References of "Journal of molecular biology"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailTemporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32
Pavlova, Olga; Lavysh, Daria; Klimuk, Evgeny et al

in Journal of Molecular Biology (2012), 416

Escherichia coli phage phiEco32 encodes two proteins that bind to host RNA polymerase (RNAP): gp79, a novel protein, and gp36, a distant homolog of σ(70) family proteins. Here, we investigated the ... [more ▼]

Escherichia coli phage phiEco32 encodes two proteins that bind to host RNA polymerase (RNAP): gp79, a novel protein, and gp36, a distant homolog of σ(70) family proteins. Here, we investigated the temporal pattern of phiEco32 and host gene expression during infection. Host transcription shutoff and three distinct bacteriophage temporal gene classes (early, middle, and late) were revealed. A combination of bioinformatic and biochemical approaches allowed identification of phage promoters recognized by a host RNAP holoenzyme containing the σ(70) factor. These promoters are located upstream of early phage genes. A combination of macroarray data, primer extension, and in vitro transcription analyses allowed identification of six promoters recognized by an RNAP holoenzyme containing gp36. These promoters are characterized by a single-consensus element tAATGTAtA and are located upstream of the middle and late phage genes. Curiously, gp79, an inhibitor of host and early phage transcription by σ(70) holoenzyme, activated transcription by the gp36 holoenzyme in vitro. [less ▲]

Detailed reference viewed: 52 (0 UL)
Full Text
Peer Reviewed
See detailDesign and structure of an equilibrium protein folding intermediate: a hint into dynamical regions of proteins.
Ayuso-Tejedor, Sara; Espinosa Angarica, Vladimir UL; Bueno, Marta et al

in Journal of molecular biology (2010), 400(4), 922-34

Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for ... [more ▼]

Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for their fully physicochemical understanding are complicated by their characteristic low populations at equilibrium. We stabilize here with a single mutation the equilibrium intermediate of apoflavodoxin thermal unfolding and determine its solution structure by NMR. It consists of a large native region identical with that observed in the X-ray structure of the wild-type protein plus an unfolded region. Small-angle X-ray scattering analysis indicates that the calculated ensemble of structures is consistent with the actual degree of expansion of the intermediate. The unfolded region encompasses discontinuous sequence segments that cluster in the 3D structure of the native protein forming the FMN cofactor binding loops and the binding site of a variety of partner proteins. Analysis of the apoflavodoxin inner interfaces reveals that those becoming destabilized in the intermediate are more polar than other inner interfaces of the protein. Natively folded proteins contain hydrophobic cores formed by the packing of hydrophobic surfaces, while natively unfolded proteins are rich in polar residues. The structure of the apoflavodoxin thermal intermediate suggests that the regions of natively folded proteins that are easily responsive to thermal activation may contain cores of intermediate hydrophobicity. [less ▲]

Detailed reference viewed: 77 (1 UL)
Peer Reviewed
See detailAllostery: absence of a change in shape does not imply that allostery is not at play.
Tsai, Chung-Jung; del Sol Mesa, Antonio UL; Nussinov, Ruth

in Journal of molecular biology (2008), 378(1), 1-11

Allostery is essential for controlled catalysis, signal transmission, receptor trafficking, turning genes on and off, and apoptosis. It governs the organism's response to environmental and metabolic cues ... [more ▼]

Allostery is essential for controlled catalysis, signal transmission, receptor trafficking, turning genes on and off, and apoptosis. It governs the organism's response to environmental and metabolic cues, dictating transient partner interactions in the cellular network. Textbooks taught us that allostery is a change of shape at one site on the protein surface brought about by ligand binding to another. For several years, it has been broadly accepted that the change of shape is not induced; rather, it is observed simply because a larger protein population presents it. Current data indicate that while side chains can reorient and rewire, allostery may not even involve a change of (backbone) shape. Assuming that the enthalpy change does not reverse the free-energy change due to the change in entropy, entropy is mainly responsible for binding. [less ▲]

