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Li W, Song J, Tu H, Jiang S, Pan B, Li J, Zhao Y, Chen L, Xu Q. Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation. Mol Ecol Resour 2024; 24:e13989. [PMID: 38946220 DOI: 10.1111/1755-0998.13989] [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: 02/18/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jie Song
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Huaming Tu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jiazhen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yongpeng Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
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Uniacke-Lowe S, Stanton C, Hill C, Ross RP. The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins. Microorganisms 2024; 12:1346. [PMID: 39065114 PMCID: PMC11278639 DOI: 10.3390/microorganisms12071346] [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: 05/16/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.
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Affiliation(s)
- Shona Uniacke-Lowe
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
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Kacirani A, Uralcan B, Domingues TS, Haji-Akbari A. Effect of Pressure on the Conformational Landscape of Human γD-Crystallin from Replica Exchange Molecular Dynamics Simulations. J Phys Chem B 2024; 128:4931-4942. [PMID: 38685567 DOI: 10.1021/acs.jpcb.4c00178] [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
Human γD-crystallin belongs to a crucial family of proteins known as crystallins located in the fiber cells of the human lens. Since crystallins do not undergo any turnover after birth, they need to possess remarkable thermodynamic stability. However, their sporadic misfolding and aggregation, triggered by environmental perturbations or genetic mutations, constitute the molecular basis of cataracts, which is the primary cause of blindness in the globe according to the World Health Organization. Here, we investigate the impact of high pressure on the conformational landscape of wild-type HγD-crystallin using replica exchange molecular dynamics simulations augmented with principal component analysis. We find pressure to have a modest impact on global measures of protein stability, such as root-mean-square displacement and radius of gyration. Upon projecting our trajectories along the first two principal components from principal component analysis, however, we observe the emergence of distinct free energy basins at high pressures. By screening local order parameters previously shown or hypothesized as markers of HγD-crystallin stability, we establish correlations between a tyrosine-tyrosine aromatic contact within the N-terminal domain and the protein's end-to-end distance with projections along the first and second principal components, respectively. Furthermore, we observe the simultaneous contraction of the hydrophobic core and its intrusion by water molecules. This exploration sheds light on the intricate responses of HγD-crystallin to elevated pressures, offering insights into potential mechanisms underlying its stability and susceptibility to environmental perturbations, crucial for understanding cataract formation.
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Affiliation(s)
- Arlind Kacirani
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Betül Uralcan
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemical Engineering, Boğaziçi University, Istanbul 34342, Turkey
| | - Tiago S Domingues
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Graduate Program in Applied Mathematics, Yale University, New Haven, Connecticut 06520, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
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4
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Uniacke-Lowe S, Johnson CN, Stanton C, Hill C, Ross P. Winogradskyella bathintestinalis sp. nov., isolated from the intestine of the deep-sea loosejaw dragonfish, Malacosteus niger. Int J Syst Evol Microbiol 2023; 73:10.1099/ijsem.0.006135. [PMID: 37877999 PMCID: PMC7615552 DOI: 10.1099/ijsem.0.006135] [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: 10/26/2023] Open
Abstract
A novel bacterial strain, APC 3343T, was isolated from the intestine of a deep-sea loosejaw dragon fish, Malacosteus niger, caught at a depth of 1000 m in the Northwest Atlantic Ocean. Cells were aerobic, rod-shaped, yellow/orange-pigmented, non-motile and Gram-negative. Growth of strain APC 3343T was observed at 4-30 °C (optimum, 21-25 °C), pH 5.5-10 (optimum, pH 7-8) and 0.5-8 % (w/v) NaCl (optimum, 2-4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain APC 3343T was most closely related to members of the genus Winogradskyella, with the most closely related type strains being Winogradskyella algae Kr9-9T (98.46 % identity), Winogradskyella damuponensis F081-2T (98.07 %), Winogradskyella eximia CECT 7946T (97.93 %), Winogradskyella litoriviva KMM 6491T (97.79 %) and Winogradskyella endarachnes HL2-2T (97.79 %). Major fatty acids (>10 % of total) were iso-C16 : 0 3-OH, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). Polar lipids were phosphatidylethanolamine, three unknown aminolipids and eight unknown lipids. The draft genome sequence was 3.8 Mb in length with a G+C content of 33.43 mol%. Based on the phenotypic characteristics and phylogenetic analysis, strain APC 3343T is deemed to be a novel species of the genus Winogradskyella, and for which the name Winogradskyella bathintestinalis sp. nov. is proposed. The type strain of this species is APC 3343T (=DSM 115832T=NCIMB 15464T).
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Affiliation(s)
- Shona Uniacke-Lowe
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
| | - Crystal N. Johnson
- Department of Biochemistry & Microbiology, Oklahoma State University – Center for Health Sciences, Tulsa, Oklahoma, USA
| | - Catherine Stanton
- APC Microbiome Ireland, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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5
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Uniacke-Lowe S, Collins FWJ, Hill C, Ross RP. Bioactivity Screening and Genomic Analysis Reveals Deep-Sea Fish Microbiome Isolates as Sources of Novel Antimicrobials. Mar Drugs 2023; 21:444. [PMID: 37623725 PMCID: PMC10456417 DOI: 10.3390/md21080444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
With the increase in antimicrobial resistance and the subsequent demand for novel therapeutics, the deep-sea fish microbiome can be a relatively untapped source of antimicrobials, including bacteriocins. Previously, bacterial isolates were recovered from the gut of deep-sea fish sampled from the Atlantic Ocean.In this study, we used in vitro methods to screen a subset of these isolates for antimicrobial activity, and subsequently mined genomic DNA from isolates of interest for bacteriocin and other antimicrobial metabolite genes. We observed antimicrobial activity against foodborne pathogens, including Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis and Micrococcus luteus. In total, 147 candidate biosynthetic gene clusters were identified in the genomic sequences, including 35 bacteriocin/RiPP-like clusters. Other bioactive metabolite genes detected included non-ribosomal peptide synthases (NRPS), polyketide synthases (PKS; Types 1 and 3), beta-lactones and terpenes. Moreover, four unique bacteriocin gene clusters were annotated and shown to encode novel peptides: a class IIc bacteriocin, two class IId bacteriocins and a class I lanthipeptide (LanM subgroup). Our dual in vitro and in silico approach allowed for a more comprehensive understanding of the bacteriocinogenic potential of these deep-sea isolates and an insight into the antimicrobial molecules that they may produce.
