Open Access

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)

  • Hajnalka Kiss1, 2,
  • Markus Nett3,
  • Nicole Domin3,
  • Karin Martin3,
  • Julia A. Maresca4, 5,
  • Alex Copeland1,
  • Alla Lapidus1,
  • Susan Lucas1,
  • Kerrie W. Berry1,
  • Tijana Glavina Del Rio1,
  • Eileen Dalin1,
  • Hope Tice1,
  • Sam Pitluck1,
  • Paul Richardson1,
  • David Bruce1, 2,
  • Lynne Goodwin1, 2,
  • Cliff Han1, 2,
  • John C. Detter1, 2,
  • Jeremy Schmutz2,
  • Thomas Brettin1, 2,
  • Miriam Land1, 6,
  • Loren Hauser1, 6,
  • Nikos C. Kyrpides1,
  • Natalia Ivanova1,
  • Markus Göker7,
  • Tanja Woyke1,
  • Hans-Peter Klenk7 and
  • Donald A. Bryant4
Standards in Genomic Sciences20115:5030356

https://doi.org/10.4056/sigs.2194987

Published: 31 December 2011

Abstract

Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95T is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

Keywords

Chemoorganoheterotrophic Gram-negative gliding ensheathed filaments free-living predator Herpetosiphonaceae Chloroflexi DOEM2005

Introduction

Strain 114-95T (= ATCC 23779 = DSM 785 = CCUG 48726) is the type strain of Herpetosiphon aurantiacus, which in turn is the type species of the genus Herpetosiphon [1,2]. Because most of the species were reclassified as members of other genera in 1998 [3], only one other species currently remains in this genus: H. geysericola (Copeland 1936) Lewin 1970. The genus name, meaning gliding tube, was derived from the Greek words herpeton, gliding animal or reptile, and siphon, tube or pipe [4]. The species epithet is derived from the Neo-Latin adjective aurantiacus, meaning orange-colored [4]. Strain 114-95T was originally isolated from the slimy coating of a freshwater alga (Chara sp.) in Birch Lake, Minnesota (USA), but strains belonging to the species were also isolated from well water, cow dung, hot springs and marine shores [1]. H. aurantiacus 114-95T is capable of predation of other bacteria and can thereby destroy whole colonies [5]. It has even been suggested that Herpetosiphon spp. are capable of facultative predation by a wolf pack strategy, in which a quorum of predatory cells is required to degrade the prey organism by excreted hydrolytic enzymes [6]. Here we present a summary classification and a set of features for H. aurantiacus 114-95T, together with the description of the complete genome and its annotation.

Classification and features

A representative genomic 16S rRNA sequence of H. aurantiacus strain 114-95T was compared using NCBI BLAST [7,8] 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 [9] and the relative frequencies of taxa and keywords (reduced to their stem [10]) were determined, weighted by BLAST scores. The most frequently occurring genera were Herpetosiphon (82.9%), Chloroflexus (9.9%), ‘Kouleothrix’ (4.5%), Oscillochloris (2.2%) and ‘Chlorothrix’ (0.5%) (46 hits in total). Regarding the 13 hits to sequences from members of the species, the average identity within HSPs was 99.8%, whereas the average coverage by HSPs was 96.9%. Regarding the two hits to sequences from other members of the genus, the average identity within HSPs was 97.8%, whereas the average coverage by HSPs was 94.2%. Among all other species, the one yielding the highest score was Herpetosiphon geysericola (NR_028694), which corresponded to an identity of 97.8% and an HSP coverage of 94.2%. (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 JF098937 (‘skin popliteal fossa clone ncd1008d03c1’), which showed an identity of 98.2% and an HSP coverage of 88.3%. The most frequently occurring keywords within the labels of environmental samples that yielded hits were ‘soil’ (4.2%), ‘microbi’ (4.1%), ‘geyser’ (3.3%), ‘geotherm’ (2.9%) and ‘mat’ (2.8%) (204 hits in total). Environmental samples that yielded hits of a higher score than the highest scoring species were not found. These keywords fit well with the ecological properties reported for strain 114-95T in the original description [1].

Figure 1 shows the phylogenetic neighborhood of H. aurantiacus in a tree based upon 16S rRNA. The sequences of the five 16S rRNA gene copies in the genome differ from each other by up to two nucleotides, and differ by up to seven nucleotides from the previously published 16S rRNA sequence (M34117), which contains 64 ambiguous base calls.
Figure 1.

