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Serebryany E, Martin RW, Takahashi GR. The Functional Significance of High Cysteine Content in Eye Lens γ-Crystallins. Biomolecules 2024; 14:594. [PMID: 38786000 PMCID: PMC11118217 DOI: 10.3390/biom14050594] [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: 03/28/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Cataract disease is strongly associated with progressively accumulating oxidative damage to the extremely long-lived crystallin proteins of the lens. Cysteine oxidation affects crystallin folding, interactions, and light-scattering aggregation especially strongly due to the formation of disulfide bridges. Minimizing crystallin aggregation is crucial for lifelong lens transparency, so one might expect the ubiquitous lens crystallin superfamilies (α and βγ) to contain little cysteine. Yet, the Cys content of γ-crystallins is well above the average for human proteins. We review literature relevant to this longstanding puzzle and take advantage of expanding genomic databases and improved machine learning tools for protein structure prediction to investigate it further. We observe remarkably low Cys conservation in the βγ-crystallin superfamily; however, in γ-crystallin, the spatial positioning of Cys residues is clearly fine-tuned by evolution. We propose that the requirements of long-term lens transparency and high lens optical power impose competing evolutionary pressures on lens βγ-crystallins, leading to distinct adaptations: high Cys content in γ-crystallins but low in βB-crystallins. Aquatic species need more powerful lenses than terrestrial ones, which explains the high methionine content of many fish γ- (and even β-) crystallins. Finally, we discuss synergies between sulfur-containing and aromatic residues in crystallins and suggest future experimental directions.
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Affiliation(s)
- Eugene Serebryany
- Department of Physiology & Biophysics, Stony Brook University, SUNY, Stony Brook, NY 11794, USA
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, SUNY, Stony Brook, NY 11794, USA
| | - Rachel W. Martin
- Department of Chemistry, UCI Irvine, Irvine, CA 92697-2025, USA
- Department of Molecular Biology & Biochemistry, UCI Irvine, Irvine, CA 92697-3900, USA
| | - Gemma R. Takahashi
- Department of Molecular Biology & Biochemistry, UCI Irvine, Irvine, CA 92697-3900, USA
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2
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Lerebours A, Regini J, Quinlan RA, Wada T, Pierscionek B, Devonshire M, Kalligeraki AA, Uwineza A, Young L, Girkin JM, Warwick P, Smith K, Hoshino M, Uesugi K, Yagi N, Terrill N, Shebanova O, Snow T, Smith JT. Evaluation of cataract formation in fish exposed to environmental radiation at Chernobyl and Fukushima. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:165957. [PMID: 37543314 DOI: 10.1016/j.scitotenv.2023.165957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/05/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023]
Abstract
Recent studies apparently finding deleterious effects of radiation exposure on cataract formation in birds and voles living near Chernobyl represent a major challenge to current radiation protection regulations. This study conducted an integrated assessment of radiation exposure on cataractogenesis using the most advanced technologies available to assess the cataract status of lenses extracted from fish caught at both Chernobyl in Ukraine and Fukushima in Japan. It was hypothesised that these novel data would reveal positive correlations between radiation dose and early indicators of cataract formation. The structure, function and optical properties of lenses were analysed from atomic to millimetre length scales. We measured the short-range order of the lens crystallin proteins using Small Angle X-Ray Scattering (SAXS) at both the SPring-8 and DIAMOND synchrotrons, the profile of the graded refractive index generated by these proteins, the epithelial cell density and organisation and finally the focal length of each lens. The results showed no evidence of a difference between the focal length, the epithelial cell densities, the refractive indices, the interference functions and the short-range order of crystallin proteins (X-ray diffraction patterns) in lens from fish exposed to different radiation doses. It could be argued that animals in the natural environment which developed cataract would be more likely, for example, to suffer predation leading to survivor bias. But the cross-length scale study presented here, by evaluating small scale molecular and cellular changes in the lens (pre-cataract formation) significantly mitigates against this issue.
