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

J 2024

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

JURECKOVA, Katerina, Marketa NYKRYNOVA, Eva SLANINOVA, Hugo FLEURIOT-BLITMAN, Veronique AMSTUTZ et. al.

Basic information

Original name

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

Authors

JURECKOVA, Katerina (203 Czech Republic), Marketa NYKRYNOVA (203 Czech Republic), Eva SLANINOVA (203 Czech Republic), Hugo FLEURIOT-BLITMAN, Veronique AMSTUTZ, Kristyna HERMANKOVA (203 Czech Republic), Matěj BEZDÍČEK (203 Czech Republic, belonging to the institution), Katerina MRAZOVA (203 Czech Republic), Kamila HRUBANOVA (203 Czech Republic), Manfred ZINN, Stanislav OBRUCA (203 Czech Republic) and Karel SEDLAR (203 Czech Republic)

Edition

Computational and Structural Biotechnology Journal, AMSTERDAM, Elsevier, 2024, 2001-0370

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 6.000 in 2022

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1016/j.csbj.2024.06.023

UT WoS

001261996700001

Keywords in English

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

Abstract

V originále

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 wildtype 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.

Citovat

JURECKOVA, Katerina, Marketa NYKRYNOVA, Eva SLANINOVA, Hugo FLEURIOT-BLITMAN, Veronique AMSTUTZ, Kristyna HERMANKOVA, Matěj BEZDÍČEK, Katerina MRAZOVA, Kamila HRUBANOVA, Manfred ZINN, Stanislav OBRUCA and Karel SEDLAR. Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum. Computational and Structural Biotechnology Journal. AMSTERDAM: Elsevier, 2024, vol. 23, December 2024, p. 2681-2694. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2024.06.023.

@article{2423158,
   author = {Jureckova, Katerina and Nykrynova, Marketa and Slaninova, Eva and FleuriotandBlitman, Hugo and Amstutz, Veronique and Hermankova, Kristyna and Bezdíček, Matěj and Mrazova, Katerina and Hrubanova, Kamila and Zinn, Manfred and Obruca, Stanislav and Sedlar, Karel},
   article_location = {AMSTERDAM},
   article_number = {December 2024},
   doi = {http://dx.doi.org/10.1016/j.csbj.2024.06.023},
   keywords = {Rhodospirillum rubrum; RNA-Seq; Transcriptome; Genome; Depolymerase knock-out; Gene ontology; Metabolism; Fructose; Acetate; Polyhydroxyalkanoates},
   language = {eng},
   issn = {2001-0370},
   journal = {Computational and Structural Biotechnology Journal},
   title = {Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum},
   url = {https://www.sciencedirect.com/science/article/pii/S2001037024002204?via%3Dihub},
   volume = {23},
   year = {2024}
}

TY  - JOUR
ID  - 2423158
AU  - Jureckova, Katerina - Nykrynova, Marketa - Slaninova, Eva - Fleuriot-Blitman, Hugo - Amstutz, Veronique - Hermankova, Kristyna - Bezdíček, Matěj - Mrazova, Katerina - Hrubanova, Kamila - Zinn, Manfred - Obruca, Stanislav - Sedlar, Karel
PY  - 2024
TI  - Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum
JF  - Computational and Structural Biotechnology Journal
VL  - 23
IS  - December 2024
SP  - 2681-2694
EP  - 2681-2694
PB  - Elsevier
SN  - 20010370
KW  - Rhodospirillum rubrum
KW  - RNA-Seq
KW  - Transcriptome
KW  - Genome
KW  - Depolymerase knock-out
KW  - Gene ontology
KW  - Metabolism
KW  - Fructose
KW  - Acetate
KW  - Polyhydroxyalkanoates
UR  - https://www.sciencedirect.com/science/article/pii/S2001037024002204?via%3Dihub
N2  - 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 wildtype 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.
ER  -

JURECKOVA, Katerina, Marketa NYKRYNOVA, Eva SLANINOVA, Hugo FLEURIOT-BLITMAN, Veronique AMSTUTZ, Kristyna HERMANKOVA, Matěj BEZDÍČEK, Katerina MRAZOVA, Kamila HRUBANOVA, Manfred ZINN, Stanislav OBRUCA and Karel SEDLAR. Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum. \textit{Computational and Structural Biotechnology Journal}. AMSTERDAM: Elsevier, 2024, vol.~23, December 2024, p.~2681-2694. ISSN~2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2024.06.023.

Detailed Information on Publication Record