Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. Item Type Article Authors Stackebrandt, Erko; Chertkov, Olga; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan- Fang; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Pan, Chongle; Rohde, Manfred; Gronow, Sabine; Göker, Markus; Detter, John C; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Woyke, Tanja; Kyrpides, Nikos C; Klenk, Hans-Peter Citation Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. 2013, 8 (2):228-38 Stand Genomic Sci DOI 10.4056/sigs.3617113 Journal Standards in genomic sciences Rights Archived with thanks to Standards in genomic sciences Download date 01/10/2021 19:56:40 Link to Item http://hdl.handle.net/10033/311146 This is an Open Access-journal’s PDF published in Stackebrandt, E., Chertkov, O., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J.-F., Tapia, R., Goodwin, L.A., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Mikhailova, N., Huntemann, M., Pati, A., Chen, A., Palaniappan, K., Land, M., Pan, C., Rohde, M., Gronow, S., Göker, M., Detter, J.C., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Woyke, T., Kyrpides, N.C., Klenk, H.-P. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (HT), and emendation of the species Turneriella parva (2013) Standards in Genomic Sciences, 8 (2), pp. 228- 238. Standards in Genomic Sciences (2013) 8:228-238 DOI:10.4056/sigs.3617113 Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (HT), and emendation of the species Turneriella parva Erko Stackebrandt1, Olga Chertkov2,3, Alla Lapidus3, Matt Nolan3, Susan Lucas3, Nancy Hammon3, Shweta Deshpande3, Jan-Fang Cheng3, Roxanne Tapia2,3, Lynne A. Goodwin2,3, Sam Pitluck3, Konstantinos Liolios3, Ioanna Pagani3, Natalia Ivanova3, Konstantinos Mavromatis3, Natalia Mikhailova3, Marcel Huntemann3, Amrita Pati3, Amy Chen4, Krishna Palaniappan4, Miriam Land3,5, Chongle Pan3,5, Manfred Rohde6, Sabine Gronow1, Markus Göker1, John C. Detter2, James Bristow3, Jonathan A. Eisen3,7, Victor Markowitz4, Philip Hugenholtz3,8, Tanja Woyke3, Nikos C. Kyrpides3, and Hans-Peter Klenk1* 1 Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 DOE Joint Genome Institute, Walnut Creek, California, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Hans-Peter Klenk Keywords: Gram-negative, motile, axial filaments, helical, flexible, non-sporulating, aerobic, mesophile, Leptospiraceae, GEBA Turneriella parva Levett et al. 2005 is the only species of the genus Turneriella which was es- tablished as a result of the reclassification of Leptospira parva Hovind-Hougen et al. 1982. Together with Leptonema and Leptospira, Turneriella constitutes the family Leptospiraceae, within the order Spirochaetales. Here we describe the features of this free-living aerobic spi- rochete together with the complete genome sequence and annotation. This is the first com- plete genome sequence of a member of the genus Turneriella and the 13th member of the family Leptospiraceae for which a complete or draft genome sequence is now available. The 4,409,302 bp long genome with its 4,169 protein-coding and 45 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain HT (= DSM 21527 = NCTC 11395 = ATCC tubules when detached for negative staining BAA-1111) is the type strain of Turneriella parva preparation and the base composition of DNA [1]. The strain was isolated from contaminated differed from that of other Leptospira species [2]. Leptospira culture medium [2] and was originally DNA-DNA hybridization [3] and enzyme activity thought to be affiliated with Leptospira [2] be- [4] studies revealed sufficient differences be- cause of morphological similarities to other tween other Leptospira species and L. parva that members of the genus. Strain HT was designated the ‘Subcommittee on the Taxonomy of as a separate species because of certain morpho- Leptospira’ [5] decided to exclude L. parva from logical and molecular differences: cells were the genus Leptospira and assign it as the type shorter and were more tightly wound, the sur- strain of a new genus: ‘Turneria’ as ‘Turneria face layer formed blebs instead of cross-striated parva’. The genus was named in honor of Leslie The Genomic Standards Consortium Stackebrandt et al. Turner, an English microbiologist who made de- authoritative source for nomenclature or classifi- finitive contributions to the knowledge of lepto- cation.) The highest-scoring environmental se- spirosis [1]. However, as the generic name is also quence was DQ017943 (Greengenes short name in use in