Polymorphism in an androgen-regulated mouse gene is the result of the insertion of a B1 repetitive element into the transcription unit

Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis

In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. “Adaptive potential” and “evolutionary potential” are proposed as the extremes of a continuum of “intra-genomic potential” due to TE-Thrust. Specific data is given, indicating “adaptive potential” being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of “evolutionary potential” is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.

Two isoforms of the kidney androgen-regulated protein are encoded by two alleles of a single gene in OFl mice

Two cDNA clones coding for two forms of the mouse kidney androgen-regulated protein (KAP) distinguished by their electrophoretic mobilities on SDS gel electrophoresis have been isolated from libraries prepared from strains of mice having one (BALB/c) or two (OFl) forms of the KAP protein. The corresponding mRNAs have identical sizes, as well as identical sequences in their 5' non-translated regions. The size difference observed between the two proteins is due to two point mutations in the coding region of the KAP mRNA, leading to two amino-acid changes one of which resulted in the substitution of a glycine for a glutamic acid. As shown byin vitrotranscription/translation experiments, these two amino-acid differences are responsible for the shift in the apparent molecular weight of the protein on SDS gels. Both forms of the protein are more abundant in males than in females.

In vitrotranslation of kidney RNAs isolated from six different strains and species of mice revealed the presence of other forms of the KAP protein, characterized by small variations of their molecular weights. Southern blot analysis data are consistent with the presence of only onekapgene in the mouse genome. A restriction fragment length polymorphism has been observed, which does not correlate with the protein polymorphism, indicating the presence of another allele in the OF1 mouse genome.

Characterization of the murine gene encoding 1-Cys peroxiredoxin and identification of highly homologous genes

A new type of peroxiredoxin, named 1-Cys peroxiredoxin (1-Cys Prx), reduces hydrogen peroxide with the use of electrons from unidentified electron donor(s). We have isolated the mouse gene encoding 1-Cys Prx (CP-3) and shown that it is comprised of five exons and four introns. Analysis of 5' flanking regions revealed binding sequences of several putative transcription factors such as Sp1, Pit-1a, c-Jun, c-Myc and YY1. It is noticeable that several potential Sp1 binding sites assigned the -60 through -96bp from putative transcription initiation site. The gel shift assays showed that Sp1 and Pit-1a bind specifically to each binding site in 1-Cys Prx promoter. We also isolated two highly related genes such as CP-2 and CP-5. These genes are encoded by single exons, and show 85% of nucleotide sequence homology with the CP-3. The structural features of these genes suggest that they might be intronless genes derived from the CP-3 by the mechanism involving retrotransposition. In addition, our data suggest that they are inserted to a specific site of the mouse L1 repetitive element. The 1-Cys Prx was actively transcribed in a variety of adult tissues as well as in the developing embryos. These results suggest that only the 1-Cys Prx gene might be relevant for studying the function of the 1-Cys Prx in the murine system.

Complete nucleotide sequence, origin of isoform and functional characterization of the mouse hepsin gene

Hepsin, a type-II membrane-associated serine protease, has been implicated in cell growth and development as well as possible initiation of blood coagulation. Here, we report on the complete nucleotide sequence, functional characterization of key structural features and the promoter of the mouse hepsin gene. The gene has a size of approximately 17 kb, and is composed of 12, 13, or 14 exons depending on alternative intron splicings - one in the 5'-UTR and the other two in the second intron. The latter two, which occur in approximately half of the hepsin transcripts, generate a hepsin mRNA species with an extra exon, which is responsible for producing a hepsin isoform with a unique 20-residue sequence inserted in the cytoplasmic portion of hepsin. Most hepsin transcripts have the 5'-UTR intron spliced, and its splicing can occur independently of the other alternative splicings. The transcriptional initiation site was determined to be 636 bp upstream of the first ATG site in a cytidine-rich region. The 5'-flanking region of hepsin up to nucleotide 274 showed a substantial promoter activity in HepG2 cells, with its expression activity sevenfold higher in the presence of the 5'-UTR intron sequence in comparison to that without the intron sequence. The basal promoter region contains potential binding sites for several transcription factors including SP1, AP2, C/EBP, LF-A1, and E box, which may be responsible for ubiquitous, but liver- and kidney-preferred tissue expression of the hepsin gene.

