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Xu Z, Asakawa S. A model explaining mRNA level fluctuations based on activity demands and RNA age. PLoS Comput Biol 2021; 17:e1009188. [PMID: 34297727 PMCID: PMC8336849 DOI: 10.1371/journal.pcbi.1009188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/04/2021] [Accepted: 06/17/2021] [Indexed: 11/19/2022] Open
Abstract
Cellular RNA levels typically fluctuate and are influenced by different transcription rates and RNA degradation rates. However, the understanding of the fundamental relationships between RNA abundance, environmental stimuli, RNA activities, and RNA age distributions is incomplete. Furthermore, the rates of RNA degradation and transcription are difficult to measure in transcriptomic experiments in living organisms, especially in studies involving humans. A model based on activity demands and RNA age was developed to explore the mechanisms of RNA level fluctuations. Using single-cell time-series gene expression experimental data, we assessed the transcription rates, RNA degradation rates, RNA life spans, RNA demand, accumulated transcription levels, and accumulated RNA degradation levels. This model could also predict RNA levels under simulation backgrounds, such as stimuli that induce regular oscillations in RNA abundance, stable RNA levels over time that result from long-term shortage of total RNA activity or from uncontrollable transcription, and relationships between RNA/protein levels and metabolic rates. This information contributes to existing knowledge. Detected cellular RNA levels usually fluctuate. The understanding of the fundamental relationships between RNA level fluctuations, the rates of RNA degradation and transcription, environmental stimuli, RNA activities, and RNA age distributions is incomplete. In the present research, we developed a model based on the demands of RNA (related to intrinsic and/or extrinsic information), RNA age (determines the survival time and biological activity of an RNA), transcription, and RNA degradation to explain the mechanism underlying intracellular RNA level fluctuations. We also explored applicability of the model for analysing dynamic processes between interacting biomolecules, such as the relationship between RNA and protein level fluctuations. Using single-cell time-series gene expression experimental data, we assessed some biological parameters, such as transcription rates, RNA degradation rates, and RNA life spans. This model could also predict RNA levels under simulation backgrounds, such as stimuli that induce regular oscillations in RNA abundance, stable RNA levels over time that result from long-term shortage of total RNA activity or from uncontrollable transcription, and relationships between RNA/protein levels and metabolic rates. This information contributes to existing knowledge and provides a new perspective for future studies.
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Affiliation(s)
- Zhongneng Xu
- Department of Ecology, Jinan University, Guangzhou, China
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail: ,
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Affiliation(s)
- J Graw
- GSF National Research Center for Environment and Health, Laboratory of Molecular Eye Development, Neuherberg, Germany
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Eiberg H, Lund AM, Warburg M, Rosenberg T. Assignment of congenital cataract Volkmann type (CCV) to chromosome 1p36. Hum Genet 1995; 96:33-8. [PMID: 7607651 DOI: 10.1007/bf00214183] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Congenital cataract, type Volkmann (McKusick no 115665, gene symbol CCV) is an autosomal dominant eye disease. The disease is characterized by a progressive, central and zonular cataract, with opacities both in the embryonic, fetal and juvenile nucleus and around the anterior and posterior Y-suture. We examined blood samples from 91 members of a Danish pedigree comprising 426 members, by using highly informative short tandem repeat polymorphisms and found the closest linkage of the disease gene (CCV) to a (CA)n dinucleotide repeat polymorphism at locus D1S243 (Zmax = 14.04 at theta M = 0.025 theta F = 0.000), at a penetrance of 0.90. Using two additional chromosome 1 markers, we were able to map the CCV gene in the sequence 1pter-(CCV, D1S243)-D1S468-D1S214. The (enolase 1) gene has been mapped to this area; however, a mutation described in this gene did not give eye disease.
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Affiliation(s)
- H Eiberg
- University Institute of Medical Biochemistry & Genetics, Department of Medical Genetics B24.4, Danish Centre for Genome Research, Copenhagen
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Lund AM, Eiberg H, Rosenberg T, Warburg M. Autosomal dominant congenital cataract; linkage relations; clinical and genetic heterogeneity. Clin Genet 1992; 41:65-9. [PMID: 1544213 DOI: 10.1111/j.1399-0004.1992.tb03634.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Congenital cataract is a heterogeneous disorder. Approximately one third of the cases are hereditary. A large family with autosomal dominant congenital cataract is described here. Clinical examinations showed variable expressivity, but all affected persons were eventually operated, most of them in the first or second decade of life. Linkage relations with a number of polymorphic marker systems were studied, all of them being negative. Among the 21 systems studied were Fy, HP, D16S4 and CRYG. The present autosomal dominant congenital cataract is termed the Volkman cataract, after the ancestor in the pedigree, and is genotypically different from the Marner cataract found in another large Danish pedigree.
