Open Access

Complete genome sequence of Tsukamurella paurometabola type strain (no. 33T)

  • A. Christine Munk1, 2,
  • Alla Lapidus1,
  • Susan Lucas1,
  • Matt Nolan1,
  • Hope Tice1,
  • Jan-Fang Cheng1,
  • Tijana Glavina Del Rio1,
  • Lynne Goodwin1, 2,
  • Sam Pitluck1,
  • Konstantinos Liolios1,
  • Marcel Huntemann1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Natalia Mikhailova1,
  • Amrita Pati1,
  • Amy Chen3,
  • Krishna Palaniappan3,
  • Roxanne Tapia1, 2,
  • Cliff Han1, 2,
  • Miriam Land1, 4,
  • Loren Hauser1, 4,
  • Yun-Juan Chang1, 4,
  • Cynthia D. Jeffries1, 4,
  • Thomas Brettin1, 4,
  • Montri Yasawong5,
  • Evelyne-Marie Brambilla6,
  • Manfred Rohde5,
  • Johannes Sikorski6,
  • Markus Göker6,
  • John C. Detter1, 2,
  • Tanja Woyke1,
  • James Bristow1,
  • Jonathan A. Eisen1, 7,
  • Victor Markowitz3,
  • Philip Hugenholtz1, 8,
  • Nikos C. Kyrpides1 and
  • Hans-Peter Klenk6
Standards in Genomic Sciences20114:4030342

https://doi.org/10.4056/sigs.1894556

Published: 1 July 2011

Abstract

Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The species is not only of interest because of its isolated phylogenetic location, but also because it is a human opportunistic pathogen with some strains of the species reported to cause lung infection, lethal meningitis, and necrotizing tenosynovitis. This is the first completed genome sequence of a member of the genus Tsukamurella and the first genome sequence of a member of the family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

obligately aerobicnon-motilemesophilicchemoorganotrophicGram-positivemetachromatic granulesopportunistic pathogen Tsukamurellaceae GEBA

Introduction

Strain no. 33T (= DSM 20162 = ATCC 8368 = JCM 10117) is the type strain of the species Tsukamurella paurometabola, which in turn is the type species of the genus Tsukamurella [1,2]. Currently, there are eleven species within the genus Tsukamurella [1,3], which is named in honor of Michio Tsukamura, a Japanese microbiologist [1]. The species epithet derives from the Greek words paurus meaning little and metabolus meaning changeable, referring to a metabolism that is little changeable [1]. Strain no. 33T was first isolated from the mycetome and ovaries of Cimex lectularis (bedbug) in a study on the bacterial flora of Hexapoda by Edward A. Steinhaus in 1941 [2]. T. paurometabola was formerly also known as Corynebacterium paurometabolum (basonym) [1,4] as well as under its heterotypic synonym Rhodococcus aurantiacus [5,6], until Collins et al. revised the controversial taxonomic position of the species in 1988 [1] and J. P. Euzéby corrected the species epithet according to the rules of to the International Code of Nomenclature of Bacteria (1990 Revision) [7]. T. paurometabola is known, albeit rarely, to be an opportunistic pathogen for humans, especially in patients with predisposing conditions, such as immunosuppression (leukemia, solid tumors, and HIV infection) [8,9], chronic lung disease (tuberculosis) [9], and most often indwelling foreign bodies (long-term use of indwelling catheters) [1013]. Here we present a summary classification and a set of features for T. paurometabola no. 33T, together with the description of the complete genomic sequencing and annotation.

Classification and features

The phylogenetic neighborhood of T. paurometabola no. 33T in a 16S rRNA based tree is shown in Figure 1. The sequences of the two identical 16S rRNA gene copies in the genome differ by one nucleotide from the previously published 16S rRNA sequence (AF283280).
Figure 1.

