Sequence of the chicken delta 2 crystallin gene and its intergenic spacer. Extreme homology with the delta 1 crystallin gene

Patterns of Crystallin Gene Expression in Differentiation State Specific Regions of the Embryonic Chicken Lens

Purpose

Transition from lens epithelial cells to lens fiber cell is accompanied by numerous changes in gene expression critical for lens transparency. We identify expression patterns of highly prevalent genes including ubiquitous and enzyme crystallins in the embryonic day 13 chicken lens.

Methods

Embryonic day 13 chicken lenses were dissected into central epithelial cell (EC), equatorial epithelial cell (EQ), cortical fiber cell (FP), and nuclear fiber cell (FC) compartments. Total RNA was prepared, subjected to high-throughput unidirectional mRNA sequencing, analyzed, mapped to the chicken genome, and functionally grouped.

Results

A total of 77,097 gene-specific transcripts covering 17,450 genes were expressed, of which 10,345 differed between two or more lens subregions. Ubiquitous crystallin gene expression increased from EC to EQ and was similar in FP and FC. Highly expressed crystallin genes fell into three coordinately expressed groups with R² ≥ 0.93: CRYAA, CRYBB2, CRYAB, and CRYBA2; CRYBB1, CRYBA4, CRYGN, ASL1, and ASL; and CRYBB3 and CRYBA1. The highly expressed transcription factors YBX1, YBX3, PNRC1, and BASP1 were coordinately expressed with the second group of crystallins (r² > 0.88).

Conclusions

Although it is well known that lens crystallin gene expression changes during the epithelial to fiber cell transition, these data identify for the first time three distinct patterns of expression for specific subsets of crystallin genes, each highly correlated with expression of specific transcription factors. The results provide a quantitative basis for designing functional experiments pinpointing the mechanisms governing the landscape of crystallin expression during fiber cell differentiation to attain lens transparency.

Disruption of a salt bridge dramatically accelerates subunit exchange in duck delta2 crystallin

Intragenic complementation is a unique property of oligomeric enzymes with which to study subunit-subunit interactions. Complementation occurs when different subunits, each possessing distinct mutations that render the individual homomutant proteins inactive, interact to form a heteromutant protein with partial recovery of activity. In this paper, complementation events between human argininosuccinate lyase (ASL) and its homolog, duck delta2 crystallin, were characterized. Different active site mutants in delta2 crystallin complement by the regeneration of native-like active sites as reported previously for ASL. The complementarity of the ASL and delta2 crystallin subunit interfaces was illustrated by the in vivo formation of active hybrid tetramers from inactive ASL and inactive delta2 crystallin mutants. Subunits of both ASL and delta2 crystallin do not dissociate and reassociate in vitro at room temperature, even after 6 days of incubation, indicating that the multimerization interface is very strong. However, disruption of a salt bridge network in the tetrameric interface of delta2 crystallin caused a drastic acceleration of subunit dissociation. Double mutants combining these interface mutants with active site mutants of delta2 crystallin were able to dissociate and reassociate to form active tetramers in vitro within hours. These results suggest that exchange of subunits may occur without unfolding of the monomer. Intragenic complementation in these interface mutants occurs by reintroducing the native salt bridge interaction upon hetero-oligomerization. Our studies demonstrate the value of intragenic complementation as a tool for investigating subunit-subunit interactions in oligomeric proteins.

Guanidine hydrochloride induced reversible dissociation and denaturation of duck delta2-crystallin

The tetrameric delta2-crystallin from duck lens exhibits a reversible dissociation-denaturation process in solutions containing guanidine hydrochloride (GdnHCl). Sigmoidal or biphasic curves for the dissociation/denaturation processes, obtained using different methods of structural analysis, as a function of GdnHCl concentration were not coincidental with each other. delta2-crystallin in 0.91 M GdnHCl existed primarily as a monomer, which had no endogenous argininosuccinate lyase activity. After dilution of the GdnHCl-treated protein, the monomers reassociated into tetramers with concomitant recovery of enzyme activity. The sigmoidal recovery of enzyme activity demonstrates a cooperative hysteretic reactivation process. When the concentration of GdnHCl was higher than 1.2 M, various partially unfolded soluble forms of delta2-crystallin were produced from the dissociated monomers as shown by size-exclusion chromatography. The formation of a partially unfolded intermediate during the dissociation-denaturation process is proposed.

Lens-preferred activity of chicken delta 1- and delta 2-crystallin enhancers in transgenic mice and evidence for retinoic acid-responsive regulation of the delta 1-crystallin gene

There are two tandemly linked delta-crystallin genes [5' delta 1 -delta 2 3'] in the chicken, with the delta 1-crystallin gene being expressed much more highly (50-100-fold) in the embryonic lens than the delta 2-crystallin gene. Previous transfection experiments have shown that a lens-preferred enhancer exists in the third intron of each chicken delta-crystallin gene. In the present investigation we have used transgenic mice to establish that both the chicken delta 1- and delta 2-crystallin enhancers are preferentially active in the mouse lens in combination with their homologous promoter and the chloramphenicol acetyltransferase (CAT) reporter gene. The promoter/ CAT constructs lacking the enhancers were inactive in the transgenic mice. In one case, a truncated delta 2-crystallin promoter (-308/+24) in combination with the enhancer was also active in the Purkinje cells of the cerebellum of the transgenic mice, which could prove useful in future experiments. Finally, retinoic acid receptors (RAR beta) activated the delta 1-crystallin, but not the delta 2-crystallin enhancer in teh recombinant plasmids in cotransfected embryonic chicken lens epithelial cells treated with retinoic acid. This activation did not occur when using the care enhancer (fragment B4) lacking surrounding flanking sequences (fragment B3 and B5) of the enhancer. Together these experiments show that the chicken delta-crystallin enhancers show lens-preference in transgenic mice despite the absence of delta-crystallin in this species and add retinoic acid nuclear receptors to the growing list of transcription factors (including Pax-6, Sox-2, and delta EF3) that directly or indirectly contribute to the high expression of the delta 1-crystallin gene in the lens.