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Affiliation(s)
- A M Lund
- Division of Pediatric Ophthalmology and Handicaps, Gentofte Hospital, Denmark
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Shiels A, Griffin CS, Muggleton-Harris AL. Immunochemical comparison of the major intrinsic protein of eye-lens fibre cell membranes in mice with hereditary cataracts. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1097:318-24. [PMID: 1742336 DOI: 10.1016/0925-4439(91)90087-p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Expression of the major intrinsic protein (MIP) of eye-lens fibre cell membranes was compared in normal (DBA), cataractous (CAT, LOP, NCT) and chimaeric (CBA-LOP) mice at different stages of development using immunofluorescence microscopy and immunoblotting techniques. MIP of apparent molecular mass 26 kDa was detected in extracts of adult DBA, LOP and CBA-LOP lenses, but only low molecular mass (less than 26 kDa) immunoreactive proteins were detected in similar extracts from adult CAT and NCT lenses. The corresponding MIP distribution patterns confirmed the highly organised fibre-cell histology in embryonic DBA and adult CBA-LOP lenses and also highlighted the severe fibre-cell degeneration in the LOP lens. In contrast, however, no immunoreactive MIP was detected in situ in embryonic CAT and NCT lenses. These results suggest that a structural alteration of MIP occurs during embryonic lens development in the cataractous CAT (dominant) and NCT (recessive) mutant mice.
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Affiliation(s)
- A Shiels
- Department of Haematology, St Mary's Hospital Medical School, Imperial College of Science, Technology and Medicine, London, U.K
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Shiels A, Griffin CS, Muggleton-Harris AL. Restriction fragment length polymorphisms associated with the gene for the major intrinsic protein of eye-lens fibre cell membranes in mice with hereditary cataracts. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1097:81-5. [PMID: 1677593 DOI: 10.1016/0925-4439(91)90028-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cloned cDNAs coding for eye-lens fibre cell-membrane proteins, MIP and MP70, were used to detect restriction fragment length polymorphisms (RFLPs) in genomic DNA from inbred mice with autosomally inherited cataracts. Whereas distinct RFLPs associated with the MIP gene were identified in the Cba Cat and Nct mutants, no such genetic variation was associated with the MP70 gene. RFLPs associated with the mouse MIP gene may provide informative DNA markers in gene linkage studies of murine hereditary cataracts.
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Affiliation(s)
- A Shiels
- Department of Haematology, St Mary's Hospital Medical School, Imperial College of Science, Technology and Medicine, London, U.K
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Sankaranarayanan K. Ionizing radiation and genetic risks. II. Nature of radiation-induced mutations in experimental mammalian in vivo systems. Mutat Res 1991; 258:51-73. [PMID: 2023600 DOI: 10.1016/0165-1110(91)90028-t] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This paper reviews data on the nature of spontaneous and radiation-induced mutations in the mouse. The data are from studies using a variety of endpoints scorable at the morphological or the biochemical level and include pre-selected as well as unselected loci at which mutations can lead to recessive or dominant phenotypes. The loci used in the morphological recessive specific-locus tests permit the recovery of a wide spectrum of induced changes. Important variables that affect the nature of radiation-induced mutations (assessed primarily using tests for viability of homozygotes) include: germ cell stage, type of irradiation and the locus. Most of the results pertain to irradiated stem cell spermatogonia. The data on morphological specific-locus mutations show that overall, more than two-thirds of the X- or gamma-ray-induced mutations are lethal when homozygous. This proportion may be lower for those that occur spontaneously, but the numbers of tested mutants are small. For spontaneous mutations, there is evidence for the occurrence of mosaics and for proviral insertions. Most or all tested induced enzyme activity variants, dominant visibles (recovered in specific-locus experiments) and dominant skeletal mutations are lethal when homozygous and this is true of 50% of dominant cataract mutations, but again, the numbers of tested mutants are small. Electrophoretic mobility variants, which are known to be due to base-pair changes, are seldom induced by irradiation. At the histocompatibility loci, no radiation-induced mutations have been recovered, presumably because deletions are incompatible with survival even in heterozygotes. All these findings are consistent with the view that in mouse germ cells, most radiation-induced mutations are DNA deletions. Some mutations (in the morphological specific-locus tests) which had previously been inferred to be deletions on the basis of genetic analyses have now been shown to be DNA deletions by molecular methods. However, the possibility cannot be excluded that at least a small proportion of induced mutations may be intragenic changes. The data on the rates of induction of recessive lethals and of dominant skeletal and dominant cataract mutations (and proportions of the latter two which are homozygous lethal) can be used to estimate the proportions of recessive lethals which are expressed as skeletal abnormalities or cataracts. These calculations show that about 10% of recessive lethals manifest themselves as skeletal and less than 0.2% as cataract mutations.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- K Sankaranarayanan
- MGC Department of Radiation Genetics and Chemical Mutagenesis, Sylvius Laboratories, State University of Leiden, The Netherlands
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Bodker FS, Lavery MA, Mitchell TN, Lovrien EW, Maumenee IH. Microphthalmos in the presumed homozygous offspring of a first cousin marriage and linkage analysis of a locus in a family with autosomal dominant cerulean congenital cataracts. AMERICAN JOURNAL OF MEDICAL GENETICS 1990; 37:54-9. [PMID: 2240043 DOI: 10.1002/ajmg.1320370113] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A family with autosomal dominant congenital cataracts was studied to determine clinical variability. A total of 159 relatives was ascertained; 17 affected and 19 normal individuals were evaluated and their blood sampled for inclusion in the linkage analysis. The disease was compatible with normal to mildly decreased visual acuity until adult life in all affected except the product of a consanguineous marriage of affected first cousins who was born with bilateral microphthalmos and dense congenital cataracts, attributed to homozygosity of the cataract gene. There were no extraocular abnormalities; the patient was of normal intelligence. Twenty-three markers were typed, 18 of which were informative. Linkage could be excluded for all 18 markers at short distances.
