Duplicated plastid and triplicated cytosolic isozymes of triosephosphate isomerase in maize (Zea mays L.)

We studied electrophoretic variation and inheritance of triosephosphate isomerase (TPI) isozymes in maize (Zea mays L.). In contrast to most diploid plants, in maize, TPI exists as multiple isozymes in both the plastid and cytosolic subcellular compartments. Phenotypes result from the overlay of two independent sets of isozymes and allozymes, representing the plastid (encoded by the nuclear genes Tpi1 and Tpi2) and cytosolic (encoded by Tpi3, Tpi4, and Tpi5) systems. All possible intragenic and intergenic dimeric enzymes are formed between polypeptides within each subcellular compartment. No heterodimers are formed between plastid and cytosolic polypeptides. Extensive surveys of accessions of land races and inbred lines revealed 22 allelic variants for the five loci. Most alleles have been formally validated by segregation analysis. We describe two null alleles at Tpi4, distinguished by their relative abilities to form intergenic heterodimers with polypeptides specified by Tpi3 and Tpi5. Linkage analyses and crosses with B-A translocation stocks were effective in determining the chromosome locations of all five loci. Duplicated genes for both the plastid and cytosolic isozymes were localized to genomic regions that possess numerous other redundant sequences. We placed Tpi1 on the long arm of chromosome 7, approximately 23 centimorgans (cM) distal to g11; we localized its duplicate--Tpi2--17 cM distal to v4 on the long arm of chromosome 2. The triplicate loci encoding cytosolic TPIs reside on chromosomes 3 and 8. Tpi4 is approximately equidistant (11 cM) from d1 and Lg3, near the centromere of chromosome 3. Tpi3 and Tpi5 are located on distal ends of the most poorly marked maize chromosome; Tpi3 is 29 cM distal to Idh 1 on 8L, and Tpi5 is on 8S or near the centromere on 8L. In contrast to most duplicated maize sequences, which often occur in parallel linkages on different chromosomes, Tpi3 and Tpi5 provide an example of intrachromosomal gene duplication. Several of the Tpi loci are located in sparsely mapped regions of the genome, and Tpi1 is the first isozyme marker for chromosome 7.     

Temporal Variation for the Expression of Catalase in DROSOPHILA MELANOGASTER: Correlations between Rates of Enzyme Synthesis and Levels of Translatable Catalase-Messenger RNA

Two variants that alter the temporal expression of catalase have been isolated from a set of third chromosome substitution lines. Each variant has been mapped to a cytogenetic interval flanked by the visible markers st (3-44.0) and cu (3-50.0) at a map position of 47.0, which is within or near the interval 75D-76A previously identified as containing the catalase structural gene on the bases of dosage responses to segmental aneuploidy. Each variant operates by modulating the rate of enzyme synthesis and the level of translatable catalase-mRNA.     

Characterization and expression of the gene encoding membralin, an evolutionary conserved protein expressed in the central nervous system

We have identified a novel gene that encodes an evolutionary conserved protein that we name membralin since it contains multiple transmembrane regions. The human gene C19orf6 localizes to chromosome 19p13.3. Splice variant membralin-1 is encoded by 11 exons, translating into 620 amino acids. In addition, we found evidence for two additional splice variants in the human. The mouse gene ORF61 localizes to chromosome 10. We cloned two splice variants in mouse: membralin-1, which is encoded by 12 exons, translating into 574 amino acids, and membralin-2, which translates into 598 amino acids. The existence of rat membralin-1 (574 amino acids long) is, so far, only supported by in situ hybridization result, whereas the existence of rat membralin-2 (598 amino acids long) is strongly supported by overlapping ESTs. Gene homologues were also identified in fruit-fly (CG8405, chromosome 2R 52; two splice variants), nematode (chromosome III), and Arabidopsis thaliana (chromosome 1). Sequence analysis revealed no closely related genes, suggesting that membralin represents the sole member of a unique protein family.     

Comparative mapping of genes from human chromosome 12 by genetic linkage mapping in cattle.

