Fiziol. rast. genet. 2023, vol. 55, no. 6, 519-527, doi:

New strains of streptomycetes in which genomes clusters of genes for agarose catabolism were revealed

Polishchuk L.V.

  • D.K. Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine 154 Akademika Zabolotnogo St., Kyiv, 03143, Ukraine

Agarose is a polysaccharide found in the cell walls of red algae. Most of the detected agarolytic microorganisms are gram-negative bacteria from several taxonomically diverse groups, but a few gram-positive ones were also detected, for example — Bacillus sp. MK03, Streptomyces coelicolor A3(2). S. coelicolor A3(2) destroys agarose with 3 different hydrolases: two extracellular b-agarases (DagA and DagB), and an intracellular a-neoagarobiose hydrolase ScJC117. The aim of the work was to identify streptomycetes strains whose genomes contain sequences similar to genes encoding proteins of the agarolytic system of S. coelicolor A3(2). The objects of study were nucleotide sequences of streptomycetes deposited into databases of The National Center for Biotechnology Information (USA). Analysis of the primary structures of streptomycete DNAs was done using BLASTN programs on the NCBI server. BLASTN-analysis of information on databases NCBI revealed presence of five such strains (Streptomyces sp. SID7813, Streptomyces sp. NRRL B-16638, Streptomyces sp. ME02-6977A, Streptomyces sp. SM1, Streptomyces sp. S4.7). Their sequences contain fragments similar to S. coelicolor A3(2) genes that code agarolytic enzymes and a special NA2-transport system of neoagarobiose. Based on the similarity of the sequences of their «housekeeping genes» (rpoB, rrnA, gyrB, atpB, trpB, recA), conclusions were made about the closely related relationships of 4 strains (Streptomyces sp. SID7813, Streptomyces sp. NRRL B-16638, Streptomyces sp. ME02-6977A, Streptomyces sp. SM1) and S. coelicolor A3(2). The strain Streptomyces sp. S4.7 is related to the strains of other species (S. niveus).

Keywords: Streptomyces sp., agarase, hydrolysis, transport system, genetic affinity

Fiziol. rast. genet.
2023, vol. 55, no. 6, 519-527

Full text and supplemented materials

Free full text: PDF  


1. Fu, X.T. & Kim, S.M. (2010). Agarase: review of major sources, categories, purification method, enzyme characteristics and applications. Mar. Drugs, 8, No. 1, pp. 200-218.

2. Wang, J., Jiang, X., Mou, H. & Guan, H. (2004). Anti-oxidation of agar oligosaccharides produced by agarase from a marine bacterium. J. Appl. Phycol., 16, No. 333-340.

3. Yamaura, I.T., Matsumoto, M., Funatsu, H. & Shigeiri, S.T. (1991). Purification and some properties of agarase from Pseudomonas sp. PT-5. Agric. Biol. Chem., 55, No. 10, 2531-2536.

4. Zang, W. &. Li, S. (2007) Cloning, characterization and molecular application of a beta-agarase gene from Vibrio sp. strain V134. Appl. Environ. Microbiol., 73, No. 9, pp. 2825-2831.

5. ServHn-Gonz«lez, L., Jensen, M.R., White, J. & Bibb, M. (1994). Transcriptional regulation of the four promoters of the agarase gene (dagA) of Streptomyces coelicolor A3(2). Microbiology (Reading), 140, No. 10, pp. 2555-2565.

6. Buttner, M.J., Fearnley, I.M. & Bibb, M.J. (1987). The agarase gene (dagA) of Streptomyces coelicolor A3(2): nucleotide sequence and transcriptional analysis. Mol. Gen. Genet., 209, No. 1, pp. 101-109.

7. Parro, V. & Mellado, R.P. (1993). Heterologous recognition in vivo of promoter sequences from the Streptomyces coelicolor dagA gene. FEMS Microbiol. Let., 106, No. 3, pp. 347-356.

8. Temuujin, U., Chi, W-J., Lee, S-U., Chang, U-K. & Hong, S-K. (2011). Overexpression and biochemical characterization of DagA from Streptomyces coelicolor A3(2): an endo-type b-agarase producing neoagarotetraose and neoagarohexaose. Appl. Microbiol. Biotechnol., 92, No. 4, pp. 749-759.

9. Suzuki, H., Sawai, Y., Suzuki, T. & Kawai, K. (2002). Purification and characterization of an extracellular alpha-neoagarooligosaccharide hydrolase from Bacillus sp. MK03. J. Bio­sci. Bioeng., 93, No. 5, pp. 456-463.

10. Grubbs K.J., Bleich, R.M. & Santa Maria, K.C. (2017). Large-scale bioinformatics analysis of Bacillus genomes uncovers conserved roles of natural products in bacterial physiology. mSystems, 2, No. 6, e00040-17.

11. Chi, W.J., Chang, Y.K. & Hong, S.K. (2012). Agar degradation by microorganisms and agar-degrading enzymes. Appl. Microbiol. Biotechnol., 94, No. 4, pp. 917-930.

12. Jiang, C., Liu, Z., Cheng, D. & Mao, X. (2020). Agarose degradation for utilization: Enzymes, pathways, metabolic engineering methods and products. Biotechnol. Adv., 45, 107641.

13. Stanier, R.Y. (1942). Agar decomposing strains of the Actinomyces coelicolor species group. J. Bacteriol., 44. No. 5, pp. 555-570.

14. Erikson, D. (1948). Differentiation of the vegetative and sporogenous phases of the actinomycetes. 3. Variation in the Actinomyces coelicolor species-group. J. Gen. Microbiol., 2, No. 3, pp. 252-259.

15. Vandamme, P., Pot, B. &. Gillis, M. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev., 60, No. 2, pp., 407-438.

16. Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P.A.D., K¬mpfer, P., Maiden, M.C.J., Nesme, X., RossellЩ-Mora, R., Swings, J., Trтpe, H.G., Vauterin, L., Ward, A.C. & Whitman, W.B. (2002). Report of the Ad Hoc Committee for the reevaluation of the species definition in bacteriology. Int. J. System. Evol. Microbiol., 52, No. 3, pp. 1043-1047.

17. Goodfellow, M., Kumar, Y., Labeda, D.P. & Sembiring, L. (2007). The Streptomyces violaceusniger clade: a home for streptomycetes with rugose ornamented spores. Antonie Van Leeuwenhoek, 92, No. 2. pp. 173-199.