Open Access

Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type strain (IP3-3T)

  • Trent A. Key1,
  • Dray P. Richmond1,
  • Kimberly S. Bowman1,
  • Yong-Joon Cho2,
  • Jongsik Chun2,
  • Milton S. da Costa3,
  • Fred A. Rainey4 and
  • William M. Moe1Email author
Standards in Genomic Sciences201611:44

https://doi.org/10.1186/s40793-016-0165-7

Received: 13 August 2015

Accepted: 31 May 2016

Published: 23 June 2016

Abstract

Dehalogenimonas alkenigignens IP3-3T is a strictly anaerobic, mesophilic, Gram negative staining bacterium that grows by organohalide respiration, coupling the oxidation of H2 to the reductive dehalogenation of polychlorinated alkanes. Growth has not been observed with any non-polyhalogenated alkane electron acceptors. Here we describe the features of strain IP3-3T together with genome sequence information and its annotation. The 1,849,792 bp high-quality-draft genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus. The genome contains 29 predicted reductive dehalogenase genes, a large majority of which lack cognate genes encoding membrane anchoring proteins.

Keywords

Chloroflexi Dehalococcoidia Reductive dechlorination 1,2-dichloroethane 1,2-dichloropropane 1,2,3-trichloropropane

Introduction

Strain IP3-3T (=JCM 17062, =NRRL B-59545) is the type strain of the species Dehalogenimonas alkenigignens [1]. Currently, two pure cultures of D. alkenigignens have been described, namely, D. alkenigignens strains IP3-3T and SBP-1 [1]. Both strains were isolated from chlorinated alkane- and alkene-contaminated groundwater collected at a Superfund Site near Baton Rouge, Louisiana (USA) [1]. Construction of 16S rRNA gene libraries indicated that bacteria closely related or identical to D. alkenigignens were present at high relative abundance in the groundwater where strains IP3-3T and SBP-1 were first isolated [1].

Strains of D. alkenigignens possess the unique trait of growing via organohalide respiration, a process in which halogenated organic compounds are utilized as terminal electron acceptors. In particular, they are able to reductively dehalogenate a variety of polychlorinated alkanes that are of environmental concern on account of their potential to cause adverse health effects and their widespread occurrence as soil and groundwater pollutants [14]. In this report, we present a summary classification and a set of features for D. alkenigignens IP3-3T together with the description of the draft genomic sequence and annotation.

Organism information

Classification and features

Dehalogenimonas alkenigignens is a member of the order Dehalococcoidales , class Dehalococcoidia , of the phylum Chloroflexi (Table 1). Based on 16S rRNA gene sequences, the closest related type strains are Dehalogenimonas lykanthroporepellens BL-DC-9T [1, 5] and Dehalococcoides mccartyi 195T [6], with sequence identities of 96.2 and 90.6 %, respectively [1].
Table 1

Classification and general features of Dehalogenimonas alkenigignens strain IP3-3T according to the MIGS recommendations [55]

MIGS ID

Property

Term

Evidence codea

 

Classification

Domain Bacteria

TAS [56]

  

Phylum Chloroflexi

TAS [57, 58]

  

Class Dehalococcoidia

TAS [6]

  

Order Dehalococcoidales

TAS [6]

  

Family Not reported

 
  

Genus Dehalogenimonas

TAS [5]

  

Species Dehalogenimonas alkenigignens

TAS [1]

  

Type strain IP3-3T

TAS [1]

 

Gram stain

Negative

TAS [1]

 

Cell shape

Coccoid, irregular

TAS [1]

 

Motility

Non-motile

TAS [1]

 

Sporulation

Nonsporulating

TAS [1]

 

Temperature range

18–42 °C

TAS [1]

 

Optimum temperature

32–34 °C

TAS [1]

 

pH range; Optimum

6.0–8.0; 6.5–7.5

TAS [1]

 

Carbon source

Not reported

 

MIGS-6

Habitat

Groundwater

TAS [1, 2]

MIGS-6.3

Salinity

<2 % NaCl (w/v)

TAS [1]

MIGS-22

Oxygen requirement

Obligate anaerobic

TAS [1]

MIGS-15

Biotic relationship

Free-living

NAS

MIGS-14

Pathogenicity

Non-pathogen

NAS

MIGS-4

Geographic location

Louisiana, USA

TAS [1]

MIGS-5

Sample collection

2009

IDA

MIGS-4.1

Latitude

30.590270

TAS [1]

MIGS-4.2

Longitude

−91.221288

TAS [1]

MIGS-4.4

Altitude

22 m

IDA

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 [59]

Figure 1 shows the phylogenetic neighborhood of D. alkenigignens strain IP3-3T in a 16S rRNA gene based phylogenetic dendrogram. The sequence of the lone 16S rRNA gene copy in the draft genome is identical to the previously published 16S rRNA gene sequence (JQ994266).
Fig. 1

Phylogenetic tree showing the position of D. alkenigignens IP3-3T (shown in bold) relative to the other species of the genus Dehalogenimonas and type species of other genera within the phylum Chloroflexi. The tree was inferred from 1392 aligned nucleotide positions of the 16S rRNA gene sequence using the Neighbor-Joining method within the MEGA v4.0.2 package [60]. Scale bar represents 2 substitutions per 100 nucleotide positions. Numbers at branching points denote support values from 1000 bootstrap replicates if larger than 70 %. Lineages with published genomes are: Anaerolinea thermophila UNI-1T (AP012029), Ardenticatena maritima 110ST (LGKN00000000), Bellilinea caldifistulae GOMI-1T (BBXX00000000), Caldilinea aerophila STL-6-O1T (AP012337), Chloroflexus aurantiacus J-10-flT (CP000909), Dehalococcoides mccartyi 195 T (CP000027), Dehalogenimonas alkenigignens IP3-3T (LFDV00000000), Dehalogenimonas lykanthroporepellens BL-DC-9T (CP002084), Herpetosiphon aurantiacus DSM 785T (CP000875), Kallotenue papyrolyticum JKG1T (JAGA00000000), Ktedonobacter racemifer SOSP1-21T (ADVG00000000), Leptolinea tardivitalis YMTK-2T (LGCK00000000), Levilinea saccharolytica KIBI-1 T (BBXZ00000000), Longilinea arvoryzae KOME-1T (BBXY00000000), Nitrolancea hollandica LbT (CAGS00000000), Ornatilinea apprima P3M-1T (LGCL00000000), Oscillochloris trichoides DG-6T (ADVR00000000), Roseiflexus castenholzii DSM 13941T (CP000804), Sphaerobacter thermophiles DSM 20745T (CP001823), “Thermanaerothrix daxensis” GNS-1 (LGKO00000000), “Thermobaculum terrenum” YNP1 (CP001825), Thermomicrobium roseum DSM 5159T (CP001275), and Thermorudis peleae KI4 T (JQMP00000000)