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Affiliation(s)
- F S Bodker
- Wilmer Ophthalmological Institute, Johns Hopkins Hospital, Baltimore, Maryland 21205
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Russell P, Chambers C. Interaction of an altered beta-crystallin with other proteins in the Philly mouse lens. Exp Eye Res 1990; 50:683-7. [PMID: 2373162 DOI: 10.1016/0014-4835(90)90114-a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An altered beta B2-crystallin is synthesized in the lens of the Philly mouse. This beta B2 has a more acidic isoelectric point than the beta B2 that is isolated from normal mouse lens. The altered beta B2 is immunologically reactive with antibody to the amino terminal of the beta B2-crystallin, but appears to be present in only very small quantities in the Philly lens. When the soluble proteins are isolated from the Philly lens and chromatographed by gel exclusion chromatography, the beta B2 can be found primarily in the heavy molecular weight fraction. Some immunoreactive material was also found throughout the higher molecular weight beta-crystallin region, beta H, and the lower molecular weight region, beta L. These results would indicate that the altered beta B2-crystallin in the Philly lens can interact with the other beta-crystallins in the lens; however, interactions of the beta B2-crystallin with the other proteins of the lens may cause rapid aggregation of the cellular proteins leading to the formation of the heavy molecular weight material. The increased number of these aggregates may eventually lead to the cataract formation in the Philly mouse.
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Affiliation(s)
- P Russell
- National Institutes of Health, Bethesda, MD 20892
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Abstract
The increasing use of animal models in the study of cataract has been one of the most important trends in lens research over the last two decades. The number of animal models available for both hereditary congenital cataracts and for maturity-onset cataracts has grown substantially during this time. Analysis of some of these systems by biochemical and molecular biology techniques has resulted in significant and often surprising insights into the basic biology of the lens, as well as the process of cataractogenesis. The following is a brief overview of those animal models for which biochemical studies have been reported.
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Affiliation(s)
- J S Zigler
- Laboratory of Mechanisms of Ocular Disease, National Eye Institute, National Institutes of Health, Bethesda, MD 20892
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12
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Jiang YJ, Chiou SH, Chang WC. Lens crystallin changes associated with amphibian metamorphosis: involvement of a beta-crystallin polypeptide. Biochem Biophys Res Commun 1989; 164:1423-30. [PMID: 2590209 DOI: 10.1016/0006-291x(89)91829-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Lens crystallins isolated from the tadpole and frog lenses were compared with regard to the developmental changes of crystallin compositions. The major changes during the process of metamorphosis were (1) the total contents of alpha- and gamma-crystallins decrease from more than 70% to less than 60% and (2) one of the major beta-crystallin polypeptides increases from less than 1% to about 6% and (3) an amphibian-specific rho-crystallin also increases from about 6% to more than 10% of total soluble proteins of the lens. We have characterized the metamorphosis-dependent beta-crystallin polypeptide by peptide mapping and sequence determination of the protease-digested fragments. This polypeptide showed very high sequence homology to that of the major beta Bp-crystallin chain reported for the mammalian lenses. The changes of the relative abundance of various crystallins and the gradually-elevated levels of the expression of this beta Bp-like crystallin in the developing lens during metamorphosis may also have some bearing on the maintenance of lens stability in the adult frog lenses.
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Affiliation(s)
- Y J Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, R.O.C
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Graw J, Kratochvilova J, Löbke A, Reitmeir P, Schäffer E, Wulff A. Characterization of Scat (suture cataract), a dominant cataract mutation in mice. Exp Eye Res 1989; 49:469-77. [PMID: 2792238 DOI: 10.1016/0014-4835(89)90055-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The autosomal, dominant mutation Scat (suture-cataract) was found in (101/El x C3H/El)F1-hybrid mice. The severity of the cataract is dependent on the gene dose. The mutation causes an anterior suture opacity in heterozygotes amd microphthalmia with vacuolated lenses in homozygotes. In histological sections of lenses the heterozygotes exhibit a hydropic swelling of lens epithelium, whereas in homozygotes interruption and degeneration of lens fibers as well as clefts and folds of the capsule were observed. The mutation has a complete penetrance and constant expressivity. The body weight of the mutants is not altered; the mutation has no effects on fertility or viability. The lens wet and dry weights are diminished (more pronounced in the homozygotes). The water content of the lens is enhanced only in the homozygous Scat mutants. Biochemically, the lenticular content of water-soluble proteins is decreased in the homozygous Scat mutants. By electrophoresis, in the lenses of homozygous Scat mutants a different pattern of water-soluble proteins could be observed. The lenses of both, heterozygous and homozygous Scat mutants exhibit enhanced Na+,K+-ATPase activity and a decreased ATP concentration. The genetical, morphological or biochemical data suggest that the effect of the Scat mutation is distinct from other described cataract mutations in mice.
