Use of lipid composition and metabolism to examine structure and activity of estuarine detrital microflora

Earlier studies have shown that the activity of the estuarine detrital microflora measured by various enzyme activities, muramic acid and adenosine 5'-triphosphate (ATP) content, heterotrophic potentials, and respiratory activities correlates with the incorporation of C and P into the microbial lipids. In this study, these lipids were reproducibly fractionated into neutral lipid, glycolipid, and phospholipid classes. Distinct differences between the active microflora of oak leaves, sweet gum leaves, and pine needles were evidenced both in the rate of lipid synthesis and in the proportions of neutral lipids, glycolipids, and phospholipids. Successional changes in the microflora of leaves incubated in a semitropical estuary, previously suggested by ATP-to-muramic acid ratios and scanning electron micrography, were reflected in changes in the proportions of C in major lipid classes when analyzed from the same type of detritus. Short incubation times with C gave lipid compositions rich in phospholipids that are typical for the faster-growing bacterial populations; longer incubation with C gave lipid compositions richer in neutral and glycolipids, more characteristic of slower-growing eukaryotes or morphologically more complex prokaryotes. The metabolism of the lipids of the estuarine detrital microflora was examined by a pulse-chase experiment with C. Glycolipids lost C at a rate equal to the loss of C of the slow component of muramic acid. Individual phospholipids lost C from their backbone glycerol esters at different rates.

Binding of inositol 1,4,5-trisphosphate (IP3) and adenophostin A to the N-terminal region of the IP3 receptor: thermodynamic analysis using fluorescence polarization with a novel IP3 receptor ligand

Inositol 1,4,5-trisphosphate (IP(3)) receptors (IP(3)R) are intracellular Ca(2+) channels. Their opening is initiated by binding of IP(3) to the IP(3)-binding core (IBC; residues 224-604 of IP(3)R1) and transmitted to the pore via the suppressor domain (SD; residues 1-223). The major conformational changes leading to IP(3)R activation occur within the N terminus (NT; residues 1-604). We therefore developed a high-throughput fluorescence polarization (FP) assay using a newly synthesized analog of IP(3), fluorescein isothiocyanate (FITC)-IP(3), to examine the thermodynamics of IP(3) and adenophostin A binding to the NT and IBC. Using both single-channel recording and the FP assay, we demonstrate that FITC-IP(3) is a high-affinity partial agonist of the IP(3)R. Conventional [(3)H]IP(3) and FP assays provide similar estimates of the K(D) for both IP(3) and adenophostin A in cytosol-like medium at 4 degrees C. They further establish that the isolated IBC retains the ability of full-length IP(3)R to bind adenophostin A with approximately 10-fold greater affinity than IP(3). By examining the reversible effects of temperature on ligand binding, we established that favorable entropy changes (T Delta S) account for the greater affinities of both ligands for the IBC relative to the NT and for the greater affinity of adenophostin A relative to IP(3). The two agonists differ more substantially in the relative contribution of Delta H and T Delta S to binding to the IBC relative to the NT. This suggests that different initial binding events drive the IP(3)R on convergent pathways toward a similar open state.

Regulation of inositol 1,4,5-trisphosphate receptors by cAMP independent of cAMP-dependent protein kinase

In HEK cells stably expressing type 1 receptors for parathyroid hormone (PTH), PTH causes a sensitization of inositol 1,4,5-trisphosphate receptors (IP(3)R) to IP(3) that is entirely mediated by cAMP and requires cAMP to pass directly from type 6 adenylyl cyclase (AC6) to IP(3)R2. Using DT40 cells expressing single subtypes of mammalian IP(3)R, we demonstrate that high concentrations of cAMP similarly sensitize all IP(3)R isoforms to IP(3) by a mechanism that does not require cAMP-dependent protein kinase (PKA). IP(3) binding to IP(3)R2 is unaffected by cAMP, and sensitization is not mediated by the site through which ATP potentiates responses to IP(3). In single channel recordings from excised nuclear patches of cells expressing IP(3)R2, cAMP alone had no effect, but it increased the open probability of IP(3)R2 activated by a submaximal concentration of IP(3) alone or in combination with a maximally effective concentration of ATP. These results establish that cAMP itself increases the sensitivity of all IP(3)R subtypes to IP(3). For IP(3)R2, this sensitization results from cAMP binding to a novel site that increases the efficacy of IP(3). Using stably expressed short hairpin RNA to reduce expression of the G-protein, G alpha(s), we demonstrate that attenuation of AC activity by loss of G alpha(s) more substantially reduces sensitization of IP(3)R by PTH than does comparable direct inhibition of AC. This suggests that G alpha(s) may also specifically associate with each AC x IP(3)R complex. We conclude that all three subtypes of IP(3)R are regulated by cAMP independent of PKA. In HEK cells, where IP(3)R2 selectively associates with AC6, G alpha(s) also associates with the AC x IP(3)R signaling junction.

