1
|
Mathur S, Haynes E, Allender MC, Gibbs HL. Genetic mechanisms and biological processes underlying host response to ophidiomycosis (snake fungal disease) inferred from tissue-specific transcriptome analyses. Mol Ecol 2024; 33:e17210. [PMID: 38010927 DOI: 10.1111/mec.17210] [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: 04/06/2023] [Revised: 07/28/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023]
Abstract
Emerging infectious diseases in wildlife species caused by pathogenic fungi are of growing concern, yet crucial knowledge gaps remain for diseases with potentially large impacts. For example, there is detailed knowledge about host pathology and mechanisms underlying response for chytridiomycosis in amphibians and white-nose syndrome in bats, but such information is lacking for other more recently described fungal infections. One such disease is ophidiomycosis, caused by the fungus Ophidiomyces ophidiicola, which has been identified in many species of snakes, yet the biological mechanisms and molecular changes occurring during infection are unknown. To gain this information, we performed a controlled experimental infection in captive Prairie rattlesnakes (Crotalus viridis) with O. ophidiicola at two different temperatures: 20 and 26°C. We then compared liver, kidney, and skin transcriptomes to assess tissue-specific genetic responses to O. ophidiicola infection. Given previous histopathological studies and the fact that snakes are ectotherms, we expected highest fungal activity on skin and a significant impact of temperature on host response. Although we found fungal activity to be localized on skin, most of the differential gene expression occurred in internal tissues. Infected snakes at the lower temperature had the highest host mortality whereas two-thirds of the infected snakes at the higher temperature survived. Our results suggest that ophidiomycosis is likely a systemic disease with long-term effects on host response. Our analysis also identified candidate protein coding genes that are potentially involved in host response, providing genetic tools for studies of host response to ophidiomycosis in natural populations.
Collapse
Affiliation(s)
- Samarth Mathur
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - Ellen Haynes
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, USA
| | - Matthew C Allender
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Brookfield Zoo, Chicago Zoological Society, Brookfield, Illinois, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
2
|
Rahman MS, Billah MM, Rangel V, Cantu E. Elevated temperature triggers increase in global DNA methylation, 5-methylcytosine expression levels, apoptosis and NOx levels in the gonads of Atlantic sea urchin. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110899. [PMID: 37673203 DOI: 10.1016/j.cbpb.2023.110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/24/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
Global warming is one of the greatest threats to living organisms. Among them, marine invertebrates are severely impacted on reproductive fitness by rising seawater surface temperatures due to climate change (e.g., massive heat waves). In this study, we used highly sensitive radioimmunoassay, immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), in situ TUNEL assay, luminescence assay, and colorimetric assay techniques to investigate the impacts of high temperatures on global DNA methylation, cellular apoptosis, and nitrative stress in gonads of Atlantic sea urchin (Arbacia punctulata, a commercially important species). Young adult sea urchins were exposed to 24, 28, and 32 °C for one week in a controlled laboratory setting. High temperatures (28 and 32 °C) markedly increased global DNA methylation (around 1.1-1.5-fold in testes and ~ 1.7-fold in ovaries) and 5-methylcytosine (5-mC) levels in gonads (around 2.7- to ~5.1-fold in ovaries and ~ 3.5- to ~6.2-fold in testes) compared with controls (24 °C). The number of apoptotic nuclei in gonads was much higher in high-temperature groups. The caspase activity also increased significantly (P < 0.05) in gonads in high-temperature groups. Nitrate/nitrites (NOx, a biomarker of reactive nitrogen species) levels were increased around 2.6- to ~5.2-fold in testes and ~ 1.9- to ~3.8-fold in ovaries in high-temperature groups. Collectively, these outcomes indicate that high temperatures drastically induce global DNA methylation, 5-mC expression levels, cellular apoptosis, and NOx levels in the gonads of Atlantic sea urchin.
