Open Access

Complete genome sequence of Actinosynnema mirum type strain (101T)

  • Miriam Land1, 2,
  • Alla Lapidus1,
  • Shanmugam Mayilraj3, 4,
  • Feng Chen1,
  • Alex Copeland1,
  • Tijana Glavina Del Rio1,
  • Matt Nolan1,
  • Susan Lucas1,
  • Hope Tice1,
  • Jan-Fang Cheng1,
  • Olga Chertkov1, 5,
  • David Bruce1, 5,
  • Lynne Goodwin1, 5,
  • Sam Pitluck1,
  • Manfred Rohde6,
  • Markus Göker3,
  • Amrita Pati1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Amy Chen7,
  • Krishna Palaniappan7,
  • Loren Hauser1, 2,
  • Yun-Juan Chang1, 2,
  • Cynthia C. Jeffries1, 2,
  • Thomas Brettin1, 5,
  • John C. Detter1, 5,
  • Cliff Han1, 5,
  • Patrick Chain1, 8,
  • Brian J. Tindall3,
  • Jim Bristow1,
  • Jonathan A. Eisen1, 9,
  • Victor Markowitz7,
  • Philip Hugenholtz1,
  • Nikos C. Kyrpides1 and
  • Hans-Peter Klenk3
Standards in Genomic Sciences20091:1010046

DOI: 10.4056/sigs.21137

Published: 20 July 2009

Abstract

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actinosynnemataceae, a rapidly growing family within the actinobacterial suborder Pseudonocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

Synnemata motile spores soluble pigments mesophile aerobic aerial and substrate mycelium nocardicin A producer Actinosynnemataceae

Introduction

Strain 101T (DSM 43827 = ATCC 29888 = NBRC 14064, and other culture collections) is the type strain of Actinosynnema mirum, which is the type species of the genus Actinosynnema [1] (Figure 1). A. mirum was described by Hasegawa et al. in 1978 [1] as an aerobic actinobacterium which forms synnemata (compacted groups of erect hyphae which bear conidia) with zoospores [1]. The organism is of interest due to its position in the tree of life where the small genus Actino-synnema, currently comprising only two species, is located on a rather long branch within the rapidly growing actinobacterial suborder Pseudo-nocardineae [2]. We here present a summary classification and a set of features for A. mirum strain 101T (Table 1), together with the description of the complete genomic sequencing and annotation.
Figure 1.

Phylogenetic tree highlighting the position of A. mirum 101T relative to all type strains of the genus and to the type strains of the type species of all other genera within the family. The tree was inferred from 1,491 aligned characters [5,6] of the 16S rRNA gene sequence under the maximum likelihood criterion [7] and rooted in accordance with current actinobacterial taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with a type strain genome-sequencing project registered in GOLD [8] are printed in blue; published genomes in bold.

Table 1.

Classification and general features of A. mirum 101T in accordance with the MIGS recommendations [13]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

 
 

Phylum Actinobacteria

 
 

Class Actinobacteria

TAS [2]

 

Order Actinomycetales

TAS [2]

 

Suborder Pseudonocardineae

TAS [2]

 

Family Actinosynnemataceae

TAS [11]

 

Genus Actinosynnema

TAS [1]

 

Species Actinosynnema mirum

TAS [1]

 

Type strain 101

 
 

Gram stain

positive

TAS [1]

 

Cell shape

hyphae, aerial and substrate mycelium

TAS [1]

 

Motility

cells nonmotile; spores motile

TAS [1]

 

Sporulation

sporulating

TAS [1]

 

Temperature range

mesophilic

TAS [1]

 

Optimum temperature

10–30°C

TAS [1]

 

Salinity

no growth at 5g NaCl/l

TAS [1]

MIGS-22

Oxygen requirement

essentially aerobic; moderate growth under CO2 atmosphere

TAS [1]

 

Carbon source

glucose, maltose, mannose, cellobiose

TAS [1]

 

Energy source

chemoorganotrophic

TAS [1]

MIGS-6

Habitat

soil, river side

TAS [1]

MIGS-15

Biotic relationship

free-living

NAS

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [14]

 

Isolation

grass blade

TAS [1]

MIGS-4

Geographic location

Raritan River, New Jersey

TAS [1]

MIGS-5

Sample collection time

September 1976

TAS [1]

MIGS-4.1

Latitude - Longitude

40.491816, −74.322087

NAS

MIGS-4.2

 

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

not reported

 

Evidence codes - IDA: Inferred from Direct Assay (first time in publication); TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [15]. If the evidence code is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements.

