Expression and purification of the cynR regulatory gene product: CynR is a DNA-binding protein

Molecular level insight of thiocyanate degradation by Pseudomonas putida TDB-1 under a high arsenic and alkaline condition

It is a big challenge to bioremediate thiocyanate pollution in the gold extraction heap leaching tailings and surrounding soils with high contents of arsenic and alkali. Here, a novel thiocyanate-degrading bacterium Pseudomonas putida TDB-1 was successfully applied to completely degrade 1000 mg/L thiocyanate under a high arsenic (400 mg/L) and alkaline condition (pH = 10). It also leached the contents of thiocyanate from 1302.16 to 269.72 mg/kg in the gold extraction heap leaching tailings after 50 h. The maximum transformation rates of S and N in thiocyanate to the two finial products of SO₄^2- and NO₃^- were 88.98 % and 92.71 %, respectively. Moreover, the genome sequencing confirmed that the biomarker gene of thiocyanate-degrading bacterium, CynS was identified in the strain TDB-1. The bacterial transcriptome revealed that critical genes, such as CynS, CcoNOQP, SoxY, tst, gltBD, arsRBCH and NhaC, etc. in the thiocyanate degradation, S and N metabolisms, and As and alkali resistance were significantly up-regulated in the groups with 300 mg/L SCN^- (T300) and with 300 mg/L SCN^- and 200 mg/L As (TA300). In addition, the protein-protein interaction network showed that the glutamate synthase encoding by gltB and gltD served as central node to integrate the S and N metabolism pathways with thiocyanate as substrate. The results of our study provide a novel molecular level insight for the dynamic gene expression regulation of thiocyanate degradation by the strain TDB-1 with a severe arsenic and alkaline stress.

Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model

BACKGROUND

The goal of most programs developed to find transcription factor binding sites (TFBSs) is the identification of discrete sequence motifs that are significantly over-represented in a given set of sequences where a transcription factor (TF) is expected to bind. These programs assume that the nucleotide conservation of a specific motif is indicative of a selective pressure required for the recognition of a TF for its corresponding TFBS. Despite their extensive use, the accuracies reached with these programs remain low. In many cases, true TFBSs are excluded from the identification process, especially when they correspond to low-affinity but important binding sites of regulatory systems.

RESULTS

We developed a computational protocol based on molecular and structural criteria to perform biologically meaningful and accurate phylogenetic footprinting analyses. Our protocol considers fundamental aspects of the TF-DNA binding process, such as: i) the active homodimeric conformations of TFs that impose symmetric structures on the TFBSs, ii) the cooperative binding of TFs, iii) the effects of the presence or absence of co-inducers, iv) the proximity between two TFBSs or one TFBS and a promoter that leads to very long spurious motifs, v) the presence of AT-rich sequences not recognized by the TF but that are required for DNA flexibility, and vi) the dynamic order in which the different binding events take place to determine a regulatory response (i.e., activation or repression). In our protocol, the abovementioned criteria were used to analyze a profile of consensus motifs generated from canonical Phylogenetic Footprinting Analyses using a set of analysis windows of incremental sizes. To evaluate the performance of our protocol, we analyzed six members of the LysR-type TF family in Gammaproteobacteria.

CONCLUSIONS

The identification of TFBSs based exclusively on the significance of the over-representation of motifs in a set of sequences might lead to inaccurate results. The consideration of different molecular and structural properties of the regulatory systems benefits the identification of TFBSs and enables the development of elaborate, biologically meaningful and precise regulatory models that offer a more integrated view of the dynamics of the regulatory process of transcription.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation

The cynTSX operon enables Escherichia coli K-12 to degrade and use cyanate as a sole nitrogen source. The promoter of this operon is positively regulated by cyanate and the CynR protein. CynR, a member of the LysR family of regulatory proteins, binds specifically to a 136-bp DNA fragment containing both the cynR and the cynTSX promoters. In this study, we report the results of DNase I digestion studies showing that CynR protects a 60-bp region on the cynR coding strand and a 56-bp sequence on the cynTSX coding strand. CynR binding was not affected by cyanate or its structural homolog azide, a gratuitous inducer of the operon. However, CynR-induced bending of two different DNA fragments was detected. The amount of bending was decreased by cyanate.