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Affiliation(s)
- J Graw
- GSF-Institut für Säugeliergenetik, Neuherberg, Federal Republic of Germany
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Alteration of a developmentally regulated, heat-stable polypeptide in the lens of the Philly mouse. Implications for cataract formation. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37412-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Barrett DJ, Sparkes RS, Gorin MB, Bhat SP, Spence MA, Marazita ML, Bateman JB. Genetic linkage analysis of autosomal dominant congenital cataracts with lens-specific DNA probes and polymorphic phenotypic markers. Ophthalmology 1988; 95:538-44. [PMID: 3174013 DOI: 10.1016/s0161-6420(88)33153-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The authors studied a four-generation family with autosomal dominant congenital cataracts (ADCCs) using linkage analysis with 23 polymorphic phenotypic markers and DNA restriction fragment length polymorphisms (RFLPs) detected by lens-specific DNA probes. A total of 19 family members were studied and the ten affected members had embryonal lens opacities. Close linkage was rejected with DNA probes encoding beta-crystallin, gamma-crystallin, and the major intrinsic protein of the lens fiber membrane (MIP) excluding defects of these genes as the cause of the cataract in this family. No statistically significant lod scores were produced with the polymorphic phenotypic markers. These results support the genetic heterogeneity of ADCCs.
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Affiliation(s)
- D J Barrett
- Jules Stein Eye Institute, UCLA School of Medicine 90024-1771
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Cooper DN, Jay M, Bhattacharya S, Jay B. Molecular genetic approaches to the analysis of human ophthalmic disease. Eye (Lond) 1987; 1 ( Pt 6):699-721. [PMID: 3331606 DOI: 10.1038/eye.1987.114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this review of the recent literature, the contribution that the new techniques of molecular genetics has made in the analysis and diagnosis of human ophthalmic conditions is presented and discussed. Among the disorders reviewed are X-linked retinitis pigmentosa, Norrie's disease, gyrate atrophy and retinoblastoma, and there are also sections on crystallins and visual pigments.
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Affiliation(s)
- D N Cooper
- Haematology Department, King's College Hospital School of Medicine, Denmark Hill, London
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Clark JI, Carper D. Phase separation in lens cytoplasm is genetically linked to cataract formation in the Philly mouse. Proc Natl Acad Sci U S A 1987; 84:122-5. [PMID: 3467344 PMCID: PMC304154 DOI: 10.1073/pnas.84.1.122] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The variation of the phase-separation temperature, Tc, in lenses was studied during the postnatal development of three genetically different mouse strains: Swiss-Webster, Philly, and the (Swiss-Webster x Philly)F1 hybrid. The general behavior of Tc during early postnatal development has two stages: in stage I, Tc increased to a maximum and then, in stage II, Tc decreased. Philly mice are a strain that develops hereditary cataracts about 36 days following birth. In F1 hybrids of Philly and Swiss-Webster mice, cataracts appeared about 49 days following birth, approximately equal to 13 days later in development than in the Philly mice. In the Philly and hybrid mice, stage I and stage II were followed by stage III in which Tc reached a minimum value and then increased toward body temperature. The values of Tc at birth, the slope of the increase during stage I, and the maximum Tc were characteristic for each mouse strain. These results establish that the behavior of the temperature of the phase separation Tc in mouse lens is linked to the genetic strain of the mice and that the value of Tc at birth is an early indicator of lenses that will develop cataracts and lenses that will develop normally.
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Lubsen NH, Renwick JH, Tsui LC, Breitman ML, Schoenmakers JG. A locus for a human hereditary cataract is closely linked to the gamma-crystallin gene family. Proc Natl Acad Sci U S A 1987; 84:489-92. [PMID: 3025877 PMCID: PMC304234 DOI: 10.1073/pnas.84.2.489] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Within the human gamma-crystallin gene cluster polymorphic Taq I sites are present. These give rise to three sets of allelic fragments from the gamma-crystallin genes. Together these restriction fragment length polymorphisms define eight possible haplotypes, three of which (Q, R, and S) were found in the Dutch and English population. A fourth haplotype (P) was detected within a family in which a hereditary Coppock-like cataract of the embryonic lens nucleus occurs in heterozygotes. Haplotype P was found only in family members who suffered from cataract, and all family members who suffered from cataract had haplotype P. The absolute correlation between the presence of haplotype P and cataract within this family shows that the gamma-crystallin gene cluster and the locus for the Coppock-like cataract are closely linked [logarithm of odds (lod) score of 7.58 at its maximum at phi = 0]. This linkage provides genetic evidence that the primary cause of a cataract in humans could possibly be a lesion in a crystallin gene.
