A study of the reactivity of S(VI)-F containing warheads with nucleophilic amino-acid side chains under physiological conditions.

Sulfonyl fluorides (SFs) have recently emerged as a promising warhead for the targeted covalent modification of proteins. Despite numerous examples of the successful deployment of SFs as covalent probe compounds, a detailed exploration of the factors influencing the stability and reactivity of SFs has not yet appeared. In this work we present an extensive study on the influence of steric and electronic factors on the reactivity and stability of the SF and related SVI-F groups. While SFs react rapidly with N-acetylcysteine, the resulting adducts were found to be unstable, rendering SFs inappropriate for the durable covalent inhibition of cysteine residues. In contrast, SFs afforded stable adducts with both N-acetyltyrosine and N-acetyllysine; furthermore, we show that the reactivity of arylsulfonyl fluorides towards these nucleophilic amino acids can be predictably modulated by adjusting the electronic properties of the warhead. These trends were largely conserved when the covalent reaction occurred within a protein binding pocket. We have also obtained a crystal structure depicting covalent modification of the catalytic lysine of a tyrosine kinase (FGFR1) by the ATP analog 5'-O-3-((fluorosulfonyl)benzoyl)adenosine (m-FSBA). Highly reactive warheads were demonstrated to be unstable with respect to hydrolysis in buffered aqueous solutions, indicating that warhead reactivity must be carefully tuned to provide optimal rates of protein modification. Our results demonstrate that the reactivity of SFs complements that of more commonly studied acrylamides, and we hope that this work spurs the rational design of novel SF-containing covalent probe compounds and inhibitors, particularly in cases where a suitably positioned cysteine residue is not present.

Behavioral screening for cocaine sensitivity in mutagenized zebrafish.

Understanding the molecular basis of addiction could be greatly aided by using forward genetic manipulation to lengthen the list of candidate genes involved in this complex process. Here, we report that zebrafish exhibit cocaine-induced conditioned place preference. In a pilot screen of 18 F(2) generation families of mutagenized fish, we found three with abnormally low responses to cocaine. This behavior was inherited by the F(3) generation in a manner that suggests the abnormalities were because of dominant mutations in single genes. Performance profiles in secondary behavioral screens measuring visual dark-adaptation and learning suggest that the defects were the result of mutations in distinct genes that affect dopaminergic signaling in the retina and brain.

The perplexed and confused mutations affect distinct stages during the transition from proliferating to post-mitotic cells within the zebrafish retina.

To identify and study genes essential for vertebrate retinal development, we are screening zebrafish embryos for mutations that disrupt retinal histogenesis. Key steps in retinogenesis include withdrawal from mitosis by multipotent neuroepithelial cells, specification to particular cell types, migration to the appropriate laminar positions, and molecular and morphological differentiation. In this study, we have identified two recessive mutations that affect the transition of proliferating neuroepithelial cells to postmitotic retinal cells. Both the perplexed and confused mutant phenotypes were initially detectable when the first retinal neuroepithelial cells began to leave the cell cycle. At this time, each mutant retina showed increased cell death and a lack of morphological differentiation. Cell death was found to be apoptotic in both perplexed and confused retinas based on TUNEL analysis and activation of caspase-3. TUNEL-phosphoRb-BrdU colocalization studies indicated that the perplexed mutation caused death in cells transitioning from a proliferative to postmitotic state. For the confused mutation, TUNEL-phosphoRb-BrdU analysis revealed that only a subset of postmitotic cells were induced to activate apoptosis. Mosaic analysis demonstrated that within the retina the perplexed mutation functions noncell-autonomously. Furthermore, whole lens or eye cup transplantations indicated that the retinal defect was intrinsic to the retina. Mosaic analysis with confused embryos showed this mutation acts cell-autonomously. From these studies, we conclude that the perplexed and confused genes are essential at distinct stages during the transition from proliferating to postmitotic cells within the zebrafish retina.

Synapse formation is arrested in retinal photoreceptors of the zebrafish nrc mutant.

