An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species

A hallmark of the Gram-positive bacteria, such as the soil-dwelling bacterium Bacillus subtilis, is their cell wall. Here, we report that d -leucine and flavomycin, biofilm inhibitors targeting the cell wall, activate the β-lactamase PenP. This β-lactamase contributes to ampicillin resistance in B. subtilis under all conditions tested. In contrast, both Spo0A, a master regulator of nutritional stress, and the general cell wall stress response, differentially contribute to β-lactam resistance under different conditions. To test whether β-lactam resistance and β-lactamase genes are widespread in other Bacilli, we isolated Bacillus species from undisturbed soils, and found that their genomes can encode up to five β-lactamases with differentiated activity spectra. Surprisingly, the activity of environmental β-lactamases and PenP, as well as the general stress response, resulted in a similarly reduced lag phase of the culture in the presence of β-lactam antibiotics, with little or no impact on the logarithmic growth rate. The length of the lag phase may determine the outcome of the competition between β-lactams and β-lactamases producers. Overall, our work suggests that antibiotic resistance genes in B. subtilis and related species are ancient and widespread, and could be selected by interspecies competition in undisturbed soils.     

GALNT3, a gene associated with hyperphosphatemic familial tumoral calcinosis, is transcriptionally regulated by extracellular phosphate and modulates matrix metalloproteinase activity

GALNT3 encodes UDP-N-acetyl-alpha-d-galactosamine: polypeptide N-acetylgalactosaminyl-transferarase 3 (ppGalNacT3), a glycosyltransferase which has been suggested to prevent proteolysis of FGF23, a potent phosphaturic protein. Accordingly, loss-of-function mutations in GALNT3 cause hyperphosphatemic familial tumoral calcinosis (HFTC), a rare autosomal recessive disorder manifesting with increased kidney reabsorption of phosphate, resulting in severe hyperphosphatemia and widespread ectopic calcifications. Although these findings definitely attribute a role to ppGalNacT3 in the regulation of phosphate homeostasis, little is currently known about the factors regulating GALNT3 expression. In addition, the effect of decreased GALNT3 expression in peripheral tissues has not been explored so far. In the present study, we demonstrate that GALNT3 expression is under the regulation of a number of factors known to be associated with phosphate homeostasis, including inorganic phosphate itself, calcium and 1,25-dihydroxyvitamin D(3). In addition, we show that decreased GALNT3 expression in human skin fibroblasts leads to increased expression of FGF7 and of matrix metalloproteinases, which have been previously implicated in the pathogenesis of ectopic calcification. Thus, the present data suggest that ppGalNacT3 may play a role in peripheral tissues of potential relevance to the pathogenesis of disorders of phosphate metabolism.     

The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework

The hologenome theory of evolution emphasizes the role of microorganisms in the evolution of animals and plants. The theory posits that the holobiont (host plus all of its symbiont microbiota) is a unit of selection in evolution. Genetic variation in the holobiont that can occur either in the host and/or in the microbial symbiont genomes (together termed hologenome) can then be transmitted to offspring. In addition to the known modes of variation, i.e. sexual recombination, chromosomal rearrangement and mutation, variation in the holobiont can occur also via two mechanisms that are specific to the hologenome theory: amplification of existing microorganisms and acquisition of novel strains from the environment. These mechanisms are Lamarckian in that (i) they are regulated by ‘use and disuse’ (of microbes) and (ii) the variations in the hologenome are transmitted to offspring, thus satisfying also the Lamarckian principle of ‘inheritance of acquired characteristics’. Accordingly, the hologenome theory incorporates Lamarckian aspects within a Darwinian framework, accentuating both cooperation and competition within the holobiont and with other holobionts.     

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry

Background  

Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L < N), the consecutive windows folding problem is to compute the minimal free energy (MFE) for the folding of each of the L-sized substrings of S. The consecutive windows folding problem can be naively solved in O(NL³) by applying any of the classical cubic-time RNA folding algorithms to each of the N-L windows of size L. Recently an O(NL²) solution for this problem has been described.     

