Mouse carbonic anhydrase III: nucleotide sequence and expression studies

Adipose Tissue Transcriptome by Serial Analysis of Gene Expression

OBJECTIVE

To describe the genomic expression profile or transcriptome of adipose tissue using the serial analysis of gene expression method.

RESEARCH METHODS AND PROCEDURES

The serial analysis of gene expression strategy is based on isolation of short sequences (tags), which usually correspond to unique transcripts, and on their concatenation into long DNA molecules, which are then cloned and sequenced. Experiments were performed with mRNA from retroperitoneal adipose tissue of male C57BL6 mice.

RESULTS

We isolated 45,996 tags corresponding to more than 17,000 different genes. Eighty-eight genes were expressed at more than 0.1% of the total population and represented 26% of the mRNA population identified. The most expressed genes were: carbonic anhydrase 3 (1.97%), cytochrome c oxidase (COX) 1 (1.47%), COX2 (1.25%), diazepam binding inhibitor (1.04%), a novel transcript (0.87%), COX3 (0.55%), fatty acid-binding protein 4 (0.55%), and NADH dehydrogenase 4 (0.52%). Other genes known to be expressed in adipose tissue, such as uncoupling protein 2, angiotensinogen, adipsin, and insulin-like growth factor 1, were found at a lower level. Several tags corresponding to novel transcripts were also found.

DISCUSSION

To our knowledge, the present results provide for the first time a quantitative description of the transcriptome in adipose tissue.

Assessment of the swine protein-annotated oligonucleotide microarray

The specificity and utility of the swine protein-annotated oligonucleotide microarray, or Pigoligoarray (http://www.pigoligoarray.org), has been evaluated by profiling the expression of transcripts from four porcine tissues. Tools for comparative analyses of expression on the Pigoligoarray were developed including HGNC identities and comparative mapping alignments with human orthologs. Hybridization results based on the Pigoligoarray's sets of control, perfect match (PM) and deliberate mismatch (MM) probes provide an important means of assessing non-specific hybridization. Simple descriptive diagnostic analyses of PM/MM probe sets are introduced in this paper as useful tools for detecting non-specific hybridization. Samples of RNA from liver, brain stem, longissimus dorsi muscle and uterine endothelium from four pigs were prepared and hybridized to the arrays. Of the total 20,400 oligonucleotides on the Pigoligoarray, 12,429 transcripts were putatively differentially expressed (DE). Analyses for tissue-specific expression [over-expressed in one tissue with respect to all the remaining three tissues (q < 0.01)] identified 958 DE transcripts in liver, 726 in muscle, 286 in uterine endothelium and 1027 in brain stem. These hybridization results were confirmed by quantitative PCR (QPCR) expression patterns for a subset of genes after affirming that cDNA and amplified antisense RNA (aRNA) exhibited similar QPCR results. Comparison to human ortholog expression confirmed the value of this array for experiments of both agricultural importance and for tests using pigs as a biomedical model for human disease.

A novel renal carbonic anhydrase type III plays a role in proximal tubule dysfunction

Dysfunction of the proximal tubule (PT) is associated with variable degrees of solute wasting and low-molecular-weight proteinuria. We measured metabolic consequences and adaptation mechanisms in a model of inherited PT disorders using PT cells of ClC-5-deficient (Clcn5Y/-) mice, a well-established model of Dent's disease. Compared to cells taken from control mice, those from the mutant mice had increased expression of markers of proliferation (Ki67, proliferative cell nuclear antigen (PCNA), and cyclin E) and oxidative scavengers (superoxide dismutase I and thioredoxin). Transcriptome and protein analyses showed fourfold induction of type III carbonic anhydrase in a kidney-specific manner in the knockout mice located in scattered PT cells. Kidney-specific carbonic anhydrase type III (CAIII) upregulation was confirmed in other mice lacking the multiligand receptor megalin and in a patient with Dent's disease due to an inactivating CLCN5 mutation. The type III enzyme was specifically detected in the urine of mice lacking ClC-5 or megalin, patients with Dent's disease, and in PT cell lines exposed to oxidative stress. Our study shows that lack of PT ClC-5 in mice and men is associated with CAIII induction, increased cell proliferation, and oxidative stress.