Phylogenetic tree highlighting the position of H. aurantiacus relative to the other type strains within the phylum Chloroflexi. The tree was inferred from 1,350 aligned characters [11,12] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [13]. Rooting was done initially using the midpoint method [14] 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 100 ML bootstrap replicates [15] (left) and from 1,000 maximum parsimony bootstrap replicates [16] (right) if the value is larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are labeled with one asterisk, and those also listed as ‘Complete and Published’ with two asterisks (see [18,19] and AP012029 for Anaerolinea thermophila, CP002084 for Dehalogenimonas lykanthroporepellens, CP001337 for Chloroflexus aggregans, CP000909 C. aurantiacus, and CP000804 for Roseiflexus castenholzii).

Table 1.

Classification and general features of H. aurantiacus 114-95T according to the MIGS recommendations [20] and the NamesforLife database [21].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [22]

 

Phylum Chloroflexi

TAS [23,24]

 

Class Chloroflexi

TAS [23,24]

 

Order Herpetosiphonales

TAS [25]

 

Family Herpetosiphonaceae

TAS [26]

 

Genus Herpetosiphon

TAS [1,2,27]

 

Species Herpetosiphon aurantiacus

TAS [1,2]

 

Type strain 114-95

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

cylindrical in unbranched sheathed filaments

TAS [1]

 

Motility

gliding

TAS [1]

 

Sporulation

not reported

 
 

Temperature range

not reported

 
 

Optimum temperature

about 30 °C

NAS

 

Salinity

not reported

 

MIGS-22

Oxygen requirement

oxic

NAS

 

Carbon source

probably carbohydrates

TAS [1]

 

Energy metabolism

chemoorganoheterotroph

TAS [1]

MIGS-6

Habitat

diverse: coating of Chara sp., lake and well water, cow dung, hot springs, marine shores

TAS [1]

MIGS-15

Biotic relationship

free living

NAS

MIGS-14

Pathogenicity

none known

NAS

 

Biosafety level

1

TAS [28]

 

Isolation

slimy coating of Chara sp.

TAS [1]

MIGS-4

Geographic location

Birch Lake, Minnesota, USA

TAS [1]

MIGS-5

Sample collection time

1961

NAS

MIGS-4.1

Latitude

45.04

 

MIGS-4.2

Longitude

94.42

 

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

390 m

NAS

Evidence codes - 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 [29].

Cells of H. aurantiacus strain 114-95T are cylindrical measuring 1–1.5 µm by 5–10 µm (Figure 2) [1]. Cells are organized in sheathed filaments of 500 µm length or more [1]. However, the existence of a sheath in the classical sense has been questioned in an analysis of the fine structure of the cells [30]. Cells of strain 114-95T stain Gram-negative, are not flagellated but are motile via gliding and divide by the formation of a transverse septum [1]. Colonies are flat, spreading, and rough, and produce an orange pigment [1]. Pigment analyses of a related strain, H. giganteus Hp a2, showed that this strain produces γ-carotene, as well as glycosylated and acyl-glycosylated derivatives of 1′-hydroxy-4-keto-gamma-carotene [31]. Strain 115-95T is catalase-positive and hydrolyzes starch, gelatine, casein and tributyrin but not cellulose [1].
Figure 2.

Scanning electron micrograph of a multicellular filament of H. aurantiacus 114-95T.

Chemotaxonomy

Data on the structure of the cell wall, quinones, cellular and polar lipids of strain 114-95T are not available, although H. giganteus Hp a2 was reported to produce menaquinones 6 and 7 [31]. Members of the Chloroflexi do not contain a lipopolysaccharide-containing outer membrane and the peptidoglycan is a variant that usually contains L-ornithine as the diamino acid [32].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing as part of the DOE Joint Genome Institute Program DOEM 2005. The genome project is deposited in the Genomes On Line Database [17] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Three genomic Sanger libraries: 3 kb pUC, 8 kb pMCL200 and fosmid pcc1Fos libraries.

MIGS-29

Sequencing platforms

ABI3730

MIGS-31.2

Sequencing coverage

11.0 × Sanger

MIGS-30

Assemblers

phrap

MIGS-32

Gene calling method

Prodigal, GenePRIMPCritica

 

INSDC ID

CP000875 (chromosome)

 

CP000876 (plasmid HAU01)

 

CP000877 (plasmid HAU02)

 

GenBank Date of Release

November 13, 2007

 

GOLD ID

Gc00677

 

NCBI project ID

16523

 

Database: IMG

2508501111

MIGS-13

Source material identifier

DSM 785

 

Project relevance

Biotechnology

Strain history

The history of strain 114-95T originates with J. G. Holt, who deposited the strain in the ATCC collection in 1961, from which it was distributed to the DSMZ and the CCUG [33].

