- Open Access
Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)
- Matt Nolan1,
- Johannes Sikorski2,
- Marlen Jando2,
- Susan Lucas1,
- Alla Lapidus1,
- Tijana Glavina Del Rio1,
- Feng Chen1,
- Hope Tice1,
- Sam Pitluck1,
- Jan-Fang Cheng1,
- Olga Chertkov1, 3,
- David Sims1, 3,
- Linda Meincke1, 3,
- Thomas Brettin1, 3,
- Cliff Han1, 3,
- John C. Detter1, 3,
- David Bruce1, 3,
- Lynne Goodwin1, 3,
- Miriam Land1, 4,
- Loren Hauser1, 4,
- Yun-Juan Chang1, 4,
- Cynthia D. Jeffries1, 4,
- Natalia Ivanova1,
- Konstantinos Mavromatis1,
- Natalia Mikhailova1,
- Amy Chen5,
- Krishna Palaniappan5,
- Patrick Chain1, 3,
- Manfred Rohde6,
- Markus Göker2,
- Jim Bristow1,
- Jonathan A. Eisen1, 7,
- Victor Markowitz5,
- Philip Hugenholtz1,
- Nikos C. Kyrpides1 and
- Hans-Peter Klenk2
- Published: 28 February 2010
Abstract
Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The ‘pinkish coiled Streptomyces-like organism with a spore case’ was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Keywords
- sporangia
- vegetative and aerial mycelia
- aerobic
- non-motile
- non-motile spores
- Gram-positive
- Streptosporangiaceae
- S. cloviforme
- GEBA
Introduction
Strain NI 9100T (= DSM 43021 = ATCC 12428 = JCM 3005) is the type strain of the species Streptosporangium roseum, which is the type species of the genus Streptosporangium, the type genus of the actinobacterial suborder Streptosporanineae [1–4]. S. roseum NI 9100T was isolated from vegetable garden soil and first described by Crouch in 1955 [2,4]. The name derives from ‘strepto’ from Greek meaning ‘coiled’ combined with ‘sporangium’, Latin for ‘spore case’, to mean ‘streptomyces-like’ but with sporangia [2,4]. The species epithet ‘roseum’ derives from the pinkish color on potato dextrose agar [2]. Here we present a summary classification and a set of features for S. roseum NI 9100T, together with the description of the complete genomic sequencing and annotation.
Classification and features
Phylogenetic tree highlighting the position of S. roseum NI 9100T relative to the type strains of the other species within the genus (1a) except for S. claviforme (see text). The tree was inferred from 1,411 and aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood criterion [10] and either rooted with the results of Figure 1b (Figure 1a) or rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [11] are shown in blue, published genomes in bold.
Phylogenetic tree highlighting the position of S. roseum NI 9100T relative to the type strains of the other genera within the family Streptosporanginea. The tree was inferred from 1,369 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood criterion [10] and either rooted with the results of Figure 1b (Figure 1a) or rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [11] are shown in blue, published genomes in bold.
