Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 to elucidate role of furfural stress during acetone butanol ethanol fermentation

The so-called clp genes, which encode components of the Clp proteolytic complex, are widespread among bacteria. The Bifidobacterium breve UCC 2003 genome contains a clpB gene with significant homology to predicted clpB genes from other members of the Actinobacteridae group. The heat- and osmotic-inducibility of the B. breve UCC 2003 clpB homologue was verified by slot-blot analysis, while Northern blot and primer extension analyses showed that the clpB gene is transcribed as a monocistronic unit with a single promoter. The role of a hspR homologue, known to control the regulation of clpB and dnaK gene expression in other high G+C content bacteria was investigated by gel mobility shift assays. Moreover the predicted 3D structure of HspR provides further insight into the binding mode of this protein to the clpB promoter region, and highlights the key amino acid residues believed to be involved in the protein–DNA interaction.

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Transcriptional Analysis of the Toxin-Coding Plasmid pBtoxis from Bacillus thuringiensis subsp. israelensis

Applied and Environmental Microbiology ◽

10.1128/aem.72.3.1771-1776.2006 ◽

2006 ◽

Vol 72 (3) ◽

pp. 1771-1776 ◽

Cited By ~ 13

Author(s):

Claudia Stein ◽

Gareth W. Jones ◽

Tanya Chalmers ◽

Colin Berry

Keyword(s):

Gene Regulation ◽

Bacillus Thuringiensis ◽

Transcriptional Regulators ◽

Transcriptional Analysis ◽

Host Bacterium ◽

Large Plasmid ◽

Coding Sequences ◽

Physiological Processes ◽

Insecticidal Toxins

ABSTRACT In Bacillus thuringiensis subsp. israelensis all of the insecticidal toxins are encoded on a single, large plasmid, pBtoxis. Sequencing of this plasmid revealed 125 potential coding sequences, many of which have predicted functions in gene regulation and physiological processes, such as germination. As a first step in understanding the possible role of pBtoxis in its host bacterium, a survey of the transcription of genes with predicted functions was carried out. Whereas many coding sequences, including those previously identified as probable pseudogenes, were not transcribed, mRNA was detected for 29 of the 40 sequences surveyed. Several of these sequences, including eight with similarities to the sequences of known transcriptional regulators, may influence wider gene regulation and thus may alter the phenotype of the host bacterium.

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Acetone–Butanol–Ethanol Fermentation From Palm Oil Mill Effluent Using Clostridium acetobutylicum

Developments in Sustainable Chemical and Bioprocess Technology ◽

10.1007/978-1-4614-6208-8_5 ◽

2013 ◽

pp. 35-41 ◽

Cited By ~ 1

Author(s):

A. S. Japar ◽

M. S. Takriff ◽

J. M. Jahim ◽

A. A. H. Kadhum

Keyword(s):

Palm Oil ◽

Ethanol Fermentation ◽

Clostridium Acetobutylicum ◽

Palm Oil Mill Effluent ◽

Palm Oil Mill ◽

Acetone Butanol Ethanol

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Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

10.1101/234930 ◽

2017 ◽

Cited By ~ 1

Author(s):

Lovorka Stojic ◽

Aaron Lun ◽

Jasmin Mangei ◽

Patrice Mascalchi ◽

Valentina Quarantotti ◽

...

Keyword(s):

Antisense Oligonucleotides ◽

Noncoding Rna ◽

Specific Activity ◽

Transcriptional Analysis ◽

Clonal Variation ◽

Loss Of Function ◽

Negative Controls ◽

Whole Transcriptome ◽

Target Effects

ABSTRACTLoss-of-function (LOF) methods, such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing, provide unparalleled power for studying the biological function of genes of interest. When coupled with transcriptomic analyses, LOF methods allow researchers to dissect networks of transcriptional regulation. However, a major concern is nonspecific targeting, which involves depletion of transcripts other than those intended. The off-target effects of each of these common LOF methods have yet to be compared at the whole-transcriptome level. Here, we systematically and experimentally compared non-specific activity of RNAi, antisense oligonucleotides and CRISPR interference (CRISPRi). All three methods yielded non-negligible offtarget effects in gene expression, with CRISPRi exhibiting clonal variation in the transcriptional profile. As an illustrative example, we evaluated the performance of each method for deciphering the role of a long noncoding RNA (lncRNA) with unknown function. Although all LOF methods reduced expression of the candidate lncRNA, each method yielded different sets of differentially expressed genes upon knockdown as well as a different cellular phenotype. Therefore, to definitively confirm the functional role of a transcriptional regulator, we recommend the simultaneous use of at least two different LOF methods and the inclusion of multiple, specifically designed negative controls.

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DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

Journal of Bacteriology ◽

10.1128/jb.01524-07 ◽

2008 ◽

Vol 190 (6) ◽

pp. 2231-2238 ◽

Cited By ~ 16

Author(s):

Melanie Zaparty ◽

Alexander Zaigler ◽

Claudia Stamme ◽

Jörg Soppa ◽

Reinhard Hensel ◽

...

Keyword(s):

Carbohydrate Metabolism ◽

Dna Microarray ◽

Transcript Level ◽

Open Reading Frames ◽

Transcriptional Analysis ◽

Heterotrophic Growth ◽

Thermoproteus Tenax ◽

Central Carbohydrate Metabolism ◽

Reading Frames

ABSTRACT In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed.

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