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.

Základní údaje

Originální název

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

Autoři

JURECKOVA, Katerina (203 Česká republika), Marketa NYKRYNOVA (203 Česká republika), Eva SLANINOVA (203 Česká republika), Hugo FLEURIOT-BLITMAN, Veronique AMSTUTZ, Kristyna HERMANKOVA (203 Česká republika), Matěj BEZDÍČEK (203 Česká republika, domácí), Katerina MRAZOVA (203 Česká republika), Kamila HRUBANOVA (203 Česká republika), Manfred ZINN, Stanislav OBRUCA (203 Česká republika) a Karel SEDLAR (203 Česká republika)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.000 v roce 2022

Organizační jednotka

Lékařská fakulta

DOI

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

UT WoS

001261996700001

Klíčová slova anglicky

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

Štítky

14110212, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 8. 2024 10:35, Mgr. Tereza Miškechová

Anotace

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 a Karel SEDLAR. Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum. Computational and Structural Biotechnology Journal. AMSTERDAM: Elsevier, 2024, roč. 23, December 2024, s. 2681-2694. ISSN 2001-0370. Dostupné z: 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 a 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, roč.~23, December 2024, s.~2681-2694. ISSN~2001-0370. Dostupné z: https://dx.doi.org/10.1016/j.csbj.2024.06.023.

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