1
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Church MC, Workman JL. The SWI/SNF chromatin remodeling complex: a critical regulator of metabolism. Biochem Soc Trans 2024; 52:1327-1337. [PMID: 38666605 DOI: 10.1042/bst20231141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
The close relationship between chromatin and metabolism has been well-studied in recent years. Many metabolites have been found to be cofactors used to modify chromatin, and these modifications can in turn affect gene transcription. One chromatin-associated factor responsible for regulating transcription is the SWI/SNF complex, an ATP-dependent chromatin remodeler conserved throughout eukaryotes. SWI/SNF was originally described in yeast as regulating genes involved in carbon source metabolism and mating type switching, and its mammalian counterpart has been extensively studied for its role in diseases such as cancer. The yeast SWI/SNF complex is closely associated with activation of stress response genes, many of which have metabolic functions. It is now recognized that this is a conserved function of the complex, and recent work has shown that mammalian SWI/SNF is also a key regulator of metabolic transcription. Emerging evidence suggests that loss of SWI/SNF introduces vulnerabilities to cells due to this metabolic influence, and that this may present opportunities for treatment of SWI/SNF-deficient cancers.
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Affiliation(s)
- Michael C Church
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
| | - Jerry L Workman
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
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2
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Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. RESEARCH SQUARE 2024:rs.3.rs-4477977. [PMID: 38883712 PMCID: PMC11177979 DOI: 10.21203/rs.3.rs-4477977/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. Here, we focus on the first two domains of coronavirus nucleocapsid proteins: the disordered N-terminal domain (NTD) and the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system for exploring the interplay between an IDR adjacent to a folded domain and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved dynamic and disordered RNA:protein complex is found across nucleocapsid protein orthologs despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Present Address, Program In Cellular and Molecular Medicine (PCMM), Boston Children’s Hospital, Boston, MA, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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3
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Wu Z, Pope SD, Ahmed NS, Leung DL, Hajjar S, Yue Q, Anand DM, Kopp EB, Okin D, Ma W, Kagan JC, Hargreaves DC, Medzhitov R, Zhou X. Control of Inflammatory Response by Tissue Microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.592432. [PMID: 38798655 PMCID: PMC11118380 DOI: 10.1101/2024.05.10.592432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Inflammation is an essential defense response but operates at the cost of normal functions. Whether and how the negative impact of inflammation is monitored remains largely unknown. Acidification of the tissue microenvironment is associated with inflammation. Here we investigated whether macrophages sense tissue acidification to adjust inflammatory responses. We found that acidic pH restructured the inflammatory response of macrophages in a gene-specific manner. We identified mammalian BRD4 as a novel intracellular pH sensor. Acidic pH disrupts the transcription condensates containing BRD4 and MED1, via histidine-enriched intrinsically disordered regions. Crucially, decrease in macrophage intracellular pH is necessary and sufficient to regulate transcriptional condensates in vitro and in vivo, acting as negative feedback to regulate the inflammatory response. Collectively, these findings uncovered a pH-dependent switch in transcriptional condensates that enables environmental sensing to directly control inflammation, with a broader implication for calibrating the magnitude and quality of inflammation by the inflammatory cost.
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Affiliation(s)
- Zhongyang Wu
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Scott D. Pope
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Nasiha S. Ahmed
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Diana L. Leung
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stephanie Hajjar
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Qiuyu Yue
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Diya M. Anand
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Elizabeth B. Kopp
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Daniel Okin
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02115
| | - Weiyi Ma
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonathan C. Kagan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Diana C. Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ruslan Medzhitov
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine
| | - Xu Zhou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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4
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Cascarina SM, Ross ED. Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life. PLoS Comput Biol 2024; 20:e1011372. [PMID: 38748749 PMCID: PMC11132505 DOI: 10.1371/journal.pcbi.1011372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 05/28/2024] [Accepted: 05/04/2024] [Indexed: 05/29/2024] Open
Abstract
Low-complexity domains (LCDs) in proteins are typically enriched in one or two predominant amino acids. As a result, LCDs often exhibit unusual structural/biophysical tendencies and can occupy functional niches. However, for each organism, protein sequences must be compatible with intracellular biomolecules and physicochemical environment, both of which vary from organism to organism. This raises the possibility that LCDs may occupy sequence spaces in select organisms that are otherwise prohibited in most organisms. Here, we report a comprehensive survey and functional analysis of LCDs in all known reference proteomes (>21k organisms), with added focus on rare and unusual types of LCDs. LCDs were classified according to both the primary amino acid and secondary amino acid in each LCD sequence, facilitating detailed comparisons of LCD class frequencies across organisms. Examination of LCD classes at different depths (i.e., domain of life, organism, protein, and per-residue levels) reveals unique facets of LCD frequencies and functions. To our surprise, all 400 LCD classes occur in nature, although some are exceptionally rare. A number of rare classes can be defined for each domain of life, with many LCD classes appearing to be eukaryote-specific. Certain LCD classes were consistently associated with identical functions across many organisms, particularly in eukaryotes. Our analysis methods enable simultaneous, direct comparison of all LCD classes between individual organisms, resulting in a proteome-scale view of differences in LCD frequencies and functions. Together, these results highlight the remarkable diversity and functional specificity of LCDs across all known life forms.