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Affiliation(s)
- Adélaïde Lerebours
- School of the Environment, Geography and Geosciences, University of Portsmouth, Portsmouth PO1 3QL, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Justyn Regini
- School of Optometry and Vision Sciences, University of Cardiff, Cardiff CA10 3AT, United Kingdom
| | - Roy A Quinlan
- Department of Biosciences, University of Durham, Upper Mountjoy, Stockton Road, Durham DH1 3LE, United Kingdom
| | - Toshihiro Wada
- Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima City, Japan
| | - Barbara Pierscionek
- Medical Technology Research Centre, Anglia Ruskin University, Bishop Hall Lane, Chelmsford CM1 1SQ, United Kingdom
| | - Martin Devonshire
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Alexia A Kalligeraki
- Department of Biosciences, University of Durham, Upper Mountjoy, Stockton Road, Durham DH1 3LE, United Kingdom
| | - Alice Uwineza
- Department of Biosciences, University of Durham, Upper Mountjoy, Stockton Road, Durham DH1 3LE, United Kingdom
| | - Laura Young
- Department of Biosciences, University of Durham, Upper Mountjoy, Stockton Road, Durham DH1 3LE, United Kingdom
| | - John M Girkin
- Department of Physics, University of Durham, South Road, Durham DH1 3LE, United Kingdom
| | - Phil Warwick
- GAU-Radioanalytical, University of Southampton, NOCS, European way, SO14 6HT Southampton,United Kingdom
| | - Kurt Smith
- Centre for Radiochemistry Research, School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Masato Hoshino
- Japan Synchrotron Radiation Research Institute (Spring-8), 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute (Spring-8), 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Naoto Yagi
- Japan Synchrotron Radiation Research Institute (Spring-8), 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Nick Terrill
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Olga Shebanova
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Tim Snow
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Jim T Smith
- School of the Environment, Geography and Geosciences, University of Portsmouth, Portsmouth PO1 3QL, United Kingdom.
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3
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Stounberg J, Thomsen TB, Heredia BD, Hüssy K. Eyes and ears: A comparative approach linking the chemical composition of cod otoliths and eye lenses. JOURNAL OF FISH BIOLOGY 2022; 101:985-995. [PMID: 35817955 PMCID: PMC9796464 DOI: 10.1111/jfb.15159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Fish eye lenses are a protein-based chronological recorder of microchemical constituents that are a potentially useful tool for interpretations of environmental, ecological and life-history experienced by fish. Here, we present the first study with data on the chemical composition of eye lenses from Baltic cod examined using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) and compare these spatially resolved data to otoliths from the same fish also analysed by LA-ICPMS, measuring the isotopes 27 Al, 137 Ba, 43 Ca, 52 Cr, 65 Cu, 57 Fe, 39 K, 7 Li, 25 Mg, 55 Mn, 31 P, 208 Pb, 85 Rb, 45 Sc, 29 Si, 88 Sr, 47 Ti, 50 V, 149 Yb, 66 Zn and 90 Zr. Comparison of the variation in element concentrations between eye lenses and otoliths from the same individuals showed minor similarities, suggesting a different governance in the uptake processes. A strong overlap between the concentric growth rings in the eye lenses and the otolith Sr periodicity was observed, where each consecutive minima in the chemical profile with high accuracy correspond to the width of each lens ring. No comparable trends were seen between growth rings and all other elements measured from both lenses and otoliths. The characteristic rings observed in cod eye lenses do not seem to represent seasonal fluctuation nor are they found to be directly linked to age. With this research, we provide a baseline study identifying elements in corresponding eye lenses and otoliths that show potential for unravelling the environmental and biological conditions experienced by fish.