Up-regulation of crystallin mRNAs in form-deprived chick eyes

Form-deprivation of chicks during early postnatal development results in ocular enlargement and great myopic refractive error (form-deprivation myopia). Previous studies have indicated that the retina, RPE and choroid play important roles in ocular enlargement in form-deprivation myopia. We aimed to isolate genes up-regulated in the retina-RPE-choroid of form-deprived chick eyes. A suppression subtractive hybridization method was used to compare mRNA expression in the retina-RPE-choroid of form-deprived and control eyes. One up-regulated cDNA was isolated and identified as part of chick delta1-crystallin cDNA. Northern blot and RT-PCR analyses demonstrated that delta1-crystallin mRNA was up-regulated in the retina-RPE at day 7 after form-deprivation treatment. Semi-quantitative RT-PCE analysis of the expression of several transcription factors indicated that Sox1 and Sox3 were upregulated in parallel with delta1-crystallin mRNA in form-deprived eyes. Northern blot analysis demonstrated that alphaA-, betaA3/A1-, betaB1-, and betaB2-crystallin mRNAs were also up-regulated in form-deprived eyes. Although the detailed mechanisms and functions of the crystallin family genes in the retina-RPE-choroid of form-deprived eyes remain unclear, results of our study suggests that form-deprivation affects the expression of these genes in chick eyes.

Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate

Delta-crystallin, the major soluble protein component of avian and reptilian eye lenses, is highly homologous to the urea cycle enzyme, argininosuccinate lyase (ASL). In duck lenses, there are two highly homologous delta crystallins, delta I and delta II, that are 94% identical in amino acid sequence. While delta II crystallin has been shown to exhibit ASL activity in vitro, delta I is enzymatically inactive. The X-ray structure of a His to Asn mutant of duck delta II crystallin (H162N) with bound argininosuccinate has been determined to 2.3 A resolution using the molecular replacement technique. The overall fold of the protein is similar to other members of the superfamily to which this protein belongs, with the active site located in a cleft formed by three different monomers in the tetramer. The active site of the H162N mutant structure reveals that the side chain of Glu 296 has a different orientation relative to the homologous residue in the H91N mutant structure [Abu-Abed et al. (1997) Biochemistry 36, 14012-14022]. This shift results in the loss of the hydrogen bond between His 162 and Glu 296 seen in the H91N and turkey delta I crystallin structures; this H-bond is believed to be crucial for the catalytic mechanism of ASL/delta II crystallin. Argininosuccinate was found to be bound to residues in each of the three monomers that form the active site. The fumarate moiety is oriented toward active site residues His 162 and Glu 296 and other residues that are part of two of the three highly conserved regions of amino acid sequence in the superfamily, while the arginine moiety of the substrate is oriented toward residues which belong to either domain 1 or domain 2. The analysis of the structure reveals that significant conformational changes occur on substrate binding. The comparison of this structure with the inactive turkey delta I crystallin reveals that the conformation of domain 1 is crucial for substrate affinity and that the delta I protein is almost certainly inactive because it can no longer bind the substrate.

Structural comparison of the enzymatically active and inactive forms of delta crystallin and the role of histidine 91

The major soluble protein component of avian and reptilian eye lenses, delta crystallin, is highly homologous to the urea cycle enzyme, argininosuccinate lyase (ASL). In duck lenses there are two highly homologous delta crystallins, termed delta I and delta II, that are 94% identical in amino acid sequence. While delta II crystallin has been shown to exhibit ASL activity in vitro, delta I crystallin is inactive. The X-ray structure of a His to Asn mutant of duck delta II crystallin (H91N) has been determined to 2.5 A resolution using the molecular replacement technique. The overall fold of the protein is similar to other members of the superfamily to which this protein belongs, with the active site located in a cleft between three different monomers of the tetrameric protein. A reexamination of the kinetic properties of the H91N mutant reveals that the mutant has 10% wild-type activity. The Vmax of the mutant protein is identical to that of the wild-type protein, but a 10-fold increase in the Michaelis constant is seen, suggesting that His 91 is involved in binding the substrate. In an effort to determine the reasons for the loss of enzymatic activity in delta I crystallin, a structural comparison of the H91N mutant with the enzymatically inactive turkey delta I crystallin has been performed. This study revealed a remarkable similarity in the overall structures of the two proteins. Three regions of secondary structure do differ significantly between the two models; these include the N-terminal tail, a loop containing residues 76-91, and a cis versus trans peptide linkage at residue Thr 322. The cis to trans peptide variation appears to be an interspecies difference between turkey and duck and is therefore not directly involved in the loss of enzymatic activity. All the residues implicated in the catalytic mechanism are conserved in both the active and inactive proteins, and given the linearity of the relationship between the enzymatic activity of duck delta I/delta II heterotetramers and their delta II content (Piatigorsky & Horwitz, 1996), it is evident from the structure that only one of the three domains that contributes to the active site is responsible for the loss of activity in the delta I protein. Given the structural differences found in domain 1 (N-terminal tail and 76-91 loop), we postulate that these differences are responsible for the loss of catalytic activity in the delta I crystallin protein and that the delta I protein is inactive because it no longer binds the substrate.

