Modular Complex Research Articles

Modulation of the microbial fermentation in the gut by fermentable carbohydrates

This review considers fermentable carbohydrates and their role in maintaining health through their availability as fuel for the gut microbiota. The microbiota possesses remarkably diverse function, and is likely modifiable by diet. Therefore a diet rich in varied fermentable carbohydrates such as dietary fibre, glycosylated polyphenolics, glucosinolates and other plant glycans, applied in a sustained fashion may promote microbial diversity leading to improved health. This may be achieved by increasing the flexibility of the microbiota's capability to interact with diverse dietary environments, or via increasing production of short chain fatty acids (SCFAs) from the fermentation of carbohydrates. A higher functional modular complexity is indicative of gut health, whilst SCFAs may reduce the risk of developing gastrointestinal disorders, cancer, and cardiovascular disease.

Modular biosynthesis branches out

Rings in biologically active molecules confer rigidity that helps the molecules to bind strongly and selectively to their targets. A ring-forming mechanism has been identified that involves a biochemically unusual reaction. See Letter p.124 Polyketide synthases (PKSs) are modular enzyme complexes that produce polyketides, a large class of secondary metabolites — otherwise known as natural products. In this manuscript, the authors identify and characterize a novel PKS module from the endofungal bacterium Burkholderia rhizoxinica that catalyses a vinylogous addition of a malonyl unit to an unsaturated thioester, generating a branch in the growing polyketide chain. This enzymological activity is very unusual; all previously studied PKS modules catalyse the head-to-tail fusion of acyl and malonyl units, yielding a linear polyketide chain. This newly discovered reaction provides a simple mechanism by which structural diversity of polyketide natural products can be increased.

Competitive and Non-competitive Regulation of Calcium-dependent Inactivation in CaV1.2 L-type Ca2+ Channels by Calmodulin and Ca2+-binding Protein 1

CaV1.2 interacts with the Ca(2+) sensor proteins, calmodulin (CaM) and calcium-binding protein 1 (CaBP1), via multiple, partially overlapping sites in the main subunit of CaV1.2, α1C. Ca(2+)/CaM mediates a negative feedback regulation of Cav1.2 by incoming Ca(2+) ions (Ca(2+)-dependent inactivation (CDI)). CaBP1 eliminates this action of CaM through a poorly understood mechanism. We examined the hypothesis that CaBP1 acts by competing with CaM for common interaction sites in the α1C- subunit using Förster resonance energy transfer (FRET) and recording of Cav1.2 currents in Xenopus oocytes. FRET detected interactions between fluorescently labeled CaM or CaBP1 with the membrane-attached proximal C terminus (pCT) and the N terminus (NT) of α1C. However, mutual overexpression of CaM and CaBP1 proved inadequate to quantitatively assess competition between these proteins for α1C. Therefore, we utilized titrated injection of purified CaM and CaBP1 to analyze their mutual effects. CaM reduced FRET between CaBP1 and pCT, but not NT, suggesting competition between CaBP1 and CaM for pCT only. Titrated injection of CaBP1 and CaM altered the kinetics of CDI, allowing analysis of their opposite regulation of CaV1.2. The CaBP1-induced slowing of CDI was largely eliminated by CaM, corroborating a competition mechanism, but 15-20% of the effect of CaBP1 was CaM-resistant. Both components of CaBP1 action were present in a truncated α1C where N-terminal CaM- and CaBP1-binding sites have been deleted, suggesting that the NT is not essential for the functional effects of CaBP1. We propose that CaBP1 acts via interaction(s) with the pCT and possibly additional sites in α1C.

Modular Construction of Topologically Complex Polycyclic Acetals by Tether‐Controlled Domino Reactions

AbstractLead tetraacetate mediated oxidative cleavage of octalin‐diols (1 and 1′), tethered by variously substituted arenes placed at the angular position (C11), show switchable regioselectivity effects. A highly selective set of regiochemical outcomes can be achieved, producing a range of polycyclic acetals through competing domino paths (A–E). The modular complexity inherent in the type‐1 domino precursors is derived from the C11 configuration, where the course of ring‐forming processes is controlled from the chirality at a remote stereocenter (C11). For methylene‐tethered type‐1′ precursors, the regiochemical outcome is mainly determined by controlling the reaction parameters.

