Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

BMC Genomics
Karel SedlarIvo Provaznik

Abstract

Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabol...Continue Reading

References

Jun 1, 2000·Nature·H OchmanE A Groisman
Dec 20, 2000·Bioinformatics·K RutherfordB Barrell
Sep 9, 2004·Microbiology and Molecular Biology Reviews : MMBR·Harald BrüssowWolf-Dietrich Hardt
Jun 28, 2005·Nucleic Acids Research·Laurent Noé, Gregory Kucherov
Oct 4, 2005·Journal of Bacteriology·Keith V Alsaker, Eleftherios T Papoutsakis
Apr 18, 2008·Omics : a Journal of Integrative Biology·Samuel V AngiuoliOwen White
Oct 22, 2008·Applied and Environmental Microbiology·Bryan P TracyEleftherios T Papoutsakis
Nov 8, 2008·Bioinformatics·Tim CarverJulian Parkhill
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Nov 6, 2009·Nature·Hubertus J E BeaumontPaul B Rainey
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Mar 9, 2010·Current Opinion in Biotechnology·Bryan P TracyEleftherios T Papoutsakis
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Oct 17, 2012·Bioinformatics·Evguenia KopylovaHélène Touzet
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Jul 2, 2014·Genome Biology·Nicholas F LahensJohn B Hogenesch
Dec 3, 2014·Current Opinion in Microbiology·Ian Goodhead, Alistair C Darby
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jan 30, 2015·Microbiology and Molecular Biology Reviews : MMBR·Mohab A Al-HinaiEleftherios T Papoutsakis
May 5, 2016·Nucleic Acids Research·David ArndtDavid S Wishart
Mar 14, 2017·Biotechnology for Biofuels·Anja PoehleinPeter Dürre
Sep 17, 2017·BMC Bioinformatics·Matthias Zytnicki

❮ Previous
Next ❯

Citations

Oct 23, 2019·Biotechnology for Biofuels·Karel SedlarIvo Provaznik
May 5, 2020·Frontiers in Bioengineering and Biotechnology·Seong Woo KwonYu-Sin Jang
Nov 24, 2020·Frontiers in Bioengineering and Biotechnology·Maryna VasylkivskaPetra Patakova
Jan 8, 2021·Applied Microbiology and Biotechnology·Barbora BranskaPetra Patakova
Jul 29, 2018·Metabolic Engineering·Kamil CharubinEleftherios T Papoutsakis
Apr 27, 2021·Applied Microbiology and Biotechnology·Mamou DialloAna M López-Contreras

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq
transcription profiling
flow cytometry
Flow

Software Mentioned

Rsubread
gplots
PhiSpy
Trinity
SAM
ChemStation
2100 Bioanalyzer Expert
BLAST +
Bioconductor
PHASTER

Related Concepts

Related Feeds

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.