Publication detail

Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum

JUREČKOVÁ, K. NYKRÝNOVÁ, M. SLANINOVÁ, E. FLEURIOT-BLITMAN, H. AMSTUTZ, V. HEŘMÁNKOVÁ, K. BEZDÍČEK, M. MRÁZOVÁ, K. HRUBANOVÁ, K. ZINN, M. OBRUČA, S. SEDLÁŘ, K.

Original Title

Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum

Type

journal article in Web of Science

Language

English

Original Abstract

Purple photosynthetic bacteria (PPB) are versatile microorganisms capable of producing various value-added chemicals, e.g., biopolymers and biofuels. They employ diverse metabolic pathways, allowing them to adapt to various growth conditions and even extreme environments. Thus, they are ideal organisms for the Next Generation Industrial Biotechnology concept of reducing the risk of contamination by using naturally robust extremophiles. Unfortunately, the potential of PPB for use in biotechnology is hampered by missing knowledge on regulations of their metabolism. Although Rhodospirillum rubrum represents a model purple bacterium studied for polyhydroxyalkanoate and hydrogen production, light/chemical energy conversion, and nitrogen fixation, little is known regarding the regulation of its metabolism at the transcriptomic level. Using RNA sequencing, we compared gene expression during the cultivation utilizing fructose and acetate as substrates in case of the wild-type strain R. rubrum DSM 467T and its knock-out mutant strain that is missing two polyhydroxyalkanoate synthases PhaC1 and PhaC2. During this first genome-wide expression study of R. rubrum, we were able to characterize cultivation-driven transcriptomic changes and to annotate non-coding elements as small RNAs.

Keywords

Rhodospirillum rubrum; RNA-Seq; Transcriptome; Genome; Depolymerase knock-out; Gene ontology; Metabolism; Fructose; Acetate; Polyhydroxyalkanoates

Authors

JUREČKOVÁ, K.; NYKRÝNOVÁ, M.; SLANINOVÁ, E.; FLEURIOT-BLITMAN, H.; AMSTUTZ, V.; HEŘMÁNKOVÁ, K.; BEZDÍČEK, M.; MRÁZOVÁ, K.; HRUBANOVÁ, K.; ZINN, M.; OBRUČA, S.; SEDLÁŘ, K.

Released

26. 6. 2024

Publisher

Elsevier

ISBN

2001-0370

Periodical

Computational and Structural Biotechnology Journal

Year of study

23

Number

December 2024

State

Kingdom of Sweden

Pages from

2681

Pages to

2694

Pages count

14

URL

https://www.sciencedirect.com/science/article/pii/S2001037024002204

Full text in the Digital Library

http://hdl.handle.net/11012/249379

BibTex

@article{BUT188890,
  author="Kateřina {Šabatová} and Markéta {Jakubíčková} and Eva {Slaninová} and Hugo {Fleuriot-Blitman} and Véronique {Amstutz} and Kristýna {Heřmánková} and Matěj {Bezdíček} and Kateřina {Mrázová} and Kamila {Hrubanová} and Manfred {Zinn} and Stanislav {Obruča} and Karel {Sedlář}",
  title="Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum",
  journal="Computational and Structural Biotechnology Journal",
  year="2024",
  volume="23",
  number="December 2024",
  pages="2681--2694",
  doi="10.1016/j.csbj.2024.06.023",
  issn="2001-0370",
  url="https://www.sciencedirect.com/science/article/pii/S2001037024002204"
}