We describe the effects of a recessive mutation on visual behavior, the electroretinogram (ERG), and photoreceptor structure in zebrafish. At 6 d post-fertilization (dpf), no optokinetic reflex could be elicited in no optokinetic response c (nrc) mutant animals under any test condition. The animals exhibited ERG responses at 5-7 dpf that were markedly abnormal and could be categorized into two groups. The first showed an initial negative a-wave followed by a delayed positive b-wave of small amplitude. Often a second ERG-like response was recorded after the initial b-wave. The second group showed only a large negative a-wave; an initial b-wave was not evident. In most recordings additional oscillatory waves varying in number, amplitude, and time course were observed. Multiple responses at the cessation of long-duration flashes were also observed. Light and electron microscopy revealed that the cone photoreceptor pedicles of nrc fish were highly abnormal. Although the appropriate number of synaptic ribbons formed in these terminals, they "floated" in the terminal, unassociated with postsynaptic processes or arciform densities. The few processes invaginating the nrc pedicles resembled those of horizontal cells. Invaginating bipolar cell processes were rare, but basal contacts were observed on pedicle surfaces. The severity of the mutation did not change between 6 and 8 dpf, showing that there is neither a delay in development nor a degeneration of the terminals; rather, nrc pedicle development appears arrested. Bipolar cell terminals in the inner plexiform layer made normal ribbon synapses; thus, the mutation appears to affect only the outer retina.

The pineal gland in wild-type and two zebrafish mutants with retinal defects.

Light and transmission electron microscopy were used to characterize the ultrastructural features of the pineal glands of wild-type and two mutant zebrafish strains that have retinal defects. Particular attention was given to the pineal photoreceptors. Photoreceptors in the pineal gland appear quite similar to retinal cone photoreceptors, having many of the same structural characteristics including outer segment disk membranes often confluent with the plasma membrane, calycal processes surrounding the outer segments, and classic connecting cilia. The pineal photoreceptor terminals differ from photoreceptor terminals in the retina in that they have short synaptic ribbons and make dyad synapses which may or may not be invaginated. Pineal photoreceptors in two zebrafish mutants with abnormal retinal photoreceptors were also studied. Pineal photoreceptors in the niezerka (nie) mutant degenerate, as they do in the retina, indicating that pineal and retinal photoreceptors share at least some genes. However, the synaptic terminals of no optokinetic response c (nrc) pineal photoreceptors are normal, suggesting that this mutation is specific to the retina.

Small molecule developmental screens reveal the logic and timing of vertebrate development.

Much has been learned about vertebrate development by random mutagenesis followed by phenotypic screening and by targeted gene disruption followed by phenotypic analysis in model organisms. Because the timing of many developmental events is critical, it would be useful to have temporal control over modulation of gene function, a luxury frequently not possible with genetic mutants. Here, we demonstrate that small molecules capable of conditional gene product modulation can be identified through developmental screens in zebrafish. We have identified several small molecules that specifically modulate various aspects of vertebrate ontogeny, including development of the central nervous system, the cardiovascular system, the neural crest, and the ear. Several of the small molecules identified allowed us to dissect the logic of melanocyte and otolith development and to identify critical periods for these events. Small molecules identified in this way offer potential to dissect further these and other developmental processes and to identify novel genes involved in vertebrate development.

The zebrafish young mutation acts non-cell-autonomously to uncouple differentiation from specification for all retinal cells.

Embryos from mutagenized zebrafish were screened for disruptions in retinal lamination to identify factors involved in vertebrate retinal cell specification and differentiation. Two alleles of a recessive mutation, young, were isolated in which final differentiation and normal lamination of retinal cells were blocked. Early aspects of retinogenesis including the specification of cells along the inner optic cup as retinal tissue, polarity of the retinal neuroepithelium, and confinement of cell divisions to the apical pigmented epithelial boarder were normal in young mutants. BrdU incorporation experiments showed that the initiation and pattern of cell cycle withdrawal across the retina was comparable to wild-type siblings; however, this process took longer in the mutant. Analysis of early markers for cell type differentiation revealed that each of the major classes of retinal neurons, as well as non-neural Müller glial cells, are specified in young embryos. However, the retinal cells fail to elaborate morphological specializations, and analysis of late cell-type-specific markers suggests that the retinal cells were inhibited from fully differentiating. Other regions of the nervous system showed no obvious defects in young mutants. Mosaic analysis demonstrated that the young mutation acts non-cell-autonomously within the retina, as final morphological and molecular differentiation was rescued when genetically mutant cells were transplanted into wild-type hosts. Conversely, differentiation was prevented in wild-type cells when placed in young mutant retinas. Mosaic experiments also suggest that young functions at or near the cell surface and is not freely diffusible. We conclude that the young mutation disrupts the post-specification development of all retinal neurons and glia cells.