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Affiliation(s)
- Jonathan Stounberg
- National Institute of Aquatic ResourcesTechnical University of DenmarkLyngbyDenmark
| | | | | | - Karin Hüssy
- National Institute of Aquatic ResourcesTechnical University of DenmarkLyngbyDenmark
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Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures. Mol Genet Genomics 2022; 297:1627-1642. [PMID: 36006456 PMCID: PMC9596584 DOI: 10.1007/s00438-022-01947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/12/2022] [Indexed: 11/01/2022]
Abstract
The catfish Ancistrus triradiatus belongs to the species-rich family Loricariidae. Loricariids display remarkable traits such as herbivory, a benthic lifestyle, the absence of scales but the presence of dermal bony plates. They are exported as ornamental fish worldwide, with escaped fishes becoming a threat locally. Although genetic and phylogenetic studies are continuously increasing and developmental genetic investigations are underway, no genome assembly has been formally proposed for Loricariidae yet. We report a high-quality genome assembly of Ancistrus triradiatus using long and short reads, and a newly assembled transcriptome. The genome assembly is composed of 9530 scaffolds, including 85.6% of ray-finned fish BUSCOs, and 26,885 predicted protein-coding genes. The genomic GC content is higher than in other catfishes, reflecting the higher metabolism associated with herbivory. The examination of the SCPP gene family indicates that the genes presumably triggering scale loss when absent, are present in the scaleless A. triradiatus, questioning their explanatory role. The analysis of the opsin gene repertoire revealed that gene losses associated to the nocturnal lifestyle of catfishes were not entirely found in A. triradiatus, as the UV-sensitive opsin 5 is present. Finally, most gene family expansions were related to immunity except the gamma crystallin gene family which controls pupil shape and sub-aquatic vision. Thus, the genome of A. triradiatus reveals that fish herbivory may be related to the photic zone habitat, conditions metabolism, photoreception and visual functions. This genome is the first for the catfish suborder Loricarioidei and will serve as backbone for future genetic, developmental and conservation studies.
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Kapitunova AI, Dominova IN, Zhukov VV. γM Crystallin Genes in the Eye Lens of a Juvenile Common Carp Cyprinus carpio: Transcription Levels and Phylogenetic Aspect. J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rocha MA, Sprague-Piercy MA, Kwok AO, Roskamp KW, Martin RW. Chemical Properties Determine Solubility and Stability in βγ-Crystallins of the Eye Lens. Chembiochem 2021; 22:1329-1346. [PMID: 33569867 PMCID: PMC8052307 DOI: 10.1002/cbic.202000739] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/17/2020] [Indexed: 11/10/2022]
Abstract
βγ-Crystallins are the primary structural and refractive proteins found in the vertebrate eye lens. Because crystallins are not replaced after early eye development, their solubility and stability must be maintained for a lifetime, which is even more remarkable given the high protein concentration in the lens. Aggregation of crystallins caused by mutations or post-translational modifications can reduce crystallin protein stability and alter intermolecular interactions. Common post-translational modifications that can cause age-related cataracts include deamidation, oxidation, and tryptophan derivatization. Metal ion binding can also trigger reduced crystallin solubility through a variety of mechanisms. Interprotein interactions are critical to maintaining lens transparency: crystallins can undergo domain swapping, disulfide bonding, and liquid-liquid phase separation, all of which can cause opacity depending on the context. Important experimental techniques for assessing crystallin conformation in the absence of a high-resolution structure include dye-binding assays, circular dichroism, fluorescence, light scattering, and transition metal FRET.
