Maturation of the yeast plasma membrane [H+]ATPase involves phosphorylation during intracellular transport.

In this study we show that the plasma membrane [H+]ATPase of Saccharomyces cerevisiae is phosphorylated on multiple Ser and Thr residues in vivo. Phosphorylation occurs during the movement of newly synthesized ATPase from the ER to the cell surface, as revealed by the analysis of temperature-sensitive sec mutants blocked at successive steps of the secretory pathway. Two-dimensional phosphopeptide analysis of the ATPase indicates that, although most sites are phosphorylated at or before arrival in secretory vesicles, some phosphopeptides are unique to the plasma membrane. Phosphorylation of plasma membrane-specific site(s) is associated with increased ATPase activity during growth on glucose. Upon glucose starvation, dephosphorylation occurs concomitantly with a decrease in enzymatic activity, and both are rapidly reversed (within 2 min) upon readdition of glucose. We suggest that reversible, site-specific phosphorylation serves to adjust ATPase activity in response to nutritional signals.

The sequence of the human genome.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Metabolic modulation of stoichiometry in a proton pump.

The current-voltage characteristics of the ATP-dependent proton pump in the plasma membrane of Neurospora have been explored under varied metabolic conditions imposed by mutation and by differential respiratory inhibition. The reversal potential, or presumed equilibrium potential, for the pump was observed at about -400 mV under energy-replete conditions, and at about -200 mV during a stable metabolic downshift of 55 percent. Steady-state levels of adenine nucleotides and inorganic phosphate, however, were not affected by this partial energy restriction, so that under both normal and restricted conditions the apparent free energy of ATP hydrolysis remained near -500 mV. The results suggest that a normal pump stoichiometry of 1 H+ extruded/1 ATP split is modified to 2 H+/1 ATP, by chronic energy restriction.

Genetic regulation of phosphate transport system II in Neurospora.

Phosphate transport system II, previously shown to be responsible for high-affinity phosphate uptake under conditions of phosphorus starvation, is regulated by at least three genes: pcon-nuc-2, preg, and nuc-1. nuc-1 and nuc-2 mutants cannot be derepressed for phosphate transport system II, while pconc and pregc mutants are partially constitutive.

Kinetics and pH-dependence of glycine-proton symport in Saccharomyces cerevisiae.

Interactions between intracellular pH (pHi) and H+-coupled transmembrane transport of glycine have been studied by means of 31P-NMR, using both aerobic and 'energy starved' cells of the yeast Saccharomyces cerevisiae. The general features of glycine transport in the yeast strain used (NCYC 239) are similar to those already reported for Saccharomyces carlsbergensis and S. cerevisiae, there being two kinetically distinct glycine uptake systems, with pH-independent K1/2 values near 14 and 0.4mM, respectively, but pH-dependent maximal velocities. Glycine transport itself has no measurable effect on pHi in aerobic cells, and only a marginal effect in energy-starved cells, but changes of pHi, imposed by extracellular addition of butyric acid, strongly influence glycine transport. Indeed, the dependence of glycine influx (in energy-starved cells) upon cytoplasmic H+ concentration appears to be third order, showing Hill slopes of 2.7-3.0. A crucial kinetic role for cytoplasmic pH in glycine transport is further indicated by a proportionality between the decline of flux and the decline of pHi produced by various metabolic inhibitors and uncouplers. Extracellular pH (pHo), by contrast, has only a weak effect on glycine influx, showing a Hill slope of 0.5. The major observations can be accommodated by a simple cyclic carrier scheme, in which 2 or more protons are transported along with glycine, but only one extracellular proton binding site dissociates in the testing range, with a pK near 5.5. The model requires a finite membrane potential, which must be somewhat sensitive to both pHi and pHo, and accommodates the discrepancy between measured net proton flux (one per glycine) and the kinetically required proton flux (two or more per glycine) by shunting through other proton-conducting pathways in the yeast membrane.

Small lipid-soluble cations are not membrane voltage probes for Neurospora or Saccharomyces.

