Arrangement Of Motifs Research Articles

Recognition of mandelate stereoisomers by chiral porphyrin hosts: prediction of stereopreference in guest binding a priori using a simple binding model?

Rigid porphyrin hosts that mimic the spatial arrangement of mandelate recognition motifs lead to stereoselective receptors and illustrate how subtle structural differences in host design have significant impact on guest recognition. The porphyrin hosts are obtained with minimal synthetic effort from readily available chiral amine precursors and are modular in design. The chiral recognition properties of the porphyrin-based hosts with chiral carboxylate-containing guests and chiral amines are described. UV/vis and 1H NMR spectroscopic results indicate some of these porphyrin hosts undergo an induced fit conformational change upon guest binding.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and 'through-DNA' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex.

Analysis of the Ush2a Gene in Medaka Fish (Oryzias latipes)

Patients suffering from Usher syndrome (USH) exhibit sensorineural hearing loss, retinitis pigmentosa (RP) and, in some cases, vestibular dysfunction. USH is the most common genetic disorder affecting hearing and vision and is included in a group of hereditary pathologies associated with defects in ciliary function known as ciliopathies. This syndrome is clinically classified into three types: USH1, USH2 and USH3. USH2 accounts for well over one-half of all Usher cases and mutations in the USH2A gene are responsible for the majority of USH2 cases, but also for atypical Usher syndrome and recessive non-syndromic RP. Because medaka fish (Oryzias latypes) is an attractive model organism for genetic-based studies in biomedical research, we investigated the expression and function of the USH2A ortholog in this teleost species. Ol-Ush2a encodes a protein of 5.445 aa codons, containing the same motif arrangement as the human USH2A. Ol-Ush2a is expressed during early stages of medaka fish development and persists into adulthood. Temporal Ol-Ush2a expression analysis using whole mount in situ hybridization (WMISH) on embryos at different embryonic stages showed restricted expression to otoliths and retina, suggesting that Ol-Ush2a might play a conserved role in the development and/or maintenance of retinal photoreceptors and cochlear hair cells. Knockdown of Ol-Ush2a in medaka fish caused embryonic developmental defects (small eyes and heads, otolith malformations and shortened bodies with curved tails) resulting in late embryo lethality. These embryonic defects, observed in our study and in other ciliary disorders, are associated with defective cell movement specifically implicated in left-right (LR) axis determination and planar cell polarity (PCP).

Structural basis of regulation and oligomerization of human cystathionine β-synthase, the central enzyme of transsulfuration

Cystathionine β-synthase (CBS) controls the flux of sulfur from methionine to cysteine, a precursor of glutathione, taurine, and H2S. CBS condenses serine and homocysteine to cystathionine with the help of three cofactors, heme, pyridoxal-5'-phosphate, and S-adenosyl-l-methionine. Inherited deficiency of CBS activity causes homocystinuria, the most frequent disorder of sulfur metabolism. We present the structure of the human enzyme, discuss the unique arrangement of the CBS domains in the C-terminal region, and propose how they interact with the catalytic core of the complementary subunit to regulate access to the catalytic site. This arrangement clearly contrasts with other proteins containing the CBS domain including the recent Drosophila melanogaster CBS structure. The absence of large conformational changes and the crystal structure of the partially activated pathogenic D444N mutant suggest that the rotation of CBS motifs and relaxation of loops delineating the entrance to the catalytic site represent the most likely molecular mechanism of CBS activation by S-adenosyl-l-methionine. Moreover, our data suggest how tetramers, the native quaternary structure of the mammalian CBS enzymes, are formed. Because of its central role in transsulfuration, redox status, and H2S biogenesis, CBS represents a very attractive therapeutic target. The availability of the structure will help us understand the pathogenicity of the numerous missense mutations causing inherited homocystinuria and will allow the rational design of compounds modulating CBS activity.

The effect of pattern sizes on blue plates and blue motif arrangements on white plates on the appetite for Japanese food.

The effect of pattern sizes on blue plates and blue motif arrangements on white plates on the appetite for Japanese food.

