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Plant bZIP G-box binding factors. Modular structure and activation mechanisms.

In this review we sum-up the knowledge about bZIP G-box binding factors (GBFs), which possess an N-terminal, proline-rich domain. The GBF has been one of the most extensively studied transcription factor family. Based on protein sequence homology with yeast and animal basic leucine-zipper (bZIP) transcription factors, bioinformatic studies have identified their main structural domains (proline-rich, basic and leucine-zipper), which have been further functionally characterized by in vitro and in vivo experiments. Recent reports have led to the discovery of other GBF-specific short amino-acid sequences that may take part in the regulation of gene expression by post-transcriptional modifications or interaction with other proteins such as bZIP enhancing factors or plant 14-3-3-like proteins. We identified a GBF region, called the 'multifunctional mosaic region', that may be implicated in cytoplasmic retention, translocation to the nucleus and regulation of transcription. We also identified many conserved protein motifs that suggest a modular structure for GBFs. At the whole plant level, GBFs have been shown to be involved in developmental and physiological processes in response to major cues such as light or hormones. Nevertheless, it remains difficult to assign a physiological role to a particular GBF protein modular structure. Finally, bringing together these different aspects of GBF studies we propose a model describing the puzzling transduction pathway involving GBFs from cytoplasmic events of signal transduction to the regulation of gene expression in the nucleus.

Amino Acid Sequence↗

Analysis of a binding difference between the two dsRNA-binding domains in TRBP reveals the modular function of a KR-helix motif.

Double-stranded RNA-binding proteins constitute a large family with conserved domains called dsRBDs. One of these, TRBP, a protein that binds HIV-1 TAR RNA, has two dsRBDs (dsRBD1 and dsRBD2), as indicated by computer sequence homology. However, a 24-amino-acid deletion in dsRBD2 completely abolishes RNA binding, suggesting that only one domain is functional. To analyse further the similarities and differences between these domains, we expressed them independently and measured their RNA-binding affinities. We found that dsRBD2 has a dissociation constant of 5.9 x 10-8 M, whereas dsRBD1 binds RNA minimally. Binding analysis of 25-amino-acid peptides in TRBP and other related proteins showed that only one peptide in TRBP and one in Drosophila Staufen bind TAR and a GC-rich TAR-mimic RNA. Whereas a 25-mer peptide derived from dsRBD2 (TR5) bound TAR RNA, the equivalent peptide in dsRBD1 (TR6) did not. Molecular modelling indicates that this difference can mainly be ascribed to the replacement of Arg by His residues. Mutational analyses in homologous peptides also show the importance of residues K2 and L3. Analysis of 15-amino-acid peptides revealed that, in addition to TR13 (from TRBP dsRBD2), one peptide in S6 kinase has RNA-binding properties. On the basis of previous and the present results, we can define, in a broader context than that of TRBP, the main outlines of a modular KR-helix motif required for binding TAR. This structural motif exists independently from the dsRBD context and therefore has a modular function.

Amino Acid Sequence↗

Modularity and dissociation in the evolution of gene expression territories in development.

Modularity is a salient feature of development and crucial to its evolution. This paper extends modularity to include the concept of gene expression territory, as established for sea urchin embryos. Territories provide a mechanism for partitioning of the cells of a rapidly developing embryo into functional units of a feeding larva. Territories exhibit the characteristics of modules. The paper asks if the embryo and the nonfeeding larva of the direct-developing sea urchin Heliocidaris erythrogramma are organized into gene expression territories, and if its territories correspond to the canonical territories of the pluteus. An analysis of cell lineage and gene expression data for H. erythrogramma shows that skeletogenic cell, coelomic, and vegetal plate gene expression territories are conserved, although they arise from cell lineages distinct from those of the pluteus, and the overall morphology of the larva differs from that of a pluteus. The ectoderm, as in indirect developers, is divided into territories. However, the oral ectodermal territory characteristic of the pluteus is absent in H. erythrogramma. Oral ectoderm is restored in hybrids of H. erythrogramma eggs fertilized by Heliocidaris tuberculata sperm. This indicates that embryonic modules evolve by changes in expression of dominant regulatory genes within territories and that entire modules can be eliminated in evolution of embryos.