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Affiliation(s)
- Shona Uniacke-Lowe
- Department of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, T12 K8AF Cork, Ireland
- Teagasc Food Research Centre, P61 C996 Fermoy, Ireland
| | | | - Colin Hill
- Department of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, T12 K8AF Cork, Ireland
| | - R Paul Ross
- Department of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, T12 K8AF Cork, Ireland
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6
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Goldstone JV, Lamb DC, Kelly SL, Lepesheva GI, Stegeman JJ. Structural modeling of cytochrome P450 51 from a deep-sea fish points to a novel structural feature in other CYP51s. J Inorg Biochem 2023; 245:112241. [PMID: 37209461 PMCID: PMC10330650 DOI: 10.1016/j.jinorgbio.2023.112241] [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: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
Cytochromes P450 (CYP), enzymes involved in the metabolism of endogenous and xenobiotic substrates, provide an excellent model system to study how membrane proteins with unique functions have catalytically adapted through evolution. Molecular adaptation of deep-sea proteins to high hydrostatic pressure remains poorly understood. Herein, we have characterized recombinant cytochrome P450 sterol 14α-demethylase (CYP51), an essential enzyme of cholesterol biosynthesis, from an abyssal fish species, Coryphaenoides armatus. C. armatus CYP51 was heterologously expressed in Escherichia coli following N-terminal truncation and purified to homogeneity. Recombinant C. armatus CYP51 bound its sterol substrate lanosterol giving a Type I binding spectra (KD 15 μM) and catalyzed lanosterol 14α-demethylation turnover at 5.8 nmol/min/nmol P450. C. armatus CYP51 also bound the azole antifungals ketoconazole (KD 0.12 μM) and propiconazole (KD 0.54 μM) as determined by Type II absorbance spectra. Comparison of C. armatus CYP51 primary sequence and modeled structures with other CYP51s identified amino acid substitutions that may confer an ability to function under pressures of the deep sea and revealed heretofore undescribed internal cavities in human and other non-deep sea CYP51s. The functional significance of these cavities is not known. PROLOGUE: This paper is dedicated in memory of Michael Waterman and Tsuneo Omura, who as good friends and colleagues enriched our lives. They continue to inspire us.
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Affiliation(s)
- Jared V Goldstone
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - David C Lamb
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea SA2 8PP, UK
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea SA2 8PP, UK
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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7
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Almeida AVM, Vaz MGMV, Castro NVD, Genuário DB, Oder JC, Souza PAMD, Martins SB, Machado M, Nunes-Nesi A, Araújo WL. How diverse a genus can be: An integrated multi-layered analysis into Desmonostoc (Nostocaceae, Cyanobacteriota). Syst Appl Microbiol 2023; 46:126422. [PMID: 37119668 DOI: 10.1016/j.syapm.2023.126422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/29/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
Cyanobacteria (Phylum Cyanobacteriota) are Gram-negative bacteria capable of performing oxygenic photosynthesis. Although the taxonomic classification of cyanobacteria was for a long time based primarily on morphological characters, the application of other techniques (e.g. molecular phylogeny), especially in recent decades, has contributed to a better resolution of cyanobacteria systematics, leading to a revision of the phylum. Although Desmonostoc occurs as a new genus/cluster and some species have been described recently, relatively few studies have been carried out to elucidate its diversity, which encompasses strains from different ecological origins, or examine the application of new characterization tools. In this context, the present study investigated the diversity within Desmonostoc, based on morphological, molecular, metabolic, and physiological characteristics. Although the usage of physiological parameters is unusual for a polyphasic approach, they were efficient in the characterization performed here. The phylogenetic analysis based on 16S rRNA gene sequences put all studied strains (25) into the D1 cluster and indicated the emergence of novel sub-clusters. It was also possible to observe that nifD and nifH exhibited different evolutionary histories within the Desmonostoc strains. Collectively, metabolic and physiological data, coupled with the morphometric data, were in general, in good agreement with the separation based on the phylogeny of the 16S rRNA gene. Furthermore, the study provided important information on the diversity of Desmonostoc strains collected from different Brazilian biomes by revealing that they were cosmopolitan strains, acclimatized to low luminous intensities, with a large metabolic diversity and great biotechnological potential.
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Affiliation(s)
- Allan Victor M Almeida
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | | | - Naira Valle de Castro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Diego Bonaldo Genuário
- Biodiversita Tecnologia Microbiana, 13148-153 Paulínia, São Paulo, Brazil; Laboratório de Microbiologia Ambiental, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, São Paulo, Brazil
| | - Jean Coutinho Oder
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | | | - Sandy Bastos Martins
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Mariana Machado
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil.
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McClain CR, Bryant SR, Hanks G, Bowles MW. Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans. ASTROBIOLOGY 2022; 22:1009-1028. [PMID: 35549348 DOI: 10.1089/ast.2021.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.
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Affiliation(s)
- Craig R McClain
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - S River Bryant
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Granger Hanks
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
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9
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Madyarova E, Shirokova Y, Gurkov A, Drozdova P, Baduev B, Lubyaga Y, Shatilina Z, Vishnevskaya M, Timofeyev M. Metabolic Tolerance to Atmospheric Pressure of Two Freshwater Endemic Amphipods Mostly Inhabiting the Deep-Water Zone of the Ancient Lake Baikal. INSECTS 2022; 13:insects13070578. [PMID: 35886754 PMCID: PMC9325015 DOI: 10.3390/insects13070578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/03/2022]
Abstract
Simple Summary Deep-water habitats are the largest ecosystem on the planet: over half of the Earth’s surface is covered with a water layer deeper than 200 m and remains poorly explored. Lake Baikal is the only freshwater body inhabited by animals adapted to the deep-water zone independently from their marine counterparts. Comparing these convergently evolved freshwater and marine animals is invaluable for revealing the basic mechanisms of adaptation to high hydrostatic pressure. However, laboratory experiments on deep-water organisms still usually require lifting them to the water’s surface and exposing them to potentially hazardous decompression, while endemics from Lake Baikal are poorly studied in this regard. Here, we compared metabolic reactions to such pressure decreases in two Baikal deep-water amphipods (shrimp-like crustaceans) from the genus Ommatogammarus: one species is known to tolerate pressures close to atmospheric levels, while the second was only observed at the pressures from 5 atm and above. We expected that the energy metabolism of the shallower-dwelling species would function better under the atmospheric pressure but found no substantial differences. Thus, despite some difference in long-term survival at atmospheric pressure, both species are suitable for laboratory studies as freshwater model objects adapted to large pressure variations. Abstract Lake Baikal is the only freshwater reservoir inhabited by deep-water fauna, which originated mostly from shallow-water ancestors. Ommatogammarus flavus and O. albinus are endemic scavenger amphipods (Amphipoda, Crustacea) dwelling in wide depth ranges of the lake covering over 1300 m. O. flavus had been previously collected close to the surface, while O. albinus has never been found above the depth of 47 m. Since O. albinus is a promising model species for various research, here we tested whether O. albinus is less metabolically adapted to atmospheric pressure than O. flavus. We analyzed a number of energy-related traits (contents of glucose, glycogen and adenylates, as well as lactate dehydrogenase activity) and oxidative stress markers (activities of antioxidant enzymes and levels of lipid peroxidation products) after sampling from different depths and after both species’ acclimation to atmospheric pressure. The analyses were repeated in two independent sampling campaigns. We found no consistent signs of metabolic disturbances or oxidative stress in both species right after lifting. Despite O. flavus surviving slightly better in laboratory conditions, during long-term acclimation, both species showed comparable reactions without critical changes. Thus, the obtained data favor using O. albinus along with O. flavus for physiological research under laboratory conditions.