Small lipid-soluble cations, such as tetraphenylphosphonium (TPP+) and tetraphenylarsonium (TPA+) are frequently used as probes of membrane voltage (delta psi, or Vm) for small animal cells, organelles, and vesicles. Because much controversy has accompanied corresponding measurements on 'walled' eukaryotic cells (plants, fungi), we studied their transport and relation to Vm in the large-celled fungus Neurospora crassa-where Vm can readily be determined with microelectrodes-as well as in the most commonly used model eukaryotic cell, the yeast Saccharomyces cerevisiae. We found no reasonable conditions under which the distribution of TPP+ or TPA+, between the cytoplasm (i) and extracellular solution (o), can serve to estimate Vm, even roughly, in either of these organisms. When applied at probe concentrations (i.e., < or = 100 microM, which did not depolarize the cells nor deplete ATP), TPP+ stabilized at ratios (i/o) below 30 in both organisms. That would imply apparent Vm values positive to -90 mV, in the face of directly measured Vm values (in Neurospora) negative to -180 mV. When applied at moderate or high concentrations (1-30 mM), TPP+ and TPA+ induced several phases of depolarization and changes of membrane resistance (Rm), as well as depletion of cytoplasmic energy stores. Only the first phase depolarization, occurring within the perfusion-turnover time and accompanied by a nearly proportionate decline of Rm, could have resulted from TPP+ or TPA+ currents per se. And the implied currents were small. Repeated testing, furthermore, greatly reduced the depolarizing effects of these lipid-soluble ions, implicating an active cellular response to decrease membrane permeability.

Cation effluxes associated with the uptake of TPP+, TPA+, and TPMP+ by Neurospora: evidence for a predominantly electroneutral influx process.

Previously observed anomalies in the transport of lipid-soluble cations (LSI's) - presumed voltage-probe ions-by intact fungal cells [1] prompted a systematic investigation of ion exchanges induced by high (millimolar) concentrations of the particular species tetraphenylphosphonium ion (TPP+), tetraphenylarsonium ion (TPA+), and triphenylmethylphosphonium ion (TPMP+). With low extracellular free Ca2+ (no calcium added to the medium), influx of the LSI's was biphasic, indicating rapid entry into the cytoplasm followed by sequestration into a subcompartment. The latter process, especially, was strongly inhibited by extracellular Ca2+ (1 mM). Contrary to the expectation for electrophoretically driven entry of LSI's into fungal cells, no major efflux of protons (acidification of the medium) could be measured; in fact, significant alkalinization of the medium was observed. The major cellular inorganic cations, K+ or Na+ (under different conditions), were released during LSI uptake, but with kinetic behavior which clearly ruled out direct coupling to the uptake of TPP+, TPA+, or TPMP+. The major mechanism for entry of these lipid-soluble cations into Neurospora appears to be electroneutral diffusion in combination with one or more hydrophilic anions. Subsequent penetration of the fungal vacuoles would result in binding of LSI's to storage polyanions (viz., polyphosphate) and concomitant displacement of the normal vacuolar cations, such as basic amino acids and polyamines, thus leading to alkalinization of the extracellular medium. The observed effluxes of cytoplasmic K+ and Na+ should result independently from energetic changes (i.e., uncoupling of the mitochondrial) and are most easily described by simple, but asynchronous, changes in the average rate constants for entry and exit of the alkali-metal cations.

Stoichiometry of H+/amino acid cotransport in Neurospora crassa revealed by current-voltage analysis.

Coupling of ions to the uptake of neutral and basic amino acids via a general amino acid transport system (System II), was studied in a mutant of Neurospora crassa (bat mtr) which lacks other transport systems for these solutes. All amino acids tested--including ones bearing no net charge--elicited rapid membrane depolarization, as expected for ion-coupled transport. (Since amino acid transport in Neurospora is not dependent on extracellular Na+ or K+, the associated ion is presumed to be H+.) Although the 14C-labeled amino acid fluxes through System II are largely independent of the identity of the amino acid, the depolarization caused by basic amino acids (L-lysine and L-ornithine) is 60-70% greater than that for neutral amino acids (e.g. L-leucine). This difference is consistent with a constant H+/amino acid stoichiometry of 2, the extra charge for lysine and ornithine being that on the amino acid itself, so that the charge ratio basic:neutral amino acids is 3:2. When actual membrane charge flow associated with amino acid uptake was compared with measured 14C-labeled amino acid influx, ratios of 2.07 charges/mol L-leucine and 3.40 charges/mol L-lysine were obtained, again in accord with a constant translocation stoichiometry of 2H+/amino acid. The advantages of this electrical method for estimating H+/solute stoichiometry in cotransport are discussed in relation to more familiar methods.

"Action potentials" in Neurospora crassa, a mycelial fungus.

