BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3025-3) contains supplementary material, which is available to authorized users.
Fungal laccases have been extensively exploited for industrial purposes and there is a wealth of information available regarding their reaction mechanism, biological role and several molecular aspects, including cloning, heterologous expression and transcriptional analyses. Here we present the reconstruction of the fungal laccase loci evolution inferred from the comparative analysis of 48 different sequences. The topology of the phylogenetic trees indicate that a single monophyletic branch exists for fungal laccases and that laccase isozyme genes may have evolved independently, possibly through duplication-divergence events. Laccases are copper-containing enzymes generally identified by the utilization of substituted p-diphenol substrates. Interestingly, our approach permitted the assignment of two copper-containing oxidases, preliminarily catalogued as laccases, to a different evolutionary group, distantly related to the main branch of bona fide laccases.
I N a recent paper in the Transactions of the Linnean Society, dealing with the results of a re-investigation of Brongniart's genus of fossil Gymnospermous seeds Stephanospcrmum, the opinion was expressed that a considerable number of the radially symmetrical forms of seeds of Permo-carboniferous age (Radiosperms) possessed the same fundamental type of organisation as StepUanospermnm itself.' The present communication deals with two additional seeds from this provisional group, viz.
BOTANY IN ENGLAND": A REPLY. I N the September number of the jfounial of Botany, Mr. James Britten deals at considerable length with the portion of my Presidential Address to the Botanical Section at the recent Meeting of the British Association at York, which was printed under the title " Botany in England." As Mr. Britten's criticism seemed based on a misapprehension of the drift of my remarks, and as it was printed in a medium often consulted by Systematic Botanists, 1 naturally sent a reply which I hoped might be inserted in a forthcoming number of the same Journal. In his capacity of Editor, however, Mr. Britten did not see his way to insert my reply in the form in which I had written it. As 1 was unable, in my turn, to fall in with the restrictions imposed by Mr. Britten, hospitality for a rejoinder had to be sought elsewhere. It is under these circumstances that the present note appears in the pages of the NEW PHVTOLOGIST. Whilst welcoming any criticisms that Mr. Britten may think fit to make, 1 may, perhaps, be permitted to express the hope that the tone which animates his recent utterance may find no permanent place in botanical controversy. When one's shortcomings are so rudely exposed, there is the temptation to emulate one's critic and take reprisals. In my York Address 1 endeavoured to shew that in the general advance of Botany in this country during the last twenty-five years our great centres of Systematic Botany had become encased, as it were, in a sort of watertight compartment, and this from causes inherent in their organisation. 1 do not think it can be seriously questioned that the Herbaria pursue their work apart. One has only to turn to the utterances of men so well qualified to speak for Systematic Botany as Sir George King and Sir William Thiselton-Dyer. The former speaks of its neglect and decadence'; the latter > Presidential Address to Section K. Brit. Assoc, Dover, 1899, p. 16.
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