- Open Access
High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway
- Published: 15 June 2014
Abstract
Here we report the 8 Mb high quality draft genome of Streptomyces sp. strain AW19M42, together with specific properties of the organism and the generation, annotation and analysis of its genome sequence. The genome encodes 7,727 putative open reading frames, of which 6,400 could be assigned with COG categories. Also, 62 tRNA genes and 8 rRNA operons were identified. The genome harbors several gene clusters involved in the production of secondary metabolites. Functional screening of the isolate was positive for several enzymatic activities, and some candidate genes coding for those activities are listed in this report. We find that this isolate shows biotechnological potential and is an interesting target for bioprospecting.
Keywords
- Bioprospecting
- enzymes
- metabolites
- Streptomyces
- Actinobacteria
Introduction
The filamentous and Gram-positive genus Streptomyces, belonging to the phylum Actinobacteria [1], are attractive organisms for bioprospecting being the largest antibiotic-producing genus discovered in the microbial world so far [2]. These species have also been exploited for heterologous expression of a variety of secondary metabolites [3]. Additionally, these species harbor genes coding for enzymes that can be applicable in industry and biotechnology [4,5].
Since the first, complete Streptomyces genome was published [6], a number of strains isolated from terrestrial environments have been reported [7–11]. Genomic investigations on Streptomyces from marine sources have, however, just recently begun [12–16].
Here, we present the draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a marine source, together with the description of genome properties and annotation. Results from functional enzyme screening of the bacterium are also reported.
Classification and features
Classification and general features of Streptomyces sp. strain AW19M42 according to the MIGS recommendations [17]
MIGS ID | Property | Term | Evidence code |
---|---|---|---|
Current classification | Domain Bacteria | TAS [18] | |
Phylum Actinobacteria | TAS [1] | ||
Class Actinobacteria | TAS [19] | ||
Subclass Actinobacteridae | |||
Order Actinomycetales | |||
Suborder Streptomycineae | |||
Family Streptomycetaceae | |||
Genus Streptomyces | |||
Species Streptomyces sp. | NAS | ||
Strain AW19M42 | IDA | ||
Gram stain | Gram positive | NDA | |
Cell shape | Branched mycelia | NDA | |
Motility | Dispersion of spores | NDA | |
Sporulation | Sporulating | NDA | |
Temperature range | Range not determined, grows at 15°C and 28°C | IDA | |
MIGS-6.3 | Salinity | Not determined, but survives 50% natural sea water | IDA |
MIGS-22 | Oxygen requirements | Aerobic | NDA |
Carbon source | Not reported | ||
Energy source | Not reported | ||
MIGS-6 | Habitat | Inner organs of sea squirt | IDA |
MIGS-15 | Biotic relationship | Free-living | IDA |
MIGS-14 | Pathogenicity | Non-pathogenic | NDA |
Biosafety level | 1 | ||
MIGS-4 | Geographic location | Hellmofjorden, Norway | IDA |
MIGS-5 | Sample collection time | April 2010 | IDA |
MIGS-4.1 | Latitude | N67 49.24316 | IDA |
MIGS-4.2 | Longitude | E16 28.99465 | IDA |
MIGS-4.3 | Depth | 77.35 m | IDA |
Phylogenetic tree indicating the phylogenetic relationship of Streptomyces sp. strain AW19M42 relative to other Streptomyces species. The phylogenetic tree was made by comparing the 16S rDNA sequence of the Streptomyces sp. strain AW19M42 to the closest related sequences from both validated type strains and unidentified isolates. S. venezuelea is used as outgroup. All positions containing gaps and missing data were eliminated. There were a total of 1,389 positions in the final dataset. The bar shows the number of base substitutions per site.