The cells of D. alkenigignens IP3-3T are Gram negative staining, non-spore forming, irregular cocci to disk-shaped with a diameter of 0.4–1.1 μm [1] (Fig. 2). The strain was isolated in liquid medium using a dilution-to-extinction approach. Growth of the strain was not observed on agar plates even after long term (2 months) incubation [1]. The temperature range for growth of strain IP3-3T is between 18 °C and 42 °C with an optimum between 30 °C and 34 °C [1]. The pH range for growth is 6.0 to 8.0 with an optimum of 7.0 to 7.5 [1]. The strain grows in the presence of <2 % (w/v) NaCl and is resistant to ampicillin and vancomycin at concentrations of 1.0 and 0.1 g/l, respectively [1].
Fig. 2

Scanning electron micrograph of cells of D. alkenigignens strain IP3-3T

D. alkenigignens IP3-3T is a strictly anaerobic chemotroph, coupling utilization of H2 as an electron donor and polychlorinated aliphatic alkanes as electron acceptors for growth. The chlorinated compounds known to be reductively dehalogenated include 1,2-dichloroethane, 1,2-dichloropropane, 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane, and 1,2,3-trichloropropane [1]. In all of the reductive dechlorination reactions characterized to date, strain IP3-3T appears to exclusively utilize vicinally halogenated alkanes as electron acceptors via dihaloelimination reactions (i.e., simultaneous removal of two chlorine atoms from adjacent carbon atoms with concomitant formation of a carbon-carbon double bond) [1]. Strain IP3-3T does not utilize carbon tetrachloride (tetrachloromethane), 1-chlorobenzene, chloroform, 1-chloropropane, 2-chloropropane, 1,2-dichlorobenzene, 1,1-dichloroethane, cis-1,2-dichloroethene, trans-1,2-dichloroethene, methylene chloride (dichloromethane), tetrachloroethene, 1,1,1-trichloroethane, or vinyl chloride as electron acceptors [1]. Growth is not supported by acetate, butyrate, citrate, ethanol, fructose, fumarate, glucose, lactate, lactose, methanol, methyl ethyl ketone, propionate, pyruvate, succinate, or yeast extract in the absence of H2 [1].

Although sufficiently high chlorinated alkane concentrations were found to become inhibitory, D. alkenigignens IP3-3T was shown to reductively dehalogenate 1,2-dichloroethane, 1,2-dichloropropane, and 1,1,2-trichloroethane when present at initial aqueous-phase concentrations as high as 9.81 ± 0.98, 5.05 ± .29, and 3.49 ± 0.31 mM, respectively [4]. When grown in the presence of mixtures of chlorinated alkanes, preferential dechlorination of 1,1,2-trichloroethane over both 1,2-dichloroethane and 1,2-dichloropropane was observed [3]. 1,2-Dichloroethane in particular was not dechlorinated until 1,1,2-trichloroethane reached low concentrations. In contrast, D. alkenigignens IP3-3T concurrently dechlorinated 1,2-dichloroethane and 1,2-dichloropropane over a comparably large concentration range [3].

Chemotaxonomic data

The major cellular fatty acids of D. alkenigignens IP3-3T are C18:1 ω9c, C16:0, C14:0, and C16:1 ω9c [1]. The same fatty acids were also present in the closely related D. alkenigignens strain SBP-1 [1]. Cellular fatty acids present in lower proportions include C18:0, C18:3 ω6c(6,9,12), and unidentified fatty acids with equivalent chain lengths of 11.980, 13.768, 13.937, and 15.056 [1].

Genome sequencing information

Genome project history

D. alkenigignens IP3-3T was chosen for genome sequencing because it is the type strain of the species and because of the importance of organohalide respiration in the field of environmental biotechnology and bioremediation. A summary of the project information is shown in Table 2. The D. alkenigignens strain IP3-3T genome project is deposited in the Genomes OnLine Database [7] and the genome sequence is available from GenBank.
Table 2

Genome sequencing project information for Dehalogenimonas alkenigignens IP3-3T

MIGS ID

Property

Term

MIGS 31

Finishing quality

Improved high-quality draft

MIGS-28

Libraries used

Three libraries: 454 Titanium standard library, 454 paired-end library (8 kb insert size), and Illumina TruSeq library

MIGS 29

Sequencing platforms

454 Titanium standard, 454 Titanium paired-end, Illumina MiSeq

MIGS 31.2

Fold coverage

42.35× (454 standard), 29.86× (454 paired-end), 583.50× (Illumina)

MIGS 30

Assemblers

Roche gsAssembler 2.6, CLCbio CLC Genomics Workbench 6.5.1

MIGS 32

Gene calling method

Prodigal

 

Locus Tag

DEALK

 

Genbank ID

LFDV00000000

 

GenBank Date of Release

December 15, 2015

 

GOLD ID

Gp0085286

 

BIOPROJECT

PRJNA261058

MIGS 13

Source Material Identifier

IP3-3T (=JCM 17062 = NRRL B-59545)

 

Project relevance

Bioremediation, Environmental, Tree of Life

Growth conditions and genomic DNA preparation

D. alkenigignens strain IP3-3T (=JCM 17062, =NRRL B-59545) was cultured in liquid anaerobic basal medium [1] supplemented with 2 mM 1,2-dichloropropane. Cells were harvested from 9.9 L culture medium by centrifugation after at least 50 % of the starting 1,2-dichloropropane was dehalogenated. Total DNA was extracted using a GenElute Bacterial Genomic DNA kit (Sigma-Aldrich) following the manufacturer’s recommended protocol. Eluted DNA was concentrated using ethanol precipitation, air dried, and reconstituted in TE buffer (10 mM Tris–HCl, 0.5 mM EDTA, pH 9.0).

Genome sequencing and assembly

The genome of D. alkenigignens IP3-3T was sequenced using a combination of Illumina [8] and 454 technologies [9]. A total of three libraries were constructed, a 454 Titanium standard library which generated 234,711 reads (42.35-fold coverage; 78.34 Mb), a 454 Titanium paired-end libraries with insert size of 8 kb which generated 238,686 reads (29.86-fold coverage; 55.23 Mb), and an Illumina paired-end library which generated 7,147,715 reads (read length 150 bp; 583.50-fold coverage; 1079.35 Mb). Libraries were prepared using 454 standard and paired-end protocols and the Illumina TruSeq DNA sample preparation protocol, as provided by each manufacturer.

