Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape

BMC Genomics
Marta IrlaVolker F Wendisch

Abstract

Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising candidate for biotechnological applications is evident. The B. methanolicus MGA3 genome consists of a 3,337,035 nucleotides (nt) circular chromosome, the 19,174 nt plasmid pBM19 and the 68,999 nt plasmid pBM69. 3,218 protein-coding regions were annotated on the chromosome, 22 on pBM19 and 82 on pBM69. In the present study, the RNA-seq approach was used to comprehensively investigate the transcriptome of B. methanolicus MGA3 in order to improve the genome annotation, identify novel transcripts, analyze conserved sequence motifs involved in gene expression and reveal operon structures. For this aim, two different cDNA library preparation methods were applied: one which allows characterization of the whole transcriptome and another which includes enrichment of primary transcript 5'-ends. Analysis of the primary transcriptome data enabled the detection of 2,167 putative transcription start sites (TSSs) which were categorized into 1,642 TSSs located in the upstream region (5'-UTR) of known protein-coding genes an...Continue Reading

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Citations

Jun 3, 2016·Microbial Cell Factories·Marc CarnicerStephanie Heux
Sep 19, 2017·Biotechnology and Bioengineering·Benjamin M WoolstonGregory Stephanopoulos
Feb 18, 2020·Biotechnology and Applied Biochemistry·Kerstin SchultenkämperVolker F Wendisch
Feb 19, 2017·Applied Microbiology and Biotechnology·Simone Balzer LeTrygve Brautaset
Jan 7, 2018·BMC Genomics·Angela KranzTino Polen
Dec 14, 2018·ELife·Sung Hyun KimCees Dekker
Jan 23, 2020·Journal of Bacteriology·Tomoya KozakaiTohru Suzuki
Aug 17, 2019·Frontiers in Microbiology·Marina Gil LópezVolker F Wendisch
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May 12, 2018·Microorganisms·Eivind B DrejerTrygve Brautaset
May 1, 2021·International Journal of Molecular Sciences·Marta IrlaTrygve Brautaset

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Datasets Mentioned

BETA
CP007740
CP007741

Methods Mentioned

BETA
PCR
electrophoresis
cDNA library
RNA seq
RNA-seq

Software Mentioned

BLAST
Illumina instrument
ORF finder
ARNold
SARUMAN
MiSeq Desktop Sequencer
ReadXplorer
Improbizer
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