Classification and features

No closely related cultivated strains are known from the literature that can be linked to the species A. mirum. Curiously, the 16S rRNA gene sequences of the type strains from the two subspecies within the second species of the genus Actinosynnema, A. pretiosum subsp. auranticum (AB303364) and A. pretiosum subsp. pretiosum (AB303365) [3], seem to have an equally or even higher degree of similarity to the 16S rRNA gene sequence derived from the genome sequence reported here than the previously reported gene sequences of strain 101T (see Figure 1). None of the phylotypes reported from environmental screenings or genomic surveys could be linked to A. mirum with a convincing degree of sequence similarity (maximal observed degree of similarity 92%; status June 2009).

A. mirum strain 101T cells are non-motile with fine hyphae which form aerial and substrate mycelia. Both the aerial and substrate mycelia are about 0.5 to 1.0 µm in diameter. Aerial mycelia are long branching hyphae, white to pale yellow in color (Figure 2). The substrate mycelia are also long, branching hyphae, white to yellowish orange, and penetrate into the agar medium and form synnemata [1]. Cells stain Gram-positive and are non-acid fast [1].
Figure 2.

Scanning electron micrograph (SEM) of A. mirum 101T. More SEMs of A. mirum can be found in the Compendium of the Actinobacteria, by Joachim M. Wink, University of Braunschweig.

A. mirum is capable of producing a yellowish-brown soluble pigment on tyrosine agar and a pale greenish pigment on oatmeal agar [1]. Capable of hydrolyzing starch, casein, tyrosine and gelatin, but not xanthine, hypoxanthine, adenine and urea [1]; produces nitrate reductase and phosphatase. Positive for utilization of tartrate, pyruvate, lactate and malate, but negative for benzoate, acetate, citrate and succinate [1]. Acid is produced aerobically from fructose, lactose, maltose, D-mannitol, L-arabinose, D-melibiose, D-mannose, L-rhamnose, xylose, dextrin, galactose, glucose, trehalose, raffinose, starch, sucrose, cellobiose, glycogen and adonitol, but not from inositol, sorbitol, D-ribose, salicin, inulin, glycerol, dulcitol, erythritol, α-methyl-D-glucoside and α-methyl-D-mannoside. A. mirum is a producer of nocardicin antibiotics [4] and inhibits the growth of several Gram-positive bacteria including: Bacillus megaterium, Sarcina lutea, Mycobacterium smegmatis; as well as the filamentous fungi, Aspergillus niger, Penicillium notatum and the yeasts, Saccharomyces cerevisiae and Candida tropicalis.

Figure 1 shows the phylogenetic neighborhood of A. mirum strain 101T in a 16S rRNA based tree. The sequences of the five 16S rRNA genes in the A. mirum genome differ by no more than one nucleotide (nt) from each other, and by up to six nts from the previously reported reference sequences derived from NBRC 14064 (AF328679) and from DSM 43827 (X84447). The differences between the genome data and the previously reported 16S rRNA gene sequence are probably due to sequencing errors in the previously reported sequence data.

Chemotaxonomy

The peptidoglycan of A. mirum contains meso-diaminopimelic acid in addition to alanine, glutamic acid and glucosamine. Galactose and mannose are present in the cell wall sugars, whereas madurose is absent. Cell wall type III has been detected, as well as whole-cell sugar pattern of type C [1]. The fatty acid pattern of strain 101T is dominated by saturated straight chain acids, C17:0 (15.2%), C16:0 (4.8%), C15:0 (2.6%), and branched chain acids, anteiso-(ai-)C13:0 (11.6%), ai-C15:0 (5.9%), ai-C17:0 (4.5%), ai-C11:0 (2.3%), and iso-(i-)C12:0 (11.3%), i-C16:0 (7.5%), i-C14:0 (3.5%), i-C15:0 (2.1%), i-C11:0 (1.5%). Unsaturated straight chain acids play only a limited role: C17:1 cis9 (11.3%), and C16:1 cis9 (3.4%) are present, whereas unsaturated branched chain fatty acids are absent. Minor amounts of hydroxylated fatty acids were detected: C16:1 2OH (1.0%), ai-C15:0 2OH (0.9%), and C15:0 3OH (0.5%) [Cellular fatty acids data from RM Kroppenstedt, DSMZ, unpublished]. The published literature on the fatty acid patterns is, however, contradictory, with Hasegawa et al. [3], and Yassin et al [9]. emphasizing the presence of branched chain fatty acids (including a 10-methyl C18:0), but neither unsaturated nor hydroxylated fatty acids are reported. The major polar lipids present are: diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidyl inositol mannosides (PIM) and phosphatidylinositol (PI) [9]. Hydroxy-phosphatidylethanolamine (OH-PE) has been reported by some authors [10,12], but not by others [9,10]. MK-9(H4) and MK-9(H6) are the predominant menaquinones [9].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genomes OnLine Database [8] and the complete genome sequence in GenBank (CP001630). 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

Two genomic libraries: 8kb pMCL200 and fosmid pcc1Fos Sanger libraries.

