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Lee CJ, Choi BH, Kim SS, Kim DNJ, Kim TH, Choi JM, Pak Y, Park JS. Intermolecular Interactions between Cysteine and Aromatic Amino Acids with a Phenyl Moiety in the DNA-Binding Domain of Heat Shock Factor 1 Regulate Thermal Stress-Induced Trimerization. Biochemistry 2024; 63:1307-1321. [PMID: 38688031 DOI: 10.1021/acs.biochem.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
In this study, we investigated the trimerization mechanism and structure of heat shock factor 1 (HSF1) using western blotting, tryptophan (Trp) fluorescence spectroscopy, and molecular modeling. First, we examined the DNA-binding domains of human (Homo sapiens), goldfish (Carassius auratus), and walleye pollock (Gadus chalcogrammus) HSF1s by mutating key residues (36 and 103) that are thought to directly affect trimer formation. Human, goldfish, and walleye pollock HSF1s contain cysteine at residue 36 but cysteine (C), tyrosine (Y), and phenylalanine (F), respectively, at residue 103. The optimal trimerization temperatures for the wild-type HSF1s of each species were found to be 42, 37, and 20 °C, respectively. Interestingly, a mutation experiment revealed that trimerization occurred at 42 °C when residue 103 was cysteine, at 37 °C when it was tyrosine, and at 20 °C when it was phenylalanine, regardless of the species. In addition, it was confirmed that when residue 103 of the three species was mutated to alanine, trimerization did not occur. This suggests that in addition to trimerization via disulfide bond formation between the cysteine residues in human HSF1, trimerization can also occur via the formation of a different type of bond between cysteine and aromatic ring residues such as tyrosine and phenylalanine. We also confirmed that at least one cysteine is required for the trimerization of HSF1s, regardless of its position (residue 36 or 103). Additionally, it was shown that the trimer formation temperature is related to growth and survival in fish.
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Affiliation(s)
- Chang-Ju Lee
- Department of Chemistry and Chemistry, Institute of Functional Materials in Pusan National University, Busan 609-735, Korea
| | - Bo-Hee Choi
- Department of Chemistry and Chemistry, Institute of Functional Materials in Pusan National University, Busan 609-735, Korea
| | - So-Sun Kim
- East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangneung-si 25435, Republic of Korea
| | - David Nahm-Joon Kim
- Department of Chemistry and Chemistry, Institute of Functional Materials in Pusan National University, Busan 609-735, Korea
| | - Tae-Hwan Kim
- Department of Chemistry and Chemistry, Institute of Functional Materials in Pusan National University, Busan 609-735, Korea
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry, Institute of Functional Materials in Pusan National University, Busan 609-735, Korea
| | - Youngshang Pak
- Department of Chemistry and Chemistry, Institute of Functional Materials in Pusan National University, Busan 609-735, Korea
| | - Jang-Su Park
- Department of Chemistry and Chemistry, Institute of Functional Materials in Pusan National University, Busan 609-735, Korea
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Desvignes T, Bista I, Herrera K, Landes A, Postlethwait JH. Cold-Driven Hemoglobin Evolution in Antarctic Notothenioid Fishes Prior to Hemoglobin Gene Loss in White-Blooded Icefishes. Mol Biol Evol 2023; 40:msad236. [PMID: 37879119 PMCID: PMC10651078 DOI: 10.1093/molbev/msad236] [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: 05/25/2023] [Revised: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023] Open
Abstract
Expression of multiple hemoglobin isoforms with differing physiochemical properties likely helps species adapt to different environmental and physiological conditions. Antarctic notothenioid fishes inhabit the icy Southern Ocean and display fewer hemoglobin isoforms, each with less affinity for oxygen than temperate relatives. Reduced hemoglobin multiplicity was proposed to result from relaxed selective pressure in the cold, thermally stable, and highly oxygenated Antarctic waters. These conditions also permitted the survival and diversification of white-blooded icefishes, the only vertebrates living without hemoglobin. To understand hemoglobin evolution during adaptation to freezing water, we analyzed hemoglobin genes from 36 notothenioid genome assemblies. Results showed that adaptation to frigid conditions shaped hemoglobin gene evolution by episodic diversifying selection concomitant with cold adaptation and by pervasive evolution in Antarctic notothenioids compared to temperate relatives, likely a continuing adaptation to Antarctic conditions. Analysis of hemoglobin gene expression in adult hematopoietic organs in various temperate and Antarctic species further revealed a switch in hemoglobin gene expression underlying hemoglobin multiplicity reduction in Antarctic fish, leading to a single hemoglobin isoform in adult plunderfishes and dragonfishes, the sister groups to icefishes. The predicted high hemoglobin multiplicity in Antarctic fish embryos based on transcriptomic data, however, raises questions about the molecular bases and physiological implications of diverse hemoglobin isoforms in embryos compared to adults. This analysis supports the hypothesis that the last common icefish ancestor was vulnerable to detrimental mutations affecting the single ancestral expressed alpha- and beta-globin gene pair, potentially predisposing their subsequent loss.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Iliana Bista