pH-induced reversible dissociation of tetrameric duck lens delta-crystallin

Animal lenses constitute many soluble proteins, which play a prominent role in eyes' light transparency. delta2-Crystallin, one of the major taxon-specific crystallins in duck lens, is a tetrameric protein consisting of four identical subunits, which contain endogenous argininosuccinate lyase activity. Under a neutral pH environment in this work, the protein was cross-linked with glutaraldehyde as tetrameric and dimeric forms with tetramer as the major form. Under acidic conditions, the protein was time-dependently dissociated into monomers with amino acid residues of pKa values 6.29+/-0.45 and 7.17+/-0.49 being involved in the monomer-monomer interactions and 6.20+/-0.10 and 8.88+/-0.07 in the dimer-dimer interactions. Duck lens delta2-crystallin thus possesses a double dimer structure (alpha2)2 with stronger monomer-monomer interactions than the dimer-dimer interactions. The acidic protein solution's reneutralization caused rapid reassociation of monomers into dimers and tetramers. The tetramer-dimer-monomer dissociation-reassociation thus is a pH-dependent freely interconvertible process.

Characterization and enzyme activity of argininosuccinate lyase/delta-crystallin of the embryonic duck lens

Argininosuccinate lyase (ASL)/delta-crystallin, a major soluble protein of the transparent eye lens of birds and reptiles, is a mixture of tetramers comprising all possible combinations of two similar polypeptides (delta 1 and delta 2). Only the delta 2 polypeptide has ASL activity. In the present investigation we have purified each of the 5 major isoforms (delta A to delta E, pI 5.2 to 5.8) of delta-crystallin tetramers from the embryonic duck lens by isoelectric focussing and established by peptide sequencing that the delta 1 and delta 2 polypeptides are encoded in the previously identified, linked delta 1 and delta 2 genes, respectively. The relative amounts of the different tetramers in the 14-day-old embryonic lens were consistent with equal expression of the 2 delta-crystallin genes and no preference for assembly of the 2 delta polypeptides. The relative amount of ASL activity of the tetramers was a linear function of the relative amount of their delta 2 polypeptides, with delta A (only delta 1) lacking enzymatic activity altogether. delta B (3 delta 1:1 delta 2), delta C (2 delta 1:2 delta 2), delta D (1 delta 1:3 delta 2) and delta E (4 delta 2) all gave normal Michaelis-Menten kinetics for fumarate production from argininosuccinate at 40 degrees C and had a similar Km (average Km for mixture was 0.15 mM). delta E had a Km of 0.187 mM and a Vmax of 9 mumol/min per mg protein. Unlike bovine and like human ASL, both reported previously, embryonic duck ASL/delta-crystallin showed no evidence of cooperativity or activation by GTP. Each isoform had a similar far ultraviolet circular dichroism spectrum and thermal stability between 20 degrees C and 60 degrees C, with denaturation occurring at 65 degrees C. Our data suggest that gene duplication, structural modifications leading to greater thermal stability of the delta 1 and delta 2 polypeptides, and selective loss of ASL activity in the delta 1 polypeptide all occurred during the recruitment of ASL for a refractive role in the duck lens, resulting in the generation of ASL isoenzymes.

The chicken beta A4- and beta B1-crystallin-encoding genes are tightly linked

Analysis of the 5' flanking region of the chicken beta B1-crystallin-encoding gene (beta B1-cry) revealed regions of sequence homology with the bovine beta A4-crystallin-encoding gene (beta A4-cry). Subsequently, the chicken beta A4-cry cDNA sequence was determined, and it was demonstrated that beta A4- and beta B1-cry are linked head to head in the chicken chromosome with 2147 nucleotides (nt) of intergenic spacer. Chicken beta A4-cry contains six exons, with the first exon being noncoding. Chicken beta A4-cry is the smallest beta-cry ever described, due to the small size of its introns which range in length from 68 to 96 nt. While three polymorphisms were noted between some cDNA clones and the genomic sequence, Southern blot analysis demonstrated that beta A4-cry exists as a single copy in the chicken genome. Northern blot analysis indicated that beta A4-cry is a lens-specific transcript which is expressed at higher levels in the embryo than in the adult. The beta A4-cry mRNA is present at 400-fold lower levels than the beta B1-cry mRNA in the 14-day embryonic chicken lens, and at 2000-fold lower levels than the beta B1-cry mRNA in the adult lens. These results are consistent with the idea that the beta-cry family was once clustered in the chromosome as the gamma-cry family is today, and raises the possibility that the relatively low expression of beta A4-cry is mechanistically linked to the high expression of beta B1-cry in the chicken lens.

Exploring the role of histidines in the catalytic activity of duck delta-crystallins using site-directed mutagenesis

The duck delta 2-crystallin gene encodes an enzymatically-active argininosuccinate lyase while the delta 1-crystallin gene product, although 94% identical, is enzymatically inactive. Four histidine residues in the duck delta 2-crystallin. His91, His110, His162 and His178, were converted to asparagine residues in an effort to define the role of histidines in the catalytic process of this enzyme-crystallin and to explain the lack of enzyme activity in the delta 1-crystallin protein. The recombinant mutant proteins were expressed in E. coli and purified to homogeneity for analysis. These four residues were chosen because they fall within highly conserved regions of argininosuccinate lyases from several species. This analysis revealed that change of His91 or His162 for asparagine resulted in complete loss of activity. The His110 enzyme had a reduced Vmax and the His178 enzyme was near normal in its kinetic properties. These data confirm the roles of histidine in the catalytic process of this enzyme-crystallin and suggest that the change of His91 to Gln91 observed in the duck and chicken delta 1-crystallin molecules may be sufficient to account for the lack of enzymatic activity of those proteins.

