Frequency of polymorphisms for alleles encoding for liver proteins of domesticated mice

Three different inbred strains of mice have been crossed with a lethal albino line (cch/c3H) and the liver polypeptides of the parents and offspring examined by two-dimensional polyacrylamide gel electrophoresis for evidences of protein polymorphisms, different alleles of which have gone to fixation in different strains. In the battery of polypeptides considered most favorable for scoring, 3.3 +/- 1.6 percent of the battery exhibited paired variants and 1.6 +/- 1.2 percent, unpaired. An adjustment for the fact the same allele of a biallelic polymorphism may go to fixation in two inbred lines of common ancestry leads to the suggestion that in the stock from which these inbred lines were ultimately derived, there were some 11.0 percent paired and 5.3 percent unpaired polymorphisms in the average mouse. This is about half the frequency of polymorphisms observed in wild European Mus musculus musculus and Mus musculus domesticus with one-dimensional electrophoresis of blood plasma and erythrocyte proteins. Three explanations were considered for the lower estimated frequency for liver protein polymorphisms: the difference is real, the apparent difference is due to the lower resolving power of two-dimensional gels, or the mouse strains from which the present inbred lines were drawn had already, lost through inbreeding, a considerable amount of their genetic variation before the inbreeding leading to the present strains commenced.     

An evolutionary switch in tissue-specific gene expression. Abundant expression of alpha 1-antitrypsin in the kidney of a wild mouse species

alpha 1-Antitrypsin (AT), one of the major proteinase inhibitors in mammalian serum, is generally considered to be synthesized exclusively in the liver. We have found that a wild-derived Mus species, Mus caroli, expresses AT mRNA in kidney at levels approaching that in liver; no other mouse, inbred or wild-derived, exhibits this striking property. Liver and kidney mRNAs from M. caroli encode very similar AT polypeptides that are distinct from that encoded by Mus musculus liver mRNA. In vivo, liver AT is secreted into the bloodstream, while kidney AT, which is processed differently from the liver protein, is excreted into the urine. Analysis of RNA from a hybrid between M. musculus and M. caroli indicates that a cis-acting genetic element may be responsible for the difference in AT expression. Restriction enzyme digestion patterns of AT genomic sequences in M. caroli DNA are considerably different from those in M. musculus; in addition, these sequences are undermethylated in liver DNA from M. musculus and in liver and kidney DNA from M. caroli, reflecting the respective patterns of expression. Further studies of the altered tissue specificity of AT expression that is apparent in these two related species should lead to new insights into the nature and evolution of genetic determinants of tissue-specific phenotypes.     

Characterization of Polypeptides Corresponding to Clones of Maize Zein mRNAS

Zeins, the storage proteins of maize (Zea mays) are a complex group of polypeptides encoded by a large multigene family. The α-zein proteins, which account for about 70% of the total, show both size and charge heterogeneity. Although clones corresponding to several different alpha zeins have been characterized, it has not been possible to correlate these sequences with individual zein polypeptides. By translating in Xenopus oocytes RNAs transcribed in vitro from cloned zein mRNAs, we were able to identify the encoded proteins among native zeins or zeins synthesized in oocytes with total zein mRNA. There was no correlation between the isoelectric points of these proteins and the homology of their coding DNA sequences, as the proteins encoded by two closely homologous cDNAs migrated with greater charge heterogeneity than those encoded by less homologous clones. In addition, the size of the proteins as determined by SDS polyacrylamide gel electrophoresis did not always correlate with the length of the protein deduced from the DNA sequence. The ability to match cloned zein sequences to individual native proteins will enable the genetic mapping of cloned genes as well as the analysis of their translational regulation.     

A single locus in the mouse encodes both myosin light chains 1 and 3, a second locus corresponds to a related pseudogene

Two loci have been characterized in the mouse Mus musculus, which are homologous to the mRNAs encoding myosin light chains MLC1_F and MLC3_F, two proteins with a common -COOH terminal sequence. One of these loci is an intronless pseudogene, absent from the mouse species Mus spretus; alterations in its nucleotide sequence preclude it from generating a functional MLC1_F or MLC3_F. The other contains the genetic information for the two proteins. The part common to both proteins is encoded by five exons, which cover about 6.5 kb. Genetic information specific for the N-terminal sequences is encoded in four exons, at 3.5 and 14.3 kb for MLC1_F, and 3.8 and 4.5 kb for MLC3_F, upstream of the first common exon. Each 5′ terminus has a TATA-like consensus sequence about 30 bases upstream of the cap site. The pseudogene is not genetically linked to the functional MLC1_F/MLC3_F locus in the genome of Mus musculus.     