Loci from human chromosome 12 were mapped in cattle to compare the gene order between species. Polymorphisms were detected in cattle in six loci that had been mapped with high precision in humans. Four of these loci, LALBA, SLC2A3, SYT1, and TPI1, mapped to bovine chromosome 5, and one, PLA2G1B, mapped to bovine chromosome 17. The sixth locus, SLC2A3L, due to a fragment produced by the SLC2A3 primers, maps to the telomeric region of BTA18. The differences in gene order between human chromosome 12 and cattle chromosome 5, when these loci are added to others already mapped in cattle, show evidence of significant rearrangement in gene order requiring several evolutionary events. There is also evidence in cattle chromosome 5 of the interspersal of material conserved on human chromosome 22 into the material conserved on human chromosome 12, consistent with ZOOFISH analyses. This analysis indicates that the larger block near the centromere is conserved on the long arm of human chromosome 12 and the smaller block near the telomere is conserved as part of the short arm of human chromosome 12. The level of variation detected in the amplified cattle DNA was approximately 1 variant per 464 nucleotides of haploid DNA using single-strand conformation polymorphism analysis. This corresponds to a per individual level of 1 variant per 1, 961 nucleotides of haploid DNA. This confirms lower genetic variability in cattle compared to humans but indicates the potential for millions of single nucleotide polymorphisms in cattle.     

Genomic organization of the mouse Msh4 gene producing bicistronic, chimeric and antisense mRNA

By degenerate PCR and screening of mouse testis cDNA library, we have identified seven cDNAs from the meiotic recombination gene Msh4. Variant alpha and probably beta are likely involved in meiotic DNA recombination. Other variants have distinctive structures; variant epsilon, theta; and iota form a bicistronic operon, while variant delta contains antisense RNA for the endoplasmic reticulum (ER) chaperon Hspa5 gene and small open reading frame (ORF) identical to epsilon ORF2. Analysis of the exon-intron structures revealed unusual genomic organizations: the first three exons of delta and the first exon of epsilon are respectively mapped to the Hspa5 locus on chromosome 2 and the Pcbp3 locus on chromosome 10; the remaining exons of both variants are mapped to the Msh4 locus on chromosome 3. The first exon of variant beta is located on chromosome 16, while the others are located on chromosome 3. Synthesis of these mRNAs is assumed to require interchromosomal trans-splicing alone (beta and epsilon) or in combination with converse-splicing (delta). Most Msh4 variant mRNAs are mainly expressed in testis, but a small amount of each variant except for epsilon is also expressed in brain, heart, thymus, ovary and embryonic head. Enhanced green fluorescent protein (EGFP) fusion experiments showed that all the ORFs are translated, and most of those proteins are localized to a particular subcellular compartment. It also appeared that expression of variant delta induces cell death. This study suggests that the dynamic interchromosomal (intergenic) trans-splicing generates functional diversity of the mouse Msh4 gene.     

Molecular characterization of the NPC1L1 variants identified from cholesterol low absorbers

Niemann-Pick C1-like 1 (NPC1L1) is an essential protein for dietary cholesterol absorption. Nonsynonymous (NS) variants of NPC1L1 in humans have been suggested to associate with cholesterol absorption variations. However, information concerning the characteristics and mechanism of these variants in cholesterol uptake is limited. In this study, we analyzed the cholesterol uptake ability of the 19 reported NS variants of NPC1L1 identified from cholesterol low absorbers. Among these variants, L110F, R306C, A395V, G402S, T413M, R693C, R1214H, and R1268H could partially mediate cellular cholesterol uptake and were categorized as partially dysfunctional variants. The other 11 variants including T61M, N132S, D398G, R417W, G434R, T499M, S620C, I647N, G672R, S881L, and R1108W could barely facilitate cholesterol uptake, and were classified into the severely dysfunctional group. The partially dysfunctional variants showed mild defects in one or multiple aspects of cholesterol-regulated recycling, subcellular localization, glycosylation, and protein stability. The severely dysfunctional ones displayed remarkable defects in all these aspects and were rapidly degraded through the ER-associated degradation (ERAD) pathway. In vivo analyses using adenovirus-mediated expression in mouse liver confirmed that the S881L variant failed to localize to liver canalicular membrane, and the mice showed defects in biliary cholesterol re-absorption, while the G402S variant appeared to be similar to wild-type NPC1L1 in mouse liver. This study suggests that the dysfunction of the 19 variants on cholesterol absorption is due to the impairment of recycling, subcellular localization, glycosylation, or stability of NPC1L1.     

