1
|
Brom JA, Petrikis RG, Nieukirk GE, Bourque J, Pielak GJ. Protecting Lyophilized Escherichia coli Adenylate Kinase. Mol Pharm 2024; 21:3634-3642. [PMID: 38805365 DOI: 10.1021/acs.molpharmaceut.4c00356] [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] [Indexed: 05/30/2024]
Abstract
Drying protein-based drugs, usually via lyophilization, can facilitate storage at ambient temperature and improve accessibility but many proteins cannot withstand drying and must be formulated with protective additives called excipients. However, mechanisms of protection are poorly understood, precluding rational formulation design. To better understand dry proteins and their protection, we examine Escherichia coli adenylate kinase (AdK) lyophilized alone and with the additives trehalose, maltose, bovine serum albumin, cytosolic abundant heat soluble protein D, histidine, and arginine. We apply liquid-observed vapor exchange NMR to interrogate the residue-level structure in the presence and absence of additives. We pair these observations with differential scanning calorimetry data of lyophilized samples and AdK activity assays with and without heating. We show that the amino acids do not preserve the native structure as well as sugars or proteins and that after heating the most stable additives protect activity best.
Collapse
Affiliation(s)
- Julia A Brom
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), 3250 Genome Sciences Building, Chapel Hill, North Carolina 27599-3290, United States
| | - Ruta G Petrikis
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), 3250 Genome Sciences Building, Chapel Hill, North Carolina 27599-3290, United States
| | - Grace E Nieukirk
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), 3250 Genome Sciences Building, Chapel Hill, North Carolina 27599-3290, United States
| | - Joshua Bourque
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), 3250 Genome Sciences Building, Chapel Hill, North Carolina 27599-3290, United States
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina at Chapel Hill (UNC-CH), 3250 Genome Sciences Building, Chapel Hill, North Carolina 27599-3290, United States
- Department of Biochemistry & Biophysics, UNC-CH, Chapel Hill, North Carolina 27599, United States
- Lineberger Cancer Center, UNC-CH, Chapel Hill, North Carolina 27599, United States
- Integrative Program for Biological and Genome Sciences, UNC-CH, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
2
|
Sugiura K, Yoshida Y, Hayashi K, Arakawa K, Kunieda T, Matsumoto M. Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome. ZOOLOGICAL LETTERS 2024; 10:11. [PMID: 38902818 PMCID: PMC11191345 DOI: 10.1186/s40851-024-00233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND In gonochoristic animals, the sex determination pathway induces different morphological and behavioral features that can be observed between sexes, a condition known as sexual dimorphism. While many components of this sex differentiation cascade show high levels of diversity, factors such as the Doublesex-Mab-3-Related Transcription factor (DMRT) are widely conserved across animal taxa. Species of the phylum Tardigrada exhibit remarkable diversity in morphology and behavior between sexes, suggesting a pathway regulating this dimorphism. Despite the wealth of genomic and zoological knowledge accumulated in recent studies, the sexual differences in tardigrades genomes have not been identified. In the present study, we focused on the gonochoristic species Paramacrobiotus metropolitanus and employed omics analyses to unravel the molecular basis of sexual dimorphism. RESULTS Transcriptome analysis between sex-identified specimens revealed numerous differentially expressed genes, of which approximately 2,000 male-biased genes were focused on 29 non-male-specific genomic loci. From these regions, we identified two Macrobiotidae family specific DMRT paralogs, which were significantly upregulated in males and lacked sex specific splicing variants. Furthermore, phylogenetic analysis indicated all tardigrade genomes lack the doublesex ortholog, suggesting doublesex emerged after the divergence of Tardigrada. In contrast to sex-specific expression, no evidence of genomic differences between the sexes was found. We also identified several anhydrobiosis genes that exhibit sex-biased expression, suggesting a possible mechanism for protection of sex-specific tissues against extreme stress. CONCLUSIONS This study provides a comprehensive analysis for analyzing the genetic differences between sexes in tardigrades. The existence of male-biased, but not male-specific, genomic loci and identification of the family specific male-biased DMRT subfamily provides the foundation for understanding the sex determination cascade. In addition, sex-biased expression of several tardigrade-specific genes which are involved their stress tolerance suggests a potential role in protecting sex-specific tissue and gametes.
