Tracing silicate weathering processes in the permafrost-dominated Lena River watershed using lithium isotopes

Increasing global temperatures are causing widespread changes in the Arctic, including permafrost thawing and altered freshwater inputs and trace metal and carbon fluxes into the ocean and atmosphere. Changes in the permafrost active layer thickness can affect subsurface water flow-paths and water-rock interaction times, and hence weathering processes. Riverine lithium isotope ratios (reported as δ7Li) are tracers of silicate weathering that are unaffected by biological uptake, redox, carbonate weathering and primary lithology. Here we use Li isotopes to examine silicate weathering processes in one of the largest Russian Arctic rivers: the Lena River in eastern Siberia. The Lena River watershed is a large multi-lithological catchment, underlain by continuous permafrost. An extensive dataset of dissolved Li isotopic compositions of waters from the Lena River main channel, two main tributaries (the Aldan and Viliui Rivers) and a range of smaller sub-tributaries are presented from the post-spring flood/early-summer period at the onset of active layer development and enhanced water-rock interactions. The Lena River main channel (average δ7Lidiss ∼ 19‰) has a slightly lower isotopic composition than the mean global average of 23‰ (Huh et al., 1998a). The greatest range of [Li] and δ7Lidiss are observed in catchments draining the south-facing slopes of the Verkhoyansk Mountain Range. South-facing slopes in high-latitude, permafrost-dominated regions are typically characterised by increased summer insolation and higher daytime temperatures relative to other slope aspects. The increased solar radiation on south-facing catchments promotes repeated freeze-thaw cycles, and contributes to more rapid melting of snow cover, warmer soils, and increased active layer thaw depths. The greater variability in δ7Li and [Li] in the south-facing rivers likely reflect the greater infiltration of melt water and enhanced water-rock interactions within the active layer. A similar magnitude of isotopic fractionation is observed between the low-lying regions of the Central Siberian Plateau (and catchments draining into the Viliui River), and catchments draining the Verkhoyansk Mountain Range into the Aldan River. This is in contrast to global rivers in non-permafrost terrains that drain high elevations or areas of rapid uplift, where high degrees of physical erosion promote dissolution of freshly exposed primary rock typically yielding low δ7Lidiss, and low-lying regions exhibit high riverine δ7Li values resulting from greater water-rock interaction and formation of secondary mineral that fractionates Li isotopes. Overall, the range of Li concentrations and δ7Lidiss observed within the Lena River catchment are comparable to global rivers located in temperate and tropical regions. This suggests that cryogenic weathering features specific to permafrost regions (such as the continual exposure of fresh primary minerals due to seasonal freeze-thaw cycles, frost shattering and salt weathering), and climate (temperature and runoff), are not a dominant control on δ7Li variations. Despite vastly different climatic and weathering regimes, the same range of riverine δ7Li values globally suggests that the same processes govern Li geochemistry – that is, the balance between primary silicate mineral dissolution and the formation (or exchange with) secondary minerals. This has implications for the use of δ7Li as a palaeo-weathering tracer for interpreting changes in past weathering regimes

The two C-terminal tyrosines stabilize occluded Na/K pump conformations containing Na or K ions

Interactions of the three transported Na ions with the Na/K pump remain incompletely understood. Na/K pump crystal structures show that the extended C terminus of the Na,K–adenosine triphosphatase (ATPase) α subunit directly contacts transmembrane helices. Deletion of the last five residues (KETYY in almost all Na/K pumps) markedly lowered the apparent affinity for Na activation of pump phosphorylation from ATP, a reflection of cytoplasmic Na affinity for forming the occluded E1P(Na3) conformation. ATPase assays further suggested that C-terminal truncations also interfere with low affinity Na interactions, which are attributable to extracellular effects. Because extracellular Na ions traverse part of the membrane’s electric field to reach their binding sites in the Na/K pump, their movements generate currents that can be monitored with high resolution. We report here electrical measurements to examine how Na/K pump interactions with extracellular Na ions are influenced by C-terminal truncations. We deleted the last two (YY) or five (KESYY) residues in Xenopus laevis α1 Na/K pumps made ouabain resistant by either of two kinds of point mutations and measured their currents as 10-mM ouabain–sensitive currents in Xenopus oocytes after silencing endogenous Xenopus Na/K pumps with 1 µM ouabain. We found the low affinity inhibitory influence of extracellular Na on outward Na/K pump current at negative voltages to be impaired in all of the C-terminally truncated pumps. Correspondingly, voltage jump–induced transient charge movements that reflect pump interactions with extracellular Na ions were strongly shifted to more negative potentials; this signals a several-fold reduction of the apparent affinity for extracellular Na in the truncated pumps. Parallel lowering of Na affinity on both sides of the membrane argues that the C-terminal contacts provide important stabilization of the occluded E1P(Na3) conformation, regardless of the route of Na ion entry into the binding pocket. Gating measurements of palytoxin-opened Na/K pump channels additionally imply that the C-terminal contacts also help stabilize pump conformations with occluded K ions