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Sparkes RS, Mohandas T, Heinzmann C, Gorin MB, Zollman S, Horwitz J. Assignment of a human beta-crystallin gene to 17cen-q23. Hum Genet 1986; 74:133-6. [PMID: 3770741 DOI: 10.1007/bf00282076] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The gene map assignment of a human beta-crystallin gene to 17cen-q23 has been made using a bovine probe in the study of human-mouse and human-Chinese hamster somatic cell hybrids containing parts of human chromosome 17.
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den Dunnen JT, Moormann RJ, Lubsen NH, Schoenmakers JG. Concerted and divergent evolution within the rat gamma-crystallin gene family. J Mol Biol 1986; 189:37-46. [PMID: 3783678 DOI: 10.1016/0022-2836(86)90379-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The nucleotide sequences of six rat gamma-crystallin genes have been determined. All genes have the same mosaic structure: the first exons contain a relatively short (25 to 44 base-pair) 5' non-coding region and the first nine base-pairs of the coding sequence, the second exons encode protein motifs I and II, while protein motifs III and IV are encoded by the third exons. The third exons also contain a 60 to 67-base-pair long 3' non-coding region. In the gamma 1-2 gene, the splice acceptor site of the third exon has been shifted three base-pairs upstream. Hence, the protein product of this gene is one amino acid residue longer. The first introns, though varying in length from 85 to 100 base-pairs, are conserved in sequence. The second introns vary considerably in length (0.9 X 10(3) to 1.9 X 10(3) base-pairs) and sequence. The second exons of the genes show concerted evolution and have undergone multiple gene conversions. In contrast, the third exons show divergent evolution. From the sequences of the third exons, an evolutionary tree of the gene family was constructed. This tree suggests that three of the present genes derive directly from the genes that originated from a tandem duplication of a two-gene cluster. Two duplications of the last gene of the four-gene cluster then yielded the other three genes. Region a' of the third exon, encoding protein motif III, is variable, while the region encoding protein motif IV (b') is constant. We postulate that this variability in region a' is due to a period of radiation after each gene duplication. A comparison of the rat sequences with those of orthologous sequences from other species shows that the variation in region a' is now preserved. Hence, it might specify the specific functional property of each gamma-crystallin protein within the lens.
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Carper D, Smith-Gill SJ, Kinoshita JH. Immunocytochemical localization of the 27K beta-crystallin polypeptide in the mouse lens during development using a specific monoclonal antibody: implications for cataract formation in the Philly mouse. Dev Biol 1986; 113:104-9. [PMID: 3943659 DOI: 10.1016/0012-1606(86)90112-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Philly mouse develops a hereditary cataract about 5 weeks after birth. Although the causative agent is not known, data suggest that there is a correlation between cataract formation and the selective absence of a 27 kilodalton (27K) beta-crystallin lens polypeptide. The ontogeny of the 27K beta-crystallin polypeptide was examined in normal mice in order to evaluate its role in normal development and determine what impact its absence may have on the Philly mouse lens. A monoclonal antibody was used with the PAP method to immunocytochemically localize the 27K polypeptide in lenses of normal mice during development. beta-Crystallins detected with polyclonal antisera were found in differentiated fiber cells throughout the lens. In contrast, the 27K beta-crystallin polypeptide detected with a specific monoclonal antibody was not found in the fiber cells of the inner part of the lens (nucleus), but was specifically localized in the fiber cells of the outer part of the lens called the cortex. The polypeptide was found only in elongating and differentiated fiber cells and not in mitotically active epithelial cells. Although a minor component of the 2-day-old lens, the 27K polypeptide comprised a large portion of the 16-day-old lens including the anterior and posterior poles. These data show that the 27K polypeptide is a minor component of the embryonic lens, but becomes a major contributor to the postnatal lens. The 27K beta-crystallin lens polypeptide is abundant in the fiber cells of the normal postnatal mouse lens. The absence of the 27K polypeptide in the Philly mouse may contribute to the observed failure of fiber cells to differentiate in the Philly mouse after birth or may be deleterious in some other manner to normal lens development. The selective absence of the 27K beta-crystallin polypeptide, a defect which precedes cataract formation in the Philly mouse, is intriguing since it suggests a relationship between this major lens polypeptide and lens clarity.
