1
|
Patra SK, Vemulawada C, Soren MM, Sundaray JK, Panda MK, Barman HK. Molecular characterization and expression patterns of Nanog gene validating its involvement in the embryonic development and maintenance of spermatogonial stem cells of farmed carp, Labeo rohita. J Anim Sci Biotechnol 2018; 9:45. [PMID: 29992021 PMCID: PMC5994655 DOI: 10.1186/s40104-018-0260-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 04/25/2018] [Indexed: 12/24/2022] Open
Abstract
Background The homeobox containing transcription factor Nanog plays crucial roles in embryonic development/proliferation and/or maintenance of spermatogonial stem cells (SSCs) via interacting with transcription factors such as Oct4 and Sox2 in mammals. However, knowledge of its exact mechanistic pathways remains unexploited. Very little is known about teleost Nanog. Information on the Nanog gene of farmed rohu carp (Labeo rohita) is lacking. We cloned and characterized the Nanog gene of rohu carp to understand the expression pattern in early developmental stages and also deduced the genomic organization including promoter elements. Results Rohu Nanog (LrNanog) cDNA comprised an open reading frame of 1,161 nucleotides bearing a structural homeodomain; whereas, the genomic structure contained four exons and three introns suggesting that it is homologous to mammalian counterparts. Phylogenetically, it was closely related to freshwater counterparts. Protein sequence (386 AA of 42.65 kDa) comparison revealed its low similarity with other vertebrate counterparts except that of the conserved homeodomain. Tissue distribution analysis revealed the existence of LrNanog transcripts only in adult gonads. The heightened abundances in the ovary and proliferating spermatogonia suggested its participations in maternal inheritance and male germ cell development. The potentiating abundances from fertilized egg onwards peaking at blastula stage vis- à-vis decreasing levels from gastrula stage onwards demonstrated its role in embryonic stem cell development. We also provided evidence of its presence in SSCs by western blotting analysis. Further, the promoter region was characterized, predicting a basal core promoter and other consensus elements. Conclusion The molecular characterization of LrNanog and its documented expression profiling at transcript and protein levels are indicative of its functional linkage with embryonic/spermatogonial stem cell maintenance. This is the first report of LrNanog genomic organization including its promoter sequence information with predicted regulatory elements of a large-bodied carp species. This will be useful for elucidating its mechanism expression in future. Nanog could be used as a potential biomarker for proliferating carp SSCs.
Collapse
Affiliation(s)
- Swagat K Patra
- 1Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| | - Chakrpani Vemulawada
- 1Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| | - Meenati M Soren
- 1Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| | - Jitendra K Sundaray
- 1Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| | - Manoj K Panda
- 2Center of Biotechnology, Siksha 'O' Anusandhan University, Bhubaneswar, India
| | - Hirak K Barman
- 1Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002 India
| |
Collapse
|
2
|
Parolini M, Bini L, Magni S, Rizzo A, Ghilardi A, Landi C, Armini A, Del Giacco L, Binelli A. Exposure to cocaine and its main metabolites altered the protein profile of zebrafish embryos. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 232:603-614. [PMID: 28993024 DOI: 10.1016/j.envpol.2017.09.097] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/13/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
Illicit drugs have been identified as emerging aquatic pollutants because of their widespread presence in freshwaters and potential toxicity towards aquatic organisms. Among illicit drug residues, cocaine (COC) and its main metabolites, namely benzoylecgonine (BE) and ecgonine methyl ester (EME), are commonly detected in freshwaters worldwide at concentration that can induce diverse adverse effects to non-target organisms. However, the information of toxicity and mechanisms of action (MoA) of these drugs, mainly of COC metabolites, to aquatic species is still fragmentary and inadequate. Thus, this study was aimed at investigating the toxicity of two concentrations (0.3 and 1.0 μg/L) of COC, BE and EME similar to those found in aquatic ecosystems on zebrafish (Danio rerio) embryos at 96 h post fertilization through a functional proteomics approach. Exposure to COC and both its metabolites significantly altered the protein profile of zebrafish embryos, modulating the expression of diverse proteins belonging to different functional classes, including cytoskeleton, eye constituents, lipid transport, lipid and energy metabolism, and stress response. Expression of vitellogenins and crystallins was modulated by COC and both its main metabolites, while only BE and EME altered proteins related to lipid and energy metabolism, as well as to oxidative stress response. Our data confirmed the potential toxicity of low concentrations of COC, BE and EME, and helped to shed light on their MoA on an aquatic vertebrate during early developmental period.
