Genome based analysis for the bioactive potential of streptomyces spectabilis strain yim 121038

VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE FACULTY OF BIOTECHNOLOGY  GRADUATION THESIS TITLE: “GENOME-BASED ANALYSIS FOR THE BIOACTIVE POTENTIAL OF STREPTOMYCES SPECTABILIS STRAIN YIM 121038” Hanoi, 3/2021 VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE FACULTY OF BIOTECHNOLOGY  GRADUATION THESIS TITLE: “GENOME-BASED ANALYSIS FOR THE BIOACTIVE POTENTIAL OF STREPTOMYCES SPECTABILIS STRAIN YIM 121038” Student’s name : Vu Thi Thuy Tien ID : 610780 Class : K61-CNSHE Supervisors : Dinh Truong Son, Ph.D Hanoi, 3/ 2021 COMMITMENT I assure that the whole research process was performed by myself under the scientific guidance of Ph.D Dinh Truong Son I assure that all research contents, results and information in my thesis is completely honest and unpublished Hanoi, February 24th 2021 Student Vu Thi Thuy Tien i ACKNOWLEDGEMENTS First and foremost, I would like to express deeply my gratitude to my supervisors Ph.D Dinh Truong Son who have supported me complete my thesis with their patience and knowledge Moreover, their guidance helped me in the period of writing of this thesis I would like to thank all my teachers in Faculty of Biotechnology, especially Department of Plant Biotechnology They provided useful scientific knowledge as well as technique for me This is one of the most important things to help me to successful my thesis I would like to thank Department of Plant Biotechnology where supported financial for my thesis I thank my lab-mate for her meaning contribution I will appreciate the time when we were working together Last but not least, I would specifically like to thank my family, especially my parents who have loved me, cared for me, trusted me and given the best study condition Hanoi, February 24th 2021 Student Vu Thi Thuy Tien ii CONTENTS COMMITMENT i ACKNOWLEDGEMENTS ii CONTENTS iii ABBREVIATION v LIST OF TABLES vi LIST OF FIGURES .vii ABSTRACT ix PART I INTRODUCTION 1.1 Preface 1.2 Purposes and requirements 1.2.1 Purposes 1.2.2 Requirements PART II LITERATURE OVERVIEW 2.1 Introduction of Streptomyces 2.1.1 Taxonomy 2.1.2 Characteristics of Streptomyces 2.1.3 Secondary Metabolites of Streptomyces 2.1.4 Antibiotics produced by Streptomyces 2.2 Genome mining of Streptomyces 11 2.2.1 Genome mining 11 2.2.2 Role of Bioinformatics in Natural Product Discovery by Genome Mining 12 2.2.3 Genome mining in Streptomyces 12 PART III MATERIALS AND METHODS 15 3.1 Materials 15 3.2 Research equipment 15 3.3 Study contents and study methods 15 3.3.1 Study contents 15 3.3.2 Study methods 16 PART IV RESULTS AND DISCUSSION 22 4.1 General genomic features Streptomyces sp YIM 121038 22 iii 4.2 Phylogeny of Streptomyces sp YIM 121038 29 4.3 Biosynthetic gene clusters for secondary metabolites of Streptomyces sp YIM 121038 30 4.4 Genome annotation, functional analysis of Streptomyces sp YIM 121038 37 4.5 Pathway of secondary metabolite biosynthesis of Zorbamycin in Streptomyces sp YIM 121038 (Antitumor potential of strain YIM 121038) 50 PART V CONCLUSION AND SUGGESTION 56 Conclusion 56 Suggestion 56 REFERENCES 57 APPENDIX 65 