A survey of canine expressed sequence tags and a display of their annotations through a flexible web-based interface.

We have initially sequenced approximately 8,000 canine expressed sequence tags (ESTs) from several complementary DNA (cDNA) libraries: testes, whole brain, and Madin-Darby canine kidney (MDCK) cells. Analysis of these sequences shows that they provide partial sequence information for about 5%-10% of the canine genes. An analysis pipeline has been created to cluster the ESTs and to map individual ESTs as well as clustered ESTs to both the human genome and the human proteome. Gene ontology (GO) terms have been assigned to the ESTs and clusters based on their top matches to the International Protein Index (IPI) set of human proteins. The data generated is stored in a MySQL relational database for analysis and display. A Web-based Perl script has been written to display the analyzed data to the scientific community.

K(+)-channel transgenes reduce K(+) currents in Paramecium, probably by a post-translational mechanism.

PAK11 is 1 of more than 15 members in a gene family that encodes K(+)-channel pore-forming subunits in Paramecium tetraurelia. Microinjection of PAK11 DNA into macronuclei of wild-type cells results in clonal transformants that exhibit hyperexcitable swimming behaviors reminiscent of certain loss-of-K(+)-current mutants. PAK2, a distant homolog of PAK11, does not have the same effect. But PAK1, a close homolog of PAK11, induces the same hyperexcitability. Cutting the PAK11 open reading frame (ORF) with restriction enzymes before injection removes this effect entirely. Microinjection of PAK11 ORF flanked by the calmodulin 5' and 3' UTRs also induces the same hyperexcitable phenotype. Direct examination of transformed cells under voltage clamp reveals that two different Ca(2+)-activated K(+)-specific currents are reduced in amplitude. This reduction does not correlate with a deficit of PAK11 message, since RNA is clearly produced from the injected transgenes. Insertion of a single nucleotide at the start of the PAK11 ORF does not affect the RNA level but completely abolishes the phenotypic transformation. Thus, the reduction of K(+) currents by the expression of the K(+)-channel transgenes reported here is likely to be the consequence of a post-translational event. The complexity of behavioral changes, possible mechanisms, and implications in Paramecium biology are discussed.

A two-cell biosensor that couples neuronal cells to optically monitored fish chromatophores.

A two-cell biosensor was developed that uses optically detected changes in naturally colored fish chromatophores to measure the neurosecretory output of mammalian neuronal cells. The specific version of the biosensor described here is a continuous flow device that places red-pigmented, dendritic erythrophore cells directly downstream of an immobilized population of PC12 neuronal cells, a well-established model cell-line having neuroendocrine function. Agents known to stimulate catecholamine neurosecretion (secretagogues) were presented to the PC12 cells. It was found that the varying level of neurosecretion from the PC12 cells was measurable by judging the degree of pigment aggregation in the erythrophores. Increases in catecholamine secretion and consequent pigment aggregation were observed for several known secretagogues, including receptor agonists (ATP, acetylcholine), membrane depolarizing agents (high K(+) concentration), and specific neurotoxins (black widow spider venom, alpha-latrotoxin). This particular two-cell biosensor, which is applicable to the detection of any agents that affect the levels of catecholamine secretion from PC12 cells, demonstrates the general principle that the breadth of sensitivity of a biosensor is increased by employing coupled cell types.

Isolation and characterization of magbane, a magnesium-lethal mutant of paramecium.

Discerning the mechanisms responsible for membrane excitation and ionic control in Paramecium has been facilitated by the availability of genetic mutants that are defective in these pathways. Such mutants typically are selected on the basis of behavioral anomalies or resistance to ions. There have been few attempts to isolate ion-sensitive strains, despite the insights that might be gained from studies of their phenotypes. Here, we report isolation of "magbane," an ion-sensitive strain that is susceptible to Mg2+. Whereas the wild type tolerated the addition of > or =20 mm MgCl2 to the culture medium before growth was slowed and ultimately suppressed (at >40 mm), mgx mutation slowed growth at 10 mm. Genetic analysis indicated that the phenotype resulted from a recessive single-gene mutation that had not been described previously. We additionally noted that a mutant that was well described previously (restless) is also highly sensitive to Mg2+. This mutant is characterized by an inability to control membrane potential when extracellular K+ concentrations are lowered, due to inappropriate regulation of a Ca2+-dependent K+ current. However, comparing the mgx and rst mutant phenotypes suggested that two independent mechanisms might be responsible for their Mg2+ lethality. The possibility that mgx mutation may adversely affect a transporter that is required for maintaining low intracellular Mg2+ is considered.

