J1-crystallins of the cubomedusan jellyfish lens constitute a novel family encoded in at least three intronless genes

Mollusc Crystallins: Physical and Chemical Properties and Phylogenetic Analysis

The purpose of the present study was to perform bioinformatic analysis of crystallin diversity in aquatic molluscs based on the sequences in the NCBI Protein database. The objectives were as follows: (1) analysis of some physical and chemical properties of mollusc crystallins, (2) comparison of mollusc crystallins with zebrafish and cubomedusa Tripedalia cystophora crystallins, and (3) determination of the most probable candidates for the role of gastropod eye crystallins. The calculated average GRAVY values revealed that the majority of the seven crystallin groups, except for μ- and ζ-crystallins, were hydrophilic proteins. The predominant predicted secondary structures of the crystallins in most cases were α-helices and coils. The highest values of refractive index increment (dn/dc) were typical for crystallins of aquatic organisms with known lens protein composition (zebrafish, cubomedusa, and octopuses) and for S-crystallin of Pomacea canaliculata. The evolutionary relationships between the studied crystallins, obtained from multiple sequence alignments using Clustal Omega and MUSCLE, and the normalized conservation index, calculated by Mirny, showed that the most conservative proteins were Ω-crystallins but the most diverse were S-crystallins. The phylogenetic analysis of crystallin was generally consistent with modern mollusc taxonomy. Thus, α- and S-, and, possibly, J1A-crystallins, can be assumed to be the most likely candidates for the role of gastropod lens crystallins.

Light modulated cnidocyte discharge predates the origins of eyes in Cnidaria

Complex biological traits often originate by integrating previously separate parts, but the organismal functions of these precursors are challenging to infer. If we can understand the ancestral functions of these precursors, it could help explain how they persisted and how they facilitated the origins of complex traits. Animal eyes are some of the best studied complex traits, and they include many parts, such as opsin-based photoreceptor cells, pigment cells, and lens cells. Eye evolution is understood through conceptual models that argue these parts gradually came together to support increasingly sophisticated visual functions. Despite the well-accepted logic of these conceptual models, explicit comparative studies to identify organismal functions of eye precursors are lacking. Here, we investigate how precursors functioned before they became part of eyes in Cnidaria, a group formed by sea anemones, corals, and jellyfish. Specifically, we test whether ancestral photoreceptor cells regulated the discharge of cnidocytes, the expensive single-use cells with various functions including prey capture, locomotion, and protection. Similar to a previous study of Hydra, we show an additional four distantly related cnidarian groups discharge significantly more cnidocytes when exposed to dim blue light compared with bright blue light. Our comparative analyses support the hypothesis that the cnidarian ancestor was capable of modulating cnidocyte discharge with light, which we speculate uses an opsin-based phototransduction pathway homologous to that previously described in Hydra. Although eye precursors might have had other functions like regulating timing of spawning, our findings are consistent with the hypothesis that photoreceptor cells which mediate cnidocyte discharge predated eyes, perhaps facilitating the prolific origination of eyes in Cnidaria.

The cuticular nature of corneal lenses in Drosophila melanogaster

The dioptric visual system relies on precisely focusing lenses that project light onto a neural retina. While the proteins that constitute the lenses of many vertebrates are relatively well characterized, less is known about the proteins that constitute invertebrate lenses, especially the lens facets in insect compound eyes. To address this question, we used mass spectrophotometry to define the major proteins that comprise the corneal lenses from the adult Drosophila melanogaster compound eye. This led to the identification of four cuticular proteins: two previously identified lens proteins, drosocrystallin and retinin, and two newly identified proteins, Cpr66D and Cpr72Ec. To determine which ommatidial cells contribute each of these proteins to the lens, we conducted in situ hybridization at 50% pupal development, a key age for lens secretion. Our results confirm previous reports that drosocrystallin and retinin are expressed in the two primary corneagenous cells-cone cells and primary pigment cells. Cpr72Ec and Cpr66D, on the other hand, are more highly expressed in higher order interommatidial pigment cells. These data suggest that the complementary expression of cuticular proteins give rise to the center vs periphery of the corneal lens facet, possibly facilitating a refractive gradient that is known to reduce spherical aberration. Moreover, these studies provide a framework for future studies aimed at understanding the cuticular basis of corneal lens function in holometabolous insect eyes.