Disruption of the olfactoretinal centrifugal pathway may relate to the visual system defect in night blindness b mutant zebrafish.

We describe here a dominant mutation, night blindness b (nbb), which causes an age-related visual system defect in zebrafish. At 4-5 months of age, dark-adapted nbb(+/-) mutants show abnormal visual threshold fluctuations when measured behaviorally. Light sensitizes the animals; thus early dark adaptation of nbb(+/-) fish is normal. After 2 hr of dark adaptation, however, visual thresholds of nbb(+/-) mutants are raised on average 2-3 log units, and rod system function is not detectable. Electroretinograms recorded from nbb(+/-) mutants are normal, but ganglion cell thresholds are raised in prolonged darkness, suggesting an inner retinal defect. The visual defect of nbb(+/-) mutants may be likely caused by an abnormal olfactoretinal centrifugal innervation; in nbb(+/-) mutants, the olfactoretinal centrifugal projection to the retina is disrupted, and the number of retinal dopaminergic interplexiform cells is reduced. A similar visual defect as shown by nbb(+/-) mutants is observed in zebrafish in which the olfactory epithelium and olfactory bulb have been excised. Homozygous nbb fish display an early onset neural degeneration throughout the CNS and die by 7-8 d of age.

Effects of dopamine depletion on visual sensitivity of zebrafish.

The visual sensitivity of zebrafish in which the retinal dopaminergic interplexiform cells (DA-IPCs) were destroyed by 6-hydroxydopamine was measured behaviorally. During the first 6-8 min of dark adaptation, visual thresholds of DA-IPC-depleted animals were similar to those of control animals. Thereafter, their visual thresholds were elevated so that by 14-18 min of dark adaptation, they were 2-3 log units above those of control animals. In DA-IPC-depleted animals, the electroretinogram was normal in terms of light sensitivity and waveform, but the light threshold for eliciting a ganglion cell discharge was raised by 1.8 log units as compared with control animals. No obvious rod system function was detected in DA-IPC-depleted animals as measured behaviorally. Partial rescue of the behavioral visual sensitivity loss in DA-IPC-depleted animals occurred when dopamine or a long-acting dopamine agonist (2-amino-6, 7-dihydroxy-1, 2, 3, 4-tetrahydronaphthalene hydrobromide) were injected intraocularly. Our data suggest that the principal visual defect shown by DA-IPC-depleted animals is attributable to effects occurring in the inner retina, mainly on rod signals. We also show that dopamine is involved in mediating the effect of the circadian clock on visual sensitivity.

A single amino acid in the second transmembrane domain of GABA rho subunits is a determinant of the response kinetics of GABAC receptors.

The rho subunits that constitute the gamma-aminobutyric acid (GABA)C receptors of retinal neurons form a unique subclass of ligand-gated chloride channels that give rise to sustained GABA-evoked currents that exhibit slow offset (deactivation) kinetics. We exploited this property to examine the molecular mechanisms that govern the disparate response kinetics and pharmacology of perch GABA rho1B and rho2A subunits expressed in Xenopus oocytes. Using a combination of domain swapping and site-directed mutagenesis, we identified the residues at amino acid position 320 in the second transmembrane domain as an important determinant of the receptor kinetics of GABAC receptors. When the site contains a proline residue, as in wild-type rho1 subunits, the receptor deactivates slowly; when serine occupies the site, as in wild-type rho2 subunits, the time course of deactivation is more rapid. In addition, we found that the same site also altered the pharmacology of GABA rho receptors, e.g., when the serine residue of the rho2A receptor was changed to proline, the response of the mutant receptor to imidazole-4-acetic acid (I4AA) mimicked that of the rho1B receptor. However, despite gross changes in receptor pharmacology, the apparent binding affinity for the drug was not significantly altered. These findings provide further evidence that the second transmembrane domain is involved in the gating mechanism that governs the response properties of the various rho receptor subunits. It is noteworthy that the proline residue in native rho1 subunits and the serine residue of rho2 subunits are well conserved in all species, a good indication that the presence of multiple GABA rho subunits serves to generate GABAC receptors that display the wide range of response kinetics observed on various types of retinal neurons.

Erratum: Temporal and spatial patterns of opsin gene expression in the zebrafish (Danio rerio): corrections with additions.