The 454 Titanium standard data and the 454 paired-end data were assembled with gsAssembler ver. 2.6 (Roche). Illumina data were assembled with CLC Genomics Workbench ver. 6.5.1 (CLCbio). Each of the resulting scaffolds and contigs were integrated using CodonCode Aligner ver. 3.7.1 (CodonCode Corporation). Also, Illumina sequencing reads were mapped to the final contigs to correct misassembles and base errors. The final assembly generated one scaffold including two contigs representing 1,849,792 bp based on 655.71× coverage of 454 and Illumina sequencing data.

Genome annotation

Genes were identified using Prodigal [10] as part of the JGI’s microbial annotation pipeline [11] followed by a round of manual curation using the JGI GenePRIMP pipeline [12]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [13], RNAMMer [14], Rfam [15], TMHMM [16], ARAGORN [17], bSECISearch [18], and signal [19]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes - Expert Review platform [20].

Genome properties

The draft genome of D. alkenigignens strain IP3-3T has a total length of 1,849,792 bp with 55.88 % G + C content (Table 3 and Fig. 3). Of the 1988 genes predicted, 1936 were protein-coding genes and 52 were RNAs. The majority of the protein-coding genes (74.9 %) were assigned a putative function, and the remaining were annotated as hypothetical proteins. The distribution of the predicted protein coding genes into COG functional categories is presented in Table 4.
Table 3

Genome statistics for Dehalogenimonas alkenigignens IP3-3T

Attribute

Value

% of Total

Genome size (bp)

1,849,792

100.00 %

DNA coding (bp)

1,667,990

90.17 %

DNA G + C (bp)

1,033,591

55.88 %

DNA scaffolds

1

 

Total genes

1988

100.00 %

Protein coding genes

1936

97.38 %

RNA genes

52a

2.62 %

Pseudo genes

4

0.20 %

Genes in internal clusters

1270

63.88 %

Genes with function prediction

1489

74.90 %

Genes assigned to COGs

1164

58.55 %

Genes with Pfam domains

1505

75.70 %

Genes with signal peptides

57

2.87 %

Genes with transmembrane helices

455

22.89 %

CRISPR repeats

0

0 %

a The genome contains a single large subunit rRNA (23S-5S) locus and a single, orphan, small subunit rRNA (16S) locus

Fig. 3

Graphical circular map of the largest contig. From the outside to the center: RNA genes (rRNAs in red and tRNAs in blue), genes on the reverse strand (colored according to the COGs categories), genes on the forward strand (colored according to the COGs categories), GC skew (where yellow indicates positive values and blue indicates negative values), GC ratio (shown in red/green, which indicates positive/negative, respectively)

Table 4

Number of protein coding genes of Dehalogenimonas alkenigignens IP3-3T associated with general COG functional categories

Code

Value

%agea

Description

J

156

12.06

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

70

5.41

Transcription

L

69

5.33

Replication, recombination and repair

B

2

0.15

Chromatin structure and dynamics

D

10

0.77

Cell cycle control, Cell division, chromosome partitioning

V

17

1.31

Defense mechanisms

T

68

5.26

Signal transduction mechanisms

M

29

2.24

Cell wall/membrane biogenesis

N

11

0.85

Cell motility

U

14

1.08

Intracellular trafficking and secretion

O

77

5.95

Posttranslational modification, protein turnover, chaperones

C

99

7.65

Energy production and conversion

G

46

3.55

Carbohydrate transport and metabolism

E

142

10.97

Amino acid transport and metabolism

F

50

3.86

Nucleotide transport and metabolism

H

91

7.03

Coenzyme transport and metabolism

I

45

3.48

Lipid transport and metabolism

P

82

6.34

Inorganic ion transport and metabolism

Q

14

1.08

Secondary metabolites biosynthesis, transport and catabolism

R

124

9.58

General function prediction only

S

66

5.10

Function unknown

-

824

41.45

Not in COGs

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

Insights from the genome sequence

Comparative genomics

The draft genome of D. alkenigignens IP3-3T is 163,282 bp larger than that of D. lykanthroporepellens BL-DC-9T (1,686,510 bp) and 380,072 bp larger than Dehalococcoides mccartyi 195T (1,469,720 bp). Although the genomes of D. alkenigignens IP3-3T, D. lykanthroporepellens BL-DC-9T [21], and Dehalococcoides mccartyi strains [2224] contain similar number of rRNA and tRNA encoding genes, they lack overall synteny and differ in their GC content, gene density, and percentage of sequence that encodes proteins.

BLAST comparisons of protein sets of D. alkenigignens IP3-3T and D. lykanthroporepellens BL-DC-9T revealed that the two strains contain 1154 protein coding genes in common (bidirectional best hits, 20-95 % identity at the predicted protein level). Bidirectional best-hit comparisons indicated that D. alkenigignens IP3-3T contains 782 protein-coding genes with no homologs in D. lykanthroporepellens BL-DC-9T. The latter contained 566 protein-coding genes with no homologs in D. alkenigignens IP3-3T. Genome-specific genes identified in D. alkenigignens IP3-3T and D. lykanthroporepellens BL-DC-9T included those that encoded transposases, restriction endonucleases, acetyltransferases, permeases, reductases, hydrogenases, and dehalogenases. Some of these strain-specific genes were associated with IS elements.

Nine signature indels (insertions or deletions) specific for predicted proteins of the class Dehalococcoidia (which at present includes only the genera Dehalococcoides and Dehalogenimonas ) were recently reported based on the results of comparative analyses of previously reported genomes [25]. Of the nine proteins in which conserved signature indels were reported as specific for the class Dehalococcoidia [25], all were found to be present in the predicted proteins of D. alkenigignens IP3-3T, including those for a GTP binding protein LepA (DEALK_16110), F0F1-type ATP synthase alpha subunit (DEALK_14680), imidazoleglycerol-phosphate dehydratase (DEALK_15410), glycine/serine hydroxymethyltransferase (DEALK_18820), adenylate kinase (DEALK_03090), hydrogenase formation/expression protein HypD (DEALK_04300), DNA gyrase subunit A (DEALK_05640), excinuclease ABC subunit A (DEALK_13870), and ribulose-phosphate 3-epimerase (DEALK_13610). Of the conserved signature proteins (CSPs) that were reported previously to be specific for the class Dehalococcoidia [25], however, several did not have homologs in D. alkenigignens IP3-3T (DET0078, DET0236, DET0307, DET0767, DET1026, DET1283, and DET1511). Furthermore, four conserved signature proteins reported as specific for the genus Dehalococcoides [25] (DET0939, DET1011, DET1322, and DET1557) were found to have homologs in Dehalogenimonas alkenigignens IP3-3T (DEALK_12980, DEALK_11520, DEALK_01350, and DEALK_19030, respectively), indicating that these proteins are not as narrowly confined to the genus Dehalococcoides as once thought.