Collapse
Affiliation(s)
- Md Saydur Rahman
- School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
| | - Mohammad Maruf Billah
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Victor Rangel
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Esmirna Cantu
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| |
Collapse
|
3
|
Liu A, Zeng F, Wang L, Zhen H, Xia X, Pei H, Dong C, Zhang Y, Ding J. High temperature influences DNA methylation and transcriptional profiles in sea urchins (Strongylocentrotus intermedius). BMC Genomics 2023; 24:491. [PMID: 37641027 PMCID: PMC10464075 DOI: 10.1186/s12864-023-09616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND DNA methylation plays an important role in life processes by affecting gene expression, but it is still unclear how DNA methylation is controlled and how it regulates gene transcription under high temperature stress conditions in Strongylocentrotus intermedius. The potential link between DNA methylation variation and gene expression changes in response to heat stress in S. intermedius was investigated by MethylRAD-seq and RNA-seq analysis. We screened DNA methylation driver genes in order to comprehensively elucidate the regulatory mechanism of its high temperature adaptation at the DNA/RNA level. RESULTS The results revealed that high temperature stress significantly affected not only the DNA methylation and transcriptome levels of S. intermedius (P < 0.05), but also growth. MethylRAD-seq analysis revealed 12,129 CG differential methylation sites and 966 CWG differential methylation sites, and identified a total of 189 differentially CG methylated genes and 148 differentially CWG methylated genes. Based on KEGG enrichment analysis, differentially expressed genes (DEGs) are mostly enriched in energy and cell division, immune, and neurological damage pathways. Further RNA-seq analysis identified a total of 1968 DEGs, of which 813 genes were upregulated and 1155 genes were downregulated. Based on the joint MethylRAD-seq and RNA-seq analysis, metabolic processes such as glycosaminoglycan degradation, oxidative phosphorylation, apoptosis, glutathione metabolism, thermogenesis, and lysosomes are regulated by DNA methylation. CONCLUSIONS High temperature affected the DNA methylation and expression levels of genes such as MOAP-1, GGT1 and RDH8, which in turn affects the metabolism of HPSE, Cox, glutathione, and retinol, thereby suppressing the immune, energy metabolism, and antioxidant functions of the organism and finally manifesting as stunted growth. In summary, the observations in the present study improve our understanding of the molecular mechanism of the response to high temperature stress in sea urchin.
Collapse
Affiliation(s)
- Anzheng Liu
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Fanshuang Zeng
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
| | - Hao Zhen
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Xinglong Xia
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Honglin Pei
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Changkun Dong
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Yanmin Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| |
Collapse
|
4
|
An X, Li N, Zhang S, Han Y, Zhang Q. Integration of proteome and metabolome profiling to reveal heat stress response and tolerance mechanisms of Serratia sp. AXJ-M for the bioremediation of papermaking black liquor. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131092. [PMID: 36857821 DOI: 10.1016/j.jhazmat.2023.131092] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/12/2023] [Accepted: 02/24/2023] [Indexed: 05/20/2023]
Abstract
The use of thermophilic bacteria for treating paper black liquor seems to be an efficient bioremediation strategy. In our previous work, the lignin-degrading bacterium Serratia sp. AXJ-M exhibited excellent heat tolerance ability. However, the molecular mechanism of its response to heat stress is unknown. Therefore, the heat stress response of AXJ-M was investigated using morphological and analytical methods. A comparative genomics analysis revealed interesting insights into the adaptability of the genetic basis of AXJ-M to harsh environments. Moreover, TMT quantitative proteomic analysis and parallel reaction monitoring (PRM) assays revealed that proteins related to both component systems, ABC transporters, carbohydrate, and amino metabolism, energy metabolism, etc., were differentially expressed. The non-targeted metabolome analysis revealed that the metabolic pathways associated with the fatty acid and amino acid biosynthesis and metabolism, together with the TCA cycle were most significantly enriched. Furthermore, integrated omics suggested that AXJ-M made metabolic adaptations to compensate for the increased energy demand caused by adverse environmental stimuli. The dominant heat regulator HspQ mediated heat adaptation of AXJ-M at high temperatures and modulated DyP expression. To summarize, the present study sheds light on the effect of high temperature on the lignin-degrading bacterium and its tolerance and underlying regulatory mechanisms.
Collapse
Affiliation(s)
- Xuejiao An
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China.
| | - Ningjian Li
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Shulin Zhang
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Yanyan Han
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qinghua Zhang
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
| |
Collapse
|
5
|
Hao P, Han L, Quan Z, Jin X, Li Y, Wu Y, Zhang X, Wang W, Gao C, Wang L, Wang H, Zhang W, Chang Y, Ding J. Integrative mRNA-miRNA interaction analysis associated with the immune response of Strongylocentrotus intermedius to Vibrio harveyi infection. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108577. [PMID: 36773712 DOI: 10.1016/j.fsi.2023.108577] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/08/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China and has experienced mass mortality owing to outbreaks of bacterial diseases such as black mouth disease. This has caused serious economic losses to the sea urchin farming industry. To investigate the immune response mechanism of S. intermedius with different tube feet colors in response to Vibrio harveyi infection, we examined the different tube feet-colored S. intermedius under V. harveyi challenge and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. We obtained 1813 differentially expressed genes (DEGs), 28 DE miRNAs, and 303 DE miRNA-DEG pairs in different tube feet-colored S. intermedius under V. harveyi challenge. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the most significant DEGs were associated with the Notch signaling and phagosome pathways. The target genes of immune-related miRNAs (miR-71, miR-184, miR-193) and genes (CALM1, SPSB4, DMBT, CSRP1) in S. intermedius were predicted and validated. This study provides insight into the molecular mechanisms that regulate genes involved in the immune response of S. intermedius infected with V. harveyi.