The cloning and molecular analysis of pawn-B in Paramecium tetraurelia.

Pawn mutants of Paramecium tetraurelia lack a depolarization-activated Ca(2+) current and do not swim backward. Using the method of microinjection and sorting a genomic library, we have cloned a DNA fragment that complements pawn-B (pwB/pwB). The minimal complementing fragment is a 798-bp open reading frame (ORF) that restores the Ca(2+) current and the backward swimming when expressed. This ORF contains a 29-bp intron and is transcribed and translated. The translated product has two putative transmembrane domains but no clear matches in current databases. Mutations in the available pwB alleles were found within this ORF. The d4-95 and d4-96 alleles are single base substitutions, while d4-662 (previously pawn-D) harbors a 44-bp insertion that matches an internal eliminated sequence (IES) found in the wild-type germline DNA except for a single C-to-T transition. Northern hybridizations and RT-PCR indicate that d4-662 transcripts are rapidly degraded or not produced. A second 155-bp IES in the wild-type germline ORF excises at two alternative sites spanning three asparagine codons. The pwB ORF appears to be separated from a 5' neighboring ORF by only 36 bp. The close proximity of the two ORFs and the location of the pwB protein as indicated by GFP-fusion constructs are discussed.

Ca(2+) current-deficient pawn mutants are promoted to queens during chronic depolarization of Paramecium tetraurelia.

Chronic KCl-induced depolarization of Paramecium tetraurelia enhances Ca(2+)-dependent backward swimming behavior over a period of 8-24 hr. Here, we investigated the electrophysiological mechanisms underlying this adaptive phenomenon using voltage-clamp techniques. Cells that had been adapted to 20 mm KCl showed several significant changes in the properties of the Ca(2+) current that mediates ciliary reversal in Paramecium (I(Ca)), including a positive shift in voltage sensitivity and a significant slowing of inactivation. In seeking an explanation for these changes, we examined the effects of chronic depolarization on mutants that do not normally express a Ca(2+) current or swim backward. Surprisingly, pawn B mutant cells slowly regained the ability to reverse their cilia during KCl exposure with a time course that mirrored behavioral adaptation of the wild type. This behavior was accompanied by expression of a novel Ca(2+) current (I(QUEEN)) whose voltage sensitivity was shifted positive with respect to the wild-type Ca(2+) current and that was slow to inactivate. Coincidental expression of I(QUEEN) in the wild type during adaptation would readily explain the observed changes in I(Ca) kinetics. We also examined the effects of chronic depolarization on Dancer, a mutant suggested previously to have an I(Ca) inactivation defect. The mutant phenotype could be suppressed or exaggerated greatly by manipulating extracellular KCl concentration, suggesting that Dancer lesion instead causes inappropriate regulation of I(QUEEN).

Correlation between loss of a Mg2+ conductance and an adaptation defect in a mutant of Paramecium tetraurelia.

Paramecium tetraurelia responds to chronic KCl-induced depolarization by swimming backward, but the ciliate recovers within seconds and then undergoes a prolonged adaptation period during which sensitivity to external stimuli is altered radically. We examined the role of Mg2+ in this phenomenon, prompted by finding that mutations in the eccentric-A gene both suppressed a Mg(2+)-specific conductance and prevented adaptation. Adaptation of the wild type proceeded normally when extracellular Mg2+ was varied from 0-20 mM, however, suggesting that channel-mediated Mg2+ fluxes were not involved. In seeking alternative explanations for the eccentric mutant phenotype, we ascertained that there was an osmotic component to adaptation but that K(+)-induced depolarization was the primary stimulus. We also noted that wild-type and eccentric mutant cells depolarized by equivalent amounts in KCl, suggesting that the genetic lesion must lie downstream of membrane-potential change. We also examined whether the adaptation-induced behavioral changes and, indeed, the defect in eccentric might be explained in terms of Mg2+ and Na+ efflux during behavioral testing, but experimental observations failed to support this notion. Finally, we consider the possibility that eccentric gene mutation prevents adaptation by interfering with intracellular free Mg2+ homeostasis in Paramecium.