Genome sequencing and annotation
Genome sequencing project information
MIGS ID | Property | Term |
---|---|---|
MIGS-31 | Finishing quality | Improved high quality draft |
MIGS-28 | Libraries used | One Illumina Paired-End library |
MIGS-29 | Sequencing platforms | Illumina HiSeq2000 |
MIGS-31.2 | Fold coverage | 350× |
MIGS-30 | Assemblers | CLC paired-end assembly |
MIGS-32 | Gene calling method | Glimmer 3 |
Genbank ID | CBRG000000000 | |
Genbank Date of Release | September 11, 2013 | |
GOLD ID | Gi0070794 | |
Project relevance | Bioprospecting |
Genome properties
Genome statistics, including nucleotide content and gene count levels
Attribute | Value | % of totala |
---|---|---|
Genome size (bp) | 8,008,851 | 100 |
DNA coding region (bp) | 6,979,999 | 87.2 |
DNA G+C content (bp) | 4,951,797 | 70.6 |
Total genes | 7,813 | n/a |
rRNA operons | 8 | n/a |
tRNA genes | 62 | n/a |
Protein-coding genes | 7,727 | 100 |
Genes assigned to COGs | 6,400 | 82.8 |
Genes with signal peptides | 987 | 12.8 |
Genes with transmembrane helices | 1,660 | 21.5 |
Number of genes associated with the 25 general COG functional categories
Code | Value | %agea | Description |
---|---|---|---|
J | 264 | 3.4 | Translation |
A | 1 | 0.0 | RNA processing and modification |
K | 836 | 10.8 | Transcription |
L | 330 | 4.3 | Replication, recombination and repair |
B | 5 | 0.1 | Chromatin structure and dynamics |
D | 71 | 0.9 | Cell cycle control, mitosis and meiosis |
Y | 0 | 0.0 | Nuclear structure |
V | 159 | 2.1 | Defense mechanisms |
T | 442 | 5.7 | Signal transduction mechanisms |
M | 338 | 4.3 | Cell wall/membrane biogenesis |
N | 28 | 0.4 | Cell motility |
Z | 6 | 0.1 | Cytoskeleton |
W | 0 | 0.0 | Extracellular structures |
U | 79 | 1.0 | Intracellular trafficking and secretion |
O | 200 | 2.6 | Posttranslational modification, protein turnover, chaperones |
C | 409 | 5.3 | Energy production and conversion |
G | 665 | 8.6 | Carbohydrate transport and metabolism |
E | 730 | 9.4 | Amino acid transport and metabolism |
F | 123 | 1.6 | Nucleotide transport and metabolism |
H | 262 | 3.4 | Coenzyme transport and metabolism |
I | 330 | 4.3 | Lipid transport and metabolism |
P | 435 | 5.6 | Inorganic ion transport and metabolism |
Q | 417 | 5.4 | Secondary metabolites biosynthesis, transport and catabolism |
R | 1,181 | 15.3 | General function prediction only |
S | 465 | 6.0 | Function unknown |
- | 1,327 | 17.2 | Not in COGs |
All putative protein coding sequences were assigned KEGG orthology [39], and mapped onto pathways using the KEGG Automatic Annotation Server (KAAS) server [40]. The analysis revealed that Streptomyces sp. strain AW19M42 harbors several genes related to biosynthesis of secondary metabolites. We have identified genes that map to the streptomycin biosynthesis pathway (glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24), dTDP-glucose 4,6-dehydratase (EC 4.2.1.46) and dTDP-4-dehydrorhamnose reductase (EC 1.1.1.133)). Also, several genes map to the pathways for biosynthesis of siderophore group nonribosomal peptides, biosynthesis of type II polyketide product pathway and polyketide sugar unit biosynthesis. Interestingly, two clusters, comprising five genes, both mapped to the biosynthesis of type II polyketide backbone pathway. These genes clusters comprise genes STREP_3146-3150 and STREP_4370-4374. This suite of genes may contribute to a distinct profile of secondary metabolites production.
Insights from the Genome Sequence
Degradation halos around colonies of Streptomyces sp. AW19M42 growing on agar plates supplemented with A, skim milk, B, gelatin, C, tributyrin, D, DNA, E, chitin and F, starch.
Candidate genes coding for putative lipase, caseinase, gelatinase and DNase activities identified in Streptomyces sp. strain AW19M42 draft genome.
