Structure and chromosome assignment of the murine p36 (calpactin I heavy chain) gene

Isolation and characterization of annexin 2 pseudogene in Rattus norvegicus

Annexin 2 is a calcium-regulated, phospholipid-binding protein present in endothelial cells, macrophages and some tumor cells. Annexin 2 is a substrate for a variety of protein kinases, and plays roles in the regulation of endocytosis, exocytosis and thrombolysis. We have determined the nucleotide sequence of a rat genomic DNA fragment that hybridized to a rat annexin 2 DNA complementary to RNA (cDNA) probe. Sequence analysis revealed that it was an intronless rat annexin 2, consisting of a start-to-stop-codon-length copy of the processed transcript. This pseudogene contained 33 point mutations and two deletion sites in the coding region as compared with the cDNA, and thus displayed typical features of a retroposon. Transitions were more frequent than transversions, and the most frequent type of mutation was G to A transition. We isolated a phage clone that contained a functional rat annexin 2 genomic fragment including coding exons 3 and 4. Polymerase chain reaction and subsequent sequence analysis revealed an intron of approximately 4 kbp at the same site as in humans and mice. Whereas the annexin 2 gene or its cDNA homologues have been detected in various species from Xenopus to humans, its pseudogene has been reported only in humans. In the present study, we demonstrated the presence of an annexin 2 pseudogene in rats.

In vivo modulation of annexins I, II and V expression by thyroxine and methylthiouracil

Regulation of annexin concentration and localization were investigated in thyroid tissues of hypothyroid [methylthiouracil (MeSur) treatment], euthyroid (control) and hyperthyroid [thyroxine (T4) treatment] rats. A low level of circulating thyroid hormones induces a decrease of total thyroid calcium-binding protein concentration when compared with the concentration in unstimulated animals. Conversely, concentrations of annexins I, II and V increase. The accumulation of these proteins in two subcellular compartments (cytosolic and particulate fractions) can be reversed by addition of thyroid hormones. The finding of a specific increase in annexins concentration in thyroid-hormone-deficient rats, with a general decrease of the total calcium-binding protein content points to a very important role of these proteins in the cells. Furthermore, hyperthyroidisnt gives opposite results. To investigate the transduction pathway of annexins I-, II- and V-induced biosynthesis by thyroid hormones in thyroid glands, we used cultured pig thyroid cells as in vitro model system. In previous work [16], we have shown that annexin concentrations and localization are under TSH control via the adenylate cyclase pathway. In the presence of MeSur (in the culture medium), the protein-binding iodine remains low, indicative of weak thyroid hormone synthesis (data not shown) and that the annexins content is unchanged. These results suggest that, in thyroid tissue, an indirect mechanism links thyroid hormones to annexin expressions via the TSH feed-back loop, and excludes autocrine regulation.

Complete structure of the murine p36 (annexin II) gene. Identification of mRNAs for both the murine and the human gene with alternatively spliced 5' noncoding exons

p36 (also termed annexin II) is a 39 kDa Ca2+/phospholipid-binding, membrane-associated protein that is a protein-tyrosine kinase substrate. We report here studies of the noncoding exons of p36, which combined with our earlier studies of the coding exons, allow us to conclude that the murine p36 gene is 34 kb in length with 14 exons. Comparison of the genes coding for mouse and human p36 (annexin II) and mouse, rat and human p35 (annexin I) and pigeon cp35 (an annexin I-related protein) shows strong genomic structural conservation supporting the hypothesis that these genes had a common ancestor. Both human and murine p36 mRNAs were found to be alternatively spliced in their 5' noncoding region. In both cases exon 2 is a cassette exon, which is present in a small fraction of p36 mRNAs. In type 1 mouse p36 mRNA the first noncoding 44 base exon 1 is joined to exon 3, the first of the 12 coding exons. In type 2 mRNA a 70 base noncoding exon (exon 2) is inserted between exon 1 and exon 3. Type 1 mRNA was present in all cell types studied as revealed by Northern analysis and primer extension, whereas type 2 mRNA could only be detected by RACE or PCR, indicating that it is of very low abundance. The major transcription start site of the mouse p36 gene was mapped by primer extension to be 61 bp upstream of the AUG initiation codon, which corresponds to type 1 mRNA, The murine p36 gene enhancer/promoter region contains a putative TATA box and several other potential regulatory sequences. The two alternatively-spliced human p36 mRNAs differ by the presence or absence of a noncoding 81 base exon (exon 2) inserted after exon 1, with exon 2-containing mRNAs representing approximately 10% of total p36 mRNA. The 300 bp spanning the promoter and exons 1-3 of the human and murine p36 genes show strong sequence homology immediately before and after the major transcription start site except in the region corresponding to exon 2, where homology is more limited.

