A Specific Endogenous Reference for Genetically Modified Common Bean (Phaseolus vulgaris L.) DNA Quantification by Real-Time PCR Targeting Lectin Gene

The Embrapa 5.1 genetically modified (GM) common bean was approved for commercialization in Brazil. Methods for the quantification of this new genetically modified organism (GMO) are necessary. The development of a suitable endogenous reference is essential for GMO quantification by real-time PCR. Based on this, a new taxon-specific endogenous reference quantification assay was developed for Phaseolus vulgaris L. Three genes encoding common bean proteins (phaseolin, arcelin, and lectin) were selected as candidates for endogenous reference. Primers targeting these candidate genes were designed and the detection was evaluated using the SYBR Green chemistry. The assay targeting lectin gene showed higher specificity than the remaining assays, and a hydrolysis probe was then designed. This assay showed high specificity for 50 common bean samples from two gene pools, Andean and Mesoamerican. For GM common bean varieties, the results were similar to those obtained for non-GM isogenic varieties with PCR efficiency values ranging from 92 to 101 %. Moreover, this assay presented a limit of detection of ten haploid genome copies. The primers and probe developed in this work are suitable to detect and quantify either GM or non-GM common bean.     

A Peptide Derived from G0/G1 Switch Gene 2 Acts as Noncompetitive Inhibitor of Adipose Triglyceride Lipase

The protein G₀/G₁ switch gene 2 (G0S2) is a small basic protein that functions as an endogenous inhibitor of adipose triglyceride lipase (ATGL), a key enzyme in intracellular lipolysis. In this study, we identified a short sequence covering residues Lys-20 to Ala-52 in G0S2 that is still fully capable of inhibiting mouse and human ATGL. We found that a synthetic peptide corresponding to this region inhibits ATGL in a noncompetitive manner in the nanomolar range. This peptide is highly selective for ATGL and does not inhibit other lipases, including hormone-sensitive lipase, monoacylglycerol lipase, lipoprotein lipase, and patatin domain-containing phospholipases 6 and 7. Because increased lipolysis is linked to the development of metabolic disorders, the inhibition of ATGL by G0S2-derived peptides may represent a novel therapeutic tool to modulate lipolysis.     

Distinct Amino Acids in the C-Linker Domain of the Arabidopsis K+ Channel KAT2 Determine Its Subcellular Localization and Activity at the Plasma Membrane