Ca(2+) channels on the move

The versatility of Ca(2+) as an intracellular messenger derives largely from the spatial organization of cytosolic Ca(2+) signals, most of which are generated by regulated openings of Ca(2+)-permeable channels. Most Ca(2+) channels are expressed in the plasma membrane (PM). Others, including the almost ubiquitous inositol 1,4,5-trisphosphate receptors (IP(3)R) and their relatives, the ryanodine receptors (RyR), are predominantly expressed in membranes of the sarcoplasmic or endoplasmic reticulum (ER). Targeting of these channels to appropriate destinations underpins their ability to generate spatially organized Ca(2+) signals. All Ca(2+) channels begin life in the cytosol, and the vast majority are then functionally assembled in the ER, where they may either remain or be dispatched to other membranes. Here, by means of selective examples, we review two issues related to this trafficking of Ca(2+) channels via the ER. How do cells avoid wayward activity of Ca(2+) channels in transit as they pass from the ER via other membranes to their final destination? How and why do some cells express small numbers of the archetypal intracellular Ca(2+) channels, IP(3)R and RyR, in the PM?

IP3 receptors: some lessons from DT40 cells

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are intracellular Ca2+ channels that are regulated by IP3 and Ca2+ and are modulated by many additional signals. These properties allow them to initiate and, via Ca2+-induced Ca2+ release, regeneratively propagate Ca2+ signals evoked by receptors that stimulate formation of IP3. The ubiquitous expression of IP3R highlights their importance, but it also presents problems when attempting to resolve the behavior of defined IP3R. DT40 cells are a pre-B-lymphocyte cell line in which high rates of homologous recombination afford unrivalled opportunities to disrupt endogenous genes. DT40-knockout cells with both alleles of each of the three IP3R genes disrupted provide the only null-background for analysis of homogenous recombinant IP3R. We review the properties of DT40 cells and consider three areas where they have contributed to understanding IP3R behavior. Patch-clamp recording from the nuclear envelope and Ca2+ release from intracellular stores loaded with a low-affinity Ca2+ indicator address the mechanisms leading to activation of IP(3)R. We show that IP3 causes intracellular IP3R to cluster and re-tune their responses to IP3 and Ca2+, better equipping them to mediate regenerative Ca2+ signals. Finally, we show that DT40 cells reliably count very few IP3R into the plasma membrane, where they mediate about half the Ca2+ entry evoked by the B-cell antigen receptor.

Synthetic partial agonists reveal key steps in IP3 receptor activation

Inositol 1,4,5-trisphosphate receptors (IP(3)Rs) are ubiquitous intracellular Ca2+ channels. IP(3) binding to the IP(3)-binding core (IBC) near the N terminus initiates conformational changes that lead to opening of a pore. The mechanisms underlying this process are unresolved. We synthesized 2-O-modified IP(3) analogs that are partial agonists of IP(3)R. These are similar to IP(3) in their interactions with the IBC, but they are less effective than IP(3) in rearranging the relationship between the IBC and the N-terminal suppressor domain (SD), and they open the channel at slower rates. IP(3)R with a mutation in the SD occupying a position similar to the 2-O substituent of the partial agonists has a reduced open probability that is similar for full and partial agonists. Bulky or charged substituents from either the ligand or the SD therefore block obligatory coupling of the IBC and the SD. Analysis of DeltaG for ligand binding shows that IP(3) is recognized by the IBC and conformational changes then propagate entirely via the SD to the pore.

