We performed chromatin immunoprecipitation-microarray analysis to investigate differences in function between StpA and H-NS in Escherichia coli cells. StpA binding regions essentially overlap those of H-NS in wild-type cells, while they are reduced to one-third in the hns mutant. The H-NS binding profile was unaffected by stpA inactivation.

The Hha and YdgT proteins are suggested to modulate the expression of horizontally acquired genes by interacting with H-NS and StpA, which play central roles in the transcriptional silencing of such genes. However, it is also possible that Hha/YdgT repress gene expression independently of H-NS/StpA, as we have not fully understood the molecular mechanism through which Hha/YdgT modulate H-NS/StpA activity. To gain further insight into the basic functions of Hha/YdgT, we analysed the impact of hha/ydgT double inactivation on the transcriptome profile of Escherichia coli K-12, and compared the effects with that of hns/stpA double inactivation. In addition, we examined the effects of hha/ydgT inactivation on the chromosomal binding of H-NS, and conversely the effects of hns/stpA inactivation on the chromosomal binding of Hha. Our results demonstrated that the chromosomal binding of Hha requires H-NS/StpA, and is necessary for the repression of a subset of genes in the H-NS/StpA regulon. Furthermore, the distribution of H-NS binding around Hha/YdgT-dependent and -independent genes suggests that Hha/YdgT proteins modulate formation of the H-NS/StpA-DNA complex.

Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches.

In this study, 65 yeast strains were isolated from different environmental samples contaminated with various petroleum hydrocarbons such as activated sludges and soil samples from automobile workshops. The yeast isolates were tested for biosurfactant production using various screening methods such as parafilm M test, oil displacement assay, drop collapse assay, determination of surface tension reduction, and emulsification index. Nineteen of the isolates were found positive for biosurfactant production and their molecular characterizations were carried out by sequencing analysis of the ITS1-5.8S-ITS2 region and D1/D2 domain of 26S rDNA. The results indicated that these strains were from a wide range of yeast genera including Rhodotorula, Candida, Yarrowia, Geotrichum, Galactomyces, and Cystobasidium. The studies to determine the emulsification index revealed that the biosurfactants produced by Yarrowia lipolytica strains (TEMGS33, TEMOS12, and TEMOS14) and Apiotrichum loubieri strain (TEMOS16) were the most potent and capable of forming stable emulsions with emulsion index (E ) up to 68%. In addition, quantitative measurements of the surface tension reduction of the biosurfactants produced by these strains were carried out by Du Noüy ring method. Biosurfactants produced from Yarrowia lipolytica strain TEMGS33 and Apiotrichum loubieri strain TEMOS16 gave the best results reducing the surface tension to 34.7 ± 1.15 and 35.3 ± 0.55 mN m , respectively. Based on these data, biosurfactants from Yarrawia lipolytica strains (TEMGS33, TEMOS12, and TEMOS14) and Apiotrichum loubieri strain (TEMOS16) showed promising results and might be implemented in numerous industrial fields such as bioremediation and food industry.

Rhizopus oryzae accumulates and degrades trehalose in response to environmental stress conditions such as heat, osmotic stress, nitrogen starvation and pH. When heat stress was applied to R. oryzae, the trehalose content of the cells was increased from 0.9 to 4.8 mg/g dw and when the stress was relieved it decreased back to 1.1 mg/g dw. Under osmotic stress and nitrogen starvation, trehalose content was increased by 3.5 and 3 fold, respectively. The decrease in external pH increased trehalose level up to 2.6 mg/g dw from 1.1 mg/g dw. Increased trehalose level decreased back to normal after pH stress was relieved. These results indicate that trehalose accumulates and acts as a stress protectant in R. oryzae.