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt 60325, Germany
- Senckenberg Research Institute, Frankfurt 60325, Germany
| | - Karina Herrera
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Audrey Landes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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Collins T, Feller G. Psychrophilic enzymes: strategies for cold-adaptation. Essays Biochem 2023; 67:701-713. [PMID: 37021674 DOI: 10.1042/ebc20220193] [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: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023]
Abstract
Psychrophilic organisms thriving at near-zero temperatures synthesize cold-adapted enzymes to sustain cell metabolism. These enzymes have overcome the reduced molecular kinetic energy and increased viscosity inherent to their environment and maintained high catalytic rates by development of a diverse range of structural solutions. Most commonly, they are characterized by a high flexibility coupled with an intrinsic structural instability and reduced substrate affinity. However, this paradigm for cold-adaptation is not universal as some cold-active enzymes with high stability and/or high substrate affinity and/or even an unaltered flexibility have been reported, pointing to alternative adaptation strategies. Indeed, cold-adaptation can involve any of a number of a diverse range of structural modifications, or combinations of modifications, depending on the enzyme involved, its function, structure, stability, and evolutionary history. This paper presents the challenges, properties, and adaptation strategies of these enzymes.
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Affiliation(s)
- Tony Collins
- Department of Biology, Center of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
| | - Georges Feller
- Department of Life Sciences, Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, 4000 Liège, Belgium
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Cheng CHC, Rivera-Colón AG, Minhas BF, Wilson L, Rayamajhi N, Vargas-Chacoff L, Catchen JM. Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus-The Closest Ancestral Proxy of Antarctic Cryonotothenioids. Genes (Basel) 2023; 14:1196. [PMID: 37372376 DOI: 10.3390/genes14061196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus' phylogenetic position. We additionally curated E. maclovinus' repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses.
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Affiliation(s)
- Chi-Hing Christina Cheng
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Bushra Fazal Minhas
- Informatics Program, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Loralee Wilson
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Niraj Rayamajhi
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Luis Vargas-Chacoff
- Laboratorio de Fisiología de Peces, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia 5090000, Chile
- Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia 5090000, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Julian M Catchen
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
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Bilyk KT, Zhuang X, Papetti C. Positive and Relaxed Selective Pressures Have Both Strongly Influenced the Evolution of Cryonotothenioid Fishes during Their Radiation in the Freezing Southern Ocean. Genome Biol Evol 2023; 15:evad049. [PMID: 36951069 PMCID: PMC10078794 DOI: 10.1093/gbe/evad049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
Abstract
Evolution in the chronic cold of the Southern Ocean has had a profound influence on the physiology of cryonotothenioid fishes. However, the suite of genetic changes underlying the physiological gains and losses in these fishes is still poorly surveyed. By identifying the genomic signatures of selection, this study aims to identify the functional classes of genes that have been changed following two major physiological transitions: the onset of freezing temperatures and the loss of hemoproteins. Looking at the changes that followed the onset of freezing temperatures, positive selective pressure was found among a set of broadly acting gene regulatory factors, suggesting a route through which cryonotothenioid gene expression has been retooled for life in the cold. Further, genes related to the cell cycle and cellular adhesion were found under positive selection suggesting that both present key challenges to life in freezing waters. By contrast, genes showing signatures of the relaxation of selective pressure showed a narrower biological impact, acting on genes related to mitochondrial function. Finally, although chronic cold-water temperatures appear correlated with substantial genetic change, the loss of hemoproteins resulted in little observable change in protein-coding genes relative to their red-blooded relatives. Combined, the influence of positive and relaxed selection shows that long-term exposure to cold has led to profound changes in cryonotothenioid genomes that may make it challenging for them to adapt to a rapidly changing climate.