The genome of D. alkenigignens IP3-3T contains 47 tRNA genes, including those for all 20 standard amino acids as well as the less common amino acid selenocysteine. Consistent with the presence of a selC gene (DEALK_t00110) encoding a selenocysteine-inserting tRNA (tRNAsec), D. alkenigignens strain IP3-3T also contains genes that are putatively involved in synthesis of selenocysteine (DEALK_04960-04970) and a GTP-dependent selenocysteine-specific elongation factor (DEALK_04950) that forms a quaternary complex with selenocysteine-tRNAsec and the selenocysteine inserting sequence (SECIS), a hairpin loop found immediately downstream of the UGA codon in selenoprotein-encoding mRNA [26]. This complex facilitates reading through the UGA codon and incorporation of selenocysteine instead of translation termination [27]. Also consistent with the presence of the genes encoding the synthesis and incorporation of selenocysteine, D. alkenigignens strain IP3-3T contains multiple genes encoding putative selenocysteine-containing proteins including a selenophosphate synthase (DEALK_04975) and formate dehydrogenase (DEALK_19115) that have internal in-frame UGA stop codons followed by putative SECIS elements [18].

A number of microorganisms accumulate low molecular weight organic compounds commonly referred to as “compatible solutes” that help the microorganisms survive osmotic stress but do not interfere with metabolism [28]. Ectoine is a compatible solute of many mesophilic bacteria capable of survival at high salt concentrations [28], while mannosylglycerate is a compatible solute accumulated by many thermophilic organisms [29]. Homologs of a gene encoding a bifunctional mannosylglycerate synthase (mgsD) are found in Dehalococcoides mccartyi strains (e.g., DET1363) and D. lykanthroporepellens BL-DC-9T (Dehly_0877), an unusual occurrence for mesophilic bacteria [21, 29]. Comparative analysis revealed that D. alkenigignens IP3-3T contains a homologous gene (DEALK_12650, 55–70 % protein identity). This expands the range of mesophilic species containing genes putatively involved in the biosynthesis of mannosylglycerate. D. alkenigignens IP3-3T, however, lacks the operon (ectABC) encoding putative homologs of the enzymes involved in ectoine biosynthesis and regulation that were found to be present in D. lykanthroporepellens BL-DC-9T (Dehly_1306, Dehly_1307, Dehly_1308). The presence of these ectoine encoding genes in D. lykanthroporepellens BL-DC-9T but not D. alkenigignens IP3-3T may account for the ability of the former to reductively dechlorinate polychlorinated alkanes in the presence of higher NaCl concentrations than was observed for D. alkenigignens IP3-3T [1].

Reductive dehalogenases

Genes encoding the enzymes characterized to date that are involved in catalyzing the reductive dehalogenation of chlorinated solvents are organized in rdhAB operons encoding a ~500 aa protein (RdhA) that functions as a reductive dehalogenase and a ~90 aa hydrophobic protein with transmembrane helices (RdhB) that is thought to anchor the RdhA to the cytoplasmic membrane [3041]. D. alkenigignens IP3-3T contains several loci, accounting for 2.38 % of the genome, related to rdhA and/or rdhB genes scattered throughout the genome. The multiple rdhA and rdhB ORFs of D. alkenigignens IP3-3T have 32–97 % and 32–43 % identities at the predicted protein level, respectively. The closest homologs for most of the D. alkenigignens IP3-3T rdhA ORFs (Table 5) are found among Dehalogenimonas lykanthroporepellens BL-DC-9T, Dehalococcoides mccartyi strains, or uncultured bacteria. A twin-arginine motif followed by a stretch of hydrophobic amino acids, was identified in the N-terminus of a large majority (27 of 29) of the predicted RdhA sequences (Table 5). Consistent with the presence of the twin-arginine sequence in the N-terminus of most of its RdhA sequences, D. alkenigignens IP3-3T contains an operon encoding proteins that constitute a putative twin-arginine translocation (TAT) system (DEALK_04830-04860). This specialized system is involved in the secretion of folded proteins across the bacterial inner membrane into the periplasmic space [42, 43]. Dehalogenimonas lykanthroporepellens BL-DC-9T also contains an operon encoding an analogous TAT system that is related to the TAT system of D. alkenigignens IP3-3T (55–86 % protein identity).
Table 5

Characteristics of putative reductive dehalogenases (rdhA) of Dehalogenimonas alkenigignens IP3-3T

Locus tag

ORF size (bp)

mol% G + C

Protein size (aa)

TAT Signal Sequence

Fe-S binding motif #1

Fe-S binding motif #2

Cognate rdhB

Closest homolog

Accession/locus tag

Identity

Size (aa)

