Global gene expression during stringent response in <it>Corynebacterium glutamicum </it>in presence and absence of the <it>rel </it>gene encoding (p)ppGpp synthase

• Main Authors: Kalinowski Jörn, Brockmann-Gretza Olaf
• Format: Article
• Language: English
• Published: BMC 2006-09-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/7/230

<p/> <p>Background</p> <p>The stringent response is the initial reaction of microorganisms to nutritional stress. During stringent response the small nucleotides (p)ppGpp act as global regulators and reprogram bacterial transcription. In this work, the genetic network controlled by the stringent response was characterized in the amino acid-producing <it>Corynebacterium glutamicum</it>.</p> <p>Results</p> <p>The transcriptome of a <it>C. glutamicum rel </it>gene deletion mutant, unable to synthesize (p)ppGpp and to induce the stringent response, was compared with that of its <it>rel</it>-proficient parent strain by microarray analysis. A total of 357 genes were found to be transcribed differentially in the <it>rel</it>-deficient mutant strain. In a second experiment, the stringent response was induced by addition of DL-serine hydroxamate (SHX) in early exponential growth phase. The time point of the maximal effect on transcription was determined by real-time RT-PCR using the histidine and serine biosynthetic genes. Transcription of all of these genes reached a maximum at 10 minutes after SHX addition. Microarray experiments were performed comparing the transcriptomes of SHX-induced cultures of the <it>rel</it>-proficient strain and the <it>rel </it>mutant. The differentially expressed genes were grouped into three classes. Class A comprises genes which are differentially regulated only in the presence of an intact <it>rel </it>gene. This class includes the non-essential sigma factor gene <it>sigB </it>which was upregulated and a large number of genes involved in nitrogen metabolism which were downregulated. Class B comprises genes which were differentially regulated in response to SHX in both strains, independent of the <it>rel </it>gene. A large number of genes encoding ribosomal proteins fall into this class, all being downregulated. Class C comprises genes which were differentially regulated in response to SHX only in the <it>rel </it>mutant. This class includes genes encoding putative stress proteins and global transcriptional regulators that might be responsible for the complex transcriptional patterns detected in the <it>rel </it>mutant when compared directly with its <it>rel</it>-proficient parent strain.</p> <p>Conclusion</p> <p>In <it>C. glutamicum </it>the stringent response enfolds a fast answer to an induced amino acid starvation on the transcriptome level. It also showed some significant differences to the transcriptional reactions occuring in <it>Escherichia coli </it>and <it>Bacillus subtilis</it>. Notable are the <it>rel</it>-dependent regulation of the nitrogen metabolism genes and the <it>rel</it>-independent regulation of the genes encoding ribosomal proteins.</p>