A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex

Background

Cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Many cubozoans have a particularly potent sting, effected by stinging structures called nematocysts; cubozoans have well-developed light sensation, possessing both image-forming lens eyes and light-sensitive eye spots; and some cubozoans have complex mating behaviors, including aggregations, copulation and internal fertilization. The cubozoan Alatina alata is emerging as a cnidarian model because it forms predictable monthly nearshore breeding aggregations in tropical to subtropical waters worldwide, making both adult and larval material reliably accessible. To develop resources for A. alata, this study generated a functionally annotated transcriptome of adult and larval tissue, applying preliminary differential expression analyses to identify candidate genes involved in nematogenesis and venom production, vision and extraocular sensory perception, and sexual reproduction, which for brevity we refer to as “venom”, “vision” and “sex”.

Results

We assembled a transcriptome de novo from RNA-Seq data pooled from multiple body parts (gastric cirri, ovaries, tentacle (with pedalium base) and rhopalium) of an adult female A. alata medusa and larval planulae. Our transcriptome comprises ~32 K transcripts, after filtering, and provides a basis for analyzing patterns of gene expression in adult and larval box jellyfish tissues. Furthermore, we annotated a large set of candidate genes putatively involved in venom, vision and sex, providing an initial molecular characterization of these complex features in cubozoans. Expression profiles and gene tree reconstruction provided a number of preliminary insights into the putative sites of nematogenesis and venom production, regions of phototransduction activity and fertilization dynamics in A. alata.

Conclusions

Our Alatina alata transcriptome significantly adds to the genomic resources for this emerging cubozoan model. This study provides the first annotated transcriptome from multiple tissues of a cubozoan focusing on both the adult and larvae. Our approach of using multiple body parts and life stages to generate this transcriptome effectively identified a broad range of candidate genes for the further study of coordinated processes associated with venom, vision and sex. This new genomic resource and the candidate gene dataset are valuable for further investigating the evolution of distinctive features of cubozoans, and of cnidarians more broadly.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2944-3) contains supplementary material, which is available to authorized users.

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms

Background

Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families.

Results

We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository (http://bitbucket.org/osiris_phylogenetics/pia/) and we demonstrate PIA on a publicly-accessible web server (http://galaxy-dev.cnsi.ucsb.edu/pia/).

Conclusions

Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0350-x) contains supplementary material, which is available to authorized users.

Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous cofactor participating in numerous redox reactions. It is also a substrate for regulatory modifications of proteins and nucleic acids via the addition of ADP-ribose moieties or removal of acyl groups by transfer to ADP-ribose. In this study, we use in-depth sequence, structure and genomic context analysis to uncover new enzymes and substrate-binding proteins in NAD-utilizing metabolic and macromolecular modification systems. We predict that Escherichia coli YbiA and related families of domains from diverse bacteria, eukaryotes, large DNA viruses and single strand RNA viruses are previously unrecognized components of NAD-utilizing pathways that probably operate on ADP-ribose derivatives. Using contextual analysis we show that some of these proteins potentially act in RNA repair, where NAD is used to remove 2'-3' cyclic phosphodiester linkages. Likewise, we predict that another family of YbiA-related enzymes is likely to comprise a novel NAD-dependent ADP-ribosylation system for proteins, in conjunction with a previously unrecognized ADP-ribosyltransferase. A similar ADP-ribosyltransferase is also coupled with MACRO or ADP-ribosylglycohydrolase domain proteins in other related systems, suggesting that all these novel systems are likely to comprise pairs of ADP-ribosylation and ribosylglycohydrolase enzymes analogous to the DraG-DraT system, and a novel group of bacterial polymorphic toxins. We present evidence that some of these coupled ADP-ribosyltransferases/ribosylglycohydrolases are likely to regulate certain restriction modification enzymes in bacteria. The ADP-ribosyltransferases found in these, the bacterial polymorphic toxin and host-directed toxin systems of bacteria such as Waddlia also throw light on the evolution of this fold and the origin of eukaryotic polyADP-ribosyltransferases and NEURL4-like ARTs, which might be involved in centrosomal assembly. We also infer a novel biosynthetic pathway that might be involved in the synthesis of a nicotinate-derived compound in conjunction with an asparagine synthetase and AMPylating peptide ligase. We use the data derived from this analysis to understand the origin and early evolutionary trajectories of key NAD-utilizing enzymes and present targets for future biochemical investigations.