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Affiliation(s)
- Kevin T Bilyk
- Department of Biology, Montclair State University, New Jersey
| | - Xuan Zhuang
- Department of Biological Sciences, University of Arkansas, Fayetteville
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Pacchini S, Piva E, Schumann S, Irato P, Pellegrino D, Santovito G. An Experimental Study on Antioxidant Enzyme Gene Expression in Trematomus newnesi ( Boulenger, 1902) Experimentally Exposed to Perfluoro-Octanoic Acid. Antioxidants (Basel) 2023; 12:antiox12020352. [PMID: 36829911 PMCID: PMC9951861 DOI: 10.3390/antiox12020352] [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: 12/31/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Antarctica is the continent with the lowest local human impact; however, it is susceptible to pollution from external sources. Emerging pollutants such as perfluoroalkyl substances pose an increasing threat to this environment and therefore require more in-depth investigations to understand their environmental fate and biological impacts. The present study focuses on expression analysis at the transcriptional level of genes coding for four antioxidant enzymes (sod1, sod2, gpx1, and gpx4) in the liver and kidney of an Antarctic fish species, Trematomus newnesi (Boulenger, 1902). mRNA levels were also assessed in fish exposed to 1.5 μg/L of perfluoro-octanoic acid for 10 days. The kidney showed a higher level of expression than the liver in wildlife specimens. In the liver, the treatment induced an increase in gene expression for all the considered enzymes, whereas in the kidney, it induced a general decrease. The obtained results advance the scientific community's understanding of how the potential future presence of anthropogenic contaminants in the Southern Ocean can affect the antioxidant system of Antarctic fishes. The presence of pollutants belonging to the perfluoroalkyl substances in the Southern Ocean needs to be continuously monitored in parallel with this type of research.
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Affiliation(s)
- Sara Pacchini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Elisabetta Piva
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Sophia Schumann
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Paola Irato
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Daniela Pellegrino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy
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Ametrano A, Picchietti S, Guerra L, Giacomelli S, Oreste U, Coscia MR. Comparative Analysis of the pIgR Gene from the Antarctic Teleost Trematomus bernacchii Reveals Distinctive Features of Cold-Adapted Notothenioidei. Int J Mol Sci 2022; 23:ijms23147783. [PMID: 35887127 PMCID: PMC9321927 DOI: 10.3390/ijms23147783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
The IgM and IgT classes were previously identified and characterized in the Antarctic teleost Trematomus bernacchii, a species belonging to the Perciform suborder Notothenoidei. Herein, we characterized the gene encoding the polymeric immunoglobulin receptor (pIgR) in the same species and compared it to the pIgR of multiple teleost species belonging to five perciform suborders, including 11 Antarctic and 1 non-Antarctic (Cottoperca gobio) notothenioid species, the latter living in the less-cold peri-Antarctic sea. Antarctic pIgR genes displayed particularly long introns marked by sites of transposable elements and transcription factors. Furthermore, analysis of T. bernacchii pIgR cDNA unveiled multiple amino acid substitutions unique to the Antarctic species, all introducing adaptive features, including N-glycosylation sequons. Interestingly, C. gobio shared most features with the other perciforms rather than with the cold-adapted relatives. T. bernacchii pIgR transcripts were predominantly expressed in mucosal tissues, as indicated by q-PCR and in situ hybridization analysis. These results suggest that in cold-adapted species, pIgR preserved its fundamental role in mucosal immune defense, although remarkable gene structure modifications occurred.
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Affiliation(s)
- Alessia Ametrano
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy; (S.P.); (L.G.)
| | - Laura Guerra
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy; (S.P.); (L.G.)
| | - Stefano Giacomelli
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Umberto Oreste
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
- Correspondence: ; Tel.: +39-081-6132556
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Tissue-Specific and Differential Cold Responses in the Domesticated Cold Tolerant Fugu. FISHES 2022. [DOI: 10.3390/fishes7040159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Domestication can be defined as the artificial selection in animals to achieve morphological, physiological, and developmental conformity to human needs, with the aim of improving various limitations in species under a human feeding environment. The future sustainability of aquaculture may rely partly on the availability of numerous domesticated fish species. However, the underlying adaptive mechanisms that result in the domestication of fish are still unclear. Because they are poikilothermic, temperature is a key environmental element that affects the entire life of fish, so studying the association between physiological and behavioral changes in low-temperature domesticated fish can provide a model for understanding the response mechanisms of fish under cold stress. Through 5 generations and 10 years of artificial selection at low temperatures, we used cold-tolerant fugu as a biological model to compare transcriptome changes in brain and liver tissues to study the effects of cold stress on fish. It was found that the expression of genes such as apoptosis, p53, oxidative phosphorylation, and mitochondrial β-oxidation in the brain of cold-tolerant fugu was significantly lower than the wild type due to cold stress, while excessive energy metabolism would lead to the production of reactive oxygen species (ROS) and exacerbate the brain damage, thus causing rollover and coma. Meanwhile, under cold stress, the signaling pathways involved in glycogenolysis and lipid metabolism, such as insulin signaling, adipocytokines, and mTOR signaling pathways, were significantly up-regulated in the liver of cold-tolerant fugu. Although the mitochondrial β-oxidation pathway was increased in cold-tolerant fugu liver tissues, the transcriptome was not enriched in apoptotic. These phenomena predict that in response to low-temperature conditions, cold-tolerant fugu employs a dynamic inter-organ metabolic regulation strategy to cope with cold stress and reduce damage to brain tissues.
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