Publication detail

Identification and Characterization of Sol Operon in Clostridium Pasteurianum NRRL B-598 Genome

SEDLÁŘ, K. ŠKUTKOVÁ, H. KOLEK, J. PATÁKOVÁ, P. PROVAZNÍK, I.

Original Title

Identification and Characterization of Sol Operon in Clostridium Pasteurianum NRRL B-598 Genome

English Title

Identification and Characterization of Sol Operon in Clostridium Pasteurianum NRRL B-598 Genome

Type

conference paper

Language

en

Original Abstract

Bacteria that belong to the genus Clostridium are a diverse group of rod-shaped anaerobes including a large number of solvent-producing species. However, these species are widely studied due to their utilization in biotechnology, the strain Clostridium pasteurianum NRRL B-598 has been used in only a few studies. This strain is characterized by its genetic stability and oxygen insensitivity. In this work, we present a bioinformatics analysis (mining) of the genome we sequenced recently. The strain NRRL B-598 genome was assembled to the contig level and annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). However, automatic annotation predicted 5,547 genes; it frequently failed in gene accurate denomination and further manual analysis was needed. Using BLAST homology search, we have determined a position of sol operon consisting of 4 genes: ald (aldehyde dehydrogenase), ctfA (CoA transferase subunit A), ctfB (CoA transferase subunit B), and adc (acetoacetate decarboxylase). These genes code enzymes involved in solvent production which are transcribed jointly. Analysis showed quite differences in sol operon content among clostridia. For example, amino acid sequences of these genes share as high as 96-99% similarity with corresponding sol genes of Clostridium beijerinckii NCIMB 8052, which are also carried by chromosomal DNA. This could be one of the reasons of strain NRRL B-598 genetic stability. On the other hand, sol operon in Clostridium acetobutylicum ATCC 824 genome is carried by plasmid and it consists of only 3 genes with significantly lower similarities to corresponding NRRL B-598 genes.

English abstract

Bacteria that belong to the genus Clostridium are a diverse group of rod-shaped anaerobes including a large number of solvent-producing species. However, these species are widely studied due to their utilization in biotechnology, the strain Clostridium pasteurianum NRRL B-598 has been used in only a few studies. This strain is characterized by its genetic stability and oxygen insensitivity. In this work, we present a bioinformatics analysis (mining) of the genome we sequenced recently. The strain NRRL B-598 genome was assembled to the contig level and annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). However, automatic annotation predicted 5,547 genes; it frequently failed in gene accurate denomination and further manual analysis was needed. Using BLAST homology search, we have determined a position of sol operon consisting of 4 genes: ald (aldehyde dehydrogenase), ctfA (CoA transferase subunit A), ctfB (CoA transferase subunit B), and adc (acetoacetate decarboxylase). These genes code enzymes involved in solvent production which are transcribed jointly. Analysis showed quite differences in sol operon content among clostridia. For example, amino acid sequences of these genes share as high as 96-99% similarity with corresponding sol genes of Clostridium beijerinckii NCIMB 8052, which are also carried by chromosomal DNA. This could be one of the reasons of strain NRRL B-598 genetic stability. On the other hand, sol operon in Clostridium acetobutylicum ATCC 824 genome is carried by plasmid and it consists of only 3 genes with significantly lower similarities to corresponding NRRL B-598 genes.

Keywords

Clostridium, Sol operon, biotechnology

RIV year

2014

Released

07.04.2014

Location

Mikulov

ISBN

978-80-86238-61-6

Book

2. mezinárodní chemicko-technologická konference, SBORNÍK ABSTRAKT A PLNÝCH TEXTŮ

Edition

1

Edition number

1

Pages from

1

Pages to

5

Pages count

5

BibTex


@inproceedings{BUT109040,
  author="Karel {Sedlář} and Helena {Škutková} and Jan {Kolek} and Petra {Patáková} and Ivo {Provazník}",
  title="Identification and Characterization of Sol Operon in Clostridium Pasteurianum NRRL B-598 Genome",
  annote="Bacteria that belong to the genus Clostridium are a diverse group of rod-shaped anaerobes including a large number of solvent-producing species. However, these species are widely studied due to their utilization in biotechnology, the strain Clostridium pasteurianum NRRL B-598 has been used in only a few studies. This strain is characterized by its genetic stability and oxygen insensitivity. In this work, we present a bioinformatics analysis (mining) of the genome we sequenced recently. The strain NRRL B-598 genome was assembled to the contig level and annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). However, automatic annotation predicted 5,547 genes; it frequently failed in gene accurate denomination and further manual analysis was needed. Using BLAST homology search, we have determined a position of sol operon consisting of 4 genes: ald (aldehyde dehydrogenase), ctfA (CoA transferase subunit A), ctfB (CoA transferase subunit B), and adc (acetoacetate decarboxylase). These genes code enzymes involved in solvent production which are transcribed jointly. Analysis showed quite differences in sol operon content among clostridia. For example, amino acid sequences of these genes share as high as 96-99% similarity with corresponding sol genes of Clostridium beijerinckii NCIMB 8052, which are also carried by chromosomal DNA. This could be one of the reasons of strain NRRL B-598 genetic stability. On the other hand, sol operon in Clostridium acetobutylicum ATCC 824 genome is carried by plasmid and it consists of only 3 genes with significantly lower similarities to corresponding NRRL B-598 genes.",
  booktitle="2. mezinárodní chemicko-technologická konference, SBORNÍK ABSTRAKT A PLNÝCH TEXTŮ",
  chapter="109040",
  doi="10.13140/2.1.3688.6402",
  edition="1",
  howpublished="electronic, physical medium",
  year="2014",
  month="april",
  pages="1--5",
  type="conference paper"
}