Correlation Between Crystallization Behavior and Network Structure in GeS2–Ga2S3–CsI Chalcogenide Glasses

Diagram of the phase transformation behavior of GeS2–Ga2S3–CsI glasses is realized in this article and the structure‐property dependence of the chalcogenide glasses is elucidated using differential scanning calorimetry and Raman spectroscopy. We observe the compositional threshold of crystallization behavior locates at x = 6–7 mol% in (100−x)(0.8GeS2–0.2Ga2S3)–xCsI glasses, which is confirmed by the thermodynamic studies. Structural motifs are derived from the Raman result that [Ge(Ga)S4], [S2GeI2], [S3GaI], and [S3Ga–GaS3] were identified to exist in this glass network. Combined with the information of structural threshold, local arrangement of these structural motifs is proposed to explain all the experimental observations, which provides a new way to understand the correlation between crystallization behavior and network structure in chalcogenide glasses.

Structure and Dynamics of the Fish Eye Lens Protein, γM7-Crystallin

The vertebrate eye lens contains high concentrations of crystallins. The dense lenses of fish are particularly abundant in a class called γM-crystallin whose members are characterized by an unusually high methionine content and partial loss of the four tryptophan residues conserved in all γ-crystallins from mammals which are proposed to contribute to protection from UV-damage. Here, we present the structure and dynamics of γM7-crystallin from zebrafish (Danio rerio). The solution structure shares the typical two-domain, four-Greek-key motif arrangement of other γ-crystallins, with the major difference noted in the final loop of the N-terminal domain, spanning residues 65-72. This is likely due to the absence of the conserved tryptophans. Many of the methionine residues are exposed on the surface but are mostly well-ordered and frequently have contacts with aromatic side chains. This may contribute to the specialized surface properties of these proteins that exist under high molecular crowding in the fish lens. NMR relaxation data show increased backbone conformational motions in the loop regions of γM7 compared to those of mouse γS-crystallin and show that fast internal motion of the interdomain linker in γ-crystallins correlates with linker length. Unfolding studies monitored by tryptophan fluorescence confirm results from mutant mouse γS-crystallin and show that unfolding of a βγ-crystallin domain likely starts from unfolding of the variable loop containing the more fluorescently quenched tryptophan residue, resulting in a native-like unfolding intermediate.

Computational Discovery of Transcriptional Regulatory Modules in Fungal Ribosome Biogenesis Genes Reveals Novel Sequence and Function Patterns

Genes involved in ribosome biogenesis and assembly (RBA) are responsible for ribosome formation. In Saccharomyces cerevisiae, their transcription is regulated by two dissimilar DNA motifs. We were interested in analyzing conservation and divergence of RBA transcription regulation machinery throughout fungal evolution. We have identified orthologs of S. cerevisiae RBA genes in 39 species across fungal phylogeny and searched upstream regions of these gene sets for DNA sequences significantly similar to S. cerevisiae RBA regulatory motifs. In addition to confirming known motif arrangements comprising two different motifs in a set of S. cerevisiae close relatives or two instances of the same motif (that we refer to as modules), we have also discovered novel modules in a group of fungi closely related to Neurospora crassa. Despite a single nucleotide difference between consensus sequences of RBA motifs, modules associated with S, cerevisiae group and N. crassa group displayed consistently different characteristics with respect to preferred module organization and several other module properties. For a given species, we have found a correlation between the configuration of the RBA module and significant enrichment in a set of specific Gene Ontology biological processes. We have identified several likely new candidates for a role in ribosome biogenesis in S. cerevisiae based on the combined evidence of RBA module presence in the upstream regions, functional annotation information and microarray expression profiles. We believe that this approach will be useful in terms of generating hypotheses about functional roles of genes for which only fragmentary data from a single source are available.

Genome-Wide Screens for In Vivo Tinman Binding Sites Identify Cardiac Enhancers with Diverse Functional Architectures

The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP) from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ∼50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

Application of Abstract Motifs Extracted In Aquatic Animal on Garments

Application of Abstract Motifs Extracted In Aquatic Animal on Garments

Vapour and mechanically induced chromic behaviour of platinum complexes with a dimer-of-dimer motif and the effects of heterometal ions

