|
1
|
Zhang H, Zhou Y, Yang Z. Genetic adaptations of marine invertebrates to hydrothermal vent habitats. Trends Genet 2024:S0168-9525(24)00181-1. [PMID: 39277449 DOI: 10.1016/j.tig.2024.08.004] [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: 06/02/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 09/17/2024]
Abstract
Hydrothermal vents are unique habitats like an oases of life compared with typical deep-sea, soft-sediment environments. Most animals that live in these habitats are invertebrates, and they have adapted to extreme vent environments that include high temperatures, hypoxia, high sulfide, high metal concentration, and darkness. The advent of next-generation sequencing technology, especially the coming of the new era of omics, allowed more studies to focus on the molecular adaptation of these invertebrates to vent habitats. Many genes linked to hydrothermal adaptation have been studied. We summarize the findings related to these genetic adaptations and discuss which new techniques can facilitate studies in the future.
Collapse
Affiliation(s)
- Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Yang Zhou
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Zhuo Yang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
|
2
|
Heo SY, Kang N, Kim EA, Kim J, Lee SH, Ahn G, Oh JH, Shin AY, Kim D, Heo SJ. Purification and Molecular Docking Study on the Angiotensin I-Converting Enzyme (ACE)-Inhibitory Peptide Isolated from Hydrolysates of the Deep-Sea Mussel Gigantidas vrijenhoeki. Mar Drugs 2023; 21:458. [PMID: 37623739 PMCID: PMC10456528 DOI: 10.3390/md21080458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/15/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023] Open
Abstract
The objective of this study was to prepare an angiotensin I-converting enzyme (ACE)-inhibitory peptide from the hydrothermal vent mussel, Gigantidas vrijenhoeki. The G. vrijenhoeki protein was hydrolyzed by various hydrolytic enzymes. The peptic hydrolysate exhibited the highest ACE-inhibitory activity and was fractionated into four molecular weight ranges by ultrafiltration. The <1 kDa fraction exhibited the highest ACE inhibitory activity and was found to have 11 peptide sequences. Among the analyzed peptides, KLLWNGKM exhibited stronger ACE inhibitory activity and an IC50 value of 0.007 μM. To investigate the ACE-inhibitory activity of the analyzed peptides, a molecular docking study was performed. KLLWNGKM exhibited the highest binding energy (-1317.01 kcal/mol), which was mainly attributed to the formation of hydrogen bonds with the ACE active pockets, zinc-binding motif, and zinc ion. These results indicate that G. vrijenhoeki-derived peptides can serve as nutritional and pharmacological candidates for controlling blood pressure.
Collapse
Affiliation(s)
- Seong-Yeong Heo
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (S.-Y.H.); (N.K.); (E.-A.K.); (J.K.)
- Department of Marine Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Nalae Kang
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (S.-Y.H.); (N.K.); (E.-A.K.); (J.K.)
| | - Eun-A Kim
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (S.-Y.H.); (N.K.); (E.-A.K.); (J.K.)
| | - Junseong Kim
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (S.-Y.H.); (N.K.); (E.-A.K.); (J.K.)
| | - Seung-Hong Lee
- Department of Pharmaceutical Engineering, Soonchunhyang University, Asan 31538, Republic of Korea;
| | - Ginnae Ahn
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu 59626, Republic of Korea;
| | - Je Hyeok Oh
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan 49111, Republic of Korea; (J.H.O.); (A.Y.S.); (D.K.)
| | - A Young Shin
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan 49111, Republic of Korea; (J.H.O.); (A.Y.S.); (D.K.)
| | - Dongsung Kim
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan 49111, Republic of Korea; (J.H.O.); (A.Y.S.); (D.K.)
| | - Soo-Jin Heo
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (S.-Y.H.); (N.K.); (E.-A.K.); (J.K.)
- Department of Marine Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| |
Collapse
|
|
3
|
Zhao B, Gao S, Zhao M, Lv H, Song J, Wang H, Zeng Q, Liu J. Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae. BMC Genomics 2022; 23:738. [PMID: 36324074 PMCID: PMC9628169 DOI: 10.1186/s12864-022-08940-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Background Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length. Results In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972 bp, 20,482, and 17,786 bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater. Conclusions Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08940-8.
Collapse
Affiliation(s)
- Baojun Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Shengtao Gao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Mingyang Zhao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hongyu Lv
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Jingyu Song
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
|
4
|
Identification and Phylogenetic Analysis of Chitin Synthase Genes from the Deep-Sea Polychaete Branchipolynoe onnuriensis Genome. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10050598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chitin, one of the most abundant biopolymers in nature, is a crucial material that provides sufficient rigidity to the exoskeleton. In addition, chitin is a valuable substance in both the medical and industrial fields. The synthesis of chitin is catalyzed by chitin synthase (CHS) enzymes. Although the chitin synthesis pathway is highly conserved from fungi to invertebrates, CHSs have mostly only been investigated in insects and crustaceans. Especially, little is known about annelids from hydrothermal vents. To understand chitin synthesis from the evolutionary view in a deep-sea environment, we first generated the whole-genome sequencing of the parasitic polychaete Branchipolynoe onnuriensis. We identified seven putative CHS genes (BonCHS1-BonCHS7) by domain searches and phylogenetic analyses. This study showed that most crustaceans have only a single copy or two gene copies, whereas at least two independent gene duplication events occur in B. onnuriensis. This is the first study of CHS obtained from a parasitic species inhabiting a hydrothermal vent and will provide insight into various organisms’ adaptation to the deep-sea hosts.
Collapse
|
|
5
|
Emami-Khoyi A, Le Roux R, Adair MG, Monsanto DM, Main DC, Parbhu SP, Schnelle CM, van der Lingen CD, Jansen van Vuuren B, Teske PR. Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run. Genes (Basel) 2021; 12:genes12030368. [PMID: 33806647 PMCID: PMC8001748 DOI: 10.3390/genes12030368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.
Collapse
Affiliation(s)
- Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Rynhardt Le Roux
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Matthew G. Adair
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Daniela M. Monsanto
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Shilpa P. Parbhu
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Claudia M. Schnelle
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Carl D. van der Lingen
- Branch: Fisheries Management, Department of Environment, Forestry and Fisheries, Private Bag X2, Vlaeberg 8012, South Africa;
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
- Correspondence:
| |
Collapse
|