Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module

Bacterial toxin-antitoxin (TA) systems are operons that code for a stable toxic protein and a labile antitoxin. TA modules are widespread on the chromosomes of free-living Bacteria and Archaea, where they presumably act as stress response elements. The chromosome of Escherichia coli K-12 encodes four known TA pairs, as well as the dinJ-yafQ operon, which is hypothesized to be a TA module based on operon organization similar to known TA genes. Induction of YafQ inhibited cell growth, but its toxicity was counteracted by coexpression of dinJ cloned on a separate plasmid. YafQ(His)(6) and DinJ proteins coeluted in Ni(2+)-affinity and gel filtration chromatography, implying the formation of a specific and stable YafQ-DinJ protein complex with an estimated molecular mass of c. 37.3 kDa. Induction of YafQ reduced protein synthesis up to 40% as judged by incorporation of [(35)S]-methionine, but did not influence the rates of DNA and RNA synthesis. Structure modelling of E. coli YafQ revealed its structural relationship with bacterial toxins of known structure suggesting that it might act as a sequence-specific mRNA endoribonuclease.     

The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures

Non-coding RNAs (ncRNAs) are regulatory molecules encoded in the intergenic or intragenic regions of the genome. In prokaryotes, biocomputational identification of homologs of known ncRNAs in other species often fails due to weakly evolutionarily conserved sequences, structures, synteny and genome localization, except in the case of evolutionarily closely related species. To eliminate results from weak conservation, we focused on RNA structure, which is the most conserved ncRNA property. Analysis of the structure of one of the few well-studied bacterial ncRNAs, 6S RNA, demonstrated that unlike optimal and consensus structures, suboptimal structures are capable of capturing RNA homology even in divergent bacterial species. A computational procedure for the identification of homologous ncRNAs using suboptimal structures was created. The suggested procedure was applied to strongly divergent bacterial species and was capable of identifying homologous ncRNAs.     

Galactoglucomannan oligosaccharides inhibition of elongation growth is in pea epicotyls coupled with peroxidase activity

The effect of galactoglucomannan oligosaccharides — GGMOs, GGMOs-r (GGMOs with reduced reducing ends), and GGMOs-g (GGMOs with reduced number of d-galactose units) on peroxidase activity was determined in pea epicotyls. GGMOs didn’t significantly modify the activity of soluble peroxidases. However, cell wall-associated peroxidases activity increased after GGMOs and GGMOs-r treatment, while in the presence of GGMOs-g this activity was significantly lower. These results are inversely related to the GGMOs, GGMOs-r, and GGMOs-g effect on elongation growth induced by 2,4-D (2,4-dichlorophenoxyacetic acid) in pea epicotyls. It can be concluded that GGMOs evoked inhibition of the elongation growth induced by auxin is probably associated with cell wall modifications catalysed by peroxidase.     

Benzimidazole design,synthesis, and docking to build selective carbonic anhydrase VA inhibitors

The similarity of human carbonic anhydrase (CA) active sites makes it difficult to design selective inhibitors for one or several CA isoforms that are drug targets. Here we synthesize a series of compounds that are based on 5-[2-(benzimidazol-1-yl)acetyl]-2-chloro-benzenesulfonamide (1a) which demonstrated picomolar binding affinity and significant selectivity for CA isoform five A (VA), and explain the structural influence of inhibitor functional groups to the binding affinity and selectivity. A series of chloro-substituted benzenesulfonamides bearing a heterocyclic tail, together with molecular docking, was used to build inhibitors that explore substituent influence on the binding affinity to the CA VA isoform.     

Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops

Grb2-associated binder 1 (GAB1) is a scaffold protein involved in numerous interactions that propagate signaling by growth factor and cytokine receptors. Here we explore in silico and validate in vivo the role of GAB1 in the control of mitogenic (Ras/MAPK) and survival (phosphatidylinositol 3-kinase (PI3K)/Akt) signaling stimulated by epidermal growth factor (EGF). We built a comprehensive mechanistic model that allows for reliable predictions of temporal patterns of cellular responses to EGF under diverse perturbations, including different EGF doses, GAB1 suppression, expression of mutant proteins, and pharmacological inhibitors. We show that the temporal dynamics of GAB1 tyrosine phosphorylation is significantly controlled by positive GAB1-PI3K feedback and negative MAPK-GAB1 feedback. Our experimental and computational results demonstrate that the essential function of GAB1 is to enhance PI3K/Akt activation and extend the duration of Ras/MAPK signaling. By amplifying positive interactions between survival and mitogenic pathways, GAB1 plays the critical role in cell proliferation and tumorigenesis.     

Truncation of the peptide sequence in bifunctional ligands with mu and delta opioid receptor agonist and neurokinin 1 receptor antagonist activities

The optimization and truncation of our lead peptide-derived ligand TY005 possessing eight amino-acid residues was performed. Among the synthesized derivatives, NP30 (Tyr¹-DAla²-Gly³-Phe⁴-Gly⁵-Trp⁶-O-[3′,5′-Bzl(CF₃)₂]) showed balanced and potent opioid agonist as well as substance P antagonist activities in isolated tissue-based assays, together with significant antinociceptive and antiallodynic activities in vivo.     

