Concerning the regulation of the whole set of carbohydrate-degrading enzymes, the complex pattern of adaptive gene control certainly needs further investigation.
Among the complex pattern of adaptive gene control for carbohydrate hydrolysis, the enhanced need for carbohydrates during periods of anaerobiosis is probably related to the strong hypoxic induction of cellubiohydrolase, which may serve for a degradation of structural polysaccharides.
Also, the differential expression pattern of genes that control metabolism and transport of potassium, iron, copper and sulphur ions suggests that they may influence directly the pathogen adaptation to the host environment.
This connection may be one of the mechanisms underlying the different patterns of gene expression control; it was already briefly discussed in Tian et al. [ 2].
We suggest that Tpt1 might have a somewhat general role in establishing an embryonic pattern of gene expression because it controls transcription of oct4 and nanog.
In tomato, as for Arabidopsis, we observed a bi-directional regulatory crosstalk between the clock machinery and photoreceptors which allowed the latter to determine significant changes on the temporal transcription pattern of genes under the control of the first.
The exception was the menin over-expressing line (UAS-Mnn1), which displayed a pattern of gene expression resembling that of control embryos subjected to a longer 1 hr heat shock treatment (Fig. 6A, lanes 5 and 6).
In addition, FSHD muscle progenitors had a unique pattern of gene dysregulation compared with analogous control cells.
In addition, we recently reported that the ability of CEC to respond to inflammatory stimuli by changing the pattern of gene expression is in part controlled by transcriptional activity [ 8, 9] and in part at the post-transcriptional level via small non coding RNAs termed microRNAs [ 16, 17].
This oscillating pattern of gene regulation may reflect a homeostatic control mechanism that is gradually adjusting the gill to the new zinc depleted condition.
