Open Access

Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)

  • Alex Copeland1,
  • Ahmet Zeytun1, 2,
  • Montri Yassawong3,
  • Matt Nolan1,
  • Susan Lucas1,
  • Nancy Hammon1,
  • Shweta Deshpande1,
  • Jan-Fang Cheng1,
  • Cliff Han1, 2,
  • Roxanne Tapia1, 2,
  • Lynne A. Goodwin1, 2,
  • Sam Pitluck1,
  • Konstantinos Mavromatis1,
  • Konstantinos Liolios1,
  • Ioanna Pagani1,
  • Natalia Ivanova1,
  • Natalia Mikhailova1,
  • Amrita Pati1,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land1, 5,
  • Loren Hauser1, 5,
  • Cynthia D. Jeffries1, 5,
  • Evelyne-Marie Brambilla6,
  • Manfred Rohde7,
  • Johannes Sikorski6,
  • Rüdiger Pukall6,
  • Markus Göker6,
  • John C. Detter1, 2,
  • Tanja Woyke1,
  • James Bristow1,
  • Jonathan A. Eisen1, 8,
  • Victor Markowitz4,
  • Philip Hugenholtz1, 9,
  • Nikos C. Kyrpides1,
  • Hans-Peter Klenk6 and
  • Alla Lapidus1
Standards in Genomic Sciences20126:6020240

https://doi.org/10.4056/sigs.2756060

Published: 25 May 2012

Abstract

Deinococcus proteolyticus (ex Kobatake et al. 1973) Brook and Murray 1981 is one of currently 47 species in the genus Deinococcus within the family Deinococcaceae. Strain MRPT was isolated from feces of Lama glama and possesses extreme radiation resistance, a trait is shares with various other species of the genus Deinococcus, with D. proteolyticus being resistant up to 1.5 Mrad of gamma radiation. Strain MRPT is of further interest for its carotenoid pigment. The genome presented here is only the fifth completed genome sequence of a member of the genus Deinococcus (and the forth type strain) to be published, and will hopefully contribute to a better understanding of how members of this genus adapted to high gamma- or UV ionizing-radiation. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,886,836 bp long genome with its four large plasmids of lengths 97 kbp, 132 kbp, 196 kbp and 315 kbp harbors 2,741 protein-coding and 58 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

strictly aerobic non-motile chemoorganotrophic proteolytic radioresistant mesophile carotenoid pigments tetrad-forming cocci Gram-positive Deinococcaceae GEBA

Introduction

Strain MRPT, also known as Kobatake strain MRP (= DSM 20540 = ATCC 35074 = JCM 6276) is the type strain of Deinococcus proteolyticus [1], one of currently 47 validly named species in the genus Deinococcus [2]. The genus name is derived from the latinized Greek word deinos meaning ‘strange or unusual’ and the Neo-Latin word coccus meaning ‘a grain or berry’, yielding the Neo-Latin ‘Deinococcus’, meaning the ‘unusual coccus’ [1]. The species epithet is derived from the Neo-Latin word proteolyticus, meaning proteolytic [1]. Strain MRPT was isolated in the early 1970s from feces of Lama glama by Kobatake et al.. and became known under its synonym “Micrococcus radioproteolyticus” [3], which according to Rule 12a of the Bacteriological Code was an illegitimate species epithet because it expressed more than one single concept [1]. The genus name “Micrococcus” was not considered for the Approved Lists of Bacterial Names published by Skerman et al. in 1980 [4]. In 1981 Brooks and Murray posited the family Deinococcaceae and the genus Deinococcus, with D. radiodurans as the type species of the type genus and D. proteolyticus as one out of three other members of the novel genus [1]. Many strains of the family Deinococcaceae are resistant to high levels of gamma and ultraviolet radiation [1]. Cells of deinococci are spherical or rod shaped [5]. Several distinct cell wall layers have been observed in thin sections and the cell wall contains lipoprotein [1]. The natural habitat of the members of genus Deinococcus was unknown for a long time, largely because of the recognition was not easy [6]. Plasmids of strain MRPT were previously analyzed by Mackay et al. [7], and survival of repeated lyophilisation was studied by Rýznar and Drásil [8]. The Genes hsp70 [9], hps40 [10], and SSB genes were sequenced [11], primarily for phylogenetic analyses. The members of the genus Deinococcus have been isolated from diverse environments [1215], usually selected and characterized by survival after high-dose irradiation [6]. To date no further isolates of D. proteolyticus have been reported. Here, we present a summary classification and a set of features for D. proteolyticus MRPT, together with the description of the complete genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of D. proteolyticus MRPT was compared using NCBI BLAST [16,17] 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 [18] and the relative frequencies of taxa and keywords (reduced to their stem [19]) were determined, weighted by BLAST scores. The most frequently occurring genus was Deinococcus (100.0%) (85 hits in total). Regarding the two hits to sequences from members of the species, the average identity within HSPs was 99.8%, whereas the average coverage by HSPs was 98.4%. Regarding the 52 hits to sequences from other members of the genus, the average identity within HSPs was 92.0%, whereas the average coverage by HSPs was 95.1%. Among all other species, the one yielding the highest score was Deinococcus piscis (DQ683348), which corresponded to an identity of 98.0% and an HSP coverage of 98.5%. (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 JF171367 (‘skin antecubital fossa clone ncd1964b12c1’), which showed an identity of 95.1% and an HSP coverage of 89.1%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘skin’ (20.6%), ‘fossa’ (10.2%), ‘forearm’ (9.2%), ‘volar’ (8.8%) and ‘antecubit’ (6.7%) (165 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found.

