Interactions of cardiac glycosides with cells and membranes Properties and structural aspects of two receptor sites for ouabain in erythrocytes

The existence of two types of binding sites for ouabain in human erythrocyte membranes is described. Receptor sites designated as ‘type I’, which may be identical to the K⁺-insensitive sites of intact cells, were detected at concentrations of ouabain as low as 10⁻⁷ M. The ‘type II’ receptor sites require the inclusion of Mg²⁺ + P_i to form complexes with ouabain; they may be identical to the K⁺-sensitive sites of intact cells. These sites were saturated at approx. 5 · 10⁻⁷ M ouabain but could not be detected at higher concentrations. The range of ouabain concentrations at which ‘type I’ receptors start to predominate (i.e. 5 · 10⁻⁸–5 · 10⁻⁷ M) was termed ‘critical digitalis concentrations’. The process of binding reached equilibrium within 1 and 4 h for ‘type I’ and ‘type II’ sites, respectively. The dissociation constant for ‘type II’ receptor-ouabain complexes was 7.6 · 10⁻⁹ M.Under similar experimental conditions, rat erythrocyte membranes exhibited only non-saturable sites.Alterations in the proportions of the two types of receptors were demonstrated by preincubation of the membranes, in the presence or absence of Mg²⁺ + P_i, prior to the addition of ouabain. In the first case, ‘type II receptor-ouabain’ complexes were stabilized at about 50% of the untreated membranes and ‘type I-ouabain’ complexes slowly approached equilibrium over a period of 24 h. In the latter instance, ‘type I’ receptors were not detected, and only ‘type II-ouabain’ complexes prevailed.     

Periovulatory changes in ovarian prostaglandin formation and their hormonal control in the rat

The concentration of prostaglandins of the E-group (PGE) and F-group (PGF) and the activity of prostaglandin-synthetase in rat ovaries increased on the evening of the day of proestrus and reached a peak at 5.00 h on the following morning, i.e. about the time of ovulation. Enzyme activity and PG concentrations receded to basal levels by 10.00 h on the day of estrus. These changes were prevented when the proestrous gonadotropin surge was blocked by administration of nembutal, and could be restored by administration of either LH or of FSH freed of LH contamination. The spontaneous preovulatory rise in prostaglandin concentration was about 6-fold for PGF and 30-fold for PGE, compared with values observed during the remainder of the cycle, whereas the rise in prostaglandin synthetase activity was only about 1.7-fold. The LH effect on PG accumulation had a latency of 2–4 h, which argues for enzyme synthesis rather than activation of preformed enzyme as the mechanism responsible. The small magnitude of the change in enzymic activity suggests that LH may, in addition, augment the availability of PG precursors. The results are compatible with the concept that prostaglandins play a physiological role in the gonadotropin-induced process of follicular rupture.     

The Mycobacterium tuberculosis Ku C-terminus is a multi-purpose arm for binding DNA and LigD and stimulating ligation

Bacterial non-homologous end joining requires the ligase, LigD and Ku. Ku finds the break site, recruits LigD, and then assists LigD to seal the phosphodiester backbone. Bacterial Ku contains a core domain conserved with eukaryotes but has a unique C-terminus that can be divided into a minimal C-terminal region that is conserved and an extended C-terminal region that varies in sequence and length between species. Here, we examine the role of Mycobacterium tuberculosis Ku C-terminal variants, where we removed either the extended or entire C-terminus to investigate the effects on Ku–DNA binding, rates of Ku-stimulated ligation, and binding affinity of a direct Ku–LigD interaction. We find that the extended C-terminus limits DNA binding and identify key amino acids that contribute to this effect through alanine-scanning mutagenesis. The minimal C-terminus is sufficient to stimulate ligation of double-stranded DNA, but the Ku core domain also contributes to stimulating ligation. We further show that wildtype Ku and the Ku core domain alone directly bind both ligase and polymerase domains of LigD. Our results suggest that Ku-stimulated ligation involves direct interactions between the Ku core domain and the LigD ligase domain, in addition to the extended Ku C-terminus and the LigD polymerase domain.     

PRIESSTESS: interpretable,high-performing models of the sequence and structure preferences of RNA-binding proteins

Modelling both primary sequence and secondary structure preferences for RNA binding proteins (RBPs) remains an ongoing challenge. Current models use varied RNA structure representations and can be difficult to interpret and evaluate. To address these issues, we present a universal RNA motif-finding/scanning strategy, termed PRIESSTESS (Predictive RBP-RNA InterpretablE Sequence-Structure moTif regrESSion), that can be applied to diverse RNA binding datasets. PRIESSTESS identifies dozens of enriched RNA sequence and/or structure motifs that are subsequently reduced to a set of core motifs by logistic regression with LASSO regularization. Importantly, these core motifs are easily visualized and interpreted, and provide a measure of RBP secondary structure specificity. We used PRIESSTESS to interrogate new HTR-SELEX data for 23 RBPs with diverse RNA binding modes and captured known primary sequence and secondary structure preferences for each. Moreover, when applying PRIESSTESS to 144 RBPs across 202 RNA binding datasets, 75% showed an RNA secondary structure preference but only 10% had a preference besides unpaired bases, suggesting that most RBPs simply recognize the accessibility of primary sequences.     

Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves

Predicting whether microbial invaders will colonize an environment is critical for managing natural and engineered ecosystems, and controlling infectious disease. Invaders often face competition by resident microbes. But how invasions play out in communities dominated by facilitative interactions is less clear. We previously showed that growth medium toxicity can promote facilitation between four bacterial species, as species that cannot grow alone rely on others to survive. Following the same logic, here we allowed other bacterial species to invade the four-species community and found that invaders could more easily colonize a toxic medium when the community was present. In a more benign environment instead, invasive species that could survive alone colonized more successfully when the residents were absent. Next, we asked whether early colonists could exclude future ones through a priority effect, by inoculating the invaders into the resident community only after its members had co-evolved for 44 weeks. Compared to the ancestral community, the co-evolved resident community was more competitive toward invaders and less affected by them. Our experiments show how communities may assemble by facilitating one another in harsh, sterile environments, but that arriving after community members have co-evolved can limit invasion success.Subject terms: Microbial ecology, Microbial ecology     

Interactions of the receptor for insulin-like growth factor II with mannose-6-phosphate and antibodies to the mannose-6-phosphate receptor

Recently, the sequence of the human receptor for insulin-like growth factor II (IGF-II) was found to be 80% identical [Morgan et al., (1987) Nature 329, 301-307] to the sequence of a partial clone of the bovine cation-independent mannose-6-phosphate receptor [Lobel et al., (1987) Proc. Natl. Acad. Sci. USA 84, 2233-2237]. In the present study, the purified receptor for insulin-like growth factor II (IGF-II) was found to react with two different polyclonal antibodies to the purified mannose-6-phosphate receptor. Moreover, mannose-6-phosphate was found to stimulate the binding of labeled IGF-II to the IGF-II receptor by two-fold. This effect had the same specificity and affinity as the reported binding of mannose-6-phosphate to its receptor; mannose-1-phosphate and mannose had no effect on the binding of labeled IGF-II to its receptor, and the half-maximally effective concentration of mannose-6-phosphate was 0.3 mM. Also, mannose-6-phosphate did not affect labeled IGF-II binding to the insulin receptor. These results support the hypothesis that a single protein of Mr-250,000 binds both IGF-II and mannose-6-phosphate. Furthermore, they indicate that mannose-6-phosphate can modulate the interaction of IGF-II to its receptor.     

Serpentine soils promote ectomycorrhizal fungal diversity

Serpentine soils impose physiological stresses that limit plant establishment and diversity. The degree to which serpentine soils entail constraints on other organisms is, however, poorly understood. Here, I investigate the effect of serpentine soils on ectomycorrhizal (ECM) fungi by conducting a reciprocal transplant experiment, where serpentine and nonserpentine ECM fungal communities were cultured in both their native and non-native soils. Contrary to expectation, serpentine soils hosted higher fungal richness compared to nonserpentine, and most species were recovered from serpentine soil, suggesting ECM fungi are not overall specialized or strongly affected by serpentine edaphic constraints.     

Patent protection for structural genomics-related inventions

Recently there have been some important developments with respect to the patentability of inventions in the field of structural genomics. The leaders of the European Patent Office (EPO), Japan Patent Office (JPO) and the United States Patent Office (USPTO) came together for a trilateral meeting to conduct a comparative study on protein 3-dimensional (3-D) structure related claims in an effort to come to a mutual understanding about the examination of such inventions. The three patent offices were presented with eight different cases: 1) 3-D structural data of a protein per se; 2) computer-readable storage medium encoded with structural data of a protein; 3) protein defined by its tertiary structure; 4) crystals of known proteins; 5) binding pockets and protein domains; 6) and 7) are both directed to in silico screening methods directed to a specific protein; and 8) pharmacophores. The preliminary conclusions reached at the trilateral meeting provide clarity regarding the types of inventions that may be patentable given a specific set of scientific facts in a patent application. Therefore, the guidance provided by this study will help inventors, attorneys and other patent practitioners who file for patent protection on structural genomics-based inventions both here and abroad comply with the patentability requirements of each office.Abbreviations: (Not Applicable)