Linkage and expression of the argininosuccinate lyase/delta-crystallin genes of the duck: insertion of a CR1 element in the intergenic spacer

delta-Crystallin is the major component of the lenses of most birds and reptiles. In the chicken there are two closely linked, tandemly oriented genes. Almost all of the delta-crystallin of the embryonic chicken lens is produced by the 5' delta 1 gene. This high lens activity has been attributed to an enhancer in intron 3. The 3' delta 2 gene encodes the enzyme argininosuccinate lyase (ASL) which is expressed at a low level in the chicken lens. Both chicken delta-crystallin genes are also expressed slightly in heart and brain, with ASL/delta 2 predominating over delta 1. In the duck (Anas platyrhynchos), ASL/delta 2-crystallin serves as both enzyme and crystallin, resulting in very high levels of ASL activity in the lens. Here we show by genomic cloning that the ASL/delta- crystallin locus is highly conserved between duck and chicken, with the two duck delta-crystallin genes closely linked in tandem. The 4.6 kbp intergenic spacer in the duck locus is 79% identical to the 4 kbp chicken spacer, except for the existence of a 615 bp CR1 element, highly reiterated in the duck genome, 1.8 kbp upstream of the duck ASL/delta 2 gene. The CR1 sequence is a truncated LINE element containing the 3' half of an open reading frame for a retroviral pol-like reverse transcriptase. Sequence analysis revealed (i) that intron 3 of the duck ASL/delta 2 gene is very similar (80%) to intron 3 of the chicken delta 1 and ASL/delta 2 genes, especially in the region of the chicken delta 1 enhancer core (93% identical) and (ii) that the 3' boundary of exon 2 of the duck ASL/delta 2 gene has undergone a recent splice-site slippage event, resulting in a two amino acid insertion in the encoded polypeptide. Finally, reverse transcription/polymerase chain reaction experiments established that both delta-crystallin genes are equally expressed to a high level in the embryonic duck lens; by contrast, both delta-crystallin genes produce a low amount of mRNA in the heart and brain of the embryonic duck, with the enzymatically active ASL/delta 2 being preferentially expressed.

Cloning of cDNAs encoding argininosuccinate lyase and arginase from Rana catesbeiana liver and regulation of their mRNAs during spontaneous and thyroid hormone-induced metamorphosis

Thyroid hormones are responsible for a change in the expression of many target genes during amphibian metamorphosis. In this study we cloned and sequenced cDNAs encoding two of the five urea cycle enzymes, argininosuccinate lyase and arginase, from adult liver of Rana catesbeiana. The cDNAs for the bullfrog argininosuccinate lyase and arginase encoded proteins of 467 and 321 amino acids with predicted molecular weights of 52,257 and 35,088, which were 72-75 and 64-68% identical to the mammalian enzymes, respectively. The accumulation of the mRNAs for argininosuccinate lyase and arginase in liver increased 26 and 4-times in a coordinated manner during spontaneous metamorphosis. Thyroid hormone-treatment induced about 5 and 10-times accumulation of mRNAs for argininosuccinate lyase and arginase in liver from premetamorphosing tadpoles within 4 days. These results suggest that the mRNA levels of the two enzymes in liver are upregulated by thyroid hormone during metamorphosis.

Sequence-specific scission of DNA by RNAs linked to a chemical nuclease

RNAs linked to the chemical nuclease 1,10-phenanthroline-copper cut double-stranded DNA of complementary sequence. This cleavage reaction is applicable to all sequences and can be used to measure the distance between marker genes in base pairs, map the size of a transcription unit and define positions of chromosomal breakpoints.

Differential expression of the two delta-crystallin genes in lens and non-lens tissues: shift favoring delta 2 expression from embryonic to adult chickens

Chicken argininosuccinate lyase (ASL)/delta-crystallin, a lens enzyme-crystallin, is encoded in two linked genes (delta 1 and delta 2); only the delta 2 polypeptide contains ASL activity. Here we have quantified delta 1- and delta 2-crystallin mRNA in the lens, cornea, neural retina, heart, and brain at different stages of embryonic development and in 1-wk-old and 1-yr-old chickens by the polymerase chain reaction using internal delta 1 and delta 2 RNA standards. The delta 1/delta 2 mRNA ratio differed for every tissue and was regulated during development. In the embryo there was more delta 1 than delta 2 mRNA in the lens (50-100 times), cornea (3-4 times), and neural retina (2-20 times), about equal amounts of delta 1 and delta 2 mRNA in the heart, and more delta 2 mRNA in the brain (15 times). delta 1-Crystallin mRNA differentially decreased in every tissue after hatching; by contrast, the delta 2 mRNA remained about the same except for the lens, where it decreased 50-fold between 1 wk and 1 yr after hatching. In the 1-yr-old chicken, the delta 2/delta 1 mRNA ratios were 7 in the lens, 175 in the cornea, 22 in the neural retina, 107 in the heart, and 136 in the brain, indicating that delta 2-crystallin is strongly favored in all adult tissues of the chicken. The excess of delta 1 to delta 2 mRNA in the embryonic lens, cornea, and neural retina is intriguing, and suggests some connection with developing transparent eye tissues. Finally, we raise the possibility that expression of both delta-crystallin genes may create tetrameric ASL isoenzymes (perhaps with different specific activities). The unexpected predominance of delta 2 mRNA in the 1-yr-old lens suggests that both the enzymatic and refractive functions of ASL/delta-crystallin are operative and spatially separated, with the enzymatic role present in the cortical fibers and the refractive role in the center of the lens.

