Characterization of myo-inositol utilization by Corynebacterium glutamicum: the stimulon, identification of transporters, and influence on L-lysine formation

Although numerous bacteria possess genes annotated iol in their genomes, there have been very few studies on the possibly associated myo-inositol metabolism and its significance for the cell. We found that Corynebacterium glutamicum utilizes myo-inositol as a carbon and energy source, enabling proliferation with a high maximum rate of 0.35 h-1. Whole-genome DNA microarray analysis revealed that 31 genes respond to myo-inositol utilization, with 21 of them being localized in two clusters of >14 kb. A set of genomic mutations and functional studies yielded the result that some genes in the two clusters are redundant, and only cluster I is necessary for catabolizing the polyol. There are three genes which encode carriers belonging to the major facilitator superfamily and which exhibit a >12-fold increased mRNA level on myo-inositol. As revealed by mutant characterizations, one carrier is not involved in myo-inositol uptake whereas the other two are active and can completely replace each other with apparent Kms for myo-inositol as a substrate of 0.20 mM and 0.45 mM, respectively. Interestingly, upon utilization of myo-inositol, the L-lysine yield is 0.10 mol/mol, as opposed to 0.30 mol/mol, with glucose as the substrate. This is probably not only due to myo-inositol metabolism alone since a mixture of 187 mM glucose and 17 mM myo-inositol, where the polyol only contributes 8% of the total carbon, reduced the L-lysine yield by 29%. Moreover, genome comparisons with other bacteria highlight the core genes required for growth on myo-inositol, whose metabolism is still weakly defined.     

