membrane-binding. J Biol Chem 2019; 294:3454-3463. [PMID: 30610115 DOI: 10.1074/jbc.ra118.004571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/20/2018] [Indexed: 12/11/2022] Open
Abstract
Annexin proteins function as Ca2+-dependent regulators of membrane trafficking and repair that may also modulate membrane curvature. Here, using high-resolution confocal imaging, we report that the intestine-specific annexin A13 (ANX A13) localizes to the tips of intestinal microvilli and determined the crystal structure of the ANX A13a isoform to 2.6 Å resolution. The structure revealed that the N terminus exhibits an alternative fold that converts the first two helices and the associated helix-loop-helix motif into a continuous α-helix, as stabilized by a domain-swapped dimer. We also found that the dimer is present in solution and partially occludes the membrane-binding surfaces of annexin, suggesting that dimerization may function as a means for regulating membrane binding. Accordingly, as revealed by in vitro binding and cellular localization assays, ANX A13a variants that favor a monomeric state exhibited increased membrane association relative to variants that favor the dimeric form. Together, our findings support a mechanism for how the association of the ANX A13a isoform with the membrane is regulated.
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Affiliation(s)
| | | | | | | | | | | | - Suli Mao
- Cell and Developmental Biology, and
| | | | - T M Iverson
- From the Departments of Pharmacology, .,Biochemistry.,the Center for Structural Biology, and.,the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232
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López-Rodríguez JC, Martínez-Carmona FJ, Rodríguez-Crespo I, Lizarbe MA, Turnay J. Molecular dissection of the membrane aggregation mechanisms induced by monomeric annexin A2. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:863-873. [DOI: 10.1016/j.bbamcr.2018.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 01/15/2023]
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