We report here a reexamination of the developmental expression of cone opsins in the zebrafish retina. The red- and blue-sensitive opsins appear at 51 h postfertilization (hpf) whereas ultraviolet (UV) opsin is not seen until after 55 hpf. More cells show red cone opsin expression than blue at 51 and 55 hpf, indicating the sequence of cone opsin expression in zebrafish is first red, then blue, and finally UV. Curiously, morphological development of the cones is in reverse order; UV cones appear quite mature by day 6-7 postfertilization (pf), but morphologically, red cones do not appear adult-like until 15-20 days pf.

Early retinal development in the zebrafish, Danio rerio: light and electron microscopic analyses.

The morphological differentiation of the zebrafish retina was analyzed by using light (LM) and transmission electron (TEM) microscopy between the time of initial ganglion cell differentiation (approximately 32 hours postfertilization; hpf) and shortly after the point when the retina appears functional (approximately 74 hpf), i.e., when all major cell types and basic synaptic connections are in place. The results show that the inner retinal neurons, like the photoreceptor and ganglion cells, differentiate first within the ventronasal region, and differentiation subsequently spreads asymmetrically into the nasal and dorsal regions before reaching the ventrotemporal retina. In addition, we show that the attenuation of the optic stalk occurs in parallel with ganglion cell differentiation between 32 and 40 hpf. The first conventional synapses appear within the inner plexiform layer simultaneously with the first photoreceptor outer segment discs at 60 hpf; functional ribbon triads arise within photoreceptor synaptic terminals at 65 hpf; and synaptic ribbons occur within bipolar cell axon terminals at the time larvae exhibit their first visual responses (approximately 70 hpf). Although development is initially more advanced within the ventronasal region between 50 and 60 hpf, development across the retina rapidly equilibrates such that it is relatively comparable within all quadrants of the central retina by 70 hpf. An area within the temporal retina characterized by tightly packed and highly tiered cones emerges with subsequent development. Retinal differentiation in the zebrafish corresponds with that generally described in other vertebrates and can be correlated with the development of visual and electroretinographic responses in the animal.

Molecular and pharmacological properties of GABA-rho subunits from white perch retina.

Five gamma-aminobutyric acid (GABA)-rho subunits were cloned from a white perch retinal cDNA library and expressed in Xenopus oocytes. The deduced amino acid sequences indicated that all are highly homologous to the GABA-rho subunits cloned from mammalian retinas; two clones (perch-rho 1A and perch-rho 1B) were in the rho 1 family, two (perch-rho 2A and perch-rho 2B) were in the rho 2 family, and one clone has been tentatively identified as a perch-rho 3 subunit. When expressed in Xenopus oocytes, all but one of the subunits (rho 3) formed functional homooligomeric receptors. However, the receptors expressed by each of the GABA-rho subunits displayed unique response properties that distinguished one from the other. For example, receptors formed by perch-rho 1B subunits were more sensitive to GABA than the receptors formed by other GABA-rho subunits, the dose-response curves for the various receptors revealed different Hill coefficients, and there were differences in the kinetics of the GABA-induced currents. In addition, the GABA-mediated current-voltage curve for rho 2 receptors was approximately linear, whereas the responses from rho 1 receptors showed outward rectification. A further division in the properties of the GABA-rho subunits was revealed in their responses to imidazole-4-acetic acid (I4AA); the drug behaved as an antagonist on A-type rho receptors and a partial agonist on the B-type rho receptors. These results suggest that there is a large diversity of GABAC receptors in the vertebrate retina, probably formed by homooligomeric and heterooligomeric combinations of GABA rho subunits, that exhibit different functional properties.

Zebrafish visual sensitivity is regulated by a circadian clock.

We have recently developed a behavioral assay, based on the escape response of fish to a threatening object, to analyze quantitatively the visual sensitivity of zebrafish. During the course of dark adaptation, we measure the threshold light intensity required to evoke an escape response. Under a normal light-dark (LD) cycle, thresholds for both the cone and rod systems are considerably lower in late afternoon hours than in early morning hours. Over a period of 24 h, zebrafish are most sensitive to visual stimuli prior to light off and least sensitive prior to light on. Under conditions of constant illumination, this rhythm of visual sensitivity persists for several days but is gradually lost. In constant light (LL), the rhythm persists 1-2 days; thereafter, visual thresholds at all times of the day converge at a level similar to thresholds measured in late afternoon hours in control animals. In constant darkness (DD). the rhythm persists at least 5 days; thereafter, it dampens to a level about a half-log unit less sensitive to that measured in the late afternoon hours in control animals. These data suggest that visual sensitivity in zebrafish is regulated by an endogenous circadian clock which functions to decrease the visual sensitivity.