A common protocadherin tail: Multiple protocadherins share the same sequence in their cytoplasmic domains and are expressed in different regions of brain

To study the diversity of protocadherins, a rat brain cDNA library was screened using a cDNA for the cytoplasmic domain of human protocadherin Pcdh2 as a probe. The resultant clones contained three different types. One type corresponds to rat Pcdh2; the other two types are distinct from Pcdh2 but contain the same sequence in their cytoplasmic domains and part of the 3′ flanking sequence. To clarify the structure of the proteins defined by the new clones, a putative entire coding sequence corresponding to one of the clones was determined. The overall structure is essentially the same as Pcdh2, indicating that the proteins defined by this clone, and probably by other clones, belong to the protocadherin family. Two PCR experiments and an RNase protection assay showed the existence of the corresponding mRNAs in rat brain preparations. Human and mouse cDNA clones with the same sequence properties were also isolated. Taken together, these results indicate that the clones are not cloning artifacts and that corresponding mRNAs are actually expressed in brains of various species. The results of in situ hybridization showed that the mRNAs corresponding to these clones were expressed in different regions in brain. Since protocadherins encoded by these mRNAs are likely to have different specificity in their interaction and share a common activity at their cytoplasmic domains, these protocadherins may provide a molecular basis, in part, to support the complex cell-cell interaction in brain.     

Characterization of a Radish Nuclear Gene Expressed during Late Seed Maturation

To study long-lived mRNAs stored in radish (Raphanus sativus) seed, we have selected clones from a dry seed cDNA library by differential screening. One of these clones, p8B6, whose mRNAs are abundant in the dry seed, was characterized. This clone hybridizes to an RNA class of approximately 600 nucleotides whose accumulation begins during the desiccation phase, reaches its maximum level in the dry seed, and is no longer detectable in 12 hour old seedlings. mRNAs hybrid-selected by p8B6 encode four polypeptides, but only two are compatible with the size class of RNAs detected by Northern analysis. Three of them have previously been identified as major `early germination' polypeptides, and their synthesis has been shown to be induced prematurely in immature embryos by a desiccation treatment. The protein deduced from the p8B6 nucleotide sequence is 9 kilodaltons in size, highly hydrophilic, rich in Gly and Glu, and contains no Cys, Trp, and lie. The amino acid sequence shares good homology with that of two recently described seed proteins: a cotton late embryogenesis abundant protein and the wheat early methionine-labeled protein. Southern blot analysis suggests that the p8B6 sequence belongs to a very small gene family. The exact function of the product encoded by p8B6 remains to be determined.     

Genetics of intracisternal-A-particle-related envelope-encoding proviral elements in mice.

Intracisternal-A-particle-related envelope-encoding (IAPE) proviral elements in the mouse genome encode and express an envelope-like protein that may allow transmission of IAPEs as infectious agents. To test IAPE mobility and potential transmission in mice, we have analyzed the distribution of IAPE elements in the genomes of Mus spretus and Mus musculus inbred strains and wild-caught animals. Potential full-length (IAPE-A) proviral elements are present as repetitive copies in DNA from male but not female animals of M. musculus inbred strains and Mus musculus castaneus. Analysis of IAPE-cellular junction fragments indicates that fixation of most IAPEs in the germ line occurred in M. musculus and M. spretus after speciation but before M. musculus inbred strains were derived.     

Chromosomal phylogeny of Muridae: a study of 10 genera

The karyotypes of 10 different species of the family Muridae (Acomys airensis, Arvicanthis niloticus, Hylomyscus stella, Malacomys longipes, Mastomys huberti, Myomys daltoni, Mus musculus, Rattus norvegicus, Thamnomys gazellae, and Uranomys ruddi) are compared by different banding techniques. From a reconstruction of the presumed ancestral karyotype of the Muridae the sequence of the various rearrangements leading to the present karyotypes is proposed in order to determine their phylogenetic relationships. In particular, the present karyotypes of the mouse and rat differ from the ancestral one by at least 12 and 7 rearrangements, respectively. A clear tendency for accumulation of a specific type of rearrangement in a given branch of the cladogram is observed. In regard to the mouse, a large number of translocations, with break points situated in the proximal part of the long arms, have occurred, which conserved the acrocentric form of the ancestral chromosomes but led to multiple recombinations of the bands.     

Extraordinary sequence divergence at Tsga8, an X-linked gene involved in mouse spermiogenesis

The X chromosome plays an important role in both adaptive evolution and speciation. We used a molecular evolutionary screen of X-linked genes potentially involved in reproductive isolation in mice to identify putative targets of recurrent positive selection. We then sequenced five very rapidly evolving genes within and between several closely related species of mice in the genus Mus. All five genes were involved in male reproduction and four of the genes showed evidence of recurrent positive selection. The most remarkable evolutionary patterns were found at Testis-specific gene a8 (Tsga8), a spermatogenesis-specific gene expressed during postmeiotic chromatin condensation and nuclear transformation. Tsga8 was characterized by extremely high levels of insertion-deletion variation of an alanine-rich repetitive motif in natural populations of Mus domesticus and M. musculus, differing in length from the reference mouse genome by up to 89 amino acids (27% of the total protein length). This population-level variation was coupled with striking divergence in protein sequence and length between closely related mouse species. Although no clear orthologs had previously been described for Tsga8 in other mammalian species, we have identified a highly divergent hypothetical gene on the rat X chromosome that shares clear orthology with the 5' and 3' ends of Tsga8. Further inspection of this ortholog verified that it is expressed in rat testis and shares remarkable similarity with mouse Tsga8 across several general features of the protein sequence despite no conservation of nucleotide sequence across over 60% of the rat-coding domain. Overall, Tsga8 appears to be one of the most rapidly evolving genes to have been described in rodents. We discuss the potential evolutionary causes and functional implications of this extraordinary divergence and the possible contribution of Tsga8 and the other four genes we examined to reproductive isolation in mice.     