Shaker K⁺ channels form the major K⁺ conductance of the plasma membrane in plants. They are composed of four subunits arranged around a central ion-conducting pore. The intracellular carboxy-terminal region of each subunit contains several regulatory elements, including a C-linker region and a cyclic nucleotide-binding domain (CNBD). The C-linker is the first domain present downstream of the sixth transmembrane segment and connects the CNBD to the transmembrane core. With the aim of identifying the role of the C-linker in the Shaker channel properties, we performed subdomain swapping between the C-linker of two Arabidopsis (Arabidopsis thaliana) Shaker subunits, K⁺ channel in Arabidopsis thaliana2 (KAT2) and Arabidopsis thaliana K⁺ rectifying channel1 (AtKC1). These two subunits contribute to K⁺ transport in planta by forming heteromeric channels with other Shaker subunits. However, they display contrasting behavior when expressed in tobacco mesophyll protoplasts: KAT2 forms homotetrameric channels active at the plasma membrane, whereas AtKC1 is retained in the endoplasmic reticulum when expressed alone. The resulting chimeric/mutated constructs were analyzed for subcellular localization and functionally characterized. We identified two contiguous amino acids, valine-381 and serine-382, located in the C-linker carboxy-terminal end, which prevent KAT2 surface expression when mutated into the equivalent residues from AtKC1. Moreover, we demonstrated that the nine-amino acid stretch ₃₁₂TVRAASEFA₃₂₀ that composes the first C-linker α-helix located just below the pore is a crucial determinant of KAT2 channel activity. A KAT2 C-linker/CNBD three-dimensional model, based on animal HCN (for Hyperpolarization-activated, cyclic nucleotide-gated K⁺) channels as structure templates, has been built and used to discuss the role of the C-linker in plant Shaker inward channel structure and function.In plants, potassium channels from the Shaker family dominate the plasma membrane (PM) conductance to K⁺ in most cell types and play crucial roles in sustained K⁺ transport (Blatt et al., 2012; Hedrich, 2012; Sharma et al., 2013). Plant Shaker channels, like their homologs in animals (Craven and Zagotta, 2006; Wahl-Schott and Biel, 2009), belong to the six transmembrane-one pore (6TM-1P) cation channel superfamily. Functional channels are tetrameric proteins arranged around a central pore (Daram et al., 1997; Urbach et al., 2000; Dreyer et al., 2004). These channels can result from the assembly of Shaker subunits encoded by the same gene (homotetramers) or by different Shaker genes (heterotetramers). Heterotetramerization has been extensively reported within the inwardly rectifying Shaker channel group (five members in Arabidopsis [Arabidopsis thaliana]) and increased channel functional diversity (Jeanguenin et al., 2008; Lebaudy et al., 2008a).Based on in silico sequence analyses, plant Shaker subunits display a short cytosolic N-terminal domain, followed by the 6TM-1P hydrophobic core, and a long C-terminal cytosolic region in which several domains can be identified. The first one, named C-linker (about 80 amino acids in length), is followed by a cyclic nucleotide-binding domain (CNBD), an ankyrin domain (involved in protein-protein interaction; Lee et al., 2007, Grefen and Blatt, 2012), and a domain named K_HA (Ehrhardt et al., 1997) rich in hydrophobic and acidic residues. Sequence analysis of plant Shaker channels indicates that, among these cytosolic domains, the highest levels of similarity are displayed by the C-linker and the CNBD domains. Interestingly, both domains are also highly conserved in some members from the animal K⁺ channel superfamily, like Hyperpolarization-activated, cyclic nucleotide-gated K⁺ channel (HCN), K⁺ voltage-gated channel, subfamily H (KCNH), and Cyclic-nucleotide-gated ion channel (CNGC). In these animal 6TM-1P channels, the roles of C-linker and CNBD domains have been extensively investigated via crystal structure analyses (Zagotta et al., 2003; Brelidze et al., 2012), whereas plant Shaker channels are still poorly characterized at the structural level (Dreyer et al., 2004; Gajdanowicz et al., 2009; Naso et al., 2009; Garcia-Mata et al., 2010).Aiming at investigating the structure-function relationship of plant Shaker channels, we have used the Arabidopsis Shaker subunit K⁺ channel in Arabidopsis thaliana2 (KAT2) as a model. We developed a subdomain-swapping strategy between KAT2 and another Shaker subunit displaying distinctive features, Arabidopsis thaliana K⁺ rectifying channel1 (AtKC1). The KAT2 subunit can form homomeric or heteromeric inwardly rectifying K⁺ channels at the PM and has been shown to be strongly expressed in guard cells, where it provides a major contribution to the membrane conductance to K⁺ (Pilot et al., 2001; Lebaudy et al., 2008b). In contrast, the behavior of AtKC1 is more complex. In planta, this subunit is coexpressed with other inwardly rectifying Shaker subunits, including KAT2, in different plant tissues (Jeanguenin et al., 2011), and in roots, direct evidence has been obtained that AtKC1 is involved in functional heterotetrameric channel formation with AKT1 (Reintanz et al., 2002; Honsbein et al., 2009). However, experiments performed in tobacco (Nicotiana tabacum) mesophyll protoplasts have revealed that when expressed alone, AtKC1 is entrapped in the endoplasmic reticulum (ER). However, in tobacco protoplasts and Xenopus laevis oocytes, coexpression of AtKC1 with KAT2 or other inwardly rectifying Shaker subunits (AKT1, KAT1, or AKT2) gives rise to functional heteromeric channels (Duby et al., 2008; Jeanguenin et al., 2011). In Arabidopsis, it is interesting that evidence of the AtKC1 retention in the ER compartment, in the absence of other Shaker subunits, is lacking, since in the native tissues, AtKC1 is always expressed with its inward partners, with which it is able to form heteromeric channels.Here, we took advantage of the unique behavior of AtKC1 when expressed in heterologous systems to investigate the structure-function relationship of the C-linker of KAT2 by sequence exchange between these two channel subunits and by site-directed mutagenesis. The C-linker domain, which, to our knowledge, had never been studied as such in plant Shaker channels before, could be predicted to play crucial roles in channel properties due to its strategic location between the channel transmembrane core and the cytoplasmic CNBD domain. The resulting KAT2-AtKC1 chimeras were expressed in tobacco mesophyll protoplasts and in X. laevis oocytes for investigating their subcellular localization and measuring their activity at the cell membrane. Here, we show that two amino acids present in the C-linker are important for channel subcellular location and that a stretch of nine amino acids forming a short helix just below the membrane, downstream of the sixth transmembrane segment of the channel hydrophobic core, is involved in channel gating. The obtained experimental results are discussed in relation with a KAT2 C-linker/CNBD three-dimensional (3D) model based on animal HCN channels as structure templates.     