Collapse
Affiliation(s)
- Kenta Sugiura
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Yoshida
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Kohei Hayashi
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihoji, Tsuruoka, Yamagata, 997-0017, Japan
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takekazu Kunieda
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Midori Matsumoto
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan.
| |
Collapse
|
3
|
Olgenblum GI, Hutcheson BO, Pielak GJ, Harries D. Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels. Chem Rev 2024; 124:5668-5694. [PMID: 38635951 PMCID: PMC11082905 DOI: 10.1021/acs.chemrev.3c00752] [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: 10/12/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/20/2024]
Abstract
Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.
Collapse
Affiliation(s)
- Gil I. Olgenblum
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Brent O. Hutcheson
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
- Department
of Chemistry, Department of Biochemistry & Biophysics, Integrated
Program for Biological & Genome Sciences, Lineberger Comprehensive
Cancer Center, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel Harries
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| |
Collapse
|
4
|
Sanchez‐Martinez S, Nguyen K, Biswas S, Nicholson V, Romanyuk AV, Ramirez J, Kc S, Akter A, Childs C, Meese EK, Usher ET, Ginell GM, Yu F, Gollub E, Malferrari M, Francia F, Venturoli G, Martin EW, Caporaletti F, Giubertoni G, Woutersen S, Sukenik S, Woolfson DN, Holehouse AS, Boothby TC. Labile assembly of a tardigrade protein induces biostasis. Protein Sci 2024; 33:e4941. [PMID: 38501490 PMCID: PMC10949331 DOI: 10.1002/pro.4941] [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: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.
Collapse
Affiliation(s)
| | - K. Nguyen
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Biswas
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - V. Nicholson
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. V. Romanyuk
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
| | - J. Ramirez
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - S. Kc
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - A. Akter
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - C. Childs
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. K. Meese
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| | - E. T. Usher
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - G. M. Ginell
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - F. Yu
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
| | - E. Gollub
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - M. Malferrari
- Dipartimento di Chimica “Giacomo Ciamician”Università di BolognaBolognaItaly
| | - F. Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
| | - G. Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiTUniversità di BolognaBolognaItaly
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o Dipartimento di Fisica e Astronomia (DIFA)Università di BolognaBolognaItaly
| | - E. W. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - F. Caporaletti
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. Giubertoni
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Woutersen
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. Sukenik
- Quantitative Systems Biology ProgramUniversity of California MercedMercedCaliforniaUSA
- Department of Chemistry and BiochemistryUniversity of California MercedMercedCaliforniaUSA
| | - D. N. Woolfson
- School of ChemistryUniversity of BristolBristolUK
- Max Planck‐Bristol Centre for Minimal BiologyUniversity of BristolBristolUK
- School of BiochemistryUniversity of Bristol, Biomedical Sciences BuildingBristolUK
| | - A. S. Holehouse
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSt. LouisMissouriUSA
- Center for Biomolecular CondensatesWashington University in St. LouisSt. LouisMissouriUSA
| | - T. C. Boothby
- Department of Molecular BiologyUniversity of WyomingLaramieWyomingUSA
| |
Collapse
|
5
|
Kang D, Yang MJ, Kim H, Park C. Protective roles of highly conserved motif 1 in tardigrade cytosolic-abundant heat soluble protein in extreme environments. Protein Sci 2024; 33:e4913. [PMID: 38358259 PMCID: PMC10868442 DOI: 10.1002/pro.4913] [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: 05/08/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/16/2024]
Abstract
Tardigrades are remarkable microscopic animals that survive harsh conditions such as desiccation and extreme temperatures. Tardigrade-specific intrinsically disordered proteins (TDPs) play an essential role in the survival of tardigrades in extreme environments. Cytosolic-abundant heat soluble (CAHS) protein, a key TDP, is known to increase desiccation tolerance and to protect the activity of several enzymes under dehydrated conditions. However, the function and properties of each CAHS domain have not yet been elucidated in detail. Here, we aimed to elucidate the protective role of highly conserved motif 1 of CAHS in extreme environmental conditions. To examine CAHS domains, three protein constructs, CAHS Full (1-229), CAHS ∆Core (1-120_184-229), and CAHS Core (121-183), were engineered. The highly conserved CAHS motif 1 (124-142) in the CAHS Core formed an amphiphilic α helix, reducing the aggregate formation and protecting lactate dehydrogenase activity during dehydration-rehydration and freeze-thaw treatments, indicating that CAHS motif 1 in the CAHS Core was essential for maintaining protein solubility and stability. Aggregation assays and confocal microscopy revealed that the intrinsically disordered N- and C-terminal domains were more prone to aggregation under our experimental conditions. By explicating the functions of each domain in CAHS, our study proposes the possibility of using engineered proteins or peptides derived from CAHS as a potential candidate for biological applications in extreme environmental stress responses.
