Open Access

Genome sequence of Lysobacter dokdonensis DS-58T, a gliding bacterium isolated from soil in Dokdo, Korea

  • Min-Jung Kwak1,
  • Soon-Kyeong Kwon1,
  • Jung-Hoon Yoon2 and
  • Jihyun F. Kim1Email author
Standards in Genomic Sciences201510:123

DOI: 10.1186/s40793-015-0116-8

Received: 21 March 2015

Accepted: 25 November 2015

Published: 9 December 2015

Abstract

Lysobacter dokdonensis DS-58, belonging to the family Xanthomonadaceae, was isolated from a soil sample in Dokdo, Korea in 2011. Strain DS-58 is the type strain of L. dokdonensis. In this study, we determined the genome sequence to describe the genomic features including annotation information and COG functional categorization. The draft genome sequence consists of 25 contigs totaling 3,274,406 bp (67.24 % G + C) and contains 3,155 protein coding genes, 2 copies of ribosomal RNA operons, and 48 transfer RNA genes. Among the protein coding genes, 75.91 % of the genes were annotated with a putative function and 87.39 % of the genes were assigned to the COG category. In the genome of L. dokdonensis, a large number of genes associated with protein degradation and antibiotic resistance were detected.

Keywords

Dokdo Xanthomonadaceae Protease Peptidase Soil bacterium

Introduction

The genus Lysobacter was firstly described by Christensen and Cook in 1979 as high G + C Gram-negative bacterium with gliding motility [1]. In the past, Lysobacter species were classified as “unidentified myxobacters” due to their high G + C ratio and gliding motility. However, the genus Lysobacter has features distinctive from myxobacteria and had been proposed as a new genus of Gammaproteobacteria . Lysobacter species are ubiquitous and have been found in a variety of environments such as soil, water, and the rhizosphere. Currently, more than 30 Lysobacter species were registered in the GenBank taxonomy database and among them, 28 species have been validly published [2]. Some of the Lysobacter species were known to produce several kinds of lytic enzymes and antibiotics [3] and have an antimicrobial activity against plant pathogens [4]. Moreover, several Lysobacter species are known to produce bioactive natural products such as cyclodepsipeptide, cyclic lipodepsipeptide, cephem-type β-lactam, and polycyclic tetramate macrolactam [5]. Despite their ubiquitous distribution, many identified species, and possible usefulness as a biocontrol agent, deciphered Lysobacter genomes are relatively limited. Here, we present the genome sequence and the genomic information of Lysobacter dokdonensis DS-58T (KCTC 12822 T = DSM1 7958 T), which is the type strain of the species.

Organism information

Classification and features

L. dokdonensis DS-58T is a Gram-staining-negative, non-motile, and rod-shaped bacterium and was isolated from the soil sample in Dokdo, an island in the East Sea, Korea, in 2011 [6]. L. dokdonensis DS-58 grows at the temperature range of 4 to 38 °C, the pH range of 6.0 to 8.0, and the NaCl concentration of 0 to 0.5 % (w/v) [6]. Colony size of L. dokdonensis DS-58 is about 1.0 – 2.0 mm on nutrient agar medium and the cell size is 1.0–5.0 μm long and 0.4–0.8 μm wide [6] (Fig. 1). L. dokdonensis DS-58 can assimilate dextrin, Tween 40, maltose, α-ketobutyric acid, alaninamide, l-alanine, l-alanyl glycine, and l-glutamic acid as a carbon source [6]. Minimum information about a genome sequence (MIGS) for L. dokdonensis DS-58 is described in Table 1. Phylogenetically, L. dokdonensis DS-58 belongs to the family Xanthomonadaceae of the class Gammaproteobacteria , and the 16S rRNA gene showed the highest sequence similarity (96.93 %) with L. niastensis GH41-7. However, a phylogenetic tree based on the 16S rRNA gene showed that the strain DS-58 is located in the deep branch of the genus Lysobacter (Fig. 2).
Fig. 1