Growth conditions and DNA isolation

H. aurantiacus strain 114-95T (DSM 785) was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ). Cells for DNA isolation were grown at 28 °C in the recommended CY liquid medium under oxic conditions with gentle shaking. DNA was isolated by the cetyl trimethylammonium bromide protocol recommended and described by the Joint Genome Institute [34]. The purity, quality and size of the bulk gDNA preparation were assessed according to DOE-JGI guidelines [34] and were consistent with JGI quality-control standards.

Genome sequencing and assembly

The genome was sequenced using a combination of 3 kb, 8 kb and fosmid DNA libraries. All general aspects of library construction and sequencing can be found at the JGI website [34]. The draft assembly contained 160 contigs in 51 scaffolds. The Phred/Phrap-/Consed software package was used for sequence assembly and quality assessment [35]. Possible mis-assemblies were corrected with Dupfinisher [36]. Gaps between contigs were closed by editing in Consed, custom priming, or PCR amplification. A total of 3,856 additional reactions and two shatter libraries were needed to close gaps and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. Together, all libraries provided 11.0 × coverage of the genome. There are 85,815 total reactions in the final assembly.

Genome annotation

Genes were identified using Prodigal [37] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [38]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform [39]

Genome properties

The genome consists of a circular chromosome (6,346,587 bp) and two circular plasmids, pHAU01 (339,639 bp) and pHAU02 (88,204 bp), respectively with an overall G+C content of 50.9% (Table 3, Figure 3, Figure 4, Figure 5 and Figure 6). These are the only plasmids that have been identified to date among the seventeen Chloroflexi strains whose genomes have been sequenced. Interestingly, the GC content of the chromosome (50.7%) is notably lower than that of pHAU01 (53.7%) or pHAU02 (53.1%). Plasmid pHAU02 is predicted to encode 71 proteins, and pHAU01 is predicted to encode 231 potential proteins, which included a variety of transposases, phage recombinases and integrases, a CRISPR and CRISPR-associated gene cluster, and a variety of predicted transcription regulators. Neither plasmid encodes a product known to be essential for cell viability. Of the 5,654 genes predicted, 5,577 were protein-coding genes, and 77 encoded RNAs; 82 pseudogenes were identified. The majority of the protein-coding genes (67.4%) 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 (not drawn to scale with plasmids). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 4.

Graphical circular map of the plasmid pHAU01. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 5.

Graphical circular map of the plasmid pHAU02 (not drawn to scale with chromosome). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 6.

Chromosome of H. aurantiacus strain 114-95T oriented to the dnaA gene (top). The inner ring shows a normalized plot of GC skew, while the center ring shows a normalized plot of GC content. The outer circle shows the distribution of secondary metabolite gene clusters. Biosynthetic gene clusters associated with thiotemplate-based assembly (PKS, NRPS) are depicted in red and bacteriocin loci are marked in black.

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

6,785,430

100.00%

DNA coding region (bp)

5,654,495

88.21%

DNA G+C content (bp)

3,453,669

50.90%

Number of replicons

3

 

Extrachromosomal elements

2

 

Total genes

5,654

100.00%

RNA genes

77

1.36%

rRNA operons

5

 

Protein-coding genes

5,577

98.64%

Pseudogenes

82

 

Genes with function prediction

3,812

67.42%

Genes in paralog clusters

505

8.93%

Genes assigned to COGs

3,831

67.76%

Genes assigned Pfam domains

3,766

66.61%

Genes with signal peptides

1,071

18.94%

Genes with transmembrane helices

1,495

26.44%

CRISPR repeats

11

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

176

4.1

Translation, ribosomal structure and biogenesis

A

3

0.1

RNA processing and modification

K

370

8.7

Transcription

L

213

5.4

Replication, recombination and repair

B

2

0.1

Chromatin structure and dynamics

D

35

0.8

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

93

2.2

Defense mechanisms

T

393

9.2

Signal transduction mechanisms

M

261

6.1

Cell wall/membrane/envelope biogenesis

N

14

0.3

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

56

1.3

Intracellular trafficking and secretion, and vesicular transport

O

142

3.3

Posttranslational modification, protein turnover, chaperones

C

205

4.8

Energy production and conversion

G

276

6.5

Carbohydrate transport and metabolism

E

307

7.2

Amino acid transport and metabolism

F

92

2.2

Nucleotide transport and metabolism

H

174

4.1

Coenzyme transport and metabolism

I

128

3.0

Lipid transport and metabolism

P

172

4.0

Inorganic ion transport and metabolism

Q

143

3.4

Secondary metabolites biosynthesis, transport and catabolism*

R

647

15.1

General function prediction only

S

349

8.2

Function unknown

-

1,823

32.2

Not in COGs

* manual annotation yielded 6.4% genes in the secondary metabolites biosynthesis, transport and catabolism category.