Robustness and adaptation reveal plausible cell cycle controlling subnetwork in Saccharomyces cerevisiae

Biological systems are often organized spatially and temporally by multi-scale functional subsystems (modules). A specific subcellular process often corresponds to a subsystem composed of some of these interconnected modules. Accurate identification of system-level modularity organization from the large scale networks can provide valuable information on subsystem models of subcellular processes or physiological phenomena. Computational identification of functional modules from the large scale network is the key approach to solve the complexity of modularity in the past decade, but the overlapping and multi-scale nature of modules often renders unsatisfactory results in these methods. Most current methods for modularity detection are optimization-based and suffered from the drawback of size resolution limit. It is difficult to trace the origin of the unsatisfactory results, which may be due to poor data, inappropriate objective function selection or simply resulted from natural evolution, and hence no system-level accurate modular models for subcellular processes can be offered. Motivated by the idea of evolution with robustness and adaption as guiding principles, we propose a novel approach that can identify significant multi-scale overlapping modules that are sufficiently accurate at the system and subsystem levels, giving biological insights for subcellular processes. The success of our evolution strategy method is demonstrated by applying to the yeast protein-protein interaction network. Functional subsystems of important physiological phenomena can be revealed. In particular, the cell cycle controlling network is selected for detailed discussion. The cell cycle subcellular processes in yeast can be successfully dissected into functional modules of cell cycle control, cell size check point, spindle assembly checkpoint, and DNA damage check point in G2/M and S phases. The interconnections between check points and cell cycle control modules provide clues on the signal stimulus entries of check points into the cell cycle, which are consistent with experimental findings. This evolution strategy method can be applied adequately to extract the plausible yeast cell cycle subnetworks from the whole network. Connections between modules in the obtained cell cycle subnetworks reveal significant cell cycle control mechanisms. This method can also be useful when applied to other biological systems at various temporal and spatial scales for example, the gene transcription networks, and biological systems from mesoscopic scale, e.g cortical network in brain, to subcellular molecular networks.

Insight into the structural versatility of the Ln(III)[15-metallacrown-5] platform by comparing analogs with Ni(II), Cu(II), and Zn(II) ring ions

The promise for tuning the molecular recognition and physical properties of coordination driven assemblies through metal ion substitutions has prompted this structural investigation into the structural versatility of Ln(III)[15-metallacrownM(II),L-5]3+ complexes. The structural versatility of this molecular class is expanded through the synthesis of Ln(III)[15-metallacrownZn(II),picHA-5](NO3)3, the first Ln(III)[15-metallacrownM(II),L-5]3+ with Zn(II) metal ions. X-ray crystallography reveals the pentagonal macrocycle has a severely ruffled face, which is attributed to a non-equatorial alignment of the picHA ligands by the square pyramidal Zn(II) ions. ESI-MS and 1H NMR suggest the complex maintains its integrity in pyridine. Comparison of the Eu(III)[15-metallacrownM(II),picHA-5]3+ structures with Ni(II), Cu(II), and Zn(II) reveal elongated M(II)–NpicHA bond lengths and bending of the picHA chelates at the ring metals with Zn(II). Surprisingly, the metallacrowns provide similar coordination environments for the central Eu(III) ion despite the structural differences in the ring. Differences in the visible absorption spectra of the Eu(III)[15-metallacrownM(II),picHA-5]3+ complexes with Ni(II), Cu(II), and Zn(II) demonstrate that the electronics of the metallacrown platform can be varied through ring ion substitutions. The ability of Ln(III)[15-metallacrownM(II),L-5] complexes to accommodate ring ions with disparate coordination geometries is unique for coordination driven assemblies and has implications for the design of modular complexes with tunable magnetic and electronic properties.

The role of Ypt/Rab GTPases in Traffic Coordination

Transport between cellular compartments is mediated by vesicles that bud from one compartment and fuse with the next. Ypt/Rab GTPases and their effectors mediate all the known aspects of vesicular transport, from formation and motility, to targeting and fusion. An attractive idea is that in addition to regulating individual transport steps, Ypt/Rabs also integrate these steps into whole pathways and coordinate them with other cellular processes. In yeast, three Ypts regulate the exocytic pathway: Ypt1 regulates entry to the Golgi, Ypt31/32 control exit from the Golgi, and Sec4 regulates fusion of Golgi vesicles with the plasma membrane (PM). We have uncovered three types of Ypt‐mediated coordination mechanisms. First, we found that Ypt31/32 and Sec4 interact with common proteins to couple Ypt31/32‐mediated vesicle formation and motility with Sec4‐mediated vesicle tethering and fusion. Second, we propose that sequential activation of Ypt1 and Ypt31/32 by the modular complex TRAPP coordinates Golgi entry and exit, thus integrating these two transport steps into a whole pathway. Third, we identified novel effectors of Ypt1 and Ypt31/32 that coordinate the exocytic pathway with other cellular process like autophagy and PM recycling. In summary, we propose Ypt/Rab interactions and sequential activation as mechanisms by which these highly conserved GTPases coordinate trafficking inside cells.