Animals↗

Mutants highlight the modular control of butterfly eyespot patterns.

The eyespots on butterfly wings are thought to be serially homologous pattern elements. Yet eyespots differ greatly in number, shape, color, and size, within and among species. To what extent do these serially homologues have separate developmental identities, upon which selection acts to create diversity? We examined x-ray-induced mutations for the eyespots of the nymphalid butterfly Bicyclus anynana that highlight the modular control of these serially homologous wing pattern elements. These mutations reduce or eliminate individual eyespots, or groups of eyespots, with no further effect on the wing color pattern. The collection of mutants highlights a greater potential developmental repertoire than that observed across the genus Bicyclus. We studied in detail one such mutation, of codominant effect, that causes the elimination of two adjacent eyespots on the ventral hindwing. By analyzing the expression of genes known to be involved in eyespot formation, we found an alteration in the differentiation of the "organizing" cells at the eyespot's center. No such cells differentiate in the wing subdivisions lacking the two eyespots in the mutants. We propose several developmental models, based on wing compartmentalization in Drosophila, that provide the first framework for thinking about the molecular evolution of butterfly wing pattern modularity.

Animals↗

The use of a modular rotating hinge component in salvage revision total knee arthroplasty.

Revision total knee arthroplasty (TKA) using a second-generation modular rotating hinge design was performed on 16 knees in 15 patients over a 5-year period. Follow-up of 2 to 6 years (mean, 51 months) was obtained in 14 knees in 13 patients. Indications for revision were aseptic loosening of a hinged prosthesis (8 knees), loosening and bone loss associated with chronic extensor mechanism disruption (2 knees), component instability with chronic medial collateral ligament disruption (3 knees), and comminuted distal femur fracture (1 knee). Clinical and radiographic results were reviewed and compared with 87 patients who underwent revision TKA using a standard condylar revision design during the same period. Early results showed comparable postoperative knee scores and range of motion between the 2 groups despite the use of the rotating hinge component in more complex revision cases. No patient has exhibited radiographic evidence of definite component loosening. Alignment of 5 degrees to 10 degrees of valgus in the frontal plane and within 2 degrees of neutral in the sagittal plane was achieved consistently. Short-term clinical and radiographic results are encouraging and suggest that a second-generation modular rotating hinge component can be used successfully in selected salvage revision cases.

Adult↗

Clinical experience with a modular noncemented femoral component in revision total hip arthroplasty: 4- to 7-year results.

A series of 163 revision total hip arthroplasties performed using a modular proximally porous-coated device was reviewed. Twenty patients died before achieving minimum follow-up, and 13 hips with Paprosky type IV femora were excluded. One patient was lost to follow-up. Minimum 4-year clinical data on the remaining 129 hips showed an improvement in modified Harris hip scores, from an average of 47.7 to 87.5. Spot welds at the sleeve-bone interface were found in 83 of the 102 hips with minimum radiographic follow-up. The aseptic failure rate was 2.9%; these hips showed progressive subsidence, with 1 resulting in the only repeat revision in the series. Three hips had osteolytic lesions of <5 mm; none threatened implant stability. There were no complications related to modularity.

Adult↗

The long-term success of modular proximal fixation stems in revision total hip arthroplasty.

A prospective study was carried out on the use of a proximally modular, proximal ingrowth noncemented stem in hip revision surgery. There were 109 short stems and 211 long stems. The mean follow-up was 7 years (range, 2-12 years). No revisions were required in the short-stem group for aseptic loosening; 3 (1.4%) revisions were required in the long-stem group. Lucency was absent in 91.7% of short-stem cases, was low grade in 7.2%, and was high grade in 1.1%. In the long-stem group, lucency was absent in 72.9% of cases, was low grade in 24.5%, and was high grade in 2.6%. No measurable subsidence occurred in the short-stem group, and 5 mm of subsidence occurred early in 2 of the long-stem group. This subsidence stabilized subsequently. Osteolysis distal to the sleeve was not observed. A proximal ingrowth, proximally modular stem can be used in revision hip surgery.