Heterodinuclear complexes, syn-[MPt(μ-pyt)2(bpy)2](n+) (syn-[MPt], M = Pd(2+), Au(3+), Hpyt = pyridine-2-thiol, bpy = 2,2'-bipyridine), were synthesized as a selective geometrical isomer by stepwise complexation. X-ray analyses of the hexafluorophosphate salts of these complexes proved their dinuclear structures with short M···Pt distances (2.9084(4) Å for syn-[PdPt] and 2.9071(4) Å for syn-[AuPt]), similar to the homodinuclear complex (2.9292(2) Å for syn-[PtPt]). In the syn-[PdPt] crystal, two dinuclear motifs are arranged closely in a head-to-head manner with a short Pt···Pt distance (3.3757(3) Å), forming a dimer-of-dimer structure as in the case of syn-[PtPt], whereas the corresponding crystal of syn-[AuPt] has a discrete arrangement of the dinuclear motifs. By the isomerisation of syn-[PdPt], anti-[PdPt] with equivalent environments of the Pd(2+) and Pt(2+) ions was also obtained successfully. Syn-[PdPt](PF6)2 exhibits vapochromic behaviour based on the absorption/desorption of CH3CN vapour, similar to that observed for syn-[PtPt](PF6)2. The reversible structural transformations induced by the uptake and release of CH3CN molecules were investigated by powder and single-crystal X-ray diffraction studies. These revealed that the vapochromic behaviour was based on the interconversion between two phases, the dimer-of-dimer structure with a short Pt···Pt distance and a π-π stacked arrangement with no Pt···Pt intermolecular interaction. The introduction of the heterometal ions enabled control of the colour region: orange ↔ red for syn-[PdPt] vs. light red ↔ dark red for syn-[PtPt], reflecting the weaker metal-metal interaction between Pd(2+) and Pt(2+) ions in the dinuclear motif. In addition, these complexes were found to exhibit mechanochromic behaviour based on a crystal-to-amorphous transformation upon grinding, and the reconstruction of the crystal structures by vapour sorption.

Arabidopsis Calmodulin-binding Protein IQ67-Domain 1 Localizes to Microtubules and Interacts with Kinesin Light Chain-related Protein-1

Calcium (Ca(2+)) is a key second messenger in eukaryotes and regulates diverse cellular processes, most notably via calmodulin (CaM). In Arabidopsis thaliana, IQD1 (IQ67 domain 1) is the founding member of the IQD family of putative CaM targets. The 33 predicted IQD proteins share a conserved domain of 67 amino acids that is characterized by a unique arrangement of multiple CaM recruitment motifs, including so-called IQ motifs. Whereas IQD1 has been implicated in the regulation of defense metabolism, the biochemical functions of IQD proteins remain to be elucidated. In this study we show that IQD1 binds to multiple Arabidopsis CaM and CaM-like (CML) proteins in vitro and in yeast two-hybrid interaction assays. CaM overlay assays revealed moderate affinity of IQD1 to CaM2 (K(d) ∼ 0.6 μm). Deletion mapping of IQD1 demonstrated the importance of the IQ67 domain for CaM2 binding in vitro, which is corroborated by interaction of the shortest IQD member, IQD20, with Arabidopsis CaM/CMLs in yeast. A genetic screen of a cDNA library identified Arabidopsis kinesin light chain-related protein-1 (KLCR1) as an IQD1 interactor. The subcellular localization of GFP-tagged IQD1 proteins to microtubules and the cell nucleus in transiently and stably transformed plant tissues (tobacco leaves and Arabidopsis seedlings) suggests direct interaction of IQD1 and KLCR1 in planta that is supported by GFP∼IQD1-dependent recruitment of RFP∼KLCR1 and RFP∼CaM2 to microtubules. Collectively, the prospect arises that IQD1 and related proteins provide Ca(2+)/CaM-regulated scaffolds for facilitating cellular transport of specific cargo along microtubular tracks via kinesin motor proteins.

COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets

In multi-cellular organisms, spatiotemporal activity of cis-regulatory DNA elements depends on their occupancy by different transcription factors (TFs). In recent years, genome-wide ChIP-on-Chip, ChIP-Seq and DamID assays have been extensively used to unravel the combinatorial interaction of TFs with cis-regulatory modules (CRMs) in the genome. Even though genome-wide binding profiles are increasingly becoming available for different TFs, single TF binding profiles are in most cases not sufficient for dissecting complex regulatory networks. Thus, potent computational tools detecting statistically significant and biologically relevant TF-motif co-occurrences in genome-wide datasets are essential for analyzing context-dependent transcriptional regulation. We have developed COPS (Co-Occurrence Pattern Search), a new bioinformatics tool based on a combination of association rules and Markov chain models, which detects co-occurring TF binding sites (BSs) on genomic regions of interest. COPS scans DNA sequences for frequent motif patterns using a Frequent-Pattern tree based data mining approach, which allows efficient performance of the software with respect to both data structure and implementation speed, in particular when mining large datasets. Since transcriptional gene regulation very often relies on the formation of regulatory protein complexes mediated by closely adjoining TF binding sites on CRMs, COPS additionally detects preferred short distance between co-occurring TF motifs. The performance of our software with respect to biological significance was evaluated using three published datasets containing genomic regions that are independently bound by several TFs involved in a defined biological process. In sum, COPS is a fast, efficient and user-friendly tool mining statistically and biologically significant TFBS co-occurrences and therefore allows the identification of TFs that combinatorially regulate gene expression.

Characterization of a set of novel meiotically-active promoters in Arabidopsis

BackgroundHomologous recombination, together with selection, laid the foundation for traditional plant breeding. The recombination process that takes place during meiotic cell division is crucial for the creation of novel variations of highly desired traits by breeders. Gaining control over this process is important for molecular breeding to achieve more precise, large-scale and quicker plant improvement. As conventional ubiquitous promoters are neither tissue-specific nor efficient in driving gene expression in meiocytes, promoters with high meiotic activities are potential candidates for manipulating the recombination process. So far, only a few meiotically-active promoters have been reported. Recently developed techniques to profile the transcriptome landscape of isolated meiocytes provided the means to discover promoters from genes that are actively expressed in meiosis.ResultsIn a screen for meiotically-active promoters, we examined ten promoter sequences that are associated with novel meiotic candidate genes. Each promoter was tested by expressing a GFP reporter gene in Arabidopsis. Characterization of regulatory regions revealed that these meiotically-active promoters possessed conserved motifs and motif arrangement. Some of the promoters unite optimal properties which are invaluable for meiosis-directed studies such as delivering specific gene expression in early meiosis I and/or meiosis II. Furthermore, the examination of homologs of the corresponding genes within green plants points to a great potential of applying the information from Arabidopsis to other species, especially crop plants.ConclusionsWe identified ten novel meiotically-active promoters; which, along with their homologs, are prime candidates to specifically drive gene expression during meiosis in plants and can thus provide important tools for meiosis study and crop breeding.

Structure ofEscherichia coliBamD and its functional implications in outer membrane protein assembly

The outer membrane protein complex (BAM complex) plays an important role in outer membrane protein (OMP) assembly in Escherichia coli. The BAM complex includes the integral β-barrel protein BamA as well as four lipoproteins: BamB, BamC, BamD and BamE. One of these lipoproteins, BamD, isessential for the survival of Escherichia coli. The structure of BamD at 2.6 Å resolution shows that this lipoprotein is composed of ten α-helices that form five tetratricopeptide-repeat (TPR) motifs. The arrangement of the BamD motifs is similar to that in the periplasmic part of BamA. One of the ten α-helices, α10, which has been shown to be important for theassembly of the BAM complex, is located in the very C-terminal region of BamD. A deep groove between TPR domains 4 and 5 is also observed. This groove, as well as the surface around α10, may provide binding sites for other components of the BAM complex. The C-terminal region ofBamD serves as a platform for interactions with other components of the BAM complex. The N-terminal region shares structural similarity to other proteins whose functions are related to assistance in or regulation of secretion. Therefore, this region is likely to play an important role in the insertion of other outer membrane proteins.