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Overbeek PA, Chepelinsky AB, Khillan JS, Piatigorsky J, Westphal H. Lens-specific expression and developmental regulation of the bacterial chloramphenicol acetyltransferase gene driven by the murine alpha A-crystallin promoter in transgenic mice. Proc Natl Acad Sci U S A 1985; 82:7815-9. [PMID: 3865198 PMCID: PMC390860 DOI: 10.1073/pnas.82.23.7815] [Citation(s) in RCA: 192] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Two lines of transgenic mice with one to two copies of a DNA fragment containing nucleotides -364 to +45 of the murine alpha A-crystallin gene linked to the bacterial chloramphenicol acetyltransferase (CAT) gene expressed the CAT gene only in their eye lenses. Both CAT activity and alpha A-crystallin were first detected in eyes at approximately 12.5 days of embryonic development, suggesting that the alpha A-CAT fusion gene and the endogenous alpha A-crystallin gene are co-regulated during lens development in the transgenic mice. These experiments show that the murine alpha A-crystallin gene contains a short, cis-acting, tissue-specific regulatory sequence at its 5' end that can target the expression of the bacterial CAT gene, and probably foreign eukaryotic genes, specifically to the ocular lens.
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Kaye NW, Church RL, Piatigorsky J, Petrash JM, Lalley PA. Assignment of the mouse alpha A-crystallin structural gene to chromosome 17. Curr Eye Res 1985; 4:1263-8. [PMID: 4085253 DOI: 10.3109/02713688509017685] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
alpha A2-crystallin is one of the major water-soluble proteins of the mammalian lens. Using a cloned cDNA probe coding for mouse alpha A2-crystallin and Southern blot hybridization, DNA isolated from a panel of somatic cell hybrids prepared from mouse fibroblasts or mouse spleen cells fused with Chinese hamster fibroblasts was probed to determine the chromosomal localization of the alpha A2-crystallin structural gene. We have located this gene on mouse chromosome 17.
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24
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Shiono T, Kador PF, Kinoshita JH. Stimulation of the hexose monophosphate pathway by pyrroline-5-carboxylate reductase in the lens. Exp Eye Res 1985; 41:767-75. [PMID: 3841659 DOI: 10.1016/0014-4835(85)90185-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Addition of pyrroline-5-carboxylate (P5C) or its precursors to rat lenses cultured for 24 hr in TC-199 medium containing 14C-glucose results in an apparent concentration-dependent increase in hexose monophosphate-pentose (HMP) pathway activity. Addition of proline, the reduction product of P5C, did not result in an increase, suggesting that stimulation of the HMP pathway is related to the reduction of P5C to proline by the enzyme P5C reductase. No apparent feedback inhibition on P5C reductase was observed. Stimulation of HMP pathway activity by P5C was also observed in the lenses of Philly and Nakano mouse, two models of congenital osmotic cataracts. Compared with its genetic control, the Swiss--Webster mouse, generally no difference in the lenticular levels of HMP pathway activity was observed in the Philly mouse--even after the onset of cataract. Stimulation of the HMP pathway in the Philly lens by P5C, however, was consistently lower than its control. In the lenses from the Nakano mouse and its genetic control, the Balb/c mouse, no difference in the percentage stimulation of the HMP pathway resulting from the addition of P5C was observed, but HMP pathway activity in the Nakano lens was consistently lower than that of the control.
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25
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den Dunnen JT, Jongbloed RJ, Geurts van Kessel AH, Schoenmakers JG. Human lens gamma-crystallin sequences are located in the p12-qter region of chromosome 2. Hum Genet 1985; 70:217-21. [PMID: 2991114 DOI: 10.1007/bf00273445] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The human gamma-crystallin genes constitute a multigene family whose members are only expressed in the eye lens. The chromosomal location of these sequences has been determined by screening a panel of human/rodent hybrid cell lines containing overlapping subsets of human chromosomes for the presence of human gamma-crystallin sequences. By correlating these genomic hybridization data with the chromosomal constitution of the somatic cell hybrids, all human gamma-crystallin sequences could be assigned to chromosome 2. The use of human/hamster cell hybrids derived from human Burkitt lymphoma cells carrying a reciprocal translocation between human chromosomes 2 and 8, allowed a further localization of the sequences to the region 2p12-qter.
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26
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Carper D, Russell P, Sanyal S. Comparison of the lens crystallin proteins from normal, rd, and rds mutant mice utilizing specific monoclonal antibodies. Exp Eye Res 1985; 40:757-61. [PMID: 4007083 DOI: 10.1016/0014-4835(85)90145-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The lens proteins from three lines of congenic mice which are homozygous for the gene retinal degeneration (rd) or retinal degeneration slow (rds) or carrying the normal alleles (normal) were analyzed by SDS-PAGE and by immunological reactivity to specific monoclonal antibodies. The lens proteins of normal, rd, and rds mice showed a similar developmental pattern between postnatal day 0 and postnatal day 30. The expression of the 25000 molecular weight (MW) beta-crystallin polypeptide which appears postnatally in the normal lens was not affected by retinal abnormalities in the mutant mice. It is concluded that the regulation of the 25000 MW beta-crystallin polypeptide is not dependent upon differentiation or maintenance of the photoreceptor outer segments or continued presence of the photoreceptor cells.
