Skip to main content
SpringerLink
Log in

Comparative genome-wide analysis of novel Streptomyces isolates RC1831 and RC1832: deciphering the role of functional carbohydrate (CAZy) active genes including chitinase for production of chitosan

  • Original Article
  • Published:
3 Biotech Aims and scope Submit manuscript

Abstract

This work compares two bacterial isolates Streptomyces barkulensis RC1831 and Streptomyces chitinovorans RC1832 isolated from Chilika Lake sediments in Odisha, India, using whole-genome sequence analysis. According to the results of the genome analysis, the RC1831 genome has a chromosome with 6,383,258 bp (72.9% GC) and 6145 coding sequences and 66 RNA, while the RC1832 genome has a chromosome with 6,055,792 bp (73.1% GC) and 5824 coding sequences and 63 RNA. Further analysis of the carbohydrate active enzyme (CAZyme) revealed that RC1831 contains 78 glycoside hydrolase family genes, whereas RC1832 includes 50 glycoside hydrolases that have the potential to regulate the chitin-degrading enzymes. KAAS (KEGG Automatic Annotation Server) and AntiSMASH online tool V3.0.5 were used to identify a biosynthetic gene cluster in the isolated strain's genome. The detailed comparative analysis of the genes between the strains will help to gain better insight of chitin and other carbohydrate polymer degradation and secondary metabolite production in both the strains as well as the evolutionary relationship and possibilities of industrial application of these strains. Chitosan production might be explained by genes for the chitin breakdown pathway found in the genome sequence, but genes for later-stage conversion were not found. One significant biomolecule with a wide range of industrial uses is chitosan. Therefore, using these microbes to produce chitosan offers a viable waste disposal solution.

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

Access this article

Log in via an institution

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
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Data Availability

The data about the strain RC1831 is publicly available at https://doi.org/10.1099/ijs.0.056614-0 and for RC1832 it is https://doi.org/10.1099/ijsem.0.001176.

References

  • Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16–W21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:1–15

    Article  Google Scholar 

  • Bai Y, Eijsink VGH, Kielak AM, van Veen JA, de Boer W (2016) Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 18:38–49

    Article  CAS  PubMed  Google Scholar 

  • Behera T, Himadri AM, Kumari K, Gouda SK, Das S, Ray L (2022) Exploration of genomic and functional features of chitinolytic bacterium Streptomyces chilikensis RC1830, isolated from Chilika Lake India. 3 Biotech 12:120

    Article  Google Scholar 

  • Bibb MJ (2005) Regulation of secondary metabolism in Streptomycetes. Curr Opin Microbiol 8:208–215

    Article  CAS  PubMed  Google Scholar 

  • Chen J, Liu Y, Diep P, Mahadevan R (2021) Genomic analysis of a newly isolated Acidithiobacillus ferridurans JAGS strain reveals its adaptation to acid mine drainage’. Minerals 11:74

    Article  CAS  Google Scholar 

  • Dilip CV, Mulaje SS, Mohalkar RY (2013) A review on actinomycetes and their biotechnological application. Int J Pharm Sci Res 4:1730

    Google Scholar 

  • Gomez-Escribano JP, Alt S, Bibb MJ (2016) Next generation sequencing of actinobacteria for the discovery of novel natural products. Mar Drugs 14:78

    Article  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354–D357

    Article  CAS  PubMed  Google Scholar 

  • Khedher B, Mariem KG, Rolain J-M, Ruimy R, Croce O (2022) Application and challenge of 3rd generation sequencing for clinical bacterial studies. Int J Mol Sci 23:1395

    Article  PubMed  PubMed Central  Google Scholar 

  • Kieser, Tobias, Mervyn J Bibb, Mark J Buttner, Keith F Chater, and David A Hopwood. (2000). Practical Streptomyces genetics, John Innes Foundation Norwich, Norwich, England

  • Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B (2014) ’The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495

    Article  CAS  PubMed  Google Scholar 

  • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ray L, Mishra SR, Panda AN, Rastogi G, Pattanaik AK, Adhya TK, Suar M, Raina V (2014) Streptomyces barkulensis sp. nov., isolated from an estuarine lake. Int J Syst Evol Microbiol 64:1365–1372

    Article  CAS  PubMed  Google Scholar 

  • Ray L, Mishra SR, Panda AN, Das S, Rastogi G, Pattanaik AK, Adhya TK, Suar M, Raina V (2016) Streptomyces chitinivorans sp. nov., a chitinolytic strain isolated from estuarine lake sediment. Int J Syst Evol Microbiol 66:3241–3248

    Article  CAS  PubMed  Google Scholar 

  • Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu L, Zhaobin Dong Lu, Fang YL, Wei Z, Guo H, Zhang G, Gu YQ, Coleman-Derr D, Xia Q (2019) OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 47:W52–W58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India

    Suchismita Nivedita, Subhransu Sekhar Behera, Himadri Tanaya Behera, Sudhansu Kumar Gouda, Ananta Narayana Panda & Lopamudra Ray

Authors
  1. Suchismita Nivedita
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Subhransu Sekhar Behera
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Himadri Tanaya Behera
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sudhansu Kumar Gouda
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ananta Narayana Panda
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Lopamudra Ray
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

LR, HTB, and SN: conceptualization, methodology. SN, LR, HTB, SSB, SKG: data curation, writing, original draft preparation, visualization, investigation. SN, SSB, LR: writing. LR: reviewing and editing.

Corresponding author

Correspondence to Lopamudra Ray.

Ethics declarations

Conflict of interests

The research was carried out without any financial or commercial ties that could be construed as having a conflict of interest among the authors.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 925 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Nivedita, S., Behera, S.S., Behera, H.T. et al. Comparative genome-wide analysis of novel Streptomyces isolates RC1831 and RC1832: deciphering the role of functional carbohydrate (CAZy) active genes including chitinase for production of chitosan. 3 Biotech 14, 114 (2024). https://doi.org/10.1007/s13205-024-03936-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s13205-024-03936-5

Keywords

Search

Navigation