Insights into the genome

The phylum Chloroflexi is fascinatingly diverse and includes chlorophototrophs (Chloroflexales) as well as Gram-positive spore-forming organisms (Ktedonobacteria), reductive dehalogenating bacteria (Dehalococcoidetes), obligately aerobic heterotrophic thermophiles (Thermomicrobia), obligately anaerobic heterotrophs (Anaerolineae, Caldilineae), and marine organisms for which no example has yet been cultivated (e.g., SAR202 cluster). H. aurantiacus is described as an aerobic heterotroph from the order Herpetosiphonales, one of two orders within the class Chloroflexi. All characterized members of the other order, Chloroflexales, are chlorophototrophs. These include organisms from the genera Chloroflexus, Roseiflexus, Oscillochloris, Chloronema, Chlorothrix, and Heliothrix [40]. An organism that appears to be most similar although not very closely related to members of Anaerolinea has also recently been shown to be chlorophototrophic [41]. The genome sequence strongly supports the conclusion that H. aurantiacus is not a chlorophyll-based phototroph or an autotroph. Other than genes for carotenoid biosynthesis, a trait that is very widely distributed among members of all three kingdoms of life, no genes specifically used for photosynthetic light harvesting, electron transport, or chlorophyll biosynthesis were identified in the H. aurantiacus genome. Moreover, although Chloroflexus spp. and Roseiflexus spp. possess the genetic capacity to fix bicarbonate/CO2 by the 3-hydroxypropionate cycle, the corresponding genes are absent in H. aurantiacus [40,42].

Based upon the genes for carotenogenesis that are found in the H. aurantiacus genome, one can predict potential carotenoids that might be produced by this organism. The genome encodes homologs of crtB (phytoene synthase, crtI (phytoene desaturase), crtO (carotene 4-ketolase), crtD (hydroxyneurosporene dehydrogenase) and cruA (lycopene cyclase), and this combination of enzymes should allow this organism to produce γ-carotene derivatives with a keto-group at the 4 position. Additionally, the genome encodes cruF (γ-carotene 1′,2′-hydratase), cruC (1′-OH glycosyltransferase), and cruD, (acyl transferase) [4345]. The presence of these genes would allow H. aurantiacus to synthesize monocyclic carotenoids carrying glycosyl, or glycosyl-fatty acyl ester moieties, attached to the 1′-OH group at the ψ–end of the molecule. This biosynthetic potential is in good agreement with the carotenoid contents of H. giganteus strain Hpa2 [31] and Roseiflexus spp. strains. The former produces γ-carotene and its glycosyl and fatty acyl-glycoside ester derivatives, while the latter produce γ-carotene, 4-keto-myxocoxanthin-glucoside, and 4-keto-myxocoxanthin-glucoside fatty acyl esters [44,46].

Scanning of the H. aurantiacus genome for siderophore biosynthetic genes revealed the presence of a cluster with remarkable similarity to that of the myxobacterial iron chelator myxochelin [47]. The annotated locus (Haur_01919–Haur_01928) contains a complete set of genes for the production of 2,3-dihydroxybenzoic acid, including open reading frames encoding isochorismate synthase (Haur_01921), isochorismate hydrolase (Haur_01923) and 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (Haur_01919). Additional genes in the operon are proposed to be involved in siderophore transport and iron utilization. Direct comparison with the myxochelin (mxc) cluster from Myxococcus xanthus DK1622 reveals the absence of an aminotransferase gene analogous to mxcL. Since mxcL is crucial for the formation of myxochelin B [47], H. aurantiacus probably only produces the biosynthetic predecessor mxyochelin A for iron sequestration. Homologs of genes involved in gliding motility in Myxococcus xanthus [48,49] and Flavobacterium johnsoniae [5053] were not found in the H. aurantiacus genome. The genes required for gliding in H. aurantiacus and other members of the Chloroflexi have not yet been identified.

One of the most interesting and unique findings within the H. aurantiacus genome was the abundance of gene loci involved in secondary metabolism. Chloroflexi genomes were screened via BLASTP alignment against a representative library of conserved biosynthetic enzymes, a method proven useful in the analysis of the Salinispora tropica genome [54]. Apart from genes involved in fatty acid and carotenoid biosynthesis, no hits were obtained for the chlorophototrophic Chloroflexi (Table 5). On the other hand, families of genes encoding enzymes of secondary metabolism were found to be highly overrepresented in the H. aurantiacus genome. A total of fourteen biosynthetic gene clusters were identified and annotated, 11 of which are specific for this organism (Table 6). The combined length of these clusters is estimated to be 448.6 kb, i.e. 6.6% of the H. aurantiacus genome is dedicated to natural product assembly. The biosynthetic capacity for secondary metabolite production of H. aurantiacus is thus comparable to that of other specialist producers of secondary metabolites, such as Actinobacteria and Myxobacteria [55,56]. The distribution of the biosynthetic loci on the H. aurantiacus chromosome seems non-random, with seven of them being located between 1.8 and 2.7 Mb clockwise from the replication origin, i.e. 50% of all clusters are concentrated in a region covering only 14% of the chromosome.
Table 5.