iv ABBREVIATION antiSMASH Antibiotics & Secondary Metabolite Analysis Shell ARTS Antibiotics Resistant Target Seeker BGCs Biosynthetic gene clusters CAZyme Cacbohydrate active enzyme COG Clusters of Orthologous Groups GBDP Genome BLAST Distance Phylogeny GGDC Genome-to-Genome Distance Calculator GO Gene Ontology KEGG Kyoto Encyclopedia of Genes and Genomes NRPSs Non-ribosomal peptide synthetases PKSs Polyketide synthases smBGCs Biosynthetic gene clusters of secondary metabolites TYGS The Type (Strain) Genome ZBM Zorbamycin v LIST OF TABLES Table 2.1 List of some antibiotics produced by Streptomyces sp 10 Table 2.2 Current genome mining studies on Streptomyces species 13 Table 3.1 List of 15 related strains of Streptomyces 17 Table 4.1 Genome features of Streptomyces sp YIM 121038 provided by NCBI, EZBioCloud 22 Table 4.2 Number of genes of COG functional category of Streptomyces sp YIM 121038 26 Table 4.3 List of Streptomyces sp YIM 121038 and other species 29 Table 4.4 List of putative secondary metabolite producing biosynthetic clusters as predicted by antiSMASH version 5.2.0 33 Table 4.5 Species distribution of Streptomyces sp YIM 121038 39 Table 4.6 Top- hit species distribution of Streptomyces sp YIM 121038 41 Table 4.7 Gene ontology categories after Blast2GO analysis 45 Table 4.8 Deduced functions of gens in the ZBM biosynthetic gene cluster and comparison genes in the ZBM biosynthetic gene cluster of S Flavoviridis to Streptomyces sp YIM 121038 55 vi LIST OF FIGURES Figure 3.1 General schematic diagram 15 Figure 3.2 Schematic representation of the Blast2GO application 20 Figure 4.1 Features of the genome of Streptomyces sp YIM 121038 provided by EZBioCloud 23 Figure 4.2 Features of the genome of Streptomyces sp YIM 121038 provided by ARTS 23 Figure 4.3 Features of the genome of Streptomyces sp YIM 121038 provided by GeneMark 24 Figure 4.4 Circular map of the Streptomyces sp YIM 121038 25 Figure 4.5 Color codes for gene functions presented in Table 4.2 28 Figure 4.6 Relationship of Streptomyces sp YIM 121038 with 15 related Streptomyces species 30 Figure 4.7 Secondary metabolite producing biosynthetic clusters as predicted by antiSMASH version 5.2.0 31 Figure 4.8 antiSMASH biosynthetic gene clusters and their predicted core structure for a Lanthipeptide b NRPS c T1PKS-NRPS d T3PKS-NRPS e NRPSbacteriocin clusters from Streptomyces sp YIM 121038 32 Figure 4.9 Blast2GO functional annotation results overview of Streptomyces sp YIM 121038 37 Figure 4.10 Number of sequences with length of Streptomyces sp YIM 121038 38 Figure 4.11 Species distribution chart of Streptomyces sp YIM 121038 after blastx to NCBI nr 38 Figure 4.12 Top- Hit species distribution chart of Streptomyces sp YIM 121038 after blastx to NCBI nr 40 Figure 4.13 E-value distribution for sequences of Streptomyces sp YIM 121038 42 Figure 4.14 InterProScan Results Chart 42 Figure 4.15 Mapping database sourses of 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table: Supplemental table Number of sequences with length of Streptomyces sp YIM 121038 Length No.Seqs Length (bp) No.Seqs Length (bp) No.Seqs Length (bp) No.Seqs (bp) 90 1010 31 1915 2925 95 1015 19 