A Distal Modular Enhancer Complex Acts to Control Pituitary- and Nervous System-Specific Expression of the LHX3 Regulatory Gene

Lin-11, Isl-1, and Mec-3 (LIM)-homeodomain (HD)-class transcription factors are critical for many aspects of mammalian organogenesis. Of these, LHX3 is essential for pituitary gland and nervous system development. Pediatric patients with mutations in coding regions of the LHX3 gene have complex syndromes, including combined pituitary hormone deficiency and nervous system defects resulting in symptoms such as dwarfism, thyroid insufficiency, infertility, and developmental delay. The pathways underlying early pituitary development are poorly understood, and the mechanisms by which the LHX3 gene is regulated in vivo are not known. Using bioinformatic and transgenic mouse approaches, we show that multiple conserved enhancers downstream of the human LHX3 gene direct expression to the developing pituitary and spinal cord in a pattern consistent with endogenous LHX3 expression. Several transferable cis elements can individually guide nervous system expression. However, a single 180-bp minimal enhancer is sufficient to confer specific expression in the developing pituitary. Within this sequence, tandem binding sites recognized by the islet-1 (ISL1) LIM-HD protein are essential for enhancer activity in the pituitary and spine, and a pituitary homeobox 1 (PITX1) bicoid class HD element is required for spatial patterning in the developing pituitary. This study establishes ISL1 as a novel transcriptional regulator of LHX3 and describes a potential mechanism for regulation by PITX1. Moreover, these studies suggest models for analyses of the transcriptional pathways coordinating the expression of other LIM-HD genes and provide tools for the molecular analysis and genetic counseling of pediatric patients with combined pituitary hormone deficiency.

Automated modular complex MPPA-SSi12 – a breakthrough technology for “liquid” cementation

Automated modular complex MPPA-SSi12 – a breakthrough technology for “liquid” cementation

THE THOMPSON–HIGMAN MONOIDS Mk,i: THE ${\mathcal J}$-ORDER, THE ${\mathcal D}$-RELATION, AND THEIR COMPLEXITY

The Thompson–Higman groups Gk,ihave a natural generalization to monoids, called Mk,i, and inverse monoids, called Invk,i. We study some structural features of Mk,iand Invk,iand investigate the computational complexity of related decision problems. The main interest of these monoids is their close connection with circuits and circuit complexity.The maximal subgroups of Mk,1and Invk,1are isomorphic to the groups Gk,j(1 ≤ j ≤ k - 1); so we rediscover all the Thompson–Higman groups within Mk,1.Deciding the Green relations [Formula: see text] and [Formula: see text] of Mk,1, when the inputs are words over a finite generating set of Mk,1, is in P.When a circuit-like generating set is used for Mk,1then deciding [Formula: see text] is coDP-complete (where DP is the complexity class consisting of differences of sets in NP). The multiplier search problem for [Formula: see text] is xNPsearch-complete, whereas the multiplier search problems of [Formula: see text] and [Formula: see text] are not in xNPsearch unless NP = coNP. The class of search problems xNPsearch is introduced as a slight generalization of NPsearch.Deciding [Formula: see text] for Mk,1when the inputs are words over a circuit-like generating set, is ⊕k-1• NP -complete; for any h ≥ 2, ⊕h•NP is a modular counting complexity class, whose verification problems are in NP. Related problems for partial circuits are the image size problem (which is # • NP-complete), and the image size modulo h problem (which is ⊕h•NP-complete). For Invk,1over a circuit-like generating set, deciding [Formula: see text] is ⊕k-1P-complete. It is interesting that the little known complexity classes coDP and ⊕k-1•NP play a central role in Mk,1.