Biochemical characterization of crystallins from pigeon lenses: structural and sequence analysis of pigeon delta-crystallin

Crystallins from pigeon eye lenses were isolated and purified by gel-permeation chromatography and characterized by gel electrophoresis, amino-acid composition and sequence analysis. Alpha- and beta-crystallins could be obtained in relatively pure forms by single-step size-exclusion chromatography whereas an extra step of ion-exchange chromatography was needed for the separation of delta-crystallin from the beta-crystallin fraction. In contrast to most characterized vertebrate species, a large amount of glycogen is eluted as a high molecular form in the first peak of the gel filtration column. Pigeon delta-crystallin, similar to duck and reptilian delta-crystallins, exists as a tetrameric structure of about 200 kDa in the native form and is composed of one major subunit of 50 kDa with heterogeneous isoelectric points spreading in a range of 4.7 to 6.8. In contrast to those obtained from duck, goose and caiman, delta-crystallin isolated from the pigeon lens possessed very little argininosuccinate lyase activity. However, pigeon delta-crystallin can still cross-react with the antibody against enzymically active duck delta-crystallin as revealed by the sensitive immunoblotting technique. It was also shown that the delta-crystallin content of the total pigeon soluble proteins decreased with the age of the animal. Structural analysis of purified delta-crystallin fraction was made with respect to its amino-acid composition and protein primary sequence. N-terminal sequence analysis indicated the presence of blocked amino-termini in all crystallin fractions of pigeon lenses. Therefore, a sequence analysis of PCR (polymerase chain reaction) amplified delta-crystallin cDNA was employed to deduce the protein sequence of this crystallin. Structural comparison of delta-crystallin sequences from pigeon, chicken and duck lenses casts some doubts on the recent claim that His-89-->Gln mutation in the chicken delta-crystallin may account for the loss of argininosuccinate lyase activity in this avian species, as compared to high enzymic activity in the duck crystallin (Barbosa et al. (1991) J. Biol. Chem. 266, 5286-5290).

Crystallin gene expression in the process of lentoidogenesis in cultures of chicken lens epithelial cells

One alpha B- and three different beta-crystallin cDNA clones were isolated from a chicken lens cDNA library by using anti-crystallin antibodies. The sequence of alpha B-crystallin cDNA showed more than 70% homology with exons of alpha B-crystallin genes of the human and hamster. Two beta-crystallin cDNAs showed almost identical sequences with previously reported chicken beta B1- and beta A3/A1-crystallin genes. The remainder showed 80% homology of sequence with bovine beta B2-crystalline cDNA. Using these newly cloned cDNAs, in addition to cDNAs of alpha A- and delta-crystallin, we examined the expression pattern of these crystallins in the process of lentoidogenesis of cultured lens epithelial cells of the chicken. All crystallins except beta-crystallins were expressed through the period of cell culture, but three beta-crystallins were expressed only after the confluent stage. These results suggest that: (1) alpha A-, alpha B- and delta-crystallin cDNAs can be used to detect differentiation of the lens epithelial cell; and (2) beta-crystallin cDNAs are superior in the detection of chicken lens fibre differentiation in vitro to delta-crystallin cDNA, which is ectopically expressed by various non-lenticular tissues.

Characterization of the aldose reductase-encoding gene family in rat

Although the enzyme aldose reductase (AR) is implicated in the development of tissue pathology in diabetes, the exact mechanism of this involvement remains unclear. To better understand the role that expression of the aldose reductase-encoding gene (ALR) may play in diabetic complications, we have begun to analyze the gene and its regulatory regions, and we present here the sequence of four ALR genes in the rat. The putative functional gene is 14.1 kb long, has ten exons which show perfect sequence identity to the rat lens AR RNA sequence, and nine introns with classical splice-site consensus sequences. Potential regulatory elements in the 5'-flanking region of this gene include a TATA box and two CCAAT boxes. Probing rat genomic Southern blots with a fragment from the first intron indicates that there is probably only one copy of this gene in the rat genome. The other three genes are processed pseudogenes which show approx. 90% identity to the rat lens AR RNA sequence, contain no introns, and have poly(A) regions at their 3' ends. Chromosomal localization studies show the presence of ALR genes on chromosomes 3, 4 and 6 in the rat with the putative functional gene mapped on chromosome 4.

Characterization of the human argininosuccinate lyase gene and analysis of exon skipping

A cosmid clone containing the entire human argininosuccinate lyase gene was isolated and characterized. The gene is approximately 35 kb in length and is divided into 16 exons. The sequence surrounding all splice sites was determined, and one unusual 5' splice site sequence in which a GC dinucleotide occurred instead of the consensus GT dinucleotide was observed. The exon structure of the gene is identical to that of the rat and similar to that of the delta-crystallin genes in the chicken. The transcription initiation site was identified, and 252 bases 5' of that site were sequenced. Within that region, the GC content is 75%, no TATA element was observed, and multiple potential Spl and CACCC binding sites were noted. Also, a putative consensus sequence that may play a role in the regulation of urea cycle genes was identified within this region. Analysis of the structure of the mature mRNA derived from this gene revealed that the sequences encoded by exon seven were deleted in approximately 5-10% of the mature mRNA in all tissue sources examined.