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Affiliation(s)
- Megan A. Rocha
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
| | - Ashley O. Kwok
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025 (USA)
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697-2525
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7
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Roskamp KW, Paulson CN, Brubaker WD, Martin RW. Function and Aggregation in Structural Eye Lens Crystallins. Acc Chem Res 2020; 53:863-874. [PMID: 32271004 DOI: 10.1021/acs.accounts.0c00014] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Crystallins are transparent, refractive proteins that contribute to the focusing power of the vertebrate eye lens. These proteins are extremely soluble and resist aggregation for decades, even under crowded conditions. Crystallins have evolved to avoid strong interprotein interactions and have unusual hydration properties. Crystallin aggregation resulting from mutation, damage, or aging can lead to cataract, a disease state characterized by opacity of the lens.Different aggregation mechanisms can occur, following multiple pathways and leading to aggregates with varied morphologies. Studies of variant proteins found in individuals with childhood-onset cataract have provided insight into the molecular factors underlying crystallin stability and solubility. Modulation of exposed hydrophobic surface is critical, as is preventing specific intermolecular interactions that could provide nucleation sites for aggregation. Biophysical measurements and structural biology techniques are beginning to provide a detailed picture of how crystallins crowd into the lens, providing high refractivity while avoiding excessively tight binding that would lead to aggregation.Despite the central biological importance of refractivity, relatively few experimental measurements have been made for lens crystallins. Our work and that of others have shown that hydration is important to the high refractive index of crystallin proteins, as are interactions between pairs of aromatic residues and potentially other specific structural features.This Account describes our efforts to understand both the functional and disease states of vertebrate eye lens crystallins, particularly the γ-crystallins. We use a variety of biophysical techniques, notably NMR spectroscopy, to investigate crystallin stability and solubility. In the first section, we describe efforts to understand the relative stability and aggregation propensity of different γS-crystallin variants. The second section focuses on interactions of these proteins with the holdase chaperone αB-crystallin. The third, fourth, and fifth sections explore different modes of aggregation available to crystallin proteins, and the final section highlights the importance of refractive index and the sometimes conflicting demands of selection for refractivity and solubility.
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Affiliation(s)
- Kyle W. Roskamp
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Carolyn N. Paulson
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - William D. Brubaker
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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8
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Houston P, Macro N, Kang M, Chen L, Yang J, Wang L, Wu Z, Zhong D. Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin. J Am Chem Soc 2020; 142:3997-4007. [PMID: 31991083 PMCID: PMC7261499 DOI: 10.1021/jacs.9b13506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Water dynamics on the protein surface mediate both protein structure and function. However, many questions remain about the role of the protein hydration layers in protein fluctuations and how the dynamics of these layers relate to specific protein properties. The fish eye lens protein γM7-crystallin (γM7) is found in vivo at extremely high concentrations nearing the packing limit, corresponding to only a few water layers between adjacent proteins. In this study, we conducted a site-specific probing of hydration water motions and side-chain dynamics at nine selected sites around the surface of γM7 using a tryptophan scan with femtosecond spectroscopy and NMR nuclear spin relaxation (NSR). We observed correlated fluctuations between hydration water and protein side chains on the time scales of a few picoseconds and hundreds of picoseconds, corresponding to local reorientations and network restructuring, respectively. These motions are heterogeneous over the protein surface and relate to the various steric and chemical properties of the local protein environment. Overall, we found that γM7 has relatively slower water dynamics within the hydration shell than a similar β-sheet protein, which may contribute to the high packing limit of this unique protein.
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Affiliation(s)
- Patrick Houston
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Nicolas Macro
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Minhee Kang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Long Chen
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Jin Yang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Zhengrong Wu
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
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9
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Ngamniyom A, Sriyapai T, Sriyapai P. Molecular analysis of population and De Novo transcriptome sequencing of Thai medaka, Oryzias minutillus (Teleostei: Adrianichthyidae). Heliyon 2020; 6:e03079. [PMID: 31909257 PMCID: PMC6938829 DOI: 10.1016/j.heliyon.2019.e03079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/13/2019] [Accepted: 12/16/2019] [Indexed: 12/27/2022] Open
Abstract
Thai medaka (Oryzias minutillus) are alternatively known as Thai rice-fish or dwarf medaka, and they widely inhabit natural freshwater environments in all regions of Thailand. In this study, we aimed to investigate the molecular genetics of the Thai medaka population in Thailand inferred from the mitochondrial control region (D-loop) and the cytochrome c oxidase subunit 1 (coxI) sequences. Furthermore, we examined RNA sequencing (RNA-seq) of adult males and females was performed with next-generation sequencing. Together, the combination of the D-loop and coxI sequences clearly distinguished the Thai medaka populations into 2 groups, such as group 1, which generally included samples from the central, northern, western, and eastern regions of the northeastern region. In this group, the fish populations seem to be a little monophyly in which the first subpopulation comprised the main samples from the northern and central regions. The second subpopulation commonly contained fish from the eastern region and specimens from the southern part of the central region near the Gulf of Thailand. Although these subgroups related to geographical distribution, bootstrap values were low in branch considered significant for both subgroups. Group 2 consisted of almost all samples from the southern population and those from the central and southern part of the northeastern region. Group 2 was found that it was made of samples from the northeastern region and samples from the southern population. A total of 73551 unigenes were identified after gene annotation. Signal transduction was the predominant protein classification among the Thai medaka orthologous groups. A differentially expressed gene (DEG) analysis identified 6 subclusters between both sexes that were composed of 257, 131, 364, 386, 114 and 108 genes. Phototransduction was the most enriched pathway and was highly expressed in males, while viral carcinogenesis, oocyte genesis, and the complement and coagulation cascades were highly expressed in females. Further details of these DEGs are discussed below. These results suggest that Thai medaka may genetically exhibit independent populations in the geographic habitats of Thailand. Moreover, these fish also reveal the genes that are conserved in other organisms and those that may be specific to this species.