The First Description of Dominance Hierarchy in Captive Giraffe: Not Loose and Egalitarian,but Clear and Linear

Wild giraffes live in extensive groups in the fission fusion system, maintaining long social distances and loose social bonds. Within these groups, resources are widely distributed, agonistic encounters are scarce and the dominance hierarchy was reported in males only, while never deeply analysed. In captivity, the possibility to maintain inter-individual distances is limited and part of the resources is not evenly distributed. Consequently, we suggest that agonistic encounters should be more frequent, leading to the establishment of the dominance hierarchy. Based on the differences in resource-holding potential, we suggested that the rank of an individual would be affected by age and sex. Based on hypotheses of prior ownership, we tested whether rank was positively affected by the time spent in a herd and whether it was stable in adult females, which were present long-term in the same herd. We originally monitored four herds of Rothschild giraffes (Giraffa camelopardalis rothschildii) in Dvůr Králové zoo (n = 8), Liberec zoo (n = 6), and two herds in Prague zoo: Prague 1 (n = 8) and Prague 2 (n = 9). The Prague 1 and Prague 2 herds were then combined and the resulting fifth herd was observed over three consecutive years (2009, 2010, and 2011) (n = 14, 13, and 14, respectively). We revealed a significantly linear hierarchy in Dvůr Králové, Prague 2 and in the combined herd in Prague. Rank was significantly affected by age in all herds; older individuals dominated the younger ones. In females, rank was positively affected by the time spent in the herd and adult females in Prague maintained their rank during three consecutive years. This study represents the first analysis of the dominance hierarchy in the captive giraffe, and discusses the behavioural flexibility of the social structure in response to monopolisable resources in a captive environment.     

Genome size and chromosome number in Echinops (Asteraceae, Cardueae) in the Aegean and Balkan regions: technical aspects of nuclear DNA amount assessment and genome evolution in a phylogenetic frame

This work focuses on the representatives of genus Echinops (Asteraceae, Cardueae) in the Aegean and Balkan regions, from the perspective of their genome evolution. Chromosome numbers were determined by orcein staining in 14 populations of nine taxa, and DNA contents were assessed by flow cytometry in 24 populations of nine taxa. A molecular phylogeny based on the internal transcribed spacer (ITS) and trnL-trnF and including first sequences for two taxa (Echinops sphaerocephalus subsp. taygeteus and E.?spinosissimus subsp. neumayeri) provided a framework for discussing genome changes. From a methodological point of view, similar C-DNA value estimates were obtained when measuring, for a same population, fresh leaves from adult plants collected in the field and from cultivated seedlings. Conversely, despite giving the appearance of being correct (e.g., low coefficient of variation), genome size assessed using silica gel-preserved material differs significantly from values obtained for the same populations with fresh material. Nevertheless, silica gel-preserved material may still provide rough estimates of genome size for, e.g., inferring ploidy level. Suitable—non-silica gel-based—DNA amounts assessed for 23 populations range from 2C?=?6.52?pg (E.?spinosissimus subsp. neumayeri) to 2C?=?9.37?pg (E.?bannaticus). Chromosome counts were established for the first time for Echinops graecus (2n?=?32), E.?sphaerocephalus subsp. albidus (2n?=?32), E.?sphaerocephalus subsp. taygeteus (2n?=?ca.?30), and E.?spinosissimus subsp. neumayeri (2n?=?28). Genome size and chromosome number are confirmed as crucial parameters for deciphering lineage diversification within the genus Echinops.     

Biochemical properties of Hsp70 chaperone system from Meiothermus ruber

The guanidine-hydrochloride (Gdn-HCl) and thermally induced unfolding of Hsp70 from Meiothermus ruber (Mru.Hsp70) were analysed using tryptophan fluorescence and 8-anilino-1-naphthalenesulfonic acid (ANS) binding. The ANS binding to Mru.Hsp70 showed both the increase in fluorescence intensity and a shift in emission maximum. Analysis of the unfolding profile of Mru.Hsp70 indicated that Gdn-HCl induced unfolding of Mru.Hsp70 occurred through intermediate species. The tryptophan and ANS fluorescence emission spectra revealed that ATP induced conformational change increased the thermal stability of Mru.Hsp70. The data obtained are similar to those of Escherichia coli DnaK. The ATP-ase activity of chaperones is fundamental for their biological activity. It this paper we demonstrate that, in contrast to Thermus thermophilus, both Mru.Hsp40 and Mru.Hsp22 co-chaperones affect the ATP-ase activity of Mru.Hsp70. The use of truncated Mru.Hsp40 proteins showed that full-length Mru.Hsp40 is required for stimulation of ATP-ase activity of Mru.Hsp70. E. coli GrpE could act as nucleotide exchange factor the in thermophilic Hsp70 ATP hydrolysis reaction. However, the role of E. coli DnaJ in the M. ruber ATP cycle needs further analysis. We selected the new substrate laccA suitable for determination of refolding activity of thermophilic chaperones.