Adult↗

Serum levels of cobalt and chromium in a complex modular total hip arthroplasty system.

There is concern that modularity in a total hip arthroplasty system increases serum cobalt and chromium ion levels. This study measures the serum cobalt and chromium levels in patients with an Oxford Universal Hip (Corin, Cirencester, United Kingdom), which has a modular sliding mechanism; patients with a similarly manufactured hip with no sliding mechanism; and a control group. Loosening was excluded clinically and radiologically. Arthroplasty patients had statistically higher levels of serum cobalt and chromium than controls, but there was no significant difference in levels between the implanted groups.

Arthroplasty, Replacement, Hip↗

Computerized detection of clustered microcalcifications: a modular approach with non-linear filters.

The ideal computerized mammogram processing system still needs to be developed. In order to achieve maximum flexibility we suggest a modular scheme, dividing the processing sequence into functionally autonomous modules. This paper provides a general scheme for detection and/or automated recognition of microcalcifications. Some modules that perform ROI selection are introduced, using special non-linear filters designed for microcalcification detection. A first type of filter selects pixels with specific statistical local features, as compared to the local mean. Among these, only pixels satisfying particular constraints on the local standard deviation are kept. Another type of filter then checks the local mean values of gradient components, so that sharp variations, unrelated to small close objects, can be eliminated. The scheme thus applies different non-linear filters in combination, making precise identification of clustered microcalcifications possible. This modular approach seems greatly to simplify system maintenance and consistency, as well as affording a comparison of different processing techniques and parameters.

Algorithms↗

[Late outcome after implantation of the PFC modular knee system].

AIM: The objective of the current, prospective study was the evaluation of long-term results after total knee arthroplasty with the PFC-Modular-knee system. METHOD: A total of 514 total knee arthroplasties were implanted between 1991 and 1994 in 248 female and 55 male patients. Their average age amounted to 62.4 years and 449 of them (87.4%) were re-investigated within the first half-year of 2000. Clinical and radiological data were evaluated according the recommendations of the American Knee Society. RESULTS: Late complications were observed in 6.5% of the cases. They consisted of prosthetic loosening (13 knees), patella problems (11 knees), instability (2 knees), periprosthetic fractures (2 knees), and one prosthesis fracture, 18 patients complained about a therapy-resistant, chronic pain syndrome. These findings lead to revision arthroplasty in 15 cases (3.3%). Preoperative American Knee Society Score values were on average 33, 35 an 17 points and improved to mean values of about 85, 79 and 5 points. Radiological signs of prosthetic loosening were observed in 12 cases (2.7%). CONCLUSION: Long-term results after total knee arthroplasty with the PFC-Modular-knee system showed a significant improvement in the patients' complaints and clinical findings at an average of 7.8 years postoperatively. Complication and revision rates of 6.5% and 3.3%, respectively, were low when compared with the international literature and--apart from this--decreased in the course of the observation time.

Aged↗

[Modular education in diabetes and pregnancy: analysis of results of 58 pregnancies in diabetic patients with functional insulin treatment].