Scanning electron micrograph of S. roseum NI 9100T
Classification and general features of S. roseum NI 9100T according to the MIGS recommendations [12]
MIGS ID | Property | Term | Evidence code |
---|---|---|---|
Current classification | Domain Bacteria | TAS [13] | |
Phylum Actinobacteria | TAS [14] | ||
Class Actinobacteria | TAS [15] | ||
Subclass Actinobacteridae | TAS [15] | ||
Order Actinomycetales | TAS [15] | ||
Suborder Streptosporangineae | TAS [15] | ||
Family Streptosporangiaceae | |||
Genus Streptosporangium | |||
Species Streptosporangium roseum | |||
Type strain NI 9100 | |||
Gram stain | not tested, probably positive | ||
Cell shape | produces aerial mycelium | TAS [2] | |
Motility | non-motile | TAS [2] | |
Sporulation | non-motile spores | TAS [2] | |
Temperature range | mesophile, temperature range not determined, does not grow at 42°C | ||
Optimum temperature | 28°C | ||
Salinity | 2.5% NaCl | ||
MIGS-22 | Oxygen requirement | aerobic | TAS [2] |
Carbon source | several (see text), but be aware of contradicting results | ||
Energy source | carbohydrates | ||
MIGS-6 | Habitat | soil | TAS [2] |
MIGS-15 | Biotic relationship | free living | TAS [2] |
MIGS-14 | Pathogenicity | non pathogenic | NAS |
Biosafety level | 1 | TAS [22] | |
Isolation | vegetable garden soil | TAS [2] | |
MIGS-4 | Geographic location | most probably Chapel Hill, North Carolina, USA | TAS [2] |
MIGS-5 | Sample collection time | 1955 or before | TAS [2] |
MIGS-4.1 | Latitude, Longitude | 35.913, −79.055 | NAS |
MIGS-4.2 | |||
MIGS-4.3 | Depth | not reported | |
MIGS-4.4 | Altitude | not reported |
The color of the substrate mycelium is red-brown to yellow-brown [2,24]. Strain NI 9100T utilizes glucose, arabinose, sucrose, xylose, fructose, and raffinose, but not inositol, mannose, rhamnose, or cellulose [19,20]. The strain is positive for arginine dihydrolase and acetoin production (Voges Proskauer test), weakly positive for citrate utilization, lysine decarboxylase, and ornithine decarboxylase, and negative for Kohn’s gelatin gelatinase, urease, o-nitro-phenyl-galactoside β-galactosidase, tryptophan desaminase, tryptophan indole production, H2S production from sodium thiosulfate [19,20]. Starch hydrolysis and nitrate reduction are positive, but growth at 42°C and iodinin production are negative [24]. Mertz and Yao [18] reported that strain NI 9100T can utilize glycerol, arabinose, rhamnose and inositol, which is in part contradictory to other results [20,21]. Gelatin is liquefied, milk is peptonized and red-brown to purple-brown soluble pigments are produced [18]. Zhang et al. [21] describe strain NI 9100T as utilizing sorbitol and sorbose but to be negative for L-arabinose, erythrose, D-fructose, D-galactose, inositol, D-mannose, maltose, raffinose, and rhamnose, which again is in part in conflict with other studies [18–20]. Strain NI 9100T produces a secondary metabolite, the antibiotic angucycline WS 79089B, which is an inhibitor of the endothelin-converting enzyme [20]. In contrast to S. carneum, strain NI 9100T does not produce an antibiotic against Staphylococcus aureus [18].
The characteristics of the ribosomal protein AT-L30 of strain S. roseum JCM2178T in comparison to other bacteria of the genus Streptosporangium is described elsewhere [25]. These data should be taken cautiously, as according to the Japanese Collection of Microorganisms (JCM) catalogue the strain number “JCM2178” is affiliated with Aspergillus oryzae (accessed to JCM in August 09), hence the true nature of strain S. roseum JCM2178T in the study of Ochi [25] is unclear.
Chemotaxonomy
The major fatty acids (relative ratio %) are iso-C16:0 (40.0), C17:0 10-methyl (23.0), C16:0 (1.95), C16:0 10-methyl (6.0), iso-C14:0 (14.0) (Reiner Kroppenstedt, personal communication). Partly different fatty acid patterns are reported elsewhere [18–20,26,27]. The proportions of diaminopimelic acid (A2pm) in the cell wall of strain S. roseum NI 9100T are 71% meso-A2pm and 29% LL-A2pm [26]. The phospholipids of strain S. roseum NI 9100T are phosphatidylethanolamine, hydroxyphosphatidylethanolamine, ninhydrin-positive and sugar-positive phospholipids, disphosphatidylglycerol, and posphatidylinositol [1]. The menaquinone compositions are MK-9 (III, VIII-H4) (56.5%), MK-9 (H2) (37.8%), MK-9 (H0) (5.0%), and MK-9 (H6) (0.7%) [1]. Galactose and madurose are present in whole cell sugars extracts, rhamnose is absent [1]. In general, the genus Streptosporangium is characterized by the whole-cell sugar type B or C, the phospholipid type IV and of the fatty acid type 3c [1].
