Evaluation of antimicrobial potentiality and type-I polyketide synthase and nonribosomal peptide synthetase biosynthetic genes from some marine actinomycetes
Subject Areas : Microbial BiotechnologyFatemeh shayesteh 1 , Nur Syuhana Binti Zakaria 2 , Gires Usup 3 , Asmat Ahmad 4
1 - Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
2 - School of Bioscience and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia
3 - School of Environmental Science and Natural Resources, Faculty of Science and Technology, University Kebangsaan Malaysia
4 - School of Bioscience and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia
Keywords: Malaysia, Actinomycetes, Antimicrobial Activity, marine bacteria, PKS-I and NRPS genes,
Abstract :
Background and Objectives: Actinomycetes are commonly known as exceptionally prolific source of secondary metabolites with diverse biological activities. The aim of this study was to identify some actinomycete isolates from Malaysia marine environment and evaluate for type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) genes as well as antimicrobial activity. Materials and Methods: Selected isolates were identified based on their morphology and molecular properties. PKS-I and NRPS genes were detected using specific primers and the potential of their antimicrobial activity was investigated by disc diffusion method.Results: The isolates varied morphologically on the basis of colony morphology, spore chain shape, aerial and substrate mycelium formation. Based on 16S rRNA gene sequences analysis, isolates Sdstm3k, Sdtm108 and Sdts4 were highly similar to Streptomyces sp. (95 %), whereas isolates Bvpd17e and SctgJI demonstrated highest similarity to Micrococcus sp. M2-19 (99 %) and Micrococcus leteus (95 %) respectively. While isolate Sdsb2k1a and Sdts46 were unidentified. The detection of PKS-I and NRPS genes revealed that only isolates SctgJI and Sdsb2k1a had both genes. Isolates Streptomyces sp. Sdst3k1 and Streptomyces sp. Sdts4 demonstrated the strongest and broadest spectrum of antimicrobial activity against 10 human pathogens tested. Conclusion: The present study indicated that actinomycetes isolated from marine environment in Malaysia can be a good source of the discovery of new bioactive compounds.
Klugman K. Antimicrobial resistance in developing countries. Part I: recent trends and current
status. Lancet Infecti Dis. 2005; 5 (8): 481-493.
2. O’Neill J. Tackling drug-resistant infections globally: final report and recommandations
[Internet]. London (UK): The review on antimicrobial resistance. Available from https://amr
review.org/sites/default/files/160525_Final%20paper_with%20cover.pdf. 2016.
3. Jakubiec-Krzesniak K, Rajnisz-Mateusiak A, Guspiel A, Ziemska J, Solecka J. Secondary
Metabolites of Actinomycetes and their Antibacterial, Antifungal and Antiviral Properties. Pol J
Microbiol. 2018; 67 (3): 259-272.
4. Berdy J. Bioactive microbial metabolites. J Antibiot 2005; 58:1-26.
5. Cane DE, Walsh CT, Khosla C. Harnessing the biosynthetic code: combinations, permutations,
and mutation. Science. 1998; 282 (5386): 63-68.
6. Cane DE, Walsh CT. The parallel and convergent universes of polyketide synthetases and
nonribosomal peptide synthetases. Chem Biol. 1999; 6 (12): 319-325.
7. Crosa JH, Walsh CT. Genetics and assembly line enzymology of siderophore biosynthesis in
bacteria. Microbiol Mol Biol R. 2002 66 (2): 223-249.
8. Weissman KJ. Introduction to polyketide biosynthesis. In: Hopwood DA, editor. Complex
Enzymes in Microbial Natural Product Biosynthesis, Part B: Polyketides, Aminocoumarins and.
Carbohydrates Methods in Enzymology. Academic Press; 2009. pp. 3-16.
9. Munro MH, Blunt JW, Dumdei EJ, Hickford SJH, Lill RE, Li S, Battershill CN, Duckworth
AR. The discovery and development of marine compounds with pharmaceutical potential. J
Biotechnol. 1999; 70 (1-3): 15-25.
10. Blunt JW, Copp BR, Hu WP, Munro MH, Northcote PT, Prinsep MR. Marine natural
products. Nat Prod Rep. 2008; 25 (1): 35-94.
11. Zainal Abidin ZA, Abdul Malek N, Zainuddin Z, Chowdhury AJK. Selective isolation and
antagonistic activity of actinomycetes from mangrove forest of Pahang, Malaysia. Front Life Sci.
2016; 9 (1): 24-31.