Collapse
Affiliation(s)
- Donguk Kang
- Department of ChemistryGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Min June Yang
- Department of ChemistryGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Hwan Kim
- GIST Advanced Institute of Instrumental Analysis (GAIA), Bio Imaging LaboratoryGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| | - Chin‐Ju Park
- Department of ChemistryGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
| |
Collapse
|
6
|
KC S, Nguyen K, Nicholson V, Walgren A, Trent T, Gollub E, Romero S, Holehouse AS, Sukenik S, Boothby TC. Disordered proteins interact with the chemical environment to tune their protective function during drying. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582506. [PMID: 38464187 PMCID: PMC10925285 DOI: 10.1101/2024.02.28.582506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results demonstrate that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.
Collapse
Affiliation(s)
- Shraddha KC
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | - Kenny Nguyen
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | | | - Annie Walgren
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | - Tony Trent
- University of Wyoming, Department of Molecular Biology. Laramie, WY
| | - Edith Gollub
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA, USA
| | - Sofia Romero
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA, USA
| | - 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
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA, USA
| | | |
Collapse
|
7
|
Li XH, Yu CWH, Gomez-Navarro N, Stancheva V, Zhu H, Murthy A, Wozny M, Malhotra K, Johnson CM, Blackledge M, Santhanam B, Liu W, Huang J, Freund SMV, Miller EA, Babu MM. Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties. PNAS NEXUS 2024; 3:pgae006. [PMID: 38269070 PMCID: PMC10808001 DOI: 10.1093/pnasnexus/pgae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.
Collapse
Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Hongni Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Andal Murthy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michael Wozny
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ketan Malhotra
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Martin Blackledge
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| |
Collapse
|
8
|
Tanaka S, Arakawa K. Reply to Tanaka and Kunieda: Control protein GFP also shows a mesh-like structure in desiccating tardigrade cells. Proc Natl Acad Sci U S A 2023; 120:e2316451120. [PMID: 37983513 PMCID: PMC10691207 DOI: 10.1073/pnas.2316451120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Affiliation(s)
- Sae Tanaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka997-0017, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki444-8787, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka997-0017, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki444-8787, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa252-0882, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa252-0882, Japan
| |
Collapse
|
9
|
Chen SWW, Teulon JM, Pellequer JL. Cry11Aa and Cyt1Aa exhibit different structural orders in crystal topography. J Mol Recognit 2023; 36:e3047. [PMID: 37474122 DOI: 10.1002/jmr.3047] [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: 03/20/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
Cry11Aa and Cyt1Aa are two pesticidal toxins produced by Bacillus thuringiensis subsp. israelensis. To improve our understanding of the nature of their oligomers in the toxic actions and synergistic effects, we performed the atomic force microscopy to probe the surfaces of their natively grown crystals, and used the L-weight filter to enhance the structural features. By L-weight filtering, molecular sizes of the Cry11Aa and Cyt1Aa monomers obtained are in excellent agreement with the three-dimensional structures determined by x-ray crystallography. Moreover, our results show that the layered feature of a structural element distinguishes the topographic characteristics of Cry11Aa and Cyt1Aa crystals, suggesting that the Cry11Aa toxin has a better chance than Cyt1Aa for multimerization and therefore cooperativeness of the toxic actions.