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Affiliation(s)
- Ekaterina Madyarova
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
| | - Yulia Shirokova
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
| | - Anton Gurkov
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
- Baikal Research Centre, 664011 Irkutsk, Russia
| | - Polina Drozdova
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
- Baikal Research Centre, 664011 Irkutsk, Russia
| | - Boris Baduev
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
| | - Yulia Lubyaga
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
| | - Zhanna Shatilina
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
- Baikal Research Centre, 664011 Irkutsk, Russia
| | - Maria Vishnevskaya
- Research Resource Center “Chromas”, Saint-Petersburg State University, 198504 Saint Petersburg, Russia;
| | - Maxim Timofeyev
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia; (E.M.); (Y.S.); (A.G.); (P.D.); (B.B.); (Y.L.); (Z.S.)
- Correspondence:
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10
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Gerringer ME, Yancey PH, Tikhonova OV, Vavilov NE, Zgoda VG, Davydov DR. Pressure tolerance of deep-sea enzymes can be evolved through increasing volume changes in protein transitions: a study with lactate dehydrogenases from abyssal and hadal fishes. FEBS J 2020; 287:5394-5410. [PMID: 32250538 PMCID: PMC7818408 DOI: 10.1111/febs.15317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 03/15/2020] [Accepted: 03/27/2020] [Indexed: 11/28/2022]
Abstract
We explore the principles of pressure tolerance in enzymes of deep-sea fishes using lactate dehydrogenases (LDH) as a case study. We compared the effects of pressure on the activities of LDH from hadal snailfishes Notoliparis kermadecensis and Pseudoliparis swirei with those from a shallow-adapted Liparis florae and an abyssal grenadier Coryphaenoides armatus. We then quantified the LDH content in muscle homogenates using mass-spectrometric determination of the LDH-specific conserved peptide LNLVQR. Existing theory suggests that adaptation to high pressure requires a decrease in volume changes in enzymatic catalysis. Accordingly, evolved pressure tolerance must be accompanied with an important reduction in the volume change associated with pressure-promoted alteration of enzymatic activity ( Δ V PP ∘ ). Our results suggest an important revision to this paradigm. Here, we describe an opposite effect of pressure adaptation-a substantial increase in the absolute value of Δ V PP ∘ in deep-living species compared to shallow-water counterparts. With this change, the enzyme activities in abyssal and hadal species do not substantially decrease their activity with pressure increasing up to 1-2 kbar, well beyond full-ocean depth pressures. In contrast, the activity of the enzyme from the tidepool snailfish, L. florae, decreases nearly linearly from 1 to 2500 bar. The increased tolerance of LDH activity to pressure comes at the expense of decreased catalytic efficiency, which is compensated with increased enzyme contents in high-pressure-adapted species. The newly discovered strategy is presumably used when the enzyme mechanism involves the formation of potentially unstable excited transient states associated with substantial changes in enzyme-solvent interactions.
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Sung HL, Nesbitt DJ. High pressure single-molecule FRET studies of the lysine riboswitch: cationic and osmolytic effects on pressure induced denaturation. Phys Chem Chem Phys 2020; 22:15853-15866. [PMID: 32706360 DOI: 10.1039/d0cp01921f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Deep sea biology is known to thrive at pressures up to ≈1 kbar, which motivates fundamental biophysical studies of biomolecules under such extreme environments. In this work, the conformational equilibrium of the lysine riboswitch has been systematically investigated by single molecule FRET (smFRET) microscopy at pressures up to 1500 bar. The lysine riboswitch preferentially unfolds with increasing pressure, which signals an increase in free volume (ΔV0 > 0) upon folding of the biopolymer. Indeed, the effective lysine binding constant increases quasi-exponentially with pressure rise, which implies a significant weakening of the riboswitch-ligand interaction in a high-pressure environment. The effects of monovalent/divalent cations and osmolytes on folding are also explored to acquire additional insights into cellular mechanisms for adapting to high pressures. For example, we find that although Mg2+ greatly stabilizes folding of the lysine riboswitch (ΔΔG0 < 0), there is negligible impact on changes in free volume (ΔΔV0 ≈ 0) and thus any pressure induced denaturation effects. Conversely, osmolytes (commonly at high concentrations in deep sea marine species) such as the trimethylamine N-oxide (TMAO) significantly reduce free volumes (ΔΔV0 < 0) and thereby diminish pressure-induced denaturation. We speculate that, besides stabilizing RNA structure, enhanced levels of TMAO in cells might increase the dynamic range for competent riboswitch folding by suppressing the pressure-induced denaturation response. This in turn could offer biological advantage for vertical migration of deep-sea species, with impacts on food searching in a resource limited environment.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA. and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA. and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and Department of Physics, University of Colorado, Boulder, CO 80309, USA
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12
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Liang L, Chen J, Li Y, Zhang H. Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures. BMC Genomics 2020; 21:68. [PMID: 31964339 PMCID: PMC6974979 DOI: 10.1186/s12864-020-6480-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Background Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood. Results In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa. Conclusions Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.
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Affiliation(s)
- Linying Liang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiawei Chen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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13
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Chen J, Liu H, Cai S, Zhang H. Comparative transcriptome analysis of Eogammarus possjeticus at different hydrostatic pressure and temperature exposures. Sci Rep 2019; 9:3456. [PMID: 30837550 PMCID: PMC6401005 DOI: 10.1038/s41598-019-39716-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/25/2019] [Indexed: 12/19/2022] Open
Abstract
Hydrostatic pressure is an important environmental factor affecting the vertical distribution of marine organisms. Laboratory-based studies have shown that many extant shallow-water marine benthic invertebrates can tolerate hydrostatic pressure outside their known natural distributions. However, only a few studies have focused on the molecular mechanisms of pressure acclimatisation. In the present work, we examined the pressure tolerance of the shallow-water amphipod Eogammarus possjeticus at various temperatures (5, 10, 15, and 20 °C) and hydrostatic pressures (0.1–30 MPa) for 16 h. Six of these experimental groups were used for transcriptome analysis. We found that 100% of E. possjeticus survived under 20 MPa at all temperature conditions for 16 h. Sequence assembly resulted in 138, 304 unigenes. Results of differential expression analysis revealed that 94 well-annotated genes were up-regulated under high pressure. All these findings indicated that the pressure tolerance of E. possjeticus was related to temperature. Several biological processes including energy metabolism, antioxidation, immunity, lipid metabolism, membrane-related process, genetic information processing, and DNA repair are probably involved in the acclimatisation in deep-sea environments.