The mouse liver content of carbonic anhydrase III and glutathione S-tranferases A3 and P1 depend on dietary supply of methionine and cysteine

The contents of glutathione S-transferase (GST) subunits, carbonic anhydrase III (CAIII), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a 230 kDa protein are affected by protein deprivation in mouse liver. In order to know if particular amino acids control these contents, the effects of feeding for 5 days with diets containing different amino acids were examined. After an exploration using SDS-PAGE analysis, the action of selected diets was further examined by distinct techniques. The 230 kDa protein was identified as fatty acid synthase (FAS) by both mass spectrometry and amino acid sequence analyses. Dietary tests showed that: (1) a protein-free diet (PFD) increased the content of glutathione S-transferases P1 and M1, and glyceraldehyde-3-phosphate dehydrogenase, while the content of glutathione S-transferase A3, fatty acid synthase and carbonic anhydrase III decreased; (2) a protein-free diet having either methionine or cysteine preserved the normal contents of glutathione S-transferases P1, A3, M1 and carbonic anydrase III; (3) a protein-free diet having threonine preserved partially the normal contents of glutathione S-transferases P1, A3, M1 and carbonic anhydrase III; (4) a protein-free diet having methionine, threonine and cysteine prevented in part the loss of fatty acid synthase; and (5) the glyceraldehyde-3-phosphate dehydrogenase content was controlled by increased carbohydrate level and/or by lower amino acid content of diets, but not by any specific amino acid. These data indicate that methionine and cysteine exert a main role on the control of liver glutathione S-transferases A3 and P1, and carbonic anhydrase III. Thus, they emerge necessary to prevent unsafe alterations of liver metabolism caused by protein deprivation.

Transcriptome of mouse uterus by serial analysis of gene expression (SAGE): Comparison with skeletal muscle

The aim of this study was to identify the transcriptome of the normal mouse uterus by Serial Analysis of Gene Expression method. mRNA was extracted from the uterus and also from the gastrocnemius muscle of mice. Short sequences (tags), each one usually corresponding to a distinct transcript, were isolated and concatemerized into long DNA molecules which were cloned and sequenced. We detected 44,484 tags for the uterus and 42,518 tags for the muscle, representing 14,543 and 14,958 potential transcript species, respectively. Seventy-five and sixty-nine genes were expressed at more than 0.1%, thus corresponding to 37 and 34% of the mRNA population detected in the respective tissues. In both cases, the most highly expressed genes are especially involved in muscle contraction, energy metabolism, and protein synthesis. Compared to skeletal muscle, some differentially expressed genes in the uterus are likely to correspond to its specific reproductive functions. The majority of these genes remain to be characterized. More than 70% of the different tags detected in the uterus did not match any sequence in the public databases and can represent novel or poorly identified genes. This study is the first quantitative description of the transcriptome of the uterus.

Carbonic anhydrase III in liver and muscle of male rats purification and properties

Cytosolic carbonic anhydrases CAI, CAII, and CAIII from liver, and CAII, and CAIII from muscle of adult male Sprague-Dawley rats were purified to homogeneity. CAIII from liver and muscle had the same amino acid composition and were immunochemically similar. Their kinetic properties at 0 degrees C were also similar. Km(CO2) was 4 mM and kcat 3x105 s(-1). Ki was 0.4 and 0.2 M for acetazolamide and NaCl, respectively. Both CAIIIs ran as single bands on SDS-electrophoresis and high-speed centrifugation, with a mol wt of 29.3 kDa. Their hydrodynamic properties suggest that CAIII is a compact, nearly spherical molecule. It contained 0.9 M zinc per M protein. In both tissues isoelectric focusing identified neutral and acidic isoforms with pIs near 7.0 and 6.3, respectively. These forms were immunologically identical and had the same amino acid composition and mol wts. The acidic forms probably represent subspecies of CAIII in different states of oxidation. CAIII is the major soluble protein in rat liver and muscle. Its function is probably to protect proteins of these tissues from oxidation catalyzed by iron-containing degradation products of haemoglobin and myoglobin. Liver CAI and CAII and muscle CAII were identical to CAI and CAII of rat erythrocytes.