1920 2935 100 1020 39 1925 2940 100 1025 30 1930 2945 105 1030 16 1935 2950 110 11 1035 29 1940 2955 115 1040 29 1945 2960 120 1045 11 1950 2965 125 1050 27 1955 2970 130 1055 33 1960 2975 135 1060 14 1965 2990 140 1065 22 1970 2995 145 1070 27 1975 3000 150 13 1075 13 1980 3005 155 14 1080 26 1985 3010 160 1085 28 1990 3015 165 20 1090 14 1995 3045 170 21 1095 24 2000 3050 175 1100 28 2005 3060 180 26 1105 12 2010 3065 185 20 1110 22 2015 3075 190 1115 26 2020 3080 195 39 1120 13 2025 3085 200 37 1125 28 2030 3090 65 205 14 1130 24 2035 3095 210 26 1135 13 2040 3100 215 1140 27 2045 3125 220 15 1145 32 2050 3140 225 30 1150 12 2055 3150 230 37 1155 32 2060 3165 235 17 1160 25 2070 3180 240 36 1165 19 2075 3185 245 35 1170 22 2080 3200 250 1175 30 2085 3210 255 32 1180 15 2090 3215 260 22 1185 30 2095 3220 265 17 1190 23 2100 3225 270 24 1195 16 2105 3230 275 29 1200 28 2110 3245 280 17 1205 29 2115 3250 285 22 1210 17 2120 3275 290 17 1215 26 2125 3280 295 14 1220 37 2130 3285 300 23 1225 18 2135 3290 305 24 1230 37 2140 3300 310 10 1235 22 2145 3305 315 26 1240 12 2150 3315 320 27 1245 27 2155 3325 325 13 1250 30 2160 3330 330 30 1255 12 2165 3335 335 20 1260 28 2170 3340 340 1265 28 2175 3345 345 31 1270 14 2180 3350 66 350 33 1275 29 2185 3355 355 20 1280 20 2190 3360 360 29 1285 2195 3390 365 30 1290 21 2200 3420 370 14 1295 26 2205 3460 375 34 1300 13 2210 3465 380 27 1305 21 2215 3485 385 18 1310 19 2220 3500 390 33 1320 22 2225 3525 395 35 1325 18 2230 3530 400 16 1330 16 2235 3535 405 33 1335 26 2240 3540 410 39 1340 23 2250 3565 415 17 1345 2260 3570 420 45 1350 29 2265 3575 425 48 1355 23 2270 3585 430 18 1360 2275 3600 435 41 1365 16 2280 3650 440 46 1370 21 2285 3680 445 19 1375 2290 3690 450 44 1380 22 2300 3710 455 35 1385 18 2305 3720 460 31 1390 11 2310 3725 470 36 1395 18 2315 3735 475 16 1400 15 2320 3750 480 24 1405 11 2330 3780 485 40 1410 17 2340 3790 490 17 1415 16 2345 3800 495 34 1420 10 2350 3900 67 500 34 1425 12 2355 3915 505 17 1430 15 2360 3920 510 44 1435 2375 3940 515 36 1440 14 2380 3950 520 19 1445 25 2390 3960 530 41 1450 2400 3975 535 17 1455 14 2405 3990 540 33 1460 15 2410 3995 545 45 1465 2415 4100 550 20 1470 17 2420 4130 555 37 1475 14 2425 4140 560 27 1480 2430 4200 565 18 1485 19 2435 4225 570 28 1490 11 2445 4345 580 12 1495 10 2450 4370 585 38 1500 15 2455 4400 590 57 1505 20 2460 4420 595 21 1510 10 2465 4435 600 47 1515 13 2470 4445 605 39 1520 19 2490 4515 610 21 1525 12 2495 4530 615 40 1530 14 2500 4535 625 17 1535 13 2510 4560 630 44 1540 2520 4570 635 34 1545 11 2525 4590 640 18 1550 15 2530 4610 645 42 1555 2545 4660 650 37 1560 15 2550 4680 655 18 1565 10 2555 4755 68 660 52 1570 2560 4805 665 30 1575 13 2565 4920 670 27 1580 11 2570 4970 675 41 1585 2580 5235 680 44 1590 16 2580 5325 685 21 1595 13 2590 5445 690 24 1600 2595 5510 695 34 1605 13 2610 5535 700 18 1610 12 2615 5585 705 43 1615 2620 5730 710 24 1620 14 2625 5790 715 16 1625 14 2640 5795 720 36 1630 2645 6120 725 33 1635 11 2650 6185 730 16 1640 2655 6280 740 38 1645 2660 6320 745 23 1655 14 2670 6360 750 46 1660 2675 6425 755 49 1665 10 2685 6465 760 35 1670 13 2690 6610 765 53 1675 2695 6615 770 31 1680 