Collapse
Affiliation(s)
- Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Lingshu Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China; Ningbo University, Ningbo, Zhejiang, 315832, PR China
| | - Zijiao Quan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yanglei Wu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Heng Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China.
| |
Collapse
|
6
|
Lofrano G, Ubaldi F, Albarano L, Carotenuto M, Vaiano V, Valeriani F, Libralato G, Gianfranceschi G, Fratoddi I, Meric S, Guida M, Romano Spica V. Antimicrobial Effectiveness of Innovative Photocatalysts: A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:2831. [PMID: 36014697 PMCID: PMC9415964 DOI: 10.3390/nano12162831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/13/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Waterborne pathogens represent one of the most widespread environmental concerns. Conventional disinfection methods, including chlorination and UV, pose several operational and environmental problems; namely, formation of potentially hazardous disinfection by-products (DBPs) and high energy consumption. Therefore, there is high demand for effective, low-cost disinfection treatments. Among advanced oxidation processes, the photocatalytic process, a form of green technology, is becoming increasingly attractive. A systematic review was carried out on the synthesis, characterization, toxicity, and antimicrobial performance of innovative engineered photocatalysts. In recent decades, various engineered photocatalysts have been developed to overcome the limits of conventional photocatalysts using different synthesis methods, and these are discussed together with the main parameters influencing the process behaviors. The potential environmental risks of engineered photocatalysts are also addressed, considering the toxicity effects presented in the literature.
Collapse
Affiliation(s)
- Giusy Lofrano
- Department of Movement, Health and Human Sciences, University of Rome Foro Italico, Piazza Lauro De Bosis, 15, 00135 Rome, Italy; (G.L.); (F.U.); (G.G.); (V.R.S.)
| | - Francesca Ubaldi
- Department of Movement, Health and Human Sciences, University of Rome Foro Italico, Piazza Lauro De Bosis, 15, 00135 Rome, Italy; (G.L.); (F.U.); (G.G.); (V.R.S.)
| | - Luisa Albarano
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 26, 80126 Naples, Italy; (L.A.); (G.L.); (M.G.)
| | - Maurizio Carotenuto
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (M.C.); (V.V.)
| | - Vincenzo Vaiano
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (M.C.); (V.V.)
| | - Federica Valeriani
- Department of Movement, Health and Human Sciences, University of Rome Foro Italico, Piazza Lauro De Bosis, 15, 00135 Rome, Italy; (G.L.); (F.U.); (G.G.); (V.R.S.)
| | - Giovanni Libralato
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 26, 80126 Naples, Italy; (L.A.); (G.L.); (M.G.)
| | - Gianluca Gianfranceschi
- Department of Movement, Health and Human Sciences, University of Rome Foro Italico, Piazza Lauro De Bosis, 15, 00135 Rome, Italy; (G.L.); (F.U.); (G.G.); (V.R.S.)
| | - Ilaria Fratoddi
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy;
| | - Sureyya Meric
- Department of Environmental Engineering, Tekirdag Namik Kemal University, Corlu 59860, Turkey;
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 26, 80126 Naples, Italy; (L.A.); (G.L.); (M.G.)
| | - Vincenzo Romano Spica
- Department of Movement, Health and Human Sciences, University of Rome Foro Italico, Piazza Lauro De Bosis, 15, 00135 Rome, Italy; (G.L.); (F.U.); (G.G.); (V.R.S.)
| |
Collapse
|
7
|
Transcriptomes reveal the involved genes in the sea urchin Mesocentrotus nudus exposed to high flow velocities. Sci Rep 2022; 12:13493. [PMID: 35931770 PMCID: PMC9356045 DOI: 10.1038/s41598-022-17793-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 11/09/2022] Open
Abstract
Despite the importance of flow velocity in marine ecosystems, molecular mechanisms of the water flow induced behavioral and growth changes remain largely unknown in sea urchins. The present study compared the gene expressions of the sea urchin Mesocentrotus nudus at high flow velocities (10 cm/s and 20 cm/s) and low flow velocity (2 cm/s) using transcriptomes. A total of 490 and 470 differentially expressed genes (DEGs) were discovered at 10 cm/s and 20 cm/s, respectively. There were 235 up-regulated and 255 down-regulated genes at 10 cm/s, 213 up-regulated and 257 down-regulated genes at 20 cm/s, compared with sea urchins at 2 cm/s. Further, there were 72 overlapped DEGs involved in regulation at both 10 cm/s and 20 cm/s. Gene Ontology (GO) functional annotation showed that DEGs were mainly enriched to cellular process, cell part, binding, and metabolism process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that DEGs were enriched in three pathways related to amino acid metabolism and lipid metabolism. A number of genes related to growth and metabolism of sea urchins were mobilized in high flow velocity environment. We further highlighted a muscle-associated gene ankyrin-1, which is correlated with the movement of tube feet at different flow velocities. The present study provides valuable information on the molecular mechanisms of changed behaviors and growth when sea urchins are exposed to high flow velocity.