Detailed reference viewed: 130 (0 UL)
Full Text
Peer Reviewed
See detailThe role of DNA-binding specificity in the evolution of bacterial regulatory networks.
Lozada-Chavez, Irma; Espinosa Angarica, Vladimir UL; Collado-Vides, Julio et al

in Journal of molecular biology (2008), 379(3), 627-43

Understanding the mechanisms by which transcriptional regulatory networks (TRNs) change through evolution is a fundamental problem.Here, we analyze this question using data from Escherichia coli and ... [more ▼]

Understanding the mechanisms by which transcriptional regulatory networks (TRNs) change through evolution is a fundamental problem.Here, we analyze this question using data from Escherichia coli and Bacillus subtilis, and find that paralogy relationships are insufficient to explain the global or local role observed for transcription factors (TFs) within regulatory networks. Our results provide a picture in which DNA-binding specificity, a molecular property that can be measured in different ways, is a predictor of the role of transcription factors. In particular, we observe that global regulators consistently display low levels of binding specificity, while displaying comparatively higher expression values in microarray experiments. In addition, we find a strong negative correlation between binding specificity and the number of co-regulators that help coordinate genetic expression on a genomic scale. A close look at several orthologous TFs,including FNR, a regulator found to be global in E. coli and local in B.subtilis, confirms the diagnostic value of specificity in order to understand their regulatory function, and highlights the importance of evaluating the metabolic and ecological relevance of effectors as another variable in the evolutionary equation of regulatory networks. Finally, a general model is presented that integrates some evolutionary forces and molecular properties,aiming to explain how regulons grow and shrink, as bacteria tune their regulation to increase adaptation. [less ▲]

Detailed reference viewed: 134 (0 UL)
Full Text
Peer Reviewed
See detailCross-talk between iron and nitrogen regulatory networks in anabaena (Nostoc) sp. PCC 7120: identification of overlapping genes in FurA and NtcA regulons.
Lopez-Gomollon, Sara; Hernandez, Jose A.; Pellicer, Silvia et al

in Journal of molecular biology (2007), 374(1), 267-81

Nitrogen signalling in cyanobacteria involves a complex network in which the availability of iron plays an important role. In the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120, iron uptake is ... [more ▼]

Nitrogen signalling in cyanobacteria involves a complex network in which the availability of iron plays an important role. In the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120, iron uptake is controlled by FurA, while NtcA is the master regulator of nitrogen metabolism and shows a mutual dependence with HetR in the first steps of heterocyst development. Expression of FurA is modulated by NtcA and it is enhanced in a hetR(-) background. Iron starvation in cells grown in the presence of combined nitrogen causes a moderate increase in the transcription of glnA that is more evident in a ntcA(-) background. Those results evidence a tight link between the reserves of iron and nitrogen metabolism that leads us to search for target genes potentially co-regulated by FurA and NtcA. Using a bioinformatic approach we have found a significant number of NtcA-regulated genes exhibiting iron boxes in their upstream regions. Our computational predictions have been validated using electrophoretic mobility shift assay (EMSA) analysis. These candidates for dual regulation are involved in different functions such as photosynthesis (i.e. psaL, petH, rbcL, isiA), heterocyst differentiation (i.e. xisA, hanA, prpJ, nifH), transcriptional regulation (several alternative sigma factors) or redox balance (i.e. trxA, ftrC, gor). The identification of common elements overlapping the NtcA and FurA regulons allows us to establish a previously unrecognized transcriptional regulatory connection between iron homeostasis, redox control and nitrogen metabolism. [less ▲]

Detailed reference viewed: 66 (0 UL)
Peer Reviewed
See detailSpatio-temporal activation of chromatin on the human CYP24 gene promoter in the presence of 1alpha,25-Dihydroxyvitamin D3
Väisänen, Sami; Dunlop, Thomas W.; Sinkkonen, Lasse UL et al

in Journal of Molecular Biology (2005), 350(1), 65-77

The vitamin D3 24-hydroxylase gene (CYP24) is one of the most strongly induced genes known. Despite this, its induction by the hormone 1alpha,25-dihydroxyvitamin D3 (1alpha,25OH2D3) has been characterized ... [more ▼]

