Skip to main content
Springer Nature Link
Log in

Identifying miRNAs in the modulation of gene regulation associated with ammonia toxicity in catfish, Clarias magur (Linnaeus, 1758)

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Background

The small non-coding microRNAs play a vital role in post-transcriptional gene regulation associated with different physiological events such as metabolism, stress, etc. The freshwater catfish, Clarias magur, can grow within hyper ammonia containing stagnant water bodies and/or muddy substratum. We intended to identify organ-specific miRNAs associated with ammonia stress management.

Methods and results

The miRNA-libraries were generated from QC passed total RNA extracted from liver, muscle, and kidney of ammonia-treated (exposed to 25 mM NH4Cl for 14 days) and untreated catfish. The libraries were validated using High sensitivity D1000 Screen tape. The trimmed quality-filtered reads for control and treated samples of kidney were 19,406,210; 14,904,423; for liver 15,467,727; 18,582,072; and for muscle 25,081,345; 19,782,182 respectively. Total 120 known and 150 novel differentially expressed miRNAs were identified, out of which miR-200, miR-217, miR-122, miR-133, miR-145, miR-221, miR-19, miR-138, miR-34, and miR-184 were predicted to be involved in the metabolism of nitrogen. The key miRNAs targeted several genes associated with urea synthesis like Glutaminase 2, Argininosuccinate lyase, Glutamate dehydrogenase 1, Alanine aminotransferase 2-like, Aspartate aminotransferase, cytoplasmic-like, Glutamate ionotropic receptor NMDA type subunit 2A, etc.

Conclusions

This is the first report of miRNAs, which serve as a vital resource for regulating nitrogen metabolism in freshwater catfish, C. magur. The data will be resourceful for further evaluating the regulatory role of miRNAs in fishes, which grow and reproduce very well in hazardous ammonia-contaminated water bodies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Explore related subjects

Discover the latest articles and news from researchers in related subjects, suggested using machine learning.

References

  1. Chondar SL (1999) Biology of finfish and shellfish. SCSC Publishers (India), West Bengal

    Google Scholar 

  2. Saha N, Ratha BK (2007) Functional ureogenesis and adaptation to ammonia metabolism in Indian freshwater air-breathing catfishes. Fish Physiol Biochem 33:283–295. https://doi.org/10.1007/s10695-007-9172-3

    Article  CAS  Google Scholar 

  3. Wood C, Evans D (1993) Ammonia and urea metabolism and excretion [in fish]. CRC Mar Sci Ser 379–426

  4. Saha N, Ratha BK (1989) Comparative study of ureogenesis in freshwater, air-breathing teleosts. J Exp Zool 252:1–8. https://doi.org/10.1002/jez.1402520102

    Article  Google Scholar 

  5. Wilson RW, Taylor EW (1992) Transbranchial ammonia gradients and acid-base responses to high external ammonia concentration in rainbow trout (Oncorhynchus mykiss) acclimated to different salinities. J Exp Biol 166:95–112. https://doi.org/10.1242/jeb.166.1.95

    Article  CAS  PubMed  Google Scholar 

  6. Randall DJ, Tsui TKN (2002) Ammonia toxicity in fish. Mar Pollut Bull 45:17–23. https://doi.org/10.1016/S0025-326X(02)00227-8

    Article  CAS  PubMed  Google Scholar 

  7. Anderson PM (1995) 3 Urea cycle in fish: molecular and mitochondrial studies. Fish physiology. Elsevier, Amsterdam, pp 57–83. https://doi.org/10.1016/S1546-5098(08)60242-3

    Chapter  Google Scholar 

  8. Kharbuli ZY, Datta S, Biswas K et al (2006) Expression of ornithine–urea cycle enzymes in early life stages of air-breathing walking catfish Clarias batrachus and induction of ureogenesis under hyper-ammonia stress. Comp Biochem Physiol B Biochem Mol Biol 143:44–53. https://doi.org/10.1016/j.cbpb.2005.09.014

    Article  CAS  PubMed  Google Scholar 

  9. Saha N, Ratha BK (1998) Ureogenesis in Indian air-breathing teleosts: adaptation to environmental constraints. Comp Biochem Physiol A Mol Integr Physiol 120:195–208. https://doi.org/10.1016/S1095-6433(98)00026-9