Collapse
|
8
|
Hao P, Ding B, Han L, Xie J, Wu Y, Jin X, Zhang X, Wang W, Wang L, Zhang W, Chang Y, Ding J. Gene expression patterns of sea urchins (Strongylocentrotus intermedius) exposed to different combinations of temperature and hypoxia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100953. [PMID: 34942521 DOI: 10.1016/j.cbd.2021.100953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/13/2022]
Abstract
Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China, and its growth and survival are severely constrained by ocean warming and the hypoxia that often accompanies high water temperatures. To elucidate the molecular mechanisms of S. intermedius that regulate gene expression in response to multi-causal environmental stresses. We performed a de novo transcriptome analysis of coelomocyte from S. intermedius to heat (25 °C), hypoxia (2 mg/L), and the combined stress. We identified 35,635, 29,107, and 29,440 differentially expressed genes (DEGs) in S. intermedius cultured under high temperature, low oxygen, and combined stress, respectively. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that these DEGs mainly enriched the functional categories of "Protein processing in endoplasmic reticulum," and "Glutathione metabolism" by heat stress, such as HSP70, GSTO1, PDIA4. After hypoxic stress, "Notch signaling pathway" and metabolism-related pathways such as "Glycerolipid metabolism", "Pyruvate metabolism" were significantly enriched. Exposure to combined stress resulted in a two-factor additive effect at the transcriptome level and have a more extensive impact on the immune correlated pathways in S. intermedius than single stress, the expression of related immune genes (C3, C5, and AIFM2) were up-regulated. Quantitative real-time PCR (qRT-PCR) analysis of the expression of 18 DEGs confirmed the RNA-Seq results. Observations in the present study will improve the understanding of the molecular mechanism of S. intermedius in response to multi-causal environmental stress.
Collapse
Affiliation(s)
- Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Beichen Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Lingshu Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China; Ningbo University, Ningbo, Zhejiang 315832, PR China
| | - Jiahui Xie
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yanglei Wu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
| |
Collapse
|
9
|
Albarano L, Zupo V, Guida M, Libralato G, Caramiello D, Ruocco N, Costantini M. PAHs and PCBs Affect Functionally Intercorrelated Genes in the Sea Urchin Paracentrotus lividus Embryos. Int J Mol Sci 2021; 22:ijms222212498. [PMID: 34830379 PMCID: PMC8619768 DOI: 10.3390/ijms222212498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/05/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) represent the most common pollutants in the marine sediments. Previous investigations demonstrated short-term sublethal effects of sediments polluted with both contaminants on the sea urchin Paracentrotus lividus after 2 months of exposure in mesocosms. In particular, morphological malformations observed in P. lividus embryos deriving from adults exposed to PAHs and PCBs were explained at molecular levels by de novo transcriptome assembly and real-time qPCR, leading to the identification of several differentially expressed genes involved in key physiological processes. Here, we extensively explored the genes involved in the response of the sea urchin P. lividus to PAHs and PCBs. Firstly, 25 new genes were identified and interactomic analysis revealed that they were functionally connected among them and to several genes previously defined as molecular targets of response to the two pollutants under analysis. The expression levels of these 25 genes were followed by Real Time qPCR, showing that almost all genes analyzed were affected by PAHs and PCBs. These findings represent an important further step in defining the impacts of slight concentrations of such contaminants on sea urchins and, more in general, on marine biota, increasing our knowledge of molecular targets involved in responses to environmental stressors.
Collapse
Affiliation(s)
- Luisa Albarano
- Stazione Zoologica Anton Dohrn, Department of Marine Biotechnology, Villa Comunale, 80121 Naples, Italy; (L.A.); (G.L.); (N.R.)