The cloning by complementation of the pawn-A gene in Paramecium.

The genetic dissection of a simple avoidance reaction behavior in Paramecium tetraurelia has shown that ion channels are a critical molecular element in signal transduction. Pawn mutants, for example, were originally selected for their inability to swim backward, a trait that has since been shown to result from the loss of a voltage-dependent calcium current. The several genes defined by this phenotype were anticipated to be difficult to clone since the 800-ploid somatic macronucleus of P. tetraurelia is a formidable obstacle to cloning by complementation. Nonetheless, when the macronucleus of a pawn mutant (pwA/pwA) was injected with total wild-type DNA or a fractional library of DNA, its clonal descendants all responded to stimuli like the wild type. By sorting a fractional library, we cloned and sequenced a 2.3-kb fragment that restores the Ca2+ current and excitability missing in pawn-A. Data from RNase protection assays, followed by the sequencing of mutant alleles and cDNA clones, established an open reading frame. The conceptually translated product suggests a novel protein that may be glycophosphatidylinositol anchored. We also discuss the general usefulness of this method in cloning other unknown DNA sequences from Paramecium that are functionally responsible for various mutant phenotypes.

Transmembrane Mg2+ currents and intracellular free Mg2+ concentration in Paramecium tetraurelia.

The properties of Mg2+ conductances in Paramecium tetraurelia were investigated under two-electrode voltage clamp. When bathed in physiological Mg2+ concentrations (0.5 mm), depolarizing steps from rest elicited a prominent Mg2+-specific current (IMg) that has been noted previously. The dependence of this current on extracellular Mg2+ approximated that of Mg2+-induced backward swimming, demonstrating that IMg contributes to normal membrane excitation and behavior in this ciliate. Closer analysis revealed that the Mg2+ current deactivated biphasically. While this might suggest the involvement of two Mg2+-specific pathways, both tail-current components were affected similarly by current-specific mutations and they had similar ion selectivities, suggesting a common pathway. In contrast, a Mg2+ current activated upon hyperpolarization could be separated into three components. The first, IMg, had similar properties to the current activated upon depolarization. The second was a nonspecific divalent cation current (INS) that was revealed following suppression of IMg by eccentric mutation. The final current was relatively minor and was revealed following suppression of IMg and INS by obstinate A gene mutation. Reversal-potential analyses suggested that IMg and INS define two intracellular compartments that contain, respectively, low (0.4 mM) and high (8 mM) concentrations of Mg2+. Measurement of intracellular free Mg2+ using the fluorescent dye, Mag-fura-2, suggested that bulk [Mg2+]i rests at around 0.4 mM in Paramecium.

Long-term adaptation of Ca2+-dependent behaviour in Paramecium tetraurelia.

Prolonged exposure to KCl has long been recognized to modify swimming behaviour in Paramecium tetraurelia, a phenomenon known as 'adaptation'. In this study, we have investigated behavioural adaptation systematically. A 24 h exposure to 30 mmol l-1 KCl deprived cells of the ability to respond behaviourally to two established chemoeffectors. We also explored the effects of 30 mmol l-1 KCl on the duration of backward swimming induced by Ba2+ and Mg2+. A brief (60 min) exposure prevented cells from swimming backwards in response to either cation, but recovery was rapid (<60 min) following a return to control medium. Prolonged (48 h) exposure caused a more persistent loss of response to Ba2+, so that several hours was now required for recovery. Surprisingly, responses to Mg2+ reappeared during 6-8 h in KCl, with backward swimming durations increasing to more than 300 % of control values after 26 h. Thus, we can distinguish two phases to adaptation. The short-term phase is characterized by an inability to respond behaviourally to most stimuli and might be adequately explained in terms of Ca2+ channel inactivation and K+-induced shifts in membrane potential. The long-term phase is characterized by enhanced responses to Mg2+ (and also to Na+), suggesting that a more extensive reprogramming of membrane excitability may occur during chronic K+-induced depolarization.

Oscillating response to a purine nucleotide disrupted by mutation in Paramecium tetraurelia.