Targeting and clustering of IP3 receptors: key determinants of spatially organized Ca2+ signals

Inositol 1,4,5-trisphosphate receptors (IP3R) are intracellular Ca2+ channels that are almost ubiquitously expressed in animal cells. The spatiotemporal complexity of the Ca2+ signals evoked by IP3R underlies their versatility in cellular signaling. Here we review the mechanisms that contribute to the subcellular targeting of IP3R and the dynamic interplay between IP3R that underpin their ability to generate complex intracellular Ca2+ signals.

Dynamic regulation of IP3 receptor clustering and activity by IP3

Inositol 1,4,5-trisphosphate receptors (IP(3)Rs) are intracellular Ca(2+) channels. Their regulation by both IP(3) and Ca(2+) allows interactions between IP(3)Rs to generate a hierarchy of intracellular Ca(2+) release events. These can progress from openings of single IP(3)R, through near-synchronous opening of a few IP(3)Rs within a cluster to much larger signals that give rise to regenerative Ca(2+) waves that can invade the entire cell. We have used patch-clamp recording from excised nuclear membranes of DT40 cells expressing only IP(3)R3 and shown that low concentrations of IP(3) rapidly and reversibly cause IP(3)Rs to assemble into small clusters. In addition to bringing IP(3)Rs close enough to allow Ca(2+) released by one IP(3)R to regulate the activity of its neighbors; clustering also retunes the regulation of IP(3)Rs by IP(3) and Ca(2+). At resting cytosolic [Ca(2+)], lone IP(3)R are more sensitive to IP(3) and the mean channel open time (approximately 10 ms) is twice as long as for clustered IP(3)R. When the cytosolic free [Ca(2+)] is increased to 1 microM, to mimic the conditions that might prevail when an IP(3)R within a cluster opens, clustered IP(3)R are no longer inhibited and their gating becomes coupled. IP(3), by dynamically regulating IP(3)R clustering, both positions IP(3)R for optimal interactions between them and it serves to exaggerate the effects of Ca(2+) within a cluster. During the course of these studies, we have observed that nuclear IP(3)R stably express one of two single channel K(+) conductances (gamma(K) approximately 120 or 200 pS). Here we demonstrate that for both states of the IP(3)R, the effects of IP(3) on clustering are indistinguishable. These observations reinforce our conclusion that IP(3) dynamically regulates assembly of IP(3)Rs into clusters that underlie the hierarchical recruitment of elementary Ca(2+) release events.

Clustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+

The versatility of Ca2+ signals derives from their spatio-temporal organization. For Ca2+ signals initiated by inositol-1,4,5-trisphosphate (InsP3), this requires local interactions between InsP3 receptors (InsP3Rs) mediated by their rapid stimulation and slower inhibition\ by cytosolic Ca2+. This allows hierarchical recruitment of Ca2+ release events as the InsP3 concentration increases. Single InsP3Rs respond first, then clustered InsP3Rs open together giving a local 'Ca2+ puff', and as puffs become more frequent they ignite regenerative Ca2+ waves. Using nuclear patch-clamp recording, here we demonstrate that InsP3Rs are initially randomly distributed with an estimated separation of 1 m. Low concentrations of InsP3 cause InsP3Rs to aggregate rapidly and reversibly into small clusters of about four closely associated InsP3Rs. At resting cytosolic [Ca2+], clustered InsP3Rs open independently, but with lower open probability, shorter open time, and less InsP3 sensitivity than lone InsP3Rs. Increasing cytosolic [Ca2+] reverses the inhibition caused by clustering, InsP3R gating becomes coupled, and the duration of multiple openings is prolonged. Clustering both exposes InsP3Rs to local Ca2+ rises and increases the effects of Ca2+. Dynamic regulation of clustering by InsP3 retunes InsP3R sensitivity to InsP3 and Ca2+, facilitating hierarchical recruitment of the elementary events that underlie all InsP3-evoked Ca2+ signals.

Activation of IP(3) receptors by synthetic bisphosphate ligands

Combining synthesis and mutagenesis, we show that a cation–π interaction between adenine of adenophostin analogues and Arg504 of IP₃ receptors (IP₃R) is responsible for the enhanced activity of adenophostins and can replace a phosphate–receptor interaction.