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Affiliation(s)
- Jiawei Chen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Helu Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Shanya Cai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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14
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Morin PA, Foote AD, Baker CS, Hancock‐Hanser BL, Kaschner K, Mate BR, Mesnick SL, Pease VL, Rosel PE, Alexander A. Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses. Mol Ecol 2018; 27:2604-2619. [DOI: 10.1111/mec.14698] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/26/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Phillip A. Morin
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor Gwynedd UK
| | - Charles Scott Baker
- Marine Mammal Institute Hatfield Marine Science Center Oregon State University Newport Oregon
- Department of Fisheries and Wildlife College of Agricultural Sciences Corvallis Oregon
| | - Brittany L. Hancock‐Hanser
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis Albert‐Ludwigs‐University of Freiburg Freiburg Germany
| | - Bruce R. Mate
- Marine Mammal Institute Hatfield Marine Science Center Oregon State University Newport Oregon
- Department of Fisheries and Wildlife College of Agricultural Sciences Corvallis Oregon
| | - Sarah L. Mesnick
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Victoria L. Pease
- Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Patricia E. Rosel
- Southeast Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Lafayette Louisiana
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15
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Baalsrud HT, Voje KL, Tørresen OK, Solbakken MH, Matschiner M, Malmstrøm M, Hanel R, Salzburger W, Jakobsen KS, Jentoft S. Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth. Sci Rep 2017; 7:7956. [PMID: 28801564 PMCID: PMC5554263 DOI: 10.1038/s41598-017-08286-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/11/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage. We discovered a correlation between expanded numbers of Hb genes and ocean depth, with the highest numbers in species occupying shallower, epipelagic regions. Moreover, we demonstrate that the Hb genes have functionally diverged through diversifying selection. Our results suggest that the more variable environment in shallower water has led to selection for a larger Hb gene repertoire and that Hbs have a key role in adaptive processes in marine environments.
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Affiliation(s)
- Helle Tessand Baalsrud
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Kjetil Lysne Voje
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Ole Kristian Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Monica Hongrø Solbakken
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Michael Matschiner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Institute of Fisheries Ecology, Johann Heinrich von Thünen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Martin Malmstrøm
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Reinhold Hanel
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Institute of Fisheries Ecology, Johann Heinrich von Thünen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway. .,Department of Natural Sciences, Centre for Coastal Research, University of Agder, Kristiansand, Norway.
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16
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Moretti M, Dias ATC, Bello F, Altermatt F, Chown SL, Azcárate FM, Bell JR, Fournier B, Hedde M, Hortal J, Ibanez S, Öckinger E, Sousa JP, Ellers J, Berg MP. Handbook of protocols for standardized measurement of terrestrial invertebrate functional traits. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12776] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Marco Moretti
- Biodiversity and Conservation Biology Swiss Federal Research Institute WSL Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - André T. C. Dias
- Departamento de Ecologia Instituto de Biologia Roberto Alcântara Gomes Universidade do Estado do Rio de Janeiro (UERJ) Maracanã Rio de Janeiro Brazil
| | - Francesco Bello
- Institute of Botany Czech Academy of Sciences Dukelska 135 379 82 Třeboň Czech Republic
- Faculty of Sciences University of South Bohemia Na Zlate Stoce 1 370 05 České Budějovice Czech Republic
| | - Florian Altermatt
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology 8600 Dübendorf Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Steven L. Chown
- School of Biological Sciences Monash University Clayton Victoria3800 Australia
| | - Francisco M. Azcárate
- Terrestrial Ecology Group (TEG) Department of Ecology Universidad Autónoma de Madrid C/Darwin 2 28049 Madrid Spain
| | - James R. Bell
- Rothamsted Research West Common Harpenden HertfordshireAL5 2JQ UK
| | - Bertrand Fournier
- Laboratoire Chrono‐Environnement UMR 6249 CNRS Université de Bourgogne Franche‐Comté 16 route de Gray 25030 Besançon Cedex France
| | - Mickaël Hedde
- INRA AgroParisTech Université Paris‐Saclay UMR 1402 Ecosys Route de Saint‐Cyr RD 10 78026 Versailles Cedex France
| | - Joaquín Hortal
- Departamento de Biogeografía y Cambio Global Museo Nacional de Ciencias Naturales (MNCN‐CSIC) C/Jose Gutierrez Abascal 2 28006 Madrid Spain
- Centre for Ecology, Evolution and Environmental Changes (Ce3C) Faculdade de Ciências da Universidade de Lisboa (FCUL) Ed. C2, Campo Grande 1749‐06 Lisboa Portugal
| | - Sébastien Ibanez
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Savoie Mont Blanc 73376 Le Bourget‐du‐Lac France
| | - Erik Öckinger
- Department of Ecology Swedish University of Agricultural Sciences P.O. Box 7044 750 07 Uppsala Sweden
| | - José Paulo Sousa
- Centre for Functional Ecology Department of Life Sciences University of Coimbra 3000‐456 Coimbra Portugal
| | - Jacintha Ellers
- Department of Ecological Science Faculty of Earth and Life Sciences Vrije Universiteit Amsterdam De Boelelaan 1085 1081 HV Amsterdam The Netherlands
| | - Matty P. Berg
- Department of Ecological Science Faculty of Earth and Life Sciences Vrije Universiteit Amsterdam De Boelelaan 1085 1081 HV Amsterdam The Netherlands
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences University of Groningen Postbox 11103 9700 CC Groningen The Netherlands
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17
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Lindgren AR, Buckley BA, Eppley SM, Reysenbach AL, Stedman KM, Wagner JT. Life on the Edge-the Biology of Organisms Inhabiting Extreme Environments: An Introduction to the Symposium. Integr Comp Biol 2016; 56:493-9. [PMID: 27471225 DOI: 10.1093/icb/icw094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Life persists, even under extremely harsh conditions. While the existence of extremophiles is well known, the mechanisms by which these organisms evolve, perform basic metabolic functions, reproduce, and survive under extreme physical stress are often entirely unknown. Recent technological advances in terms of both sampling and studying extremophiles have yielded new insight into their evolution, physiology and behavior, from microbes and viruses to plants to eukaryotes. The goal of the "Life on the Edge-the Biology of Organisms Inhabiting Extreme Environments" symposium was to unite researchers from taxonomically and methodologically diverse backgrounds to highlight new advances in extremophile biology. Common themes and new insight that emerged from the symposium included the important role of symbiotic associations, the continued challenges associated with sampling and studying extremophiles and the important role these organisms play in terms of studying climate change. As we continue to explore our planet, especially in difficult to reach areas from the poles to the deep sea, we expect to continue to discover new and extreme circumstances under which life can persist.