Chloroflexi genome data and biosynthetic potential.

Organism

Size, Mb

Topology

 

Biosynthetic Gene Cluster

   

PKS

NRPS

PKS/NRPS

Bacteriocin

H. aurantiacus strain 114-95T

6.351

Circular

2

4

5

3

Chloroflexus aurantiacus J-10-fl

5.26

Circular

-

-

-

-

Chloroflexus aggregans DSM 9485

4.68

Circular

-

-

-

-

Roseiflexus castenholzii DSM 13941

5.72

Circular

-

-

-

-

Roseiflexus sp. RS-1

5.80

Circular

-

-

-

-

1chromosome only

Table 6.

Herpetosiphon aurantiacus strain 114-95T biosynthetic loci.

Type #

Location on the chromosome

Features

Product

Estimated Size [kb]

PKS/NRPS 1

Haur_01976-Haur_01989

2 PKS modules, 6 NRPS modules

Lipopeptide

47.7

2

Haur_02003 Haur_02024

1 PKS module, 11 NRPS modules, genes for the production of hydroxyphenylglycine

Glycopeptide

69.0

3

Haur_02147

1 PKS module, 1 NRPS module

Unknown

12.3

4

Haur_02568-Haur_02581

2 PKS modules, 3 NRPS modules

Depsipeptide

35.9

5

Haur_04184-Haur_04206

16 PKS modules, 7 NRPS modules, genes for the production of hydroxymalonyl-acyl carrier protein

Macrolide

112.6

PKS 1

Haur_00021

naringenin-chalcone synthase (type-III PKS)

Aromatic polyketide

1.1

2

Haur_00919-Haur_00937

iterative type-I PKS

Enediyne

27.5

NRPS 1

Haur_01684-Haur_01687

3 NRPS modules

Tripeptide

10.0

2

Haur_01919-Haur_01928

1 NRPS module

Myxochelin

14.0

3

Haur_02229-Haur_02262

9 NRPS modules

Nonapeptide

62.6

4

Haur_03313-Haur_3318

2 NRPS modules

Dipeptide

13.3

 

Haur_00966-

   

Bacteriocin

Haur_00988

genes for Ser/Thr dehydration and heterocycle formation LanM-like lanthionine synthetase LanM-like lanthionine synthetase

Thiazolylpeptide

24.2

1

Haur_01990-

Lantibiotic

11.0

2

Haur_02002-

Lantibiotic

7.4

3

Haur_03953-

  
 

Haur_03957

   

A striking feature of secondary metabolism in H. aurantiacus, which is also observed in myxobacterial and cyanobacterial genomes, is the preponderance of mixed polyketide synthase (PKS)-non-ribosomal peptide synthetase (NRPS) and NRPS gene clusters [56,57]. On the other hand, only two solely PKS systems were identified, including a type-III PKS of unknown function, as well as an iterative type-I PKS associated with enediyne biosynthesis (Table 6 and Figure 6). Enediyne clusters have as yet only been reported from Actinobacteria [58], and the presence of such a locus on the chromosome of H. aurantiacus is suggestive of horizontal gene transfer. Evidence for the recent acquisition of biosynthetic genes was obtained in case of the cluster designated pks-nrps5. This megacluster, which spans 112.6 kb of contiguous DNA on the chromosome (Table 6), is flanked both upstream and downstream by a number of transposon fragments. An above-average GC content of 66% as well as significant shifts of the latter in both border regions of the cluster suggest a foreign origin. The observation that horizontal gene transfer may account for the accumulation of biosynthetic genes is, to a degree, reminiscent of the evolution of the M. xanthus DK1622 genome [59].

Even though thiotemplate-based chemistry involving PKSs and NRPSs appears to be the predominant theme in natural product biosynthesis by H. aurantiacus, genomic analyses also revealed the molecular basis for the assembly and posttranslational modification of ribosomally encoded peptides [60,61]. Furthermore, various pathways to specific biosynthetic building blocks, such as the rare amino acid L-p-hydroxyphenylglycine [62] and the polyketide extender unit hydroxymalonyl-acyl carrier protein, were identified. The pathways are located adjacent to PKS and NRPS genes, which suggest that functional crosstalk is very likely to occur.