Collapse
Affiliation(s)
- Shu-Wen W Chen
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
- Rue Cyprien Jullin, Vinay, France
| | - Jean-Marie Teulon
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Jean-Luc Pellequer
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| |
Collapse
|
10
|
Sanchez-Martinez S, Ramirez JF, Meese EK, Childs CA, Boothby TC. The tardigrade protein CAHS D interacts with, but does not retain, water in hydrated and desiccated systems. Sci Rep 2023; 13:10449. [PMID: 37369754 DOI: 10.1038/s41598-023-37485-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Tardigrades are a group of microscopic animals renowned for their ability to survive near complete desiccation. A family of proteins, unique to tardigrades, called Cytoplasmic Abundant Heat Soluble (CAHS) proteins are necessary to mediate robust desiccation tolerance in these animals. However, the mechanism(s) by which CAHS proteins help to protect tardigrades during water-loss have not been fully elucidated. Here we use thermogravimetric analysis to empirically test the proposed hypothesis that tardigrade CAHS proteins, due to their propensity to form hydrogels, help to retain water during desiccation. We find that regardless of its gelled state, both in vitro and in vivo, a model CAHS protein (CAHS D) retains no more water than common proteins and control cells in the dry state. However, we find that while CAHS D proteins do not increase the total amount of water retained in a dry system, they interact with the small amount of water that does remain. Our study indicates that desiccation tolerance mediated by CAHS D cannot be simply ascribed to water retention and instead implicates its ability to interact more tightly with residual water as a possible mechanism underlying its protective capacity. These results advance our fundamental understanding of tardigrade desiccation tolerance which could provide potential avenues for new technologies to aid in the storage of dry shelf-stable pharmaceuticals and the generation of stress tolerant crops to ensure food security in the face of global climate change.
Collapse
Affiliation(s)
| | - John F Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Emma K Meese
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Charles A Childs
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Thomas C Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
| |
Collapse
|
11
|
Eicher J, Hutcheson BO, Pielak GJ. Properties of a tardigrade desiccation-tolerance protein aerogel. Biophys J 2023; 122:2500-2505. [PMID: 37149732 PMCID: PMC10323019 DOI: 10.1016/j.bpj.2023.05.002] [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: 02/09/2023] [Revised: 04/10/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Lyophilization is promising for tackling degradation during the drying and storage of protein-based drugs. Tardigrade cytosolically abundant heat soluble (CAHS) proteins are necessary and sufficient for desiccation-tolerance in vivo and protein protection in vitro. Hydrated CAHS proteins form coiled-coil-based fine-stranded, cold-setting hydrogels, but the dried protein remains largely uncharacterized. Here, we show that dried CAHS D gels (i.e., aerogels) retain the structural units of their hydrogels, but the details depend on prelyophilization CAHS concentrations. Low concentration samples (<10 g/L) form thin (<0.2 μm) tangled fibrils lacking regular structure on the micron scale. Upon increasing the concentration, the fibers thicken and form slabs comprising the walls of the aerogel pores. These changes in morphology are associated with a loss in disorder and an increase in large β sheets and a decrease in α helices and random coils. This disorder-to-order transition is also seen in hydrated gels as a function of concentration. These results suggest a mechanism for pore formation and indicate that using CAHS proteins as excipients will require attention to initial conditions because the starting concentration impacts the lyophilized product.
Collapse
Affiliation(s)
- Jonathan Eicher
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Brent O Hutcheson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina.
| |
Collapse
|
12
|
Liu J, Li RS, Zhang L, Wang J, Dong Q, Xu Z, Kang Y, Xue P. Enzyme-Activatable Polypeptide for Plasma Membrane Disruption and Antitumor Immunity Elicitation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206912. [PMID: 36932931 DOI: 10.1002/smll.202206912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/01/2023] [Indexed: 06/15/2023]
Abstract
Enzyme-instructed self-assembly of bioactive molecules into nanobundles inside cells is conceived to potentially disrupt plasma membrane and subcellular structure. Herein, an alkaline phosphatase (ALP)-activatable hybrid of ICG-CF4 KYp is facilely synthesized by conjugating photosensitizer indocyanine green (ICG) with CF4 KYp peptide via classical Michael addition reaction. ALP-induced dephosphorylation of ICG-CF4 KYp enables its transformation from small-molecule precursor into rigid nanofibrils, and such fibrillation in situ causes severe mechanical disruption of cytomembrane. Besides, ICG-mediated photosensitization causes additional oxidative damage of plasma membrane by lipid peroxidation. Hollow MnO2 nanospheres devote to deliver ICG-CF4 KYp into tumorous tissue through tumor-specific acidity/glutathione-triggered degradation of MnO2 , which is monitored by fluorescent probing and magnetic resonance imaging. The burst release of damage-associated molecular patterns and other tumor antigens during therapy effectively triggers immunogenetic cell death and improves immune stimulatory, as demonstrated by the promotion of dendritic cell maturation and CD8+ lymphocyte infiltration, as well as constraint of regulatory T cell population. Taken together, such cytomembrane injury strategy based on peptide fibrillation in situ holds high clinical promise for lesion-specific elimination of primary, abscopal, and metastatic tumors, which may enlighten more bioinspired nanoplatforms for anticancer theranostics.