Transmission electron microscopic image of Lysobacter dokdonensis DS-58

Table 1

Classification and general features of Lysobacter dokdonensis DS-58T according to the MIGS recommendations [24]

MIGS ID

Property

Term

Evidence codea

 

Classification

Domain Bacteria

TAS [25]

  

Phylum

TAS [26]

  

Class

TAS [27]

  

Order

TAS [28]

  

Family Xanthomonadaceae

TAS [29]

  

Genus Lysobacter

TAS [30, 31]

  

Species Lysobacter dokdonensis

TAS [6]

  

Strain DS-58

TAS [6]

 

Gram stain

Negative

TAS [6]

 

Cell shape

Rod

TAS [6]

 

Motility

Non-motile

TAS [6]

 

Sporulation

Non-sporulating

TAS [6]

 

Temperature range

4–38 °C

TAS [6]

 

Optimum temperature

30 °C

TAS [6]

 

pH range; Optimum

6.0–8.0; Optimum 6.5–7.5

TAS [6]

 

Carbon source

Dextrin, Tween40, Maltose, L-Alanine, L-Glutamic acid, α-Ketobutyric acid, Alaninamide, L-Alanyl glycine

TAS [6]

MIGS-6

Habitat

Soil

TAS [6]

MIGS-6.3

Salinity

0–0.5 % NaCl (w/v)

TAS [6]

MIGS-22

Oxygen requirement

Aerobic

TAS [6]

MIGS-15

Biotic relationship

Free-living

TAS [6]

MIGS-14

Pathogenicity

Unknown

NAS

MIGS-4

Geographic location

Republic of Korea

TAS [6]

MIGS-5

Sample collection

2011

TAS [6]

MIGS-4.1

Latitude

Not reported

NAS

MIGS-4.2

Longitude

Not reported

NAS

MIGS-4.4

Altitude

Not reported

NAS

a Evidence codes—IDA Inferred from Direct Assay, 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 [32]

Fig. 2

Neighbour-joining tree of the type species of the genus Lysobacter. Neighbor-joining tree based on the 16S rRNA gene sequence was constructed using MEGA 5. The evolutionary distances were calculated using Jukes-Cantor model and phylogenetic tree was generated based on the comparison of 1,379 nucleotides. Bootstrap values (percentages of 1,000 replications) greater than 50 % are shown at each node and Xanthomonas campestris ATCC 33913 (AE008922) were used as an out-group. The scale bar represents 0.005 nucleotide substitutions per site. Accession numbers of the 16S rRNA gene are presented in the parentheses. *species whose genome has been sequenced

Genome sequencing information

Genome project history

The genome sequencing and analysis of L. dokdonensis DS-58 were performed by the Laboratory of Microbial Genomics and Systems/Synthetic Biology at Yonsei University using the next generation sequencing. The genomic information was deposited in the GenBank (Accession number is JRKJ00000000). Summary of the genome project is provided in Table 2.
Table 2

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality draft

MIGS-28

Libraries used

A 500-bp paired-end library

MIGS-29

Sequencing platforms

HiSeq2000 of Illumina/Solexa

MIGS-31.2

Fold coverage

753-fold coverage

MIGS-30

Assemblers

CLC Genomics Workbench 5.1

MIGS-32

Gene calling method

Glimmer 3

 

Locus Tag

LF41

 

Genbank ID

JRKJ00000000

 

Genbank Date of Release

November 3, 2014

 

GOLD ID

Gi0043381

 

BIOPROJECT

PRJNA260566

MIGS-13

Source Material Identifier

DS-58

 

Project relevance

Environmental, Soil bacterium

Growth conditions and genomic DNA preparation

L. dokdonensis DS-58 (accession numbers of culture collection: KCTC 12822 = DSM1 7958) was routinely cultured on nutrient medium at 30 °C. Strain DS-58 forms light yellow colored colonies with average 1.0–2.0 mm of diameter in 5 days (Table 1) [6]. For the genome sequencing, single colony of L. dokdonensis DS-58 was inoculated in nutrient medium and incubated in the shacking incubator at 30 °C. Genomic DNA was extracted using chemical and enzymatic method as described in Molecular Cloning, A Laboratory Manual [7]. Cell lysis was conducted using sodium dodecyl sulfate and proteinase K. From the cell lysate, genomic DNA was purified using phenol:chloroform, precipitated using isopropanol, and finally eluted into Tris-EDTA buffer.