Assembly of the cnidarian camera-type eye from vertebrate-like components

Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of dark shielding pigment. Cnidaria as the likely sister group to the Bilateria are the earliest branching phylum with a well developed visual system. Here, we show that camera-type eyes of the cubozoan jellyfish, Tripedalia cystophora, use genetic building blocks typical of vertebrate eyes, namely, a ciliary phototransduction cascade and melanogenic pathway. Our findings indicative of parallelism provide an insight into eye evolution. Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution.

Cubozoan crystallins: evidence for convergent evolution of pax regulatory sequences

Cnidaria is the earliest-branching metazoan phylum containing a well-developed, lens-containing visual system located on specialized sensory structures called rhopalia. Each rhopalium in a cubozoan jellyfish Tripedalia cystophora has a large and a small complex, camera-type eye with a cellular lens containing distinct families of crystallins. Here, we have characterized J2-crystallin and its gene in T. cystophora. The J2-crystallin gene is composed of a single exon and encodes a 157-amino acid cytoplasmic protein with no apparent homology to known proteins from other species. The non-lens expression of J2-crystallin suggests nonoptical as well as crystallin functions consistent with the gene-sharing strategy that has been used during evolution of lens crystallins in other invertebrates and vertebrates. Although nonfunctional in transfected mammalian lens cells, the J2-crystallin promoter is activated by the jellyfish paired domain transcription factor PaxB in co-transfection tests via binding to three paired domain sites. PaxB paired domain-binding sites were also identified in the PaxB-regulated promoters of the J1A- and J1B-crystallin genes, which are not homologous to the J2-crystallin gene. Taken together with previous studies on the regulation of the diverse crystallin genes, the present report strongly supports the idea that crystallin recruitment of multifunctional proteins was driven by convergent changes involving Pax (as well as other transcription factors) in the promoters of nonhomologous genes within and between species as well as within gene families.

Eye evolution: lens and cornea as an upgrade of animal visual system

Lens-containing eyes are a feature of surprisingly broad spectrum of organisms across the animal kingdom that represent a significant improvement of simple eye composed of just photoreceptor cells and pigment cells. It is apparent that such an upgrade of animal visual system has originated numerous times during evolution since many distinct strategies to enhance light refraction through the use of lens and cornea have been utilized. In addition to having an ancient role in prototypical eye formation Pax transcription factors were convergently recruited for regulation of structurally diverse crystallins and genes affecting morphogenesis of various lens-containing eyes.

Evolution of graded refractive index in squid lenses

A lens with a graded refractive index is required for vision in aquatic animals with camera-type eyes. This optical design entails a radial gradient of protein density, with low density in external layers and high density in internal layers. To maintain the optical stability of the eye, different material properties are required for proteins in different regions of the lens. In low-density regions of the lens where slight protein aggregation causes significant light scattering, aggregation must be minimized. Squid lens S-crystallin proteins are evolutionarily derived from the glutathione S-transferase protein family. We used biochemistry, optical modelling and phylogenetics to study the evolution and material properties of S-crystallins. S-crystallins are differentially expressed in a radial gradient, suggesting a role in refractive index. This gradient in S-crystallin expression is correlated with their evolutionary history and biochemistry. S-crystallins have been under positive selection. This selection appears to have resulted in stabilization of derived S-crystallins via mutations in the dimer interface and extended electrostatic fields. These derived S-crystallins probably cause the glassy organization and stability of low refractive index lens layers. Our work elucidates the molecular and evolutionary mechanisms underlying the production and maintenance of camera-like optics in squid lenses.

