SciELO - Scientific Electronic Library Online

 
vol.48 issue1Genome sequence of Prevotella intermedia SUNY aB G8-9K-3, a biofilm forming strain with drug-resistanceGenome sequence of Bradyrhizobium embrapense strain CNPSo 2833T, isolated from a root nodule of Desmodium heterocarpon author indexsubject indexarticles search
Home Pagealphabetic serial listing  

Services on Demand

Journal

Article

Indicators

Related links

Share


Brazilian Journal of Microbiology

Print version ISSN 1517-8382On-line version ISSN 1678-4405

Braz. J. Microbiol. vol.48 no.1 São Paulo Jan./Mar. 2017

https://doi.org/10.1016/j.bjm.2016.06.013 

Genome Announcements

Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594

Raimonda Petkauskaitea  * 

Jochen Blomb 

Alexander Goesmannb 

Nomeda Kuisienea 

aVilnius University, Faculty of Natural Sciences, Department of Microbiology and Biotechnology, Vilnius, Lithuania

bJustus-Liebig-Universität Giessen, Bioinformatik und Systembiologie, Giessen, Germany


Abstract

Geobacillus thermodenitrificans DSM 101594 was isolated as a producer of extracellular thermostable pectic polysaccharide degrading enzymes. The completely sequenced genome was 3.6 Mb in length with GC content of 48.86%. A number of genes encoding enzymatic active against the high molecular weight polysaccharides of potential biotechnological importance were identified in the genome.

Keywords: Geobacilli; Polysaccharide degradation; Genome

In recent years, number of sequenced geobacilli genomes has increased substantially.1 The annotation of genomes of newly isolated geobacilli strains is extremely important as these thermophiles are one of the major sources of thermoactive and/or thermostable enzymes of biotechnological importance.

This communication presents the draft genome sequence of G. thermodenitrificans PA-3 designated as DSM 101594, a highly active pectate lyase producer. This thermophilic bacterium was isolated from a soil sample collected from the compost facility at Vilnius University Botanical Garden, Vingis Park, Vilnius, Lithuania. The strain was isolated via enrichment culture with polygalacturonic acid and subsequently apple pomace as the main source of carbon and energy. The potential of a recombinant thermostable pectate lyase (locus_tag GEPA3_0510) from G. thermodenitrificans DSM 101594 has already been demonstrated for the enzymatic production of long-chain pectic oligosaccharides, which serves as a valuable prebiotics obtained from the agro-industrial wastes.2,3

16S rRNA gene phylogenetic analysis confirmed the strain PA-3 to be G. thermodenitrificans. 16S rRNA gene sequence comparison was performed according to UPGMA algorithm implemented in MEGA 6.4

A genome assembly was constructed in order to determine the potential biotechnological applicability of G. thermodenitrificans DSM 101594 and to identify the genes of interest. Total DNA was extracted from liquid growth culture aerobically cultivated in DifcoTM Nutrient Broth (BD Diagnostics) at 60 °C overnight using GeneJETTM Genomic DNA Purification Kit (Thermo Fisher Scientific) following the manufacturer's instructions. A draft of whole-genome sequence was obtained using the next-generation sequencing (NGS); paired-end 100 cycles sequence reads were generated using Illumina HiSeq2500 system (BaseClear, Leiden, the Netherlands). FASTQ sequence reads were generated using Illumina Casava pipeline (version 1.8.3). 1,317,704 read pairs covering 213,468,048 bases were assembled using SPAdes Genome Assembler software (version 3.1.0) resulting in 208 contigs; of which 25 contigs shorter than 200 bp were discarded. The final assembly consisted of 3,646,477 bp with an average coverage of 58.5×. The genome has a GC content of 48.86%. Automated genome annotation was carried out by using GenDB software.5 The automated gene prediction identified 3,638 coding sequences (CDS), 10 rRNA regions, and 92 tRNA regions (Table 1). The direct manual annotation was performed using Pfam,6 InterProScan,7 and NCBI BLAST.