Delta-crystallin gene expression and patterns of hypomethylation demonstrate two levels of regulation for the delta-crystallin genes in embryonic chick tissues

In this study we address two questions regarding the control of delta-crystallin gene expression in chick embryos. First we have determined whether delta-crystallin mRNA is found outside of the developing lens, in which it is the predominant mRNA. We find that this mRNA can be detected, although at relatively low levels, in all embryonic tissues we have examined (from the definitive streak stage onward). This low level of transcription may be related to a second function for one or both of the delta-crystallin genes: both genes have a high degree of sequence identity to the enzyme argininosuccinate lyase. This result led us to a second set of experiments in which we reevaluated the possible role of hypomethylation in the expression of the delta-crystallin genes. Previous work showed that particular HhaI and HpaII sites in the crystallin genes undergo hypomethylation early in the process of lens differentiation when there is a burst of delta-crystallin mRNA accumulation. We not find that these sites remain methylated in nonlens tissues, implying that they cannot be required for the delta-crystallin gene activity found in these tissues. Other sites are constitutively hypomethylated, however, and may be functionally linked to this low level of gene activity. From an analysis of the kinetics of the developmentally regulated hypomethylation of HhaI and HpaII sites we also find that complete hypomethylation of these sites is not required for activating high levels of delta-crystallin transcription during lens differentiation. We do find, however, that these sites approach a fully hypomethylated state later in the lens differentiation process. Our analyses of mRNA levels and hypomethylation together lead us to propose that the delta-crystallin genes are regulated by two different mechanisms, one that leads to high levels of expression in the lens and the other which is responsible for low level expression in all other tissues in the chick embryo.

Independent regulation of two coexpressed delta-crystallin genes in chick lens and nonlens tissues

It is known that delta-crystallin is super-abundant in the early chick lens, but it is found at lower levels in certain other tissues. Ninety-nine percent of the lens delta-crystallin poly(A)+ RNA is from the delta 1-crystallin gene. We report here that the delta 1- and delta 2-crystallin genes are both transcribed in the chick lens and retina throughout embryonic development and that both RNAs are found in embryo adenohypophysis and epiphysis and in day-old posthatch chick tibiofemoral chondrocytes and striated muscle. delta 1-crystallin RNA is more abundant in lens tissues, while delta 2-crystallin RNA is more abundant in all nonlens tissues. However, delta 1-crystallin RNA is processed more efficiently than delta 2-crystallin RNA in all early embryonic tissues examined. A comparison of lens epithelium and fibers established that levels of delta 2-crystallin RNA are the same but those of delta 1-crystallin RNA are over 100-fold higher in fibers compared to epithelial cells. The evidence implies independent regulation both of transcription and of post-transcriptional events for these two genes.

Expression of the chicken 'delta 2-crystallin' gene in mouse cells: evidence for encoding of argininosuccinate lyase

In the chicken genome, downstream from the delta 1 gene, encoding delta-crystallin, a highly homologous gene called delta 2 is found, but neither its expression nor its function has been clarified. Close similarity of the delta 2 gene to mammalian argininosuccinate lyase (ASL)-encoding genes in organization and deduced amino acid sequence of the encoded protein suggested that this gene may encode chicken ASL. To test this possibility, we cloned the delta 2 gene on a plasmid, introduced it into mouse cells, and assessed expression and ASL activity in comparison with delta 1. We found that delta 2 was expressed well in fibroblastic L cells, which resulted in synthesis of a protein with a size (50 kDa) and antigenicity very close to delta-crystallin, but it was repressed in lens cells in which expression of delta 1 was activated. Transfectant L cell lines expressing delta 2 exhibited significantly higher ASL activity than those without. We conclude that the delta 2 gene codes for chicken ASL, but has a tissue specificity distinct from delta 1 in its expression.

Gene conversion and splice-site slippage in the argininosuccinate lyases/delta-crystallins of the duck lens: members of an enzyme superfamily

Argininosuccinate lyase(ASL)/delta-crystallin is a prominent example of an enzyme-crystallin with roles as both a catalyst and a major structural component of the eye lens in birds and reptiles. In chicken it appears that gene duplication and separation of function may have occurred with one gene product acting primarily as a crystallin and one primarily as an enzyme. However, two delta-crystallin-encoding genes are abundantly expressed in the lens of the embryonic duck (Anas platyrhynchos) which has extremely high ASL activity. Here the isolation and sequence analysis of full length cDNA clones for both duck delta-crystallins are described. The two delta-crystallins are highly similar (94% identical in predicted aa sequence), probably as a result of gene conversion. However, the cDNA for duck delta 2-crystallin contains an in-frame insertion of two codons, probably the result of a recent intron boundary slippage. ASL/delta-crystallin belongs to a superfamily of lyases, including fumarases, aspartases and adenylosuccinate lyase which possess some highly conserved blocks of aa sequence. There may be some clues to the tertiary structures of these conserved motifs in otherwise unrelated proteins for which three-dimensional structures are known.

Human alpha B-crystallin gene and preferential promoter function in lens

alpha B-Crystallin, first identified as a structural component of the vertebrate eye lens, is expressed at high levels in lens and at lower levels in a number of other tissues, most notably cardiac and skeletal muscle, kidney, and brain. We have cloned and sequenced the human alpha B-crystallin gene and show that it is structurally similar to its hamster homolog. We have also identified its transcription initiation site in human lens RNA. Functional analysis of a promoter fragment extending from -537 to +21 (relative to the transcription initiation site) and fused to the bacterial chloramphenicol acetyltransferase gene suggests that this fragment contains regulatory elements that function preferentially, but not exclusively, in lens. In contrast, this fragment is apparently insufficient to promote transcription in glial cells, as this construct functioned poorly in a glioblastoma-astrocytoma cell line (U-373MG) that synthesizes high levels of the endogenous alpha B-crystallin gene product.