Collapse
Affiliation(s)
- Jiahui Liu
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Rong Sheng Li
- National Demonstration Center for Experimental Chemistry and Chemical Engineering Education, School of Chemical Science and Engineering, Yunnan University, Kunming, 650091, China
| | - Lei Zhang
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China
| | - Jie Wang
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China
| | - Qi Dong
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Zhigang Xu
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Yuejun Kang
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Peng Xue
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| |
Collapse
|
13
|
Packebush MH, Sanchez-Martinez S, Biswas S, Kc S, Nguyen KH, Ramirez JF, Nicholson V, Boothby TC. Natural and engineered mediators of desiccation tolerance stabilize Human Blood Clotting Factor VIII in a dry state. Sci Rep 2023; 13:4542. [PMID: 36941331 PMCID: PMC10027729 DOI: 10.1038/s41598-023-31586-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
Biologics, pharmaceuticals containing or derived from living organisms, such as vaccines, antibodies, stem cells, blood, and blood products are a cornerstone of modern medicine. However, nearly all biologics have a major deficiency: they are inherently unstable, requiring storage under constant cold conditions. The so-called 'cold-chain', while effective, represents a serious economic and logistical hurdle for deploying biologics in remote, underdeveloped, or austere settings where access to cold-chain infrastructure ranging from refrigerators and freezers to stable electricity is limited. To address this issue, we explore the possibility of using anhydrobiosis, the ability of organisms such as tardigrades to enter a reversible state of suspended animation brought on by extreme drying, as a jumping off point in the development of dry storage technology that would allow biologics to be kept in a desiccated state under not only ambient but elevated temperatures. Here we examine the ability of different protein and sugar-based mediators of anhydrobiosis derived from tardigrades and other anhydrobiotic organisms to stabilize Human Blood Clotting Factor VIII under repeated dehydration/rehydration cycles, thermal stress, and long-term dry storage conditions. We find that while both protein and sugar-based protectants can stabilize the biologic pharmaceutical Human Blood Clotting Factor VIII under all these conditions, protein-based mediators offer more accessible avenues for engineering and thus tuning of protective function. Using classic protein engineering approaches, we fine tune the biophysical properties of a protein-based mediator of anhydrobiosis derived from a tardigrade, CAHS D. Modulating the ability of CAHS D to form hydrogels make the protein better or worse at providing protection to Human Blood Clotting Factor VIII under different conditions. This study demonstrates the effectiveness of tardigrade CAHS proteins and other mediators of desiccation tolerance at preserving the function of a biologic without the need for the cold-chain. In addition, our study demonstrates that engineering approaches can tune natural products to serve specific protective functions, such as coping with desiccation cycling versus thermal stress. Ultimately, these findings provide a proof of principle that our reliance on the cold-chain to stabilize life-saving pharmaceuticals can be broken using natural and engineered mediators of desiccation tolerance.
Collapse
Affiliation(s)
| | | | - Sourav Biswas
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Shraddha Kc
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Kenny H Nguyen
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - John F Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Vincent Nicholson
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Thomas C Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA.
| |
Collapse
|
14
|
Qin S, Zhou HX. Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526886. [PMID: 36778236 PMCID: PMC9915584 DOI: 10.1101/2023.02.02.526886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Dynamics is a crucial link between sequence and function for intrinsically disordered proteins (IDPs). NMR spin relaxation is a powerful technique for characterizing the sequence-dependent backbone dynamics of IDPs. Of particular interest is the 15N transverse relaxation rate (R2), which reports on slower dynamics (10s of ns up to 1 μs and beyond). NMR and molecular dynamics (MD) simulations have shown that local interactions and secondary structure formation slow down backbone dynamics and raise R2. Elevated R2 has been suggested to be indicators of propensities of membrane association, liquid-liquid phase separation, and other functional processes. Here we present a sequence-based method, SeqDYN, for predicting R2 of IDPs. The R2 value of a residue is expressed as the product of contributing factors from all residues, which attenuate with increasing sequence distance from the central residue. The mathematical model has 21 parameters, representing the correlation length (where the attenuation is at 50%) and the amplitudes of the contributing factors of the 20 types of amino acids. Training on a set of 45 IDPs reveals a correlation length of 5.6 residues, aromatic and long branched aliphatic amino acids and Arg as R2 promotors whereas Gly and short polar amino acids as R2 suppressors. The prediction accuracy of SeqDYN is competitive against that of recent MD simulations using IDP-specific force fields. For a structured protein, SeqDYN prediction represents R2 in the unfolded state. SeqDYN is available as a web server at https://zhougroup-uic.github.io/SeqDYNidp/ for rapid R2 prediction.