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Affiliation(s)
- Arin Ngamniyom
- Major in Environment, Faculty of Environmental Culture and Eco-tourism, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thayat Sriyapai
- Major in Environment, Faculty of Environmental Culture and Eco-tourism, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Pichapack Sriyapai
- Department of Microbiology, Faculty of Sciences, Srinakharinwirot University, Bangkok, 10110, Thailand
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10
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Bierma JC, Roskamp KW, Ledray AP, Kiss AJ, Cheng CHC, Martin RW. Controlling Liquid-Liquid Phase Separation of Cold-Adapted Crystallin Proteins from the Antarctic Toothfish. J Mol Biol 2018; 430:5151-5168. [PMID: 30414964 DOI: 10.1016/j.jmb.2018.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022]
Abstract
Liquid-liquid phase separation (LLPS) of proteins is important to a variety of biological processes both functional and deleterious, including the formation of membraneless organelles, molecular condensations that sequester or release molecules in response to stimuli, and the early stages of disease-related protein aggregation. In the protein-rich, crowded environment of the eye lens, LLPS manifests as cold cataract. We characterize the LLPS behavior of six structural γ-crystallins from the eye lens of the Antarctic toothfish Dissostichus mawsoni, whose intact lenses resist cold cataract in subzero waters. Phase separation of these proteins is not strongly correlated with thermal stability, aggregation propensity, or cross-species chaperone protection from heat denaturation. Instead, LLPS is driven by protein-protein interactions involving charged residues. The critical temperature of the phase transition can be tuned over a wide temperature range by selective substitution of surface residues, suggesting general principles for controlling this phenomenon, even in compactly folded proteins.
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Affiliation(s)
- Jan C Bierma
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA
| | - Kyle W Roskamp
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Aaron P Ledray
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA
| | - Andor J Kiss
- Center for Bioinformatics and Functional Genomics, Miami University, Oxford, OH 45056,USA.
| | - C-H Christina Cheng
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,USA
| | - Rachel W Martin
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA.
