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Kodzik N, Ciereszko A, Szczepkowska B, Malinowska A, Dietrich MA. Comparative proteomic analysis of the ovarian fluid and eggs of Siberian sturgeon. BMC Genomics 2024; 25:451. [PMID: 38714919 PMCID: PMC11077782 DOI: 10.1186/s12864-024-10309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Sturgeon species are living fossils that exhibit unique reproductive characteristics, and elucidation of the molecular processes governing the formation and quality of sturgeon eggs is crucial. However, comprehensive data on the protein composition of sturgeon ovarian fluid (OF) and eggs and their functional significance are lacking. To address this knowledge gap, the aim of the present study was to conduct a comprehensive comparative proteomic analysis of Siberian sturgeon OF and eggs using liquid chromatography-mass spectrometry (LC-MS/MS). RESULTS A total of 617 proteins were identified in OF, and 565 proteins were identified in eggs. A total of 772 proteins showed differential abundance. Among the differentially abundant proteins, 365 were more abundant in OFs, while 407 were more abundant in eggs. We identified 339 proteins unique to OFs and 287 proteins specific to eggs, and further investigated the top 10 most abundant proteins in each. The functional annotation of the OF proteins highlighted their predominant association with immune system processes, including the complement and coagulation cascade, neutrophil and leukocyte-mediated immunity, cholesterol metabolism, and regulation of the actin cytoskeleton. Analysis of egg proteins revealed enrichment in metabolic pathways, such as oxidative phosphorylation and fatty acid metabolism, and protein ubiquitination and translation. OF-specific proteins included extracellular matrix and secretory vesicles, and eggs were enriched in proteins localized to mitochondria and ribosome components. CONCLUSIONS This study presents the first comprehensive characterization of the protein composition of sturgeon OF and eggs and elucidates their distinct functional roles. These findings advance our understanding of sturgeon reproduction, OF-egg signaling and the origin of OF proteins. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium with the dataset identifier PXD044168 to ensure accessibility for further research.
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Affiliation(s)
- Natalia Kodzik
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, 10-748, Poland
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, 10-748, Poland
| | - Bożena Szczepkowska
- Department of Sturgeon Fish Breeding, Inland Fisheries Institute in Olsztyn, Pozezdrze, Pieczarki, 11-610, Poland
| | - Agata Malinowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, Warszawa, 02-106, Poland
| | - Mariola Aleksandra Dietrich
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, 10-748, Poland.
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Ocalewicz K. Quality of fish eggs and production of androgenetic and gynogenetic doubled haploids (DHs). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023:10.1007/s10695-023-01206-4. [PMID: 37296321 DOI: 10.1007/s10695-023-01206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
Induced development of haploid embryos (H) with only paternal (androgenesis) or maternal (gynogenesis) chromosomes requires irradiation of eggs before fertilization or activation of eggs with irradiated spermatozoa, respectively. To provide doubled haploids (DHs), androgenetic and gynogenetic haploid zygotes need to be subjected to the thermal or high hydrostatic pressure (HHP) shock to suppress the first mitotic cleavage and to double paternal or maternal haploid set of chromosomes. Androgenesis and mitotic gynogenesis (mito-gynogenesis) result in the generation of fully homozygous individuals in a single generation. DHs have been utilized in selective breeding programs, in studies concerning the phenotypic consequences of recessive alleles and to evaluate the impact of sex chromosomes on the early ontogeny. Moreover, the use of DHs for the NGS approach radically improves de novo the assembly of the genomes. However, reduced survival of the doubled haploids limits the wide application of androgenotes and gynogenotes. The high mortality of DHs may be only partly explained by the expression of recessive traits. Observed inter-clutch variation in the survival of DHs developing in eggs originating from different females make it necessary to take a closer look at the quality of the eggs used during induced androgenesis and gynogenesis. Moreover, the developmental competence of eggs that are subjected to irradiation before fertilization in order to deactivate maternal chromosomes when undergoing induced androgenesis and exposed to the physical shock after fertilization that leads to the duplication of the zygotes in both mito-gynogenesis and androgenesis may be also altered as irradiation and sublethal values of temperatures and hydrostatic pressure are considered as harmful for the cell organelles and biomolecules. Here, recently provided results concerning the morphological, biochemical, genomic, and transcriptomic characteristics of fish eggs showing high and low competence for androgenesis and mito-gynogenesis are reviewed.