DEALK_00310

1344

44.64

447

-

CX2CX2CX3C

CX10CX2CX3C

None

DET0876

38 %

510

DEALK_00330

1584

45.58

527

+

CX2CX2CX3C

CX11CX2CX3C

None

GY50_1378

38 %

508

DEALK_01520

1566

58.88

521

+

CX2CX2CX3C

CX9CX2CX3C

None

DGWBC_1268

43 %

500

DEALK_04890

1593

50.03

530

+

CX2CX2CX3C

CX8CX4CX3C

None

DGWBC_1769

81 %

531

DEALK_05980

1515

62.44

504

+

CX2CX2CX3C

CX2CX3C

None

DGWBC_1268

42 %

500

DEALK_05990

1542

59.27

513

+

CX2CX2CX3C

CX12CX2CX3C

None

BAI47820.1

60 %

490

DEALK_06000

1518

58.56

505

+

CX2CX2CX3C

CX12CX2CX3C

None

BAI47820.1

59 %

490

DEALK_06060

1416

59.82

471

+

CX2CX2CX3C

CX9CX4CX3C

None

Dehly_0849

68 %

475

DEALK_06310

1422

54.57

473

+

CX2CX2CX3C

CX9CX2CX3C

None

DhcVS_1421

63 %

475

DEALK_06360

1527

58.74

508

+

CX2CX2CX3C

CX12CX2CX3C

None

DGWBC_1268

44 %

500

DEALK_07340

1398

59.73

465

+

CX2CX2CX3C

CX8CX2CX3C

None

AGY79010.1

63 %

413

DEALK_07360

1398

54.01

465

+

CX2CX2CX3C

CX8CX2CX3C

None

Dehly_1582

75 %

452

DEALK_08250

1575

52.38

524

+

CX2CX2CX3C

CX10CX2CX3C

None

X793_01190

45 %

514

DEALK_08260

1566

56.64

521

+

CX2CX2CX3C

CX9CX2CX3C

None

X793_01190

42 %

514

DEALK_08270

1518

50.00

505

+

CX2CX2CX3C

CX8CX2CX3C

None

DGWBC_1584

77 %

502

DEALK_11210

1404

56.91

467

+

CX2CX2CX3C

CX8CX2CX3C

None

Dehly_0121

69 %

469

DEALK_11290

1527

61.03

508

+

CX2CX2CX3C

CX9CX2CX3C

DEALK_11280

BAG72164.1

42 %

504

DEALK_11300

1416

56.64

471

+

CX2CX2CX3C

CX2CX2CX3C

None

AGY79025.1

75 %

367

DEALK_11330

1401

59.10

466

+

CX2CX2CX3C

CX2CX2CX3C

None

AGY79025.1

77 %

367

DEALK_11430

1575

53.14

524

+

CX2CX2CX3C

CX10CX2CX3C

None

X793_01190

44 %

514

DEALK_16100

1386

55.27

461

+

CX2CX2CX3C

CX9CX4CX3C

None

Dehly_0068

69 %

460

DEALK_16320

1401

58.82

466

+

CX2CX2CX3C

CX8CX2CX3C

None

DGWBC_0119

74 %

474

DEALK_16330

1515

61.65

504

+

CX2CX2CX3C

CX9CX2CX3C

None

DGWBC_0120

80 %

502

DEALK_17120

1449

46.79

482

+

CX2CX2CX3C

CX8CX2CX3C

None

CEP66756.1

42 %

449

DEALK_17180

849

42.84

282

-

None

None

None

Dehly_1523

92 %

340

DEALK_17200

1455

44.47

484

+

CX2CX2CX3C

CX2CX3C

DEALK_17210

AGS15112.1

95 %

484

DEALK_17450

1563

58.99

520

+

CX2CX2CX3C

CX9CX2CX3C

None

X793_01190

42 %

514

DEALK_17880

1641

60.69

546

+

CX2CX2CX3C

CX2CX3C

None

DGWBC_1268

40 %

500

DEALK_19050

1506

50.60

501

+

CX2CX2CX3C

CX2CX2CX3C

DEALK_19040

DhcVS_96

61 %

496

Two conserved motifs each containing three or four cysteine residues, a feature associated with binding iron-sulfur clusters [44], were identified near the C-terminus of 28 of the 29 predicted RdhA sequences of D. alkenigignens IP3-3T. The first of these motifs had a consistent number of cysteine residues and consistent number of amino acids between the cysteine residues (CX2CX2CX3C), while the second motif was variable (Table 5). If a “full-length” rdhA is predicted to encode a protein containing a twin-arginine sequence in the N-terminus, two iron-sulfur cluster binding motifs in the C-terminus, and an intervening sequence of ~450 aa, then D. alkenigignens IP3-3T contains 27 such genes, a number appreciably larger than the 17 such genes found in Dehalogenimonas lykanthroporepellens BL-DC-9T [21]. One of the non-full length rdhA genes (DEALK_17180) contains a predicted internal stop codon that putatively prevents complete translation of what would otherwise be a 458 aa protein containing two iron-sulfur binding clusters. rdhA genes with internal stop codons have been reported previously among the genomes of other organohalide respiring strains of the genera Dehalococcoides [24] and Dehalobacter [45, 46].

Within D. alkenigignens IP3-3T, only three of the rdhA ORFs (DEALK_11290, DEALK_17200, and DEALK_19050) have a cognate rdhB (Table 6). Two additional rdhB genes (DEALK_00250 and DEALK_05730) appear to be orphans with no cognate rdhA ORF. In at least one locus (DEALK_00250), it appears that transposon insertion has truncated the rdhA gene (annotated as pseudogene DEALK_00260). The predicted RdhB sequences of strain IP3-3T each contain two or three transmembrane helices (Table 6), similar to the features of the predicted RdhB sequences of Dehalogenimonas lykanthroporepellens BL-DC-9T and Dehalococcoides mccartyi strains [21, 22, 24, 47]. The predicted RdhB sequences of D. alkenigignens IP3-3T are most closely related to the RdhB of D. lykanthroporepellens strain BL-DC-9T, Dehalococcoides mccartyi strain GY, and an uncultured bacterium designated as Dehalogenimonas sp. WBC-2 [48] (45-96 % identity at the protein level, Table 6). As was observed for D. lykanthroporepellens BL-DC-9T [21], genes putatively involved in the regulation of rdhAB operons in Dehalococcoides mccartyi strains (e.g., MarR-type or two-component transcriptional regulators [22, 24]) were not present in a majority of the rdhA loci of D. alkenigignens IP3-3T. Thus, it appears that regulation of rdh gene expression within the genus Dehalogenimonas may generally differ from that of the genus Dehalococcoides .
Table 6

Putative reductive dehalogenase membrane anchoring proteins (rdhB) of Dehalogenimonas alkenigignens IP3-3T

Locus tag

ORF size (bp)

mol% G + C

Protein size (aa)

TMa

Cognate rdhA

Closest homolog

Locus tag

Identity

Size (aa)

DEALK_00250

285

42.81

94

3

None b

GY50_1377

45 %

91

DEALK_05730

270

58.52

89

3

None

DGWBC_0212

85 %

89

DEALK_11280

294

59.52

97

3

DEALK_11290

Dehly_1504

56 %

88

DEALK_17210

228

37.28

75

2

DEALK_17200

Dehly_1525

96 %

72

DEALK_19040

279

49.46

92

3

DEALK_19050

Dehly_0276

70 %

91

a Number of transmembrane helices as predicted by TMHMM2.0 [16]

b A pseudogene (DEALK_00260) upstream of the putative rdhB gene is predicted to encode a 33 aa fragment with high sequence identity (63 %) with the C-terminus of a putative reductive dehalogenase of Dehalococcoides mccartyi 195T (DET0235)

The predicted RdhA protein encoded by the rdhAB operon comprised of DEALK_17200-17210 shares 95 % identity with the 1,2-dichloropropane reductive dehalogenases (dcpAs) recently identified in Dehalococcoides mccartyi strains KS and RC and 92 % identity with the related dcpA in D. lykanthroporepellens BL-DC-9T [39]. The putative membrane anchoring protein encoded by the rdhB (DEALK_17210) adjacent to the dcpA gene is also related (92–96 % identity at the protein level) to the RdhB cognate dcpA of D. lykanthroporepellens BL-DC-9T and Dehalococcoides mccartyi strains KS and RC [39]. Interestingly, the putative dcpA gene present in D. alkenigignens IP3-3T had mismatches with all four primers/probes that were reported [39] for use in PCR or qPCR for detection and quantification of this gene (1 mismatch with dcpA-360 F, 3 mismatches with dcpA-1257 F, and two mismatches each with dcpA-1426R and dcpA-1449R).