A Motion Direction Map in Macaque V2

In mammals, the perception of motion starts with direction-selective neurons in the visual cortex. Despite numerous studies in monkey primary and second visual cortex (V1 and V2), there has been no evidence of direction maps in these areas. In the present study, we used optical imaging methods to study the organization of motion response in macaque V1 and V2. In contrast to the findings in other mammals (e.g., cats and ferrets), we found no direction maps in macaque V1. Robust direction maps, however, were found in V2 thick/pale stripes and avoided thin stripes. In many cases direction maps were located within thick stripes and exhibited pinwheel or linear organizations. The presence of motion maps in V2 points to a newfound prominence of V2 in motion processing, for contributing to motion perception in the dorsal pathway and/or for motion cue-dependent form perception in the ventral pathway.

Abstract LB-327: Targeted microbeads for attraction and induction of specific innate immune response in the tumor microenvironment

Abstract Anti-tumor activity of molecules and cells of the innate immune system has been reported. Here we propose a method for targeting preferred innate immune cells and magnifying their tumoricidal effect at the tumor microenvironment, by modular multiple-component complexes. As a model, micro-complexes carried monoclonal anti-HER2 antibodies, lipopolysaccharide and mannose. The complexes showed high binding capacity to HER2-positive cancer cells in vitro, high induction of interleukin-1 RNA transcription by the activated monocytes and ability to mediate monocytes’ attachment to HER2-positive cells. We thus present a new vision of targeting a desired innate immune response to the tumor microenvironment. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-327.

Liposomal modular complexes for simultaneous targeted delivery of bioactive gases and therapeutics

Intrinsically echogenic liposomes (ELIP) can be adapted to encapsulate nitric oxide to facilitate ultrasound-enhanced delivery of therapeutic agents to atherosclerotic plaques. However, the NO loading of targeted ELIP caused a 93% decrease of antibody (Ab) immunoreactivity. The following hypothesis was tested: biotin/avidin-mediated coupling of NO-ELIP and Ab-conjugated ELIP will enable co-delivery of bioactive gases and ELIP that can encapsulate other agents without loss of targeting efficiency. Complex formation was initiated by addition of excess streptavidin to equal proportions of biotinylated Ab-ELIP and NO-ELIP. Fluorescence deconvolution microscopy, Coulter Multisizer 3 analysis and flow cytometry demonstrated that the ELIP coupling procedure formed mixed aggregates of ≥ 10 liposomes within 1 min. Intravascular ultrasound imaging and ELISA showed that echogenicity and targeting efficiency were completely and 69–99% retained, respectively. When complexed to NO-ELIP, ELIP bifunctionally targeted to both CD34 and ICAM-1 (BF-ELIP) increased human mononuclear cell migration through human coronary artery endothelial cell monolayers in transwell plates 4-fold relative to a nonspecific IgG-ELIP control and 2-fold relative to BF-ELIP alone. It was concluded that this novel multi-functional conjugation methodology provides a platform technology for site-specific co-delivery of bioactive gases and other agents.

MKK4/SEK1 Is Negatively Regulated through a Feedback Loop Involving the E3 Ubiquitin Ligase Itch

Cells exposed to environmental stress rapidly activate the MAPK cascade (MKKK/MKK/MAPK). The transient nature of stress signaling is a consequence of negative feedback signals that lead to kinase dephosphorylation, degradation, and sequestration, which have not been fully elucidated for MKK family members. Here, we investigated the signals that negatively regulate MKK4/SEK1, an upstream activator of the MAPKs JNK and p38/HOG1. Following exposure of cells to sorbitol, MKK4 underwent ubiquitination and degradation in a proteasome-dependent manner. MKK4 ubiquitination required JNK kinase activity. The JNK substrate Itch (a HECT domain-containing Nedd4-like ubiquitin protein ligase) bound to MKK4, ubiquitinated lysines 140 and 143, and promoted MKK4 degradation. Other E3 ligases within the MAPK modular complex did not ubiquitinate MKK4. These data suggest that MKK4 is negatively regulated through a feedback loop involving the E3 ubiquitin ligase Itch, which has a fundamental role in the mechanism that controls MKK4 protein levels.

Portrait of an Enzyme, a Complete Structural Analysis of a Multimodular β-N-Acetylglucosaminidase from Clostridium perfringens

Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens micro-toxin, which was determined using a combination of small angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.