The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation

Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-alpha-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors.

Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family

Selenoproteins are a diverse group of proteins that contain selenocysteine (Sec), the 21st amino acid. In the genetic code, UGA serves as a termination signal and a Sec codon. This dual role has precluded the automatic annotation of selenoproteins. Recent advances in the computational identification of selenoprotein genes have provided a first glimpse of the size, functions, and phylogenetic diversity of eukaryotic selenoproteomes. Here, we describe the identification of a selenoprotein family named SelJ. In contrast to known selenoproteins, SelJ appears to be restricted to actinopterygian fishes and sea urchin, with Cys homologues only found in cnidarians. SelJ shows significant similarity to the jellyfish J1-crystallins and with them constitutes a distinct subfamily within the large family of ADP-ribosylation enzymes. Consistent with its potential role as a structural crystallin, SelJ has preferential and homogeneous expression in the eye lens in early stages of zebrafish development. A structural role for SelJ would be in contrast to the majority of known selenoenzymes. The unusually highly restricted phylogenetic distribution of SelJ, its specialization, and the comparative analysis of eukaryotic selenoproteomes reveal the diversity and functional plasticity of selenoproteins and point to a mosaic evolution of the use of Sec in proteins.

Advanced optics in a jellyfish eye

Cubozoans, or box jellyfish, differ from all other cnidarians by an active fish-like behaviour and an elaborate sensory apparatus. Each of the four sides of the animal carries a conspicuous sensory club (the rhopalium), which has evolved into a bizarre cluster of different eyes. Two of the eyes on each rhopalium have long been known to resemble eyes of higher animals, but the function and performance of these eyes have remained unknown. Here we show that box-jellyfish lenses contain a finely tuned refractive index gradient producing nearly aberration-free imaging. This demonstrates that even simple animals have been able to evolve the sophisticated visual optics previously known only from a few advanced bilaterian phyla. However, the position of the retina does not coincide with the sharp image, leading to very wide and complex receptive fields in individual photoreceptors. We argue that this may be useful in eyes serving a single visual task. The findings indicate that tailoring of complex receptive fields might have been one of the original driving forces in the evolution of animal lenses.

Vertebrate-like ??-crystallins in the ocular lenses of a copepod

The diverse crystallins are water-soluble proteins that are responsible for the optical properties of cellular lenses of animal eyes. While all vertebrate lenses contain physiological stress-related alpha- and betagamma-crystallins, some also contain taxon-specific, often enzyme-related crystallins. To date, the alpha- and betagamma-crystallins have been found only in vertebrate lenses. Here we report lenses from an invertebrate, the pontellid copepod Anomalocera ornata, accumulate betagamma-crystallin family members as judged by immunocytochemistry, western immunoblotting and microsequencing. Our data provide the first example of betagamma-crystallin members in an invertebrate lens, establishing that the use of this protein family as lens crystallins is not confined to vertebrates.

Role of Pax genes in eye evolution: a cnidarian PaxB gene uniting Pax2 and Pax6 functions

PaxB from Tripedalia cystophora, a cubomedusan jellyfish possessing complex eyes (ocelli), was characterized. PaxB, the only Pax gene found in this cnidarian, is expressed in the larva, retina, lens, and statocyst. PaxB contains a Pax2/5/8-type paired domain and octapeptide, but a Pax6 prd-type homeodomain. Pax2/5/8-like properties of PaxB include a DNA binding specificity of the paired domain, activation and inhibitory domains, and the ability to rescue spa(pol), a Drosophila Pax2 eye mutant. Like Pax6, PaxB activates jellyfish crystallin and Drosophila rhodopsin rh6 promoters and induces small ectopic eyes in Drosophila. Pax6 has been considered a "master" control gene for eye development. Our data suggest that the ancestor of jellyfish PaxB, a PaxB-like protein, was the primordial Pax protein in eye evolution and that Pax6-like genes evolved in triploblasts after separation from Cnidaria, raising the possibility that cnidarian and sophisticated triploblastic eyes arose independently.

