Length heterogeneity in rat salivary gland alpha 2 mu globulin mRNAs: multiple splice-acceptors and polyadenylation sites

Wheat germ agglutinin affinity chromatography enrichment and glyco-proteomic characterization of tetrodotoxin-binding proteins from the plasma of cultured tiger pufferfish (Takifugu rubripes)

Efficient enrichment of tetrodotoxin (TTX)-binding proteins from the plasma of cultured tiger pufferfish (Takifugu rubripes) was achieved by ammonium sulfate fractionation and wheat germ agglutinin (WGA) affinity chromatography. The enrichment efficiency was validated by ultrafiltration-LC/MS-based TTX-binding assay and proteomics. Major proteins in the WGA-bound fraction were identified as isoform X1 (125 kDa) and X2 variants (88 and 79 kDa) derived from pufferfish saxitoxin and tetrodotoxin-binding protein (PSTBP) 1-like gene (LOC101075943). The 125-kDa X1 protein was found to be a novel member of the lipocalin family, having three tandemly repeated domains. X2 variants, X2α and X2β, were estimated to have two domains, and X2β is structurally related to Takifugu pardalis PSTBP2 in their domain type and arrangement. Among 11 potential N-glycosylation sites in the X2 precursor, 5 N-glycosylated Asn residues (N55, N89, N244, N308, and N449) were empirically determined. Structural relationships among PSTBP homologs and complexity of their proteoforms are discussed.

Molecular complexity of the major urinary protein system of the Norway rat, Rattus norvegicus

Major urinary proteins (MUP) are the major component of the urinary protein fraction in house mice (Mus spp.) and rats (Rattus spp.). The structure, polymorphism and functions of these lipocalins have been well described in the western European house mouse (Mus musculus domesticus), clarifying their role in semiochemical communication. The complexity of these roles in the mouse raises the question of similar functions in other rodents, including the Norway rat, Rattus norvegicus. Norway rats express MUPs in urine but information about specific MUP isoform sequences and functions is limited. In this study, we present a detailed molecular characterization of the MUP proteoforms expressed in the urine of two laboratory strains, Wistar Han and Brown Norway, and wild caught animals, using a combination of manual gene annotation, intact protein mass spectrometry and bottom-up mass spectrometry-based proteomic approaches. Cluster analysis shows the existence of only 10 predicted mup genes. Further, detailed sequencing of the urinary MUP isoforms reveals a less complex pattern of primary sequence polymorphism in the rat than the mouse. However, unlike the mouse, rat MUPs exhibit added complexity in the form of post-translational modifications, including the phosphorylation of Ser4 in some isoforms, and exoproteolytic trimming of specific isoforms. Our results raise the possibility that urinary MUPs may have different roles in rat chemical communication than those they play in the house mouse. Shotgun proteomics data are available via ProteomExchange with identifier PXD013986.

Proteomic analysis of the transition from quiescent to proliferating stages in rat liver hepatectomy model

The 70% (or 2/3) partial hepatectomy (PHx) rat liver model provides an effective medium for study of the transition and regulation of hepatocytes from quiescent to proliferating phase. Although the gene expression pattern has come under intense scrutiny, a differential proteomic study could help to reveal the mechanism of how the process is initiated and regulated. The proteomic changes were analyzed in two groups, 7 h after 70% PHx test group and sham-operation control group, by two-dimensional gel electrophoresis with 907 +/- 33 and 910 +/- 64 spots on gels, respectively. Twelve down-regulated spots and twenty-six up-regulated spots were recognized using ImageMaster software and were identified by matrix-assisted laser desorption/ionization-mass spectrometry-quadrupole time of flight mass spectrometry and/or tandem mass spectrometry reconfirmation. Some of the differential proteins were associated with stress defense, lipid metabolism, and macromolecular biosynthesis while the others were shown to be involved in regulating transcript factors associated with liver regeneration. A "proteomic model" for liver regeneration was suggested based on our data and related scientific literature to interpret the differential proteome pattern that reflected the transition of cells from quiescent to proliferating state, including but not limited to the rat liver after 70% PHx.