A Map for Horizontal Disparity in Monkey V2

The perception of visual depth is determined by integration of spatial disparities of inputs from the two eyes. Single cells in visual cortex of monkeys are known to respond to specific binocular disparities; however, little is known about their functional organization. We now show, using intrinsic signal optical imaging and single-unit physiology, that, in the thick stripe compartments of the second visual area (V2), there is a clustered organization of Near cells and Far cells, and moreover, there are topographic maps for Near to Far disparities within V2. Our findings suggest that maps for visual disparity are calculated in V2, and demonstrate parallels in functional organization between the thin, pale, and thick stripes of V2.

The TatBC complex formation suppresses a modular TatB-multimerization in Escherichia coli

Twin-arginine translocation (Tat) systems allow the translocation of folded proteins across biological membranes of most prokaryotes. In proteobacteria, a TatBC complex binds Tat substrates and initiates their translocation after recruitment of the component TatA. TatA and TatB belong to one protein family, but only TatB forms stable complexes with TatC. Here we show that TatB builds up TatA-like modular complexes in the absence of TatC. This TatB ladder ranges from about 100 to over 880kDa with 105±10kDa increments. TatC alone can form a 250kDa complex which could be a scaffold that can recruit TatB to form defined TatBC complexes.

The Role of Trs65 in the Ypt/Rab Guanine Nucleotide Exchange Factor Function of the TRAPP II Complex

The conserved modular complex TRAPP is a guanine nucleotide exchanger (GEF) for the yeast Golgi Ypt-GTPase gatekeepers. TRAPP I and TRAPP II share seven subunits and act as GEFs for Ypt1 and Ypt31/32, respectively, which in turn regulate transport into and out of the Golgi. Trs65/Kre11 is one of three TRAPP II-specific subunits. Unlike the other two subunits, Trs120 and Trs130, Trs65 is not essential for viability, is conserved only among some fungi, and its contribution to TRAPP II function is unclear. Here, we provide genetic, biochemical, and cellular evidence for the role of Trs65 in TRAPP II function. First, like Trs130, Trs65 localizes to the trans-Golgi. Second, TRS65 interacts genetically with TRS120 and TRS130. Third, Trs65 interacts physically with Trs120 and Trs130. Finally, trs65 mutant cells have low levels of Trs130 protein, and they are defective in the GEF activity of TRAPP II and the intracellular distribution of Ypt1 and Ypt31/32. Together, these results show that Trs65 plays a role in the Ypt GEF activity of TRAPP II in concert with the two other TRAPP II-specific subunits. Elucidation of the role played by Trs65 in intracellular trafficking is important for understanding how this process is coordinated with two other processes in which Trs65 is implicated: cell wall biogenesis and stress response.

Random walks along the streets and canals in compact cities: Spectral analysis, dynamical modularity, information, and statistical mechanics

Different models of random walks on the dual graphs of compact urban structures are considered. Analysis of access times between streets helps to detect the city modularity. The statistical mechanics approach to the ensembles of lazy random walkers is developed. The complexity of city modularity can be measured by an information-like parameter which plays the role of an individual fingerprint of Genius loci. Global structural properties of a city can be characterized by the thermodynamic parameters calculated in the random walk problem.

TRAPPII subunits are required for the specificity switch of a Ypt–Rab GEF

Ypt-Rab GTPases are key regulators of the various steps of intracellular trafficking. Guanine nucleotide-exchange factors (GEFs) regulate the conversion of Ypt-Rabs to the GTP-bound state, in which they interact with effectors that mediate all the known aspects of vesicular transport. An interesting possibility is that Ypt-Rabs coordinate separate steps of the transport pathways. The conserved modular complex TRAPP is a GEF for the Golgi gatekeepers Ypt1 and Ypt31/32 (Refs 5-7). However, it is not known how Golgi entry and exit are coordinated. TRAPP comes in two configurations: the seven-subunit TRAPPI is required for endoplasmic reticulum-to-Golgi transport, whereas the ten-subunit TRAPPII functions in late Golgi. The two essential TRAPPII-specific subunits Trs120 and Trs130 have been identified as Ypt31/32 genetic interactors. Here, we show that they are required for switching the GEF specificity of TRAPP from Ypt1 to Ypt31. Moreover, a trs130ts mutation confers opposite effects on the intracellular localization of these GTPases. We suggest that the Trs120-Trs130 subcomplex joins TRAPP in the late Golgi to switch its GEF activity from Ypt1 to Ypt31/32. Such a 'switchable' GEF could ensure sequential activation of these Ypts, thereby coordinating Golgi entry and exit.