The generation of a library of PCR-analyzed microsatellite variants for genetic mapping of the mouse genome

Forty-three sequences containing simple sequence repeats or microsatellites were generated from an M13 library of total genomic mouse DNA. These sequences were analyzed for size variation using the polymerase chain reaction and gel electrophoresis without the need for radiolabeling. Seventy-two percent of the sequences showed allelic size variations between different inbred strains of mouse and the wild mouse, Mus spretus; and 53% showed variation between inbred strains. Thirty-seven percent were variant between B6/J and DBA/2J, and 81% of these were resolved using minigel agarose electrophoresis alone. This approach is a useful way of generating the large number of variants that are needed to create high resolution maps of the mouse genome.     

3D3/lyric: a novel transmembrane protein of the endoplasmic reticulum and nuclear envelope, which is also present in the nucleolus

We previously performed a gene-trap screen in mouse cells with particular focus on clones in which the trapped protein-reporter fusions localise to compartments of the nucleus. Here we describe one such gene-trap line in which the fusion protein showed a unique, patchy distribution at the nuclear periphery. We have cloned the endogenous mouse and human cDNAs encoding the protein trapped in the F9/3D3 cell line. The predicted proteins (64 kDa) encoded by this novel gene are highly conserved and similar to an unpublished rat protein in sequence databases called p80 or lyric. The amino acid sequence of 3D3/lyric indicates that it may be a type-1b membrane protein with a single transmembrane domain (TMD). Antibodies against the endogenous protein recognise multiple isoforms, consistent with multiple 3D3/lyric mRNAs detected by Northern blot analysis. Subcellular fractionation and immunostaining show that 3D3/lyric is located not only principally in the endoplasmic reticulum (ER), but also in the nuclear envelope (NE), which is contiguous with this compartment. Furthermore, 3D3/lyric is also found in the nucleolus and is therefore a rare example of a protein that suggests a possible connection between this compartment and the endoplasmic reticulum.     

Molecular cloning and characterization of cDNA encoding mouse cytokeratin no. 19

We have isolated cDNA clones encoding the mouse cytokeratin No. 19 (Ck 19) from an intestinal cDNA library using synthetic oligodeoxyribonucleotides as probes. We obtained four independent clones, which correspond to about 1.4-kb of ck19 cDNA. Nucleotide sequence analysis revealed that these cDNAs encode a protein of 44,541 Da composed of 403 amino acids (aa). The deduced aa sequence defines an alpha-helical central domain, and suggests that the protein lacks a C-terminal non-alpha-helical tail segment, characteristic of the human and bovine 40-kDa keratins (Ck19). The overall aa identity between mouse Ck19 and human and bovine Ck19 is very high, 82.7% and 82.4%, respectively. The coil-forming central domain of mouse Ck19 has 45-65% similarity to other type-I Ck polypeptides, while it displays only 20-30% similarity to type-II Ck polypeptides. Northern blot analysis showed that mouse ck19 mRNA is strongly expressed in adult intestine, stomach and uterus. Interestingly, it is expressed in a placental cell line and a retinoic acid-treated mouse teratocarcinoma cell line (F9), but not in a parietal yolk sac endoderm-like cell line (PYS-2). This pattern of expression is very similar to that for the mouse gene encoding extra-embryonic endodermal cytoskeletal protein C (EndoC), suggesting they may be the same.     

Cell-free translation of silkmoth chorion mRNAs: Identification of protein precursors and characterization of cloned DNAs by hybrid-selected translation

The secretory silkmoth chorion proteins are synthesized as precursors bearing signal peptides. Precursors are detected upon cell-free translation of chorion mRNAs in the wheat germ system; they are processed into products identical in size to authentic chorion proteins when translation is performed in the presence of microsomal membranes from dog pancreas. Precursors corresponding to specific protein size classes and subclasses are identified by three approaches: comparison of precursors and products encoded by stage-specific mRNAs, comparison of precursors and products encoded by mRNAs specifically hybridizing to individual chorion cDNA clones, and comparison of relative amino acid compositions of precursors and authentic chorion proteins. Translation of stage-specific mRNA preparations indicates that, in general, the developmental changes of in vivo chorion protein synthesis are based on changes in concentrations of the corresponding mRNAs. Characterization of the precursors makes it possible to identify, for any chorion DNA clone, the protein subclass, a member of which is encoded by the clone sequence.