Craig Gatto

Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins

MicroRNAs (miRs) are small non-coding RNAs that generally function as negative regulators of target messenger RNAs (mRNAs) at the posttranscriptional level. MiRs bind to the 3′UTR of target mRNAs through complementary base pairing, resulting in target mRNA cleavage or translation repression. To date, over 15,000 distinct miRs have been identified in organisms ranging from viruses to man, and interest in miR research continues to intensify. Of note, the most enlightening aspect of miR function – the mRNAs they target – continues to be elusive. Descriptions of the molecular origins of independent miR molecules currently support the hypothesis that miR hairpin generation is based on the adjacent insertion of two related transposable elements (TEs) at one genomic locus. Thus transcription across such TE interfaces establishes many, if not the majority of functional miRs. The implications of these findings are substantial for understanding how TEs confer increased genomic fitness, describing miR transcriptional regulations, and making accurate miR target predictions. In this work, we have performed a comprehensive analysis of the genomic events responsible for the formation of all currently annotated miR loci. We find that the connection between miRs and transposable elements is more significant than previously appreciated, and more broadly, supports an important role for repetitive elements in miR origin, expression and regulatory network formation. Further, we demonstrate the utility of these findings in miR target prediction. Our results greatly expand the existing repertoire of defined miR origins, detailing the formation of 2,392 of 15,176 currently recognized miR genomic loci and supporting a mobile genetic element model for the genomic establishment of functional miRs.

Altered Na+ transport after an intracellular α-subunit deletion reveals strict external sequential release of Na+ from the Na/K pump

The Na/K pump actively exports 3 Na+ in exchange for 2 K+ across the plasmalemma of animal cells. As in other P-type ATPases, pump function is more effective when the relative affinity for transported ions is altered as the ion binding sites alternate between opposite sides of the membrane. Deletion of the five C-terminal residues from the α-subunit diminishes internal Na+ (Nai+) affinity ≈25-fold [Morth et al. (2007) Nature 450:1043–1049]. Because external Na+ (Nao+) binding is voltage-dependent, we studied the reactions involving this process by using two-electrode and inside-out patch voltage clamp in normal and truncated (ΔKESYY) Xenopus-α1 pumps expressed in oocytes. We observed that ΔKESYY (i) decreased both Nao+ and Nai+ apparent affinities in the absence of Ko+, and (ii) did not affect apparent Nao+ affinity at high Ko+. These results support a model of strict sequential external release of Na+ ions, where the Na+-exclusive site releases Na+ before the sites shared with K+ and the ΔKESYY deletion only reduces Nao+ affinity at the shared sites. Moreover, at nonsaturating Ko+, ΔKESYY induced an inward flow of Na+ through Na/K pumps at negative potentials. Guanidinium+ can also permeate truncated pumps, whereas N-methyl-D-glucamine cannot. Because guanidiniumo+ can also traverse normal Na/K pumps in the absence of both Nao+ and Ko+ and can also inhibit Na/K pump currents in a Na+-like voltage-dependent manner, we conclude that the normal pathway transited by the first externally released Na+ is large enough to accommodate guanidinium+.

FabH selectivity for anteiso branched-chain fatty acid precursors in low-temperature adaptation in Listeria monocytogenes.

Gram-positive bacteria, including Listeria monocytogenes, adjust membrane fluidity by shortening the fatty acid chain length and increasing the proportional production of anteiso fatty acids at lower growth temperatures. The first condensation reaction in fatty acid biosynthesis is carried out by beta-ketoacyl-acyl carrier protein synthase III (FabH), which determines the type of fatty acid produced in bacteria. Here, we measured the initial rates of FabH-catalyzed condensation of malonyl-acyl carrier protein and alternate branched-chain precursor acyl-CoAs utilizing affinity-purified His-tagged L. monocytogenes FabH heterologously expressed in Escherichia coli. Listeria monocytogenes FabH showed a preference for 2-methylbutyryl-CoA, the precursor of odd-numbered anteiso fatty acids, at 30 degrees C, which was further increased at a low temperature (10 degrees C), suggesting that temperature-dependent substrate selectivity of FabH underlies the increased formation of anteiso branched-chain fatty acids during low-temperature adaptation. The increased FabH preferential condensation of 2-methylbutyryl-CoA could not be attributed to a significantly higher availability of this fatty acid precursor as acyl-CoA pool levels were reduced similarly for all fatty acid precursors at low temperatures.

Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations

The Na/K pump is a P-type ATPase that exchanges three intracellular Na+ ions for two extracellular K+ ions through the plasmalemma of nearly all animal cells. The mechanisms involved in cation selection by the pumps ion-binding sites (site I and site II bind either Na+ or K+; site III binds only Na+) are poorly understood. We studied cation selectivity by outward-facing sites (high K+ affinity) of Na/K pumps expressed in Xenopus oocytes, under voltage clamp. Guanidinium+, methylguanidinium+, and aminoguanidinium+ produced two phenomena possibly reflecting actions at site III: (i) voltage-dependent inhibition (VDI) of outwardly directed pump current at saturating K+, and (ii) induction of pump-mediated, guanidinium-derivative–carried inward current at negative potentials without Na+ and K+. In contrast, formamidinium+ and acetamidinium+ induced K+-like outward currents. Measurement of ouabain-sensitive ATPase activity and radiolabeled cation uptake confirmed that these cations are external K+ congeners. Molecular dynamics simulations indicate that bound organic cations induce minor distortion of the binding sites. Among tested metals, only Li+ induced Na+-like VDI, whereas all metals tested except Na+ induced K+-like outward currents. Pump-mediated K+-like organic cation transport challenges the concept of rigid structural models in which ion specificity at site I and site II arises from a precise and unique arrangement of coordinating ligands. Furthermore, actions by guanidinium+ derivatives suggest that Na+ binds to site III in a hydrated form and that the inward current observed without external Na+ and K+ represents cation transport when normal occlusion at sites I and II is impaired. These results provide insights on external ion selectivity at the three binding sites.

The reactive nitrogen species peroxynitrite is a potent inhibitor of renal Na-K-ATPase activity

Peroxynitrite is a reactive nitrogen species produced when nitric oxide and superoxide react. In vivo studies suggest that reactive oxygen species and, perhaps, peroxynitrite can influence Na-K-ATPase function. However, the direct effects of peroxynitrite on Na-K-ATPase function remain unknown. We show that a single bolus addition of peroxynitrite inhibited purified renal Na-K-ATPase activity, with IC50 of 107+/-9 microM. To mimic cellular/physiological production of peroxynitrite, a syringe pump was used to slowly release (approximately 0.85 microM/s) peroxynitrite. The inhibition of Na-K-ATPase activity induced by this treatment was similar to that induced by a single bolus addition of equal cumulative concentration. Peroxynitrite produced 3-nitrotyrosine residues on the alpha, beta, and FXYD subunits of the Na pump. Interestingly, the flavonoid epicatechin, which prevented tyrosine nitration, was unable to blunt peroxynitrite-induced ATPase inhibition, suggesting that tyrosine nitration is not required for inhibition. Peroxynitrite led to a decrease in iodoacetamidofluorescein labeling, implying that cysteine modifications were induced. Glutathione was unable to reverse ATPase inhibition. The presence of Na+ and low MgATP during peroxynitrite treatment increased the IC50 to 145+/-10 microM, while the presence of K+ and low MgATP increased the IC50 to 255+/-13 microM. This result suggests that the EPNa conformation of the pump is slightly more sensitive to peroxynitrite than the E(K) conformation. Taken together, these results show that peroxynitrite is a potent inhibitor of Na-K-ATPase activity and that peroxynitrite can induce amino acid modifications to the pump.

Nuclear Na+/K+-ATPase plays an active role in nucleoplasmic Ca2+ homeostasis

Summary Na+/K+-ATPase, an integral membrane protein, has been studied for over a half century with respect to its transporter function in the plasma membrane, where it expels three Na+ ions from the cell in exchange for two K+ ions. In this study, we demonstrate a functioning Na+/K+-ATPase within HEK293 cell nuclei. This subcellular localization was confirmed by western blotting, ouabain-sensitive ATPase activity of the nuclear membrane fraction, immunocytochemistry and delivery of fluorescently tagged Na+/K+-ATPase &agr;- and &bgr;-subunits. In addition, we observed an overlap between nuclear Na+/K+-ATPase and Na/Ca-exchanger (NCX) when nuclei were immunostained with commercially available Na+/K+-ATPase and NCX antibodies, suggesting a concerted physiological coupling between these transporters. In keeping with this, we observed an ATP-dependent, strophanthidin-sensitive Na+ flux into the nuclear envelope (NE) lumen loaded with the Na-sensitive dye, CoroNa-Green. Analogous experiments using Fluo-5N, a low affinity Ca2+ indicator, demonstrated a similar ATP-dependent and strophanthidin-sensitive Ca2+ flux into the NE lumen. Our results reveal an intracellular physiological role for the coordinated efforts of the Na+/K+-ATPase and NCX to actively remove Ca2+ from the nucleoplasm into the NE lumen (i.e. the nucleoplasmic reticulum).

Influence of Fatty Acid Precursors, Including Food Preservatives, on the Growth and Fatty Acid Composition of Listeria monocytogenes at 37 and 10°C

ABSTRACT Listeria monocytogenes is a food-borne pathogen that grows at refrigeration temperatures and increases its content of anteiso-C15:0 fatty acid, which is believed to be a homeoviscous adaptation to ensure membrane fluidity, at these temperatures. As a possible novel approach for control of the growth of the organism, the influences of various fatty acid precursors, including branched-chain amino acids and branched- and straight-chain carboxylic acids, some of which are also well-established food preservatives, on the growth and fatty acid composition of the organism at 37°C and 10°C were studied in order to investigate whether the organism could be made to synthesize fatty acids that would result in impaired growth at low temperatures. The results indicate that the fatty acid composition of L. monocytogenes could be modulated by the feeding of branched-chain amino acid, C4, C5, and C6 branched-chain carboxylic acid, and C3 and C4 straight-chain carboxylic acid fatty acid precursors, but the growth-inhibitory effects of several preservatives were independent of effects on fatty acid composition, which were minor in the case of preservatives metabolized via acetyl coenzyme A. The ability of a precursor to modify fatty acid composition was probably a reflection of the substrate specificities of the first enzyme, FabH, in the condensation of primers of fatty acid biosynthesis with malonyl acyl carrier protein.