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Affiliation(s)
- Sean M. Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Eric D. Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
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5
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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6
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Aryan F, Detrés D, Luo CC, Kim SX, Shah AN, Bartusel M, Flynn RA, Calo E. Nucleolus activity-dependent recruitment and biomolecular condensation by pH sensing. Mol Cell 2023; 83:4413-4423.e10. [PMID: 37979585 PMCID: PMC10803072 DOI: 10.1016/j.molcel.2023.10.031] [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: 11/15/2022] [Revised: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023]
Abstract
DEAD-box ATPases are major regulators of biomolecular condensates and orchestrate diverse biochemical processes that are critical for the functioning of cells. How DEAD-box proteins are selectively recruited to their respective biomolecular condensates is unknown. We explored this in the context of the nucleolus and DEAD-box protein DDX21. We find that the pH of the nucleolus is intricately linked to the transcriptional activity of the organelle and facilitates the recruitment and condensation of DDX21. We identify an evolutionarily conserved feature of the C terminus of DDX21 responsible for nucleolar localization. This domain is essential for zebrafish development, and its intrinsically disordered and isoelectric properties are necessary and sufficient for the ability of DDX21 to respond to changes in pH and form condensates. Molecularly, the enzymatic activities of poly(ADP-ribose) polymerases contribute to maintaining the nucleolar pH and, consequently, DDX21 recruitment and nucleolar partitioning. These observations reveal an activity-dependent physicochemical mechanism for the selective recruitment of biochemical activities to biomolecular condensates.
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Affiliation(s)
- Fardin Aryan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Diego Detrés
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Claire C Luo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Skylar X Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arish N Shah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michaela Bartusel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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7
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Moses D, Ginell GM, Holehouse AS, Sukenik S. Intrinsically disordered regions are poised to act as sensors of cellular chemistry. Trends Biochem Sci 2023; 48:1019-1034. [PMID: 37657994 PMCID: PMC10840941 DOI: 10.1016/j.tibs.2023.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Intrinsically disordered proteins and protein regions (IDRs) are abundant in eukaryotic proteomes and play a wide variety of essential roles. Instead of folding into a stable structure, IDRs exist in an ensemble of interconverting conformations whose structure is biased by sequence-dependent interactions. The absence of a stable 3D structure, combined with high solvent accessibility, means that IDR conformational biases are inherently sensitive to changes in their environment. Here, we argue that IDRs are ideally poised to act as sensors and actuators of cellular physicochemistry. We review the physical principles that underlie IDR sensitivity, the molecular mechanisms that translate this sensitivity to function, and recent studies where environmental sensing by IDRs may play a key role in their downstream function.
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Affiliation(s)
- David Moses
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA.
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA; Quantitative Systems Biology Program, University of California, Merced, CA, USA.
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8
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Hajjar S, Zhou X. pH sensing at the intersection of tissue homeostasis and inflammation. Trends Immunol 2023; 44:807-825. [PMID: 37714775 PMCID: PMC10543622 DOI: 10.1016/j.it.2023.08.008] [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: 08/08/2023] [Revised: 08/13/2023] [Accepted: 08/13/2023] [Indexed: 09/17/2023]
Abstract
pH is tightly maintained at cellular, tissue, and systemic levels, and altered pH - particularly in the acidic range - is associated with infection, injury, solid tumors, and physiological and pathological inflammation. However, how pH is sensed and regulated and how it influences immune responses remain poorly understood at the tissue level. Applying conceptual frameworks of homeostatic and inflammatory circuitries, we categorize cellular and tissue components engaged in pH regulation, drawing parallels from established cases in physiology. By expressing various intracellular (pHi) and extracellular pH (pHe)-sensing receptors, the immune system may integrate information on tissue and cellular states into the regulation of homeostatic and inflammatory programs. We introduce the novel concept of resistance and adaptation responses to rationalize pH-dependent immunomodulation intertwined with homeostatic equilibrium and inflammatory control. We discuss emerging challenges and opportunities in understanding the immunological roles of pH sensing, which might reveal new strategies to combat inflammation and restore tissue homeostasis.