12. Faja O, Sharad AA, Younis KM, Usup G, Ahmad A. Isolation, screening and antibiotic
profiling of marine Actinomycetes extracts from the coastal of Peninsular Malaysia. Int J
Chemtech Res. 2017; 10 (3): 212-224.
13. Schneemann I, Kajahn I, Ohlendorf B, Zinecker H, Erhard A, Nagel K, Wiese J, Imhoff JF.
Mayamycin, a Cytotoxic Polyketide from a Streptomyces Strain Isolated from the Marine Sponge
Halichondria panacea. J Nat Prod. 2010; 73 (7):1309-1312.
14. Kennedy J, Baker PW, Piper C, Cotter PD, Walsh M, Mooij MJ, Bourke MB, Rea
MC, O'Connor PM, Ross RP, Hill C, O'Gara F, Marchesi JR, Dobson ADW. Isolation and
analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans
collected from Irish waters. Mar Biotech. 2008; 11 (3): 384-396.
15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst
Evol Microbiol. 1966; 16 (3): 313-340.
16. Piterina AV, Barlett J, Pembroke JT. Molecular analysis of bacterial community DNA in
sludge undergoing autothermal thermophilic aerobic digestion (ATAD): pitfalls and improved
methodology to enhance diversity recovery. Divers. 2010; 2 (4): 505-526.
17. Thompson JD, Higgins DG, Gibson TJ. Clustal W: Improving the sensitivity of progressive
multiple sequence alignment through sequence weighting, position-specific gap penalties and
weight matrix choice. Nucleic Acids Res. 1994; 22 (22): 4673-4680.
18. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary
genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007; 24 (8): 1596-1599.
19. Ayuso-Sacido A, Genilloud O. New PCR primers for the screening of NRPS and
PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene
sequences in major taxonomic groups. Microb Ecol. 2005; 49 (1): 10-24.
20. Hamadan J, Mikolajcik EM. Acidolin: an antibiotic produced by Lactobacillus acidophilus. J
Antibiot. 1974; 27 (8): 631-636.
21. Apella MC, Gonzalez SN, Nader de Macias ME, Romero N, Oliver G. In vitro studies on the
inhibition of the growth of Shigella sonnei by Lactobacillus casei and Lactobacillus acidophilus.
J Appl Bacteriol. 1992; 73 (6): 480-483.
22. Zhao XQ, Jiao WC, Jiang B, Yuan WJ, Yang TH, Hao SH. Screening
and identification of actinobacteria from marine sediments: investigation of potential
producers for antimicrobial agents and type I polyketides. World J Microbiol Biotechnol. 2009;
25 (5): 859-866.
23. Chen HH, Zhao GZ, Park DJ, Zhang YQ, Xu LH, Lee JC, Kim CJ, Li WJ. Micrococcus.
endophyticus sp. nov., isolated from surface-sterilized Aquilaria sinensis roots. Int J Syst Evol
Microbiol. 2009; 59: 1070-1075.
24. Stackebrandt E, Goebel BM. Taxonomic Note: A place for DNA-DNA reassociation and 16S
rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol.
1994; 44 (4): 846-849.
25. Zhu H, Guo J, Yao Q, Yang S, Deng M, et al. Streptomyces vietnamensis sp. nov., a
streptomycete with violet–blue diffusible pigment isolated from soil in Vietnam. Int J Syst Evol
Microbiol. 2007; 57: 1770-1774.
26. Okami Y, Tazaki T, Katumata S, Honda K, Suzuki M, et al. Studies on Streptomyces
kanamyceticus, producer of kanamycin. J Antibiot. 1959; 12: 252-256.
27. Petkovic H, Cullum J, Hranueli D, Hunter IS, Peric Concha N, Pigac J, Thamchaipenet A,
Vujaklija D, Long PF. Genetics of Streptomyces rimosus, the oxytetracycline producer. Microbiol
Mol Biol Rev. 2006; 70 (3): 704-728.
28. Ross A, Schugerl K. Tetracycline production by Streptomyces aureofaciens: the time lag of
production. Appl Microbiol Biotechnol. 2005; 29 (2-3): 174-180.
29. Konoshenko GI, Avraleva IV, Anisova LN, Orlova TI. Biologically active substances by a
number of strains of the actinomycin C producer Streptomyces chyrsomallus. Antibiot Khimioter.
1994; 39 (2-3): 22-25.
30. Fischbach MA, Walsh CT. Antibiotics for emerging pathogens. Science. 2009; 325 (5944):
1089-1093.