Phylogenetic tree highlighting the position of T. paurometabola relative to the other type strains within the genus Tsukamurella. The tree was inferred from 1,447 aligned characters [14,15] of the 16S rRNA gene sequence under the maximum likelihood criterion [16] and rooted with the members of the closely related genus Dietzia. 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 [17] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [18] are labeled with one asterisk, those registered as ‘Complete and Published’ with two asterisks.

A representative genomic 16S rRNA sequence of strain no. 33T was compared using NCBI BLAST under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [19] and the relative frequencies, of taxa and keywords (reduced to their stem [20]) were determined, weighted by BLAST scores. The most frequently occurring genera were Tsukamurella (34.7%), Mycobacterium (32.5%), Dietzia (20.6%) and Rhodococcus (12.1%) (220 hits in total). Regarding the seven hits to sequences from members of the species, the average identity within HSPs was 99.3%, whereas the average coverage by HSPs was 96.7%. Regarding the 45 hits to sequences from other members of the genus, the average identity within HSPs was 99.2%, whereas the average coverage by HSPs was 96.2%. Among all other species, the one yielding the highest score was Tsukamurella strandjordii, (NR_025113), which corresponded to an identity of 99.5% and a HSP coverage of 100.0%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was DQ366095 (‘on Oil Degrading Consortium oil polluted soil clone MH1 Pitesti’), which showed an identity of 99.2% and an HSP coverage of 99.0%. The most frequently occurring keywords within the labels of environmental samples which yielded hits were ‘skin’ (9.6%), ‘human’ (4.8%), ‘microbiom, tempor, topograph’ (4.2%), ‘sea’ (3.8%) and ‘sediment’ (1.8%) (30 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found. These environmental labels are in line with the locations reported for the isolation of Tsukamurella strains, such as soil, human sputum, and bed bug [2,21].

The cells of T. paurometabola are straight to slightly curved rods with a size of 0.5–0.8 × 1.0–5 µm and occur singly, in pairs, or in masses [2,21] (Figure 2). The organism is Gram-positive, weakly acid-fast (some strains are strongly acid-fast), non-sporeforming and non-motile [2,21] (Table 1). The organism contains metachromatic granules [2]. Colonies of T. paurometabola are small (diameter, 0.5–2.0 mm) with convex elevation, have entire edges (sometimes rhizoidal), are dryish but easily emulsified and are white to creamy to orange in color [3.15]. T. paurometabola is strictly aerobic and chemoorganotrophic bacterium [1]. Reaction is positive for catalase and pyrazinamidase [1]. Acid is produced from some sugars [1]. The organism does not produce nitriles from nitrates [2]. Indole is not produced by T. paurometabola [2]. The organism is non-pathogenic for guinea pigs [2]. In general T. paurometabola strains grow in the range 10°C to 35°C. Strain no. 33T does not grow at 45°C [1]. The strain did not survive heating at 60°C for 15 minutes [1]. Some strains of T. paurometabola produce acid from fructose, galactose, glucose, glycerol, inositol, manitol, mannose, sorbitol, sucrose, and trehalose [1]. Acid is not produced from L-arabinose, L-rhamnose, or D-xylose [1]. Some strains of T. paurometabola grow on ethanol, fructose, galactose, glucose, inositol, mannitol, mannose, melizitose, sorbitol, sucrose, trehalose, xylose, n-butanol, isobutanol, 2,3-butylene glycol, propanol, propylene glycol, citrate, fumarate, malate, pyruvate, and succinate [1]. The organism does not grow on adonitol, arabinose, inulin, lactose, raffinose, or rhamnose [1]. Acetamide and nicotinamide are used as sole nitrogen sources but not benzamide [1]. Acetamide, glutamate, glucosamine, monoethanolamine, and serine are used as sole sources of carbon and nitrogen [1]. T. paurometabola is able to degrade Tween 20, Tween 40, Tween 60, and Tween 80, but not adenine, casein, or elastin [1]. Some strains of T. paurometabolum degrade xanthine and tyrosine [1]. The organism produces β-galactosidase and urease, but not arylsulfatase or α-esterase [1]. T. paurometabolum is resistant to ethambutol (5 µg/ml), 5-fluorouracil (20 µg/ml), mitomycin C (10 µg/ml), and picric acid (0.2% w/v) [1]. The organism is susceptible to bleomycin (5 µg/ml) [1].
Figure 2.