- Department of Biology, University of Naples Federico II, Complesso di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy;
| | - Valerio Zupo
- Stazione Zoologica Anton Dohrn, Department of Marine Biotechnology, Villa Dohrn, Punta San Pietro, 80077 Naples, Italy;
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Complesso di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy;
- Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), Complesso Universitario di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Giovanni Libralato
- Stazione Zoologica Anton Dohrn, Department of Marine Biotechnology, Villa Comunale, 80121 Naples, Italy; (L.A.); (G.L.); (N.R.)
- Department of Biology, University of Naples Federico II, Complesso di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy;
| | - Davide Caramiello
- Stazione Zoologica Anton Dohrn, Department of Research Infrastructures for Marine Biological Resources, Marine Organisms Core Facility, Villa Comunale, 80121 Naples, Italy;
| | - Nadia Ruocco
- Stazione Zoologica Anton Dohrn, Department of Marine Biotechnology, Villa Comunale, 80121 Naples, Italy; (L.A.); (G.L.); (N.R.)
- Stazione Zoologica Anton Dohrn, Department of Marine Biotechnology, C. da Torre Spaccata, 87071 Amendolara, Italy
| | - Maria Costantini
- Stazione Zoologica Anton Dohrn, Department of Marine Biotechnology, Villa Comunale, 80121 Naples, Italy; (L.A.); (G.L.); (N.R.)
- Correspondence:
| |
Collapse
|
10
|
De novo Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Loxechinus albus Using RNA-Seq. BIOLOGY 2021; 10:biology10100995. [PMID: 34681094 PMCID: PMC8533317 DOI: 10.3390/biology10100995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary Edible red sea urchin (Loxechinus albus) is an endemic species of echinoderm distributed along the Chilean coasts. This resource has been overexploited in recent years, depleting their natural populations. At present, there are few reported gene sequences available in public databases, restricting the molecular studies associated with aquaculture for this species. The aim of this study was to present the first annotated reference transcriptome of L. albus using NGS technologies and the differential expression transcripts analysis of the evaluated tissues. The transcriptome data obtained in this study will serve as a reference for future molecular research in the edible red sea urchin and other sea urchin species. Abstract Edible red sea urchin (Loxechinus albus) is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Hence, generate a transcriptome is crucial information that will considerably enrich molecular data and promote future findings for the L. albus aquaculture. Here, we obtained transcriptomic data of the edible red sea urchin by Illumina platform. Total RNA was extracted from gonads, intestines, and coelomocytes of juvenile urchins, and samples were sequenced using MiSeq Illumina technology. A total of 91,119,300 paired-end reads were de novo assembled, 185,239 transcripts produced, and a reference transcriptome created with 38.8% GC content and an N50 of 1769 bp. Gene ontology analysis revealed notable differences in the expression profiles between gonads, intestines, and coelomocytes, allowing the detection of transcripts associated with specific biological processes and KEGG pathways. These data were validated using 12 candidate transcripts by real-time qPCR. This dataset will provide a valuable molecular resource for L. albus and other species of sea urchins.
Collapse
|
11
|
D’Alessio S, Buckley KM, Kraev I, Hayes P, Lange S. Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin ( Strongylocentrotus purpuratus) Coelomic Fluid-Novel Insights into Echinodermata Biology. BIOLOGY 2021; 10:866. [PMID: 34571743 PMCID: PMC8464700 DOI: 10.3390/biology10090866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
The purple sea urchin (Strongylocentrotus purpuratus) is a marine invertebrate of the class Echinoidea that serves as an important research model for developmental biology, cell biology, and immunology, as well as for understanding regenerative responses and ageing. Peptidylarginine deiminases (PADs) are calcium-dependent enzymes that mediate post-translational protein deimination/citrullination. These alterations affect protein function and may also play roles in protein moonlighting. Extracellular vesicles (EVs) are membrane-bound vesicles that are released from cells as a means of cellular communication. Their cargo includes a range of protein and RNA molecules. EVs can be isolated from many body fluids and are therefore used as biomarkers in physiological and pathological responses. This study assessed EVs present in the coelomic fluid of the purple sea urchin (Strongylocentrotus purpuratus), and identified both total protein cargo as well as the deiminated protein cargo. Deiminated proteins in coelomic fluid EVs were compared with the total deiminated proteins identified in coelomic fluid to assess putative differences in deiminated protein targets. Functional protein network analysis for deiminated proteins revealed pathways for immune, metabolic, and gene regulatory functions within both total coelomic fluid and EVs. Key KEGG and GO pathways for total EV protein cargo furthermore showed some overlap with deimination-enriched pathways. The findings presented in this study add to current understanding of how post-translational deimination may shape immunity across the phylogeny tree, including possibly via PAD activity from microbiota symbionts. Furthermore, this study provides a platform for research on EVs as biomarkers in sea urchin models.