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Affiliation(s)
- Annie R Lindgren
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Bradley A Buckley
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Sarah M Eppley
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Anna-Louise Reysenbach
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Kenneth M Stedman
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Josiah T Wagner
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
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18
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Saavedra LM, Quiñones RA, Gonzalez-Saldía RR, Niklitschek EJ. Aerobic and anaerobic enzymatic activity of orange roughy (Hoplostethus atlanticus) and alfonsino (Beryx splendens) from the Juan Fernandez seamounts area. FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:869-882. [PMID: 26687132 DOI: 10.1007/s10695-015-0181-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
The aerobic and anaerobic enzymatic activity of two important commercial bathypelagic species living in the Juan Fernández seamounts was analyzed: alfonsino (Beryx splendens) and orange roughy (Hoplostethus atlanticus). These seamounts are influenced by the presence of an oxygen minimum zone (OMZ) located between 160 and 250 m depth. Both species have vertical segregation; alfonsino is able to stay in the OMZ, while orange roughy remains at greater depths. In this study, we compare the aerobic and anaerobic capacity of these species, measuring the activity of key metabolic enzymes in different body tissues (muscle, heart, brain and liver). Alfonsino has higher anaerobic potential in its white muscle due to greater lactate dehydrogenase (LDH) activity (190.2 μmol NADH min(-1) g ww(-1)), which is related to its smaller body size, but it is also a feature shared with species that migrate through OMZs. This potential and the higher muscle citrate synthase and electron transport system activities indicate that alfonsino has greater swimming activity level than orange roughy. This species has also a high MDH/LDH ratio in its heart, brain and liver, revealing a potential capacity to conduct aerobic metabolism in these organs under prolonged periods of environmental low oxygen conditions, preventing lactic acid accumulation. With these metabolic characteristics, alfonsino may have increased swimming activity to migrate and also could stay for a period of time in the OMZ. The observed differences between alfonsino and orange roughy with respect to their aerobic and anaerobic enzymatic activity are consistent with their characteristic vertical distributions and feeding behaviors.
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Affiliation(s)
- L M Saavedra
- Center for the Study of Multiple-Drivers on Marine Socio-Ecological Systems (MUSELS), Universidad de Concepción, Barrio Universitario S/N, Concepción, Chile.
| | - R A Quiñones
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, O'Higgins 1695, Concepción, Chile
- Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
| | - R R Gonzalez-Saldía
- Unidad de Biotecnología Marina, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
| | - E J Niklitschek
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue Km 6, Casilla 557, Puerto Montt, ChileX Región
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19
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Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation. Int J Genomics 2014; 2014:267482. [PMID: 25309900 PMCID: PMC4182897 DOI: 10.1155/2014/267482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/19/2014] [Indexed: 11/29/2022] Open
Abstract
Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.
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20
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Wei CL, Rowe GT, Haedrich RL, Boland GS. Long-term observations of epibenthic fish zonation in the deep northern Gulf of Mexico. PLoS One 2012; 7:e46707. [PMID: 23056412 PMCID: PMC3463567 DOI: 10.1371/journal.pone.0046707] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 09/07/2012] [Indexed: 11/18/2022] Open
Abstract
A total of 172 bottom trawl/skimmer samples (183 to 3655-m depth) from three deep-sea studies, R/V Alaminos cruises (1964–1973), Northern Gulf of Mexico Continental Slope (NGoMCS) study (1983–1985) and Deep Gulf of Mexico Benthos (DGoMB) program (2000 to 2002), were compiled to examine temporal and large-scale changes in epibenthic fish species composition. Based on percent species shared among samples, faunal groups (≥10% species shared) consistently reoccurred over time on the shelf-break (ca. 200 m), upper-slope (ca. 300 to 500 m) and upper-to-mid slope (ca. 500 to 1500 m) depths. These similar depth groups also merged when the three studies were pooled together, suggesting that there has been no large-scale temporal change in depth zonation on the upper section of the continental margin. Permutational multivariate analysis of variance (PERMANOVA) also detected no significant species changes on the limited sites and areas that have been revisited across the studies (P>0.05). Based on the ordination of the species shared among samples, species replacement was a continuum along a depth or macrobenthos biomass gradient. Despite the well-known, close, negative relationship between water depth and macrofaunal biomass, the fish species changed more rapidly at depth shallower than 1,000 m, but the rate of change was surprisingly slow at the highest macrofaunal biomass (>100 mg C m−2), suggesting that the composition of epibenthic fishes was not altered in response to the extremely high macrofaunal biomass in the upper Mississippi and De Soto Submarine Canyons. An alternative is that the pattern of fish species turnover is related to the decline in macrofaunal biomass, the presumptive prey of the fish, along the depth gradient.
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Affiliation(s)
- Chih-Lin Wei
- Ocean Science Centre, Memorial University of Newfoundland, St. John's, Canada.
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21
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Lemaire B, Debier C, Calderon PB, Thomé JP, Stegeman J, Mork J, Rees JF. Precision-cut liver slices to investigate responsiveness of deep-sea fish to contaminants at high pressure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:10310-10316. [PMID: 22900608 DOI: 10.1021/es301850e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
While deep-sea fish accumulate high levels of persistent organic pollutants (POPs), the toxicity associated with this contamination remains unknown. Indeed, the recurrent collection of moribund individuals precludes experimental studies to investigate POP effects in this fauna. We show that precision-cut liver slices (PCLS), an in vitro tool commonly used in human and rodent toxicology, can overcome such limitation. This technology was applied to individuals of the deep-sea grenadier Coryphaenoides rupestris directly upon retrieval from 530-m depth in Trondheimsfjord (Norway). PCLS remained viable and functional for 15 h when maintained in an appropriate culture media at 4 °C. This allowed experimental exposure of liver slices to the model POP 3-methylcholanthrene (3-MC; 25 μM) at levels of hydrostatic pressure mimicking shallow (0.1 megapascal or MPa) and deep-sea (5-15 MPa; representative of 500-1500 m depth) environments. As in shallow water fish, 3-MC induced the transcription of the detoxification enzyme cytochrome P4501A (CYP1A; a biomarker of exposure to POPs). This induction was diminished at elevated pressure, suggesting a limited responsiveness of C. rupestris toward POPs in its native environment. This very first in vitro toxicological investigation on a deep-sea fish opens the route for understanding pollutants effects in this highly exposed fauna.