Nucleotide sequence and structure of the mouse carbonic anhydrase III gene

At least 14 distinct isozymes of carbonic anhydrase have been identified in mammals. These enzymes catalyze the hydration of carbon dioxide and are essential for regulation of cellular pH and carbon dioxide transport. Carbonic anhydrase III is highly expressed in certain tissues, including muscle and fat where it constitutes up to 25% of the soluble protein. We cloned a cDNA encoding mouse carbonic anhydrase III. This cDNA contains 1653 bp, consisting of 79 bp in the 5' UTR, a 780 bp open reading frame, and 794 bp of the 3' UTR, including two potential polyadenylation signals. Fluorescent in situ hybridization confirmed the existence of a single copy of the gene on chromosome 3. We then isolated the genomic DNA for mouse carbonic anhydrase III and analyzed its structure. The gene consists of seven exons and six introns which span 10.5 kb. The 5' flanking region of the genomic DNA is notable for a pyrimidine rich region consisting of two dinucleotide repeats containing 23 and 20 TC pairs separated by the same 15 bp spacer.

Androgen-linked control of carbonic anhydrase III expression occurs in rat perivenous hepatocytes; an immunocytochemical study

Carbonic anhydrase (CA) isozymes CAII and CAIII were assayed by a radioimmunosorbent technique in liver cytosolic fractions and in isolated hepatocytes of adult male and female rats. Male livers contained 0.16 mg of CAII and 57 mg of CAIII per g cytosolic protein. Corresponding values for female livers were 0.34 mg CAII and 4 mg CAIII. Similar values and differences between CAII and III were found in isolated hepatocytes. Neonatal and adult castration of males reduced the CAIII levels to those of the females. Treatment with testosterone for three weeks restored the copulatory behaviour in the males castrated at adult age, but restored only partially the levels of CAIII. No significant effects of the endocrine manipulations were seen on CAII. Oophorectomy, with or without testosterone substitution, had no significant effect on CAII and CAIII levels in female rats. Immunohistochemistry and histochemistry showed that the regulation of CAIII is confined to perivenous hepatocytes. CAIII can therefore serve as a useful marker in the separation of these cells. CAIII appears to belong to the proteins and enzymes of the rat liver, known to be regulated via the hypothalamo-pituitary-liver axis. It may be used as a model of gene regulation in perivenous hepatocytes.

Suppression of carbonic anhydrase III in rat liver by a dioxin-related toxic compound, coplanar polychlorinated biphenyl, 3, 3',4,4',5-pentachlorobiphenyl

A coplanar polychlorinated biphenyl, 3,3',4,4',5-pentachlorobiphenyl (PenCB), significantly suppresses the expression of rat liver carbonic anhydrase III (CAIII), an enzyme which has recently been suggested to prevent from H(2)O(2)-inducible apoptosis. Marked changes in the CAIII levels of liver cytosol were observed in rats following doses of PenCB ranging from 0.5 to 25 mg/kg body weight and maximum suppression was observed at a dose of 10 mg/kg. Northern analysis revealed that the level of CAIII mRNA in rat liver was dramatically reduced by PenCB treatment while only weak suppression was observed in pair-fed controls. Two AU-rich elements, considered as a destabilizing signal of mRNA, were found in the 3'-untranslated region of CAIII sequenced after reverse transcription-PCR and 3'-rapid amplification of the cDNA end. Dramatic decrease of CAIII in rat liver by PenCB could account for the suppression of the defense system for oxidative stress.