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Affiliation(s)
- Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Al. M. Piłsudskiego 46, 81-378, Gdynia, Poland.
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3
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Chen F, Wang Y, He J, Smith C, Xue G, Zhao Y, Peng Y, Zhang J, Liu J, Chen J, Xie P. Alternative signal pathways underly fertilization and egg activation in a fish with contrasting modes of spawning. BMC Genomics 2023; 24:167. [PMID: 37016278 PMCID: PMC10074663 DOI: 10.1186/s12864-023-09244-1] [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: 10/11/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND The processes of fertilization and egg activation are vital for early embryogenesis. However, while the mechanisms associated with key events during these processes differ among species and modes of spawning, the signal pathways underlying these processes are opaque for many fishes, including economically important species. RESULTS We investigated phenotypic traits, ultrastructure and protein expression levels in the eggs of the topmouth culter (Culter alburnus), a protected and economically important freshwater fish that exhibits two spawning modes, producing semi-buoyant eggs and adhesive eggs. Unfertilized eggs of C. alburnus were examined, as well as eggs at fertilization and 30 min post fertilization. Our results showed that in semi-buoyant eggs, energy metabolism was activated at fertilization, followed by elevated protein expression of cytoskeleton and extracellular matrix (ECM)-receptor interactions that resulted in rapid egg swelling; a recognized adaptation for lotic habitats. In contrast, in adhesive eggs fertilization initiated the process of sperm-egg fusion and blocking of polyspermy, followed by enhanced protein expression of lipid metabolism and the formation of egg envelope adhesion and hardening, which are adaptive in lentic habitats. CONCLUSION Our findings indicate that alternative signal pathways differ between modes of spawning and timing during the key processes of fertilization and egg activation, providing new insights into the molecular mechanisms involved in adaptive early embryonic development in teleost fishes.
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Affiliation(s)
- Feng Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Yeke Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Carl Smith
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Ge Xue
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanghui Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jia Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiarui Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Jun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China.
| | - Ping Xie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Donghu Experimental Station of Lake Ecosystems, Chinese Academy of Sciences, 430072, Wuhan, China.
- Institute of Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment, Yunnan University, 650500, Kunming, China.
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Bir J, Rojo-Bartolomé I, Lekube X, Diaz de Cerio O, Ortiz-Zarragoitia M, Cancio I. High production of transfer RNAs identifies the presence of developing oocytes in ovaries and intersex testes of teleost fish. MARINE ENVIRONMENTAL RESEARCH 2023; 186:105907. [PMID: 36774708 DOI: 10.1016/j.marenvres.2023.105907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
5S rRNA is highly transcribed in fish oocytes and this transcription levels can be used to identify the presence of oocytes in the intersex testes of fish exposed to xenoestrogens. Similar to 5S rRNA, tRNAs are transcribed by RNA polymerase III (Pol-III) in eukaryotes, so this study focuses in the analysis of the levels of expression of tRNAs in the gonads (ovaries and testes) of eight teleost species as a possible new oocyte molecular marker. Total RNA extracted from gonads of six commercial teleost species in the Biscay Bay, from the pollution sentinel species thicklip grey mullet (Chelon labrosus) known present intersex testes in response to xenoestrogens in Gernika estuary and from the laboratory model species Danio rerio were analysed through capillary electrophoresis. Bioanalyzer electropherograms were used to quantify the concentrations of tRNAs, 5S and 5.8S rRNA. All studied ovaries expressed significantly higher levels of tRNAs and 5S rRNA than testes. A tRNA to 5.8S rRNA index was calculated which differentiates ovaries from testes, and identifies some intersex testes in between testes and ovaries in mullets. The tRNA/5.8S ratio was highest in ovaries in previtellogenic stage, decreasing towards maturity. Thus, strong oocyte expression of tRNAs is an additional proof of high activity levels of Pol-III during early stages of oocyte development in teleost ovaries. Incidentally, we observed that miRNA concentrations were always higher in testes than ovaries. The indexing approach developed in the present study could have multiple applications in teleost reproduction research and in the development of early molecular markers of intersex condition.