Ca²⁺ release by d-myo-inositol 1,4,5-trisphosphate receptors (IP₃Rs) is widely considered to require the vicinal 4,5-bisphosphate motif of IP₃, with P-5 and P-4 engaging the α and β domains of the binding site; using synthesis and mutagenesis we show that the adenine of synthetic glyconucleotides, through an interaction with Arg504, can replace the interaction of either P-1 or P-5 with the α-domain producing, respectively, the most potent bisphosphate agonist yet synthesised and the first agonist of IP₃R without a vicinal bisphosphate motif; this will stimulate new approaches to IP₃R ligand design.

Functional ryanodine receptors in the plasma membrane of RINm5F pancreatic beta-cells

Ryanodine receptors (RyR) are Ca²⁺ channels that mediate Ca²⁺ release from intracellular stores in response to diverse intracellular signals. In RINm5F insulinoma cells, caffeine, and 4-chloro-m-cresol (4CmC), agonists of RyR, stimulated Ca²⁺ entry that was independent of store-operated Ca²⁺ entry, and blocked by prior incubation with a concentration of ryanodine that inactivates RyR. Patch-clamp recording identified small numbers of large-conductance (γ_K = 169 pS) cation channels that were activated by caffeine, 4CmC or low concentrations of ryanodine. Similar channels were detected in rat pancreatic β-cells. In RINm5F cells, the channels were blocked by cytosolic, but not extracellular, ruthenium red. Subcellular fractionation showed that type 3 IP₃ receptors (IP₃R3) were expressed predominantly in endoplasmic reticulum, whereas RyR2 were present also in plasma membrane fractions. Using RNAi selectively to reduce expression of RyR1, RyR2, or IP₃R3, we showed that RyR2 mediates both the Ca²⁺ entry and the plasma membrane currents evoked by agonists of RyR. We conclude that small numbers of RyR2 are selectively expressed in the plasma membrane of RINm5F pancreatic β-cells, where they mediate Ca²⁺ entry.

Selective coupling of type 6 adenylyl cyclase with type 2 IP3 receptors mediates direct sensitization of IP3 receptors by cAMP

Interactions between cyclic adenosine monophosphate (cAMP) and Ca²⁺ are widespread, and for both intracellular messengers, their spatial organization is important. Parathyroid hormone (PTH) stimulates formation of cAMP and sensitizes inositol 1,4,5-trisphosphate receptors (IP₃R) to IP₃. We show that PTH communicates with IP₃R via “cAMP junctions” that allow local delivery of a supramaximal concentration of cAMP to IP₃R, directly increasing their sensitivity to IP₃. These junctions are robust binary switches that are digitally recruited by increasing concentrations of PTH. Human embryonic kidney cells express several isoforms of adenylyl cyclase (AC) and IP₃R, but IP₃R2 and AC6 are specifically associated, and inhibition of AC6 or IP₃R2 expression by small interfering RNA selectively attenuates potentiation of Ca²⁺ signals by PTH. We define two modes of cAMP signaling: binary, where cAMP passes directly from AC6 to IP₃R2; and analogue, where local gradients of cAMP concentration regulate cAMP effectors more remote from AC. Binary signaling requires localized delivery of cAMP, whereas analogue signaling is more dependent on localized cAMP degradation.

How does intracellular Ca2+ oscillate: by chance or by the clock?

Ca2+ oscillations have been considered to obey deterministic dynamics for almost two decades. We show for four cell types that Ca2+ oscillations are instead a sequence of random spikes. The standard deviation of the interspike intervals (ISIs) of individual spike trains is similar to the average ISI; it increases approximately linearly with the average ISI; and consecutive ISIs are uncorrelated. Decreasing the effective diffusion coefficient of free Ca2+ using Ca2+ buffers increases the average ISI and the standard deviation in agreement with the idea that individual spikes are caused by random wave nucleation. Array-enhanced coherence resonance leads to regular Ca2+ oscillations with small standard deviation of ISIs.

Counting functional inositol 1,4,5-trisphosphate receptors into the plasma membrane

Inositol 1,4,5-trisphosphate receptors (IP(3)R) within the endoplasmic reticulum mediate release of Ca(2+) from intracellular stores. Different channels usually mediate Ca(2+) entry across the plasma membrane. In B lymphocytes and a cell line derived from them (DT40 cells), very few functional IP(3)R (approximately 2/cell) are invariably expressed in the plasma membrane, where they mediate about half the Ca(2+) entry evoked by activation of the B-cell receptor. We show that cells reliably count approximately 2 functional IP(3)R into the plasma membrane even when their conductance and ability to bind IP(3) are massively attenuated. We conclude that very small numbers of functional IP(3)R can be reliably counted into a specific membrane compartment in the absence of feedback signals from the active protein.

