1,720,972 research outputs found
Transcription factors of the MocR family: in silico comparative analysis
No full textThe MocR/GabR subfamily of chimeric proteins is widespread in bacteria and regulates a variety of biological processes. All members of this subfamily are typically composed of a winged helix-turn-helix (HTH) DNA-binding domain and a putative aminotransferase domain (AAT), belonging to the superfamily of the pyridoxal-5’-phosphate (PLP) enzymes of fold type I. The HTH-containing regions of these proteins vary from 60 to 120 residues in lenght and are similar to the winged HTH regions of bacterial transcriptional regulators of the broad GntR family. Little is known about the function of the AAT domain
and about its ability to retain some catalytic activity. Moreover, the transcriptional regulatory pathways in which the MocR proteins might be involved are not known. So far,
only a few MocR regulators have been characterized experimentally. One of these, PdxR is involved in the regulation of the divergently oriented pdxST operon, coding for the subunits of pyridoxal-5’-phosphate synthase in Corynebacterium glutamicum. Our research projects are aimed at the characterization of this regulator family through the following sub-tasks:
-give an overview of the distribution of MocR factors among the different taxonomical bacterial divisions;
-try to assess the degree of conservation of the main structural features of the AAT domain and compare them to those of the freestanding PLP enzymes;
-predict which genes are controlled by these regulators;
-identify, in the intergenic regions, the transcription factor binding sites (TFBSs).
Methods:
An ad-hoc Profile-HMM was built from a multiple sequence alignment of MocR proteins. HMM searches were carried out on the complete proteomes of each phylum reported in the taxonomy division of UniProt databank to collect most of the
members of the MocR family. A Python script was used to extract information about the location, into the genome, of gene coding MocR and their neighbors genes. All sequences of neighboring genes were compared against the Pfam database to locate known domains. Pfam domain frequency was calculated as the fraction of the proteins having that particular Pfam domain. This frequency was calculated for each Pfam domain for all proteins in the dataset. Based on these frequencies and knowledge available in the literature, a subset of convergently
transcribed pairs was selected. Pattern search and comparative genomics methods were used to detect direct and inverted repeat sequences in the intergenic regions between MocR and neighbors genes. Homology modelling techniques were applied to predict the three-dimensional structure of representative MocR members based on the B. subtilis GabR with PDB code 4MGR. The most interesting regulators will be selected for experimental
characterization
Conserved water molecules in bacterial serine hydroxymethyltransferases
No full textWater molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5’-phosphate (PLP)-dependent enzymes that catalyze the reversible conversion of L-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as ‘clusters’ and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of eleven bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments
Type I pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines.
No full textPyridoxal 5'-phosphate (PLP)-dependent enzymes of fold type I, the most studied structural class of the PLP-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. These enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (PKS) and nonribosomal peptides (NRPS). The aim of this work is to provide a proteome-wide view of the distribution and characteristics of type I domains covalently integrated in these assemblies in prokaryotes. An ad-hoc Hidden Markov profile was calculated using a sequence alignment derived from a multiple structural superposition of distantly related PLP-enzymes of fold type I. The profile was utilized to scan the sequence databank and to collect the proteins containing at least one type I domain linked to a component of an assembly line in bacterial genomes. The domains adjacent to a carrier protein were further investigated. Phylogenetic analysis suggested the presence of four PLP-dependent families: Aminotran_3, Beta_elim_lyase and Pyridoxal_deC, occurring mainly within mixed NRPS/PKS clusters, and Aminotran_1_2 found mainly in PKS clusters. Sequence similarity to the reference PLP enzymes with solved structures ranged from 24 to 42% identity. Homology models were built for each representative type I domain and molecular docking simulations with putative substrates were carried out. Prediction of the protein-protein interaction sites evidenced that the surface regions of the type I domains embedded within multienzyme assemblies were different from those of the self-standing enzymes; these structural features appear to be required for productive interactions with the adjacent domains in a multidomain context. This work provides a systematic view of the occurrence of type I domain within NRPS and PKS assembly lines and it predicts their structural characteristics using computational methods. Comparison with the corresponding stand-alone enzymes highlighted the common and different traits related to various aspects of their structure-function relationship. Therefore, the results of this work, on one hand contribute to the understanding of the functional and structural diversity of the PLP-dependent type I enzymes and, on the other, pave the way to further studies aimed at their applications in combinatorial biosynthesis
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Genomic distribution and heterogeneity of MocR-like transcriptional factors containing a domain belonging to the superfamily of the pyridoxal-5'-phosphate dependent enzymes of fold type I.
No full textBacterial proteins belonging to the MocR/GabR family are chimeric proteins incorporating a short N-terminal helix-turn-helix containing domain with DNA-binding properties, and a long C-terminal domain belonging to the superfamily of the pyridoxal-5'-phosphate enzymes of fold type I. The first purpose of this report is to give an overview of the distribution of these factors among the different taxonomical bacterial divisions and to determine the degree of conservation of the main structural features of the PLP binding domain. Complete proteomes of bacteria phyla were scanned with a hidden Markov model representative of the MocR family. Results indicate that presence of MocR factors is heterogeneous even within the single bacterial phylum: some species miss completely the factors, while others possess one or even more regulators. Absence of MocR factors is distinctive of some phyla such as Chlamydiae. The genomic distribution of MocR is, as expected, highly correlated to the size of the genome. At variance, phyla missing MocR regulators generally are characterized by compact genomes, of the order of 1.0-2.0Mb, such as the case of Mollicutes or Chlamydiae. Apparently, the minimum genome size compatible with the presence of MocR genes is around 2.0-2.5Mb. Conservation of the residues corresponding to those involved in the interaction with the cofactor pyridoxal-5'-phosphate in the homologous 2-aminoadipate aminotransferase, was analyzed in the multiple sequence alignments of MocR within each phyla considered. In the vast majority of cases, residues are conserved or conservatively replaced. This result suggests that, in most cases, MocR factors preserve at least ability to bind the cofactor and very likely some catalytic abilities
Structural properties of the linkers connecting the n- and c- terminal domains in the mocr bacterial transcriptional regulators
Full text linkPeptide inter-domain linkers are peptide segments covalently linking two adjacent domains within a protein. Linkers play a variety of structural and functional roles in naturally occurring proteins. In this work we analyze the sequence properties of the predicted linker regions of the bacterial transcriptional regulators belonging to the recently discovered MocR subfamily of the GntR regulators. Analyses were carried out on the MocR sequences taken from the phyla Actinobacteria, Firmicutes, Alpha-, Beta- and Gammaproteobacteria. The results suggest that MocR linkers display phylum-specific characteristics and unique features different from those already described for other classes of inter-domain linkers. They show an average length significantly higher: 31.8 ± 14.3 residues reaching a maximum of about 150 residues. Compositional propensities displayed general and phylum-specific trends. Pro is dominating in all linkers. Dyad propensity analysis indicate Pro–Pro as the most frequent amino acid pair in all linkers. Physicochemical properties of the linker regions were assessed using amino acid indices relative to different features: in general, MocR linkers are flexible, hydrophilic and display propensity for β-turn or coil conformations. Linker sequences are hypervariable: only similarities between MocR linkers from organisms related at the level of species or genus could be found with sequence searches. The results shed light on the properties of the linker regions of the new MocR subfamily of bacterial regulators and may provide knowledge-based rules for designing artificial linkers with desired properties. © 2016 The Author(s
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
- …