Collapse
Affiliation(s)
- Stefania D’Alessio
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | | | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Polly Hayes
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
- UCL EGA Institute for Women’s Health, Maternal and Fetal Medicine, London WC1E 6AU, UK
| |
Collapse
|
12
|
Li C, Zhao W, Qin C, Yu G, Ma Z, Guo Y, Pan W, Fu Z, Huang X, Chen J. Comparative transcriptome analysis reveals changes in gene expression in sea cucumber (Holothuria leucospilota) in response to acute temperature stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100883. [PMID: 34303260 DOI: 10.1016/j.cbd.2021.100883] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
Ambient temperature is an important abiotic factor that influences growth performance and physiological functions in sea cucumbers. To understand the molecular responses of the sea cucumber Holothuria leucospilota to acute temperature stress, we performed a de novo transcriptome analysis of body wall tissue from H. leucospilota exposed to 2 hoursh of acute heat (35 ± 1 °C) and cold stress (15 ± 1 °C). A total of 99,015 unigenes were obtained after assembly of the sequenced reads. Compared with a control group maintained at 25.0 ± 1 °C, 1169 differentially expressed unigenes (DEGs) were identified after heat stress, 781 were up-regulated and 388 were down-regulated. After cold stress, 1464 DEGs were identified; 900 were up-regulated and 564 were down-regulated. The annotation of DEGs revealed that heat shock proteins play important roles in protecting H. leucospilota from high temperature stress. Furthermore, KEGG pathway enrichment analysis showed that the categories: "Ribosome" and "Protein processing in endoplasmic reticulum" were strongly affected by heat stress. These two pathways are associated with biosynthesis and processing of proteins, and refolding of misfolded proteins. The lipid metabolism pathways "Sphingolipid metabolism" and "Ether lipid metabolism", were affected by cold stress. The RNA-Seq results for eight selected DEGs were verified the expression by quantitative real-time PCR analysis. Our results will improve the understanding of the molecular response mechanisms of H. leucospilota to ambient temperature stress.
Collapse
Affiliation(s)
- Changlin Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Wang Zhao
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Chuanxin Qin
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China.
| | - Gang Yu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China.
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Yu Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Wanni Pan
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| | - Zhengyi Fu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Xingmei Huang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China; Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Jisheng Chen
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China
| |
Collapse
|
13
|
Bultelle F, Boutet I, Devin S, Caza F, St-Pierre Y, Péden R, Brousseau P, Chan P, Vaudry D, Le Foll F, Fournier M, Auffret M, Rocher B. Molecular response of a sub-antarctic population of the blue mussel (Mytilus edulis platensis) to a moderate thermal stress. MARINE ENVIRONMENTAL RESEARCH 2021; 169:105393. [PMID: 34217095 DOI: 10.1016/j.marenvres.2021.105393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The Kerguelen Islands (49°26'S, 69°50'E) represent a unique environment due to their geographical isolation, which protects them from anthropogenic pollution. The ability of the endemic mussel, part of the Mytilus complex, to cope with moderate heat stress was explored using omic tools. Transcripts involved in six major metabolic functions were selected and the qRT-PCR data indicated mainly changes in aerobic and anaerobic energy metabolism and stress response. Proteomic comparisons revealed a typical stress response pattern with cytoskeleton modifications and elements suggesting increased energy metabolism. Results also suggest conservation of protein homeostasis by the long-lasting presence of HSP while a general decrease in transcription is observed. The overall findings are consistent with an adaptive response to moderate stresses in mussels in good physiological condition, i.e. living in a low-impact site, and with the literature concerning this model species. Therefore, local blue mussels could be advantageously integrated into biomonitoring strategies, especially in the context of Global Change.
Collapse
Affiliation(s)
- F Bultelle
- UMR-I 02 INERIS-URCA-ULH SEBIO / Environmental Stresses and Biomonitoring of Aquatic Ecosystems, FR CNRS 3730 Scale, Université Le Havre Normandie, F-76063, Le Havre Cedex, France.
| | - I Boutet
- Station Biologique de Roscoff CNRS, Laboratory Adaptation & Diversity in Marine Environment (UMR7144 CNRS-SU), Sorbonne Université, Roscoff, France.
| | - S Devin
- UMR 7360 LIEC, Université Metz-Lorraine, France.
| | - F Caza
- INRS-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, Québec, H7V 1B7, Canada.
| | - Y St-Pierre
- INRS-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, Québec, H7V 1B7, Canada.