Occasional spontaneous "action potentials" are found in mature hyphae of the fungus Neurospora crassa. They can arise either from low-level sinusoidal oscillations of the membrane potential or from a linear slow depolarization which accelerates into a rapid upstroke at a voltage 5-20 mV depolarized from the normal resting potential (near-180 mV). The "action potentials" are long-lasting, 1-2 min and at the peak reach a membrane potential near-40 mV. A 2-to 8-fold increase of membrane conductance accompanies the main depolarization, but a slight decrease of membrane conductance occurs during the slow depolarization. Two plausible mechanisms for the phenomenon are (a) periodic increases of membrane permeability to inorganic ions, particularly H+ or Cl- and (b) periodic decreases in activity of the major electrogenic pump (H+) or the Neurospora membrane, coupled with a nonlinear (inverse signoid) current-boltage relationship. Identification of action potential-like disturbances in fungi means that such behavior has now been found in all major biologic taxa which have been probed with suitable electrodes. As yet there is no obvious function for the events in fungi.

Effects of inhibitors on the plasma membrane and mitochondrial adenosine triphosphatases of Neurospora crassa.

A comparative study has been made of the effects of a variety of inhibitors on the plasma membrane ATPase and mitochondrial ATPase of Neurospora crassa. The most specific inhibitors proved to be vanadate and diethylstilbestrol for the plasma membrane ATPase and azide, oligomycin, venturicidin, and leucinostatin for mitochondrial ATPase. N,N'-Dicyclohexylcarbodiimide, octylguanidine, triphenylsulfonium chloride, and quercetin and related bioflavonoids inhibited both enzymes, although with different concentration dependences. Other compounds that were tested (phaseolin, fusicoccin, deoxycorticosterone, alachlor, salicyclic acid, N-1-napthylphthalamate, triiodobenzoic acid, cyclic AMP, cyclic GMP, theobromine, theophylline, and histamine) had no significant effect on either enzyme. Overall, the results indicate that the plasma membrane and mitochondrial ATPases are distinct enzymes, in spite of the fact that they may play related roles in H+ transport across their respective membranes.

Phosphate transport in Neurospora. Derepression of a high-affinity transport system during phosphorus starvation.

In addition to the constitutive, low-affinity phosphate-transport system described previously, Neurospora possesses a second, high-affinity system which is derepressed during phosphorus starvation. At pH 5.8, System ii has a K1/2 of about 3muM and a Jmax of 5.2 mmol/1 cell water per min. System ii reaches maximal activity after about 2 h of growth in phosphorus-free minimal medium. Its formation is blocked by cycloheximide and, once made, it appears to turn over rapidly. Addition of cycloheximide to fully derepressed cultures results in the decay of System ii with a t1/2 of 14 min, very similar to the turnoacteriol. 95, 959-966) for tryptophan transport in Neurospora. Thus, these transport systems appear to be regulated by a balance between synthesis and breakdown, as affected by intracellular pools of substrate or related compounds.

N-terminal chimeric constructs improve the expression of sarcoplasmic reticulum Ca(2+)-ATPase in yeast.

Wild-type and chimeric constructs comprising rabbit sarcoplasmic reticulum (SR) Ca(2+)-ATPase and the N-terminal cytoplasmic portion of yeast plasma membrane H(+)-ATPase were expressed in yeast under control of a heat-shock regulated promoter. The wild-type ATPase was found predominantly in endoplasmic reticulum (ER) membranes. Addition of the first 88 residues of H(+)-ATPase to the Ca(2+)-ATPase N-terminal end promoted a marked shift in the localization of chimeric H(+)/Ca(2+)-ATPase which accumulated in a light membrane fraction associated with yeast smooth ER. Furthermore, there was a three-fold increase in the overall level of expression of chimeric H(+)/Ca(2+)-ATPase. Similar results were obtained for a chimeric Ca(2+)-ATPase containing a hexahistidine sequence added to its N-terminal end. Both H(+)/Ca(2+)-ATPase and 6xHis-Ca(2+)-ATPase were functional as demonstrated by their ability to form a phosphorylated intermediate and undergo fast turnover. Conversely, a replacement chimera in which the N-terminal end of SR Ca(2+)-ATPase was replaced by the corresponding segment of H(+)-ATPase was not stably expressed in yeast membranes. These results indicate that the N-terminal segment of Ca(2+)-ATPase plays an important role in enzyme assembly and contains structural determinants necessary for ER retention of the ATPase.

