Diversity of beta-crystallin mRNAs of the chicken lens. Hybridization analysis with cDNA clones

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.

Structure and lens expression of the gene encoding chicken beta A3/A1-crystallin

The beta A1- and beta A3-crystallins are major polypeptides in the lenses of vertebrates. We present evidence that a single beta A3/A1 gene encodes these two proteins in the chicken. The beta A3/A1 gene has been sequenced and its functional promoter identified in transfection experiments. The chicken beta A3/A1 gene has the same structure as the human orthologue: six exons with standard splice sites and two alternative start codons from which the protein products are apparently translated. Northern analysis revealed an abundant 0.9-kb transcript in the lenses of 1-2-day-old chickens and no detectable transcripts in the rest of the eye, brain, heart, kidney, liver or skeletal muscle. The 5'-flanking sequence of the chicken beta A3/A1 gene is very similar to that of the human and mouse genes, suggesting conservation of important putative regulatory sequences in addition to the TATA box. A thymidine-rich element (bp -218 to -163) and a potential AP-1-binding site (bp -264 to -258) are present within the chicken 5'-flanking region. A DNA fragment from -382 to +22 of the chicken beta A3/A1 gene is sufficient to promote expression of the bacterial cat gene in transfected chicken primary lens epithelial cells, but not in transfected dermal fibroblasts.(ABSTRACT TRUNCATED AT 250 WORDS)

Accumulation of crystallin in developing chicken lens

Separation and quantitation of crystallin subunits in embryonic and post-hatched chicken lens were carried out by two-dimensional gel electrophoresis and an image analysing system in order to elucidate detail in the accumulation process of each crystallin subunit in lens differentiation. Complete separation of the subunits was possible when 7 M urea was included in the second dimension gel of the electrophoresis. In particular, beta-crystallin could be separated into more than 24 spots on the gel. These experiments showed that delta-crystallin accumulated rapidly during early development up to more than 80% of total crystallins, while beta-crystallin accumulated quickly only after hatching. In contrast with the contents of beta- and delta-crystallins, alpha-crystallin content in total crystallins was kept at approximately 18% throughout lens development. Therefore, it was concluded that crystallins accumulated in several different ways. This suggests that different regulation mechanisms work on the accumulation of each crystallin subunit and that the subunit composition of lens proteins is specific to each state of lens development.

Evidence for the extralenticular expression of members of the beta-crystallin gene family in the chick and a comparison with delta-crystallin during differentiation and transdifferentiation

The beta-crystallins are major water soluble proteins of vertebrate lens fibre cells and have previously been regarded as lens-specific proteins: however beta B2-and beta A3/A1-crystallin RNAs are transcribed and beta-crystallin polypeptides are detectable in the developing chick retina. The beta-crystallin RNA is transcribed in a subpopulation of retina cells and the number of transcribing cells and the level of beta-crystallin polypeptides increase during the differentiation of the retina. Several tissues express beta-crystallin polypeptides, but individual tissues are characterised by qualitative and quantitative differences in the beta- and delta-crystallin polypeptides expressed. The expression of beta-crystallins appears to be non-random as defined by tissue distribution, cellular localisation and ontogeny, implying a function for extralenticular beta-crystallins and a complex mechanism for the regulation of their expression.

Monoclonal antibodies to chick crystallins

Several monoclonal antibodies against chick crystallins were obtained. Immunoblot analysis indicated that the monoclonal antibodies distinguish not only the three classes of crystallin (alpha, beta and delta), but also their subclasses. Monoclonal antibodies alpha 2 and alpha 1 reacted exclusively with alpha A and alpha B, respectively, demonstrating that alpha-crystallin subclasses of the chicken are antigenically distinct. An immunohistological study utilizing these monoclonal antibodies showed that the two alpha-crystallin subclasses, alpha A and alpha B, are co-expressed in the same cells and are more concentrated in the epithelium than the fibers in 14-day-old chick embryo lenses. However, immunofluorescence suggested different distribution of alpha-crystallin subclasses within an epithelial cell. alpha A is distributed evenly in the cytoplasm, but alpha B is more concentrated in the fiber-proximal side. Using anti-beta monoclonal antibodies, it was shown that beta-crystallins are divided into three distinct subclasses according to their antigenicity: 27-kDa and 25-kDa beta-crystallins are recognized by beta 1 antibody, 26-kDa and 19-kDa beta-crystallins by beta 2 antibody, and 35-kDa beta-crystallins by beta 3 antibody. All of the anti-delta-crystallin monoclonal antibodies (delta 1 to delta 3) obtained here bound to all delta-crystallin molecular species separable by isoelectrofocusing.