Functional insulin treatment based on the patient's education for selective use of insulin for fasting, eating or correction of hyperglycaemia was used between 1985 and 1994 prospectively in 58 pregnancies (in 18 cases after conception) in 47 pregnant diabetic patients. We hypothesised that near-normalisation of glycaemia is possible throughout pregnancy by modular outpatient group education, individual counselling and functional insulin treatment. We wanted to investigate to which degree it might eliminate classical diabetes-associated neonatal complications. To avoid hospitalisation if possible and premature induction of labour, patients were taught both the primary adjustment (immediate correction of hyperglycaemia) and the secondary adjustment of the insulin dosages: correction of individual algorithms for insulin use according to daily insulin consumption and mean blood glucose MBG. A target metabolic control (HbA1c levels in the normal range, MBG < 100 and < 90 mg/dl after the 28th week of gestation respectively) was achieved in the majority of the 58 pregnancies. Severe hypoglycaemia occurred in 12 patients (21%). The gestational age at delivery was 39.0 +/- 1.6 (34-41; in 3 cases only [5%] < 37) weeks with an average birth weight of 3335 +/- 521 (1950-4450) g. The birth weight of only 5 newborn (9%) was above the 90th percentile and no one below the 10th percentile for weight of a comparable population. No cases of respiratory distress were observed. Hypoglycaemia was recorded in only 4 newborn (7%) and was comparable also to that of offsprings in non-diabetic women. Malformations were found in two offsprings whose mothers had presented first for diabetes education after conception, pregnancy being terminated in one case of meningomyelocele. Caesarean section (n = 15; 26%) was primarily due to maternal reasons. Functional insulin treatment prior to conception, modular diabetes group education, specific patient motivation for a near-normal glycaemia throughout pregnancy as well as interdisciplinary care allow pregnancy outcome in diabetic patients similar to that in non-diabetic women and thus the realisation of the 5-year targets of the WHO Declaration of St. Vincent 1989.

Adolescent↗

Stress promotes maleness in hermaphroditic modular animals.

Sex-allocation theory developed for hermaphroditic plants predicts that impaired phenotype or reduced parental survivorship caused by environmental stress should induce relatively greater allocation to the male function. We provide experimental evidence of stress-induced maleness, already well documented in flowering plants, in a modular animal. By using cloned copies of replicate genotypes, we show that the marine bryozoan Celleporella hyalina increases the ratio of male to female modules in response to diverse environmental stressors. Mating trials confirmed that paternity is determined by fair-raffle sperm competition, which should obviate local mate competition at characteristic population density and promote the advantage of increased male allocation. The demonstrated similarity to plants transcends specific physiological pathways and suggests that stress-induced bias toward male function is a general response of hermaphroditic modular organisms to impaired prospects for parental productivity or survival.

Animals↗

Modular mutagenesis of human placental ribonuclease inhibitor, a protein with leucine-rich repeats.

Human placental ribonuclease inhibitor (PRI) is a potent protein inhibitor of pancreatic ribonucleases and the homologous blood vessel-inducing protein angiogenin. Although inhibition by PRI occurs with a 1:1 stoichiometry, its primary structure is composed predominantly of seven internal leucine-rich repeats. These internal repeats were systematically deleted either singly or in combination by "modular" mutagenesis. Deletion of repeat units 3 plus 4 or repeat unit 6 results in mutants that both bind to and inhibit ribonuclease A. Therefore, the angiogenin/ribonuclease binding site in PRI must reside primarily or entirely in repeats 1, 2, 5, or 7, the short N- or C-terminal segments, or a combination of these. Deletion of repeat units 3-5, 5-6, or 5 alone results in mutants that exhibit only binding activity. Hence, the binding site cannot reside exclusively in repeat 5. Other internal deletions or N- or C-terminal deletions of 6-86% of the protein all abolish activity. These results suggest that PRI has a modular structure, with one primary structural repeat constituting one module. The approach taken may be applicable to other proteins with repeat structures.

Amino Acid Sequence↗

Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples.

The cis-regulatory systems that control developmental expression of two sea urchin genes have been subjected to detailed functional analysis. Both systems are modular in organization: specific, separable fragments of the cis-regulatory DNA each containing multiple transcription factor target sites execute particular regulatory subfunctions when associated with reporter genes and introduced into the embryo. The studies summarized here were carried out on the CyIIIa gene, expressed in the embryonic aboral ectoderm and on the Endo16 gene, expressed in the embryonic vegetal plate, archenteron, and then midgut. The regulatory systems of both genes include modules that control particular aspects of temporal and spatial expression, and in both the territorial boundaries of expression depend on a combination of negative and positive functions. In both genes different regulatory modules control early and late embryonic expression. Modular cis-regulatory organization is widespread in developmentally regulated genes, and we present a tabular summary that includes many examples from mouse and Drosophila. We regard cis-regulatory modules as units of developmental transcription control, and also of evolution, in the assembly of transcription control systems.