Cloning, sequence, and tissue distribution of a rabbit renal Na+/H+ exchanger transcript.

Rabbit kidney expresses a transcript that is similar to the human growth-factor-activatable Na+/H+ exchanger. PCR and library screening were used to clone overlapping 2.5 kb, 1.4 kb, and 1.8 kb cDNAs that together contain the entire coding region (2448 bp) and 5' untranslated region (726 bp) and part of the 3' untranslated region (128 bp) of a rabbit renal Na+/H+ exchanger transcript. The nucleotide and inferred amino acid sequences are highly conserved between rabbit and human (88% nucleotide identity, 95% amino acid identity). In rabbit, the transcript is expressed in both epithelial and non-epithelial tissues, with highest expression in stomach, brain, kidney, lung and ileum, and minimal expression in liver and skeletal muscle.

Net uptake of potassium in Neurospora. Exchange for sodium and hydrogen ions.

Net uptake of potassium by low K, high Na cells of Neurospora at pH 5.8 is accompanied by net extrusion of sodium and hydrogen ions. The amount of potassium taken up by the cells is matched by the sum of sodium and hydrogen ions lost, under a variety of conditions: prolonged preincubation, partial respiratory inhibition (DNP), and lowered [K](o). All three fluxes are exponential with time and obey Michaelis kinetics as functions of [K](o). The V(max) for net potassium uptake, 22.7 mmoles/kg cell water/min, is very close to that for K/K exchange reported previously (20 mmoles/kg cell water/min). However, the apparent K(m) for net potassium uptake, 11.8 mM [K](o), is an order of magnitude larger than the value (1 mM) for K/K exchange. It is suggested that a single transport system handles both net K uptake and K/K exchange, but that the affinity of the external site for potassium is influenced by the species of ion being extruded.

Potassium transport in Neurospora. Evidence for a multisite carrier at high pH.

At low extracellular pH (4-6), net uptake of potassium by Neurospora is a simple exponential process which obeys Michaelis kinetics as a function of [K](o). At high pH, however, potassium uptake becomes considerably more complex, and can be resolved into two distinct exponential components. The fast component (time constant = 1.2 min) is matched quantitatively by a rapid loss of sodium; it is attributed to ion exchange within the cell wall, since it is comparatively insensitive to low temperature and metabolic inhibitors. By contrast, the slower component (time constant = 10.9 min) is inhibited markedly at 0 degrees C and by CN and deoxycorticosterone, and is thought to represent carrier-mediated transport of potassium across the cell membrane. This transport process exhibits sigmoid kinetics as a function of [K](o); the data can be fitted satisfactorily by two different two-site models (one involving a carrier site and a modifier site, the other an allosteric model). Either of these models could also accommodate the simple Michaelis kinetics at low pH.

Control of intracellular pH. Predominant role of oxidative metabolism, not proton transport, in the eukaryotic microorganism Neurospora.

Recessed-tip microelectrodes were used to measure internal pH (pHi) in the fungus Neurospora, and to examine the response of pHi to several kinds of stress: changes of extracellular pH (pHo), inhibition of the principal proton pump in the plasma membrane, and inhibition of respiration. Under control conditions, at pHo = 5.8, pHi in Neurospora is 7.19 +/- 0.04. Changes of pHo between 3.9 and 9.3 affect pHi linearly but with a slope of only approximately 0.1 unit pHi per unit pHo, stable pHi being reached within 3 min of changed pHo. Despite a postulated high passive permeability of the Neurospora membrane to protons (Slayman, 1970), neither active nor passive H+ transport appears critical to pHi because (alpha) specific inhibition of the proton pump by orthovanadate has little effect on pHi, and (b) cytoplasmic acidification produced by respiratory blockade is unaffected by the size or direction of proton gradient. To convert measured changes in pHi into net proton fluxes, intracellular buffering capacity (beta i) was measured by the weak acid/weak base technique. At pHi = 7.2, beta i was (-) 35 mmol H+ (liter cell water)-1 (pH unit)-1, but beta i increased substantially in both the acid and alkaline directions, which suggests that amino acid side chains are the principal source of buffer.

A potassium-proton symport in Neurospora crassa.