Variation in the relative abundance of gamma-crystallin gene transcripts during development and ageing

The transcripts of gamma-crystallin mRNA were examined during adulthood. The mRNA transcripts were detected by Northern blot technique. Although the total RNA per lens measured remains constant during adulthood, the mRNA transcript size was observed to decline with ageing, specifically for the gamma-crystallin and not for alpha- and beta-crystallins. We could show that the relative amount of mRNA transcripts detected with the four probes decreased with ageing, with gamma 1 and gamma 2 transcripts being found at a higher level than the gamma 3 and gamma 4 transcripts.

Linkage between the beta B2 and beta B3 crystallin genes in man and rat: a remnant of an ancient beta-crystallin gene cluster

Human and rat genomic clones containing beta B2- and/or beta B3-crystallin sequences have been isolated and characterized. Both in the human and the rat genome the single-copy beta B3-crystallin gene is linked to a beta B2-crystallin gene. In both species the linked genes, separated by 20 kb in the human and 11 kb in the rat genome, are oriented head-to-tail with respect to transcription. A single copy of the beta B2-crystallin gene is present in the rat genome, in the human genome two copies of this gene are found. The second human copy could as yet not be linked to the beta B2/beta B3-crystallin gene cluster.

Alterations in crystallin gene expression during subculture of chick lens cells

We report here on the changes in crystallin gene expression during serial subculture of lens epithelial cells derived from day-old post-hatch chicks. Total cellular RNA from mass cultures were analysed by in vitro cell-free translation and by RNA blot (Northern) hybridization using a cloned delta-crystallin cDNA. Our results indicate that following subculture, lens epithelial cells which still retain the capacity for lens fibre differentiation (lentoid body formation) show a selective loss of delta-crystallin synthesis, and that this is related to the loss of delta-crystallin mRNA. The data suggest that older epithelial-cell populations give rise to lentoid bodies which in terms of crystallin gene expression closely resemble the later-formed cortical fibres of the adult chick lens. Tertiary cultures had an accelerated growth rate, formed no lentoids, contained no translatable alpha- or delta-crystallin mRNAs but still contained translatable beta-crystallin mRNAs.

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.

Preferential conservation of the globular domains of the beta A3/A1-crystallin polypeptide of the chicken eye lens

The primary structure of the beta 19/26-crystallin polypeptide of the chicken lens has been determined by cDNA sequencing and primer extension experiments. In addition, a primer extension experiment has corrected the sequence for the N-terminal arm of the murine beta 23 polypeptide, which is the homologue of the chicken beta 19/26 polypeptide. We also show that, in the chicken and mouse, the N-terminal arm of the polypeptide is encoded on two separate exons. For simplicity, we have changed the names of both chicken beta 19/26 and murine beta 23 to beta A3/A1, which is the name of the homologous bovine polypeptide. The deduced sequence of the chicken beta A3/A1 polypeptide fits the predicted three-dimensional structure involving two homologous domains, each folded into two 'Greek key' motifs, common to the beta gamma-crystallin superfamily of proteins. Comparison of the amino acid sequence of the chicken and mammalian beta A3/A1 polypeptides indicates that different regions of the protein, which are encoded on different exons, are diverging at different rates. The N-terminal extension is the fastest evolving region of the beta A3/A1 polypeptide. Hybrid-selected translation coupled with primer extension experiments suggest that a single chicken beta A3/A1 mRNA synthesizes two polypeptides, beta A3 (25 kDa) and beta A1 (23 kDa) by utilization of different translation initiation sites.

delta- and beta-Crystallin mRNA levels in the embryonic and posthatched chicken lens: temporal and spatial changes during development

The levels of delta- and beta-crystallin mRNAs were examined by cDNA hybridization in the embryonic and posthatched chicken eye lens. Four different cloned beta-crystallin cDNAs were used, allowing discrimination among different members of the beta-crystallin family. Each crystallin mRNA displayed a characteristic temporal and spatial pattern in the developing lens. delta-Crystallin mRNA accumulated rapidly during early embryonic development; by contrast, the beta-crystallin mRNAs began to accumulate rapidly near the end of embryogenesis. Both delta- and beta-crystallin mRNAs increased in the lens for the first month after hatching and began to decrease 3 months after hatching. The levels of the delta- and the different beta-crystallin mRNAs were also differentially regulated in cultured embryonic lens epithelia. The most fiber cell specific crystallin gene product in the differentiating lens was the beta 35 mRNA. These experiments provide a quantitative basis for exploring the differential expression of the delta- and beta-crystallin gene families in the chicken lens.