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Affiliation(s)
- Stephanie Hajjar
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, 300 Longwood Ave, Boston, MA 02115, USA
| | - Xu Zhou
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, 300 Longwood Ave, Boston, MA 02115, USA.
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9
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Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552128. [PMID: 37609146 PMCID: PMC10441348 DOI: 10.1101/2023.08.06.552128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function, yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. We focussed here on the first two domains of coronavirus nucleocapsid proteins, the disordered N-terminal domain (NTD) followed by the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system to explore the interplay between an IDR adjacent to a folded domain, and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved fuzzy RNA:protein complex is found across nucleocapsid protein orthologs, despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
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10
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Menezes AP, Murillo AM, de Castro CG, Bellini NK, Tosi LRO, Thiemann OH, Elias MC, Silber AM, da Cunha JPC. Navigating the boundaries between metabolism and epigenetics in trypanosomes. Trends Parasitol 2023; 39:682-695. [PMID: 37349193 DOI: 10.1016/j.pt.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
Epigenetic marks enable cells to acquire new biological features that favor their adaptation to environmental changes. These marks are chemical modifications on chromatin-associated proteins and nucleic acids that lead to changes in the chromatin landscape and may eventually affect gene expression. The chemical tags of these epigenetic marks are comprised of intermediate cellular metabolites. The number of discovered associations between metabolism and epigenetics has increased, revealing how environment influences gene regulation and phenotype diversity. This connection is relevant to all organisms but underappreciated in digenetic parasites, which must adapt to different environments as they progress through their life cycles. This review speculates and proposes associations between epigenetics and metabolism in trypanosomes, which are protozoan parasites that cause human and livestock diseases.
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Affiliation(s)
- Ana Paula Menezes
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ana Milena Murillo
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil
| | - Camila Gachet de Castro
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Natalia Karla Bellini
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | | | | | - Maria Carolina Elias
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ariel Mariano Silber
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil.
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil.
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11
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Ginell GM, Flynn AJ, Holehouse AS. SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets. Bioinformatics 2023; 39:btad488. [PMID: 37540173 PMCID: PMC10423030 DOI: 10.1093/bioinformatics/btad488] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 07/02/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
MOTIVATION The emergence of high-throughput experiments and high-resolution computational predictions has led to an explosion in the quality and volume of protein sequence annotations at proteomic scales. Unfortunately, sanity checking, integrating, and analyzing complex sequence annotations remains logistically challenging and introduces a major barrier to entry for even superficial integrative bioinformatics. RESULTS To address this technical burden, we have developed SHEPHARD, a Python framework that trivializes large-scale integrative protein bioinformatics. SHEPHARD combines an object-oriented hierarchical data structure with database-like features, enabling programmatic annotation, integration, and analysis of complex datatypes. Importantly SHEPHARD is easy to use and enables a Pythonic interrogation of largescale protein datasets with millions of unique annotations. We use SHEPHARD to examine three orthogonal proteome-wide questions relating protein sequence to molecular function, illustrating its ability to uncover novel biology. AVAILABILITY AND IMPLEMENTATION We provided SHEPHARD as both a stand-alone software package (https://github.com/holehouse-lab/shephard), and as a Google Colab notebook with a collection of precomputed proteome-wide annotations (https://github.com/holehouse-lab/shephard-colab).
