In this work, we present the draft genome sequence of Actinocorallia populi A251T consisting of 8,253,402 bp with a G + C content of 71.5 mol%. The genome sequence includes 3 5S rRNA genes, 54 tRNA genes, 28 snRNA genes and 19 CRISPRs in 26 contigs. Using the Rapid Annotation using Subsystem Technology, a total of 7766 coding DNA sequences, which were assigned to 436 subsystems, were found in the genome. And 6743 protein-coding sequences with designated functions were assigned to 19 categories in the Cluster of Orthologous Groups database. The genome contains 20 gene clusters responsible for the synthesis of secondary metabolites, including two type I polyketide synthase (PKS) gene clusters, two type III PKS gene clusters, three nonribosomal peptide synthetase (NRPS) gene clusters and two hybrid PKS/NRPS gene clusters. These results indicate that strain A251 has the ability to produce several nonribosomal polypeptides and diverse polyketides, which was verified by liquid chromatography-mass spectrometry analysis of the extraction from fermentation broth. In addition, lactones, indole and many unknown natural products are present in the metabolites. Bioactivity testing revealed anticancer and antidiabetic activities of the crude extract towards the cancer cell line HepG2. In summary, the genomic sequences and bioactive fermentation products demonstrate the potential of strain A251 in biotechnology.
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Coding DNA sequences
Nonribosomal polypeptide synthetase
Biosynthetic gene cluster
Amos B, Rolf A (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45–48
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75–90
Burge SW, Daub J, Eberhardt R et al (2013) Rfam 11.0: 10 years of RNA families. Nucl Acids Res 41:D226–D232
Challis GL, Ravel J (2000) Coelichelin, a new peptide siderophore encoded by the streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase. FEMS Microbiol Lett 187:111–114
Chang Z, Sitachitta N, Rossi JV et al (2004) Biosynthetic pathway and gene cluster analysis of curacin A, an antitubulin natural product from the tropical marine cyanobacterium. J Nat Prod 67:1356–1367
Demain AL, Sanchez S (2009) Microbial drug discovery: 80 years of progress. J Antibiot 62:5–16
Grissa I, Vergnaud G, Pourcel C (2007) Crisprfinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucl Acids Res 35:52–57
Han KY, Wu X, Jiang CL et al (2019) Three new compounds from the actinomycete Actinocorallia aurantiaca. Natural Products and Bioprospecting 9:351–354
Iinuma S, Yokota A, Hasegawa T et al (1994) Actinocorallia gen. nov., a new genus of the order Actinomycetales. Int J Syst Bacteriol 44:230–234
Kanehisa M, Goto S, Kawashima S et al (2004) The KEGG resource for deciphering the genome. Nucl Acids Res 32:D277–D280
Kumar M, Kumar P, Das P et al (2019) Draft genome of Streptomyces sp. strain 130 and functional analysis of extracellular enzyme producing genes. Mol Biol Rep 46(5):5063–5071
Lagesen K, Hallin PF, Rødland EA et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucl Acids Res 35:3100–3108
Lee SD (2006) Actinocorallia cavernae sp. nov. isolated from a natural cave in Jeju, Korea. Int J Syst Evol Microbiol 56(5):1085–1088
Lee I, Kim YO, Park SC et al (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103
Li W, Jaroszewski LA, Godzik A (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18:77–82
Li XG, Wang ZK, Lu FJ et al (2018) Actinocorallia populi sp. nov., an endophytic actinomycete isolated from a root of Populus adenopoda (maxim.). Int J Syst Evol Microbiol 68:2325–2330
Liu C, Li Y, Ye L et al (2016) Actinocorallia lasiicapitis sp. nov. an actinomycete isolated from the head of an ant (Lasius fuliginosus L.). Int J Syst Evol Microbiol 66:2172–2177
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–964
Luo R, Liu BH, Xie YL et al (2012) Soapdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18
Medema MH, Blin K, Cimermancic P et al (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucl Acids Res 39:W339–W346
Meier-kolthoff JP, Auch AF, Klenk HP et al (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 14:60
Packter NM (1993) The polyketide metabolites, D. O'Hagan Ellis Horwood, New York. Int J Biol Macromol 15(2):134
Pitcher DG, Saunders NA, Owen RJ (1989) Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156
Richter M, RossellóMóra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131
Sauma L, Sc M, Karin G et al (2006) PPAR-γ response element activity in intact primary human adipocytes: effects of fatty acids. Nutrition 22:60–68
Shao HH, Chen MJ, Fei XT et al (2019) Complete genome sequence and characterization of a polyethylene biodegradation strain, Streptomyces Albogriseolus LBX-2. Microorganisms 7:379
Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340
Skehan P, Storeng R, Scudiero D et al (1990) New colorimetric cytotoxicity assay for anticancer-drug screening. J Natl Cancer I 82:1107–1112
Sun YH, Deng ZX (2006) Polyketides and combinatorial biosynthetic approaches. Chin J Antibiot 1:6–14
Tatusov RL, Fedorova ND, Jackson JD et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinf 4:41
Tatusova TA, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucl Acids Res 44(14):6614–6624
Vichai V, Kirtikara K (2006) Sulforhodamine b colorimetric assay for cytotoxicity screening. Nat Protoc 1:1112–1116
Wayne LG, Brenner DJ, Colwell RR et al (1987) International committee on systematic bacteriology. Report of the ad hoc committee on the reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 37:463–464
Wiren NV, Klair S, Bansal S et al (1999) Nicotianamine chelates both FeIII and FeII. Implications for metal transport in plants. Plant Physiol 119:1107–1114
Zhang Z, Kudo T, Nakajima Y et al (2001) Clarification of the relationship between the members of the family Thermomonosporaceae on the basis of the 16S rDNA, 16S–23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses. Int J Syst Evol Microbiol 51:373–383
Zhang H, Yohe T, Huang L et al (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucl Acids Res 6:W95–W101
We thank the Institute of Materia Medica of Chengdu Diao pharmaceutical Corp. for conducing the anticancer and antidiabetic activity screening. This work was supported by the National Key Research and Development Program of China (2017YFB0308401); and the Opening Project of Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education (20826041C4159).
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The authors declare that there are no conflicts of interest.
This work does not contain any studies with human participants or animals performed by any of the authors.
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Li, X., Wang, Z., Gan, L. et al. Draft genome sequence of Actinocorallia populi A251T, an actinomycetes producing polyketides and nonribosomal polypeptides. 3 Biotech 10, 79 (2020). https://doi.org/10.1007/s13205-020-2070-4
- Draft genome
- Actinocorallia populi
- Genomic annotation
- Crude extract