Rat lens beta-crystallins are internally duplicated and homologous to gamma-crystallins

The nucleotide sequence of two cloned rat lens beta-crystallin cDNAs pRL beta B3-2 and pRL beta B1-3 has been determined. pRL beta B3-2 contains the complete coding information for a beta-crystallin, designated beta B3, of 210 amino acid residues. pRL beta B1-3 is incomplete at its 5' end; the 5' codogenic information which is not present in this cDNA clone was deduced from the cloned gene. pRL beta B1-3 codes for a beta-crystallin polypeptide, designated beta B1, whose full length is 247 amino acid residues. Considerable sequence homology is noted between the amino- and carboxy-terminal halves of each protein. The two rat beta-crystallins show a substantial sequence homology with each other (60%) as well as with the published sequences of rat gamma-crystallin (37%) and bovine and murine beta-crystallins (55 and 45%). All these proteins have a two-domain structure which, like the bovine gamma II-crystallin, might be folded into four remarkably similar protein motifs. Our data further indicate that the beta-crystallins can be subdivided into two groups which are evolutionarily related. Both groups are, although more distantly, also related to the gamma-crystallins.

Comparison of the crystallin mRNA populations from rat, calf and duck lens. Evidence for a longer alpha A2-mRNA and two distinct alpha B2-mRNAs in the birds

Total cytoplasmic poly(A)-containing RNA from rat, calf and duck lens was fractionated by electrophoresis in methylmercury hydroxide-containing agarose gels. RNA electrophoresed in parallel lanes was either transferred onto nitrocellulose and hybridized with total cDNA synthesized on the initial mRNA or was recovered from individual gel fractions for in vitro translation in a reticulocyte cell-free system. This allowed the identification and size-characterization of individual mRNA species encoding alpha-, beta-, gamma- and delta-crystallin polypeptides. The 14 S mRNA fraction of rat lens comprises two alpha A2-mRNAs of approximately 1250 and 1350 nucleotides and the alpha AIns-mRNA with a size similar to that of the largest alpha A2-mRNA. The calf lens 14 S mRNA fraction harbors a heterogeneous population of alpha A2-mRNA. In the same fraction another mRNA encoding a polypeptide, designated X, has been found sharing no homology with alpha A sequences. The duck lens alpha A2-mRNA appears to be 400-450 bases longer than the rat and calf lens alpha A2-mRNAs. Furthermore, in contrast to the single alpha B2-mRNA in rat and calf lens, two alpha B2-mRNAs have been identified in duck lens, one, the major species, similar in size to the alpha B2-mRNA in rat and calf lens (800 bases), and the other species 700 nucleotides longer. The large size differences among the alpha A2- and alpha B2-mRNAs most likely reside in their 3'-untranslated sequences.

Characterization of the rat gamma-crystallin gene family and its expression in the eye lens

Rat genomic clones, which together contain all of the rat genomic gamma-crystallin sequences, have been characterized. Five gamma-crystallin genes are located on a contiguous DNA region, 63 X 10(3) base-pairs long. These genes, named (5') gamma 1-1, gamma 1-2, gamma 2-2 and gamma 3-1 (3'), are all oriented head to tail. A sixth gamma-crystallin gene, named the gamma 4-1 gene, could not be linked to the gamma-crystallin gene cluster with our present set of genomic clones. Mapping experiments using single copy sequences which form the extreme 5' or 3' region of the gene cluster showed that, if the gamma 4-1 gene is located on the same chromosome, then it must be separated from the gene cluster by at least 25 X 10(3) base-pairs of DNA. All gamma-crystallin genes have a similar mosaic structure. They contain a large (0.9 X 10(3) to 1.88 X 10(3) base-pairs) intron in the middle of the gene and are further interrupted close to the 5' end of the gene. The length of the first exon varies from about 40 to about 50 base-pairs. The complementary DNA clone pRL-gamma-3 used in this study is a copy of the transcript of the gamma 3-1 gene, while the second complementary DNA clone, pRL-gamma-2, is most likely a copy of the transcript of the gamma 2-1 gene. It is further shown that rat lens messenger RNA protects fragments from the 3' ends of the four other gamma-crystallin genes against degradation by S1 nuclease, hence all six gamma-crystallin genes present in the rat genome must be transcribed in the lens. Repetitive sequences were found to be present between and around the gamma-crystallin genes. Mapping with cloned repetitive sequences showed that three different repeats, designated A, B and C, occur more than once in the gamma-crystallin gene cluster. Repeat C is also found in the gamma 4-1 region. A repetitive region 3' to the gamma 3-1 gene contains members of all three repeat families.