The purine nucleotide GTP, when added extracellularly, induces oscillations in the swimming behaviour of the protist Paramecium tetraurelia. For periods as long as 10 min the cell swims backwards and forwards repetitively. The oscillations in swimming behaviour are driven by changes in membrane potential of the cell, which in turn are caused by periodic activation of inward Mg2+- and Na+-specific currents. We screened for and isolated mutants that are defective in this response, exploiting the fact that the net result of GTP on a population of cells is repulsion. One mutant, GTP-insensitive (gin A), is not repelled by GTP. In addition, GTP fails to induce repetitive backwards swimming in gin A mutants, although they swim backwards normally in response to other stimuli. GTP fails to evoke oscillations in membrane potential or Mg2+ and Na+ currents in the mutant, although the Mg2+ and Na+ conductances are not themselves measurably affected. A small, oscillating Ca2+ current induced by GTP in the wild type, which might be part of the mechanism that generates oscillations, is also missing from gin A cells. To our knowledge, gin A is the first example of a mutant defective in a purinergic response. We discuss the possibility that the gin A lesion affects the oscillator itself.

Phenotypic and genetic analysis of "Chameleon," a paramecium mutant with an enhanced sensitivity to magnesium.

Three mutant strains of Paramecium tetraurelia with an enhanced sensitivity to magnesium have been isolated. These new "Chameleon" mutants result from partial- or codominant mutations at a single locus, Cha. Whereas the wild type responded to 5 mM Mg2+ by swimming backward for 10-15 sec, Cha mutants responded with approximately 30 sec backward swimming. Electrophysiological analysis suggested that this behavior may be caused by slowing in the rate at which a Mg(2+)-specific ion conductance deactivates following membrane excitation. This would be consistent with an observed increase in the sensitivity of Cha mutants to nickel poisoning, since Ni2+ is also able to enter the cell via this pathway. More extensive behavioral analysis showed that Cha cells also overresponded to Na+, but there was no evidence for a defect in intracellular Ca2+ homeostasis that might account for a simultaneous enhancement of both the Mg2+ and Na+ conductances. The possibility that the Cha locus may encode a specific regulator of the Mg(2+)- and Na(+)-permeabilities is considered.

Extracellular GTP causes membrane-potential oscillations through the parallel activation of Mg2+ and Na+ currents in Paramecium tetraurelia.

Paramecium tetraurelia responds to extracellular GTP (>/= 10 nm) with repeated episodes of prolonged backward swimming. These backward swimming events cause repulsion from the stimulus and are the behavioral consequence of an oscillating membrane depolarization. Ion substitution experiments showed that either Mg2+ or Na+ could support these responses in wild-type cells, with increasing concentrations of either cation increasing the extent of backward swimming. Applying GTP to cells under voltage clamp elicited oscillating inward currents with a periodicity similar to that of the membrane-potential and behavioral responses. These currents were also Mg2+- and Na+-dependent, suggesting that GTP acts through Mg2+-specific (IMg) and Na+-specific (INa) conductances that have been described previously in Paramecium. This suggestion is strengthened by the finding that Mg2+ failed to support normal behavioral or electrophysiological responses to GTP in a mutant that specifically lacks IMg ("eccentric"), while Na+ failed to support GTP responses in "fast-2," a mutant that specifically lacks INa. Both mutants responded normally to GTP if the alternative cation was provided. As IMg and INa are both Ca2+-dependent currents, the characteristic GTP behavior could result from oscillations in intracellular Ca2+ concentration. Indeed, applying GTP to cells in the absence of either Mg2+ or Na+ revealed a minor inward current with a periodicity similar to that of the depolarizations. This current persisted when known voltage-dependent Ca2+ currents were blocked pharmacologically or genetically, which implies that it may represent the activation of a novel purinergic-receptor-coupled Ca2+ conductance.

Isolation and characterization of paramecium mutants defective in their response to magnesium.

Four mutant strains of Paramecium tetraurelia with a reduced ability to respond behaviorally to Mg2+ have been isolated. Voltage-clamp analyses showed that their Mg2+ insensitivity is associated with a reduced Ca(2+)-dependent Mg2+ current. The four mutants, which have been doubled "eccentric," result from recessive mutations in two unlinked loci, xntA and xntB. Further analysis of xntA1 showed it to be unlinked to any of the behavioral mutants of P. tetraurelia described previously, but it is allelic to d4-521, a "K(+)-resistant" strain, and d4-596, a "Ba(2+)-shy" mutant. The varied pleiotropic effects of xntA1, which include increased resistance to Ni2+ and Zn2+ poisoning, suggest that the locus encodes a central regulator of cell function in Paramecium.