Zebrafish retinal mutants.

We have initiated a genetic analysis of the zebrafish visual system to identify novel molecules involved in vertebrate retinal function. Zebrafish are highly visual; they have four types of cones as well as rod photoreceptors, making it possible to study both rod and cone-mediated visual responses. To identify visual mutants, optokinetic responses of mutagenized larvae are measured in a three-generation screen for recessive mutations. By measuring visual behavior our genetic screen has been targeted towards identifying mutants that do not have gross morphological abnormalities. The electroretinogram (ERG) of optokinetic-defective mutants is recorded and their retinas are examined histologically to localize defects to the retina. In this report, we summarize our screening results and ERG and histological analyses of the five morphologically normal mutants we have analyzed to date. Additionally, the more detailed characterization of a red-blind mutant that we have isolated is summarized. Our results indicate that mutants with defects in various processes such as photoreceptor synaptic transmission, photoreceptor adaptation and cell-type specific survival and/or function can be identified using this approach.

Transposition of the mariner element from Drosophila mauritiana in zebrafish.

With the increased popularity of zebrafish (Danio rerio) for mutagenesis studies, efficient methods for manipulation of its genome are needed. One approach is the use of a transposable element as a vector for gene transfer in this species. We report here the transformation of zebrafish and germ-line transmission of the mariner element from Drosophila mauritiana. The mariner element was selected because its transposition is independent of host-specific factors. One- to two-cell-stage zebrafish embryos were coinjected with a supercoiled plasmid carrying the nonautonomous mariner element peach and mRNA encoding the transposase. Surviving larvae were reared to adulthood, and the transmission of peach to the F1 generation was tested by PCR. Four of the 12 founders, following plasmid injections on 2 different days, transmitted the element to their progeny. Inheritance of the transgene from the F1 to the F2 generation showed a Mendelian pattern. No plasmid sequences were detected by PCR or Southern blot analysis, indicating transposition of peach rather than random integration of the plasmid DNA. These data provide evidence of transformation of a vertebrate with a transposable element and support the host-independent mechanism for transposition of the mariner element. We suggest this system could be used for insertional mutagenesis or for identifying active regions of the genome in the zebrafish.

Comparative morphology of distal neurons in larval and adult zebrafish retinas.

Distal retinal cells from larval (7-10 days postfertilization) and adult zebrafish retinas were cultured in 70% L-15 medium for 4-5 d and comparable cell types identified. Four photoreceptor types were observed in adult retinal cultures, whereas only single cones were isolated from larval retinas. Horizontal cells in both larval and adult cultures were distinguished by their large size and stellate morphology and two subtypes, A and B, were recognized. Bipolar cells were readily identified in adult cultures, but rare in larval cultures. Two bipolar cell types, large and small, were distinguished. Measurements of the various cell types are provided.

A comparison of GABAC and rho subunit receptors from the white perch retina.

There is increasing evidence that GABAC receptors are composed of GABA rho subunits. In this study, we compared the properties of native GABAC receptors with those of receptors composed of a GABA rho subunit. A homologue of the GABA rho gene was cloned from a white perch (Roccus americana) retinal cDNA library. The clone (perch-s) has an open reading frame of 1422 nucleotide base pairs and encodes a predicted protein of 473 amino acids. It is highly homologous to GABA rho subunits cloned from human and rat retinas. The receptors (perch-s receptor) expressed by this gene in Xenopus oocytes show properties similar to those of the GABAC receptors present on white perch retinal neurons. GABA induced a sustained response that had a reversal potential of -27.1 +/- 3.6 mV. The EC50 for the response was 1.74 +/- 1.25 microM, a value similar to that reported for GABAC receptors. Pharmacologically, the responses were bicuculline insensitive and not modulated by either diazepam or pentobarbital as is the case for GABAC receptors. There were, however, some distinct differences between native GABAC and perch-s receptors. I4AA acts as a partial agonist on perch-s receptors whereas it is strictly an antagonist on native GABAC receptors. Picrotoxin inhibition is noncompetitive on perch-s receptors, but both competitive and noncompetitive on GABAC receptors. We conclude that GABAC receptors are formed by GABA rho subunits but that native GABAC receptors probably consist of a mixture of GABA rho subunits.