Actin bundling via LIM domains

The LIM domain is defined as a protein-protein interaction module involved in the regulation of diverse cellular processes including gene expression and cytoskeleton organization. We have recently shown that the tobacco WLIM1, a two LIM domain-containing protein, is able to bind to, stabilize and bundle actin filaments, suggesting that it participates to the regulation of actin cytoskeleton structure and dynamics. In the December issue of the Journal of Biological Chemistry we report a domain analysis that specifically ascribes the actin-related activities of WLIM1 to its two LIM domains. Results suggest that LIM domains function synergistically in the full-length protein to achieve optimal activities. Here we briefly summarize relevant data regarding the actin-related properties/functions of two LIM domain-containing proteins in plants and animals. In addition, we provide further evidence of cooperative effects between LIM domains by transiently expressing a chimeric multicopy WLIM1 protein in BY2 cells.Key words: Actin-binding proteins, actin-bundling, cysteine-rich proteins, cytoskeleton, LIM domainThe LIM domain is a ≈55 amino acid peptide domain that was first identified in 1990 as a common cystein-rich sequence found in the three homeodomain proteins LIN-11, Isl1 and MEC-3. It has since been found in a wide variety of eukaryotic proteins of diverse functions. Animals possess several families of LIM proteins, with members containing 1–5 LIM domains occasionally linked to other catalytic or protein-binding domains such as homeodomain, kinase and SH3 domains. In contrast, plants only possess two distinct sets of LIM proteins. One is plant-specific and has not been functionally characterized yet. The other one comprises proteins that exhibit the same overall structure as the animal cystein rich proteins (CRPs), i.e., two very similar LIM domains separated by a ≈50 amino acid-long interLIM domain and a relatively short and variable C-terminal domain (Fig. 1A). The mouse CRP2 protein was the first CRP reported to interact directly with actin filaments (AF) and to stabilize the latter.¹ Identical observations were subsequently described for the chicken CRP1 and tobacco WLIM1 proteins.^2,3 In addition, these two proteins were shown to arrange AF into cables both in vitro and in vivo and thus join the list of actin bundlers.Open in a separate windowFigure 1Domain maps for wild-type WLIM1 (A) and GFP-fused chimeric 3xWLIM1 (B). A. WLIM1 basically comprises a short N-terminal domain (Nt), two LIM domains (LIM1 and LIM2), an interLIM spacer (IL) and a C-terminal domain (Ct). B. 3xWLIM1 consists of three tandem WLIM1 copies. This chimeric protein has been fused in C-terminus to GFP and transiently expressed in tobacco BY2 cells.To identify the peptide domains of WLIM1 responsible for its actin-related properties/activities, we generated domain-deleted and single domain variants and submitted them to a series of in vivo and in vitro assays.⁴ Localization experiments established that both LIM domains are required to efficiently target the actin cytoskeleton in tobacco BY2 cells. High-speed (200,000 g) cosedimentation data confirmed that the actin-binding activity of WLIM1 relies on its LIM domains. Indeed, the deletion of either the first or the second LIM domain respectively resulted in a 5-fold and 10-fold decrease of the protein affinity for AF. Importantly, each single LIM domain was found able to interact with AF in an autonomous manner, although with a reduced affinity compared to the wild-type WLIM1. Low-speed (12,500 g) cosedimentation data and electron microscopy observations revealed that the actin bundling activity of WLIM1 is also triggered by its LIM domains. Surprisingly each single LIM domain was able to bundle AF in an autonomous manner, suggesting that WLIM1 has two discrete actin-bundling sites. However, the bundles induced by the variants containing only one LIM domain, i.e., LIM domain-deleted mutants and single LIM domains, differed from those induced by the full-length WLIM1. They appeared more wavy and loosely packed and formed only at relatively high protein:actin ratios. Together these data suggest that LIM domains are autonomous actin-binding and -bundling modules that function in synergy in wild-type WLIM1 to achieve optimal activities.To further assess the mechanism of cooperation between the LIM domains of plant CRP-related proteins, we generated a chimeric protein composed of three WLIM1 copies in tandem (3 × WLIM1, Fig. 1B), and transiently expressed it as a GFP-fusion in tobacco BY2 cells. We anticipated that such a six LIM domain-containing protein displays an even higher actin-bundling activity. (Fig. 2A) shows the typical actin cytoskeleton pattern in an expanding BY2 cell as visualized using the actin marker GFP-fABD2.⁵ As previously reported by Sheahan et al.,⁵ GFP-fABD2 decorated dense, transversely oriented, cortical networks as well as transvacuolar strands connecting the subcortical-perinuclear region to the cortex. Ectopic expression of WLIM1-GFP (BY2 cells normally do not express the WLIM1 gene) induced moderate but perceptible modifications of the actin cytoskeleton structure (Fig. 2B). Most AF are arranged in bundles thicker than those observed in GFP-fABD2 expressing cells and fine AF arrays are less frequently observed. As expected, this phenotype was significantly enhanced in cells transformed with the 3xWLIM1-GFP protein (Fig. 2C). Indeed, cells were almost devoided of fine AF arrays and exhibited very thick actin cables (Fig. 2C) that, at times (≈30 %), form atypical long looped structures (Fig. 2D). The appearance of such structures may result from the increase of cable stability and thickness induced by the 3xWLIM1-GFP protein, as these parameters are likely to determine, at least partially, the maximal length of actin bundles. Together the present observations support earlier data showing that LIM domains work in concert in LIM proteins to regulate actin bundling in plant cells. Strikingly, vertebrate and plant CRPs invariably contain two LIM domains. The lack, in these organisms, of CRP-related proteins combining more than two LIM domains may be explained by the fact that very thick cables, such as those induced by the artificial 3xWLIM1, may be too stable structures incompatible with the necessary high degree of actin cytoskeleton plasticity. As an exception, a muscle CRP-related protein with five LIM domains (Mlp84B) has been identified in Drosophila.⁶ However, rather than decorating actin filaments in an homogenous manner, this protein has been found to concentrate in a specialized region of the Z-discs where it stabilizes, in concert with D-titin, muscle sarcomeres.⁷Open in a separate windowFigure 2Typical actin cytoskeleton patterns in tobacco BY2 cells that have been transiently transformed, using a particle gun, with GFP-fABD2 (A), WLIM1-GFP (B), and 3xWLIM1-GFP (C and D). For each construct, more than 60 cells were analyzed by confocal microscopy. In the case of 3xWLIM1-GFP, two prevalent patterns have been observed (C and D). Bars = 20 µm.The relatively well conserved spacer length (≈50 amino acids) that separates the two LIM domains in vertebrate CRPs and related plant LIM proteins remains an intriguing feature the importance of which in actin cable organization remains to be established. Using electron microscopy we are currently evaluating the effects of the modification of the interLIM domain length on the structural properties of actin cables.     