    Article  Google Scholar 

  10. Das P, Sahoo L, Das SP et al (2020) De novo assembly and genome-wide SNP discovery in Rohu Carp, Labeo rohita. Front Genet 11:386. https://doi.org/10.3389/fgene.2020.00386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Chakrapani V, Patra SK, Mohapatra SD et al (2016) Comparative transcriptomic profiling of larvae and post-larvae of Macrobrachium rosenbergii in response to metamorphosis and salinity exposure. Genes Genomics 38:1061–1076. https://doi.org/10.1007/s13258-016-0452-0

    Article  CAS  Google Scholar 

  12. Rasal KD, Sundaray JK (2020) Status of genetic and genomic approaches for delineating biological information and improving aquaculture production of farmed rohu, Labeo rohita (Ham, 1822). Rev Aquac 12:2466–2480. https://doi.org/10.1111/raq.12444

    Article  Google Scholar 

  13. Banerjee B, Koner D, Hasan R et al (2019) Transcriptome analysis reveals novel insights in air-breathing magur catfish (Clarias magur) in response to high environmental ammonia. Gene 703:35–49. https://doi.org/10.1016/j.gene.2019.04.009

    Article  CAS  PubMed  Google Scholar 

  14. Felskie AK, Anderson PM, Wright PA (1998) Expression and activity of carbamoyl phosphate synthetase III and ornithine urea cycle enzymes in various tissues of four fish species. Comp Biochem Physiol B Biochem Mol Biol 119:355–364. https://doi.org/10.1016/S0305-0491(97)00361-1

    Article  Google Scholar 

  15. Banerjee B, Koner D, Bhuyan G, Saha N (2018) Differential expression of multiple glutamine synthetase genes in air-breathing magur catfish, Clarias magur and their induction under hyper-ammonia stress. Gene 671:85–95. https://doi.org/10.1016/j.gene.2018.05.111

    Article  CAS  PubMed  Google Scholar 

  16. Hwang HW, Mendell JT (2006) MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br J Cancer 94:776–780. https://doi.org/10.1038/sj.bjc.6603023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Huang L, Mollet S, Souquere S et al (2011) Mitochondria associate with P-bodies and modulate microRNA-mediated RNA interference. J Biol Chem 286:24219–24230. https://doi.org/10.1074/jbc.M111.240259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126–139. https://doi.org/10.1038/nrm2632

    Article  CAS  PubMed  Google Scholar 

  19. Li J, Ling Y, Huang W et al (2019) Regulatory mechanisms of miR-96 and miR-184 abnormal expressions on otic vesicle development of zebrafish following exposure to β-diketone antibiotics. Chemosphere 214:228–238. https://doi.org/10.1016/j.chemosphere.2018.09.118

    Article  CAS  PubMed  Google Scholar 

  20. Trotta E (2014) On the normalization of the minimum free energy of RNAs by sequence length. PLoS ONE 9:e113380. https://doi.org/10.1371/journal.pone.0113380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kiernan F (1833) XXIX. The anatomy and physiology of the liver. Philos Trans R Soc Lond. https://doi.org/10.1098/rstl.1833.0031

    Article  Google Scholar 

  22. Wei X, Yang Z, Liu H et al (2020) MicroRNA-125a-3p overexpression promotes liver regeneration through targeting proline-rich acidic protein 1. Ann Hepatol 19:99–106. https://doi.org/10.1016/j.aohep.2019.05.010

    Article  CAS  PubMed  Google Scholar 

  23. Klieser E, Mayr C, Kiesslich T et al (2019) The crosstalk of miRNA and oxidative stress in the liver: from physiology to pathology and clinical implications. Int J Mol Sci 20:5266. https://doi.org/10.3390/ijms20215266

    Article  CAS  PubMed Central  Google Scholar 

  24. Murray DD, Suzuki K, Law M et al (2017) Circulating miR-122 and miR-200a as biomarkers for fatal liver disease in ART-treated, HIV-1-infected individuals. Sci Rep 7:1–11. https://doi.org/10.1038/s41598-017-11405-8

    Article  CAS  Google Scholar 

  25. Pan C, Chen H, Wang L et al (2012) Down-regulation of MiR-127 facilitates hepatocyte proliferation during rat liver regeneration. PLoS ONE 7:e39151. https://doi.org/10.1371/journal.pone.0039151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Szabo G, Bala S (2013) MicroRNAs in liver disease. Nat Rev Gastroenterol Hepatol 10:542–552. https://doi.org/10.1038/nrgastro.2013.87

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Brusle J, Anadon GG (1996) The structure and function of fish liver. In: Munshi, Jsd, Dutta (eds) Fish morphology. HM Science Publishers Inc, Boston