To date, the secondary metabolome of Herpetosiphon spp. has not been explored beyond a single report on a structurally complex, natural product, siphonazole, which likely derives from a mixed PKS-NRPS assembly line [63]. The genome sequence of H. aurantiacus strain 114-95T now certainly provides a rationale for further studies of the chemistry and biology of this versatile microorganism.

Declarations

Acknowledgements

The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 and was also supported by NSF grant MCB-0523100 to D.A.B. M.N. gratefully acknowledges the German Federal Ministry of Education and Research (BMBF 0315591A) for supporting research involving genomics within the GenoMik-Transfer framework.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
Bioscience Division, Los Alamos National Laboratory
(3)
Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute
(4)
The Pennsylvania State University
(5)
Dept. of Civil and Environmental Engineering, University of Delaware
(6)
Oak Ridge National Laboratory
(7)
Leibnitz Institute DSMZ - German Collection of Microorganisms and Cell Cultures

References

  1. Holt JG, Lewin RA. Herpetosiphon aurantiacus gen. et sp. n., a new filamentous gliding organism. J Bacteriol 1968; 95:2407–2408. PubMedPubMed CentralPubMedGoogle Scholar
  2. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. doi:10.1099/00207713-30-1-225View ArticleGoogle Scholar
  3. Sly LI, Taghavi M, Fegan M. Phylogenetic heterogeneity within the genus Herpetosiphon: transfer of the marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus to the genus Lewinella gen. nov. in the Flexibacter-Bacteroides-Cytophaga phylum. Int J Syst Bacteriol 1998; 48:731–737. PubMed doi:10.1099/00207713-48-3-731View ArticlePubMedGoogle Scholar
  4. Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed doi:10.1099/00207713-47-2-590View ArticlePubMedGoogle Scholar
  5. Quinn GR. Skerman VBD. Herpetosiphon — nature’s scavenger? Curr Microbiol 1980; 4:57–62. doi:10.1007/BF02602893View ArticleGoogle Scholar
  6. Jurkevitch E. Predatory behaviors in bacteria— diversity and transitions. Microbe 2007; 2:67–73.Google Scholar
  7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Bascic local alignment search tool. J Mol Biol 1990; 215:403–410. PubMedView ArticlePubMedGoogle Scholar
  8. Korf I, Yandell M, Bedell J. BLAST, O’Reilly, Sebastopol, 2003.Google Scholar
  9. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069–5072. PubMed doi:10.1128/AEM.03006-05PubMed CentralView ArticlePubMedGoogle Scholar
  10. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137.View ArticleGoogle Scholar
  11. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452View ArticlePubMedGoogle Scholar
  12. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMedView ArticlePubMedGoogle Scholar
  13. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642View ArticlePubMedGoogle Scholar
  14. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669–674. doi:10.1111/j.1095-8312.2007.00864.xView ArticleGoogle Scholar
  15. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.Google Scholar
  16. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Kyrpides NC. The genomes on line database (GOLD) in 2009: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848PubMed CentralView ArticlePubMedGoogle Scholar
  17. Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, et al. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 2009; 4:e4207. PubMed doi:10.1371/journal.pone.0004207PubMed CentralView ArticlePubMedGoogle Scholar
  18. Pati A, LaButti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, et al. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T). Stand Genomic Sci 2010; 2:49–56. PubMed doi:10.4056/sigs.601105PubMed CentralView ArticlePubMedGoogle Scholar
  19. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  20. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.Google Scholar
  21. Woese CR, Kandier O, Wheelis ML. Towards a natural system of organisms. Proposal for the domains Archaea and Bacteria. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  22. 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; 54:2049–2051. PubMed doi:10.1099/ijs.0.03028-0View ArticlePubMedGoogle Scholar