Scanning electron micrograph of T. paurometabola no. 33T

Table 1.

Classification and general features of T. paurometabola no. 33T according to the MIGS recommendations [22] and the NamesforLife database [23]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [24]

 

Phylum “Actinobacteria

TAS [25]

 

Class Actinobacteria

TAS [26]

 

Subclass Actinobacteridae

TAS [26,27]

 

Order Actinomycetales

TAS [2629]

 

Suborder Corynebacterineae

TAS [26,27]

 

Family Tsukamurellaceae

TAS [26,27]

 

Genus Tsukamurella

TAS [1]

 

Species Tsukamurella paurometabola

TAS [1]

 

Type strain no. 33

TAS [2]

 

Gram stain

positive

TAS [2]

 

Cell shape

short rods occurring singly, in pairs or in masses

TAS [2]

 

Motility

none

TAS [2]

 

Sporulation

none

TAS [2]

 

Temperature range

10°C–35°C, not at 45°C

NAS [1]

 

Optimum temperature

not reported

 
 

Salinity

not reported

 

MIGS-22

Oxygen requirement

obligately aerobic

TAS [1]

 

Carbon source

carbohydrates

TAS [1]

 

Energy metabolism

chemoorganotroph

TAS [1]

MIGS-6

Habitat

soil, human sputum, insect microbiome

TAS [2,4]

MIGS-15

Biotic relationship

free-living

NAS

MIGS-14

Pathogenicity

infection of the lung, lethal meningitis, and necrotizing tenosynovitis

TAS [4]

 

Biosafety level

1+

TAS [30]

 

Isolation

ovaries of Cimex lectularius (bedbug)

TAS [2,4]

MIGS-4

Geographic location

most probably close to Columbus, Ohio

NAS

MIGS-5

Sample collection time

1941 or before

TAS [2]

MIGS-4.1

Latitude

not reported

 

MIGS-4.2

Longitude

not reported

 

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

not reported

 

Evidence codes - IDA: Inferred from Direct Assay (first time in publication); TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from of the Gene Ontology project [31]. If the evidence code is IDA, the property was directly observed by one of the authors or an expert mentioned in the acknowledgements.

Chemotaxonomy

The major cell wall sugars of T. paurometabola are arabinose and galactose [1], but ribose and traces of glucose have also been observed (unpublished data, DSMZ). The diagnostic amino acid of peptidoglycan is meso-diaminopimelic acid (variation A1γ); the glycan moiety of cell walls contains N-glycolyl residues [1]. Arabinogalactan is covalently attached to the peptidoglycan [32]. Long-chain highly unsaturated mycolic acids (62 to 78 carbon atoms) are present and contain one to six double bonds [1]. Fatty acid esters released on pyrolysis of mycolic acids have 20 to 22 carbon atoms [1,21]. The major polar lipids of T. paurometabola are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, and mono- and diacylated phosphatidylinositol dimannosides [1,21]. Some strains of T. paurometabola produce glycolipids [1]. The long-chain cellular fatty acids are predominantly straight-chain saturated, mono-unsaturated, and 10-methyl branched acids [1].

Menaquinones are the sole respiratory quinones, with MK-9 predominating [1]: 80% MK-9 (H0), 6.8% MK-8 (H0), 3.5% MK-7 (H0), 2.3%.MK-10 (H0) and 6.7%.MK-8 (H2) (unpublished data, DSMZ).