Regional localization of the human G protein alpha i2 (GNAI2) gene: assignment to 3p21 and a related sequence (GNAI2L) to 12p12-p13.

Gi alpha proteins, members of the G protein signal transduction family, include a small number of polypeptides: Gi alpha 1 (GNAI1), Gi alpha 2 (GNAI2), and Gi alpha 3 (GNAI3). A cDNA for the human GNAI2 gene has been isolated from a human T-cell library and is mapped by chromosomal in situ hybridization to the short arm of chromosome 3 at 3p21. A related sequence, GNAI2L, is mapped by in situ hybridization to the short arm of chromosome 12 at p12-p13. These mapping results are further supported by amplification of GNAI2-specific sequences in a monochromosomal human/rodent somatic cell hybrid containing only human chromosome 3. Of note, these assignments are to chromosome regions in which other G proteins reside. Localization of GNAI2 to 3p21 is of great interest as this region of the short arm of chromosome 3 is frequently involved in rearrangements in various human tumors.     

The histone domain of macroH2A1 contains several dispersed elements that are each sufficient to direct enrichment on the inactive X chromosome

Histone variants replace the core histones in a substantial fraction of nucleosomes, affecting chromatin structure and impacting chromatin-templated processes. In many instances incorporation of histone variants results in formation of specialized regions of chromatin. Proper localization of histone variants to distinct regions of the genome is critical for their function, yet how this specific localization is achieved remains unclear. macroH2A1 is enriched on the inactive X chromosome in female mammalian cells, where it functions to maintain gene silencing. macroH2A1 consists of a histone H2A-like histone domain and a large, globular C-terminal macro domain that is not present in other histone proteins. The histone domain of macroH2A1 is alone sufficient to direct enrichment on the inactive X chromosome when expressed in female cells, indicating that sequences important for correct localization lie in this domain. Here we investigate whether divergent sequences of the H2A variant macroH2A1 contribute to its correct localization. We mapped the regions of the macroH2A1 histone domain that are sufficient for localization to the inactive X chromosome using chimeras between H2A and the histone domain of macroH2A1. Multiple short sequences dispersed along the macroH2A1 histone domain individually supported enrichment on the inactive X chromosome when introduced into H2A. These sequences map to the surface of the macroH2A1/H2B dimer, but are buried in the crystal structure of the macroH2A1 containing nucleosome, suggesting that they may contribute to recognition by macroH2A1/H2B deposition factors.     

Chromosomal Locations of Three Human Nuclear Genes (RPSM12, TUFM, and AFG3L1) Specifying Putative Components of the Mitochondrial Gene Expression Apparatus

We have mapped the chromosomal locations of three human nuclear genes for putative components of the apparatus of mitochondrial gene expression, using a combination ofin situhybridization and interspecies hybrid mapping. The genesRPMS12(mitoribosomal protein S12, a conserved protein component of the mitoribosomal accuracy center),TUFM(mitochondrial elongation factor EF-Tu), andAFG3L1(similar to the yeast genesAfg3andRca1involved in the turnover of mistranslated or misfolded mtDNA-encoded polypeptides) were initially characterized by a combination of database sequence analysis, PCR, cloning, and DNA sequencing.RPMS12maps to chromosome 19q13.1, close to the previously mapped gene for autosomal dominant hearing loss DFNA4. TheTUFMgene is located on chromosome 16p11.2, with a putative pseudogene or variant (TUFML) located very close to the centromere of chromosome 17.AFG3L1is located on chromosome 16q24, very close to the telomere. By virtue of their inferred functions in mitochondria, these genes should be regarded as candidates of disorders sharing features with mitochondrial disease syndromes, such as sensorineural deafness, diabetes, and retinopathy.     