Genome sequencing and annotation
Genome project history
Genome sequencing project information
MIGS ID | Property | Term |
---|---|---|
MIGS-31 | Finishing quality | Finished |
MIGS-28 | Libraries used | Two Sanger libraries: 6kb pMCL200 and fosmid pcc1Fos One 454 Pyrosequence standard library |
MIGS-29 | Sequencing platforms | ABI3730, 454 GS FLX |
MIGS-31.2 | Sequencing coverage | 8.45× Sanger; 27.6× Pyrosequence |
MIGS-30 | Assemblers | Newbler, phrap |
MIGS-32 | Gene calling method | Prodigal, GenePrimp |
INSDC ID | CP001814 (genome), CP001815 (plasmid) | |
Genbank Date of Release | December 10, 2009 | |
GOLD ID | Gc01156 | |
NCBI project ID | 21083 | |
Database: IMG-GEBA | 2501799901 | |
MIGS-13 | Source material identifier | DSM 43021 |
Project relevance | Tree of Life, GEBA |
Growth conditions and DNA isolation
S. roseum NI 9100T, DSM 43021, was grown in DSMZ medium 535, Trypticase Soy Broth [28], at 28°C. DNA was isolated from 0.5–1 g of cell paste using the JGI CTAP procedure with modification ALM as described in [29].
Genome sequencing and assembly
The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov/. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 11,709 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher [30] or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 2,837 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. Together all sequence types provided 36.05× coverage of the genome. The final assembly contains 128,042 Sanger and 1,033,578 Pyrosequence reads.
Genome annotation
Genes were identified using Prodigal [31] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline (http://geneprimp.jgi-psf.org) [32]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [33].
Genome properties
Graphical circular map of the genome; plasmid not to scale. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.
Genome Statistics
Attribute | Value | % of Total |
---|---|---|
Genome size (bp) | 10,369,518 | 100.00% |
DNA coding region (bp) | 9,121,910 | 87.97% |
DNA G+C content (bp) | 7,348,162 | 70.86% |
Number of replicons | 2 | |
Extrachromosomal elements | 1 | |
Total genes | 9,501 | 100.00% |
RNA genes | 80 | 0.84% |
rRNA operons | 6 | |
Protein-coding genes | 9,421 | 99.16% |
Pseudo genes | 446 | 4.49% |
Genes with function prediction | 5,939 | 62.47% |
Genes in paralog clusters | 2,792 | 29.37% |
Genes assigned to COGs | 6,224 | 65.47% |
Genes assigned Pfam domains | 6,596 | 69.38% |
Genes with signal peptides | 2,248 | 23.65% |
Genes with transmembrane helices | 2,235 | 23.51% |
CRISPR repeats | 0 |
Number of genes associated with the general COG functional categories
Code | value | % age | Description |
---|---|---|---|
J | 226 | 2.4 | Translation, ribosomal structure and biogenesis |
A | 1 | 0.0 | RNA processing and modification |
K | 966 | 10.3 | Transcription |
L | 293 | 3.1 | Replication, recombination and repair |
B | 1 | 0.0 | Chromatin structure and dynamics |
D | 38 | 0.4 | Cell cycle control, mitosis and meiosis |
Y | 0 | 0.0 | Nuclear structure |
V | 189 | 2.0 | Defense mechanisms |
T | 511 | 5.4 | Signal transduction mechanisms |
M | 298 | 3.2 | Cell wall/membrane biogenesis |
N | 2 | 0.0 | Cell motility |
Z | 1 | 0.0 | Cytoskeleton |
W | 0 | 0.0 | Extracellular structures |
U | 43 | 0.5 | Intracellular trafficking and secretion |
O | 167 | 1.8 | Posttranslational modification, protein turnover, chaperones |
C | 424 | 4.5 | Energy production and conversion |
G | 639 | 6.8 | Carbohydrate transport and metabolism |
E | 600 | 6.4 | Amino acid transport and metabolism |
F | 124 | 1.3 | Nucleotide transport and metabolism |
H | 254 | 2.7 | Coenzyme transport and metabolism |
I | 306 | 3.2 | Lipid transport and metabolism |
P | 320 | 3.4 | Inorganic ion transport and metabolism |
Q | 315 | 3.3 | Secondary metabolites biosynthesis, transport and catabolism |
R | 974 | 10.3 | General function prediction only |
S | 473 | 5.0 | Function unknown |
- | 3187 | 33.8 | Not in COGs |
Declarations
Acknowledgements
We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1.
Authors’ Affiliations
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