The Mechanism for RNA Recognition by ANTAR Regulators of Gene Expression

ANTAR proteins are widespread bacterial regulatory proteins that have RNA–binding output domains and utilize antitermination to control gene expression at the post-initiation level. An ANTAR protein, EutV, regulates the ethanolamine-utilization genes (eut) in Enterococcus faecalis. Using this system, we present genetic and biochemical evidence of a general mechanism of antitermination used by ANTARs, including details of the antiterminator structure. The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination. The ANTAR protein dimerizes and associates with its substrate RNA in response to signal-induced phosphorylation. Furthermore, bioinformatic searches using this conserved antiterminator motif identified many new ANTAR target RNAs in phylogenetically diverse bacterial species, some comprising complex regulons. Despite the unrelatedness of the species in which they are found, the majority of the ANTAR–associated genes are thematically related to nitrogen management. These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism

Bioinformatic Characterization of P-Type ATPases Encoded Within the Fully Sequenced Genomes of 26 Eukaryotes

P-type ATPases play essential roles in numerous processes, which in humans include nerve impulse propagation, relaxation of muscle fibers, secretion and absorption in the kidney, acidification of the stomach and nutrient absorption in the intestine. Published evidence suggests that uncharacterized families of P-type ATPases with novel specificities exist. In this study, the fully sequenced genomes of 26 eukaryotes, including animals, plants, fungi and unicellular eukaryotes, were analyzed for P-type ATPases. We report the organismal distributions, phylogenetic relationships, probable topologies and conserved motifs of nine functionally characterized families and 13 uncharacterized families of these enzyme transporters. We have classified these proteins according to the conventions of the functional and phylogenetic IUBMB-approved transporter classification system (www.tcdb.org, Saier et al. in Nucleic Acids Res 34:181–186, 2006; Nucleic Acids Res 37:274–278, 2009)

Properties and expression of Na+/K+-ATPase α-subunit isoforms in the brain of the swamp eel, Monopterus albus, which has unusually high brain ammonia tolerance

10.1371/journal.pone.0084298PLoS ONE812-POLN

Protein Phosphatase 2A Interacts with the Na+,K+-ATPase and Modulates Its Trafficking by Inhibition of Its Association with Arrestin

Background: The P-type ATPase family constitutes a collection of ion pumps that form phosphorylated intermediates during ion transport. One of the best known members of this family is the Na +,K +-ATPase. The catalytic subunit of the Na +,K +-ATPase includes several functional domains that determine its enzymatic and trafficking properties. Methodology/Principal Findings: Using the yeast two-hybrid system we found that protein phosphatase 2A (PP2A) catalytic C-subunit is a specific Na +,K +-ATPase interacting protein. PP-2A C-subunit interacted with the Na +,K +-ATPase, but not with the homologous sequences of the H +,K +-ATPase. We confirmed that the Na +,K +-ATPase interacts with a complex of A- and C-subunits in native rat kidney. Arrestins and G-protein coupled receptor kinases (GRKs) are important regulators of G-protein coupled receptor (GPCR) signaling, and they also regulate Na +,K +-ATPase trafficking through direct association. PP2A inhibits association between the Na +,K +-ATPase and arrestin, and diminishes the effect of arrestin on Na +,K +-ATPase trafficking. GRK phosphorylates the Na +,K +-ATPase and PP2A can at least partially reverse this phosphorylation. Conclusions/Significance: Taken together, these data demonstrate that the sodium pump belongs to a growing list of io

Understanding Communication Signals during Mycobacterial Latency through Predicted Genome-Wide Protein Interactions and Boolean Modeling

About 90% of the people infected with Mycobacterium tuberculosis carry latent bacteria that are believed to get activated upon immune suppression. One of the fundamental challenges in the control of tuberculosis is therefore to understand molecular mechanisms involved in the onset of latency and/or reactivation. We have attempted to address this problem at the systems level by a combination of predicted functional protein∶protein interactions, integration of functional interactions with large scale gene expression studies, predicted transcription regulatory network and finally simulations with a Boolean model of the network. Initially a prediction for genome-wide protein functional linkages was obtained based on genome-context methods using a Support Vector Machine. This set of protein functional linkages along with gene expression data of the available models of latency was employed to identify proteins involved in mediating switch signals during dormancy. We show that genes that are up and down regulated during dormancy are not only coordinately regulated under dormancy-like conditions but also under a variety of other experimental conditions. Their synchronized regulation indicates that they form a tightly regulated gene cluster and might form a latency-regulon. Conservation of these genes across bacterial species suggests a unique evolutionary history that might be associated with M. tuberculosis dormancy. Finally, simulations with a Boolean model based on the regulatory network with logical relationships derived from gene expression data reveals a bistable switch suggesting alternating latent and actively growing states. Our analysis based on the interaction network therefore reveals a potential model of M. tuberculosis latency