TYRP1 and MC1R genotypes and their effects on coat color in dogs

We used PCR amplification of cDNA prepared from skin biopsies to determine the nearly full-length, protein-coding sequence of dog TYRP1, and to define sequence variants potentially responsible for the B locus. One common variant contained a premature stop codon in exon 5 (Q331ter), and the other deleted a proline residue in exon 5 (345delP). A third variant in exon 2 (S41C) occurred less frequently. We genotyped 43 brown (including brown and white) and 34 black (including tricolor, black-and-tan, and black and white) dogs. All 43 of the brown group carried two or more of these sequence variants likely to interfere with TYRP1 function, whereas 0 of 34 in the black group carried two or more of these variants (10 carried one variant). We also genotyped 13 black-nosed and 10 brown-nosed dogs whose coat color was described as red, yellow, gold, apricot, or orange (including various degrees of white). All these dogs were homozygous for a R306X MC1R variant shown to be associated with these coat color phenotypes. The black or brown nose correlated perfectly with the absence or presence of the same three TYRP1 variants described above. TYRP1 was linkage mapped to dog chromosome 11, with a SNP in exon 7.     

Defining the locus of origin of a genetically determined electrophoretic variant of a multilocus enzyme system; the calcutta-1 of human LDH system is a B-locus variant

Summary Six (four Hindus, one Sikh, and one Muslim) out of 213 individuals originating from different parts of the Indian subcontinent (namely, Andhra Pradesh, Maharashtra, Uttar Pradesh, East Punjab, and West Punjab) were found to be Calcutta-1 (CAL1) variants of lactate dehydrogenase (LDH). The CAL1 variant was originally described (and thus, generally believed at present) as an allelic variant at the LDHA locus in chromosome 11. By using an improved Cellogel electrophoretic procedure the isozyme patterns observed in the erythrocytes and leukocytes of the variant have indicated that the CAL1 is not a variant of LDHA but that of LDHB, a chromosome 12 marker. This suggestion was supported by the isozyme patterns of LDH in a set of segregating clones of man-mouse somatic cell hybrids with the variant as human partner. Moreover, the variant cosegregated consistently with the human chromosome 12 and with the markers firmly assigned to the latter but not with human chromosome 11 or its markers in these hybrids. These results confirmed that the CAL1 is an LDHB variant.     

Electrophoretic variants in three Amerindian tribes: the Baniwa, Kanamari, and Central Pano of western Brazil.

Data are presented on electrophoretic variants of 25 polypeptides found in the blood serum and erythrocytes, in 812 individuals from three Amerindian tribes, the Pano, the Baniwa, and the Kanamari. Two "private polymorphisms" were encountered, of PEPB in the Pano and CAII in the Baniwa. A single example of a different PEPB variant was encountered in the Baniwa, and two possible examples of an unstable variant of HGB A2 in the Kanamari. In addition, the well-known A variant of ACP1, the Duarte variant of GALT, the 2 variant of Hp and the 2 variant of PGM1 occurred in polymorphic proportions in all three tribes, and the TFDChi variant was present as a polymorphism in the Baniwa. These data have recently been incorporated into a treatment which concludes that the eight electrophoretically-defined "private polymorphisms" thus far encountered in Amerindian tribes can be explained by a mutation pressure of 0.7 x 10(-5)/locus/generation on the assumption of neutrality of the phenotypes in question (Neel and Thompson, '78).     

Genetic linkage and radiation hybrid mapping of the three human GABA(C) receptor rho subunit genes: GABRR1, GABRR2 and GABRR3.

GABA(C) receptors mediate rapid inhibitory neurotransmission in retina. We have mapped, in detail, the human genes which encode the three polypeptides that comprise this receptor: rho1 (GABRR1), rho2 (GABRR2) and rho3 (GABRR3). We show that GABRR1 and GABRR2 are located close together, in a region of chromosome 6q that contains loci for inherited disorders of the eye, but that GABRR3 maps to chromosome 3q11-q13.3. Our mapping data suggest that the rho polypeptide genes, which are thought to share a common ancestor with GABA(A) receptor subunit genes, diverged at an early stage in the evolution of this gene family.     