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11
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Chen Y, Sagar V, Len HS, Peterson K, Fan J, Mishra S, McMurtry J, Wilmarth PA, David LL, Wistow G. γ-Crystallins of the chicken lens: remnants of an ancient vertebrate gene family in birds. FEBS J 2016; 283:1516-30. [PMID: 26913478 DOI: 10.1111/febs.13689] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/02/2016] [Accepted: 02/18/2016] [Indexed: 11/30/2022]
Abstract
γ-Crystallins, abundant proteins of vertebrate lenses, were thought to be absent from birds. However, bird genomes contain well-conserved genes for γS- and γN-crystallins. Although expressed sequence tag analysis of chicken eye found no transcripts for these genes, RT-PCR detected spliced transcripts for both genes in chicken lens, with lower levels in cornea and retina/retinal pigment epithelium. The level of mRNA for γS in chicken lens was relatively very low even though the chicken crygs gene promoter had lens-preferred activity similar to that of mouse. Chicken γS was detected by a peptide antibody in lens, but not in other ocular tissues. Low levels of γS and γN proteins were detected in chicken lens by shotgun mass spectroscopy. Water-soluble and water-insoluble lens fractions were analyzed and 1934 proteins (< 1% false discovery rate) were detected, increasing the known chicken lens proteome 30-fold. Although chicken γS is well conserved in protein sequence, it has one notable difference in leucine 16, replacing a surface glutamine conserved in other γ-crystallins, possibly affecting solubility. However, L16 and engineered Q16 versions were both highly soluble and had indistinguishable circular dichroism, tryptophan fluorescence and heat stability (melting temperature Tm ~ 65 °C) profiles. L16 has been present in birds for over 100 million years and may have been adopted for a specific protein interaction in the bird lens. However, evolution has clearly reduced or eliminated expression of ancestral γ-crystallins in bird lenses. The conservation of genes for γS- and γN-crystallins suggests they may have been preserved for reasons unrelated to the bulk properties of the lens.
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Affiliation(s)
- Yingwei Chen
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vatsala Sagar
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hoay-Shuen Len
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine Peterson
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianguo Fan
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sanghamitra Mishra
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McMurtry
- USDA, ARS, Southern Plains Area, East College Station, TX, USA
| | - Phillip A Wilmarth
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Larry L David
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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12
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Choudhury S, Thomas JK, Sylvain NJ, Ponomarenko O, Gordon RA, Heald SM, Janz DM, Krone PH, Coulthard I, George GN, Pickering IJ. Selenium preferentially accumulates in the eye lens following embryonic exposure: a confocal X-ray fluorescence imaging study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:2255-2261. [PMID: 25607235 DOI: 10.1021/es503848s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Maternal transfer of elevated selenium (Se) to offspring is an important route of Se exposure for fish in the natural environment. However, there is a lack of information on the tissue specific spatial distribution and speciation of Se in the early developmental stages of fish, which provide important information about Se toxicokinetics. The effect of maternal transfer of Se was studied by feeding adult zebrafish a Se-elevated or a control diet followed by collection of larvae from both groups. Novel confocal synchrotron-based techniques were used to investigate Se within intact preserved larvae. Confocal X-ray fluorescence imaging was used to compare Se distributions within specific planes of an intact larva from each of the two groups. The elevated Se treatment showed substantially higher Se levels than the control; Se preferentially accumulated to highest levels in the eye lens, with lower levels in the retina, yolk and other tissues. Confocal X-ray absorption spectroscopy was used to determine that the speciation of Se within the eye lens of the intact larva was a selenomethionine-like species. Preferential accumulation of Se in the eye lens may suggest a direct cause-and-effect relationship between exposure to elevated Se and Se-induced ocular impairments reported previously. This study illustrates the effectiveness of confocal X-ray fluorescence methods for investigating trace element distribution and speciation in intact biological specimens.
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Affiliation(s)
- Sanjukta Choudhury
- Department of Geological Sciences, University of Saskatchewan , 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada
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13
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Kingsley CN, Bierma JC, Pham V, Martin RW. γS-crystallin proteins from the Antarctic nototheniid toothfish: a model system for investigating differential resistance to chemical and thermal denaturation. J Phys Chem B 2014; 118:13544-53. [PMID: 25372016 PMCID: PMC4254003 DOI: 10.1021/jp509134d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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The γS1- and γS2-crystallins,
structural eye lens proteins
from the Antarctic toothfish (Dissostichus mawsoni), are homologues of the human lens protein γS-crystallin.