Figure 1 shows the phylogenetic neighborhood of D. proteolyticus in a 16S rRNA based tree. The sequences of the three identical 16S rRNA gene copies in the genome differ by three nucleotides from the previously published 16S rRNA sequence (Y11331).
Figure 1.

Phylogenetic tree highlighting the position of D. proteolyticus relative to the type strains of the other species within the family Deinococcaceae. The tree was inferred from 1,377 aligned characters [20,21] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [22]. Rooting was done initially using the midpoint method [23] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 750 ML bootstrap replicates [24] (left) and from 1,000 maximum parsimony bootstrap replicates [25] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [26] are labeled with one asterisk, those also listed as ‘Complete and Published’ with two asterisks [2729]. The genome of D. radiodurans published by White et al. in 1999 [30] later turned out not to be from the type strain [31].

Strain MRPT is strictly aerobic, Gram-positive and non-motile [1]. Cells are spheres (Figure 2), 1.0 to 2.0 µm in diameter, occurring singly and in pairs [1]. Cells are divided into two planes to form tetrads or tablets of cells, and the cell wall consists of at least three distinct layers [1]. Resting stages of cells are not known [1]. Colonies are orange-red, smooth and convex with a regular edge [1]. Multiple carotenoids are present in the cells [1]. The organism reveals the presence of polyphosphate granules which have a delicate granular structure [41]. Optimal growth temperature is 30ºC [1], but the organism is also able to grow at 37 ºC [42]. Growth was observed in media that contained 1% of NaCl [1], but not when the media contained 5% of NaCl [42]. Strain MRPT is chemoorganotrophic with respiratory metabolism [1]. The organism produces catalase, but not β-galactosidase [42], and does not reduce nitrate to nitrite [42]. The reaction was negative for methyl red, Voges-Proskauer, indole and citrate tests [42]. Strain MRPT does not produce acid from arabinose, galactose, lactose, maltose, manitol, sorbitol, sucrose or xylose [42]. Acid with no gas was produced from glucose or fructose, when the organism was grown on peptone-water basal medium or the basal medium according to subcommittee on taxonomy of staphylococci and micrococci [1,42,43]. Esculin was hydrolyzed by strain MRPT [42]. The organism was more active in digesting proteins (milk, soya and gelatin) than D. radiodurans [1]; milk is peptonized and gelatine is liquefied by strain MRPT [1]. Strain MRPT is resistant to to gamma radiation up to 1.5 Mrad. [1].
Figure 2.

Scanning electron micrograph of D. proteolyticus MRPT

Chemotaxonomy

The cell wall of strain MRPT contains A3β type peptidoglycan [41], with L-ornithine in the peptide subunit and glycine in the interpeptide bridge [1]. The predominant fatty acid is palmitoleate, whereas branched-chain fatty acids are present in minor amounts only [1]: C16:1 (73.0%), C18:1 (7.8%), C17:1 (6.9%), C17:0 (4.8%), C16:0 (3.7%), C19:1 (2.4%), C15:1 (0.9%), and trace amounts of C14:0, C14:1 and C15:0 [42]. The fatty acid composition and the cell wall profiles of D. proteolyticus are similar to those of D. radiodurans and D. radiophilus [41,42].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [44], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [45]. The genome project is deposited in the Genome On Line Database [26] 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 1.

Classification and general features of D. proteolyticus MRPT according to the MIGS recommendations [32] and the NamesforLife database [33].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [34]

 

Phylum “Deinococcus-Thermus

TAS [35,36]

 

Class Deinococci

TAS [37,38]

 

Order Deinococcales

TAS [5]

 

Family Deinococcaceae

TAS [1,5]

 

Genus Deinococcus

TAS [1,5]

 

Species Deinococcus proteolyticus

TAS [1]

 

Type strain MRP

TAS [1]

 

Gram stain

positive

TAS [1]

 

Cell shape

spheres; singly, in pairs or tetrads

TAS [1]

 

Motility

none

TAS [1]

 

Sporulation

none

TAS [1]

 

Temperature range

mesophile

TAS [1]

 

Optimum temperature

30°C

TAS [1]

 

Salinity

1% NaCl

TAS [1]

MIGS-22

Oxygen requirement

strictly aerobic

TAS [1]

 

Carbon source

glucose

TAS [1]

 

Energy source

chemoorganotroph

TAS [1]

MIGS-6

Habitat

soil, host

TAS [3]

MIGS-15

Biotic relationship

free-living

NAS

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [39]

 

Isolation

feces of Lama glama

TAS [3]

MIGS-4

Geographic location

not reported

 

MIGS-5

Sample collection time

1973 or before

TAS [3]

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 the Gene Ontology project [40]. If the evidence code is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements.

Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Three genomic libraries: one 454 pyrosequence standard library, one 454 PE library (8 kb insert size), one Illumina library

MIGS-29

Sequencing platforms

454-GS-FLX-Titanium, Illumina GAii

MIGS-31.2

Sequencing coverage

249.0 × Illumina; 33.0 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.3, VELVET version 0.7.63, phrap version SPS - 4.24

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002536 (chromosome)

 

CP002537-40 (plasmids pDEIRP01-04)

 

Genbank Date of Release

October 7, 2011

 

GOLD ID

Gc01666

 

NCBI project ID

41911

 

Database: IMG-GEBA

649633035

MIGS-13

Source material identifier

DSM 20540

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

D. proteolyticus MRPT, DSM 20540, was grown in DSMZ medium 53 (Corynebacterium Agar) [46] at 30°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/DL for cell lysis as described in Wu et al. [45]. DNA is available through the DNA Bank Network [47].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [48]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 75 contigs in five scaffolds was converted into a phrap [49] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (721.9 Mb) was assembled with Velvet [50] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 146.0Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [49] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [48], Dupfinisher [51], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 169 additional reactions and two shatter libraries were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [52]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 282.0 × coverage of the genome. The final assembly contained 149,969 pyrosequence and 20,053,100 Illumina reads.

Genome annotation

Genes were identified using Prodigal [53] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [54]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant 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 [55].

Genome properties

The genome consist of a 2,147,060 bp long chromosome and four large circular plasmids of 315,518 bp, 195,800 bp, 132,270 bp, and 97,188 bp length, and a G+C content of 65.6% (Table 3 and Figure 3). Of the 2,799 genes predicted, 2,741 were protein-coding genes, and 58 RNAs; 85 pseudogenes were also identified. The majority of the protein-coding genes (65.0%) 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 (plasmids not shown, but accessible through the img/er pages on the JGI web pages [48]); 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 (black), GC skew (purple/olive).

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

2,886,836

100.00

DNA coding region (bp)

2,524,665

87.45

DNA G+C content (bp)

1,894,892

65.64

Number of replicons

5

 

Extrachromosomal elements

4

 

Total genes

2,799

100.00

RNA genes

58

2.07

rRNA operons

3

 

tRNA genes

47

1.68

Protein-coding genes

2,741

97.93

Pseudo genes

85

3.04

Genes with function prediction

1,818

64.95

Genes in paralog clusters

1,029

36.76

Genes assigned to COGs

2,042

72.95

Genes assigned Pfam domains

1,982

70.81

Genes with signal peptides

986

35.23

Genes with transmembrane helices

561

20.04

CRISPR repeats

3

 
Table 4.

Number of genes associated with the general COG functional categories

Code

Value

%age

Description

J

150

6.8

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

134

6.1

Transcription

L

158

7.1

Replication, recombination and repair

B

1

0.1

Chromatin structure and dynamics

D

32

1.5

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

44

2.0

Defense mechanisms

T

93

4.2

Signal transduction mechanisms

M

101

4.6

Cell wall/membrane/envelope biogenesis

N

30

1.4

Cell motility

Z

1

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

50

2.3

Intracellular trafficking, secretion, and vesicular transport

O

95

4.3

Posttranslational modification, protein turnover, chaperones

C

122

5.5

Energy production and conversion

G

105

4.8

Carbohydrate transport and metabolism

E

177

8.0

Amino acid transport and metabolism

F

75

3.4

Nucleotide transport and metabolism

H

109

4.9

Coenzyme transport and metabolism

I

80

3.6

Lipid transport and metabolism

P

119

5.4

Inorganic ion transport and metabolism

Q

38

1.7

Secondary metabolites biosynthesis, transport and catabolism

R

299

13.5

General function prediction only

S

199

9.0

Function unknown

-

757

27.1

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Katja Steenblock (DSMZ) for growing D. proteolyticus cultures. 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 599/1-2.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
Bioscience Division, Los Alamos National Laboratory
(3)
Faculty of Pharmacy, Department of Biochemistry, Mahidol University
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Oak Ridge National Laboratory
(6)
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(7)
HZI - Helmholtz Centre for Infection Research
(8)
University of California Davis Genome Center
(9)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland

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