An Efficient Approach to Mining Maximal Contiguous Frequent Patterns from Large DNA Sequence Databases

Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

BapC autotransporter protein of Bordetella pertussis is an adhesion factor

Bordetella pertussis, the causative agent of whooping cough, attaches to mucosal surfaces in upper respiratory tract, where it produces, a variety of surface-associated and secreted molecules. Among various secreted products, some of the proteins belonging to autotransporter family; pertactin (Prn), bordetella resistance to killing (BrkA) and a newly identified member, bordetella autotransporter protein-C (BapC), are investigated in this study for their adherence potential to various respiratory and non-respiratory tract specific cell lines. Our results reveal that BapC and Prn mutants adhere significantly less (p < 0.0001 and p < 0.05) respectively to human non-respiratory (HeLa-229) and murine macrophages (P-388 D-1) cells compared to their wild-type strains. Prn, BrkA and BapC share no homology in their passenger domains except existence of common motifs arginine-glycine-asparctic (RGD) and glycosaminoglycan binding site (SGXG). We have shown that RGD and SGXG motifs are present in the coiled region in Prn and BrkA proteins with the exception in BapC where R (463) of RGD and S (597) of SGXG motif were observed in beta sheet of the modeled protein structures. Therefore, there is possibility that such arrangement of motifs can confer greater probability of BapC in better selective adherence to binding sites on the HeLa-229 and P-388 D-1 cell lines.

Physical and Genomic Characteristics Identify Chicken Proventricular Necrosis Virus (R11/3 Virus) as a Novel Birnavirus

Chicken proventricular necrosis virus (CPNV), isolate R11/3, previously was isolated from transmissible viral proventriculitis-affected chickens and was determined to be the likely etiology of this disease. CPNV was identified as a birnavirus on the basis of virion size and morphology (icosahedral, approximately 75 nm in diameter, nonenveloped); buoyant density in cesium chloride (1.32 g/ml); a genome comprising bisegmented, double-stranded RNA (approximately 3.8 and 3.4 kilobase pairs); and nucleotide sequence analyses. Nucleotide sequencing of CPNV RNA, segment B, identified a single large open reading frame that encodes a 903-amino acid protein. The 903-amino acid protein was identified as the putative VP1, the viral RNA-dependent RNA polymerase (RdRp), on the basis of sequence homologies with other birnavirus VP1 proteins. The CPNV VP1 possessed the unique permuted RdRp sequence motif arrangement characteristic of birnaviruses; however, phylogenetic analyses based on VP1 demonstrated that CPNV is deeply divergent from other birnaviruses.

A Symmetry Analysis of Design Structure: 1,000 Years of Continuity and Change in Puebloan Ceramic Design

This paper postulates that cultural entities with long term structural integrity are characterized by symmetrical relationships between and among the constituent sectors of society. We demonstrate how such social relationships are embedded in the symmetrical arrangements of motifs in geometric design. We test this premise with an analysis of 1000 years of ceramic design from the northern American Southwest, AD 600-1600, with a description of the continuities and changes in the plane pattern symmetries that structure design. Two major points of change in symmetry use at c. AD 900 and AD 1300 correlate with changes in settlement type from pithouses to unit pueblos and from unit pueblos to multi-storied plaza oriented pueblos that accompanied adjustments to changes in environmental conditions. We propose that in the American Southwest the predominant use of bifold symmetry is a structural metaphor for the reciprocal social relationships basic to the organization of small puebloan agricultural communities and that the changes in these symmetries reflect the changing integration of the household into an increasingly complex social system. This interpretation of the meaning of design structure is derived from cosmological principles embedded in 20th century ritual songs of the Hopi, descendents of the prehistoric puebloans, as well as depicted in images in their 15th century kiva wall murals. We present this interpretation of the sequence of pueblo development in the American Southwest in terms of the changing symmetrical nature of the social relationships that integrated the agricultural communities as an example of the insights possible with this new approach to design analysis.

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

To gain global insights into the role of the well-known repressive splicing regulator PTB we analyzed the consequences of PTB knockdown in HeLa cells using high-density oligonucleotide splice-sensitive microarrays. The major class of identified PTB-regulated splicing event was PTB-repressed cassette exons, but there was also a substantial number of PTB-activated splicing events. PTB repressed and activated exons showed a distinct arrangement of motifs with pyrimidine-rich motif enrichment within and upstream of repressed exons, but downstream of activated exons. The N-terminal half of PTB was sufficient to activate splicing when recruited downstream of a PTB-activated exon. Moreover, insertion of an upstream pyrimidine tract was sufficient to convert a PTB-activated to a PTB-repressed exon. Our results demonstrate that PTB, an archetypal splicing repressor, has variable splicing activity that predictably depends upon its binding location with respect to target exons.