Genome sequencing and assembly

For the whole genome shotgun sequencing, a library with 500-bp insert size was prepared and paired-end genome sequencing was performed with HiSeq2000 of the Illumina/Solexa platform (Macrogen, Inc., South Korea). Sequence trimming was conducted using CLC Genomics Workbench 5.1 (CLC bio, Qiagen, Netherlands) with parameters of 0.01 quality score and none of the ambiguous nucleotide. Sequence reads below 60 bp in length were discarded. After trimming, a total of 28,810,330 reads with an average read length of 95.8 bp were generated. De novo assembly was performed with CLC Genomics Workbench with parameters of automatic word and bubble size, deletion and insertion cost of 3, mismatch cost of 2, similarity fraction of 1.0, length fraction of 0.5, and minimum contig length of 500 bp. After the de novo assembly, scaffolding was performed using SSPACE [8] and automatic gap filling was carried out with IMAGE [9]. Following the automatic gap filling, manual gap filling was conducted using CLC Genomics Workbench with the function of Find Broken Pair Mates in the end of the contigs. Basic information of the genome sequencing project is described in Table 2.

Genome annotation

Structural gene prediction was conducted using Glimmer 3 [10] in RAST server [11] with automatic fixation of errors and frame shifts. Functional assignment of the predicted protein coding sequences (CDSs) was performed using AutoFact [12] with the results of BLASTP or RPS-BLAST with Uniref100, NR, COG, and Pfam databases. For the accurate annotation, the functional assignment results from the RAST server and BLAST were compared each other. When assignment of the gene function was not the same between the results from RAST and BLAST, an additional BLASTP search was performed with NR database at NCBI and the top-hit result was selected for the annotation.

Genome properties

The draft genome sequence of the strain DS-58 consists of 25 contigs and the sum of the contigs is 3,274,406 bp (G + C content 67.24 %) (Table 3 and Fig. 3). From the genome of the strain DS-58, 3,155 CDSs, 2 copies of ribosomal RNA operons, and 48 transfer RNAs were detected. Among the predicted CDSs, 2,436 CDSs were annotated with a putative function and 2,757 CDSs were assigned to a COG category. The numbers and percentages of COG assigned genes are shown in Table 4.
Table 3

Genome Statistics

Attribute

Value

% of total

Genome size (bp)

3,274,406

100.00

DNA coding (bp)

3,006,255

91.81

DNA G + C (bp)

2,201,865

67.24

DNA contigs

25

-

Total genes

3,209

100.00

Protein coding genes

3,155

98.32

RNA genes

54

1.68

Genes with function prediction

2,436

75.91

Genes assigned to COGs

2,757

85.91

Genes with Pfam domains

2,230

69.49

Genes with signal peptides

456

14.21

Genes with transmembrane helices

767

23.90

CRISPR repeats

1

-

Fig. 3

Circular representation of the draft genome of Lysobacter dokdonensis DS-58. The first circle from inside shows the 25 contigs sorted by size. The second and the third circles indicate COG- assigned genes in color codes. Yellow circle represents the G + C content and red-blue circle is for the G + C skew. Innermost, blue-scattered spots indicate the tRNA genes and red-scattered spots indicate the rRNA genes. Red lines are to indicate connections of paired-end reads at the end of each contig

Table 4

Number of protein coding genes of Lysobacter dokdonensis DS-58 associated with the general COG functional categories