31. Xin Y, Kanagasabhapathy M, Janussen D, Xue S, Zhang W. Phylogenetic diversity of
Gram- positive bacteria cultured from Antarctic deep-sea sponges. Polar Biol. 2011; 34 (10):
1501-1512.
32. Zhou K, Zhang X, Zhang F, Li Z. Phylogenetically diverse cultivable fungal community and
polyketide synthase (PKS), non-ribosomal peptide synthase (NRPS) genes associated with the
South China Sea sponges. Microb Ecol. 2011; 62 (3): 644-654.
33. Zhao K, Penttinen P, Guan T, Xiao J, Chen Q, Xu J, Lindstrom K, Zhang L, Zhang X, Strobel
GA. The diversity and anti-microbial activity of endophytic actinomycetes isolated from
medicinal plants in Panxi plateau, China. Curr Microbiol. 2011; 62 (1): 182-190.
34. Bredholt H, Galatenko OA, Engelhardt K, Tjaervik E, Terekhova LP, Zotchev SB. Rare
actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway:
isolation, diversity and biological activity. Environ Microbiol. 2007; 9 (11): 2756-2764.
8
_||_
Klugman K. Antimicrobial resistance in developing countries. Part I: recent trends and current
status. Lancet Infecti Dis. 2005; 5 (8): 481-493.
2. O’Neill J. Tackling drug-resistant infections globally: final report and recommandations
[Internet]. London (UK): The review on antimicrobial resistance. Available from https://amr
review.org/sites/default/files/160525_Final%20paper_with%20cover.pdf. 2016.
3. Jakubiec-Krzesniak K, Rajnisz-Mateusiak A, Guspiel A, Ziemska J, Solecka J. Secondary
Metabolites of Actinomycetes and their Antibacterial, Antifungal and Antiviral Properties. Pol J
Microbiol. 2018; 67 (3): 259-272.
4. Berdy J. Bioactive microbial metabolites. J Antibiot 2005; 58:1-26.
5. Cane DE, Walsh CT, Khosla C. Harnessing the biosynthetic code: combinations, permutations,
and mutation. Science. 1998; 282 (5386): 63-68.
6. Cane DE, Walsh CT. The parallel and convergent universes of polyketide synthetases and
nonribosomal peptide synthetases. Chem Biol. 1999; 6 (12): 319-325.
7. Crosa JH, Walsh CT. Genetics and assembly line enzymology of siderophore biosynthesis in
bacteria. Microbiol Mol Biol R. 2002 66 (2): 223-249.
8. Weissman KJ. Introduction to polyketide biosynthesis. In: Hopwood DA, editor. Complex
Enzymes in Microbial Natural Product Biosynthesis, Part B: Polyketides, Aminocoumarins and.
Carbohydrates Methods in Enzymology. Academic Press; 2009. pp. 3-16.
9. Munro MH, Blunt JW, Dumdei EJ, Hickford SJH, Lill RE, Li S, Battershill CN, Duckworth
AR. The discovery and development of marine compounds with pharmaceutical potential. J
Biotechnol. 1999; 70 (1-3): 15-25.
10. Blunt JW, Copp BR, Hu WP, Munro MH, Northcote PT, Prinsep MR. Marine natural
products. Nat Prod Rep. 2008; 25 (1): 35-94.
11. Zainal Abidin ZA, Abdul Malek N, Zainuddin Z, Chowdhury AJK. Selective isolation and
antagonistic activity of actinomycetes from mangrove forest of Pahang, Malaysia. Front Life Sci.
2016; 9 (1): 24-31.
12. Faja O, Sharad AA, Younis KM, Usup G, Ahmad A. Isolation, screening and antibiotic
profiling of marine Actinomycetes extracts from the coastal of Peninsular Malaysia. Int J
Chemtech Res. 2017; 10 (3): 212-224.
13. Schneemann I, Kajahn I, Ohlendorf B, Zinecker H, Erhard A, Nagel K, Wiese J, Imhoff JF.
Mayamycin, a Cytotoxic Polyketide from a Streptomyces Strain Isolated from the Marine Sponge
Halichondria panacea. J Nat Prod. 2010; 73 (7):1309-1312.
14. Kennedy J, Baker PW, Piper C, Cotter PD, Walsh M, Mooij MJ, Bourke MB, Rea
MC, O'Connor PM, Ross RP, Hill C, O'Gara F, Marchesi JR, Dobson ADW. Isolation and
analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans
collected from Irish waters. Mar Biotech. 2008; 11 (3): 384-396.
15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst
Evol Microbiol. 1966; 16 (3): 313-340.
