Detail publikačního výsledku

Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data

JUREČKOVÁ, K.; RASCHMANOVÁ, H.; KOLEK, J.; VASYLKIVSKA, M.; BRANSKÁ, B.; PATÁKOVÁ, P.; PROVAZNÍK, I.; SEDLÁŘ, K.

Originální název

Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data

Anglický název

Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data

Druh

Článek WoS

Originální abstrakt

Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of Clostridium beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however their validation is required.

Anglický abstrakt

Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of Clostridium beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however their validation is required.

Klíčová slova

HKG; housekeeping genes; non-model organisms; biofuel; Clostridium

Klíčová slova v angličtině

HKG; housekeeping genes; non-model organisms; biofuel; Clostridium

Autoři

JUREČKOVÁ, K.; RASCHMANOVÁ, H.; KOLEK, J.; VASYLKIVSKA, M.; BRANSKÁ, B.; PATÁKOVÁ, P.; PROVAZNÍK, I.; SEDLÁŘ, K.

Rok RIV

2021

Vydáno

04.03.2021

Nakladatel

Frontiers

ISSN

1664-302X

Periodikum

Frontiers in Microbiology

Svazek

12

Číslo

1

Stát

Švýcarská konfederace

Strany od

1

Strany do

10

Strany počet

10

URL

https://www.frontiersin.org/articles/10.3389/fmicb.2021.640054/full

Plný text v Digitální knihovně

http://hdl.handle.net/11012/196506

BibTex

@article{BUT169963,
  author="Kateřina {Šabatová} and Hana {Raschmanová} and Jan {Kolek} and Maryna {Vasylkivska} and Barbora {Branská} and Petra {Patáková} and Valentýna {Provazník} and Karel {Sedlář}",
  title="Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data",
  journal="Frontiers in Microbiology",
  year="2021",
  volume="12",
  number="1",
  pages="1--10",
  doi="10.3389/fmicb.2021.640054",
  issn="1664-302X",
  url="https://www.frontiersin.org/articles/10.3389/fmicb.2021.640054/full"
}

Dokumenty

fmicb-12-640054