    Google Scholar 

  28. Dieter C, Assmann TS, Costa AR et al (2019) MiR-30e-5p and MiR-15a-5p expressions in plasma and urine of type 1 diabetic patients with diabetic kidney disease. Front Genet 10:563. https://doi.org/10.3389/fgene.2019.00563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kurahashi R, Kadomatsu T, Baba M et al (2019) MicroRNA-204-5p: a novel candidate urinary biomarker of Xp11. 2 translocation renal cell carcinoma. Cancer Sci 110:1897–1908. https://doi.org/10.1111/cas.14026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Metzinger-Le Meuth V, Fourdinier O, Charnaux N et al (2019) The expanding roles of microRNAs in kidney pathophysiology. Nephrol Dial Transplant 34:7–15. https://doi.org/10.1093/ndt/gfy140

    Article  CAS  PubMed  Google Scholar 

  31. Shang J, Sun S, Zhang L et al (2020) miR-211 alleviates ischaemia/reperfusion-induced kidney injury by targeting TGFβR2/TGF-β/SMAD3 pathway. Bioengineered 11:547–557. https://doi.org/10.1080/21655979.2020.1765501

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Van Rooij E, Sutherland LB, Liu N et al (2006) A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci USA 103:18255–18260. https://doi.org/10.1073/pnas.0608791103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Marsit CJ, Eddy K, Kelsey KT (2006) MicroRNA responses to cellular stress. Cancer Res 66:10843–10848. https://doi.org/10.1158/0008-5472.CAN-06-1894

    Article  CAS  PubMed  Google Scholar 

  34. Kamei Y, Hatazawa Y, Uchitomi R et al (2020) Regulation of skeletal muscle function by amino acids. Nutrients 12:261. https://doi.org/10.3390/nu12010261

    Article  CAS  PubMed Central  Google Scholar 

  35. Sharma M, Juvvuna PK, Kukreti H, McFarlane C (2014) Mega roles of microRNAs in regulation of skeletal muscle health and disease. Front Physiol 5:239. https://doi.org/10.3389/fphys.2014.00239

    Article  PubMed  PubMed Central  Google Scholar 

  36. Matsuzaka Y, Kishi S, Aoki Y et al (2014) Three novel serum biomarkers, miR-1, miR-133a, and miR-206 for Limb-girdle muscular dystrophy, Facioscapulohumeral muscular dystrophy, and Becker muscular dystrophy. Environ Health Prev Med 19:452–458. https://doi.org/10.1007/s12199-014-0405-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Jia H, Zhao Y, Li T et al (2017) miR-30e is negatively regulated by myostatin in skeletal muscle and is functionally related to fiber-type composition. Acta Biochim Biophys Sin (Shanghai) 49:392–399. https://doi.org/10.1093/abbs/gmx019

    Article  CAS  Google Scholar 

  38. Franceschetti T, Delany AM (2015) miRNAs in bone repair. MicroRNA in regenerative medicine. Elsevier, Amsterdam, pp 653–683. https://doi.org/10.1016/B978-0-12-405544-5.00025-3

    Chapter  Google Scholar 

  39. Felig P (1973) The glucose-alanine cycle. Metabolism 22:179–207. https://doi.org/10.1016/0026-0495(73)90269-2

    Article  CAS  PubMed  Google Scholar 

  40. Nelson DL, Lehninger AL, Cox MM (2008) Lehninger principles of biochemistry. Macmillan, London

    Google Scholar 

  41. Chew SF, Wilson JM, Ip YK, Randall DJ (2005) Nitrogen excretion and defense against ammonia toxicity. Fish Physiol 21:307–395. https://doi.org/10.1016/S1546-5098(05)21008-7

    Article  Google Scholar 

  42. Dimski DS (1994) Ammonia metabolism and the urea cycle: function and clinical implications. J Vet Intern Med 8:73–78. https://doi.org/10.1111/j.1939-1676.1994.tb03201.x

    Article  CAS  PubMed  Google Scholar 

  43. Plaitakis A, Kalef-Ezra E, Kotzamani D et al (2017) The glutamate dehydrogenase pathway and its roles in cell and tissue biology in health and disease. Biology (Basel) 6:11. https://doi.org/10.3390/biology6010011

    Article  CAS  Google Scholar 

  44. Damink SWMO, Deutz NEP, Dejong CHC et al (2002) Interorgan ammonia metabolism in liver failure. Neurochem Int 41:177–188. https://doi.org/10.1016/S0197-0186(02)00040-2

