Transcriptome analysis of thermoplasma volcanium GSS1 under extreme stress

Zabcı, Sema
In this study, to provide new insight into anti-stress mechanisms in archaea, we have carried out genome wide transcriptome analysis of Thermoplasma volcanium under severe stress conditions (i.e., heat- shock at 68 ºC, sub-lethal and lethal oxidative stress and pH stress at pH 5.0) using whole genome gene expression microarray. The change in the gene expression profile in response to three stressors indicated retardation of cell growth accompanied by down regulation of genes involved in essential cellular processes such as translation, transcription, cell motility, and energy metabolism. In addition, heat- shock resulted in the increased transcription level of genes encoding heat shock proteins (e.g., GroEL, GrpE, DnaK, and DnaJ). The highest number of up-regulated genes was recorded upon pH stress. pH stress response in T.volcanium was characterized by activation of several transporter gene products, which are crucial for maintaining intracellular pH homeostasis. Oxidative stress triggered mostly down regulation of gene expression. Up regulation of oxidoreductases, Fe-S oxidoreductases, aldo/keto reductases, and dehydrogenases as a response to oxidative stress provoked by H2O2 can be important for maintaining intracellular redox potential and detoxification of free radicals. On the other hand, activation of the carbohydrate metabolism and transport, as well as some transcriptional regulators was detected in response to three stress signals. The verification of the microarray data with qRT-PCR showed good agreement between results of the two techniques


Expression profiling of thermoplasma volcanium GSS1 under stress conditions with specific emphasis on proteasome associated regulatory VAT genes
Yılmaz, Tülay; Kocabıyık, Semra; Department of Biology (2013)
In this study differential expression of the two proteasome associated VAT genes (TVNO382 and TVN0947) of Thermoplasma volcanium GSS1 (Tpv) cells challenged by extracellular stresses, i.e., pH, heat-shock and hydrogen peroxide were investigated using quantitative RT-PCR and Western blotting/hybridization techniques. We also performed a comprehensive transcriptome analysis of the Tpv as response to environmental stresses by genome-wide expression arrays. Quantitative RT-PCR analyses revealed that VAT genes e...
Expression and activity analyses of industrially important extracellular enzymes produced by a bacilysin knock-out mutant of Bacillus Subtilis
Aytekin, Samet; Özcengiz, Gülay; Okay, Sezer; Department of Molecular Biology and Genetics (2018)
Bacilysin, the smallest peptide antibiotic known to date, is produced non-ribosomally by Bacillus subtilis by the collective actions of seven proteins transcribed from bacABCDEF operon and bacG gene. Bacilysin is a two-amino acid peptide composed of L-alanine and a modified amino acid, L-anticapsin. Bacilysin biosynthesis was shown to be strongly regulated by quorum sensing through the actions of global regulator proteins including Spo0K, Spo0H, Spo0A, ComQ/ComX, ComP/ComA as well as several Phr proteins, O...
Transcriptome profiling of wheat under heat and cold stress treatments
BALOĞLU, MEHMET CENGİZ; Oz, M. Tufan; Öktem, Hüseyin Avni; Yucel, Meral (2012-09-23)
Microarray analysis was performed to indicate effects of cold and heat stress treatments on global gene expression profiles of wheat. Two groups were generated for comparison of microarray data analysis. Cold and heat conditions were separately compared to control condition. The Affymetrix GeneChip® Wheat Genome Array contains 61,127 probe sets designed to target 55,052 wheat transcripts. Out of these more than 60,000 probes, 12,895 (21.5%) were found to be differentially expressed at least p value lower th...
Expression Analysis of TaNAC69-1 and TtNAMB-2, Wheat NAC Family Transcription Factor Genes Under Abiotic Stress Conditions in Durum Wheat (Triticum turgidum)
Baloglu, Mehmet Cengiz; Oz, Mehmet Tufan; Öktem, Hüseyin Avni; Yücel, Ayşe Meral (2012-10-01)
NAC-type plant-specific transcription factor genes encode proteins that play important roles in abiotic stress responses, as well as regulation of plant development. In the current study, expression profiles of wheat NAC-type transcription factor genes, TaNAC69-1 and TtNAMB-2, were examined under drought, salt, cold, and heat stress conditions in wheat. Based on reverse transcription quantitative PCR results, TaNAC69-1 was strongly expressed under drought, salinity, and high-temperature stress conditions. C...
Molecular cloning, characterization, and homologous expression of an endochitinase gene from Bacillus thuringiensis serovar morrisoni
Okay, Sezer; Özcengiz, Gülay (2011-01-01)
The endochitinase gene (chi3023) of Bacillus thuringiensis (Bt) serovar morrisoni strain 3023 was amplified via polymerase chain reaction (PCR) and cloned in Escherichia coli. The ORF of chi3023 (GenBank Accession Number: DQ993175) consists of 2031 nucleotides encoding a 676-residue protein with a calculated molecular mass of 74.5 kDa and a pI value of 6.0. The amino acid sequence of Chi3023 was compared with previously sequenced Bt chitinases and the phylogenetic relationships among them were determined. T...
Citation Formats
S. Zabcı, “Transcriptome analysis of thermoplasma volcanium GSS1 under extreme stress,” M.S. - Master of Science, Middle East Technical University, 2015.