Nutritional and hormonal regulation of mRNA abundance for arginine biosynthetic enzymes in kidney

Argininosuccinate synthetase and argininosuccinate lyase catalyze the synthesis of arginine from citrulline in kidney and also serve as components of the urea cycle in liver of ureotelic animals. Dietary and hormonal regulation of mRNAs encoding these enzymes have been well studied in liver but not in kidney. Messenger RNAs for these enzymes are localized within the renal cortex. Starvation and extreme variations in dietary protein content (0% vs 60% casein) produced 2.6- to 3.5-fold increases in mRNA abundance for these two enzymes in rat kidney. Argininosuccinate lyase mRNA was not induced by dibutyryl cAMP, dexamethasone, or a combination of the two agents. In contrast, argininosuccinate synthetase mRNA was induced 2-fold by dibutyryl cAMP but was unresponsive to dexamethasone. Thus, diet and hormones regulate levels of these mRNAs in rat kidney, but the responses are both qualitatively and quantitatively distinct from the responses previously reported for rat liver.

Evolutionary aspects of urea cycle enzyme genes

The functions and expression pattern of urea cycle enzymes have undergone considerable changes during the course of evolution. Sequence analyses shows that urea cycle enzymes from mammals are homologous to microbial enzymes of the arginine-metabolic pathway. Recently, an unexpected relationship was found between argininosuccinate lyase (EC 4.3.2.1), the fourth enzyme of the cycle, and delta-crystallin, a lens structural protein of birds and reptiles.

Conditions permitting the homotopic expression of lens-specific crystallin genes

delta-Crystallin is a major soluble protein of the avian and reptilian lens, and its expression is highly tissue-specific in development. In order to understand regulatory mechanisms for tissue-specific expression of delta-crystallin gene, several experimental systems were established in a heterologous combination of the chicken gene and mouse cells. The expression was ectopic in various cell types differentiated in teratomas derived from mouse teratocarcinoma or embryonic stem cells which were transformed to carry the chicken delta-crystallin genes. Cells of the same transformed lines of embryonic stem cells expressed the chicken gene homotopically in chimeric embryos produced by injecting them into the blastocysts. The homotopic expression also occurred in experimental systems consisting of the heterologous introduction of the gene (1) into various mouse cells in primary cultures, and (2) into male pronuclei of mouse fertilized eggs.

Evidence for positive and negative regulation in the promoter of the chicken delta 1-crystallin gene

We investigated the role of sequences flanking the transcription initiation site of the delta 1-crystallin gene in transient transfection assays of primary embryonic chicken lens epithelial cells or fibroblasts. Varying lengths of the 5' flanking sequence of the delta 1-crystallin gene (containing some untranslated sequence from exon 1) were fused to the bacterial chloramphenicol acetyltransferase (CAT) gene in the pSVOCAT plasmid. A plasmid carrying the bacterial beta-galactosidase gene driven by the Rous sarcoma virus (RSV) promoter was used as an internal control. Standardized results showed that the sequence located between -120 to -43 exhibited strong promoter activity; however, the promoter activity was markedly reduced (20-fold) when the upstream sequence between -603 and -120 was included in the construct. The delta 1-crystallin promoter displayed little lens preference. This upstream sequence did not reduce the activity of the Simian virus 40 (SV40) early promoter (with or without its enhancer) or the Herpes thymidine kinase promoter in transfection tests, indicating some specificity in its effect. Evidence for a delta 1-crystallin negative trans-acting factor was provided by competition experiments. Our data raise the possibility that expression of the delta 1-crystallin gene involves a negative cis-acting transcription element, a speculation which may deserve further attention in view of the gradual decrease in delta-crystallin synthesis in the developing lens.

Expression of the delta-crystallin genes in the embryonic chicken lens

The amounts of lens mRNA derived from the delta 1- and delta 2-crystallin genes of the chicken were determined by primer extension experiments using gene-specific synthetic oligonucleotides. The primer extended products were sequenced to establish the identity of the resulting cDNAs. The results indicated that most of the delta-crystallin mRNA in the 14-day-old embryonic lens contained transcripts derived from the delta 1 gene. Importantly, however, about 1-2% of the extended products were derived from delta 2 mRNA. Although not quantitative, the primer extension experiments suggested that the delta 1/delta 2 mRNA ratio may differ in the lens fiber cells during development between 6 days of embryogenesis and 3 weeks after hatching. These data provide the first demonstration for the presence of delta 2-crystallin mRNA in the chicken lens and raise the possibility that the two linked, extremely similar delta-crystallin genes are differentially regulated during development.

Lens-specific enhancer in the third intron regulates expression of the chicken delta 1-crystallin gene

We have previously shown that the tissue specificity determinant of the chicken delta 1-crystallin gene lies 3' of position -100 (Hayashi et al. 1985). Since the promoter of the gene (delta 1-crystallin promoter) did not show any tissue specificity, we examined various segments of the delta 1-crystallin gene for a tissue-specific enhancer activity by placing each segment downstream of a heterologous transcriptional unit coding for chloramphenicol acetyltransferase (CAT) and by transfecting chicken tissues in primary culture. We found that a segment spanning the third intron bears a strong lens-specific enhancer activity. This "delta 1-crystallin enhancer" activates transcription from the delta 1-crystallin promoter 20- to 40-fold in lens cells and to various degrees with other promoters. Deletion analysis of the enhancer region indicated that it covered nearly 1 kb but did not indicate clear-cut boundaries. For its enhancer effect the core region of 120 bp and associations with certain adjoining regions were required. Removal of the enhancer from the gene totally abolished delta 1-crystallin expression, and reinsertion of the enhancer in either upstream, internal, or downstream positions restored expression. We conclude that the delta 1-crystallin enhancer is an essential and major determinant for lens-specificity of delta 1-crystallin expression.