The vitamin D3 24-hydroxylase gene (CYP24) is one of the most strongly induced genes known. Despite this, its induction by the hormone 1alpha,25-dihydroxyvitamin D3 (1alpha,25OH2D3) has been characterized only partially. Therefore, we monitored the spatio-temporal, 1alpha,25OH2D3-dependent chromatin acetylation status of the human CYP24 promoter by performing chromatin immunoprecipitation (ChIP) assays with antibodies against acetylated histone 4. This was achieved by performing PCR on 25 contiguous genomic regions spanning the first 7.7 kb of the promoter. ChIP assays using antibodies against the 1alpha,25OH2D3 receptor (VDR) revealed that, in addition to the proximal promoter, three novel regions further upstream associated with VDR. Combined in silico/in vitro screening identified in three of the four promoter regions sequences resembling known VDREs and reporter gene assays confirmed the inducibility of these regions by 1alpha,25OH2D3)=. In contrast, the fourth VDR-associated promoter region did not contain any recognizable classical VDRE that could account for the presence of the protein on this region. However, re-ChIP assays monitored on all four promoter regions simultaneous association of VDR with retinoid X receptor, coactivator, mediator and RNA polymerase II proteins. These proteins showed a promoter region-specific association pattern demonstrating the complex choreography of the CYP24 gene promoter activation over 300 minutes. Thus, this study reveals new information concerning the regulation of the CYP24 gene by 1alpha,25OH2D3, and is a demonstration of the simultaneous participation of multiple, structurally diverse response elements in promoter activation in a living cell. [less ▲]

Detailed reference viewed: 32 (8 UL)
Full Text
Peer Reviewed
See detailComparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes.
Espinosa Angarica, Vladimir UL; Gonzalez, Abel D.; Vasconcelos, Ana T. et al

in Journal of molecular biology (2005), 354(1), 184-99

Experimental data on the Escherichia coli transcriptional regulation has enabled the construction of statistical models to predict new regulatory elements within its genome. Far less is known about the ... [more ▼]

Experimental data on the Escherichia coli transcriptional regulation has enabled the construction of statistical models to predict new regulatory elements within its genome. Far less is known about the transcriptional regulatory elements in other gamma-proteobacteria with sequenced genomes, so it is of great interest to conduct comparative genomic studies oriented to extracting biologically relevant information about transcriptional regulation in these less studied organisms using the knowledge from E. coli. In this work, we use the information stored in the TRACTOR_DB database to conduct a comparative study on the mechanisms of transcriptional regulation in eight gamma-proteobacteria and 38 regulons. We assess the conservation of transcription factors binding specificity across all the eight genomes and show a correlation between the conservation of a regulatory site and the structure of the transcription unit it regulates. We also find a marked conservation of site-promoter distances across the eight organisms and a correspondence of the statistical significance of co-occurrence of pairs of transcription factor binding sites in the regulatory regions, which is probably related to a conserved architecture of higher-order regulatory complexes in the organisms studied. The results obtained in this study using the information on transcriptional regulation in E. coli enable us to conclude that not only transcription factor-binding sites are conserved across related species but also several of the transcriptional regulatory mechanisms previously identified in E. coli. [less ▲]

Detailed reference viewed: 73 (1 UL)
Peer Reviewed
See detailAutomatic methods for predicting functionally important residues.
del Sol Mesa, Antonio UL; Pazos, Florencio; Valencia, Alfonso

in Journal of molecular biology (2003), 326(4), 1289-302

Sequence analysis is often the first guide for the prediction of residues in a protein family that may have functional significance. A few methods have been proposed which use the division of protein ... [more ▼]