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Affiliation(s)
- Benjamin Lemaire
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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22
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Cottin D, Brown A, Oliphant A, Mestre NC, Ravaux J, Shillito B, Thatje S. Sustained hydrostatic pressure tolerance of the shallow water shrimp Palaemonetes varians at different temperatures: Insights into the colonisation of the deep sea. Comp Biochem Physiol A Mol Integr Physiol 2012; 162:357-63. [DOI: 10.1016/j.cbpa.2012.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 04/07/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
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23
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Asante KA, Agusa T, Kubota R, Mochizuki H, Ramu K, Nishida S, Ohta S, Yeh HM, Subramanian A, Tanabe S. Trace elements and stable isotope ratios (delta(13)C and delta(15)N) in fish from deep-waters of the Sulu Sea and the Celebes Sea. MARINE POLLUTION BULLETIN 2010; 60:1560-1570. [PMID: 20483434 DOI: 10.1016/j.marpolbul.2010.04.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 04/20/2010] [Accepted: 04/23/2010] [Indexed: 05/29/2023]
Abstract
Trace elements (TEs) and stable isotope ratios (delta(15)N and delta(13)C) were analyzed in fish from deep-water of the Sulu Sea, the Celebes Sea and the Philippine Sea. Concentrations of V and Pb in pelagic fish from the Sulu Sea were higher than those from the Celebes Sea, whereas the opposite trend was observed for delta(13)C. High concentrations of Zn, Cu and Ag were found in non-migrant fish in deep-water, while Rb level was high in fish which migrate up to the epipelagic zone, probably resulting from differences in background levels of these TEs in each water environment or function of adaptation to deep-water by migrant and non-migrant species. Arsenic level in the Sulu Sea fish was positively correlated with delta(15)N, indicating biomagnification of arsenic. To our knowledge, this is the first study on relationship between diel vertical migration and TE accumulation in deep-water fish.
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Affiliation(s)
- Kwadwo Ansong Asante
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan
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Brindley AA, Pickersgill RW, Partridge JC, Dunstan DJ, Hunt DM, Warren MJ. Enzyme sequence and its relationship to hyperbaric stability of artificial and natural fish lactate dehydrogenases. PLoS One 2008; 3:e2042. [PMID: 18446214 PMCID: PMC2323112 DOI: 10.1371/journal.pone.0002042] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 03/11/2008] [Indexed: 11/18/2022] Open
Abstract
The cDNAs of lactate dehydrogenase b (LDH-b) from both deep-sea and shallow living fish species, Corphaenoides armatus and Gadus morhua respectively, have been isolated, sequenced and their encoded products overproduced as recombinant enzymes in E. coli. The proteins were characterised in terms of their kinetic and physical properties and their ability to withstand high pressures. Although the two proteins are very similar in terms of their primary structure, only 21 differences at the amino acid level exist between them, the enzyme from the deep-sea species has a significantly increased tolerance to pressure and a higher thermostability. It was possible to investigate whether the changes in the N-terminal or C-terminal regions played a greater role in barophilic adaptation by the construction of two chimeric enzymes by use of a common restriction site within the cDNAs. One of these hybrids was found to have even greater pressure stability than the recombinant enzyme from the deep-living fish species. It was possible to conclude that the major adaptive changes to pressure tolerance must be located in the N-terminal region of the protein. The types of changes that are found and their spatial location within the protein structure are discussed. An analysis of the kinetic parameters of the enzymes suggests that there is clearly a trade off between Km and kcat values, which likely reflects the necessity of the deep-sea enzyme to operate at low temperatures.
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Affiliation(s)
- Amanda A Brindley
- Department of Biosciences, University of Kent, Canterbury, Kent, United Kingdom.
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Gooday AJ. Benthic foraminifera (Protista) as tools in deep-water palaeoceanography: environmental influences on faunal characteristics. ADVANCES IN MARINE BIOLOGY 2003; 46:1-90. [PMID: 14601411 DOI: 10.1016/s0065-2881(03)46002-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Foraminiferal research lies at the border between geology and biology. Benthic foraminifera are a major component of marine communities, highly sensitive to environmental influences, and the most abundant benthic organisms preserved in the deep-sea fossil record. These characteristics make them important tools for reconstructing ancient oceans. Much of the recent work concerns the search for palaeoceanographic proxies, particularly for the key parameters of surface primary productivity and bottom-water oxygenation. At small spatial scales, organic flux and pore-water oxygen profiles are believed to control the depths at which species live within the sediment (their 'microhabitats'). Epifaunal/shallow infaunal species require oxygen and labile food and prefer relatively oligotrophic settings. Some deep infaunal species can tolerate anoxia and are closely linked to redox fronts within the sediment; they consume more refractory organic matter, and flourish in relatively eutrophic environments. Food and oxygen availability are also key factors at large (i.e. regional) spatial scales. Organic flux to the sea floor, and its seasonality, strongly influences faunal densities, species compositions and diversity parameters. Species tend to be associated with higher or lower flux rates and the annual flux range of 2-3 g Corg m-2 appears to mark an important faunal boundary. The oxygen requirements of benthic foraminifera are not well understood. It has been proposed that species distributions reflect oxygen concentrations up to fairly high values (3 ml l-1 or more). Other evidence suggests that oxygen only begins to affect community parameters at concentrations < 0.5 ml l-1. Different species clearly have different thresholds, however, creating species successions along oxygen gradients. Other factors such as sediment type, hydrostatic pressure and attributes of bottom-water masses (particularly carbonate undersaturation and current flow) influence foraminiferal distributions, particularly on continental margins where strong seafloor environmental gradients exist. Epifaunal species living on elevated substrata are directly exposed to bottom-water masses and flourish where suspended food particles are advected by strong currents. Biological interactions, e.g. predation and competition, must also play a role, although this is poorly understood and difficult to quantify. Despite often clear qualitative links between environmental and faunal parameters, the development of quantitative foraminiferal proxies remains problematic. Many of these difficulties arise because species can tolerate a wide range of non-optimal conditions and do not exhibit simple relationships with particular parameters. Some progress has been made, however, in formulating proxies for organic fluxes and bottom-water oxygenation. Flux proxies are based on the Benthic Foraminiferal Accumulation Rate and multivariate analyses of species data. Oxygen proxies utilise the relative proportions of epifaunal (oxyphilic) and deep infaunal (low-oxygen tolerant) species. Yet many problems remain, particularly those concerning the calibration of proxies, the closely interwoven effects of oxygen and food availability, and the relationship between living assemblages and those preserved in the permanent sediment record.