Conservation of delta-crystallin gene structure between ducks and chickens

A cloned chicken delta-crystallin cDNA was used to identify two putative delta-crystallin genes in the duck by Southern blot hybridization. A DNA fragment containing most of one of these genes was isolated from a library made in bacteriophage lambda Charon 28A containing genomic DNA from 14-day-old embryonic ducks. Electron microscopy, partial gene sequencing, primer extension analysis using duck mRNA, and comparison with the well-characterized chicken delta-crystallin genes suggest that our cloned duck delta-crystallin gene, like the chicken delta-crystallin genes, is 8-10 kb long and contains 17 exons. Hybridization and sequencing data show great similarity between the homologous 5' untranslated and coding exons of the duck and chicken delta-crystallin genes. Overall, the homologous introns also appear to have approximately 30% sequence similarity, and have been subject to deletion/insertion events. Our partial characterization of duck delta-crystallin gene sequences suggests that this avian and reptilian crystallin family has been conserved during evolution, as have the other crystallin gene families that are expressed in the eye lens.

Recruitment of enzymes as lens structural proteins

Crystallins, the principal components of the lens, have been regarded simply as soluble, structural proteins. It now appears that the major taxon-specific crystallins of vertebrates and invertebrates are either enzymes or closely related to enzymes. In terms of sequence similarity, size, and other physical characteristics delta-crystallin is closely related to argininosuccinate lyase, tau-crystallin to enolase, and SIII-crystallin to glutathione S-transferase; moreover, it has recently been demonstrated that epsilon-crystallin is an active lactate dehydrogenase. Enzymes may have been recruited several times as lens proteins, perhaps because of the developmental history of the tissue or simply because of evolutionary pragmatism (the selection of existing stable structures for a new structural role).

Complete nucleotide sequence of the chicken alpha A-crystallin gene and its 5' flanking region

The chicken alpha A-crystallin gene and 2.6 kb of its 5' flanking sequence have been isolated and characterized by electron microscopy and sequencing. The structural gene is 4.5 kb long and contains two introns, each approx. 1 kb in length. The first intron divides codons 63 and 64, and the second intron divides codons 104 and 105, as in rodents. There is little indication that the insert exon of rodents (an alternatively spliced sequence) is present in complete form in the chicken alpha A-crystallin gene; small stretches of similarity to this sequence were found throughout the gene. The 5' flanking sequence of the chicken alpha A-crystallin gene shows considerable sequence similarity with other mammalian alpha B-crystallin genes. In addition, one consensus sequence (GCAGCATGCCCTCCTAG) present in the 5' flanking region of the chicken alpha A-crystallin gene was found in the 5' flanking region of most reported crystallin genes.

Expression of the delta 1-crystallin gene: salt-dependent alteration in the cell-free synthesis of delta-crystallin polypeptides

We have investigated the origins of the two major size classes of delta-crystallin polypeptides (48 kDa and 50 kDa on sodium dodecyl sulfate-urea-polyacrylamide gels) in the chicken lens. Both the 48-kDa and 50-kDa polypeptides were produced by cell-free translation in a salt-dependent (Na+, K+, acetate and Cl-) pattern from mRNA derived from a cloned delta 1-crystallin cDNA. The salt-dependent alteration in the ratio of cell-free synthesis of the 48-kDa to 50-kDa delta-crystallin polypeptides was greatly enhanced by capping of the delta 1 mRNA. Translation of the delta 1 mRNA containing a premature termination codon suggested that the larger delta-crystallin band contains two polypeptides which differ in their N-terminal one-third. In vitro transcription/translation analysis of several mutant delta 1 cDNA clones and immunoblot analysis of authentic delta-crystallin with antisera raised to peptides contained in delta-crystallin showed that neither alternative initiation at two in-phase AUG codons nor alternative termination at sites on the delta 1 mRNA are responsible for generating the two sizes of the delta-crystallin polypeptides. Taken together our data suggest (but do not prove) that delta-crystallin heterogeneity is generated by co-translational modification of the primary polypeptide encoded in the delta 1-crystallin gene.

The eye lens crystallins: ambiguity as evolutionary strategy

Comparative studies of the different families of lens-specific proteins of the vertebrates, the crystallins, and their genes reveal several interesting evolutionary features. The origin of alpha-crystallin can be traced back to the small heat shock proteins, while the superfamily of beta gamma-crystallins shows structural similarities with a bacterial spore coat protein. The crystallins display a great diversity within and between species, as well as during development. Ambiguous transcription, mRNA-processing, and translation contribute to this diversity of the crystallins and their expression. These mechanisms include the occurrence of atypical poly-A addition signals, alternative splicing, and the use of two initiation codons on a single mRNA.

Two delta-crystallin polypeptides are derived from a cloned delta 1-crystallin cDNA

Previous studies have shown that there are 2 similar delta-crystallin genes (delta 1 and delta 2) and at least 2 delta-crystallin polypeptides in the chicken eye lens. We show here that both delta-crystallin polypeptides can be synthesized from mRNA transcribed in vitro from a cloned delta 1-crystallin cDNA. Both polypeptides co-migrate in SDS-urea-polyacrylamide electrophoresis with their authentic counterparts isolated from 15-day-old embryonic chicken lenses, and both react with sheep anti-chicken delta-crystallin serum. Screening nearly 900 delta-crystallin cDNA clones from a 15-day-old embryonic lens library with an oligonucleotide probe specific for exon 2 of the delta 2-crystallin gene failed to detect any delta 2 cDNA clones, indicating that the delta 2 gene produces little or no mRNA in the lens at this stage of development. Our results suggest that both of the observed delta-crystallin polypeptides are derived from mRNA transcribed from the delta 1 gene, with heterogeneity arising at the translational or co-translational level.