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27
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den Dunnen JT, Moormann RJ, Schoenmakers JG. Rat lens beta-crystallins are internally duplicated and homologous to gamma-crystallins. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 824:295-303. [PMID: 3879970 DOI: 10.1016/0167-4781(85)90035-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
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.
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28
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Garber AT, Winkler C, Shinohara T, King CR, Inana G, Piatigorsky J, Gold RJ. Selective loss of a family of gene transcripts in a hereditary murine cataract. Science 1985; 227:74-7. [PMID: 3964960 DOI: 10.1126/science.3964960] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The eye lens of the Fraser mouse contains a dominantly inherited cataract with reduced amounts of seven distinct but homologous gamma crystallins encoded by a family of gamma-crystallin genes. The results of experiments with cultured lenses, cell-free RNA translation, and Northern blot hybridization indicated a specific loss of the family of gamma-crystallin messenger RNA's in the Fraser mouse lens. Southern blot hybridization of genomic DNA's from normal and Fraser mice showed no differences in gamma-crystallin coding sequences.
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29
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Abstract
A cataract is an opacity of the lens causing a reduction of visual function. The organogenesis of the lens in various mammals is similar. Therefore, a cataract mutation in mice can be directly compared with cataracts in man. Screening for dominant cataracts in mice was combined with the scoring of specific locus mutations. This combination increases the number of scorable loci, allows the comparison of unselected and selected loci and makes possible a systematic comparison of dominant and recessive mutations. In a combined experiment, dominant cataract and specific locus mutations were scored in the same offspring of mice after treatment of spermatogonia. In radiation experiments the induced frequency of dominant cataracts in spermatogonia was after single exposure 4.5 - 5.5 X 10(-5) mutations/gamete/Gy and for specific locus mutations 1.6 - 2.8 X 10(-5) mutations/locus/Gy. In experiments with ethylnitrosourea (ENU) the induced frequency of dominant cataracts was 0.7 - 1.3 X 10(-5) (mutations/gamete)/(mg ENU/kg body weight) and for specific locus mutations 2.6 - 3.3 X 10(-6) (mutations/locus)/(mg ENU/kg body weight). The radiation-induced mutation rate can be used for the direct estimation of the genetic risk in humans. The genetically significant population dose for 19 000 offspring in Hiroshima and Nagasaki was estimated to be 1.1 X 10(6) man-rem, absorbed at high dose rate. For the 19 000 offspring one would expect less than 1 radiation-induced dominant cataract and a total of 20 - 25 dominant mutations. If the number of dominant and recessive loci are equal one would expect in addition the induction of 250 recessive mutations in this population. Chemically induced dominant cataract mutations could be used to determine the allowable level of exposure for a single compound. The genetically characterized mutations will be an ideal source for studies in the field of developmental genetics. The investigation of alpha-, beta-, and gamma-crystallins by electrophoretic methods, the activity determinations of enzymes and the systematic use of cDNA hybridization may lead to an understanding of the genesis of dominant cataracts in mice and man.
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30
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Carper D, Russell P, Shinohara T, Kinoshita JH. Differential synthesis of rat lens proteins during development. Exp Eye Res 1985; 40:85-94. [PMID: 3979459 DOI: 10.1016/0014-4835(85)90110-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Developmental regulation of crystallin protein synthesis was observed in rat lenses between embryonic day 19 and postnatal day 21. Studies on lenses incubated in [35S]-methionine and on lens messenger RNAs translated in a reticulocyte lysate showed that several new polypeptides were synthesized in the lens beginning approximately 1 week after birth. One new polypeptide which had a molecular weight of 27 000 comigrated with the beta crystallins on SDS-PAGE and became a predominant component in older lenses. By crossed rocket immunoelectrophoresis and isoelectric focusing, synthesis of several native beta crystallins and one gamma crystallin was detected only in the postnatal lens. Many crystallin proteins were synthesized in the embryonic and the postnatal lens and did not change during the time period studied. These data suggest a differential regulation of the crystallin proteins during development. It appears that the lens undergoes a transition from embryonic to adult crystallin expression during the first weeks after birth. Factors such as maturation of the retina may be necessary for this transition.
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31
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den Dunnen JT, Moormann RJ, Cremers FP, Schoenmakers JG. Two human gamma-crystallin genes are linked and riddled with Alu-repeats. Gene 1985; 38:197-204. [PMID: 4065573 DOI: 10.1016/0378-1119(85)90218-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A human genomic cosmid clone, pHcos gamma-1, has been isolated containing two closely linked gamma-crystallin genes, oriented in the same direction. The sequence of these genes and their 5' and 3' flanking regions has been determined. The coding regions of both genes are interrupted by two introns. The first introns (94 and 100 bp, respectively) are located in the 5' region of the genes. The second introns (2.82 and 0.95 kb, respectively) divide the genes into two halves, each encoding a structural domain of the gamma-crystallin protein. The coding regions of the two genes show 80% homology. Due to a mutation in the splice acceptor site of the second intron of the first gene, the coding region of its third exon is 3 bp longer than that of the second gene. In the flanking regions several conserved sequence elements were found, including those elements that are known to be necessary for the correct expression of eukaryotic genes. The flanking and intronic regions of the genes contain 'simple sequence' DNA and Alu repeats. The Alu repeats are usually clustered, contain truncated elements, and are often located near simple sequence DNA.