Rearrangements in the Relative Orientation of Cytoplasmic Domains Induced by a Membrane-anchored Protein Mediate Modulations in Kv Channel Gating

Interdomain interactions between intracellular N and C termini have been described for various K⁺ channels, including the voltage-gated Kv2.1, and suggested to affect channel gating. However, no channel regulatory protein directly affecting N/C interactions has been demonstrated. Most Kv2.1 channel interactions with regulatory factors occur at its C terminus. The vesicular SNARE that is also present at a high concentration in the neuronal plasma membrane, VAMP2, is the only protein documented to affect Kv2.1 gating by binding to its N terminus. As its binding target has been mapped near a site implicated in Kv2.1 N/C interactions, we hypothesized that VAMP2 binding to the N terminus requires concomitant conformational changes in the C terminus, which wraps around the N terminus from the outside, to give VAMP2 access. Here, we first determined that the Kv2.1 N terminus, although crucial, is not sufficient to convey functional interaction with VAMP2, and that, concomitant to its binding to the “docking loop” at the Kv2.1 N terminus, VAMP2 binds to the proximal part of the Kv2.1 C terminus, C1a. Next, using computational biology approaches (ab initio modeling, docking, and molecular dynamics simulations) supported by molecular biology, biochemical, electrophysiological, and fluorescence resonance energy transfer analyses, we mapped the interaction sites on both VAMP2 and Kv2.1 and found that this interaction is accompanied by rearrangements in the relative orientation of Kv2.1 cytoplasmic domains. We propose that VAMP2 modulates Kv2.1 inactivation by interfering with the interaction between the docking loop and C1a, a mechanism for gating regulation that may pertain also to other Kv channels.Interdomain interactions between intracellularly located N and C termini have been described for various K⁺ channels, including inwardly rectifying Kir2.3 and Kir6.2 (1, 2), small conductance Ca²⁺-activated (hSK3) (3), and voltage-gated Kv2.1 (4) and Kv4.1 (5) channels. In the case of Kv2.1, two modes of interaction have been proposed: an association of the distal part of Kv2.1 C terminus (termed CTA domain; amino acids (aa) 741–853)⁴ with aa 67 and 75 of the Kv2.1 N terminus (4); or an association between the proximal part of the Kv2.1 C terminus (aa 444–477) and the predicted loop structure (aa 55–71) in the N-terminal T1 domain (6). In addition, involvement of the S4-S5 linker in this interaction has been suggested (7). Although these studies propose two different C-terminal sites, they indicate a specific loop in the N terminus of Kv2.1 (6, 8), which could be functionally related to the Shaker and Shal docking loops in the lateral part of their T1 domains (9, 10). These latter loops are responsible for the subfamily-specific association with β-subunits (Kvβ and KChIP, respectively). Further, the interaction between the N and C cytoplasmic termini (N/C interaction) of Kv2.1 has been shown to be dynamic and voltage-dependent and to involve structural rearrangements between these domains, which could affect both activation and inactivation gating of the channel (4, 6, 7). These rearrangements can be clearly detected with fluorescence resonance energy transfer (FRET) (11). A similar N/C interaction has been shown to affect gating of the closely related Kv4.1 channel (5, 12).It is conceivable that the specific packaging of Kv2.1 cytoplasmic termini (a relatively long C terminus (>400 aa) wrapping the N terminus (<190 aa) from the outside (4)) not only supports multiple interactions between the termini but also reflects the fact that most of the interactions of the channel with intracellular and membrane-bound regulatory factors occur at the C terminus, including channel phosphorylation (13–15), clustering through a unique proxinal restriction and clustering signal (16), and protein-protein interactions with both the plasma membrane SNAREs, syntaxin 1A and SNAP-25 (17–19), and the MiRP2 (KCNE3) peptide (20). For the Kv2.1 N terminus, on the other hand, there are only two examples of protein-protein interactions: a transient association with KChAP (21), which does not affect channel function; and an interaction with the vesicular SNARE partner VAMP2 (synaptobrevin 2), which is also present at a high concentration in the neuronal plasma membrane and enhances channel inactivation (8). Specifically, VAMP2 has been shown to associate with the extension of a docking loop in the lateral part of the T1 domain (8) near the site of interaction with the C terminus (4, 6). Thus, it is reasonable to hypothesize that interaction with VAMP2 will affect the N/C interaction, similar to proton-mediated Kir2.3 (1) and Kir1.1 (22) N/C interactions or the ATP-dependent Kir6.2 (2) N/C interaction. To date, no protein molecule that directly affects N/C interactions in a K⁺ channel has been demonstrated. Because VAMP2 was the first protein documented to affect Kv2.1 channel gating by binding to a specific N-terminal site, which is probably masked by the C terminus, we have put forward the idea that its interaction with the Kv2.1 N terminus requires conformational changes in the C terminus that will enable its access to the N terminus.Here we endeavored to gain a mechanistic and structural understanding of the Kv2.1-VAMP2 interaction. Based on our evidence, we propose that VAMP2 modulates Kv2.1 gating by interfering with the Kv2.1 cytoplasmic N/C interaction.     