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Affiliation(s)
- Joyanta Bir
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Basque Country, Spain; Fisheries and Marine Resources Technology Discipline, School of Life Sciences, Khulna University, Khulna, 9208, Bangladesh
| | - Iratxe Rojo-Bartolomé
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Basque Country, Spain
| | - Xabier Lekube
- Biscay Bay Environmental Biospecimen Bank (BBEBB), Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Basque Country, Spain
| | - Oihane Diaz de Cerio
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Basque Country, Spain
| | - Maren Ortiz-Zarragoitia
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Basque Country, Spain
| | - Ibon Cancio
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Basque Country, Spain.
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5
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Yilmaz O, Jensen AM, Harboe T, Møgster M, Jensen RM, Mjaavatten O, Birkeland E, Spriet E, Sandven L, Furmanek T, Berven FS, Wargelius A, Norberg B. Quantitative proteome profiling reveals molecular hallmarks of egg quality in Atlantic halibut: impairments of transcription and protein folding impede protein and energy homeostasis during early development. BMC Genomics 2022; 23:635. [PMID: 36071374 PMCID: PMC9450261 DOI: 10.1186/s12864-022-08859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Background Tandem mass tag spectrometry (TMT labeling-LC-MS/MS) was utilized to examine the global proteomes of Atlantic halibut eggs at the 1-cell-stage post fertilization. Comparisons were made between eggs judged to be of good quality (GQ) versus poor quality (BQ) as evidenced by their subsequent rates of survival for 12 days. Altered abundance of selected proteins in BQ eggs was confirmed by parallel reaction monitoring spectrometry (PRM-LC-MS/MS). Correspondence of protein levels to expression of related gene transcripts was examined via qPCR. Potential mitochondrial differences between GQ and BQ eggs were assessed by transmission electron microscopy (TEM) and measurements of mitochondrial DNA (mtDNA) levels. Results A total of 115 proteins were found to be differentially abundant between GQ and BQ eggs. Frequency distributions of these proteins indicated higher protein folding activity in GQ eggs compared to higher transcription and protein degradation activities in BQ eggs. BQ eggs were also significantly enriched with proteins related to mitochondrial structure and biogenesis. Quantitative differences in abundance of several proteins with parallel differences in their transcript levels were confirmed in egg samples obtained over three consecutive reproductive seasons. The observed disparities in global proteome profiles suggest impairment of protein and energy homeostasis related to unfolded protein response and mitochondrial stress in BQ eggs. TEM revealed BQ eggs to contain significantly higher numbers of mitochondria, but differences in corresponding genomic mtDNA (mt-nd5 and mt-atp6) levels were not significant. Mitochondria from BQ eggs were significantly smaller with a more irregular shape and a higher number of cristae than those from GQ eggs. Conclusion The results of this study indicate that BQ Atlantic halibut eggs are impaired at both transcription and translation levels leading to endoplasmic reticulum and mitochondrial disorders. Observation of these irregularities over three consecutive reproductive seasons in BQ eggs from females of diverse background, age and reproductive experience indicates that they are a hallmark of poor egg quality. Additional research is needed to discover when in oogenesis and under what circumstances these defects may arise. The prevalence of this suite of markers in BQ eggs of diverse vertebrate species also begs investigation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08859-0.
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Affiliation(s)
- Ozlem Yilmaz
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway.
| | | | - Torstein Harboe
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | - Margareth Møgster
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | | | - Olav Mjaavatten
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Even Birkeland
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Endy Spriet
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Linda Sandven
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Birgitta Norberg
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
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Zolotarenko AD, Shitova MV. Transcriptome Studies of Salmonid Fishes of the Genius Oncorhynchus. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542207016x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Mercer M, Jang S, Ni C, Buszczak M. The Dynamic Regulation of mRNA Translation and Ribosome Biogenesis During Germ Cell Development and Reproductive Aging. Front Cell Dev Biol 2021; 9:710186. [PMID: 34805139 PMCID: PMC8595405 DOI: 10.3389/fcell.2021.710186] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/07/2021] [Indexed: 01/21/2023] Open
Abstract
The regulation of mRNA translation, both globally and at the level of individual transcripts, plays a central role in the development and function of germ cells across species. Genetic studies using flies, worms, zebrafish and mice have highlighted the importance of specific RNA binding proteins in driving various aspects of germ cell formation and function. Many of these mRNA binding proteins, including Pumilio, Nanos, Vasa and Dazl have been conserved through evolution, specifically mark germ cells, and carry out similar functions across species. These proteins typically influence mRNA translation by binding to specific elements within the 3′ untranslated region (UTR) of target messages. Emerging evidence indicates that the global regulation of mRNA translation also plays an important role in germ cell development. For example, ribosome biogenesis is often regulated in a stage specific manner during gametogenesis. Moreover, oocytes need to produce and store a sufficient number of ribosomes to support the development of the early embryo until the initiation of zygotic transcription. Accumulating evidence indicates that disruption of mRNA translation regulatory mechanisms likely contributes to infertility and reproductive aging in humans. These findings highlight the importance of gaining further insights into the mechanisms that control mRNA translation within germ cells. Future work in this area will likely have important impacts beyond germ cell biology.