16. Piterina AV, Barlett J, Pembroke JT. Molecular analysis of bacterial community DNA in
sludge undergoing autothermal thermophilic aerobic digestion (ATAD): pitfalls and improved
methodology to enhance diversity recovery. Divers. 2010; 2 (4): 505-526.
17. Thompson JD, Higgins DG, Gibson TJ. Clustal W: Improving the sensitivity of progressive
multiple sequence alignment through sequence weighting, position-specific gap penalties and
weight matrix choice. Nucleic Acids Res. 1994; 22 (22): 4673-4680.
18. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary
genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007; 24 (8): 1596-1599.
19. Ayuso-Sacido A, Genilloud O. New PCR primers for the screening of NRPS and
PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene
sequences in major taxonomic groups. Microb Ecol. 2005; 49 (1): 10-24.
20. Hamadan J, Mikolajcik EM. Acidolin: an antibiotic produced by Lactobacillus acidophilus. J
Antibiot. 1974; 27 (8): 631-636.
21. Apella MC, Gonzalez SN, Nader de Macias ME, Romero N, Oliver G. In vitro studies on the
inhibition of the growth of Shigella sonnei by Lactobacillus casei and Lactobacillus acidophilus.
J Appl Bacteriol. 1992; 73 (6): 480-483.
22. Zhao XQ, Jiao WC, Jiang B, Yuan WJ, Yang TH, Hao SH. Screening
and identification of actinobacteria from marine sediments: investigation of potential
producers for antimicrobial agents and type I polyketides. World J Microbiol Biotechnol. 2009;
25 (5): 859-866.
23. Chen HH, Zhao GZ, Park DJ, Zhang YQ, Xu LH, Lee JC, Kim CJ, Li WJ. Micrococcus.
endophyticus sp. nov., isolated from surface-sterilized Aquilaria sinensis roots. Int J Syst Evol
Microbiol. 2009; 59: 1070-1075.
24. Stackebrandt E, Goebel BM. Taxonomic Note: A place for DNA-DNA reassociation and 16S
rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol.
1994; 44 (4): 846-849.
25. Zhu H, Guo J, Yao Q, Yang S, Deng M, et al. Streptomyces vietnamensis sp. nov., a
streptomycete with violet–blue diffusible pigment isolated from soil in Vietnam. Int J Syst Evol
Microbiol. 2007; 57: 1770-1774.
26. Okami Y, Tazaki T, Katumata S, Honda K, Suzuki M, et al. Studies on Streptomyces
kanamyceticus, producer of kanamycin. J Antibiot. 1959; 12: 252-256.
27. Petkovic H, Cullum J, Hranueli D, Hunter IS, Peric Concha N, Pigac J, Thamchaipenet A,
Vujaklija D, Long PF. Genetics of Streptomyces rimosus, the oxytetracycline producer. Microbiol
Mol Biol Rev. 2006; 70 (3): 704-728.
28. Ross A, Schugerl K. Tetracycline production by Streptomyces aureofaciens: the time lag of
production. Appl Microbiol Biotechnol. 2005; 29 (2-3): 174-180.
29. Konoshenko GI, Avraleva IV, Anisova LN, Orlova TI. Biologically active substances by a
number of strains of the actinomycin C producer Streptomyces chyrsomallus. Antibiot Khimioter.
1994; 39 (2-3): 22-25.
30. Fischbach MA, Walsh CT. Antibiotics for emerging pathogens. Science. 2009; 325 (5944):
1089-1093.
31. Xin Y, Kanagasabhapathy M, Janussen D, Xue S, Zhang W. Phylogenetic diversity of
Gram- positive bacteria cultured from Antarctic deep-sea sponges. Polar Biol. 2011; 34 (10):
1501-1512.
32. Zhou K, Zhang X, Zhang F, Li Z. Phylogenetically diverse cultivable fungal community and
polyketide synthase (PKS), non-ribosomal peptide synthase (NRPS) genes associated with the
South China Sea sponges. Microb Ecol. 2011; 62 (3): 644-654.
33. Zhao K, Penttinen P, Guan T, Xiao J, Chen Q, Xu J, Lindstrom K, Zhang L, Zhang X, Strobel
GA. The diversity and anti-microbial activity of endophytic actinomycetes isolated from
medicinal plants in Panxi plateau, China. Curr Microbiol. 2011; 62 (1): 182-190.
34. Bredholt H, Galatenko OA, Engelhardt K, Tjaervik E, Terekhova LP, Zotchev SB. Rare
actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway:
isolation, diversity and biological activity. Environ Microbiol. 2007; 9 (11): 2756-2764.
8