Enigma of the abundant water-soluble cytoplasmic proteins of the cornea: the "refracton" hypothesis

It is accepted that the taxon-specific, multifunctional crystallins (small heat-shock proteins and enzymes) serve structural roles contributing to the transparent and refractive properties of the lens. The transparent cornea also accumulates unexpectedly high proportions of taxon-specific, multifunctional proteins particularly, but not only, in the epithelium. For example, aldehyde dehydrogenase 3 (ALDH3) is the main water-soluble protein in corneal epithelial cells of most mammals (but ALDH1 predominates in the rabbit), whereas gelsolin predominates in the zebrafish corneal epithelium. Moreover, some invertebrates (e.g., squid and scallop) accumulate proteins in their corneas that are similar to their lens crystallins. Pax-6, among other transcription factors, is implicated in development and tissue-specific gene expression of the lens and cornea. Environmental factors appear to influence gene expression in the cornea, but not the lens. Although no direct proof exists, the diverse, abundant corneal proteins may have evolved a crystallinlike role, in addition to their enzymatic or cytoskeletal functions, by a gene sharing mechanism similar to the lens crystallins. Consequently, it is proposed that the cornea and lens be considered as a single refractive unit, called here the "refracton," to emphasize their similarities and common function.

J3-crystallin of the jellyfish lens: similarity to saposins

J3-crystallin, one of the three major eye-lens proteins of the cubomedusan jellyfish (Tripedalia cystophora), shows similarity to vertebrate saposins, which are multifunctional proteins that bridge lysosomal hydrolases to lipids and activate enzyme activity. Sequence alignment of deduced J3-crystallin indicates two saposin-like motifs arranged in tandem, each containing six cysteines characteristic of this protein family. The J3-crystallin cDNA encodes a putative precursor analogous to vertebrate prosaposins. The J3-crystallin gene has seven exons, with exons 2-4 encoding the protein. Exon 3 encodes a circularly permutated saposin motif, called a swaposin, found in plant aspartic proteases. J3-crystallin RNA was found in the cubomedusan lens, statocyst, in bands radiating from the pigmented region of the ocellus, in the tentacle tip by in situ hybridization, and in the embryo and larva by reverse transcription-PCR. Our data suggest a crystallin role for the multifunctional saposin protein family in the jellyfish lens. This finding extends the gene sharing evolutionary strategy for lens crystallins to the cnidarians and indicates that the putative primordial saposin/swaposin J3-crystallin reflects both the chaperone and enzyme connections of the vertebrate crystallins.

Retinoic acid X receptor in the diploblast, Tripedalia cystophora

Nuclear hormone receptors comprise a characteristic family of transcription factors found in vertebrates, insects and nematodes. Here we show by cDNA and gene cloning that a Cnidarian, Tripedalia cystophora, possesses a retinoid receptor (jRXR) with remarkable homology to vertebrate retinoic acid X receptors (RXRs). Like vertebrate RXRs, jRXR binds 9-cis retinoic acid (Kd = 4 x 10(-10) M) and binds to the DNA sequence, PuGGTCA as a monomer in vitro. jRXR also heterodimerizes with Xenopus TR beta on a thyroid responsive element of a direct repeat separated by 4 bp. A jRXR binding half-site capable of interacting with (His6)jRXR fusion protein was identified in the promoters of three T. cystophora crystallin genes that are expressed highly in the eye lens of this jellyfish. Because crystallin gene expression is regulated by retionoid signaling in vertebrates, the jellyfish crystallin genes are candidate in vivo targets for jRXR. Finally, an antibody prepared against (His6)jRXR showed that full-length jRXR is expressed at all developmental stages of T. cystophora except the ephydra, where a smaller form replaces is. These data show that Cnidaria, a diploblastic phylum ancestral to the triploblastic invertebrate and subsequent vertebrate lineages, already have an RXR suggesting that RXR is an early component of the regulatory mechanisms of metazoa.