| | - R Péden
- UMR-I 02 INERIS-URCA-ULH SEBIO / Environmental Stresses and Biomonitoring of Aquatic Ecosystems, FR CNRS 3730 Scale, Université Le Havre Normandie, F-76063, Le Havre Cedex, France; UMR-I 02 INERIS-URCA-ULH SEBIO / Environmental Stresses and Biomonitoring of Aquatic Ecosystems, Université de REIMS Champagne-Ardenne, Campus Moulin de la Housse, 51687, Reims, France.
| | - P Brousseau
- Institut des Sciences de la mer, Le Parc de la rivière Mitis, Sainte-Flavie, Québec, G0J 2L0, Canada.
| | - P Chan
- Normandie Univ, UNIROUEN, Plateforme PISSARO, IRIB, 76821, Mont-Saint-Aignan, France.
| | - D Vaudry
- Normandie Univ, UNIROUEN, Plateforme PISSARO, IRIB, 76821, Mont-Saint-Aignan, France; Normandie Univ, UNIROUEN, INSERM U1239 DC2N, 76821, Mont-Saint-Aignan, France.
| | - F Le Foll
- UMR-I 02 INERIS-URCA-ULH SEBIO / Environmental Stresses and Biomonitoring of Aquatic Ecosystems, FR CNRS 3730 Scale, Université Le Havre Normandie, F-76063, Le Havre Cedex, France.
| | - M Fournier
- Institut des Sciences de la mer, Le Parc de la rivière Mitis, Sainte-Flavie, Québec, G0J 2L0, Canada.
| | - M Auffret
- UMR CNRS 6539-LEMAR/ Laboratoire des Sciences de l'Environnement Marin, Technopôle Brest-Iroise, 29280, Plouzané, France.
| | - B Rocher
- UMR-I 02 INERIS-URCA-ULH SEBIO / Environmental Stresses and Biomonitoring of Aquatic Ecosystems, FR CNRS 3730 Scale, Université Le Havre Normandie, F-76063, Le Havre Cedex, France.
| |
Collapse
|
14
|
Integrated miRNA-mRNA analysis provides potential biomarkers for selective breeding in bay scallop (Argopecten irradians). Genomics 2021; 113:2744-2755. [PMID: 34091007 DOI: 10.1016/j.ygeno.2021.05.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/10/2021] [Accepted: 05/30/2021] [Indexed: 11/23/2022]
Abstract
Growth traits were compared between selected Argopecten irradians (BA) and non-selected A. irradians (NA; as a control). The results indicated that 1) the BA line exhibited greater average body weight and adductor muscle wet weight increase compared with the NA line at the same age of 10 months. 2) Comparative and integrated microRNA (miRNA) and mRNA transcriptome analyses identified 3373 differentially expressed genes (DEGs), 33 differentially expressed miRNAs (DEMs), and 39 "DEM-DEG" pairs in the BA line compared with the control. DEGs, DEMs, and "DEM-DEG" pairs involved in insulin signaling, immune related pathways, and actin cytoskeleton regulation were identified as candidates correlated with growth improvement in the BA line. A total of 259 positively selected genes were also identified. Collectively, our observations in this study will enrich the molecular information for A. irradians and provide potential biomarkers for future selective breeding and new seed creation in scallops.
Collapse
|
15
|
Delorme NJ, Frost EJ, Sewell MA. Effect of acclimation on thermal limits and hsp70 gene expression of the New Zealand sea urchin Evechinus chloroticus. Comp Biochem Physiol A Mol Integr Physiol 2020; 250:110806. [DOI: 10.1016/j.cbpa.2020.110806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022]
|
16
|
Chen Y, Li Y, Zhan Y, Hu W, Sun J, Zhang W, Song J, Li D, Chang Y. Identification of molecular markers for superior quantitative traits in a novel sea cucumber strain by comparative microRNA-mRNA expression profiling. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100686. [PMID: 32413829 DOI: 10.1016/j.cbd.2020.100686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 01/21/2023]
Abstract
To investigate the adaptability of Apostichopus japonicus (A. japonicus) strain "Anyuan No. 1" in the South China Sea, field monitoring and microRNA-mRNA integrated analyses were conducted between "Anyuan No. 1" and a regular A. japonicus population from Wendeng (Shandong Province, as a control) in the Xiapu farming area in Fujian Province, China. The results showed that "Anyuan No. 1" exhibited greater body weight increase and a higher number of papillae compared to the control during two and a half months of field monitoring. Comparative microRNA (miRNA) and mRNA transcriptome analyses identified 12 differentially expressed miRNAs (DEMs) and 165 differentially expressed genes (DEGs) in "Anyuan No. 1" compared to the control. Long-chain specific acyl-CoA dehydrogenase (ACADL), transmembrane protein 251 (TMEM251), dehydrogenase/reductase SDR family protein 7-like (Dhrs7), insulin-like growth factor-binding protein 7 (IGFBP-7), CDK5 regulatory subunit-associated protein 1 (CDK5RAP1), visual pigment-like receptor peropsin, 39S ribosomal protein, miR-10, miR-153, miR-7, and miR-3529 were identified as gene and miRNA candidates correlated with superior economic traits in "Anyuan No. 1". Collectively, "Anyuan No. 1" is suitable for large-scale cultivation extension due to its better adaptability to the South China Sea area. Furthermore, we identified "miR10-ACADL" as a potential module for further molecular marker-assisted selective breeding of A. japonicus.