One 454 pyrosequence standard library

MIGS-29

Sequencing platforms

ABI3730, 454 GS FLX

MIGS-31.2

Sequencing coverage

8.9x Sanger; 20x pyrosequence

MIGS-30

Assemblers

Newbler version 1.1.02.15, phrap

MIGS-32

Gene calling method

Prodigal

 

Genbank ID

CP001630

 

Genbank Date of Release

not available

 

GOLD ID

Gc01024

 

NCBI project ID

19705

 

Database: IMG-GEBA

2501533214

MIGS-13

Source material identifier

DSM 43827

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

A. mirum strain 101T, DSM 44827, was grown in DSMZmedium535 (GYM Streptomyces Medium at 28°C. DNA was isolated from 1–1.5 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) with a modified lysis buffer (1 ml achromopeptidase and 0.5 ml lysostaphin added) and one hour incubation at 37°C.

Genome sequencing and assembly

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found on the JGIwebsite. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 10,493 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [16]. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. 1,564 Sanger finishing reads were produced 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 sequence types provided 28.9x coverage of the genome. The final assembly contains 105,508 Sanger reads in addition to the 454 based pseudo reads.

Genome annotation

Genes were identified using Prodigal [17] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [18]. 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 IntegratedMicrobialGenomes (IMG-ER) platform [19].

Genome properties

The genome is 8,248,144 bp long and comprises one circular chromosome with a 73.7% GC content (Table 3 and Figure 3). Of the 7,174 genes predicted, 7100 were protein coding genes, and 74 RNAs., One hundred and eight four pseudogenes were also identified. The majority of genes (67.3%) of the genes were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The prop-erties and the statistics of the genome are summarized in Table 3. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

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

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

8,248,144

 

DNA Coding region (bp)

7,331,694

88.89%

DNA G+C content (bp)

6,079,614

73.71%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

7174

 

RNA genes

74

1.07%

rRNA operons

5

 

Protein-coding genes

7100

98.93%

Pseudo genes

184

2.56%

Genes with function prediction

4835

67.37%

Genes in paralog clusters

1404

19.56%

Genes assigned to COGs

4487

62.52%

Genes assigned Pfam domains

4849

67.56%

Genes with signal peptides

1722

23.99%

Genes with transmembrane helices

1590

21.15%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the 21 general COG functional categories

Code

Value

%

Description

J

182

2.6

Translation, ribosomal structure and biogenesis

A

2

0.0

RNA processing and modification

K

607

8.5

Transcription

L

173

2.4

Replication, recombination and repair

B

2

0.0

Chromatin structure and dynamics

D

34

0.5

Cell cycle control, mitosis and meiosis

Y

0

0.0

Nuclear structure

V

96

1.4

Defense mechanisms

T

389

5.5

Signal transduction mechanisms

M

210

3.0

Cell wall/membrane biogenesis

N

45

0.6

Cell motility

Z

1

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

46

0.6

Intracellular trafficking and secretion

O

149

2.1

Posttranslational modification, protein turnover, chaperones

C

306

4.3

Energy production and conversion

G

441

6.2

Carbohydrate transport and metabolism

E

425

6.0

Amino acid transport and metabolism

F

108

1.5

Nucleotide transport and metabolism

H

223

3.1

Coenzyme transport and metabolism

I

226

3.2

Lipid transport and metabolism

P

241

3.4

Inorganic ion transport and metabolism

Q

265

3.7

Secondary metabolites biosynthesis, transport and catabolism

R

670

9.4

General function prediction only

S

328

4.6

Function unknown

-

2613

36.8

Not in COGs

Declarations

Acknowledgements

We gratefully acknowledge the help of Marlen Jando for growing A. mirum cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
Oak Ridge National Laboratory
(3)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(4)
Microbial Type Culture Collection, Institute of Microbial Technology
(5)
Bioscience Division, Los Alamos National Laboratory
(6)
HZI - Helmholtz Centre for Infection Research
(7)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(8)
Lawrence Livermore National Laboratory
(9)
University of California Davis Genome Center

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Copyright

© The Author(s) 2009