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Affiliation(s)
- Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, United States
- Center for Biomolecular Condensates, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, MO 63130, United States
| | - Aidan J Flynn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, United States
- Center for Biomolecular Condensates, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, MO 63130, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, United States
- Center for Biomolecular Condensates, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, MO 63130, United States
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12
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Xie Y, Liu T, Gresham D, Holt LJ. mRNA condensation fluidizes the cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542963. [PMID: 37398029 PMCID: PMC10312499 DOI: 10.1101/2023.05.30.542963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The intracellular environment is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cell physiology. When exposed to stress, mRNAs released after translational arrest condense with RNA binding proteins, resulting in the formation of membraneless RNA protein (RNP) condensates known as processing bodies (P-bodies) and stress granules (SGs). However, the impact of the assembly of these condensates on the biophysical properties of the crowded cytoplasmic environment remains unclear. Here, we find that upon exposure to stress, polysome collapse and condensation of mRNAs increases mesoscale particle diffusivity in the cytoplasm. Increased mesoscale diffusivity is required for the efficient formation of Q-bodies, membraneless organelles that coordinate degradation of misfolded peptides that accumulate during stress. Additionally, we demonstrate that polysome collapse and stress granule formation has a similar effect in mammalian cells, fluidizing the cytoplasm at the mesoscale. We find that synthetic, light-induced RNA condensation is sufficient to fluidize the cytoplasm, demonstrating a causal effect of RNA condensation. Together, our work reveals a new functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to effectively respond to stressful conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Department of Biology, New York University, New York, New York, United States
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
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13
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Simpson-Lavy K, Kupiec M. Glucose Inhibits Yeast AMPK (Snf1) by Three Independent Mechanisms. BIOLOGY 2023; 12:1007. [PMID: 37508436 PMCID: PMC10376661 DOI: 10.3390/biology12071007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
Snf1, the fungal homologue of mammalian AMP-dependent kinase (AMPK), is a key protein kinase coordinating the response of cells to a shortage of glucose. In fungi, the response is to activate respiratory gene expression and metabolism. The major regulation of Snf1 activity has been extensively investigated: In the absence of glucose, it becomes activated by phosphorylation of its threonine at position 210. This modification can be erased by phosphatases when glucose is restored. In the past decade, two additional independent mechanisms of Snf1 regulation have been elucidated. In response to glucose (or, surprisingly, also to DNA damage), Snf1 is SUMOylated by Mms21 at lysine 549. This inactivates Snf1 and leads to Snf1 degradation. More recently, glucose-induced proton export has been found to result in Snf1 inhibition via a polyhistidine tract (13 consecutive histidine residues) at the N-terminus of the Snf1 protein. Interestingly, the polyhistidine tract plays also a central role in the response to iron scarcity. This review will present some of the glucose-sensing mechanisms of S. cerevisiae, how they interact, and how their interplay results in Snf1 inhibition by three different, and independent, mechanisms.
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Affiliation(s)
- Kobi Simpson-Lavy
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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14
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Irvali D, Schlottmann FP, Muralidhara P, Nadelson I, Kleemann K, Wood NE, Doncic A, Ewald JC. When yeast cells change their mind: cell cycle "Start" is reversible under starvation. EMBO J 2023; 42:e110321. [PMID: 36420556 PMCID: PMC9841329 DOI: 10.15252/embj.2021110321] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic cells decide in late G1 phase of the cell cycle whether to commit to another round of division. This point of cell cycle commitment is termed "Restriction Point" in mammals and "Start" in the budding yeast Saccharomyces cerevisiae. At Start, yeast cells integrate multiple signals such as pheromones and nutrients, and will not pass Start if nutrients are lacking. However, how cells respond to nutrient depletion after the Start decision remains poorly understood. Here, we analyze how post-Start cells respond to nutrient depletion, by monitoring Whi5, the cell cycle inhibitor whose export from the nucleus determines Start. Surprisingly, we find that cells that have passed Start can re-import Whi5 into the nucleus. In these cells, the positive feedback loop activating G1/S transcription is interrupted, and the Whi5 repressor re-binds DNA. Cells which re-import Whi5 become again sensitive to mating pheromone, like pre-Start cells, and CDK activation can occur a second time upon replenishment of nutrients. These results demonstrate that upon starvation, the commitment decision at Start can be reversed. We therefore propose that cell cycle commitment in yeast is a multi-step process, similar to what has been suggested for mammalian cells.
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Affiliation(s)
- Deniz Irvali
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Fabian P Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | | | - Iliya Nadelson
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Katja Kleemann
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - N Ezgi Wood
- The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Doncic
- The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer C Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
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15
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Xie Y, Gresham D, Holt L. Increased mesoscale diffusivity in response to acute glucose starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523352. [PMID: 36711511 PMCID: PMC9882054 DOI: 10.1101/2023.01.10.523352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Macromolecular crowding is an important parameter that impacts multiple biological processes. Passive microrheology using single particle tracking is a powerful means of studying macromolecular crowding. Here we monitored the diffusivity of self-assembling fluorescent nanoparticles (μNS) in response to acute glucose starvation. mRNP diffusivity was reduced upon glucose starvation as previously reported. In contrast, we observed increased diffusivity of μNS particles. Our results suggest that, upon glucose starvation, mRNP granule diffusivity may be reduced due to changes in physical interactions, while global crowding in the cytoplasm may be reduced.