Evolutionary origins of retroposon lineages of Mhc class II Ab alleles

Major histocompatibility complex (Mhc) class II Ab genes have evolved into three distinct lineages. While lineage 2 alleles differ from lineage 1 alleles by the insertion of a retroposon in intron 2, the basis for the extremely large intron 2 in lineage 3 alleles has heretofore been undetermined. In this report, we demonstrate by nucleotide sequencing that the genomic sequences of prototypic alleles from all three lineages diverge significantly and that lineage 3 is derived from lineage 2 by two insertional events in intron 2. One insert, composed of a member of B1 short interspersed repetitive elements (SINEs), occurs 508 base pairs (bp) 3' of exon 2, and the other, 1141 bp 3' of exon 2 within the retroposon that distinguishes lineage 2 from lineage 1. To assess the evolutionary stability of these lineages and the extent of ancestral polymorphisms of Ab within Mus species, we extended our restriction site polymorphism analysis to include 86 alleles from 120 independently derived H2 haplotypes from 12 separate species and subspecies of Mus. A phylogenetic tree revealing the relationships of these Ab alleles with respect to restriction site polymorphisms, but excluding the retroposon insertions, demonstrated that these lineages have distinctive genomic structures beyond the retroposon polymorphisms. In summary, these mouse Ab genes were produced from successive retroposon insertion events. Lineage 1 and 2 were detected in a variety of Mus species, including Mus caroli, indicating that these lineages diverged more than 2 million years ago. Lineage 3 alleles were found only in the Mus musculus subspecies, suggesting that it diverged from lineage 2 more recently. These results indicate that all three lineages of Ab have persisted through several speciation events in the genus Mus.

Insertional mutations in mammals and mammalian cells

The retroposon sequences, their mechanisms of transposition and the occurrence of insertional mutation in the mammalian genome are reviewed. Insertional mutations fall into two broad categories: those due to the disruption of a gene following the physical integration of a foreign DNA sequence result in loss of gene product and would be expected to be associated with a recessive mutation. A second class of insertional mutation is well documented in which upon integration the promoter/enhancer activities inherent in the retroposon genome exert their influence on neighboring genes. This promoter/enhancer activity of integrated retroposons may have effects over relatively long distances and thus limit the possibilities of establishing an association between retroposon integration and mutation. It is emphasized that a systematic search for insertional mutations in the mammalian genome involves an extensive two-dimensional array of possible retroposon sequences and mutant alleles. Present results represent only a small portion of the total array. Future studies promise to be fruitful in efforts to isolate genes through insertional tagging, to characterize the mechanisms of retroposon transposition, as well as to study the stability of the mammalian genome.

The structure of the mouse lipoprotein lipase gene: a B1 repetitive element is inserted into the 3' untranslated region of the mRNA

The catabolism of triglycerides-rich lipoproteins and the subsequent uptake of free fatty acids by muscle and adipose tissue is dependent on the enzyme lipoprotein lipase (LPL). To better understand the regulation of this enzyme, we have isolated and characterized the mouse LPL gene. The gene is 28 kb in length and comprises 10 exons which encode a 4.0-kb mRNA. In this report, almost 6 kb of DNA sequence is presented, including 1251 bp 5' to the gene, over 4 kb of exon and exon-intron junctions, and 583 bp 3' to the gene. RNA from differentiated 3T3-L1 adipocytes was used in primer extension and RNase protection assays to show that the 5' untranslated region is not interrupted by an intron and the start site of transcription is 199 bp 5' to the ATG codon that begins translation. The first exon codes for the 5' untranslated region and the signal peptide of 27 amino acids and 2 amino acids of the mature protein, exons 2-9 code for 445 amino acids of the mature protein. These exons are short and vary in length from 102 to 287 bp. The 10th exon codes for the 3' untranslated region and is 2346 bp long. This exon contains a single copy of a B1 repetitive element of 152 bp followed by a 169-bp homopurine stretch. These elements are flanked by a pair of 16-bp direct repeats. The mouse gene is similar in size to the human, which also contains 10 exons in similar locations. There is a high degree of sequence homology between the two genes, 5' region (700 bp), 75%; 5' untranslated region, 74%; coding region, 88%; 3' untranslated region, 75%. The most striking difference is the absence of the B1 repetitive element and homopurine region in the human 3' untranslated region. This information about the mouse LPL gene may lead to a better understanding of its regulation and role in plasma lipoprotein metabolism.