The hybrid histidine kinase Slr1759 of the cyanobacterium Synechocystis sp. PCC 6803 contains FAD at its PAS domain

The cyanobacterium Synechocystis sp. PCC 6803 harbours 47 histidine kinases (Hiks). Among these are hybrid histidine kinases with one or two response regulator domains as well as numerous Hiks with several sensory domains. One example is the hybrid histidine kinase Slr1759 (Hik14) that has two PAS domains arranged in tandem linked to a predicted GAF domain. Here, we show that a Slr1759 derivative recombinantly expressed in Escherichia coli has a flavin cofactor. Using truncated Slr1759 variants, it is shown that the flavin associates with the first PAS domain. The cofactor reconstitutes the activity of d-amino acid oxidase apoprotein from pig kidney, indicating that the flavin derivative is FAD. Furthermore, the Slr1759 histidine kinase domain indeed undergoes autophosphorylation in vitro. The phosphorylated product of a recombinant Slr1759 derivative is sensitive to acids, pointing to a histidine residue as the phosphate-accepting group.     

Bronchoalveolar lavage fluid from preterm infants with chorioamnionitis inhibits alveolar epithelial repair

Background

Preterm infants are highly susceptible to lung injury. While both chorioamnionitis and antenatal steroids induce lung maturation, chorioamnionitis is also associated with adverse lung development. We investigated the ability of bronchoalveolar lavage fluid (BALF) from ventilated preterm infants to restore alveolar epithelial integrity after injury in vitro, depending on whether or not they were exposed to chorioamnionitis or antenatal steroids. For this purpose, a translational model for alveolar epithelial repair was developed and characterised.

Methods

BALF was added to mechanically wounded monolayers of A549 cells. Wound closure was quantified over time and compared between preterm infants (gestational age < 32 wks) exposed or not exposed to chorioamnionitis and antenatal steroids (≥ 1 dose). Furthermore, keratinocyte growth factor (KGF) and vascular endothelial growth factor (VEGF) were quantified in BALF, and their ability to induce alveolar epithelial repair was evaluated in the model.