Table 1 Genome features of Geobacillus thermodenitrificans DSM 101594. 

Features Chromosome
Length (bp) 3,646,477
G+C content (%) 48.86
ORFs 3638
rRNA regions 10
tRNA regions 92

Determined genome sequence was compared using EDGAR8 software with the genome sequences of other geobacilli, including the phylogenetically nearest strains, G. thermodenitrificans NG80-29 and G. thermodenitrificans DSM 465.10 The analysed G. thermodenitrificans DSM 101594 genome revealed an adaptational trait that enforces this thermophile to occupy the environmental niches rich in insoluble high molecular weight polysaccharides. A 60 kbp long region, previously not identified in any other geobacilli genomes encoding genes for the utilisation of a broad range of polysaccharides and genes of polysaccharide degradation product transport systems, is the key finding of this trait. The ability of G. thermodenitrificans DSM 101594 to use different polysaccharides for nutrition demonstrates flexible adaptation to available energy and/or carbon sources. Finally, a substantial number of genes encoding powerful biocatalysts was annotated in the genome of this strain.

Nucleotide sequence accession numbers

Draft genome sequence for G. thermodenitrificans DSM 101594 has been deposited at GenBank under accession no. LIDX00000000. The version described in this paper is version LIDX01000000.

Acknowledgements

This study was funded by “TermozymOS’ project of the National Research Programme “Healthy and Safe Food” by the Lithuanian Science Council (project no. SVE-08/2011). We acknowledge the access to resources within the de.NBI network financially supported by the BMBF grant FKZ 031A533.

References

1 Benson DA, Cavanaugh M, Clark K, et al. GenBank. Nucleic Acids Res. 2013;(41 (Database issue)):D36-D42. [ Links ]

2 Petkauskaite R, Lukosius D, Dębski J, et al. Identification of proteins involved in starch and polygalacturonic acid degradation using LC-MS. Cent Eur J Biol. 2014;9(7):708-716. [ Links ]

3 Kieraite I, Petkauskaite R, Jasilionis A, Kuisiene N. Evaluation of potential of free and immobilized thermophilic bacterial enzymes in the degradation of agro-industrial wastes. Arch Biol Sci. 2015;67(1):161-172. [ Links ]

4 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary genetics analysis Version 6.0. Mol Biol Evol. 2013;30(12):2725-2729. [ Links ]

5 Meyer F, Goesmann A, McHardy AC, et al. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003;31(8):2187-2195. [ Links ]

6 Punta M, Coggill PC, Eberhardt RY, et al. The Pfam protein families database. Nucleic Acids Res. 2012;(40 (Database issue)):D290-D301. [ Links ]

7 Quevillon E, Silventoinen V, Pillai S, et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005;33(suppl 2):W116-W120. [ Links ]

8 Blom J, Albaum SP, Doppmeier D, et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinform. 2009;10:154, http://dx.doi.org/10.1186/1471-2105-10-154. [ Links ]

9 Feng L, Wang W, Cheng J, et al. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep subsurface oil reservoir. Proc Natl Acad Sci U S A. 2007;104(13):5602-5607. [ Links ]

10 Yao N, Ren Y, Wang W. Genome sequence of a thermophilic bacillus. Geobacillus thermodenitrificans DSM 465. Genome Announc. 2013;1(6):e01046-e1113, http://dx.doi.org/10.1128/genomeA.01046-13. [ Links ]

Received: March 29, 2016; Accepted: June 9, 2016

*Corresponding author at: E-mail: Sauletekio ave. 7, LT-10257 Vilnius, Lithuania. E-mail: raimonda.petkauskaite@gf.vu.lt (R. Petkauskaite).

Conflicts of interest

The authors declare no conflicts of interest.

Creative Commons License This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivative License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium provided the original work is properly cited and the work is not changed in any way.