The B gene of pea encodes a defective flavonoid 3',5'-hydroxylase, and confers pink flower color

The inheritance of flower color in pea (Pisum sativum) has been studied for more than a century, but many of the genes corresponding to these classical loci remain unidentified. Anthocyanins are the main flower pigments in pea. These are generated via the flavonoid biosynthetic pathway, which has been studied in detail and is well conserved among higher plants. A previous proposal that the Clariroseus (B) gene of pea controls hydroxylation at the 5' position of the B ring of flavonoid precursors of the anthocyanins suggested to us that the gene encoding flavonoid 3',5'-hydroxylase (F3'5'H), the enzyme that hydroxylates the 5' position of the B ring, was a good candidate for B. In order to test this hypothesis, we examined mutants generated by fast neutron bombardment. We found allelic pink-flowered b mutant lines that carried a variety of lesions in an F3'5'H gene, including complete gene deletions. The b mutants lacked glycosylated delphinidin and petunidin, the major pigments present in the progenitor purple-flowered wild-type pea. These results, combined with the finding that the F3'5'H gene cosegregates with b in a genetic mapping population, strongly support our hypothesis that the B gene of pea corresponds to a F3'5'H gene. The molecular characterization of genes involved in pigmentation in pea provides valuable anchor markers for comparative legume genomics and will help to identify differences in anthocyanin biosynthesis that lead to variation in pigmentation among legume species.     

Soluble and particulate inositol 1,4,5-trisphosphate 5-phosphatases show common antigenic determinants

Inositol 1,4,5-trisphosphate 5-phosphatase catalyses the dephosphorylation of the phosphate in the 5-position from inositol 1,4,5-trisphosphate and inositol 1,3,4,5-tetrakisphosphate. One particulate and two soluble enzymes were previously described in bovine brain. In this study, we have obtained a precipitating antiserum against soluble type I inositol 1,4,5-trisphosphate 5-phosphatase. The particulate, but not the soluble type II enzyme, was immunoprecipitated by the serum. Inositol 1,4,5-triphosphate 5-phosphatase activity from crude extracts of rat brain, human platelets and rat liver were immmunoprecipitated by the same antibodies, suggesting the existence of common antigenic determinant among inositol 1,4,5-trisphosphate 5-phosphatases of diverse sources.     

Progress in outgrowth culture from rabbit tracheal explants: Balance between proliferation and maintenance of differentiated state in epithelial cells

Summary Primary cultures of rabbit tracheal cells were obtained as outgrowths from explants of tracheal mucosa. A 30% collagen substratum containing serum and minimal essential medium was required for obtaining an outgrowth of epithelial cells keeping their differentiated characteristics. The tracheal epithelial cells obtained near the explant in the first days of culture presented morphologic similarities with normal tracheal epithelium. Cultures contained basal cells and epithelial polarized cells that exhibited apical tight junctions and desmosomes. Ciliated cells stayed functional during all time culture. Their number slightly increased at the beginning of the culture and then stayed constant when the total number of cells increased. Development of the outgrowth was rapid and significant inasmuch as the outgrowth surface reached 30 times that of the explant after less than 8 days. This was linked to cellular proliferation, as demonstrated by the incorporation of bromodeoxyuridine (BrdU) in phase-S nuclei and the revelation of BrdU using an immunofluorescence technique. The epithelial nature of the outgrowth cells and the absence of contamination with fibroblasts were established by positive staining with anti-keratin antibody and by negative staining with anti-vimentin antibody, respectively. This work was supported by DRET and by CIFRE grant awarded to S. R.     