Collapse
Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| |
Collapse
|
15
|
In vivo expression vector derived from anhydrobiotic tardigrade genome enables live imaging in Eutardigrada. Proc Natl Acad Sci U S A 2023; 120:e2216739120. [PMID: 36693101 PMCID: PMC9945988 DOI: 10.1073/pnas.2216739120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Water is essential for life, but anhydrobiotic tardigrades can survive almost complete dehydration. Anhydrobiosis has been a biological enigma for more than a century with respect to how organisms sustain life without water, but the few choices of genetic toolkits available in tardigrade research have been a challenging circumstance. Here, we report the development of an in vivo expression system for tardigrades. This transient transgenic technique is based on a plasmid vector (TardiVec) with promoters that originated from an anhydrobiotic tardigrade Ramazzottius varieornatus. It enables the introduction of GFP-fused proteins and genetically encoded indicators such as the Ca2+ indicator GCaMP into tardigrade cells; consequently, the dynamics of proteins and cells in tardigrades may be observed by fluorescence live imaging. This system is applicable for several tardigrades in the class Eutardigrada: the promoters of anhydrobiosis-related genes showed tissue-specific expression in this work. Surprisingly, promoters functioned similarly between multiple species, even for species with different modes of expression of anhydrobiosis-related genes, such as Hypsibius exemplaris, in which these genes are highly induced upon facing desiccation, and Thulinius ruffoi, which lacks anhydrobiotic capability. These results suggest that the highly dynamic expression changes in desiccation-induced species are regulated in trans. Tissue-specific expression of tardigrade-unique unstructured proteins also suggests differing anhydrobiosis machinery depending on the cell types. We believe that tardigrade transgenic technology opens up various experimental possibilities in tardigrade research, especially to explore anhydrobiosis mechanisms.
Collapse
|
16
|
Zhang H, Liu Q, Liang Q, Wang B, Chen Z, Wang J. Expression of tardigrade disordered proteins impacts the tolerance to biofuels in a model cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2023; 13:1091502. [PMID: 36687595 PMCID: PMC9845703 DOI: 10.3389/fmicb.2022.1091502] [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: 11/07/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Tardigrades, known colloquially as water bears or moss piglets, are diminutive animals capable of surviving many extreme environments, even been exposed to space in low Earth orbit. Recently termed tardigrade disordered proteins (TDPs) include three families as cytoplasmic-(CAHS), secreted-(SAHS), and mitochondrial-abundant heat soluble (MAHS) proteins. How these tiny animals survive these stresses has remained relatively mysterious. Cyanobacteria cast attention as a "microbial factory" to produce biofuels and high-value-added chemicals due to their ability to photosynthesis and CO2 sequestration. We explored a lot about biofuel stress and related mechanisms in Synechocystis sp. PCC 6803. The previous studies show that CAHS protein heterogenous expression in bacteria, yeast, and human cells increases desiccation tolerance in these hosts. In this study, the expression of three CAHS proteins in cyanobacterium was found to affect the tolerance to biofuels, while the tolerance to Cd2+ and Zn2+ were slightly affected in several mutants. A quantitative transcriptomics approach was applied to decipher response mechanisms at the transcriptional level further.