Rapid functional assays of intracellular Ca2+ channels

Functional assays of intracellular Ca2+ channels, such as the inositol 1,4,5-trisphosphate receptor (IP3R), have generally used 45Ca2+-flux assays, fluorescent indicators loaded within either the cytosol or the endoplasmic reticulum (ER) of single cells, or electrophysiological analyses. None of these methods is readily applicable to rapid, high-throughput quantitative analyses. Here we provide a detailed protocol for high-throughput functional analysis of native and recombinant IP3Rs. A low-affinity Ca2+ indicator (mag-fluo-4) trapped within the ER of permeabilized cells is shown to report changes in luminal free Ca2+ concentration reliably. An automated fluorescence plate reader allows rapid measurement of Ca2+ release from intracellular stores mediated by IP3R. The method can be readily adapted to other cell types or to the analysis of other intracellular Ca2+ channels. This protocol can be completed in 2-3 h.

Targeting and retention of type 1 ryanodine receptors to the endoplasmic reticulum

Most ryanodine receptors and their relatives, inositol 1,4,5-trisphosphate receptors, are expressed in the sarcoplasmic or endoplasmic reticulum (ER), where they mediate Ca(2+) release. We expressed fragments of ryanodine receptor type 1 (RyR1) in COS cells alone or fused to intercellular adhesion molecule-1 (ICAM-1), each tagged with yellow fluorescent protein, and used confocal imaging and glycoprotein analysis to identify the determinants of ER targeting and retention. Single transmembrane domains (TMD) of RyR1 taken from the first (TMD1-TMD2) or last (TMD5-TMD6) pair were expressed in the ER membrane. TMD3-TMD4 was expressed in the outer mitochondrial membrane. The TMD outer pairs (TMD1-TMD2 and TMD5-TMD6) retained ICAM-1, a plasma membrane-targeted protein, within the ER membrane. TMD1 alone provided a strong ER retention signal and TMD6 a weaker signal, but the other single TMD were unable to retain ICAM-1 in the ER. We conclude that TMD1 provides the first and sufficient signal for ER targeting of RyR1. The TMD outer pairs include redundant ER retention signals, with TMD1 providing the strongest signal.

Plasma membrane IP3 receptors

IP3Rs (inositol 1,4,5-trisphosphate receptors) are expressed in the membranes of non-mitochondrial organelles in most animal cells, but their presence and role within the plasma membrane are unclear. Whole-cell patch-clamp recording from DT40 cells expressing native or mutated IP3Rs has established that each cell expresses just two or three functional IP3Rs in its plasma membrane. Only approx. 50% of the Ca2+ entry evoked by stimulation of the B-cell receptor is mediated by store-operated Ca2+ entry, the remainder appears to be carried by the IP3Rs expressed in the plasma membrane. Ca2+ entering the cell via just two large-conductance IP3Rs is likely to have very different functional consequences from the comparable amount of Ca2+ that enters through the several thousand low-conductance store-operated channels.

Prostaglandin F2alpha increases the sensitivity of the contractile proteins to Ca2+ in human myometrium

It is not known whether agonists (other than oxytocin) increase the contractile protein sensitivity to intracellular calcium ([Ca2+]i) in human myometrium. We determined the calcium-tension relationship in the presence and absence of prostaglandin F2alpha (PGF2alpha). PGF2alpha increased the calcium sensitivity during both the contractile (rising) and relaxation (falling) phases of a contraction.

Store-operated Ca2+ entry: A STIMulating stOrai

Store-operated Ca2+ entry (SOCE) mediates much of the Ca2+ entry evoked by receptors that stimulate phospholipase C. However, for 20 years, the plasma membrane Ca2+ channel and the signal linking its activation to loss of Ca2+ from the endoplasmic reticulum (ER) have eluded detection. But the search might now be over. Two proteins, STIM1 (the ER Ca2+ sensor) and Orai1 (the Ca2+ channel), have recently been identified as the missing links in SOCE.