Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F21%3A43922713" target="_blank" >RIV/60461373:22330/21:43922713 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216305:26220/21:PU139787

Výsledek na webu

<a href="https://www.frontiersin.org/articles/10.3389/fmicb.2021.640054/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fmicb.2021.640054/full</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fmicb.2021.640054" target="_blank" >10.3389/fmicb.2021.640054</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data

Popis výsledku v původním jazyce

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 (GO) 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 C. 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. © Copyright © 2021 Jureckova, Raschmanova, Kolek, Vasylkivska, Branska, Patakova, Provaznik and Sedlar.

Název v anglickém jazyce

Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data

Popis výsledku anglicky

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 (GO) 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 C. 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. © Copyright © 2021 Jureckova, Raschmanova, Kolek, Vasylkivska, Branska, Patakova, Provaznik and Sedlar.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

20901 - Industrial biotechnology

Projekt

<a href="/cs/project/GA17-00551S" target="_blank" >GA17-00551S: Vztah mezi efluxem butanolu a tolerancí k butanolu u klostridií</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2021

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Frontiers in Microbiology

ISSN

1664-302X

e-ISSN

—

Svazek periodika

12

Číslo periodika v rámci svazku

MAR 18 2021

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

10

Strana od-do

—

Kód UT WoS článku

000635376200001

EID výsledku v databázi Scopus

2-s2.0-85103503423