Publication detail

Genomic and functional analysis of polyhydroxyalkanoates producer Rhodospirillum rubrum DSM 467

JUREČKOVÁ, K. NYKRÝNOVÁ, M. SLANINOVÁ, E. BEZDÍČEK, M. OBRUČA, S. ŠKUTKOVÁ, H. SEDLÁŘ, K.

Original Title

Genomic and functional analysis of polyhydroxyalkanoates producer Rhodospirillum rubrum DSM 467

Type

conference paper

Language

English

Original Abstract

Rhodospirillum rubrum is a bacterium capable of the production of polyhydroxyalkanoates (PHA). PHA are polyesters that bacteria primarily use as a storage of energy and carbon in a form of cytoplasmic granules. Nevertheless, PHA are also promising renewable and biodegradable alternatives to petrochemical polymers, which nowadays leads to extensive research of R. rubrum. In this study, we focused on the analysis of a genome sequence of Rhodospirillum rubrum DSM 467. We sequenced and assembled genome of R. rubrum DSM 467 by a hybrid approach using long (Oxford Nanopore) and short (Illumina) reads. Chromosome sequence is available under accession number CP077803.1 and plasmid sequence under CP077804.1 in the GenBank database. Chromosome sequence was 4 352 570 bp long, CG content was 65.4%, and 3 919 open reading frames (ORF) belonged to protein-coding sequences. Plasmid sequence was 53 835 bp long, CG content was 59.8%, and a number of ORF was 49. Functional annotation revealed that protein-coding sequences can be assigned a clusters of orthologous genes group in 90% cases for chromosome sequence and 80% cases for plasmid sequence, respectively. From available genome sequences of R. rubrum species, we created its pangenome with 4 572 genes, where we identified the core genome with 1 765 genes, accessory genome with 2 808 genes and 890 genes were unique. Genome annotation was also used for the construction of the genome-scale model of R. rubrum DSM 467 in Pathways tool. Our results will be used in further research of metabolic processes behind PHA biosynthesis in Rhodospirillum rubrum DSM 467.

Keywords

PHA; rhodospirillum rubrum DSM 467; genome

Authors

JUREČKOVÁ, K.; NYKRÝNOVÁ, M.; SLANINOVÁ, E.; BEZDÍČEK, M.; OBRUČA, S.; ŠKUTKOVÁ, H.; SEDLÁŘ, K.

Released

14. 12. 2022

Publisher

Czech Society of Industrial Chemistry

Location

Prague

ISBN

978-80-88307-11-2

Book

Proceedings of the 9th International Conference on Chemical Technology

Pages from

367

Pages to

372

Pages count

6

URL

https://www.icct.cz/cs/Amca-ICCT/media/content/2022/proceedings/ICCT2022-Proceedings.pdf

BibTex

@inproceedings{BUT180366,
  author="Kateřina {Šabatová} and Markéta {Jakubíčková} and Eva {Slaninová} and Matěj {Bezdíček} and Stanislav {Obruča} and Helena {Vítková} and Karel {Sedlář}",
  title="Genomic and functional analysis of polyhydroxyalkanoates producer Rhodospirillum rubrum DSM 467",
  booktitle="Proceedings of the 9th International Conference on Chemical Technology",
  year="2022",
  pages="367--372",
  publisher="Czech Society of Industrial Chemistry",
  address="Prague",
  isbn="978-80-88307-11-2",
  url="https://www.icct.cz/cs/Amca-ICCT/media/content/2022/proceedings/ICCT2022-Proceedings.pdf"
}