  23. Garrity GM, Holt JG. Phylum BVI. Chloroflexi phy. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 427–446.View ArticleGoogle Scholar
  24. Castenholz RW. Order II. ‘Herpetosiphonales’. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 444.Google Scholar
  25. Boone DR, Castenholz RW. Family I. ‘Herpetosiphonaceae’. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 445.View ArticleGoogle Scholar
  26. Lewin RA, Leadbetter ER. Genus Herpetosiphon Holt and Lewin 1968, 2408; emend. mut. char. In: Buchanan RE, Gibbons NE (eds), Bergey’s Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 107–109.Google Scholar
  27. BAuA. Classification of bacteria and archaea in risk groups. TRBA 2005; 466:205.Google Scholar
  28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  29. Reichenbach H, Golecki JR. The fine structure of Herpetosiphon, and a note on the taxonomy of the genus. Arch Microbiol 1975; 102:281–291. PubMed doi:10.1007/BF00428379View ArticlePubMedGoogle Scholar
  30. Kleinig H, Reichenbach H. Carotenoid glucosides and menaquinones from the gliding bacterium Herpetosiphon giganteus Hp a2. Arch Microbiol 1977; 112:307–310. PubMed doi:10.1007/BF00413098View ArticlePubMedGoogle Scholar
  31. Jürgen UJ, Meißner JD, Reichenbach H, Weckesser J. L-ornithine containing peptidoglycan-polysaccharide complex from the cell wall of the gliding bacterium Herpetosiphon aurantiacus. FEMS Microbiol Lett 1989; 60:247–250. doi:10.1016/0378-1097(89)90404-7View ArticleGoogle Scholar
  32. Verslyppe B, De Smet W, De Baets B, De Vos P, Dawyndt P. Make Histri: reconstructing the exchange history of bacterial and archaeal type strains. Syst Appl Microbiol 2011; 34:328–336. PubMed doi:10.1016/j.syapm.2011.01.004View ArticlePubMedGoogle Scholar
  33. The Joint Genome Institute. http://www.jgi.doe.gov/www.jgi.doe.gov
  34. Phrap and Phred for Windows. MacOS, Linux, and Unix. www.phrap.com
  35. Cliff S. Han, Patrick Chain. 2006. Finishing repeat regions automatically with Dupfinisher. Proceeding of the 2006 international conference on bioinformatics & computational biology. Edited by Hamid R. Arabnia & Homayoun Valafar, CSREA Press. June 26–29, 2006: 141–146.Google Scholar
  36. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119PubMed CentralView ArticlePubMedGoogle Scholar
  37. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457View ArticlePubMedGoogle Scholar
  38. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar
  39. Bryant DA, Liu Z, Li T, Zhao F, Garcia Costas AM, Klatt CG, Ward DM, Frigaard NU, Overmann J. Comparative and functional genomics of anoxygenic green bacteria from the taxa Chlorobi, Chloroflexi, and Acidobacteria. In: Advances in Photosynthesis and Respiration, Vol. 33, Functional Genomics and Evolution of Photosynthetic Systems, (Burnap, R. L. and Vermaas, W., eds.), pp. 47–102, Springer, Dordrecht, The Netherlands.Google Scholar
  40. Klatt CG, Wood JM, Rusch DB, Bateson MM, Hamamura N, Heidelberg JF, Grossman AR, Bhaya D, Cohan FM, Kühl M, et al. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J 2011; 5:1262–1278. PubMed doi:10.1038/ismej.2011.73PubMed CentralView ArticlePubMedGoogle Scholar
  41. Klatt CG, Bryant DA, Ward DM. Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats. Environ Microbiol 2007; 9:2067–2078. PubMed doi:10.1111/j.1462-2920.2007.01323.xView ArticlePubMedGoogle Scholar
  42. Maresca JA, Bryant DA. Identification of two genes encoding new carotenoid-modifying enzymes in the green sulfur bacterium Chlorobium tepidum. J Bacteriol 2006; 188:6217–6223. PubMed doi:10.1128/JB.00766-06PubMed CentralView ArticlePubMedGoogle Scholar
  43. Maresca JA, Graham JE, Bryant DA. Carotenoid biosynthesis in chlorophototrophs: the biochemical and genetic basis for structural diversity. Photosynth Res 2008; 97:121–140. PubMed doi:10.1007/s11120-008-9312-3View ArticlePubMedGoogle Scholar
  44. Graham JE, Bryant DA. The biosynthetic pathway for the synthesis of the myxol-2-fucoside in the cyanobacterium Synechococcus sp. strain PCC 7002. J Bacteriol 2009; 191:3292–3300. PubMed doi:10.1128/JB.00050-09PubMed CentralView ArticlePubMedGoogle Scholar