Collapse
Affiliation(s)
- Marco Parolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 2, I-20133 Milano, Italy.
| | - Luca Bini
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Stefano Magni
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Alessandro Rizzo
- Department of Environmental Science and Policy, University of Milan, via Celoria 2, I-20133 Milano, Italy
| | - Anna Ghilardi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Claudia Landi
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Alessandro Armini
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Luca Del Giacco
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Andrea Binelli
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| |
Collapse
|
3
|
Chakrapani V, Rasal KD, Kumar S, Mohapatra SD, Sundaray JK, Jayasankar P, Barman HK. In Silico Analysis of nsSNPs of Carp TLR22 Gene Affecting its Binding Ability with Poly I:C. Interdiscip Sci 2017; 10:641-652. [PMID: 28660537 DOI: 10.1007/s12539-017-0247-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 11/29/2022]
Abstract
Immune response mediated by toll-like receptor 22 (TLR22), only found in teleost/amphibians, is triggered by double-stranded RNA binding to its LRR (leucine-rich repeats) ecto-domain. Accumulated evidences suggested that missense mutations in TLR genes affect its function. However, information on mutation linked pathogen recognition for TLR22 was lacking. The present study was commenced for predicting the effect of non-synonymous single-nucleotide polymorphisms (nsSNPs) on the pathogen recognizable LRR domain of TLR22 of farmed carp, Labeo rohita. The sequence-based algorithms (SIFT, PROVEAN and I-Mutant2.0) indicated that three SNPs (out of 27) such as p.L159F (rs76759876) and p.L529P (rs749355507) of LRR, and p.I836M (rs750758397) of intracellular motifs could potentially disrupt protein function. The 3D structure was generated using MODELLER 9.13 and further validated by SAVEs server. The simulated molecular docking of native TLR22 and mutants with poly I:C ligand indicated that mutations positioned at p.L159F and p.L529P of the LRR region affects the binding affinity significantly. This is the first kind of study of predicting nsSNPs of teleost TLR22 with disturbed ligand binding affinity with its extra-cellular LRR domain and thereby likely hindrance in subsequent signal transduction. This study serves as a guide for in vivo evaluation of impact of mutation on immune response mediated by teleost TLR22 gene.
Collapse
Affiliation(s)
- Vemulawada Chakrapani
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Sunil Kumar
- ICAR, National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, 275103, India
| | - Shibani D Mohapatra
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Jitendra K Sundaray
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Hirak K Barman
- Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India.
| |
Collapse
|
4
|
Status and future perspectives of single nucleotide polymorphisms (SNPs) markers in farmed fishes: Way ahead using next generation sequencing. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
5
|
Identification of Deleterious Mutations in Myostatin Gene of Rohu Carp (Labeo rohita) Using Modeling and Molecular Dynamic Simulation Approaches. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7562368. [PMID: 27019850 PMCID: PMC4785247 DOI: 10.1155/2016/7562368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/13/2016] [Accepted: 01/27/2016] [Indexed: 11/18/2022]
Abstract
The myostatin (MSTN) is a known negative growth regulator of skeletal muscle. The mutated myostatin showed a double-muscular phenotype having a positive significance for the farmed animals. Consequently, adequate information is not available in the teleosts, including farmed rohu carp, Labeo rohita. In the absence of experimental evidence, computational algorithms were utilized in predicting the impact of point mutation of rohu myostatin, especially its structural and functional relationships. The four mutations were generated at different positions (p.D76A, p.Q204P, p.C312Y, and p.D313A) of MSTN protein of rohu. The impacts of each mutant were analyzed using SIFT, I-Mutant 2.0, PANTHER, and PROVEAN, wherein two substitutions (p.D76A and p.Q204P) were predicted as deleterious. The comparative structural analysis of each mutant protein with the native was explored using 3D modeling as well as molecular-dynamic simulation techniques. The simulation showed altered dynamic behaviors concerning RMSD and RMSF, for either p.D76A or p.Q204P substitution, when compared with the native counterpart. Interestingly, incorporated two mutations imposed a significant negative impact on protein structure and stability. The present study provided the first-hand information in identifying possible amino acids, where mutations could be incorporated into MSTN gene of rohu carp including other carps for undertaking further in vivo studies.
Collapse
|