Involvement of retinoic acid/retinoid receptors in the regulation of murine alphaB-crystallin/small heat shock protein gene expression in the lens

Crystallins are a diverse group of abundant soluble proteins that are responsible for the refractive properties of the transparent eye lens. We showed previously that Pax-6 can activate the alphaB-crystallin/small heat shock protein promoter via the lens-specific regulatory regions LSR1 (-147/-118) and LSR2 (-78/-46). Here we demonstrate that retinoic acid can induce the accumulation of alphaB-crystallin in N/N1003A lens cells and that retinoic acid receptor heterodimers (retinoic acid receptor/retinoid X receptor; RAR/RXR) can transactivate LSR1 and LSR2 in cotransfection experiments. DNase I footprinting experiments demonstrated that purified RAR/RXR heterodimers will occupy sequences resembling retinoic acid response elements within LSR1 and LSR2. Electrophoretic mobility shift assays using antibodies indicated that LSR1 and LSR2 can interact with endogenous RAR/RXR complexes in extracts of cultured lens cells. Pax-6 and RAR/RXR together had an additive effect on the activation of alphaB-promoter in the transfected lens cells. Thus, the alphaB-crystallin gene is activated by Pax-6 and retinoic acid receptors, making these transcription factors examples of proteins that have critical roles in early development as well as in the expression of proteins characterizing terminal differentiation.

Multifunctional lens crystallins and corneal enzymes. More than meets the eye

The abundant water-soluble proteins, called crystallins, of the transparent, refractive eye lens have been recruited from metabolic enzymes and stress-protective proteins by a process called "gene sharing." Many crystallins are also present at lower concentration in nonocular tissues where they have nonrefractive roles. The complex expression pattern of the mouse alpha B-crystallin/small heat shock protein gene is developmentally controlled at the transcriptional level by a combinatorial use of shared and lens-specific regulatory elements. A number of crystallin genes, including that for alpha B-crystallin, are activated by Pax-6, a conserved transcription factor for eye evolution. Aldehyde dehydrogenase class 3 and transketolase are metabolic enzymes comprising extremely high proportions of the water-soluble proteins of the cornea and may have structural as well as enzymatic roles, reminiscent of lens enzyme-crystallins. Inductive processes appear to be important for the corneal-preferred expression of these enzymes. The use of the same protein for entirely different functions by a gene-sharing mechanism may be a general strategy based on evolutionary tinkering at the level of gene regulation.

Genomic structure of a potassium channel toxin from Heteractis magnifica

We provide information on the gene encoding the K+ channel toxin, HmK, of the sea anemone Heteractis magnifica. A series of DNA amplifications by PCR, which included the amplification of the 5'-untranslated region of the gene, showed that an intron of 402 nucleotides separated the sequence that encodes the matured toxin from the signal peptide sequence. A second 264 nucleotide intron interrupted the 5'-untranslated region of the previously reported HmK cDNA. Two possible transcription-initiation sites were identified by primer extension analysis. Corresponding TATA-box consensus sequences, characteristic of a promoter region, were also located from PCR products of uncloned libraries of adaptor-ligated genomic DNA fragments. The coding region for matured HmK is intronless. The same is also true for other sea anemone toxins reported thus far. More notably, a similar intron-exon organization is present in other ion channel-blocking toxins from scorpions implying that molecules having similar functions share a similar organization at the genomic level suggesting a common path of evolution.