12 2705 6660 775 22 1685 10 2710 6870 780 41 1690 2715 7035 785 43 1695 12 2725 7515 790 21 1700 12 2730 7650 795 43 1705 2735 8060 800 44 1710 2745 8350 805 13 1715 2750 9160 69 810 34 1720 2755 9270 815 45 1725 2760 9270 820 19 1730 2775 9665 825 54 1735 2780 9965 830 44 1740 2795 10190 835 14 1745 2805 10205 840 38 1750 2810 10345 845 40 1755 2820 10610 850 22 1760 2825 10815 855 31 1765 2835 10895 860 37 1770 2840 10950 865 21 1775 2850 10955 870 32 1780 2855 10965 875 35 1785 2865 11000 880 15 1790 2870 11190 885 44 1795 2875 11270 890 41 1800 2880 11785 895 26 1805 2885 12330 900 39 1810 2890 12730 905 41 1815 2895 13015 910 17 1820 2910 13440 920 34 1825 2915 13710 925 24 1830 2920 14160 930 46 1835 2925 14200 935 41 1840 2935 14325 940 17 1845 2940 14920 945 45 1850 2945 15005 950 39 1855 2950 15035 955 19 1860 2855 15090 70 960 41 1865 2865 15510 965 41 1870 2870 15650 970 22 1875 2875 15660 975 38 1880 2880 15935 980 32 1885 2885 17205 985 23 1890 2890 17510 990 43 1895 2895 18570 995 32 1900 2910 19715 1000 15 1905 2915 19950 1005 41 1910 2920 22260 Supplemental table E-value distribution for sequences of Streptomyces sp YIM 121038 E-Value Hits E-Value (1e-X) Hits E-Value (1e-X) (1e-X) E-Value Hits Hits (1e-X) 407 49 582 94 669 139 652 409 50 610 95 656 140 622 395 51 528 96 708 141 588 320 52 542 97 634 142 603 429 53 562 98 735 143 596 383 54 554 99 746 144 660 10 494 55 581 100 723 145 637 11 477 56 670 101 710 146 613 12 473 57 633 102 706 147 654 13 496 58 695 103 659 148 715 14 517 59 590 104 674 149 710 15 478 60 605 105 709 150 658 16 475 61 624 106 717 151 623 17 433 62 631 107 757 152 674 18 427 63 619 108 675 153 689 71 19 428 64 684 109 669 154 645 20 500 65 674 110 629 155 707 21 536 66 652 111 688 156 688 22 513 67 680 112 112 157 663 23 503 68 709 113 707 158 586 24 439 69 713 114 685 159 588 25 491 70 643 115 690 160 601 26 513 71 667 116 665 161 510 27 568 72 582 117 695 162 495 28 607 73 610 118 760 163 519 29 594 74 647 119 739 164 538 30 572 75 741 120 739 165 500 31 535 76 662 121 807 166 166 32 560 77 699 122 787 167 554 33 621 78 597 123 817 168 558 34 604 79 646 124 808 169 533 35 580 80 648 125 743 170 603 36 559 81 687 126 679 171 529 37 483 82 670 127 676 172 521 38 559 83 664 128 691 173 529 39 561 84 671 129 635 174 486 40 644 85 698 130 602 175 503 41 547 86 672 131 666 176 541 42 531 87 629 132 649 177 497 43 529 88 624 133 661 178 533 44 532 89 684 134 603 179 490 45 627 90 769 135 660 180 53956 46 557 91 763 136 630 47 549 92 745 137 574 48 560 93 733 138 594 72 Supplemental table GO level distribution for Streptomyces sp YIM 121038 GO Level GO Annotations Biological Process Level GO Annotations Molecular Function (P) Level Annotations Cellular Component (F) (C) 0 0 0 1 21 100 301 1704 91 213 637 586 213 2088 1612 562 2160 113 663 1021 29 520 578 70 503 769 11 10 321 10 97 10 11 670 11 35 11 12 226 12 12 13 75 13 13 12 20 12 12 15 15 15 73 Supplemental figure: Supplemental figure Four similar aa sequences which able produce Orf30, Orf 26, ZbmD, ZbmL Supplemental figure Results running local blast in Blast2GO of similar aa sequences which able produce Orf30, Orf 26, ZbmD, ZbmL 74