Combined ion flux and electrophysiological measurements have been used to characterized active transport of potassium by cells of Neurospora crassa that have been moderately starved of K+ and then maintained in the presence of millimolar free calcium ions. These conditions elicit a high-affinity (K1/2 = 1-10 microM) potassium uptake system that is strongly depolarizing. Current-voltage measurements have demonstrated a K+-associated inward current exceeding (at saturation) half the total current normally driven outward through the plasma membrane proton pump. Potassium activity ratios and fluxes have been compared quantitatively with electrophysiological parameters, by using small (approximately 15 micron diam) spherical cells of Neurospora grown in ethylene glycol. All data are consistent with a transport mechanism that carries K ions inward by cotransport with H ions, which move down the electrochemical gradient created by the primary proton pump. The stoichiometry of entry is 1 K ion with 1 H ion; overall charge balance is maintained by pumped extrusion of two protons, to yield a net flux stoichiometry of 1 K+ exchanging for 1 H+. The mechanism is competent to sustain the largest stable K+ gradients that have been measured in Neurospora, with no direct contribution from phosphate hydrolysis or redox processes. Such a potassium-proton symport mechanism could account for many observations reported on K+ movement in other fungi, in algae, and in higher plants.

Isolation of an ion channel gene from Arabidopsis thaliana using the H5 signature sequence from voltage-dependent K+ channels.

A degenerate oligonucleotide corresponding to the K+ channel signature sequence (TMTTVGYGD) was used to isolate the genomic and cDNA forms of a new channel gene, AKT3, from Arabidopsis thaliana. The deduced protein sequence has a predicted membrane topography similar to Shaker-like K+ channels. Three distinct modules comprise the carboxyl-terminal half: a nucleotide-binding motif, an ankyrin repeat domain, and a polyglutamate track. Xenopus oocytes injected with cRNA exhibited an inward-rectifying K+ current, demonstrating that the AKT3 polypeptide is a functional transport protein. Two other Arabidopsis K+ transporters (AKT1 and KAT1) share 60% homology with AKT3; together these proteins constitute a family of plant inward-rectifying K+ channels.

NSC1: a novel high-current inward rectifier for cations in the plasma membrane of Saccharomyces cerevisiae.

The plasma membrane of the yeast Saccharomyces cerevisiae possesses a non-specific cation 'channel', tentatively dubbed NSC1, which is blocked by normal (mM) calcium and other divalent metal ions, is unblocked by reduction of extracellular free divalents below approximately 10 microM, and is independent of the identified potassium channel and porters in yeast, Duk1p, Trk1p, and Trk2p. Ion currents through NSC1, observed by means of whole-cell patch recording, have the following characteristics: Large amplitude, often exceeding 1 nA of K+/ cell at -200 mV, in tetraploid yeast, sufficient to double the normal intracellular K+ concentration within 10 s; non-saturation at large negative voltages; complicated activation kinetics, in which approximately 50% of the total current arises nearly instantaneously with a voltage-clamp step, while the remainder develops as two components, with time constants of approximately 100 ms and approximately 1.3 s; and voltage independence of both the activation time constants and the associated fractional current amplitudes.

The presumed potassium carrier Trk2p in Saccharomyces cerevisiae determines an H+-dependent, K+-independent current.

Ionic currents related to the major potassium uptake systems in Saccharomyces cerevisiae were examined by whole cell patch-clamping, under K+ replete conditions. Those currents have the following properties. They (1) are inward under all conditions investigated, (2) arise instantaneously with appropriate voltage steps, (3) depend solely upon the moderate affinity transporter Trk2p, not upon the high affinity transporter Trk1p. They (4) appear to be independent of the extracellular K+ concentration, (5) are also independent of extracellular Ca2+, Mg2+ and Cl- but (6) are strongly dependent on extracellular pH, being large at low pH (up to several hundred pA at -200 mV and pH 4) and near zero at high pH (above 7.5). They (7) increase in proportion to log[H+]o, rather than directly in proportion to the proton concentration and (8) behave kinetically as if each transporter cycle moved one proton plus one (high pH) or two (low pH) other ions, as yet unidentified. In view of background knowledge on K+ transport related to Trk2p, the new results suggest that the K+ status of yeast cells modulates both the kinetics of Trk2p-mediated transport and the identity of ions involved. That modulation could act either on the Trk2 protein itself or on interactions of Trk2 with other proteins in a hypothetical transporter complex. Structural considerations suggest a strong analogy to the KtrAB system in Vibrio alginolyticus and/or the TrkH system in Escherichia coli.