    Article  Google Scholar 

  45. Dolomatov SI, Shekk PV, Zukow W, Kryukova MI (2011) Features of nitrogen metabolism in fishes. Rev Fish Biol Fish 21:733–737. https://doi.org/10.1007/s11160-011-9212-z

    Article  Google Scholar 

  46. His T (2001) The metabolism of nitrogen and amino acids. Biochem Chem React Living Cells 2:1359

    Google Scholar 

  47. Mommsen TP, Walsh PJ (1992) Biochemical and environmental perspectives on nitrogen metabolism in fishes. Experientia 48:583–593. https://doi.org/10.1007/BF01920243

    Article  CAS  Google Scholar 

  48. Ip YK, Chew SF (2018) Air-breathing and excretory nitrogen metabolism in fishes. Acta Histochem 120:680–690. https://doi.org/10.1016/j.acthis.2018.08.013

    Article  CAS  PubMed  Google Scholar 

  49. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12. https://doi.org/10.14806/ej.17.1.200

    Article  Google Scholar 

  50. Kalvari I, Argasinska J, Quinones-Olvera N et al (2018) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 46:D335–D342. https://doi.org/10.1093/nar/gkx1038

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors are thankful to the Director, ICAR-Central Institute of Freshwater Aquaculture (CIFA), Bhubaneswar, India; and North-Eastern Hill University (NEHU), Shillong, India for providing research facility.

Funding

This work was supported by a research project sanctioned to NS and HKB by the Indian Council of Agricultural Research—National Agricultural Science Fund (NASF/ABA-7011/1018-19/240), New Delhi, India.

Author information

Author notes

  1. Kananbala Patra

    Present address: Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India

  2. Kiran D. Rasal

    Present address: ICAR-Central Institute of Fisheries Education, Yari Road, Panch Marg, Versova, Mumbai, Maharashtra, 400061, India

Authors and Affiliations

  1. Fish Genetics & Biotechnology Division, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India

    Kananbala Patra, Rupali Rajaswini, Binita Murmu, Kiran D. Rasal, Lakshman Sahoo & Hirak Kumar Barman

  2. Fish Nutrition & Physiology Division, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India

    Ashis Saha

  3. Biochemical Adaptation Lab., Department of Zoology, North-Eastern Hill University, Shillong, 793022, India

    Nirmalendu Saha & Debaprasad Koner

Authors
  1. Kananbala Patra
    View author publications

    Search author on:PubMed Google Scholar

  2. Rupali Rajaswini
    View author publications

    Search author on:PubMed Google Scholar

  3. Binita Murmu
    View author publications

    Search author on:PubMed Google Scholar

  4. Kiran D. Rasal
    View author publications

    Search author on:PubMed Google Scholar

  5. Lakshman Sahoo
    View author publications

    Search author on:PubMed Google Scholar

  6. Ashis Saha
    View author publications

    Search author on:PubMed Google Scholar

  7. Nirmalendu Saha
    View author publications

    Search author on:PubMed Google Scholar

  8. Debaprasad Koner
    View author publications

    Search author on:PubMed Google Scholar

  9. Hirak Kumar Barman
    View author publications

    Search author on:PubMed Google Scholar

Contributions

HKB, LS, and AS were responsible for project designing and executions. NS and DK conducted NH4Cl treatment experiments and organ collections. KP and KDR participated in sequencing, analyzing, and compiling data. RR and BM conducted qPCR analysis and statistical analysis. All authors contributed to preparing and finalizing the manuscript.

Corresponding author

Correspondence to Hirak Kumar Barman.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

The study was approved by the Institutional Animal Ethics Committee (IAEC) of North-Eastern Hill University, Shillong, India (NEC/IEC/2018/016). The study was part of routine laboratory-based investigations using catfishes without involving any human experimentations.

Consent for publication

Yes.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (TIF 18842 kb)

Fig. 1 WEGO plot. Gene Ontology Distribution of miRNAs (a) in 5′-UTR targeted by miRNA, and (b) in 3′-UTR targeted by miRNA

Supplementary file2 (DOCX 23 kb)

Supplementary file3 (DOCX 16 kb)

Supplementary file4 (DOCX 22 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Patra, K., Rajaswini, R., Murmu, B. et al. Identifying miRNAs in the modulation of gene regulation associated with ammonia toxicity in catfish, Clarias magur (Linnaeus, 1758). Mol Biol Rep 49, 6249–6259 (2022). https://doi.org/10.1007/s11033-022-07424-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-022-07424-y

Keywords