Modulation of gene and protein expression by carbon tetrachloride in the rat liver

The gene and protein expression changes after exposure to a toxic compound might help elucidate its mechanism of action. In this paper we investigated the effect of carbon tetrachloride (CCl(4)) on the gene and protein expression in rat livers. Adult Wistar rats were administered CCl(4) and livers were harvested 6 or 24 h thereafter. The analysis of mitochondrial proteins on 2D gels showed the upregulation of two proteins involved in stress (catalase and uricase). Among the downregulated proteins, enzymes related to the metabolism of lipids and aminoacids were affected. Additionally, alpha-2-macroglobulin and senescence marker protein, two proteins whose decrease in expression has been connected to hepatocyte damage, were decreased. Several of the upregulated genes are involved in stress response, DNA and protein damage, and repair. Genes coding for several enzymes involved in different metabolic pathways, including some P450, were downregulated in the treated animals. In conclusion, a single dose of CCl(4) caused gene and protein expression changes that can be related to its mechanism of toxicity. Results from both technologies support previous publications and provide possible new toxicity markers. However, the correlation between gene and protein expression at a given time point is less apparent, partly as a result of different regulatory mechanisms between gene and protein expression.

Crystal structure of aphrodisin, a sex pheromone from female hamster

We have solved the crystal structure of aphrodisin, a pheromonal protein inducing a copulatory behaviour in male hamster, using MAD methods with selenium, at 1.63 A resolution. The monomeric protein belongs to the lipocalin family, and possesses a disulfide bridge in a loop between strands 2 and 3. This disulfide bridge is characteristic of a family of lipocalins mainly identified in rodents, and is analogous to the fifth disulfide bridge of the long neurotoxins, such as alpha cobratoxin. An elongated electron density was found inside the buried cavity, which might represent a serendipitous ligand of unknown origin. The analysis of the water accessible surfaces of the side-chains bordering the cavity indicates that Phe76 may be the door for the natural ligand to access the cavity. This residue defines the entry of the cavity as belonging to the consensus for lipocalins. The face bearing Phe76 might also serve for the interaction with the receptor.

Cloning, post-translational modifications, heterologous expression and ligand-binding of boar salivary lipocalin

Boar submaxillary glands produce the sex-specific salivary lipocalin (SAL), which binds steroidal sex pheromones as endogenous ligands. The cDNA encoding SAL was cloned and sequenced. From a single individual, two protein isoforms, differing in three amino acid residues, were purified and structurally characterized by a combined Edman degradation/MS approach. These experiments ascertained that the mature polypeptide is composed of 168 amino acid residues, that one of the three putative glycosylation sites is post-translationally modified and the structure of the bound glycosidic moieties. Two of the cysteine residues are paired together in a disulphide bridge, whereas the remaining two occur as free thiols. SAL bears sequence similarity to other lipocalins; on this basis, a three-dimensional model of the protein has been built. A SAL isoform was expressed in Escherichia coli in good yields. Protein chemistry and CD experiments verified that the recombinant product shows the same redox state at the cysteine residues and that the same conformation is observed as in the natural protein, thus suggesting similar folding. Binding experiments on natural and recombinant SAL were performed with the fluorescent probe 1-aminoanthracene, which was efficiently displaced by the steroidal sex pheromone, as well as by several odorants.

Three subsets of genes whose tissue specific expression is sex and age-dependent can be identified within the rat alpha 2u-globulin family

The rat alpha 2u-globulins are encoded by a multigene family whose 20-25 members are subjected to multihormonal regulation that is dependent upon the sex of the animal, the developmental stage and the tissue being examined. Using RT-PCR and diagnostic restriction analysis of the products, we have examined the specificity of the expression of different members of the gene family. All family members can be classified into three subsets, depending on how the amplified cDNA responds to digestion with ApaLI, SstI and VspI. Subset A contains the restriction sites for both ApaLI and SstI but not VspI and typifies the genes expressed in the salivary glands of both mature and juvenile animals of both sexes, where it is the only subset expressed. This subset of genes also accounts for all the transcripts observed in the kidneys and mammary glands of juvenile males. Although subset A was represented in the transcript populations of all the other tissues examined, its proportion relative to the total varied greatly. The two other subsets were subset V, which contains only the restriction site for VspI, and subset N, which lacks all three restriction sites. In all the other tissues examined, two or all three of the subsets were expressed, usually in a manner that was unique to the sex and age of the tissue in question. The proportion of each of the three alpha 2u-globulin subsets in the alpha 2u-globulin gene family was determined by quantitation of the restriction products of amplified genomic DNA. Interestingly, the most prevalent subset in the genome (N) has the most limited tissue expression pattern, but is found in liver and preputial glands, the tissues expressing the most substantial quantities of alpha 2u-globulin. These results indicate the complexity of the regulation of the alpha 2u-globulins and point to the necessity for gene specific analyses if the expression of the family is to be understood in molecular terms.