New non-lethal calmodulin mutations in Paramecium. A structural and functional bipartition hypothesis.

The mechanisms by which calmodulin coordinates its numerous molecular targets in living cells remain largely unknown. To further understand how this pivotal Ca(2+)-binding protein functions in vivo, we isolated and studied nine new Paramecium behavioral mutants defective in calmodulin. Nucleotide sequences of mutant calmodulin genes indicated single amino-acid substitutions in mutants cam4(E104K), cam5-1 (D95G), cam6 (A102V), cam7 (H135R), cam14-1 (G59S) and cam15 (D50G). In addition, we encountered a second occurrence of three identified substitutions; they are cam1-2 (S101F), cam5-2 (D95G) and cam14-2 (G59S). Most of these mutational changes occurred in sites that have been highly conserved throughout evolution. Furthermore, most of these changes were not among the amino acids known to interact with the basic amphiphilic peptides of calmodulin targets. Consistent with our previous finding [Kink, J. A., Maley, M. E., Preston R. R., Ling, K.-Y., Wallen-Friedman, M. A., Saimi, Y. & Kung, C. (1990) Cell 62, 165-174], mutants that under-reacted to certain stimuli (allele number above 10) had substitutions in the N-terminal lobe of calmodulin, and those that over-reacted (below 10) had substitutions in the C-terminal lobe. No mutations were found in the central helix that connects the lobes. Thus, through undirected in vivo mutation analyses of Paramecium, we discovered that each of the two lobes of calmodulin has a distinct role in regulating the function of a specific ion channel and eventually the behavior of Paramecium. We, therefore, propose a hypothesis of functional bipartition of calmodulin that reflects its structural bipartition.

Inhibition of Mg2+ current by single-gene mutation in Paramecium.

"Eccentric" is a newly-isolated mutant of Paramecium tetraurelia that fails to swim backwards in response to Mg2+. In the wild type, this backward swimming results from Mg2+ influx via a Mg(2+)-specific ion conductance (IMg). Voltage-clamp analysis confirmed that, as suspected, step changes in membrane potential over a physiological range fail to elicit IMg from eccentric. Further electrophysiological investigation revealed a number of additional ion-current defects in eccentric: (i) The Ca2+ current activated upon depolarization inactivates more slowly in eccentric than in the wild type, and it requires longer to recover from this inactivation. (ii) The Ca(2+)-dependent Na+ current deactivates significantly faster in the mutant. (iii) The two K+ currents observed upon hyperpolarization are reduced by > 60% in eccentric. It is difficult to envision how these varied pleiotropic effects could result from loss of a single ion current. Rather, they suggest that the eccentric mutation affects a global regulatory system. Two plausible hypotheses are discussed.

Calcium current activated upon hyperpolarization of Paramecium tetraurelia.

Hyperpolarization of Paramecium tetraurelia under conditions where K+ currents are suppressed elicits an inward current that activates rapidly toward a peak at 25-80 ms and decays thereafter. This peak current (Ihyp) is not affected by removing Cl ions from the microelectrodes used to clamp membrane potential, or by changing extracellular Cl- concentration, but is lost upon removing extracellular Ca2+. Ihyp is also lost upon replacing extracellular Ca2+ with equimolar concentrations of Ba2+, Co2+, Mg2+, Mn2+, or Sr2+, suggesting that the permeability mechanism that mediates Ihyp is highly selective for Ca2+. Divalent cations also inhibit Ihyp when introduced extracellularly, in a concentration- and voltage-dependent manner. Ba2+ inhibits Ihyp with an apparent dissociation constant of 81 microM at -110 mV, and with an effective valence of 0.42. Ihyp is also inhibited reversibly by amiloride, with a dissociation constant of 0.4 mM. Ihyp is not affected significantly by changes in extracellular Na+, K+, or H+ concentration, or by EGTA injection. Also, it is unaffected by manipulations or mutations that suppress the depolarization-activated Ca2+ current or the various Ca(2+)-dependent currents of Paramecium. We suggest that Ihyp is mediated by a novel, hyperpolarization-activated calcium conductance that is distinct from the one activated by depolarization.