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Affiliation(s)
- Ying Xie
- New York University, School of Medicine, Institute for Systems Genetics, New York, USA
- New York University, Center for Genomics and Systems Biology, Department of Biology, New York, USA
| | - David Gresham
- New York University, Center for Genomics and Systems Biology, Department of Biology, New York, USA
| | - Liam Holt
- New York University, School of Medicine, Institute for Systems Genetics, New York, USA
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16
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Xie Y, Gresham D, Holt LJ. Increased mesoscale diffusivity in response to acute glucose starvation. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000729. [PMID: 36908311 PMCID: PMC9996311 DOI: 10.17912/micropub.biology.000729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/14/2023]
Abstract
Macromolecular crowding is an important property of cells that impacts multiple biological processes. Passive microrheology using single particle tracking is a powerful means of studying macromolecular crowding. Here we monitored the diffusivity of self-assembling fluorescent nanoparticles (μNS) and mRNPs ( GFA1 -PP7) in response to acute glucose starvation. mRNP diffusivity was reduced upon glucose starvation as previously reported. By contrast, we observed increased diffusivity of μNS particles. Our results suggest that, upon glucose starvation, mRNP granule diffusivity may be reduced due to increased physical interactions, whereas macromolecular crowding in the cytoplasm may be globally reduced.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Department of Biology, New York University, New York, New York, United States
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States
- Correspondence to: David Gresham (
)
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Correspondence to: Liam J Holt (
)
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17
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MoSnf5 Regulates Fungal Virulence, Growth, and Conidiation in Magnaporthe oryzae. J Fungi (Basel) 2022; 9:jof9010018. [PMID: 36675839 PMCID: PMC9861326 DOI: 10.3390/jof9010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Snf5 (sucrose nonfermenting) is a core component of the SWI/SNF complexes and regulates diverse cellular processes in model eukaryotes. In plant pathogenic fungi, its biological function and underlying mechanisms remain unexplored. In this study, we investigated the biological roles of MoSnf5 in plant infection and fungal development in the rice blast pathogen Magnaporthe oryzae. The gene deletion mutants of MoSNF5 exhibited slower vegetative hyphal growth, severe defects in conidiogenesis, and impaired virulence and galactose utilization capacities. Domain dissection assays showed that the Snf5 domain and the N- and C-termini of MoSnf5 were all required for its full functions. Co-immunoprecipitation and yeast two-hybrid assays showed that MoSnf5 physically interacts with four proteins, including a transcription initiation factor MoTaf14. Interestingly, the ∆MoTaf14 mutants showed similar phenotypes as the ∆Mosnf5 mutants on fungal virulence and development. Moreover, assays on GFP-MoAtg8 expression and localization showed that both the ∆Mosnf5 and ∆MoTaf14 mutants were defective in autophagy. Taken together, MoSnf5 regulates fungal virulence, growth, and conidiation, possibly through regulating galactose utilization and autophagy in M. oryzae.
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [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: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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Identification of Genes Promoting Growth of Ustilago maydis on Biomolecules Released from Cells Killed by Oxidation. J Fungi (Basel) 2022; 8:jof8090957. [PMID: 36135682 PMCID: PMC9503528 DOI: 10.3390/jof8090957] [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: 07/21/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Much headway has been made in understanding the numerous strategies that enable microorganisms to counteract various types of environmental stress, but little is known about how microbial populations recover after a massive death caused by exposure to extreme conditions. Using the yeast-like fungus Ustilago maydis as a model, our recent post-stress regrowth under starvation (RUS) studies have demonstrated that this organism reconstitutes devastated populations with remarkable efficiency. Subsequently, we have identified four RUS-gene products. Two of these, Did4 and Tbp1, play parallel roles in protecting the genome. To identify additional molecular components, we took a molecular-genetic and a transcriptomic approach. By employing a simple and novel screening method, we identified five RUS-deficient mutants (snf8, slm1, vrg4, snf5, hsf1), three of which (snf8, slm1, and hsf1) displayed sensitivity to different genotoxic agents, indicating that the corresponding gene products have roles in genome protection. The global transcriptomic changes of cells grown in supernatants derived from peroxide-treated cell suspensions revealed sets of uniquely expressed genes. Importantly, among the genes induced by the substrates was Chk1, which encodes a protein kinase required for checkpoint-mediated cell cycle arrest in response to DNA damage. Mutants of U. maydis deleted of Chk1 are severely incapacitated in RUS.
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Lee B, Jaberi-Lashkari N, Calo E. A unified view of low complexity regions (LCRs) across species. eLife 2022; 11:e77058. [PMID: 36098382 PMCID: PMC9470157 DOI: 10.7554/elife.77058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
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Affiliation(s)
- Byron Lee
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nima Jaberi-Lashkari
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
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