Putative gene | Annotation | Size (aa) |
---|---|---|
Lipase | ||
STREP_0737 | Lipase | 273 |
STREP_1671 | Triacylglycerol lipase | 266 |
STREP_1821 | G-D-S-L family lipolytic protein | 281 |
STREP_2698 | Lipase class 2 | 297 |
STREP_2704 | Triacylglycerol lipase | 269 |
STREP_4585 | Secreted hydrolase | 268 |
STREP_5662 | Lipase or acylhydrolase family protein | 367 |
STREP_6665 | Esterase/lipase | 259 |
STREP_6850 | Esterase/lipase | 429 |
STREP_7611 | Triacylglycerol lipase | 366 |
Gelatinase | ||
STREP_5784 | Peptidase M4 thermolysin | 523 |
STREP_6038 | Peptidase M4 thermolysin | 680 |
STREP_3662 | Peptidase M4 thermolysin | 358 |
Caseinase | ||
STREP_0198 | Putative secreted serine protease | 361 |
STREP_0258 | Protease | 278 |
STREP_0974 | Protease | 488 |
STREP_1078 | Serine protease | 388 |
STREP_1313 | M6 family metalloprotease domain-containing protein | 398 |
STREP_1389 | M6 family metalloprotease domain protein | 1,389 |
STREP_2216 | Putative secreted subtilisin-like serine protease | 511 |
STREP_2239 | metalloprotease | 296 |
STREP_3135 | Metalloprotease domain protein | 127 |
STREP_3964 | ATP-dependent protease La | 808 |
STREP_3975 | ATP-dependent metalloprotease FtsH | 673 |
STREP_4000 | Streptogrisin-B-Pronase enzyme B SGPB/Serine protease B | 299 |
STREP_5179 | ATP-dependent Clp protease proteolytic subunit | 222 |
STREP_5180 | ATP-dependent Clp protease, ATP-binding subunit ClpX | 432 |
STREP_5944 | Protease | 527 |
STREP_5945 | Protease | 534 |
STREP_6196 | Protease | 383 |
STREP_6570 | Protease | 701 |
STREP_6821 | Putative protease | 352 |
STREP_7179 | Serine protease | 635 |
STREP_7580 | Protease | 856 |
DNase | ||
STREP_0436 | Exodeoxyribonuclease VII, large subunit | 403 |
STREP_0437 | Exodeoxyribonuclease VII small subunit | 91 |
STREP_1352 | Exodeoxyribonuclease III Xth | 268 |
STREP_1969 | TatD-related deoxyribonuclease | 1,969 |
STREP_2155 | Deoxyribonuclease V | 220 |
STREP_2430 | Deoxyribonuclease/rho motif-related TRAM | 452 |
STREP_4206 | Deoxyribonuclease | 776 |
STREP_6678 | Probable endonuclease 4 - Endodeoxyribonuclease | 275 |
Chitinase | ||
STREP_2729 | Chitinase, glycosyl hydrolase 18 family | 628 |
STREP_5817 | Chitinase, glycosyl hydrolase 18 family | 424 |
STREP_5513 | Carbohydrate-binding CenC domain protein | 577 |
STREP_3508 | Glycoside hydrolase family protein | 609 |
STREP_4257 | Putative endochitinase | 350 |
STREP_6187 | Chitinase, glycosyl hydrolase 19 family | 297 |
STREP_6188 | Chitinase, glycosyl hydrolase 19 family | 291 |
Amylase | ||
STREP_1696 | Glycoside hydrolase starch-binding protein | 573 |
STREP_5789 | Secreted alpha-amylase | 458 |
STREP_7405 | Malto-oligosyltrehalose synthase | 834 |
STREP_1697 | Alpha-1,6-glucosidase, pullulanase-type | 1,774 |
Conclusion
The 8 Mb draft genome belonging to Streptomyces sp. strain AW19M42, originally isolated from a marine sea squirt in the sub-Arctic region of Norway has been deposited at ENA/DDBJ/GenBank under accession number CBRG000000000. The isolate was successfully screened for several enzymatic activities that are applicable in biotechnology and candidate genes coding for the enzyme activities were identified in the genome. Streptomyces sp. strain AW19M42 will serve as a source of functional enzymes and other bioactive chemicals in future bioprospecting projects.
Declarations
Acknowledgements
This work was supported by the Research Council of Norway (Grant no. 192123). We would like to acknowledge Kristin E. Hansen and Seila Pandur for technical assistance during bacterial isolation and nucleic acid extraction. The sequencing service was provided by the Norwegian Sequencing Centre (www.sequencing.uio.no), a national technology platform hosted by the University of Oslo and supported by the “Functional Genomics” and “Infrastructure” programs of the Research Council of Norway and the Southeastern Regional Health Authorities.
Authors’ Affiliations
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