Abstract
BackgroundThe identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known.ResultsHere, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) by profiling transcription in a wild-type and a delta-cre1 mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes.ConclusionsOur study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.
Highlights
The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour
The results showed that - in contrast to the radial growth on plates - the Δcre1 strain grew significantly slower on only 5 of 95 carbon sources (Glycogen -37 [±4], p = 0.004; arbutin -27 [±4], p = 0.0006; adenosine -42 [±5], p = 0.022; salicin -34 [±4], p = 0.007; and amygdalin -42 [±6], p = 0.013), but on the other hand was unaffected on the majority of them
Increased growth of > 30% of the control, which would be expected if CRE1 represses growth on a given carbon source, was observed for 9 carbon sources shown in Additional File 1, Figure S3 (D-galactose +38 [±3], p = 0.0008; L-sorbose +34 [±3], p = 0.027; D-xylose +48 [±5], p = 0.002; palatinose +31 [±6], p = 0.033; maltose +58 [±6], p = 0.002; stachyose +45 [±4], p = 0.03; xylitol +37 [±4], p = 0.017; adonitol +46 [±6], p = 0.0008); and glucuronamide +73 [±3], p = 0.044)
Summary
The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. Many filamentous fungi have developed a predominantly saprobic lifestyle, in which successful competition with other microorganisms for the limited resources present in the environment is the key for survival To this end mechanisms evolved that allow a rapid adaption to changing nutrient conditions. One such wide-domain regulatory circuit is carbon catabolite repression (CCR): it allows the preferred assimilation of carbon sources of high nutritional value over others [1,2,3,4]. We chose to use chemostat cultures on D-glucose as a carbon source at two different growth rates (one repressing and one derepressing [16]) to investigate the genome-wide changes in gene expression in relation to CRE1 function, using a Δcre recombinant mutant strain of T. reesei and corresponding control strain
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