Although γS1 has the higher thermal stability of the two, it
is more susceptible to chemical denaturation by urea. The lower thermodynamic
stability of both toothfish crystallins relative to human γS-crystallin
is consistent with the current picture of how proteins from organisms
endemic to perennially cold environments have achieved low-temperature
functionality via greater structural flexibility. In some respects,
the sequences of γS1- and γS2-crystallin are typical of
psychrophilic proteins; however, their amino acid compositions also
reflect their selection for a high refractive index increment. Like
their counterparts in the human lens and those of mesophilic fish,
both toothfish crystallins are relatively enriched in aromatic residues
and methionine and exiguous in aliphatic residues. The sometimes contradictory
requirements of selection for cold tolerance and high refractive index
make the toothfish crystallins an excellent model system for further
investigation of the biophysical properties of structural proteins.
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Affiliation(s)
- Carolyn N Kingsley
- Department of Chemistry, University of California-Irvine , 1102 Natural Sciences 2, Irvine, California, 92697-2025, United States
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14
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Slingsby C, Wistow GJ. Functions of crystallins in and out of lens: roles in elongated and post-mitotic cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 115:52-67. [PMID: 24582830 PMCID: PMC4104235 DOI: 10.1016/j.pbiomolbio.2014.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 02/18/2014] [Indexed: 12/25/2022]
Abstract
The vertebrate lens evolved to collect light and focus it onto the retina. In development, the lens grows through massive elongation of epithelial cells possibly recapitulating the evolutionary origins of the lens. The refractive index of the lens is largely dependent on high concentrations of soluble proteins called crystallins. All vertebrate lenses share a common set of crystallins from two superfamilies (although other lineage specific crystallins exist). The α-crystallins are small heat shock proteins while the β- and γ-crystallins belong to a superfamily that contains structural proteins of uncertain function. The crystallins are expressed at very high levels in lens but are also found at lower levels in other cells, particularly in retina and brain. All these proteins have plausible connections to maintenance of cytoplasmic order and chaperoning of the complex molecular machines involved in the architecture and function of cells, particularly elongated and post-mitotic cells. They may represent a suite of proteins that help maintain homeostasis in such cells that are at risk from stress or from the accumulated insults of aging.
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Affiliation(s)
- Christine Slingsby
- Department of Biological Sciences, Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK.
| | - Graeme J Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, Bg 6, Rm 106, National Institutes of Health, Bethesda, MD 20892-0608, USA
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15
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Serebryany E, King JA. The βγ-crystallins: native state stability and pathways to aggregation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 115:32-41. [PMID: 24835736 DOI: 10.1016/j.pbiomolbio.2014.05.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 01/26/2023]
Abstract
The βγ-crystallins are among the most stable and long-lived proteins in the human body. With increasing age, however, they transform to high molecular weight light-scattering aggregates, resulting in cataracts. This occurs despite the presence in the lens of high concentrations of the a-crystallin chaperones. Aggregation of crystallins can be induced in vitro by a variety of stresses, including acidic pH, ultraviolet light, oxidative damage, heating or freezing, and specific amino acid substitutions. Accumulating evidence points to the existence of specific biochemical pathways of protein: protein interaction and polymerization. We review the methods used for studying crystallin stability and aggregation and discuss the sometimes counterintuitive relationships between factors that favor native state stability and those that favor non-native aggregation. We discuss the behavior of βγ-crystallins in mixtures and their chaperone ability; the consequences of missense mutations and covalent damage to the side-chains; and the evolutionary strategies that have shaped these proteins. Efforts are ongoing to reveal the nature of cataractous crystallin aggregates and understand the mechanisms of aggregation in the context of key models of protein polymerization: amyloid, native-state, and domain-swapped. Such mechanistic understanding is likely to be of value for the development of therapeutic interventions and draw attention to unanswered questions about the relationship between a protein's native state stability and its transformation to an aggregated state.
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Affiliation(s)
- Eugene Serebryany
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States.