botany and zoology, this name was ren- 'Cntrl Erpn Rnnng Wtrs Exmnd TGGE and uplnd dered illegitimate and invalidate, but was used in strm cln S-BQ2 83'), which showed an identity of the literature [6,7]. The first 16S rRNA gene- 95.6% and an HSP coverage of 97.8%. The most based study (Genbank accession number frequently occurring keywords within the labels Z21636), performed on Leptospira parva incertae of all environmental samples which yielded hits sedis, confirmed the isolated position of L. parva were 'microbi' (5.5%), 'sediment' (2.6%), 'soil' among Leptonema and Leptospira species [8], a (2.5%), 'industri' (2.1%) and 'anaerob' (1.9%) finding later supported by Morey et al. [9]. The (194 hits in total). Environmental samples which reclassification of L. parva as Turneriella parva yielded hits of a higher score than the highest com. nov. was published by Levett et al. [1], re- scoring species were not found. confirming the separate position of the type Figure 1 shows the phylogenetic neighborhood of strain [10] and an additional strain (S-308-81, T. parva HT in a 16S rRNA based tree. The se- ATCC BAA-1112) from the uterus of a sow from quences of the two identical 16S rRNA gene cop- all other leptospiras on the basis of DNA-DNA ies in the genome do not differ from the previ- hybridization and 16S rRNA gene sequence anal- ously published 16S rRNA sequence (AY293856). ysis (Genbank accession number AY293856). The strain was selected for genome sequencing be- cause of its deep branching point within the Morphology and physiology Leptospiraceae lineage. Cells of strain HT are Gram-negative, flexible and Here we present a summary classification and a helical with 0.3 µm in diameter and 3.5-7.5 µm in set of features for T. parva HT together with the length and a wavelength of 0.3-0.5 µm (Figure 2). description of the complete genomic sequencing Motility is achieved by means of two axial fila- and annotation. ments, similar to those of other leptospiras. The surface of the cells show several blebs with no ap- parent substructure when prepared for negative Classification and features staining while under the same conditions, cross- 16S rRNA gene sequence analysis striated tubules are visible in other leptospiras A representative genomic 16S rDNA sequence of [1,2]. The strain is obligately aerobic and oxidase T. parva HT was compared using NCBI BLAST positive. Slow and limited growth occurs in [11,12] under default settings (e.g., considering polysorbate albumin medium [39] at 11, 30 and only the high-scoring segment pairs (HSPs) from 37 °C. Growth is inhibited by 8-azaguanine (200 -1 -1 the best 250 hits) with the most recent release of µg ml ) and 2,6 diaminopurine (µg ml ). Lipase is the Greengenes database [13] and the relative produced, long-chain fatty acids and long-chain frequencies of taxa and keywords (reduced to fatty alcohols are utilized as carbon and energy their stem [14]) were determined, weighted by sources. L- -L-glutamate BLAST scores. The most frequently occurring arylamidase, glycine arylamidase, leucyl-glycine genera were Geobacter (48.7%), Leptospira lysine -Darylamidase,-galactosidase αactivities are (19.2%), Pelobacter (13.4%), Spirochaeta (8.1%) lacking [4]. The type strain is not pathogenic for and Turneriella (6.4%) (56 hits in total). Regard- hamstersarylamidase [1]. and α ing the single hit to sequences from members of the species, the average identity within HSPs was Chemotaxonomy 95.8%, whereas the average coverage by HSPs Information on peptidoglycan composition, major was 89.8%. Among all other species, the one cell wall sugars, fatty acids, menaquinones and yielding the highest score was Leptonema illini polar lipids is not available. The mol% G+C of DNA (AY714984), which corresponded to an identity was originally reported to be approximately 48% of 85.7% and an HSP coverage of 62.6%. (Note [3], significantly less than the G+C content in- that the Greengenes database uses the INSDC (= ferred from the genome sequence. EMBL/NCBI/DDBJ) annotation, which is not an http://standardsingenomics.org 229 Turneriella parva type strain (HT) Figure 1. Phylogenetic tree highlighting the position of T. parva relative to the type strains of the other species within the phy- lum 'Spirochaetes'. The tree was inferred from 1,318 aligned characters [15,16] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [17]. Rooting was done initially using the midpoint method [18] and then checked for its agreement with the current classification (Table 1).