Sequence analysis is often the first guide for the prediction of residues in a protein family that may have functional significance. A few methods have been proposed which use the division of protein families into subfamilies in the search for those positions that could have some functional significance for the whole family, but at the same time which exhibit the specificity of each subfamily ("Tree-determinant residues"). However, there are still many unsolved questions like the best division of a protein family into subfamilies, or the accurate detection of sequence variation patterns characteristic of different subfamilies. Here we present a systematic study in a significant number of protein families, testing the statistical meaning of the Tree-determinant residues predicted by three different methods that represent the range of available approaches. The first method takes as a starting point a phylogenetic representation of a protein family and, following the principle of Relative Entropy from Information Theory, automatically searches for the optimal division of the family into subfamilies. The second method looks for positions whose mutational behavior is reminiscent of the mutational behavior of the full-length proteins, by directly comparing the corresponding distance matrices. The third method is an automation of the analysis of distribution of sequences and amino acid positions in the corresponding multidimensional spaces using a vector-based principal component analysis. These three methods have been tested on two non-redundant lists of protein families: one composed by proteins that bind a variety of ligand groups, and the other composed by proteins with annotated functionally relevant sites. In most cases, the residues predicted by the three methods show a clear tendency to be close to bound ligands of biological relevance and to those amino acids described as participants in key aspects of protein function. These three automatic methods provide a wide range of possibilities for biologists to analyze their families of interest, in a similar way to the one presented here for the family of proteins related with ras-p21. [less ▲]

Detailed reference viewed: 75 (1 UL)
Full Text
Peer Reviewed
See detailProtein fold recognition by prediction-based threading
Rost, B.; Schneider, Reinhard UL; Sander, C.

in Journal of Molecular Biology (1997), 270(3), 471-480

In fold recognition by threading one takes the amino acid sequence of a protein and evaluates how well it fits into one of the known three-dimensional (3D) protein structures. The quality of sequence ... [more ▼]

In fold recognition by threading one takes the amino acid sequence of a protein and evaluates how well it fits into one of the known three-dimensional (3D) protein structures. The quality of sequence-structure fit is typically evaluated using inter-residue potentials of mean force or other statistical parameters. Here, we present an alternative approach to evaluating sequence-structure fitness. Starting from the amino acid sequence we first predict secondary structure and solvent accessibility for each residue. We then thread the resulting one-dimensional (1D) profile of predicted structure assignments into each of the known 3D structures. The optimal threading for each sequence-structure pair is obtained using dynamic programming. The overall best sequence-structure pair constitutes the predicted 3D structure for the input sequence. The method is fine-tuned by adding information from direct sequence-sequence comparison and applying a series of empirical filters. Although the method relies on reduction of 3D information into 1D structure profiles, its accuracy is, surprisingly, not clearly inferior to methods based on evaluation of residue interactions in 3D. We therefore hypothesise that existing 1D-3D threading methods essentially do not capture more than the fitness of an amino acid sequence for a particular 1D succession of secondary structure segments and residue solvent accessibility. The prediction-based threading method on average finds any structurally homologous region at first rank in 29% of the cases (including sequence information). For the 22% first hits detected at highest scores, the expected accuracy rose to 75%. However, the task of detecting entire folds rather than homologous fragments was managed much better; 45 to 75% of the first hits correctly recognised the fold. [less ▲]

Detailed reference viewed: 102 (0 UL)
Peer Reviewed
See detailREDEFINING THE GOALS OF PROTEIN SECONDARY STRUCTURE PREDICTION
ROST, B.; SANDER, C.; Schneider, Reinhard UL

in Journal of Molecular Biology (1994), 235(1), 13-26

Detailed reference viewed: 76 (0 UL)
Full Text
Peer Reviewed
See detailPREDICTION OF PROTEIN-STRUCTURE BY EVALUATION OF SEQUENCE-STRUCTURE FITNESS - ALIGNING SEQUENCES TO CONTACT PROFILES DERIVED FROM 3-DIMENSIONAL STRUCTURES
OUZOUNIS, C.; SANDER, C.; SCHARF, M. et al

in Journal of Molecular Biology (1993), 232(3), 805-825

Detailed reference viewed: 46 (0 UL)