Forced MyHCIIB expression following targeted genetic manipulation of conditionally immortalized muscle precursor cells

The ability to carry out gene targeting in somatic stem cells while maintaining their stem cell characteristics would have important implications for gene therapy and for the analysis of gene function. Using mouse myoblasts, we have explored this possibility by attempting to alter the promoter of a myosin heavy chain gene (MyHCIIB) characteristic of physiologically "fast" muscle so as to force its unscheduled expression in physiologically "slow" muscle fibers. Conditionally immortalized muscle precursor cells were transfected with a gene targeting construct designed to replace the MyHCIIB promoter with that for the carbonic anhydrase III gene (CAIII), which is highly expressed in slow muscle. A potentially targeted clone was isolated and differentiated in culture to form myotubes which expressed MyHCIIB. Cells from the same clone were injected into both slow and fast muscle of host mice, where they contributed to fiber formation. In slow muscle, the fibers derived from this clone did not express MyHCIIB; this may reflect an instability of the targeted MyHCIIB locus and/or a failure of the hybrid promoter to function in slow fibers in vivo. Nonetheless, we have demonstrated that a "promoter knock-in" gene targeting procedure can be used to generate unique MyHCIIB-expressing myotubes in culture and that conditionally immortalized myoblasts can be subjected to extensive passaging and genetic manipulation without losing their ability to form fibers in culture and in vivo.

Sequence comparisons and functional studies of the proximal promoter of the carbonic anhydrase 3 (CA3) gene

Carbonic anhydrase 3 (CA3) is a member of a gene family encoding proteins which catalyse the hydration of CO2 to generate protons and bicarbonate ions for cellular ion transport and pH homeostasis. In mouse embryos CA3 is expressed at high levels in notochord and skeletal muscle and here we demonstrate that this pattern of expression is the same in the developing human embryo. To investigate mechanisms controlling CA3 transcription, we have isolated and compared 2.8kb of sequence flanking exon 1 from the mouse and human genes. Several segments of high sequence identity >80% have been identified, the longest segments of which represent a proximal promoter region and a putative enhancer element. We have shown previously that in cultured cells the human 2.8kb promoter region imposes high level myogenic specific transcription of a reporter gene. However, we now show that while this promoter region directed muscle-specific expression in transgenic mouse embryos this was subject to position effects.

Decreased carbonic anhydrase III levels in the liver of the mouse mutant 'toxic milk' (tx) due to copper accumulation

The mouse mutant 'toxic milk' (tx) is characterized by marked hepatic accumulation of copper, similar to that found in patients with the genetic disorder of copper transport, Wilson disease. In addition, lactating tx females produce copper-deficient milk. To characterize further the biochemical basis of this defect, Western blots of tissue extracts from normal and tx mice were probed with various heavy-metal radioisotopes (63Ni. 65Zn and 64Cu). A 30 kDa Ni/Zn-binding polypeptide was found to be markedly decreased in the livers of the tx mice. This protein was isolated from normal adult mice using a procedure based on Ni-chelation chromatography. The amino acid sequences of two CNBr peptides were identical with portions of the mouse skeletal muscle carbonic anhydrase III (CAIII) sequence. Two other peptides sequenced had closely related sequences to that of CAIII, but with two differences in 45 amino acids. These two peptides may be derived from a novel CAIII isoform, which we term CAIIIB to distinguish it from the published form, CAIIIA. We isolated a cDNA clone corresponding to CAIIIA and used this to show that CAIIIA mRNA was also decreased in the mutant liver, but not in muscle. Copper loading of normal mice also decreased hepatic CAIIIA mRNA, suggesting that the decrease in CAIII mRNA in the tx mouse liver is a secondary consequence of the high copper levels in the liver.