  45. Takaichi S, Maoka T, Yamada M, Matsuura K, Hikawa Y, Hanada S. Absence of carotenes and presence of a tertiary methoxy group in a carotenoid from a thermophilic filamentous photosynthetic bacterium Roseiflexus castenholzii. Plant Cell Physiol 2001; 42:1355–1362. PubMed doi:10.1093/pcp/pce172View ArticlePubMedGoogle Scholar
  46. Gaitatzis N, Kunze B, Müller R. Novel insights into siderophore formation in myxobacteria. ChemBioChem 2005; 6:365–374. PubMed doi:10.1002/cbic.200400206View ArticlePubMedGoogle Scholar
  47. Nan B, Zusman DR. Uncovering the mystery of gliding motility in Myxobacteria. Annu Rev Genet 2011; 45:21–39. PubMed doi:10.1146/annurevgenet-110410-132547PubMed CentralView ArticlePubMedGoogle Scholar
  48. Luciano J, Agrebi R, Le Gall AV, Wartel M, Fiegna F, Ducret A, Brochier-Armanet C, Mignot T. Emergence and modular evolution of a novel motility machinery in bacteria. PLoS Genet 2011; 7:e1002268. PubMed doi:10.1371/journal.pgen.1002268PubMed CentralView ArticlePubMedGoogle Scholar
  49. Rhodes RG, Samarasam MN, Shrivastava A, van Baaren JM, Pochiraju S, Bollampalli S, McBride MJ. Flavobacterium johnsoniae gldN and gldO are partially redundant genes required for gliding motility and surface localization of SprB. [P]. J Bacteriol 2010; 192:1201–1211. PubMed doi:10.1128/JB.01495-09PubMed CentralView ArticlePubMedGoogle Scholar
  50. Rhodes RG, Nelson SS, Pochiraju S, McBride MJ. Flavobacterium johnsoniae sprB is part of an operon spanning the additional gliding motility genes sprC, sprD and sprF. J Bacteriol 2011; 193:599–610. PubMed doi:10.1128/JB.01203-10PubMed CentralView ArticlePubMedGoogle Scholar
  51. Rhodes RG, Pucker HG, McBride MJ. Development and use of a gene deletion strategy for Flavobacterium johnsoniae to identify the redundant gliding motility genes remF, remG, remH, and remI. J Bacteriol 2011; 193:2418–2428. PubMed doi:10.1128/JB.00117-11PubMed CentralView ArticlePubMedGoogle Scholar
  52. Rhodes RG, Samarasam MN, Van Groll EJ, McBride MJ. Mutations in Flavobacterium johnsoniae sprE result in defects in gliding motility and protein secretion. J Bacteriol 2011; 193:5322–5327. PubMed doi:10.1128/JB.05480-11PubMed CentralView ArticlePubMedGoogle Scholar
  53. Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci USA 2007; 104:10376–10381. PubMed doi:10.1073/pnas.0700962104PubMed CentralView ArticlePubMedGoogle Scholar
  54. Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 2009; 26:1362–1384. PubMed doi:10.1039/b817069jPubMed CentralView ArticlePubMedGoogle Scholar
  55. Wenzel SC, Müller R. The impact of genomics on the exploitation of the myxobacterial secondary metabolome. Nat Prod Rep 2009; 26:1385–1407. PubMed doi:10.1039/b817073hView ArticlePubMedGoogle Scholar
  56. Nett M, König GM. The chemistry of gliding bacteria. Nat Prod Rep 2007; 24:1245–1261. PubMed doi:10.1039/b612668pView ArticlePubMedGoogle Scholar
  57. Van Lanen SG, Shen B. Biosynthesis of enediyne antitumor antibiotics. Curr Top Med Chem 2008; 8:448–459. PubMed doi:10.2174/156802608783955656PubMed CentralView ArticlePubMedGoogle Scholar
  58. Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, et al. Evolution of sensory complexity recorded in a myxobacterial genome (2006). Proc Natl Acad Sci USA 2006; 103:15200–15205. PubMed doi:10.1073/pnas.0607335103PubMed CentralView ArticlePubMedGoogle Scholar
  59. Begley M, Cotter PD, Hill C, Ross RP. Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins. Appl Environ Microbiol 2009; 75:5451–5460. PubMed doi:10.1128/AEM.00730-09PubMed CentralView ArticlePubMedGoogle Scholar
  60. Brown LCW, Acker MG, Clardy J, Walsh CT, Fischbach MA. Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin. Proc Natl Acad Sci USA 2009; 106:2549–2553. PubMed doi:10.1073/pnas.0900008106View ArticleGoogle Scholar
  61. Kastner S, Müller S, Natesan L, König GM, Guthke R, Nett M. 4-Hydroxyphenylglycine biosynthesis in Herpetosiphon aurantiacus — a case of gene duplication and catalytic divergence. submittedGoogle Scholar
  62. Nett M, Erol Ö, Kehraus S, Köck M, Krick A, Eguereva E, Neu E, König GM. Siphonazole, an unusual metabolite from Herpetosiphon sp. Angew Chem Int Ed Engl 2006; 45:3863–3867. PubMed doi:10.1002/anie.200504525View ArticlePubMedGoogle Scholar

Copyright

© The Author(s) 2011