The presence of insertion sequence elements adjacent to some rdhA/rdhB loci in D. alkenigignens IP3-3T indicates their acquisition from an unknown host. Previous studies of D. lykanthroporepellens BL-DC-9T and Dehalococcoides strains have also suggested horizontal transfer of reductive dehalogenase genes [21, 49, 50]. Additionally, the genomic region downstream of the ssrA gene (DEALK_tm00010) in D. alkenigignens IP3-3T shares some synteny with the mobile genetic elements reported for vinyl chloride reductases in Dehalococcoides strains [49]. A 22 bp direct repeat of the 3’ end of the ssrA gene adjacent to one of the rdhA loci in D. alkenigignens IP3-3T (DEALK_11430) suggests that integration at the ssrA gene may have played a role in shaping the genome of D. alkenigignens IP3-3T.

It remains to be determined if D. alkenigignens IP3-3T rdhA genes lacking an rdhB ORF downstream encode functional reductive dehalogenases and whether or how they are membrane-bound. It is possible that a non-contiguous rdhB (e.g., the orphan DEALK_005730) could complement one or more of the strain IP3-3T rdhA genes lacking an rdhB ORF downstream. Alternatively, some of these genes may encode reductive dehalogenases that are not membrane bound or that are bound by an unknown mechanism. The finding that many of the D. lykanthroporepellens BL-DC-9T rdhA genes lacking cognate rdhB genes are simultaneously transcribed during the reductive dechlorination of 1,2-dichloroethane, 1,2-dichloropropane, and 1,2,3-trichloropropane [51] suggests that rdhA genes lacking a cognate rdhB may serve a purpose. An enzyme involved in the reductive dehalogenation of tetrachloroethene by Sulfurospirillum multivorans (basonym Dehalospirillum multivorans [52, 53]) was found in the cytoplasmic fraction [54], suggesting that some reductive dehalogenases are either loosely membrane-bound or soluble entities. The same may be the case for the majority of reductive dehalogenases of D. alkenigignens IP3-3T.

Conclusions

Genomic analysis of D. alkenigignens IP3-3T revealed the presence of components associated with synthesis of selenocysteine-containing proteins as well as numerous reductive dehalogenase homologous genes not previously studied. As with the related species D. lykanthroporepellens but in contrast to other dechlorinating genera, a large majority of the reductive dehalogenase homologous genes in D. alkenigignens IP3-3T lack apparent cognate genes encoding membrane anchoring components. The sequences of these diverse genes may aid future studies aimed at elucidating the strain’s mechanisms for transforming polychlorinated alkanes. The absence of genes encoding enzymes involved in ectoine biosynthesis in the genome of D. alkenigignens IP3-3T may account for the strain’s inability to dehalogenate chlorinated alkanes at higher NaCl concentrations that were observed for strains of the related species D. lykanthroporepellens .

Declarations

Acknowledgements

This research was financially supported by a consortium of petrochemical companies. The work conducted by TK was supported in part by U.S. National Science Foundation grant DGE-1247192. The authors gratefully acknowledge Xiao Ying for assistance with scanning electron microscopy.

Authors’ contributions

TK and KB carried out the microbial cultivation and genomic DNA isolation. YC and JC supervised and participated in sequencing and assembly. TK, DR, and WM participated in sequence alignment and conducted manual curation. TK, DR, KB, YC, JC, MC, FR, and WM all participated in drafting the manuscript. All authors read and approved the manuscript.

Competing interests

The authors declare that they have no competing interests.

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)
Louisiana State University
(2)
ChunLab, Inc., Seoul National University
(3)
Department of Life Sciences, University of Coimbra
(4)
University of Alaska Anchorage