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Affiliation(s)
- Marianne Mercer
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Seoyeon Jang
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chunyang Ni
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Michael Buszczak
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Neurodevelopment vs. the immune system: Complementary contributions of maternally-inherited gene transcripts and proteins to successful embryonic development in fish. Genomics 2021; 113:3811-3826. [PMID: 34508856 DOI: 10.1016/j.ygeno.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/12/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
The aim of this study was to investigate the respective contribution of maternally-inherited mRNAs and proteins to egg molecular cargo and to its developmental competence in fish using pikeperch as a model. Our study provides novel insights into the understanding of type-specific roles of maternally-inherited molecules in fish. Here we show, for the first time, that transcripts and proteins have distinct, yet complementary, functions in the egg of teleost fish. Maternally-inherited mRNAs would shape embryo neurodevelopment, while maternally-inherited proteins would rather be responsible for protecting the embryo against pathogens. Additionally, we observed that processes directly preceding ovulation may considerably affect the reproductive success by modifying expression level of genes crucial for proper embryonic development, being novel fish egg quality markers (e.g., smarca4 or h3f3a). These results are of major importance for understanding the influence of external factors on reproductive fitness in both captive and wild-type fish species.
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9
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Weber GM, Birkett J, Martin K, Dixon D, Gao G, Leeds TD, Vallejo RL, Ma H. Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability. BMC Genomics 2021; 22:448. [PMID: 34130620 PMCID: PMC8207762 DOI: 10.1186/s12864-021-07773-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Background Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The transcriptome of the unfertilized egg, therefore, has potential to provide markers for predictors of egg quality and diagnosing problems with embryo production encountered by fish hatcheries. Although levels of specific transcripts have been shown to associate with measures of egg quality, these differentially expressed genes (DEGs) have not been consistent among studies. The present study compares differences in select transcripts among unfertilized rainbow trout eggs of different quality based on eyeing rate, among 2 year classes of the same line (A1, A2) and a population from a different hatchery (B). The study compared 65 transcripts previously reported to be differentially expressed with egg quality in rainbow trout. Results There were 32 transcripts identified as DEGs among the three groups by regression analysis. Group A1 had the most DEGs, 26; A2 had 15, 14 of which were shared with A1; and B had 12, 7 of which overlapped with A1 or A2. Six transcripts were found in all three groups, dcaf11, impa2, mrpl39_like, senp7, tfip11 and uchl1. Conclusions Our results confirmed maternal transcripts found to be differentially expressed between low- and high-quality eggs in one population of rainbow trout can often be found to overlap with DEGs in other populations. The transcripts differentially expressed with egg quality remain consistent among year classes of the same line. Greater similarity in dysregulated transcripts within year classes of the same line than among lines suggests patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were identified, for each of the genes there is considerable variability in transcript abundance among eggs of similar quality and low correlations between transcript abundance and eyeing rate, making it highly improbable to predict the quality of a single batch of eggs based on transcript abundance of just a few genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07773-1.
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Affiliation(s)
- Gregory M Weber
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA.