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [33], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [34]. The genome project is deposited in the Genome On Line Database [18] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Three genomic libraries: Sanger 8 kb pMCL200 library, 40 kb (fosmid, pcc1Fos) library, 454 pyrosequence standard library

MIGS-29

Sequencing platforms

ABI3730, 454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

8.25 × Sanger; 37.9 × pyrosequence

MIGS-30

Assemblers

Newbler version 1.1.02.15, phrap

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

  

CP001966 (chromosome)

 

INSDC ID

CP001967 (plasmid Tpau01)

 

Genbank Date of Release

May 17, 2010

 

GOLD ID

Gc01341

 

NCBI project ID

29399

 

Database: IMG-GEBA

646564587

MIGS-13

Source material identifier

DSM 20162

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

T. paurometabola no. 33T, DSM 2016, was grown in medium 535 (Trypticase soy broth medium) [35] at 28°C. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram Positive DNA Purification Kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer, with modification st/LALMice for cell lysis as described in [24]. DNA is available through the DNA Bank Network [36].

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 can be found at the JGI website [37]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). Large Newbler contigs were broken into 4,920 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 adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler [38]. Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [39]. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 516 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, the combination of the Sanger and 454 sequencing platforms provided 46.15 × coverage of the genome. The final assembly contains 42,170 Sanger reads and 745,985 pyrosequencing reads.

Genome annotation

Genes were identified using Prodigal [40] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [41]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, 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 [42].

Genome properties

The genome consists of a 4,379,918 bp long chromosome and a 99,806 bp long plasmid, both with a G+C content of 68.4% (Table 3 and Figure 3). Of the 4,391 genes predicted, 4,335 were protein-coding genes, and 56 RNAs; 93 pseudogenes were also identified. The majority of the protein-coding genes (68.7%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical circular map of the chromosome. 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.

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

4,479,724

100.00%

DNA coding region (bp)

4,108,044

91.70%

DNA G+C content (bp)

3,064,083

68.40%

Number of replicons

2

 

Extrachromosomal elements

1

 

Total genes

4,391

100.00%

RNA genes

56

1.28%

rRNA operons

2

 

Protein-coding genes

4,335

98.72%

Pseudo genes

93

2.12%

Genes with function prediction

3,017

68.71%

Genes in paralog clusters

691

15.74%

Genes assigned to COGs

3,025

68.89%

Genes assigned Pfam domains

3,376

76.88%

Genes with signal peptides

1,031

23.48%

Genes with transmembrane helices

1,114

25.37%

CRISPR repeats

N.D.

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

169

5.0

Translation, ribosomal structure and biogenesis

A

1

0.0

RNA processing and modification

K

310

9.2

Transcription

L

198

5.9

Replication, recombination and repair

B

1

0.0

Chromatin structure and dynamics

D

31

0.9

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

39

1.2

Defense mechanisms

T

131

3.9

Signal transduction mechanisms

M

135

4.0

Cell wall/membrane/envelope biogenesis

N

3

0.1

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

29

0.9

Intracellular trafficking, secretion, and vesicular transport

O

102

3.0

Posttranslational modification, protein turnover, chaperones

C

217

6.4

Energy production and conversion

G

220

6.5

Carbohydrate transport and metabolism

E

274

8.1

Amino acid transport and metabolism

F

85

2.5

Nucleotide transport and metabolism

H

165

4.9

Coenzyme transport and metabolism

I

231

6.8

Lipid transport and metabolism

P

169

5.0

Inorganic ion transport and metabolism

Q

172

5.1

Secondary metabolites biosynthesis, transport and catabolism

R

430

12.7

General function prediction only

S

269

8.0

Function unknown

-

1,366

31.1

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Marlen Jando (DSMZ) for growing cultures of T. paurometabola. This work was performed under the auspices of the US Department of Energy 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, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
Bioscience Division, Los Alamos National Laboratory
(3)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(4)
Oak Ridge National Laboratory
(5)
HZI - Helmholtz Centre for Infection Research
(6)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(7)
University of California Davis Genome Center
(8)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland

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