Cloning of a housekeeping-type gene (MER5) preferentially expressed in murine erythroleukemia cells

DNA complementary to mRNA preferentially produced in murine erythroleukemia (MEL) cells was cloned from a cDNA library of anemic mouse spleen mRNAs. An open reading frame was noted in the cloned DNA, and was tentatively designated MER5. The MER5 mRNA is abundant in three MEL cell lines, but less in other tissues or cell lines. The levels of the MER5 mRNA changed periodically during MEL cell differentiation and decreased as globin mRNA accumulated. The MER5 promoter region contained no typical TATA-like sequence, but possible target sequences for AP1, AP2, SP1 and octamer-binding protein. More interestingly, this promoter contained the duplicated CACCC boxes, which are common in the adult beta-globin promoter from many species, but uncommon for promoters of other eukaryotic genes.

Isolation of the cDNA clone for mouse glycophorin, erythroid-specific membrane protein

The cDNA clone for a major mouse glycophorin, transmembrane glycoprotein of erythrocytes has been isolated from a mouse spleen erythroblast cDNA library. The primary structure of a major glycophorin indicates that the protein is a single polypeptide chain of 168 amino acids (aa) clearly organized in three domains distinct in the glycophorin of other species. A strong homology of the mouse major glycophorin with human glycophorin A or B, but not with human glycophorin C is observed only in the hydrophobic stretch of 23 nonpolar aa, indicating that the major mouse glycophorin species cloned is similar to human glycophorin A. The glycophorin mRNA is absent in all non-erythroid organs or cell lines examined. The glycophorin mRNA is induced during the differentiation of murine erythroleukemia cells with dimethyl sulfoxide.

The murine urokinase-type plasminogen activator gene

The murine urokinase-type plasminogen activator (uPA) gene has been isolated from a BALB/c liver DNA cosmid library and its nucleotide sequence established. The gene is organized into 11 exons comprising 34.7% of the 6710 base pair (bp) region spanning the interval between the presumed transcription initiation and polyadenylation sites. The transcription initiation site is flanked by common RNA polymerase II promoter elements, including a TATA box and a potential transcription factor Sp1 binding site. A large polypurine tract of the structure (AG)22(AGGG)16(AG)28 is located 79 bp upstream of the 5'-terminus. It was highly sensitive to the single-strand-specific nuclease S1, suggesting a non-B-DNA conformation of unknown significance. Consistent with the well-documented influence of adenosine cyclic 3',5'-phosphate (cAMP) on uPA gene expression, there is a dodecanucleotide homologous to proposed regulatory sequences identified in other cAMP-modulated genes. Comparison of the murine uPA gene to the previously described porcine and human uPA genes revealed an unusually high degree of evolutionary (interspecies) sequence conservation that was not limited to exons but included introns and flanking sequences as well.

Dispersed repetitive sequences of the mouse genome are differentially represented in extrachromosomal circular DNAs in vivo

Eukaryotic cells contain extrachromosomal circular (ecc) DNAs which are homologous to chromosomal sequences. We have isolated eccDNAs from whole tissues of C57BL/6 mice. Using hybridization techniques, we show that R-, MIF-, B1-, and B2-dispersed repetitive sequences of the mouse genome are differentially represented in heart, brain, and liver tissues. Moreover, we show that the relative abundance of B2 sequences in heart and liver eccDNAs is higher than the relative abundance of the other repetitive sequence families studied.