Collapse
Affiliation(s)
- Heao Zhang
- Whittle School and Studios, Shenzhen, Guangdong, China
| | - Qingyang Liu
- Whittle School and Studios, Shenzhen, Guangdong, China
| | - Qing Liang
- Shenzhen Link Spider Technology Co., Ltd., Shenzhen, China
| | - Boxiang Wang
- Shenzhen Link Spider Technology Co., Ltd., Shenzhen, China,*Correspondence: Boxiang Wang, Zixi Chen
| | - Zixi Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China,*Correspondence: Boxiang Wang, Zixi Chen
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| |
Collapse
|
17
|
Eicher JE, Brom JA, Wang S, Sheiko SS, Atkin JM, Pielak GJ. Secondary structure and stability of a gel-forming tardigrade desiccation-tolerance protein. Protein Sci 2022; 31:e4495. [PMID: 36335581 PMCID: PMC9679978 DOI: 10.1002/pro.4495] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/08/2022]
Abstract
Protein-based pharmaceuticals are increasingly important, but their inherent instability necessitates a "cold chain" requiring costly refrigeration during production, shipment, and storage. Drying can overcome this problem, but most proteins need the addition of stabilizers, and some cannot be successfully formulated. Thus, there is a need for new, more effective protective molecules. Cytosolically, abundant heat-soluble proteins from tardigrades are both fundamentally interesting and a promising source of inspiration; these disordered, monodisperse polymers form hydrogels whose structure may protect client proteins during drying. We used attenuated total reflectance Fourier transform infrared spectroscopy, differential scanning calorimetry, and small-amplitude oscillatory shear rheometry to characterize gelation. A 5% (wt/vol) gel has a strength comparable with human skin, and melts cooperatively and reversibly near body temperature with an enthalpy comparable with globular proteins. We suggest that the dilute protein forms α-helical coiled coils and increasing their concentration drives gelation via intermolecular β-sheet formation.
Collapse
Affiliation(s)
- Jonathan E. Eicher
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Julia A. Brom
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Shikun Wang
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Sergei S. Sheiko
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Joanna M. Atkin
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Gary J. Pielak
- Department of ChemistryUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| |
Collapse
|
18
|
Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022. [PMID: 35880435 PMCID: PMC9442351 DOI: 10.5483/bmbrep.2022.55.8.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biomolecular phase separation has recently attracted broad in-terest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be ex-plained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic.
Collapse
Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| |
Collapse
|
19
|
Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022; 55:363-369. [PMID: 35880435 PMCID: PMC9442351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 03/08/2024] Open
Abstract
Biomolecular phase separation has recently attracted broad interest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be explained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic. [BMB Reports 2022; 55(8): 363-369].
Collapse
Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| |
Collapse
|
20
|
Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:insects13060557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
Collapse
|
21
|
Pohl C, Effantin G, Kandiah E, Meier S, Zeng G, Streicher W, Segura DR, Mygind PH, Sandvang D, Nielsen LA, Peters GHJ, Schoehn G, Mueller-Dieckmann C, Noergaard A, Harris P. pH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils. Nat Commun 2022; 13:3162. [PMID: 35672293 PMCID: PMC9174238 DOI: 10.1038/s41467-022-30462-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominantly β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembles into helical non-amyloid fibrils. The in vitro anti-microbial activity was determined and shown to be enhanced compared to the wildtype. Plectasin contains a cysteine-stabilised α-helix-β-sheet structure, which remains intact upon fibril formation. Two protofilaments form a right-handed protein fibril. The fibril formation is reversible and follows sigmoidal kinetics with a pH- and concentration dependent equilibrium between soluble monomer and protein fibril. This high-resolution structure reveals that α/β proteins can natively assemble into fibrils. Here the authors report the cryo-EM structure of a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembling in a pH- and concentration dependent manner into helical non-amyloid fibrils. The fibrils formation is reversible, and follows a sigmoidal kinetics. The fibrils adopt a right-handed helical superstructure composed by two protofilaments, stabilized by an outer hydrophobic ring and an inner hydrophobic centre. These findings reveal that α/β proteins can natively assemble into fibrils.
Collapse
|
22
|
Veling MT, Nguyen DT, Thadani NN, Oster ME, Rollins NJ, Brock KP, Bethel NP, Lim S, Baker D, Way JC, Marks DS, Chang RL, Silver PA. Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells. ACS Synth Biol 2022; 11:1292-1302. [PMID: 35176859 DOI: 10.1021/acssynbio.1c00572] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis-protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlights the ability of DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.
Collapse
Affiliation(s)
- Mike T. Veling
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Dan T. Nguyen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Nicole N. Thadani
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michela E. Oster
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Nathan J. Rollins
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Kelly P. Brock
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Neville P. Bethel
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jeffrey C. Way
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Roger L. Chang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| |
Collapse
|