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Affiliation(s)
- Andrew J Gooday
- Southampton Oceanography Centre, European Way, Southampton SO14 3ZH, UK.
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Macgregor RB. The interactions of nucleic acids at elevated hydrostatic pressure. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:266-76. [PMID: 11983401 DOI: 10.1016/s0167-4838(01)00349-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The application of elevated hydrostatic pressure on the order of a few thousand bar provides insight into the molecular forces responsible for stabilizing the conformations and non-covalent interactions of biological molecules in aqueous solution. In particular, the parameters derived from these studies have enabled researchers to glean information regarding the importance of hydration in the energetics and kinetics of these systems. This review presents data concerned with the application of hydrostatic pressure to study the thermodynamics, kinetics, and structure of nucleic acids and the interactions between nucleic acids and proteins, enzymes, and drugs. These complexes often form extremely stable non-covalent complexes in which electrostatic interactions play an important role. The sensitivity of these interactions to pressure offers a valuable experimental tool for investigating the energetics of the complexes.
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Affiliation(s)
- Robert B Macgregor
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
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Abstract
Pressures between 10 and 100 MPa can exert powerful effects on the growth and viability of organisms. Here I describe the effects of elevated pressure in this range on mesophilic (atmospheric pressure adapted) and piezophilic (high-pressure adapted) microorganisms. Examination of pressure effects on mesophiles makes use of this unique physical parameter to aid in the characterization of fundamental cellular processes, while in the case of piezophiles it provides information on the essence of the adaptation of life to high-pressure environments, which comprise the bulk of our biosphere. Research is presented on the isolation of pressure-resistant mutants, high-pressure regulation of gene expression, the role of membrane lipids and proteins in determining growth ability at high pressure, pressure effects on DNA replication and topology as well as on cell division, and the role of extrinsic factors in modulating enzyme activity at high pressure.
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Affiliation(s)
- D H Bartlett
- Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, 8682 La Jolla Shores Drive, La Jolla, CA 92093-0202, USA.
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28
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Van Dover CL, German CR, Speer KG, Parson LM, Vrijenhoek RC. Evolution and biogeography of deep-sea vent and seep invertebrates. Science 2002; 295:1253-7. [PMID: 11847331 DOI: 10.1126/science.1067361] [Citation(s) in RCA: 206] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Deep-sea hydrothermal vents and cold seeps are submarine springs where nutrient-rich fluids emanate from the sea floor. Vent and seep ecosystems occur in a variety of geological settings throughout the global ocean and support food webs based on chemoautotrophic primary production. Most vent and seep invertebrates arrive at suitable habitats as larvae dispersed by deep-ocean currents. The recent evolution of many vent and seep invertebrate species (<100 million years ago) suggests that Cenozoic tectonic history and oceanic circulation patterns have been important in defining contemporary biogeographic patterns.
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Affiliation(s)
- C L Van Dover
- Biology Department, College of William and Mary, Williamsburg, VA 23187, USA.
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Danovaro R, Dell'Anno A, Fabiano M, Pusceddu A, Tselepides A. Deep-sea ecosystem response to climate changes: the eastern Mediterranean case study. Trends Ecol Evol 2001. [DOI: 10.1016/s0169-5347(01)02215-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cailliet GM, Andrews AH, Burton EJ, Watters DL, Kline DE, Ferry-Graham LA. Age determination and validation studies of marine fishes: do deep-dwellers live longer? Exp Gerontol 2001; 36:739-64. [PMID: 11295512 DOI: 10.1016/s0531-5565(00)00239-4] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Age determination and validation studies on deep-water marine fishes indicate they are difficult to age and often long-lived. Techniques for the determination of age in individual fish includes growth-zone analysis of vertebral centra, fin rays and spines, other skeletal structures, and otoliths (there are three sets of otoliths in most bony fish semicircular canals, each of which is made of calcium carbonate). Most have regular increments deposited as the fish (and its semicircular canals) grows. The most commonly used otolith for age determination is the largest one called the sagitta. Age validation techniques include: (1) tag-recapture, often combined with oxytetracycline injection and analysis in growth-zones of bone upon recapture; (2) analysis of growth-zones over time; and (3) radiometric approaches utilizing a known radioactive decay series as an independent chronometer in otoliths from bony fishes. We briefly summarize previous studies using these three validation approaches and present results from several of our radiometric studies on deep-water, bony fishes recently subjected to expanding fisheries. Radiometric age validation results are presented for four species of scorpaenid fishes (the bank, Sebastes rufus, and bocaccio, S. paucispinis, rockfishes, and two thornyhead species, Sebastolobus altivelis and S. alascanus). In addition, our analysis of scorpaenids indicates that longevity increases exponentially with maximum depth of occurrence. The reason that the deep-water forms of scorpaenid fishes are long-lived is uncertain. Their longevity, however, may be related to altered physiological processes relative to environmental parameters like low temperature, high pressures, low light levels, low oxygen, and poor food resources.
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Affiliation(s)
- G M Cailliet
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, CA 95039, USA.
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Mentré P, Hui Bon Hoa G. Effects of high hydrostatic pressures on living cells: a consequence of the properties of macromolecules and macromolecule-associated water. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 201:1-84. [PMID: 11057830 DOI: 10.1016/s0074-7696(01)01001-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sixty percent of the Earth's biomass is found in the sea, at depths greater than 1000 m, i.e., at hydrostatic pressures higher than 100 atm. Still more surprising is the fact that living cells can reversibly withstand pressure shifts of 1000 atm. One explanation lies in the properties of cellular water. Water forms a very thin film around macromolecules, with a heterogeneous structure that is an image of the heterogeneity of the macromolecular surface. The density of water in contact with macromolecules reflects the physical properties of their different domains. Therefore, any macromolecular shape variations involving the reorganization of water and concomitant density changes are sensitive to pressure (Le Chatelier's principle). Most of the pressure-induced changes to macromolecules are reversible up to 2000 atm. Both the effects of pressure shifts on living cells and the characteristics of pressure-adapted species are opening new perspectives on fundamental problems such as regulation and adaptation.