Molecular evidence of complex tissue- and sex-specific mRNA expression of the rat alpha(2u)-globulin multigene family

alpha(2u)-Globulin is well known to be a rat protein encoded by a highly homologous multigene family with more than twenty members. We report here the cloning and identification of major alpha(2u)-globulin mRNA species expressed in various tissues. Initially, eight individual clones (PGCL1-8) were obtained from a male preputial gland cDNA library. Data base analysis with BLAST demonstrated six mRNAs to be novel, all clones being characterized by highly conserved sequence motifs as lipocalins. All cDNAs contained an open reading frame of 543 nucleotides and encode 181 amino acid proteins showing 92.5-98.7% and 87.3-98.3% nucleic and amino acid identity, respectively. Denaturing gradient gel electrophoresis (DGGE) with sequence analysis showed that PGCL4 is a major member in the female mammary gland, and in the submaxillary and lachrymal glands of both sexes, while the counterpart in male liver and the coagulate glands was found to be PGCL1. Numbers of cDNA species including PGCL1 and PGCL4 were found in preputial glands, no sex-related difference being observed. These results directly demonstrate complex tissue- and sex-specific expression of alpha(2u)-globulins in terms of mRNA species, providing useful information for understanding regulation of the alpha(2u)-globulin multigene family.

Abundant secretory lipocalins displaying male and lactation-specific expression in adult hamster submandibular gland. cDNA cloning and sex hormone-regulated repression

We have previously identified massively expressed 24- and 20.5-kDa male-specific proteins in submandibular salivary glands (SMG) of adult hamsters. Here we report the cloning of the cDNA encoding the 24-kDa protein which we have now found to be a heterogenously N-glycosylated form of the 20.5-kDa protein. The deduced amino acid sequence indicated that the protein is a member of the lipocalin family, the two most related lipocalins being rat odorant-binding protein of nasal mucosa and aphrodisin, a pheromonal protein present in vaginal discharge and saliva of female hamsters. Northern blot analysis showed that cognate mRNA is expressed in hamster SMG and lacrimal gland (LG) displaying marked sex-hormonal repression. The sex-hormonal repression patterns showed similarities and dissimilarities between SMG and LG but they were, respectively, similar to the sex-hormonal repression pattern noted for the SMG 24/20.5-kDa male-specific proteins and for an abundant female-specific 20-kDa LG secretory protein. These SMG and LG proteins were found to be immunologically similar and secretion of the SMG proteins in saliva and their excretion in urine was detected. The male-specific and abundant expression of the SMG proteins were seen at and after sexual maturity but was not dependent on androgens. Surprisingly, a temporary male-like expression of these SMG proteins was seen in lactating females which was obliterated by oestrogen administration. Our results show that despite differences in their repression by sex hormones, the gene for SMG 24/20.5-kDa proteins is similar or identical to that of LG 20-kDa protein and their marked repression by both androgens and oestrogens might be at the transcriptional level. Moreover, they might be excellent models with which to study sex hormone repression of gene expression at the molecular level. The results of homology search and the male- and lactation-specific pressure of the SMG proteins in adult saliva and urine suggests a possibility of their involvement in olfaction-mediated chemical communication between hamsters.

cDNA cloning and sequencing reveal the major horse allergen Equ c1 to be a glycoprotein member of the lipocalin superfamily

The gene encoding the major horse allergen, designated Equus caballus allergen 1 (Equ c1), was cloned from total cDNA of sublingual salivary glands by reverse transcription-polymerase chain reaction using synthetic degenerate oligonucleotides deduced from N-terminal and internal peptide sequences of the glycosylated hair dandruff protein. A recombinant form of the protein, with a polyhistidine tail, was expressed in Escherichia coli and purified by immobilized metal affinity chromatography. The recombinant protein is able to induce a passive cutaneous anaphylaxis reaction in rat, and it behaves similarly to the native Equ c1 in several immunological tests with allergic patients' IgE antibodies, mouse monoclonal antibodies, or rabbit polyclonal IgG antibodies. Amino acid sequence identity of 49-51% with rodent urinary proteins from mice and rats suggests that Equ c1 is a new member of the lipocalin superfamily of hydrophobic ligand-binding proteins that includes several other major allergens. An RNA blot analysis demonstrates the expression of mRNA Equ c1 in liver and in sublingual and submaxillary salivary glands.