Collapse
Affiliation(s)
- Yang Chen
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yingying Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaoyao Zhan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
| | - Wanbin Hu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jingxian Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Dantong Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
| |
Collapse
|
17
|
Warming and temperature variability determine the performance of two invertebrate predators. Sci Rep 2020; 10:6780. [PMID: 32321937 PMCID: PMC7176636 DOI: 10.1038/s41598-020-63679-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 04/03/2020] [Indexed: 02/05/2023] Open
Abstract
In a warming ocean, temperature variability imposes intensified peak stress, but offers periods of stress release. While field observations on organismic responses to heatwaves are emerging, experimental evidence is rare and almost lacking for shorter-scale environmental variability. For two major invertebrate predators, we simulated sinusoidal temperature variability (±3 °C) around todays' warm summer temperatures and around a future warming scenario (+4 °C) over two months, based on high-resolution 15-year temperature data that allowed implementation of realistic seasonal temperature shifts peaking midpoint. Warming decreased sea stars' (Asterias rubens) energy uptake (Mytilus edulis consumption) and overall growth. Variability around the warming scenario imposed additional stress onto Asterias leading to an earlier collapse in feeding under sinusoidal fluctuations. High-peak temperatures prevented feeding, which was not compensated during phases of stress release (low-temperature peaks). In contrast, increased temperatures increased feeding on Mytilus but not growth rates of the recent invader Hemigrapsus takanoi, irrespective of the scale at which temperature variability was imposed. This study highlights species-specific impacts of warming and identifies temperature variability at the scale of days to weeks/months as important driver of thermal responses. When species' thermal limits are exceeded, temperature variability represents an additional source of stress as seen from future warming scenarios.
Collapse
|
18
|
Smitha PK, Vishnupriyan K, Kar AS, Anil Kumar M, Bathula C, Chandrashekara KN, Dhar SK, Das M. Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum. BMC PLANT BIOLOGY 2019; 19:405. [PMID: 31521126 PMCID: PMC6744693 DOI: 10.1186/s12870-019-1988-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/26/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the "house-keeping genes", involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of > 50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum. RESULT Five genes (TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6) identified by data-science driven analysis, along with two commonly used reference genes found in literature (PP2A1 and UBQ14) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm, BestKeeper, NormFinder and RefFinder. CONCLUSION Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.
Collapse
Affiliation(s)
- P. K. Smitha
- Department of Biotechnology, Research and Development Centre, Bharathiar University, Coimbatore, Tamil Nadu 641 046 India
- Beyond Antibody LLP, S-005 Krishna Greens, Krishna Temple Road, Dodda Bomasandra, Bangalore, Karnataka 560 097 India
| | - K. Vishnupriyan
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
| | - Ananya S. Kar
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
- School of Bio Sciences & Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632 014 India
| | - M. Anil Kumar
- Beyond Antibody LLP, S-005 Krishna Greens, Krishna Temple Road, Dodda Bomasandra, Bangalore, Karnataka 560 097 India
| | - Christopher Bathula
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
| | - K. N. Chandrashekara
- Division of Plant Physiology and Biotechnology, UPASI Tea Research Foundation, Tea Research Institute, Nirar Dam, Valparai, Coimbatore, Tamil Nadu 642 127 India
| | - Sujan K. Dhar
- Beyond Antibody LLP, S-005 Krishna Greens, Krishna Temple Road, Dodda Bomasandra, Bangalore, Karnataka 560 097 India
| | - Manjula Das
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
| |
Collapse
|
19
|
Balakirev ES. Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins. Genes (Basel) 2019; 10:E592. [PMID: 31387337 PMCID: PMC6723515 DOI: 10.3390/genes10080592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.
Collapse
Affiliation(s)
- Evgeniy S Balakirev
- National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 17 Palchevsky Street, 690041 Vladivostok, Russia.
- School of Biomedicine, Far Eastern Federal University, 8 Sukhanov Street, 690950 Vladivostok, Russia.
| |
Collapse
|