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16
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Unexpected headless and tailless fish in the stomach content of shortfin mako Isurus oxyrinchus. PLoS One 2014; 9:e88488. [PMID: 24533093 PMCID: PMC3922876 DOI: 10.1371/journal.pone.0088488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/08/2014] [Indexed: 11/28/2022] Open
Abstract
The stomach content of 113 individuals of shortfin mako Isurus oxyrinchus was analyzed. Individuals were sampled at landing in Vigo (Spain) and captured by sea-surface long-liners in the vicinity of the Azores Archipelago and between Azores and the Iberian Peninsula, in March and October 2012, and March 2013. Teleosts constituted the dominant item, mainly Atlantic saury Scomberesox saurus (87% of teleost prey). Among them, 94% were deprived of both head and the caudal fin, while the flesh and bones of the body were preserved. The presence of eye's lenses, the number of which was consistent with the number of fish remains, likely rules out the elimination of the heads before ingestion. There is no obvious explanation for this unexpected and unrecorded pattern of digestion.
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17
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Chen Y, Zhao H, Schuck P, Wistow G. Solution properties of γ-crystallins: compact structure and low frictional ratio are conserved properties of diverse γ-crystallins. Protein Sci 2013; 23:76-87. [PMID: 24214907 DOI: 10.1002/pro.2395] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 11/11/2022]
Abstract
γ-crystallins are highly specialized proteins of the vertebrate eye lens where they survive without turnover under high molecular crowding while maintaining transparency. They share a tightly folded structural template but there are striking differences among species. Their amino acid compositions are unusual. Even in mammals, γ-crystallins have high contents of sulfur-containing methionine and cysteine, but this reaches extremes in fish γM-crystallins with up to 15% Met. In addition, fish γM-crystallins do not conserve the paired tryptophan residues found in each domain in mammalian γ-crystallins and in the related β-crystallins. To gain insight into important, evolutionarily conserved properties and functionality of γ-crystallins, zebrafish (Danio rerio) γM2b and γM7 were compared with mouse γS and human γD. For all four proteins, far UV CD spectra showed the expected β-sheet secondary structure. Like the mammalian proteins, γM7 was highly soluble but γM2b was much less so. The heat and denaturant stability of both fish proteins was lower than either mammalian protein. The ability of full-length and truncated versions of human αB-crystallin to retard aggregation of the heat denatured proteins also showed differences. However, when solution behavior was investigated by sedimentation velocity experiments, the diverse γ-crystallins showed remarkably similar hydrodynamic properties with low frictional ratios and partial specific volumes. The solution behavior of γ-crystallins, with highly compact structures suited for the densely packed environment of the lens, seems to be highly conserved and appears largely independent of amino acid composition.
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Affiliation(s)
- Yingwei Chen
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, Maryland, 20892-0608
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18
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Zhao H, Chen Y, Rezabkova L, Wu Z, Wistow G, Schuck P. Solution properties of γ-crystallins: hydration of fish and mammal γ-crystallins. Protein Sci 2013; 23:88-99. [PMID: 24282025 DOI: 10.1002/pro.2394] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/06/2022]
Abstract
Lens γ crystallins are found at the highest protein concentration of any tissue, ranging from 300 mg/mL in some mammals to over 1000 mg/mL in fish. Such high concentrations are necessary for the refraction of light, but impose extreme requirements for protein stability and solubility. γ-crystallins, small stable monomeric proteins, are particularly associated with the lowest hydration regions of the lens. Here, we examine the solvation of selected γ-crystallins from mammals (human γD and mouse γS) and fish (zebrafish γM2b and γM7). The thermodynamic water binding coefficient B₁ could be probed by sucrose expulsion, and the hydrodynamic hydration shell of tightly bound water was probed by translational diffusion and structure-based hydrodynamic boundary element modeling. While the amount of tightly bound water of human γD was consistent with that of average proteins, the water binding of mouse γS was found to be relatively low. γM2b and γM7 crystallins were found to exhibit extremely low degrees hydration, consistent with their role in the fish lens. γM crystallins have a very high methionine content, in some species up to 15%. Structure-based modeling of hydration in γM7 crystallin suggests low hydration is associated with the large number of surface methionine residues, likely in adaptation to the extremely high concentration and low hydration environment in fish lenses. Overall, the degree of hydration appears to balance stability and tissue density requirements required to produce and maintain the optical properties of the lens in different vertebrate species.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, Bethesda, Maryland, 20892
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