Purification and identification of allergenic alpha (2u)-globulin species of rat urine

Amino-acid compositional and sequence analyses as well as mass spectrometric determinations of purified rat urine proteins, previously termed prealbumin and alpha(2)-euglobulin, have revealed a high homology between the two forms which have now been identified as alpha(2)-globulin species. The "prealbumin' fraction was found to correspond to alpha(2u)-globulin originating from salivary gland and the 'alpha(2)-euglobulin' fraction was identical with the major urinary protein (MUP) or alpha(2u)-globulin. The results indicate that the two major protein fractions of rat urine constitute different forms of the same parent protein, alpha(2u)-globulin, having no amino-acid sequence resemblance to prealbumin (transthyretin) of rat serum.

Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site

The dinucleotide AG, found at the 3' end of virtually all eukaryotic pre-mRNA introns, is thought to be essential for splicing. Reduction-of-function mutations in two Caenorhabditis elegans genes, the receptor tyrosine kinase gene let-23 and the collagen gene dpy-10, both alter the AG at the end of a short (ca. 50-nucleotide) intron to AA. The in vivo effects of these mutations were studied by sequencing polymerase chain reaction-amplified reverse-transcribed RNA isolated from the two mutants. As expected, we find transcripts that splice to a cryptic AG, skip an exon, and retain an unspliced intron. However, we also find significant levels of splicing at the mutated 3' splice site (AA) and at nearby non-AG dinucleotides. Our results indicate that for short C. elegans introns an AG is not required for splicing at either the correct 3' splice site or incorrect sites. Analysis of a splice site mutant involving a longer, 316-nucleotide C. elegans intron indicates that an AG is also not required there for splicing. We hypothesize that elements besides the invariant AG, e.g., an A-U-rich region, a UUUC motif, and/or a potential branch point sequence, are directing the selection of the 3' splice site and that in wild-type genes these elements cooperate so that proper splicing occurs.

Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site

The dinucleotide AG, found at the 3' end of virtually all eukaryotic pre-mRNA introns, is thought to be essential for splicing. Reduction-of-function mutations in two Caenorhabditis elegans genes, the receptor tyrosine kinase gene let-23 and the collagen gene dpy-10, both alter the AG at the end of a short (ca. 50-nucleotide) intron to AA. The in vivo effects of these mutations were studied by sequencing polymerase chain reaction-amplified reverse-transcribed RNA isolated from the two mutants. As expected, we find transcripts that splice to a cryptic AG, skip an exon, and retain an unspliced intron. However, we also find significant levels of splicing at the mutated 3' splice site (AA) and at nearby non-AG dinucleotides. Our results indicate that for short C. elegans introns an AG is not required for splicing at either the correct 3' splice site or incorrect sites. Analysis of a splice site mutant involving a longer, 316-nucleotide C. elegans intron indicates that an AG is also not required there for splicing. We hypothesize that elements besides the invariant AG, e.g., an A-U-rich region, a UUUC motif, and/or a potential branch point sequence, are directing the selection of the 3' splice site and that in wild-type genes these elements cooperate so that proper splicing occurs.

Identification of a novel transcription unit in the human insulin-like growth factor-II gene

The human insulin-like growth factor-II (hIGF-II) gene has until now been thought to be composed of eight exons, including three independent leader exons. In the present study two additional exons, one leader exon and one alternatively used ordinate exon, have been newly identified. They were abundantly expressed in human histiocytoma tissue, generating mRNA species of about 5.0 kb in length. The new leader exon shows significant sequence similarity with the rE1 exon, previously reported to be transcribed only in the rat, and is mapped at nearly the same genomic location as in the rat. On the other hand, sequence similarity with another exon in the corresponding region of the rat genome was also found. It was, however, obvious that the rat sequence would not work as an active exon, since both splice acceptor and donor sites were deviated considerably from the consensus sequences. It has thus become apparent that the complex transcription unit of a single-copy hIGF-II gene comprises at least 10 exons, including four leader exons, one alternative exon and three common protein-coding exons.

Variability of polyadenylation sites in mRNAs from human fetal liver

cDNA libraries of human fetal liver were constructed in pBR322 and lambda gt10 vectors. The libraries were screened for liver-specific clones by differential hybridization. This procedure revealed 25 and 32 liver-specific clones in plasmid and phage libraries, respectively. The majority of these clones were represented with serum albumin, fetal G gamma-globin and A gamma-globin cDNA inserts. Three types of 3'-non-coding region were found in 5 sequenced albumin cDNAs. In one type mRNA the distance between the AATAAA signal and polyadenylation site was 15 nucleotides, in 2 other types this distance was 10 and 6 nucleotides. The polyadenylation site in the G gamma-globin cDNA was located 2 nucleotides further from AATAAA signal, while in the A gamma-globin cDNA it was 2 nucleotides closer to the signal as compared with the results published previously.