Refined structure of bovine carbonic anhydrase III at 2.0 A resolution

The three-dimensional structure of bovine carbonic anhydrase III (BCA III) from red skeletal muscle cells has been determined by molecular replacement methods. The structure has been refined at 2.0 A resolution by both constrained and restrained structure-factor least squares refinement. The current crystallographic R-value is 19.2% and 121 solvent molecules have so far been found associated with the protein. The structure is highly similar to the refined structure of human carbonic anhydrase II. Some differences in amino acid sequence and structure between the two isoenzymes are discussed. In BCA III, Lys 64 and Arg 91 (His 64 and Ile 91 in HCA II) are both pointing out from the active site cavity forming salt bridges with Glu 4 and Asp 72 (His 4 and Asp 72 in HCA II), respectively. However, Arg 67 and Phe 198 (Asn 67 and Leu 198 in HCA II) are oriented towards the zinc ion and significantly reduce the volume of the active site cavity. Phe 198 particularly reduces the size of the substrate binding region at the "deep water" position at the bottom of the cavity and we suggest that this is one of the major reasons for the differences in catalytic properties of isoenzyme III as compared to isozyme II.

Nucleotide sequence of a cDNA encoding rat brain carbonic anhydrase II and its deduced amino acid sequence

A carbonic anhydrase II (CAII)-encoding cDNA clone was isolated from a rat brain lambda gt11 library. The 1459-bp cDNA codes for 260 amino acids with sequence similarity to mouse and human CAII and hybridizes to a single 1.7-kb mRNA.

CAIII a marker for early myogenesis: analysis of expression in cultured myogenic cells

Carbonic anhydrase III (CAIII) is an abundant muscle protein characteristic of adult type-1, slow-twitch, muscle fibers. We demonstrate that CAIII is not confined to mature muscle but is also expressed in cultured myogenic cells that were originally derived from adult and fetal limb muscle (G8 and C2C12) and by azacytidine treatment of 10T1/2 fibroblasts (23A2). Transcripts may accumulate in these cells to levels that correspond to 6.5% of that found in mature muscle. CAIII is expressed in mononucleate myoblasts and is abundant in those that preferentially fuse to form myotubes, and these findings contrast with those for many other muscle genes whose transcripts only accumulate on or after terminal differentiation. Preliminary promoter-function assays by transfection shows that 2.8 kb of sequence flanking the 5' end of the human CAIII gene efficiently promotes transcription of the bacterial chloramphenicol acetyltransferase gene in myogenic cells. However, none of the sequences within this region are sufficient to confer muscle-specific expression. Removal of sequences 5' to -715 bp leads to a major loss of transcriptional activity of the CAIII promoter. These results imply that the proximal CAIII promoter, which includes a putative CArG box and four potential MyoD binding sites, is not adequate for either myoblast-specific or maximal transcription.

Mapping of mouse carbonic anhydrase-3, Car-3: another locus in the homologous region of mouse chromosome 3 and human chromosome 8

At least six separate genes determining tissue- and organelle-specific isoforms of carbonic anhydrase are known. We have determined the chromosome location of one of these genes, carbonic anhydrase-3 (Car-3), in the mouse and carried out a linkage analysis of Car-1, Car-2, and Car-3. Car-3 has been assigned to band 3A2 by in situ hybridization. We identified a PstI restriction fragment length polymorphism between Mus spretus and Mus mus domesticus and, by using an interspecific backcross, showed that Car-3 is 2.4 +/- 1.7% SE from both Car-1 and Car-2, calculating genetic distance as percentage recombination. No recombinants were found between Car-1 and Car-2 in 100 backcross offspring, and when these data are combined with earlier results, these two loci are estimated to be 1.2 cM from each other at the 95% confidence interval. The three homologous carbonic anhydrase loci in man had earlier been assigned to 8q22, and the finding of linkage of Car-3 to Car-1 and Car-2 in the mouse adds another locus to the conserved segments on mouse chromosome 3 and human chromosome 8.