Actins↗

SMART, a simple modular architecture research tool: identification of signaling domains.

Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25% of our domain set could not be deduced from SwissProt and 41% could not be annotated by Pfam. SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline 1; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.

Amino Acid Sequence↗

Compact stellarators with modular coils.

Compact stellarator designs with modular coils and only two or three field periods are now available; these designs have both good stability and quasiaxial symmetry providing adequate transport for a magnetic fusion reactor. If the bootstrap current assumes theoretically predicted values a three field period configuration is optimal, but if that net current turns out to be lower, a device with two periods and just 12 modular coils might be better. There are also attractive designs with quasihelical symmetry and four or five periods whose properties depend less on the bootstrap current. Good performance requires that there be a satisfactory magnetic well in the vacuum field, which is a property lacking in a stellarator-tokamak hybrid that has been proposed for a proof of principle experiment. In this paper, we present an analysis of stability for these configurations that is based on a mountain pass theorem asserting that, if two solutions of the problem of magnetohydrodynamic equilibrium can be found, then there has to be an unstable solution. We compare results of our theory of equilibrium, stability, and transport with recently announced measurements from the large LHD experiment in Japan.

Journal Article↗

Modularity of serpins. A bifunctional chimera possessing alpha1-proteinase inhibitor and thyroxine-binding globulin properties.

An exciting application of protein engineering is the creation of proteins with novel functions by the retrofitting of native proteins. Such attempts might be facilitated by the idea of a mosaic architecture of proteins out of structural units. Even though numerous theoretical concepts deal with the delineation of structural "modules," their potential in the design of proteins has not yet been sufficiently exploited. To address this question we used a gain of function approach by designing modular chimeric molecules out of two structurally homologous but functionally diverse members of the superfamily of serine-proteinase inhibitors, alpha1-proteinase inhibitor and thyroxine-binding globulin. Substitution of two of four alpha1-proteinase inhibitor modules (Lys222 to Leu288 and Pro362 to Lys394, respectively), identified by alpha-backbone distance analysis, with their thyroxine-binding globulin homologues resulted in a bifunctional chimera with inhibition of human leukocyte elastase and high affinity thyroxine binding. To our knowledge, this is the first report on a bifunctional chimera engineered from modules of homologous globular proteins. Our results demonstrate how a modular concept can facilitate the design of new functional proteins by swapping structural units chosen from members of a protein superfamily.

Humans↗

Association of neuronal calcium channels with modular adaptor proteins.

Presynaptic voltage-gated calcium (Ca(2+)) channels mediate Ca(2+) influx into the presynaptic terminal that triggers synaptic vesicle fusion and neurotransmitter release. The immediate proximity of Ca(2+) channels to the synaptic vesicle release apparatus is critical for rapid and efficient synaptic transmission. In a series of biochemical experiments, we demonstrate a specific association of the cytosolic carboxyl terminus of the N-type Ca(2+) channel pore-forming alpha(1B) subunit with the modular adaptor proteins Mint1 and CASK. The carboxyl termini of alpha(1B) bind to the first PDZ domain of Mint1 (Mint1-1). The proline-rich region present in the carboxyl termini of alpha(1B) binds to the SH3 domain of CASK. Mint1-1 is specific for the E/D-X-W-C/S-COOH consensus, which defines a novel class of PDZ domains (class III). The Mint1-1 PDZ domain-binding motif is present only in the "long" carboxyl-terminal splice variants of N-type (alpha(1B)) and P/Q-type (alpha(1A)) Ca(2+) channels, but not in R-type (alpha(1E)) or L-type (alpha(1C)) Ca(2+) channels. Our results directly link presynaptic Ca(2+) channels to a macromolecular complex formed by modular adaptor proteins at synaptic junction and advance our understanding of coupling between cell adhesion and synaptic vesicle exocytosis.

Adaptor Proteins, Signal Transducing↗