The crystallin gene families

Recent work from our laboratory on the structure and the genetic organization of the lens beta- and gamma-crystallin gene families is reviewed briefly. In the rat six different gamma-crystallin genes are present which all have an identical distribution of exons and introns, namely a small intron after the third translation codon and a larger one within the coding region for the connecting peptide which links the two domains of the gamma-crystallins. We find five rat genes physically linked and located on a DNA segment of only 50 kilobases, whereas the sixth gene is more distant. The polypeptide sequences, as deduced from DNA sequence analysis, of these six rat and two human gamma-crystallin genes are compared and discussed in terms of structural and evolutionary aspects. The gene coding for rat beta B1a-crystallin appears to be a single-copy gene of much larger size than the gamma-crystallin genes. The beta B1 gene is not physically linked to the other beta-crystallin genes, even though the various beta genes are evolutionarily related and in that sense constitute a gene family. In contrast to the gamma-crystallin genes, the beta B1 gene has an intron not only between the domain sequence but also between the motif sequences. In addition, the exon coding for the N-terminal extension of the protein is separated by an intron from the first protein motif sequence. We anticipate that structural and genetic investigations on lens crystallin genes and their expression might provide a framework for revealing the basis of (some) hereditary disorders in the visual system.

Crystallin genes: templates for lens transparency

Analysis of recombinant DNAs provides new information on the basis of crystallin evolution and diversity. All crystallin genes contain introns. Two similar, tandemly linked chicken delta-crystallin genes, which probably arose by gene duplication, contain at least 16-17 introns. In the beta-crystallins three introns are situated between exons encoding the structural motifs of the protein, thus relating gene and protein structure. The structurally similar beta- and gamma-crystallins are coded by separate gene families which apparently arose by successive duplications of a common ancestral gene. The N-termini (5' end of gene) of the beta-crystallins appear to have diverged, while the 3' ends have been conserved. In the single murine alpha A-crystallin gene, coding information (the insert exon) for the alpha Ains peptide is contained within an intron. Alternative RNA splicing of this gene gives both the alpha A2 and the alpha Ains crystallin mRNAs. Thus, molecular genetics is providing a deeper appreciation of evolutionary events and is serving to redefine the crystallins in terms of their genes. Since the crystallins are so abundant in the lens, greater understanding of their polypeptide and gene structure should contribute to our understanding of and ability to treat cataract.

Bovine beta-crystallin complementary DNA clones. Alternating proline/alanine sequence of beta B1 subunit originates from a repetitive DNA sequence

A library of recombinant plasmids carrying complementary DNA sequences synthesized from bovine lens messenger RNAs was constructed. Clones coding for five different beta-crystallin subunits: beta B1, beta B3, beta Bp, beta s, beta A3 (and beta A1), were identified by means of hybridization selection, followed by one- and two-dimensional gel electrophoresis of the translational products. Under rather stringent conditions each of these clones hybridizes with its corresponding mRNA and does not show significant cross-hybridization with mRNAs coding for other beta-crystallins, except in the case of the homologous beta A3 and beta A1-crystallins. The beta A3 and beta A1 subunits seem to be encoded by one mRNA using two different AUG codons as start position for translation. We have also determined the nucleotide sequence of a beta B1-crystallin cDNA (pBL beta B1) which enabled us to deduce the complete amino acid sequence of the protein. The beta B1-crystallin, a characteristic component of the high molecular weight crystallin aggregate (beta H), is internally homologous both at DNA and protein level as has been reported for gamma- and other beta-crystallins. This is in agreement with the idea that these proteins had a common ancestral precursor gene that internally duplicated. The G + C content of the coding sequence of beta B1 is very high: 67% overall and even 84.2% for the first 170 nucleotides, due to a remarkable non-random codon usage. A proline/alanine repetition in the N-terminal domain of the protein is encoded by a repetitive "simple" DNA sequence.

Homology between the primary structures of the major bovine beta-crystallin chains

Partial amino acid sequences of six major subunits of bovine beta-crystallin have been determined by automatic liquid-phase Edman degradation and the dansyl-Edman procedure, complemented by amino acid analyses of peptides. The results show that, including the previously established beta Bp sequence [H. P. C. Driessen et al. (1981) Eur. J. Biochem. 121, 83-91], there exist at least seven primary gene products in bovine beta-crystallin, which exhibit 40% or more sequence homology. Two of the gene products are completely identical except for the presence in one of them of 17 additional residues at the N terminus, possibly caused by differential splicing of the same primary RNA transcript. The rate of evolutionary change of the beta chains (4% sequence change per 100 X 10(6) years) is about equally slow as that of alpha-crystallin, and the gene duplications giving rise to the different chains must have occurred very early in vertebrate evolution. The beta chains can be divided into two groups, according to sequence homology and presence of deletions/insertions and C-terminal extension, on which basis a new, rational nomenclature for the beta subunits is introduced. The N-terminal extensions of all beta chains are very different in length and sequence, even between homologous beta chains in different species. Possible explanations for this finding are discussed.