Code

Value

%agea

Description

J

168

5.32

Translation, ribosomal structure and biogenesis

A

5

0.16

RNA processing and modification

K

164

5.20

Transcription

L

120

3.80

Replication, recombination and repair

B

1

0.03

Chromatin structure and dynamics

D

34

1.08

Cell cycle control, cell division, chromosome partitioning

Y

0

0.00

Nuclear structure

V

60

1.90

Defense mechanisms

T

232

7.35

Signal transduction mechanisms

M

219

6.94

Cell wall/membrane/envelope biogenesis

N

60

1.90

Cell motility

Z

3

0.10

Cytoskeleton

W

1

0.03

Extracellular structures

U

96

3.04

Intracellular trafficking, secretion, and vesicular transport

O

119

3.77

Posttranslational modification, protein turnover, chaperones

C

142

4.50

Energy production and conversion

G

90

2.85

Carbohydrate transport and metabolism

E

184

5.83

Amino acid transport and metabolism

F

57

1.81

Nucleotide transport and metabolism

H

109

3.45

Coenzyme transport and metabolism

I

114

3.61

Lipid transport and metabolism

P

113

3.58

Inorganic ion transport and metabolism

Q

55

1.74

Secondary metabolites biosynthesis, transport and catabolism

R

308

9.76

General function prediction only

S

303

9.60

Function unknown

-

398

12.61

Not in COGs

aThe percentages are based on the total number of protein coding genes in the genome

Insights from the genome sequence

Some Lysobacter species are known to produce the secondary metabolite with antimicrobial activities [13, 14]. In the genome of L. dokdonensis DS-58, biosynthetic gene clusters for a bacteriocin and an arylpolyene were detected. The structure of bacteriocin-biosynthetic gene cluster of DS-58 was similar to the one in L. arseniciresistens ZS79 and the structure of arylpolyene-biosynthetic gene cluster was similar to the one in Xanthomonas campestris NCPPB 4392 (Fig. 4).
Fig. 4

Biosynthetic gene clusters for bacteriocin and arylpolyene. Gene clusters for biosynthesis of secondary metabolites were detected using the AntiSMASH webserver [23]. a Bacteriocin-biosynthetic gene cluster. b Arylpolyene biosynthetic gene cluster. Same colors in different strains indicate the same genes. White-colored genes are genes unrelated to the secondary metabolite gene clusters. 1, hypothetical protein (LF41_2288); 2, non-heme chloroperoxidase (LF41_2289); 3, alkylhydroperoxidase (LF41_2290); 4, membrane protein-like protein (LF41_2291); 5, 23S rRNA (guanosine-2′-O-)-methyltransferase (LF41_2292); 6, permease (LF41_2293); 7, ribonuclease T (LF41_2294); 8, hypothetical protein (LF41_2295); 9, DUF692 domain containing protein (LF41_2296); 10, hypothetical protein (LF41_2297); 11, phosphate transport system regulatory protein (LF41_2298); 12, phosphate transport ATP-binding protein (LF41_2299); 13, phosphate transport system permease protein (LF41_2300); 14, phosphate transport system permease protein (LF41_2301); 15, phosphate ABC transporter, periplasmic phosphate-binding protein (LF41_2302); 16, coproporphyrinogen-III oxidase (LF41_3101); 17, DNA polymerase I (LF41_3103); 18, DUF2785 domain containing protein (LF41_3104); 19, putative exporter (LF41_3121); 20, fatty acyl-CoA synthetase (LF41_3122); 21, acyltransferase (LF41_3123); 22, dehydratase (LF41_3124); 23, acyl carrier protein (LF41_3126); 24, monooxygenase (LF41_3127); 25, pteridine-dependent deoxygenase (LF41_3128). Strains are: Lysobacter dokdonensis DS-58, Lysobacter arseniciresistens ZS79, Arenimonas composti DSM 18010, Lysobacter daejeonensis GH1-9, Xanthomonas albilineans GPE PC73, Pseudoxanthomonas suwonensis 11–1, Xanthomonas campestris NCPPB 4392, Xanthomonas vasicola NCPPB 206, Xanthomonas gardneri ATCC 19865