A tomato ER-type Ca2+-ATPase, LCA1, has a low thapsigargin-sensitivity and can transport manganese

Recombinant Ca(2+)-ATPase from tomato (i.e. LCA1 for Lycopersicon esculentum [Since the identification and naming of LCA1, the scientific name for the tomato has been changed to Solanum lycopersicum.] Ca-ATPase) was heterologously expressed in yeast for structure-function characterization. We investigate the differences between plant and animal Ca pumps utilizing comparisons between chicken and rabbit SERCA-type pumps with Arabidopsis (ECA1) and tomato plant (LCA1) Ca(2+)-ATPases. Enzyme function was confirmed by the ability of each Ca(2+)-ATPase to rescue K616 growth on EGTA-containing agar and directly via in vitro ATP hydrolysis. We found LCA1 to be approximately 300-fold less sensitive to thapsigargin than animal SERCAs, whereas ECA1 was thapsigargin-resistant. LCA1 showed typical pharmacological sensitivities to cyclopiazonic acid, vanadate, and eosin, consistent with it being a P(IIA)-type Ca(2+)-ATPase. Possible amino acid changes responsible for the reduced plant thapsigargin-sensitivity are discussed. We found that LCA1 also complemented K616 yeast growth in the presence of Mn(2+), consistent with moving Mn(2+) into the secretory pathway and functionally compensating for the lack of secretory pathway Ca-ATPases (SPCAs) in plants.

Sodium and Proton Effects on Inward Proton Transport through Na/K Pumps

The Na/K pump hydrolyzes ATP to export three intracellular Na (Nai) as it imports two extracellular K (Ko) across animal plasma membranes. Within the protein, two ion-binding sites (sites I and II) can reciprocally bind Na or K, but a third site (site III) exclusively binds Na in a voltage-dependent fashion. In the absence of Nao and Ko, the pump passively imports protons, generating an inward current (IH). To elucidate the mechanisms of IH, we used voltage-clamp techniques to investigate the [H]o, [Na]o, and voltage dependence of IH in Na/K pumps from ventricular myocytes and in ouabain-resistant pumps expressed in Xenopus oocytes. Lowering pHo revealed that Ho both activates IH (in a voltage-dependent manner) and inhibits it (in a voltage-independent manner) by binding to different sites. Nao effects depend on pHo; at pHo where no Ho inhibition is observed, Nao inhibits IH at all concentrations, but when applied at pHo that inhibits pump-mediated current, low [Na]o activates IH and high [Na]o inhibits it. Our results demonstrate that IH is a property inherent to Na/K pumps, not linked to the oocyte expression environment, explains differences in the characteristics of IH previously reported in the literature, and supports a model in which 1), protons leak through site III; 2), binding of two Na or two protons to sites I and II inhibits proton transport; and 3), pumps with mixed Na/proton occupancy of sites I and II remain permeable to protons.

Divalent cation interactions with Na,K-ATPase cytoplasmic cation sites: implications for the para-nitrophenyl phosphatase reaction mechanism.

The interactions of divalent cations with the adenosine triphosphatase (ATPase) and para-nitrophenyl phosphatase (pNPPase) activity of the purified dog kidney Na pump and the fluorescence of fluorescein isothiocyanate (FITC)-labeled pump were determined. Sr2+ and Ba2+ did not compete with K+ for ATPase (an extracellular K+ effect). Sr2+ and Ba2+ did compete with Na+ for ATPase (an intracellular Na+ effect) and with K+ for pNPPase (an intracellular K+ effect). These results suggest that Ba2+ or Sr2+ can bind to the intracellular transport site, yet neither Ba2+ nor Sr2+ was able to activate pNPPase activity; we confirmed that Ca2+ and Mn2+ did activate. As another measure of cation binding, we observed that Ca2+ and Mn2+, but not Ba2+, decreased the fluorescence of the FITC-labeled pump; we confirmed that K+ substantially decreased the fluorescence. Interestingly, Ba2+ did shift the K+ dose-response curve. Ethane diamine inhibited Mn2+ stimulation of pNPPase (as well as K+ and Mg2+ stimulation) but did not shift the 50% inhibitory concentration (IC50) for the Mn2+-induced fluorescence change of FITC, though it did shift the IC50 for the K+-induced change. These results suggest that the Mn2+-induced fluorescence change is not due to Mn2+ binding at the transport site. The drawbacks of models in which Mn2+ stimulates pNPPase by binding solely to the catalytic site vs. those in which Mn2+ stimulates by binding to both the catalytic and transport sites are presented. Our results provide new insights into the pNPPase kinetic mechanism as well as how divalent cations interact with the Na pump.