Binding of a photoaffinity analogue of glutathione to MRP1 (ABCC1) within two cytoplasmic regions (L0 and L1) as well as transmembrane domains 10-11 and 16-17

MRP1 (or ABCC1) is an ABC membrane protein that transports a wide range of natural products as well as glutathione (GSH)-, glucuronate-, and sulfate-conjugated metabolites. In addition, free GSH is required for MRP1 to transport several chemotherapeutic drugs. However, the mechanisms regulating the influence of GSH on MRP1 is poorly understood, and the location of GSH binding site(s) within MRP1 have yet to be determined. To address these issues, we have synthesized a [(125)I] labeled azido-derivative of GSH (IAAGSH) to photoaffinity label MRP1. Our results revealed that IAAGSH labeled MRP1 with high specificity, and binding was inhibited by MRP1 substrates leukotriene C(4) and MK571. Interestingly, verapamil and vincristine enhanced IAAGSH photolabeling of MRP1, in agreement with observations that both drugs enhance GSH transport. We observed GSH to be the best inhibitor of photoaffinity labeling, as compared to oxidized glutathione (GSSG) and four different GSH alkyl derivatives. These observations indicate that IAAGSH interacted with MRP1 in a similar manner as unmodified GSH. Moreover, using eight MRP1-HA variants, each containing hemagglutinin A (HA) epitopes inserted at different sites in MRP1, we mapped the GSH binding sites in MRP1. Our GSH analogue photoaffinity labeled four MRP1 polypeptides that were located within two cytoplasmic domains in linker sequences (L0 and L1) as well as transmembrane domains 10-11 and 16-17. The photoaffinity labeling of polypeptides within L0 and L1 domains is further confirmed using two MRP1-specific monoclonal antibodies (MRPr1 and QCRL1) with epitopes within the linker domains. Taken together, this study provides the most precise information to date on the location of GSH binding sites in MRP1.     

Structural proteins and cell-free translation products of total RNA and hybrid-selected RNA from two DNA variants of vaccinia virus.

Two major variants of vaccinia virus, large (L) and small (S), differ by a deletion of 9.7 kilobase pairs. The structural proteins and the translation products of RNA transcribed in vitro from each of these variants were analyzed by gel electrophoresis. Recombinant plasmids were used to select RNA transcribed from the L variant sequences corresponding to the deletion. This RNA yielded translation products indicating that a minimum of 11 polypeptides, including two structural proteins, map within the deletion.     

Genetic variants of the Bombyx mori silkworm encoding sericin proteins of different lengths

A variant sericin polypeptide originally found by acid gel electrophoresis in the Nd-s mutant strain of the silkworm, Bombyx mori, has been analyzed genetically. The vriant polypeptide (called S-2^v) is encoded by a gene which behaves as a codominant allele of the gene encoding the standard S-2 sericin polypeptide. Linkage analysis locates these alleles at 0.0 map unit on chromosome 11. SDS-polyacrylamide gel electrophoresis shows that the molecular weight of the S-2^v variant polypeptide is lower by approximately 62,500 than that of the S-2 polypeptide. Amino acid analysis indicates that the two sericin polypeptides have similar compositions. These results are consistent with the idea that the variant allele arose by deletion within the S-2 coding sequence in the Src-2 gene locus as the result of unequal recombination.     

A unique subset of developmentally regulated surface proteins turns over rapidly during fusion of the L6 rat myoblast cell line

We have previously identified several developmentally regulated surface polypeptides in the L6 rat myoblast cell line, on the basis of their susceptibility to lactoperoxidase catalyzed iodination. An analysis of the turnover rates of these polypeptides now indicates that while the bulk of the iodinated polypeptides have a half-life of 20-30 h, four low-molecular-weight polypeptides have half lives of 2-7 h. The half-lives of all of the rapid turnover class surface polypeptides were greatly increased in cultures where fusion was inhibited by chloroquine and in nonfusing variants of the L6 cell line. In contrast, inhibition of fusion by the metalloendoprotease inhibitor 1, 10-phenanthroline did not alter the turnover of any iodinatable surface proteins. We propose that some or all of the rapid turnover class of polypeptides may be surface receptors which control cell surface alterations involved in the acquisition of fusion competence or in fusion itself.