Results

On day 0/1, BALF from infants exposed to antenatal steroids significantly increased epithelial repair (40.3 ± 35.5 vs. -6.3 ± 75.0% above control/mg protein), while chorioamnionitis decreased wound-healing capacity of BALF (-2.9 ± 87.1 vs. 40.2 ± 36.9% above control/mg protein). BALF from patients with chorioamnionitis contained less KGF (11 (0-27) vs. 0 (0-4) pg/ml) and less detectable VEGF (66 vs. 95%) on day 0. BALF levels of VEGF and KGF correlated with its ability to induce wound repair. Moreover, KGF stimulated epithelial repair dose-dependently, although the low levels in BALF suggest KGF is not a major modulator of BALF-induced wound repair. VEGF also stimulated alveolar epithelial repair, an effect that was blocked by addition of soluble VEGF receptor-1 (sVEGFr1/Flt-1). However, BALF-induced wound repair was not significantly affected by addition of sVEGFr1.

Conclusion

Antenatal steroids improve the ability of BALF derived from preterm infants to stimulate alveolar epithelial repair in vitro. Conversely, chorioamnionitis is associated with decreased wound-healing capacity of BALF. A definite role for KGF and VEGF in either process could not be established. Decreased ability to induce alveolar epithelial repair after injury may contribute to the association between chorioamnionitis and adverse lung development in mechanically ventilated preterm infants.     

The Genome of Streptococcus mitis B6 - What Is a Commensal?

Streptococcus mitis is the closest relative of the major human pathogen S. pneumoniae. The 2,15 Mb sequence of the Streptococcus mitis B6 chromosome, an unusually high-level beta-lactam resistant and multiple antibiotic resistant strain, has now been determined to encode 2100 genes. The accessory genome is estimated to represent over 40%, including 75 mostly novel transposases and IS, the prophage φB6 and another seven phage related regions. Tetracycline resistance mediated by Tn5801, and an unusual and large gene cluster containing three aminoglycoside resistance determinants have not been described in other Streptococcus spp. Comparative genomic analyses including hybridization experiments on a S. mitis B6 specific microarray reveal that individual S. mitis strains are almost as distantly related to the B6 strain as S. pneumoniae. Both species share a core of over 900 genes. Most proteins described as pneumococcal virulence factors are present in S. mitis B6, but the three choline binding proteins PcpA, PspA and PspC, and three gene clusters containing the hyaluronidase gene, ply and lytA, and the capsular genes are absent in S. mitis B6 and other S. mitis as well and confirm their importance for the pathogenetic potential of S. pneumoniae. Despite the close relatedness between the two species, the S. mitis B6 genome reveals a striking X-alignment when compared with S. pneumoniae.     

Force-Driven Separation of Short Double-Stranded DNA

Short double-stranded DNA is used in a variety of nanotechnological applications, and for many of them, it is important to know for which forces and which force loading rates the DNA duplex remains stable. In this work, we develop a theoretical model that describes the force-dependent dissociation rate for DNA duplexes tens of basepairs long under tension along their axes (“shear geometry”). Explicitly, we set up a three-state equilibrium model and apply the canonical transition state theory to calculate the kinetic rates for strand unpairing and the rupture-force distribution as a function of the separation velocity of the end-to-end distance. Theory is in excellent agreement with actual single-molecule force spectroscopy results and even allows for the prediction of the rupture-force distribution for a given DNA duplex sequence and separation velocity. We further show that for describing double-stranded DNA separation kinetics, our model is a significant refinement of the conventionally used Bell-Evans model.     

Lanthanum ions inhibit the mammalian Sec61 complex in its channel dynamics and protein transport activity

Previous electrophysiological experiments characterized the Sec61 complex, which provides the aqueous path for entry of newly-synthesized polypeptides into the mammalian endoplasmic reticulum, as a highly dynamic channel that, once activated by precursor proteins, fluctuates between main open states with mean conductances of 220 and 550 pS. Millimolar concentrations of lanthanum ions simultaneously restricted the dynamics of the Sec61 channel and inhibited translocation of polypeptides. Molecular modeling indicates that lanthanum binding sites cluster at the putative lateral gate of the Sec61 complex and suggests that structural flexibility of the lateral gate is essential for channel and protein transport activities of the Sec61 complex.