| | - Jill Birkett
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | | | | | - Guangtu Gao
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Timothy D Leeds
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Roger L Vallejo
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV, USA
| | - Hao Ma
- USDA/ARS Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Ames, IA, USA
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10
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Yilmaz O, Patinote A, Com E, Pineau C, Bobe J. Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs. BMC Genomics 2021; 22:308. [PMID: 33910518 PMCID: PMC8082894 DOI: 10.1186/s12864-021-07606-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND We previously reported the results of CRISPR/Cas9 knock-out (KO) of type-I and type-III vitellogenins (Vtgs) in zebrafish, which provided the first experimental evidence on essentiality and disparate functioning of Vtgs at different stages during early development. However, the specific contributions of different types of Vtg to major cellular processes remained to be investigated. The present study employed liquid chromatography and tandem mass spectrometry (LC-MS/MS) to meet this deficit. Proteomic profiles of zebrafish eggs lacking three type-I Vtgs simultaneously (vtg1-KO), or lacking only type III Vtg (vtg3-KO) were compared to those of wild type (Wt) eggs. Obtained spectra were searched against a zebrafish proteome database and identified proteins were quantified based on normalized spectral counts. RESULTS The vtg-KO caused severe changes in the proteome of 1-cell stage zebrafish eggs. These changes were disclosed by molecular signatures that highly resembled the proteomic phenotype of poor quality zebrafish eggs reported in our prior studies. Proteomic profiles of vtg-KO eggs and perturbations in abundances of hundreds of proteins revealed unique, noncompensable contributions of multiple Vtgs to protein and in energy homeostasis. The lack of this contribution appears to have a significant impact on endoplasmic reticulum and mitochondrial functions, and thus embryonic development, even after zygotic genome activation. Increased endoplasmic reticulum stress, Redox/Detox activities, glycolysis/gluconeogenesis, enrichment in cellular proliferation and in human neurodegenerative disease related activities in both vtg1- and vtg3-KO eggs were found to be indicators of the aforementioned conditions. Distinctive increase in apoptosis and Parkinson disease pathways, as well as the decrease in lipid metabolism related activities in vtg3-KO eggs implies compelling roles of Vtg3, the least abundant form of Vtgs in vertebrate eggs, in mitochondrial activities. Several differentially abundant proteins representing the altered molecular mechanisms have been identified as strong candidate markers for studying the details of these mechanisms during early embryonic development in zebrafish and possibly other vertebrates. CONCLUSIONS These findings indicate that the global egg proteome is subject to extensive modification depending on the presence or absence of specific Vtgs and that these modifications can have a major impact on developmental competence.
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Affiliation(s)
- Ozlem Yilmaz
- INRAE, LPGP, 35000, Rennes, France.
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway.
| | | | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset-UMR_S 1085, F-35042, Rennes cedex, France
- Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset-UMR_S 1085, F-35042, Rennes cedex, France
- Protim, Univ Rennes, F-35042, Rennes cedex, France
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11
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Żarski D, Le Cam A, Nynca J, Klopp C, Ciesielski S, Sarosiek B, Montfort J, Król J, Fontaine P, Ciereszko A, Bobe J. Domestication modulates the expression of genes involved in neurogenesis in high-quality eggs of Sander lucioperca. Mol Reprod Dev 2020; 87:934-951. [PMID: 32864792 DOI: 10.1002/mrd.23414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022]
Abstract
Pikeperch, Sander lucioperca, is a species of high interest to the aquaculture. The expansion of its production can only be achieved by furthering domestication level. However, the mechanisms driving the domestication process in finfishes are poorly understood. Transcriptome profiling of eggs was found to be a useful tool allowing understanding of the domestication process in teleosts. In this study, using next-generation sequencing, the first pikeperch transcriptome has been generated as well as pikeperch-specific microarray comprising 35,343 unique probes. Next, we performed transcriptome profiling of eggs obtained from wild and domesticated populations. We found 710 differentially expressed genes that were linked mostly to nervous system development. These results provide new insights into processes that are directly involved in the domestication of finfishes. It can be suggested that all the identified processes were predetermined by the maternally derived set of genes contained in the unfertilized eggs. This allows us to suggest that fish behavior, along with many other processes, can be predetermined at the cellular level and may have significant implications on the adaptation of cultured fish to the natural environment. This also allows to suggest that fish behavior should be considered as a very important pikeperch aquaculture selection trait.
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Affiliation(s)
- Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Aurelie Le Cam
- Fish Physiology and Genomics, UR1037 (LPGP), INRAE, Rennes, France
| | - Joanna Nynca
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Sławomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Beata Sarosiek
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Jerome Montfort
- Fish Physiology and Genomics, UR1037 (LPGP), INRAE, Rennes, France
| | - Jarosław Król
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury, Olsztyn, Poland
| | | | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Julien Bobe
- Fish Physiology and Genomics, UR1037 (LPGP), INRAE, Rennes, France
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