References

  1. Bowman KS, Nobre MF, da Costa MS, Rainey FA, Moe WM. Dehalogenimonas alkenigignens sp. nov., a chlorinated alkane dehalogenating bacterium isolated from groundwater. Int J Syst Evol Microbiol. 2013;63:1492–8. doi:10.1099/ijs.0.045054-0. pmid:22888191.View ArticlePubMedGoogle Scholar
  2. Chen J, Bowman KS, Rainey FA, Moe WM. Reassessment of PCR primers targeting 16S rRNA genes of the organohalide-respiring genus Dehalogenimonas. Biodegradation. 2014;25:747–56. doi:10.1007/s10532-014-9696-z. pmid: 24989478.View ArticlePubMedGoogle Scholar
  3. Dillehay JL, Bowman KS, Yan J, Rainey FA, Moe WM. Substrate interactions in dehalogenation of 1,2-dichloroethane, 1,2-dichloropropane, and 1,1,2-trichloroethane mixtures by Dehalogenimonas spp. Biodegradation. 2014;25:301–12. doi:10.1007/s10532-013-9661-2. pmid:23990262.View ArticlePubMedGoogle Scholar
  4. Maness AD, Bowman KS, Yan J, Rainey FA, Moe WM. Dehalogenimonas spp. can reductively dehalogenate high concentrations of 1,2-dichloroethane, 1,2-dichloropropane, and 1,1,2-trichloroethane. AMB Express. 2012;2:54. doi:10.1186/2191-0855-2-54. pmid:23046725.View ArticlePubMedPubMed CentralGoogle Scholar
  5. Moe WM, Yan J, Nobre MF, da Costa MS, Rainey FA. Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductive dehalogenating bacterium isolated from chlorinated solvent contaminated groundwater. Int J Syst Evol Microbiol. 2009;59:2692–7. doi:10.1099/ijs.0.011502-0. pmid:19625421.View ArticlePubMedGoogle Scholar
  6. Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, et al. Dehalococcoides mccartyi gen. nov., sp. nov., obligate organohalide-respiring anaerobic bacteria, relevant to halogen cycling and bioremediation, belong to a novel class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol. 2013;63:625–35. doi:10.1099/ijs.0.034926-0. pmid:22544797.View ArticlePubMedGoogle Scholar
  7. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, et al. The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012;40:D571–9. doi:10.1093/nar/gkr1100. pmid:22135293.View ArticlePubMedGoogle Scholar
  8. Bennett S. Solexa Ltd. Pharmacogenomics. 2004;5:433–8. pmid:15165179.View ArticlePubMedGoogle Scholar
  9. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376–80. doi:10.1038/nature03959. pmid:16056220.PubMedPubMed CentralGoogle Scholar
  10. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 2010;11:119. doi:10.1186/1471-2105-11-119. pmid:20211023.View ArticleGoogle Scholar
  11. Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IM-A, Pati A, Nielsen T, Markowitz VM, Kyrpides NC. The Standard Operating Procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci. 2015;10:86. doi:10.1186/s40793-015-0077-y. pmid:26512311.View ArticlePubMedPubMed CentralGoogle Scholar
  12. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, et al. GenePRIMP: a gene prediction improvement pipeline for microbial genomes. Nat Methods. 2010;7:455–7. doi:10.1038/nmeth.1457. pmid:20436475.View ArticlePubMedGoogle Scholar
  13. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64. doi:10.1093/nar/25.5.955. pmid:9023104.View ArticlePubMedPubMed CentralGoogle Scholar
  14. Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 2007;35:3100–8. doi:10.1093/nar/gkm160. pmid:17452365.View ArticlePubMedPubMed CentralGoogle Scholar
  15. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31:439–41. doi:10.1093/nar/gkg006. pmid:12520045.View ArticlePubMedPubMed CentralGoogle Scholar
  16. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Molecular Biol. 2001;305:567–80. doi:10.1006/jmbi.2000.4315. pmid:11152613.View ArticleGoogle Scholar
  17. Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004;32:11–6. doi:10.1093/nar/gkh152. pmid:14704338.View ArticlePubMedPubMed CentralGoogle Scholar
  18. Zhang Y, Gladyshev VN. An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes. Bioinformatics. 2005;21:2580–9. doi:10.1093/bioinformatics/bti400. pmid:15797911.View ArticlePubMedGoogle Scholar
  19. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Molecular Biol. 2004;340:783–95. doi:10.1016/j.jmb.2004.05.028. pmid:15223320.View ArticleGoogle Scholar
  20. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25:2271–8. doi:10.1093/bioinformatics/btp393. pmid:19561336.View ArticlePubMedGoogle Scholar
  21. Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, et al. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to “Dehalococcoides” strains. Stand Genomic Sci. 2012;6:251–64. doi:10.4056/sigs.2806097. pmid:22768368.View ArticlePubMedPubMed CentralGoogle Scholar
  22. Kube M, Beck A, Zinder SH, Kuhl H, Reinhardt R, Adrian L. Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol. 2005;23:1269–73. doi:10.1038/nbt1131. pmid:16116419.View ArticlePubMedGoogle Scholar
  23. Pöritz M, Goris T, Wubet T, Tarkka MT, Buscot F, Nijenhuis I, et al. Genome sequences of two dehalogenation specialists – Dehalococcoides mccartyi strains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region. FEMS Microbiol Lett. 2013;343:101–4. doi:10.1111/1574-6968.12160. pmid:23600617.View ArticlePubMedGoogle Scholar
  24. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, et al. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science. 2005;307:105–8. doi:10.1126/science.1102226. pmid:15637277.View ArticlePubMedGoogle Scholar
  25. Ravinesan DA, Gupta RS. Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia. Int J Syst Evol Microbiol. 2014;64:2176–81. doi:10.1099/ijs.0.057919-0. pmid: 24676731.View ArticlePubMedGoogle Scholar
  26. Donovan J, Copeland PR. Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins. BMC Evol Biol. 2009;9:229. doi:10.1186/1471-2148-9-229. pmid:19744324.View ArticlePubMedPubMed CentralGoogle Scholar
  27. Zavacki AM, Mansell JB, Chung M, Klimovitsky B, Harney JW, Berry MJ. Coupled tRNA(Sec)-dependent assembly of the selenocysteine decoding apparatus. Mol Cell. 2003;11:773–81. doi:10.1016/S1097-2765(03)00064-9. pmid:12667458.View ArticlePubMedGoogle Scholar
  28. Santos H, da Costa MS. Compatible solutes in organisms that live in hot saline environments. Environ Microbiol. 2002;4:501–9. doi:10.1046/j.1462-2920.2002.00335.x. pmid:12220406.View ArticlePubMedGoogle Scholar
  29. Empadinhas N, Albuquerque L, Costa J, Zinder SH, Santos MA, Santos H, et al. A gene from the mesophilic bacterium Dehalococcoides ethenogenes encodes a novel mannosylglycerate synthase. J Bacteriol. 2004;186:4075–84. doi:10.1128/JB.186.13.4075-4084.2004. pmid:15205409.View ArticlePubMedPubMed CentralGoogle Scholar
  30. Adrian L, Rahnenfuhrer J, Gobom J, Holscher T. Identification of a chlorobenzene reductive dehalogenase in Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol. 2007;73:7717–24. doi:10.1128/AEM.01649-07. pmid:17933933.View ArticlePubMedPubMed CentralGoogle Scholar
  31. Fung JM, Morris RM, Adrian L, Zinder SH. Expression of reductive dehalogenase genes in Dehalococcoides ethenogenes strain 195 growing on tetrachloroethene, trichloroethene, or 2,3-dichlorophenol. Appl Environ Microbiol. 2007;73:4439–45. doi:10.1128/AEM.00215-07. pmid:17513589.View ArticlePubMedPubMed CentralGoogle Scholar