In the genome of L. dokdonensis DS-58, a number of genes associated with proteolysis were detected that include 63 genes encoding peptidases and 33 genes encoding proteases. Microbial proteases are among the most important industrial enzymes due to their diverse activities and the genus Bacillus is major source of protease in the market [15, 16]. Results from the text mining of annotated gene products indicated that L. dokdonensis DS-58 has more genes encoding proteases and peptidases than other genome-sequenced Lysobacter species except for L. antibioticus ASM73109v1 and L. capsici AZ78. Moreover, in the genome of the strain DS-58, genes encoding 17 β-lactamases for degrading chemicals such as β-lactam antibiotics, biotin-biosynthetic proteins, and type IV fimbrial biogenesis proteins that could be involved in gliding motility were detected.

Distinct from other genera in the Xanthomonadaceae , Lysobacter spp. exhibit gliding motility [1]. Type IV pili-associated bacterial motility is widespread in members of diverse taxa such as Proteobacteria , Bacteroidetes , and Fibrobacteres [17] and known to be responsible for S-motility in Myxococcus and twitching motility in Lysobacter [18] as well as Pseudomonas and Neisseria [19]. Thus, there is a possibility that the gliding motility of Lysobacter is associated with type IV fimbriae. On the other hand, GltA, which is involved in A-motility of Myxococcus xanthus that best fits the definition of gliding motility [20], was detected in the genome of DS-58 (56 % identity with 88 % coverage).

Lysobacter species typically have been isolated from soil and water, but several studies indicated that Lysobacter species may survive in more diverse habitats of anaerobic or extreme-cold [21, 22]. A great diversity of secreted degrading enzymes such as proteases and ß-lactamases may contribute to the adaptation of Lysobacter species to such diverse environments. Abundant genes encoding proteases and peptidases in the genome of DS-58 may contribute to the discovery of effective and commercially useful proteolytic enzymes. Moreover, in the genome of DS-58, dozens of genes involved in the biosynthesis of type IV fimbriae were detected. The mechanism of gliding motility has not yet been clearly revealed, and we expect that the genome information of DS-58 may contribute to the genetic analysis of bacterial gliding motility.

Conclusions

L. dokdonensis DS-58, the type strain of the species, is a soil bacterium isolated from Dokdo in Korea. Through a phylogenetic analysis of the 16S rRNA gene, L. dokdonensis is located in a deep branch of the genus Lysobacter . The genome sequence of L. dokdonensis DS-58 is comprised of 25 contigs of 3,274,406 bp with G + C content of 67.24 %. In the genome of DS-58, a total of 3,155 CDSs were predicted and 87.39 % of the CDSs were functionally assigned to COG categories. Dozens of genes associated with protein degradation and resistance to antibiotics were detected. Through the genome analysis of L. dokdonensis DS-58, we report that this soil bacterium harbors a large number of peptidases and proteases, which may represent a rich source of protein-degrading enzymes.

Abbreviations

COG: 

Clusters of Orthologous Groups

NR: 

Non-redundant

Uniref: 

UniProt Reference Clusters

Pfam: 

Protein families

SSPACE: 

SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension

IMAGE: 

Iterative Mapping and Assembly for Gap Elimination

RAST: 

Rapid Annotation using Subsystem Technology

AutoFACT: 

Automatic Functional Annotation and Classification Tool

BLAST: 

Basic Local Alignment Search Tool

RPS-BLAST: 

Reversed Position Specific-BLAST

MEGA: 

Molecular Evolutionary Genetics Analysis

MIGS: 

Minimum Information about a Genome Sequence

CRISPR: 

Clustered Regularly Interspaced Short Palindromic Repeat.

Declarations

Acknowledgements

This work was financially supported by the National Research Foundation (NRF-2011-0017670) of the Ministry of Science, ICT and Future Planning, Republic of Korea.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
Department of Systems Biology and Division of Life Sciences, Yonsei University
(2)
Department of Food Science and Biotechnology, Sungkyunkwan University

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Copyright

© Kwak et al. 2015