Lens crystallins of invertebrates--diversity and recruitment from detoxification enzymes and novel proteins

The major proteins (crystallins) of the transparent, refractive eye lens of vertebrates are a surprisingly diverse group of multifunctional proteins. A number of lens crystallins display taxon-specificity. In general, vertebrate crystallins have been recruited from stress-protective proteins (i.e. the small heat-shock proteins) and a number of metabolic enzymes by a gene-sharing mechanism. Despite the existence of refractive lenses in the complex and compound eyes of many invertebrates, relatively little is known about their crystallins. Here we review for the first time the state of knowledge of invertebrate crystallins. The major cephalopod (squid, octopus, and cuttlefish) crystallins (S-crystallins) have, like vertebrate crystallins, been recruited from a stress protective metabolic enzyme, glutathione S-transferase. The presence of overlapping AP-1 and antioxidant responsive-like sequences that appear functional in transfected vertebrate cells suggest that the recruitment of glutathione S-transferase to S-crystallins involved response to oxidative stress. Cephalopods also have at least two taxon-specific crystallins: omega-crystallin, related to aldehyde dehydrogenase, and omega-crystallin, related to a superfamily of lipid-binding proteins. L-crystallin (probably identical to O-crystallin) is the major protein of the lens of the squid photophore, a specialized structure for emitting light. The use of L/omega-crystallin in the ectodermal lens of the eye and the mesodermal lens of the photophore of the squid contrasts with the recruitment of different crystallins in the ectodermal lenses of the eye and photophore of fish. S-and omega-crystallins appear to be lens-specific (some S-crystallins are also expressed in cornea) and, except for one S-crystallin polypeptide (SL11/Lops4; possibly a molecular fossil), lack enzymatic activity. The S-crystallins (except SL11/Lops4) contain a variable peptide that has been inserted by exon shuffling. The only other invertebrate crystallins that have been examined are in one marine gastropod (Aplysia, a sea hare), in jellyfish and in the compound eyes of some arthropods; all are different and novel proteins. Drosocrystallin is one of three calcium binding taxon-specific crystallins found selectively in the acellular corneal lens of Drosophila, while antigen 3G6 is a highly conserved protein present in the ommatidial crystallin cone and central nervous system of numerous arthropods. Cubomedusan jellyfish have three novel crystallin families (the J-crystallins); the J1-crystallins are encoded in three very similar intronless genes with markedly different 5' flanking sequences despite their almost identical encoded proteins and high lens expression. The numerous refractive structures that have evolved in the eyes of invertebrates contrast markedly with the limited information on their protein composition, making this field as exciting as it is underdeveloped. The similar requirement of Pax-6 (and possibly other common transcription factors) for eye development as well as the diversity, taxon-specificity and recruitment of stress-protective enzymes as crystallins suggest that borrowing multifunctional proteins for refraction by a gene sharing strategy may have occurred in invertebrates as did in vertebrates.

Convergent evolution of crystallin gene regulation in squid and chicken: the AP-1/ARE connection

Previous experiments have shown that the minimal promoters required for function of the squid SL20-1 and SL11 crystallin genes in transfected rabbit lens epithelial cells contain an overlapping AP-1/antioxidant responsive element (ARE) upstream of the TATA box. This region resembles the PL-1 and PL-2 elements of the chicken beta B1-crystallin promoter which are essential for promoter function in transfected primary chicken lens epithelial cells. Here we demonstrate by site-directed mutagenesis that the AP-1/ARE sequence is essential for activity of the squid SL20-1 and SL11 promoters in transfected embryonic chicken lens cells and fibroblasts. Promoter activity was higher in transfected lens cells than in fibroblasts. Electrophoretic mobility shift and DNase protection experiments demonstrated the formation of numerous complexes between nuclear proteins of the embryonic chicken lens and the AP-1/ARE sequences of the squid SL20-1 and SL11 crystallin promoters. One of these complexes comigrated and cross-competed with that formed with the PL-1 element of the chicken beta B1-crystallin promoter. This complex formed with nuclear extracts from the lens, heart, brain, and skeletal muscle of embryonic chickens and was eliminated by competition with a consensus AP-1 sequence. The nonfunctional mutant AP-1/ARE sequences did not compete for complex formation. These data raise the intriguing possibility that entirely different, nonhomologous crystallin genes of the chicken and squid have convergently evolved a similar cis-acting regulatory element (AP-1/ARE) for high expression in the lens.