Gigantism among Late Jurassic limulids: New ichnological evidence from the Causses Basin (Lozère,France) and comments on body-size evolution among horseshoe crabs

An abundant ichnological material composed of xiphosuran trackways and isolated traces was discovered in Upper Jurassic limestones from the Causses Basin (Causse Méjean, Lozère, France). The morphology of the imprints supports their identification as Kouphichnium isp. In contrast to the most frequent case, the trackways are composed of omnipresent pusher imprints sometime associated with leg traces, but with no telson mark. We argue that this pattern reflects actual surface traces rather than an incomplete set of undertracks. The size distribution of the sampled ichnites is broadly bimodal. This is best explained by sexual dimorphism, a phenomenon frequently observed in modern xiphosurans. Analysis of the trace fossils further suggests that several growth stages are recorded and that the horseshoe crabs were walking in a protected and flat environment like a lagoon. This area, certainly close to a mating ground, was occasionally affected by a continental influence. The biometric study of the tracks suggests a gigantic size for the trackmakers whose body may have reached 84 cm in length. This discovery complements the few reports on other gigantic horseshoe crabs in the Jurassic of Western Europe, thus casting doubt on the postulated increase in body size from the Palaeozoic to the Recent. Furthermore, a literature review shows that there are still major gaps in the record of limulid body-fossils and tracks. Thus, neither of these archives can be taken at face value for quantifying the body-size evolution of horseshoe crabs.     

Very High Surface Capacity Observed Using Si Negative Electrodes Embedded in Copper Foam as 3D Current Collectors

Cu foam is evaluated as a replacement for metal foil current collectors to create 3D composite electrodes with the objective to produce Si‐based anodes with high loadings. The electrodes are prepared by casting the slurry into the porosity of the foam. With such a design, the loading and the surface capacity can reach values as high as 10 mg cm^?2 and 10 mAh cm^?2. Compared to the common 2D design, the 3D copper framework shows a great advantage in the cycle life (more than 400 cycles at a Si loading of 10 mg cm^?2 with commercial micrometric particles) and power performance. The thinness of the composite coating on the foam walls favors a better preservation of the electronic wiring upon cycling and fast lithium ion diffusion. A higher coulombic efficiency in half cells with lithium metal as the counter electrode is achieved by using carbon nanofibers (CNF) rather than carbon black (CB). The possibility to reach, in practice, higher surface capacity could allow a significant increase in both the volumetric and gravimetric energy densities by 23% and 19%, respectively, for the Cu foam‐silicon//LiFePO₄ stack compared to the graphite/LiFePO₄ stack of traditional design.     

Rebuilding a macromolecular membrane complex at the atomic scale: Case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2

Ion channel‐coupled receptors (ICCR) are artificial proteins built from a G protein‐coupled receptor and an ion channel. Their use as molecular biosensors is promising in diagnosis and high‐throughput drug screening. The concept of ICCR was initially validated with the combination of the muscarinic receptor M2 with the inwardly rectifying potassium channel Kir6.2. A long protein engineering phase has led to the biochemical characterization of the M2‐Kir6.2 construct. However, its molecular mechanism remains to be elucidated. In particular, it is important to determine how the activation of M2 by its agonist acetylcholine triggers the modulation of the Kir6.2 channel via the M2‐Kir6.2 linkage. In the present study, we have developed and validated a computational approach to rebuild models of the M2‐Kir6.2 chimera from the molecular structure of M2 and Kir6.2. The protocol was first validated on the known protein complexes of the μ‐opioid Receptor, the CXCR4 receptor and the Kv1.2 potassium channel. When applied to M2‐Kir6.2, our protocol produced two possible models corresponding to two different orientations of M2. Both models highlights the role of the M2 helices I and VIII in the interaction with Kir6.2, as well as the role of the Kir6.2 N‐terminus in the channel opening. Those two hypotheses will be explored in a future experimental study of the M2‐Kir6.2 construct. Proteins 2014; 82:1694–1707. © 2014 Wiley Periodicals, Inc.     

Fe-S clusters, fragile sentinels of the cell

Iron-sulfur (Fe-S) clusters are ubiquitous cofactors present in a myriad of proteins controlling processes as diverse as DNA replication, photosynthesis, respiration and gene regulation. Their assembly and delivery into apo-proteins are catalysed by different multi-protein systems conserved throughout prokaryotes and eukaryotes. Because so many cellular processes are dependent upon Fe-S proteins, alteration of the Fe-S clusters or of the systems that make them has profound impact on cellular physiology. The present review aims at covering and discussing those situations wherein these highly efficient redox sensitive cofactors turn from faithful sentinels into enfeebled assistants or, worse, into dangerous insiders.