DIVERSIFICATION OF THE AFRICAN GENUS PROTEA (PROTEACEAE) IN THE CAPE BIODIVERSITY HOTSPOT AND BEYOND: EQUAL RATES IN DIFFERENT BIOMES

The Cape region of South Africa is a hotspot of flowering plant biodiversity. However, the reasons why levels of diversity and endemism are so high remain obscure. Here, we reconstructed phylogenetic relationships among species in the genus Protea, which has its center of species richness and endemism in the Cape, but also extends through tropical Africa as far as Eritrea and Angola. Contrary to previous views, the Cape is identified as the ancestral area for the radiation of the extant lineages: most species in subtropical and tropical Africa are derived from a single invasion of that region. Moreover, diversification rates have been similar within and outside the Cape region. Migration out of the Cape has opened up vast areas, but those lineages have not diversified as extensively at fine spatial scales as lineages in the Cape. Therefore, higher net rates of diversification do not explain the high diversity and endemism of Protea in the Cape. Instead, understanding why the Cape is so diverse requires an explanation for how Cape species are able to diverge and persist at such small spatial scales.     

Heparanase 2 Interacts with Heparan Sulfate with High Affinity and Inhibits Heparanase Activity

Heparanase activity is highly implicated in cell dissemination associated with tumor metastasis, angiogenesis, and inflammation. Heparanase expression is induced in many hematological and solid tumors, associated with poor prognosis. Heparanase homolog, termed heparanase 2 (Hpa2), was cloned based on sequence homology. Detailed characterization of Hpa2 at the biochemical, cellular, and clinical levels has not been so far reported, and its role in normal physiology and pathological disorders is obscure. We provide evidence that unlike heparanase, Hpa2 is not subjected to proteolytic processing and exhibits no enzymatic activity typical of heparanase. Notably, the full-length Hpa2c protein inhibits heparanase enzymatic activity, likely due to its high affinity to heparin and heparan sulfate and its ability to associate physically with heparanase. Hpa2 expression was markedly elevated in head and neck carcinoma patients, correlating with prolonged time to disease recurrence (follow-up to failure; p = 0.006) and inversely correlating with tumor cell dissemination to regional lymph nodes (N-stage; p = 0.03). Hpa2 appears to restrain tumor metastasis, likely by attenuating heparanase enzymatic activity, conferring a favorable outcome of head and neck cancer patients.     

A Dominance Hierarchy of Auditory Spatial Cues in Barn Owls

Background

Barn owls integrate spatial information across frequency channels to localize sounds in space.

Methodology/Principal Findings

We presented barn owls with synchronous sounds that contained different bands of frequencies (3–5 kHz and 7–9 kHz) from different locations in space. When the owls were confronted with the conflicting localization cues from two synchronous sounds of equal level, their orienting responses were dominated by one of the sounds: they oriented toward the location of the low frequency sound when the sources were separated in azimuth; in contrast, they oriented toward the location of the high frequency sound when the sources were separated in elevation. We identified neural correlates of this behavioral effect in the optic tectum (OT, superior colliculus in mammals), which contains a map of auditory space and is involved in generating orienting movements to sounds. We found that low frequency cues dominate the representation of sound azimuth in the OT space map, whereas high frequency cues dominate the representation of sound elevation.

Conclusions/Significance

We argue that the dominance hierarchy of localization cues reflects several factors: 1) the relative amplitude of the sound providing the cue, 2) the resolution with which the auditory system measures the value of a cue, and 3) the spatial ambiguity in interpreting the cue. These same factors may contribute to the relative weighting of sound localization cues in other species, including humans.