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Affiliation(s)
- P Mentré
- Station INRA 806, Institut de Biologie Physico-Chimique, Paris, France
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Kaarniranta K, Holmberg CI, Lammi MJ, Eriksson JE, Sistonen L, Helminen HJ. Primary chondrocytes resist hydrostatic pressure-induced stress while primary synovial cells and fibroblasts show modified Hsp70 response. Osteoarthritis Cartilage 2001; 9:7-13. [PMID: 11178942 DOI: 10.1053/joca.2000.0354] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE During joint loading, chondrocytes in the articular cartilage are subjected to gradients of high compressive hydrostatic pressure (HP). In response to diverse chemical or physical stresses, heat shock genes are induced to express heat shock proteins (Hsps). This study sought to examine the role of Hsps in baroresistance in primary bovine chondrocytes and synovial cells, as well as in primary human fibroblasts. METHODS Northern blotting was used to analyze the steady-state levels of hsp70 mRNA in the primary cells exposed to HP or heat stress. Hsp70 protein accumulation was analyzed by Western blotting, and the DNA-binding activity was examined by gel mobility shift assay. RESULTS Primary bovine chondrocytes which have been adapted to live under pressurized conditions showed negligible Hsp70 response upon HP loading, whereas primary bovine synovial cells and human fibroblasts accumulated hsp70 mRNA and protein when subjected to HP. The response was initiated without activation of the heat shock transcription factor 1. Interestingly, pre-conditioning of the barosensitive fibroblasts with HP or heat shock reduced the Hsp70 response, indicating induction of baroresistance. CONCLUSION This study suggests that Hsp70 can play an important role in the early stages of adaptation of cells to HP. Thus, the Hsp70 gene expression upon HP loading may serve as one indicator of the chondrocytic phenotype of the cells. This can be of use in the treatment of cartilage lesions.
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Affiliation(s)
- K Kaarniranta
- Department of Anatomy, University of Kuopio, Kuopio, 70211, Finland
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Bradshaw WE, Fujiyama S, Holzapfel CM. ADAPTATION TO THE THERMAL CLIMATE OF NORTH AMERICA BY THE PITCHER-PLANT MOSQUITO,WYEOMYIA SMITHII. Ecology 2000. [DOI: 10.1890/0012-9658(2000)081[1262:atttco]2.0.co;2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Chilukuri LN, Bartlett DH. Isolation and characterization of the gene encoding single-stranded-DNA-binding protein (SSB) from four marine Shewanella strains that differ in their temperature and pressure optima for growth. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 4):1163-1174. [PMID: 9141679 DOI: 10.1099/00221287-143-4-1163] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ssb gene, coding for single-stranded-DNA-binding protein (SSB), was cloned from four marine Shewanella strains that differed in their temperature and pressure optima and ranges of growth. All four Shewanella ssb genes complemented Escherichia coli ssb point and deletion mutants, with efficiencies that varied with temperature and ssb gene source. The Shewanella SSBs are the largest bacterial SSBs identified to date (24.9-26.3 kDa) and may be divided into conserved amino- and carboy-terminal regions and a highly variable central region. Greater amino acid sequence homology was observed between the Shewanella SSBs as a group (72-87%) than with other bacterial SSBs (52-69%). Analysis of the amino acid composition of the Shewanella SSBs revealed several features that could correlate with pressure or temperature adaptation. SSBs from the three low-temperature-adapted Shewanella strains were an order of magnitude more hydrophilic than that from the mesophilic strain, and differences in the distribution of eight amino acids were identified which could contribute to either the temperature or pressure adaptation of the proteins. The SSBs from all four Shewanella strains were overproduced and partially purified based upon their ability to bind single-stranded DNA. The differences found among the Shewanella SSBs suggest that these proteins will provide a useful system for exploring the adaptation of protein-protein and protein-DNA interactions at low temperature and high pressure.
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Affiliation(s)
- Lakshmi N Chilukuri
- Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
| | - Douglas H Bartlett
- Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
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Hope AJ, Partridge JC, Dulai KS, Hunt DM. Mechanisms of wavelength tuning in the rod opsins of deep-sea fishes. Proc Biol Sci 1997; 264:155-63. [PMID: 9061967 PMCID: PMC1688238 DOI: 10.1098/rspb.1997.0023] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The main object of this study was to investigate the molecular basis for changes in the spectral sensitivity of the visual pigments of deep-sea fishes. The four teleost species studied, Hoplostethus mediterraneus, Cataetyx laticeps, Gonostoma elongatum and Histiobranchus bathybius, are phylogenetically distant from each other and live at depths ranging from 500 to almost 5000 m. A single fragment of the intronless rod opsin gene was PCR-amplified from each fish and sequenced. The wavelength of peak sensitivity for the rod visual pigments of the four deep-sea species varies from 483 nm in H. mediterraneus and G. elongatum to 468 nm in C. laticeps. Six amino acids at sites on the inner face of the chromophore-binding pocket formed by the seven transmembrane a-helices are identified as candidates for spectral tuning. Substitutions at these sites involve either a change of charge, or a gain or loss of a hydroxyl group. Two of these, at positions 83 and 292, are consistently substituted in the visual pigments of all four species and are likely to be responsible for the shortwave sensitivity of the pigments. Shifts to wavelengths shorter than 480 nm may involve substitution at one or more of the remaining four sites. None of the modifications found in the derived sequences of these opsins suggest functional adaptations, such as increased content of hydroxyl-bearing or proline residues, to resist denaturation by the elevated hydrostatic pressures of the deep sea. Phylogenetic evidence for the duplication of the rod opsin gene in the Anguilliform lineage is presented.
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Affiliation(s)
- A J Hope
- School of Biological Sciences, University of Bristol, UK
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7 Pressure Effects on Shallow-Water Fishes. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s1546-5098(08)60232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Chapter 9 metabolic potentials of deep-sea fishes: A comparative approach. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s1873-0140(06)80035-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Bartlett D, Chi E. Genetic characterization of ompH mutants in the deep-sea bacterium Photobacterium sp. strain SS9. Arch Microbiol 1994; 162:323-8. [PMID: 7857197 DOI: 10.1007/bf00263779] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OmpH is an outer membrane protein produced by the deep-sea bacterium Photobacterium species strain SS9 in response to elevated hydrostatic pressure. In order to facilitate studies of the function of this protein, a series of OmpH+ and OmpH- strains were obtained from SS9 by Tn5 gene replacement mutagenesis. A previously isolated ompH::lacZ strain and a derivative of this strain harboring a plasmid expressing the wild-type ompH gene were also utilized. The acridine mutagen ICR 191 preferentially inhibited the growth of OmpH+ over OmpH- cells. Indeed, OmpH+ cultures treated with the mutagen rapidly accumulated mutants producing reduced levels of OmpH. In addition, OmpH+ cells took up the peptide Met-Leu-Phe approximately 15 times more rapidly than OmpH- cells. The results are consistent with the hypothesis that OmpH functions as a relatively large, nonspecific diffusion channel.
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Affiliation(s)
- D Bartlett
- Center for Marine Biomedicine and Biotechnology, Scripps Institution of Oceanography, University of California, La Jolla 92093-0202
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