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32
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Brahma SK, Sanyal S. Immunohistochemical studies of lens crystallins in the dysgenetic lens (dyl) mutant mice. Exp Eye Res 1984; 38:305-11. [PMID: 6373332 DOI: 10.1016/0014-4835(84)90168-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The lens in the dyl mutant mice shows a persistent lens-ectodermal connection as well as degeneration and extrusion of lens materials after the initial differentiation of the fibres. Immunohistochemical investigation of the ontogeny of the lens crystallins in this developing mutant lens has been carried out using the indirect immunofluorescence staining method with antiserum to adult mouse lens total soluble proteins. The results have been compared with those for coisogenic normal lens used as a control. In both, the first positive reaction was detectable at identical stages of lens development. A rapid increase in the intensity of fluorescence, most marked in the elongating fibre progressing through the equatorial region to the epithelium, was recorded in the mutant as well as in the normal lens. However, the stalk leading to the lens epithelium did not show any reaction. Appearance of vacuoles in the lens nucleus and cortex marked the beginning of degeneration of fibres which otherwise showed strong fluorescence. This was followed by extrusion of lens crystallin materials through the stalk. As a result, the lens became increasingly reduced and malformed but the surviving cells making up the vestigeal lens in the adult showed positive immunofluorescence. The results demonstrate that despite a failure of lens-ectoderm separation in the mutant mice, the ontogeny of the lens crystallins and differentiation of the lens up to a certain stage of development follow an apparently normal course before the commencement of cataractous degeneration.
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33
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Carper D, Smith-Gill SJ, Kinoshita JH. Production and characterization of a monoclonal antibody to bovine beta-crystallin. Curr Eye Res 1984; 3:501-7. [PMID: 6697751 DOI: 10.3109/02713688408997238] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A monoclonal antibody to a bovine lens 27K beta-crystallin polypeptide has been produced from a rat x mouse hybridoma. The antibody reacts with the 27K polypeptide of bovine, mouse, rat, and human lenses, but does not react to the 27K polypeptide of monkey lens nor does it react with any component in the Philly mouse lens which is missing the 27K polypeptide. The antibody does not recognize any of the other major bovine beta-crystallin polypeptides but does recognize a large number of native beta-crystallin proteins. The antigenic specificity and species cross-reactivity of this antibody provides an excellent opportunity to study many aspects of lens development and cataractogenesis.
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34
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Garner WH. Non-invasive techniques in the study of cataract development at the metabolic and protein molecular level. CIBA FOUNDATION SYMPOSIUM 1984; 106:248-65. [PMID: 6568977 DOI: 10.1002/9780470720875.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Metabolic changes may precede changes in lens protein structure and cataract opacification. Since many of the effects associated with cataract are oxidative in nature, changes in the redox state may be caused by alterations in the level of various metabolic intermediates such as ATP and NAD(P)H. Abnormal levels of H2O2 have been found in the aqueous fluid of cataract patients. Lenses have been treated with 1 mM-H2O2 in organ culture as a cataract model. H2O2 in this system uncouples Na+, K+-ATPase. This metabolic stress has been further evaluated non-invasively by 31P NMR to show that H2O2 can reduce ATP levels without any immediate effects on visual transparency. However, further treatment by this oxidant leads to definitive visual changes in lens clarity. These changes may be due to further changes in structural lens proteins caused by denaturation and aggregation induced by H2O2. The effects of H2O2 on isolated lens proteins is being examined in molecular detail by NMR to ascertain how the lens proteins become denatured in solution. The relevance of the H2O2 model to cataract formation can only be evaluated by using several non-invasive techniques beyond NMR, and then critically comparing the model systems with human cataract tissue samples.
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35
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Inana G, Piatigorsky J, Norman B, Slingsby C, Blundell T. Gene and protein structure of a beta-crystallin polypeptide in murine lens: relationship of exons and structural motifs. Nature 1983; 302:310-5. [PMID: 6835368 DOI: 10.1038/302310a0] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A 23,000 molecular weight beta-crystallin (beta 23) of the murine eye lens is encoded in a 4.1 +/- 0.3-kilobase gene containing three introns. Each of the four exons seems to code for a separate structural motif of the protein, whose tertiary structure was predicted by an interactive computer graphics technique based on the crystallographic structure of bovine gamma II-crystallin. The first exon also encodes a hydrophobic N-terminal peptide resembling membrane anchor sequences of other proteins. Our results indicate structural homology among the beta- and gamma-crystallin polypeptides, and link gene structure with protein structure in this superfamily of lens proteins.
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