  32. Holscher T, Gorisch H, Adrian L. Reductive dehalogenation of chlorobenzene congeners in cell extracts of Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol. 2003;69:2999–3001. doi:10.1128/AEM.69.5.2999-3001.2003. pmid:12732577.View ArticlePubMedPubMed CentralGoogle Scholar
  33. Hug L, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L. Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Philos Trans R Soc Lond B Biol Sci. 2013;368:20120322. doi:10.1098/rstb.2012.0322. pmid:23479752.View ArticlePubMedPubMed CentralGoogle Scholar
  34. Magnuson JK, Romine MF, Burris DR, Kingsley MT. Trichloroethene reductive dehalogenase from Dehalococcoides ethenogenes: sequence of tceA and substrate range characterization. Appl Environ Microbiol. 2000;66:5141–7. doi:10.1128/AEM.66.12.5141-5147.2000. pmid:11097881.View ArticlePubMedPubMed CentralGoogle Scholar
  35. Müller JA, Rosner BM, von Abendroth G, Meshulam-Simon G, McCarty PL, Spormann AM. Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution. Appl Environ Microbiol. 2004;70:4880–8. doi:10.1128/AEM.70.8.4880-4888.2004. pmid:15294827.View ArticlePubMedPubMed CentralGoogle Scholar
  36. Maillard J, Schumacher W, Vazquez F, Regeard C, Hagen WR, Holliger C. Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. Appl Environ Microbiol. 2003;69:4628–38. doi:10.1128/AEM.69.8.4628-4638.2003. pmid:12902251.View ArticlePubMedPubMed CentralGoogle Scholar
  37. Neumann A, Wohlfarth G, Diekert G. Tetrachloroethene dehalogenase from Dehalospirillum multivorans: cloning, sequencing of the encoding genes, and expression of the pceA gene in Escherichia coli. J Bacteriol. 1998;180:4140–5. pmid:9696761.PubMedPubMed CentralGoogle Scholar
  38. Nijenhuis I, Zinder SH. Characterization of hydrogenase and reductive dehalogenase activities of Dehalococcoides ethenogenes strain 195. Appl Environ Microbiol. 2005;71:1664–7. doi:10.1128/AEM.71.3.1664-1667.2005. pmid:15746376.View ArticlePubMedPubMed CentralGoogle Scholar
  39. Padilla-Crespo E, Yan J, Swift C, Wagner DD, Chourey K, Hettich RL, et al. Identification and environmental distribution of dcpA, which encodes the reductive dehalogenase catalyzing the dichloroelimination of 1,2-dichloropropane to propene in organohalide-respiring Chloroflexi. Appl Environ Microbiol. 2014;80:808–18. doi:10.1128/AEM.02927-13. pmid:24242248.View ArticlePubMedPubMed CentralGoogle Scholar
  40. Suyama A, Yamashita M, Yoshino S, Furukawa K. Molecular characterization of the PceA reductive dehalogenase of Desulfitobacterium sp. strain Y51. J Bacteriol. 2002;184:3419–28. doi:10.1128/JB.184.13.3419-3428.2002. pmid:12057934.View ArticlePubMedPubMed CentralGoogle Scholar
  41. Thibodeau J, Gauthier A, Duguay M, Villemur R, Lepine F, Juteau P, et al. Purification, cloning, and sequencing of a 3,5-dichlorophenol reductive dehalogenase from Desulfitobacterium frappieri PCP-1. Appl Environ Microbiol. 2004;70:4532–7. doi:10.1128/AEM.70.8.4532-4537.2004. pmid:15294782.View ArticlePubMedPubMed CentralGoogle Scholar
  42. Stanley NR, Palmer T, Berks BC. The twin arginine consensus motif of Tat signal peptides is involved in Sec-independent protein targeting in Escherichia coli. J Biol Chem. 2000;275:11591–6. doi:10.1074/jbc.275.16.11591. pmid:10766774.View ArticlePubMedGoogle Scholar
  43. Sargent F, Berks BC, Palmer T. Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins. FEMS Microbiol Lett. 2006;254:198–207. doi:10.1111/j.1574-6968.2005.00049.x. pmid:16445746.View ArticlePubMedGoogle Scholar
  44. Bruschi M, Guerlesquin F. Structure, function and evolution of bacterial ferredoxins. FEMS Microbiol Rev. 1988;4:155–75. doi:10.1111/j.1574-6968.1988.tb02741.x. pmid:3078742.View ArticlePubMedGoogle Scholar
  45. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, et al. Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration. Arch Microbiol. 1998;169:313–21. doi:10.1007/s002030050577. pmid:9531632.View ArticlePubMedGoogle Scholar
  46. Kruse T, Maillard J, Goodwin L, Woyke T, Teshima H, Bruce D, et al. Complete genome sequence of Dehalobacter restrictus PER-K23T. Stand Genomic Sci. 2013;8:375–88. doi:10.4056/sigs.3787426. pmid:24501624.View ArticlePubMedPubMed CentralGoogle Scholar
  47. McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, Wagner R, et al. Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet. 2009;5:e1000714. doi:10.1371/journal.pgen.1000714. pmid:19893622.View ArticlePubMedPubMed CentralGoogle Scholar
  48. Molenda O, Quaile AT, Edwards EA. Dehalogenimonas WBC-2 genome and identification of its trans-dichloroethene reductive dehalogenase, TdrA. Appl Environ Microbiol. In press. doi:10.1128/AEM.02017-15 pmid:26452554Google Scholar
  49. McMurdie PJ, Hug LA, Edwards EA, Holmes S, Spormann AM. Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides. BMC Genomics. 2011;12:287. doi:10.1186/1471-2164-12-287. pmid:21635780.View ArticlePubMedPubMed CentralGoogle Scholar
  50. Krajmalnik-Brown R, Sung Y, Ritalahti KM, Saunders FM, Löffler FE. Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiol Ecol. 2007;59:206–14. doi:10.1111/j.1574-6941.2006.00243.x. pmid:17233752.View ArticlePubMedGoogle Scholar
  51. Mukherjee K, Bowman KS, Rainey FA, Siddaramappa S, Challacombe JF, Moe WM. Dehalogenimonas lykanthroporepellens BL-DC-9T simultaneously transcribes many rdhA genes during organohalide respiration with 1,2-DCA, 1,2-DCP, and 1,2,3-TCP as electron acceptors. FEMS Microbiol Lett. 2014;354:111–8. doi:10.1111/1574-6968.12434. pmid:24673292.View ArticlePubMedGoogle Scholar
  52. Scholz-Muramatsu H, Neumann A, Meßmer M, Moore E, Diekert G. Isolation and characterization of Dehalospirillum multivorans gen. nov., sp. nov., a tetrachloroethene-utilizing, strictly anaerobic bacterium. Arch Microbiol. 1995;163:48–56. doi:10.1007/BF00262203.View ArticleGoogle Scholar
  53. Luijten MLGC. de Weert J, Smidt Hauke, Boschker HTS, de Vos WM, Schraa G, Stams AJM. Description of Sulfurospirillum halorespirans sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov. Int J Syst Evol Microbiol. 2003;53:787–93. doi:10.1099/ijs.0.02417-0. pmid:12807201.View ArticlePubMedGoogle Scholar
  54. Miller E, Wohlfarth G, Diekert G. Studies on tetrachloroethene respiration in Dehalospirillum multivorans. Arch Microbiol. 1996;166:379–87. doi:10.1007/s0020300503991. pmid:9082914.View ArticlePubMedGoogle Scholar
  55. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7. doi:10.1038/nbt1360. pmid:18464787.View ArticlePubMedPubMed CentralGoogle Scholar
  56. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9. doi:10.1073/pnas.87.12.4576. pmid:2112744.View ArticlePubMedPubMed CentralGoogle Scholar
  57. Garrity GM, Phylum HJG, BVI. Chloroflexi phy. nov. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s Manual of Systematic Bacteriology. Volume 1. 2nd ed. New York: Springer; 2001. p. 427–46.View ArticleGoogle Scholar
  58. Hugenholtz P, Stackebrandt E. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol. 2004;54:2049–51. doi:10.1099/ijs.0.03028-0. pmid:15545432.View ArticlePubMedGoogle Scholar
  59. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9. doi:10.1038/75556. pmid:10802651.View ArticlePubMedPubMed CentralGoogle Scholar
  60. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9. doi:10.1093/molbev/msm092. pmid:17488738.View ArticlePubMedGoogle Scholar

Copyright

© The Author(s). 2016