The gene encoding human annexin V has a TATA-less promoter with a high G+C content

Annexin V is a phospholipase A2 and protein kinase C inhibitory protein with calcium channel activity and an undefined role in cellular signal transduction, inflammation, growth and differentiation. Three genomic clones for human annexin V (ANX5) were characterized by restriction analysis, Southern blotting and sequencing. ANX5 spans at least 29 kb of the human genome and contains 13 exons ranging in length from 44 to 513 bp and 12 introns from 232 bp to 8 kb. The absence of a typical TATA box and the presence of high G+C content and Sp1-binding sites in its promoter characterize it as a 'housekeeping' gene and account for its broad pattern of expression. Potential binding sites for cis-regulatory elements identified in the 5'-upstream region of annexin V are consistent with its known regulation by oncogenic and growth-related stimuli. ANX5, like its chick homologue, differs from the genes encoding annexins I, II and III in features of its promoter and in the size of its exons 1, 2 and 3 in ways that may impart individuality to its regulation and function.

Molecular cloning of a novel N-terminal variant of annexin II from rat basophilic leukaemia cells

Rat annexin II cDNA clones were isolated from a rat basophilic leukaemia cell plasmid library by cross-species hybridization with a mouse probe, and fully sequenced using the dideoxy-chain-termination method. Alignment of the derived amino-acid sequence with those of other mammalian annexin II species revealed a high level of conservation, characteristic of the annexin family of proteins. One of the cDNAs isolated contained an additional six nucleotides close to the N-terminus, lying in-frame and at a point corresponding to an intron/exon boundary in the human annexin II gene. As the two rat cDNAs were identical apart from the six nucleotide insert, it is likely that these represent alternatively spliced transcripts of a single gene, rather than the products of two separate genes. The six nucleotides encode serine-glutamine and therefore introduce an additional potential phosphorylation site into a region already containing one tyrosine and two serine phosphorylation sites. The discovery of this novel annexin II variant may have important implications both for p11 binding and for regulation of annexin II function by phosphorylation.

Genomic organization and chromosomal localization of the mouse synexin gene

We have isolated and characterized the gene encoding mouse synexin, which consists of 14 exons and spans approximately 30 kbp of genomic DNA. The protein's unique N-terminal domain is encoded by six exons, and the C-terminal tetrad repeat, the site of the membrane-fusion and ion-channel domain, is encoded by seven exons. The first exon encodes the 5'-untranslated region. Analysis of synexin-gene expression in different mouse tissues shows that mRNA with exon 6 is only present in brain, heart and skeletal muscle. mRNA lacking exon 6 is expressed in all tissues we have examined. The initiation site for transcription was determined by primer-extension analysis and S1 nuclease mapping. Sequence analysis of the 1.3 kb 5'-flanking region revealed that the promoter has a TATA box located at position -25 and a number of potential promoter and regulatory elements. A CCAAT motif was not observed but CCATT is located in an appropriate position for the CCAAT motif upstream from the transcription-initiation start site. In addition, the 5'-flanking region contains two sets of palindromic sequences. Finally, we have determined that the functional synexin gene (Anx7) is located on mouse chromosome 14 and that a pseudogene (Anx7-ps1) is located on chromosome 10.

Structural evolution of the annexin supergene family

The annexin family of calcium-binding proteins is comprised of at least ten mammalian genes, with additional representatives in lower eukaryotes. Recent structural analyses of several annexin genes have provided insights into the relationship between exon organization and functional domains. We discuss the implications of these findings and speculate on the evolutionary origins of the annexin supergene family.

Divergent structure of the human synexin (annexin VII) gene and assignment to chromosome 10

The human synexin (annexin VII) gene occurs as a single copy at chromosome 10q21.1-21.2 and substantially deviates in size and in the location of splice junctions from the other two well-characterized members of the annexin gene family, lipocortin I (annexin I) and calpactin I (annexin II). The synexin gene contains 14 exons, including an alternatively spliced cassette exon, and spans approximately 34 kb of DNA. Only five of the fourteen splice junctions are conserved compared to other annexins, and the differences are particularly pronounced in the exons that encode the C-terminal third and fourth conserved repeats in the gene product. Although parallels between exons and protein domains were not apparent, we did observe clustering of splice junctions corresponding to either the unique N-terminal domain or the conserved C-terminal tetrad repeat domain, which is common to all annexins. Furthermore, a complete analysis of the 5' flanking region of the annexin VII gene revealed an entirely different set of cis-acting and enhancer elements compared to other annexin genes. We conclude that the annexin VII gene may have arisen by a divergence from the evolutionary pathway taken by both annexins I and II.

Structure of the gene encoding anchorin CII (chick annexin V)

Anchorin CII (annexin V) was first characterized as a collagen-binding protein and later identified as the chick homologue of human endonexin II, a member of the annexin gene family. Its gene (anx5) structure and sequence have been investigated to provide insight into the evolution and regulation of this important protein, and to elucidate its putative role in signal transduction and cellular differentiation. Four chick genomic clones encoding anchorin CII were isolated and characterized by restriction analysis, Southern blotting and sequencing. The anchorin CII-encoding gene spans about 24 kb and consists of 13 exons ranging in length from 50 to 561 bp, interrupted by 12 introns of 94 bp to 7 kb. Its promoter sequence contained no TATA box, but did display a high G+C content and multiple Sp1-binding sites typical of 'housekeeping' genes. Potential binding sites for transcription factors in the 5'-upstream region are consistent with regulation of anx5 expression by mitogens, oncoproteins, steroids and possibly metals. Genomic Southern blotting confirmed that chick anx5 is present as a single-copy gene.

Structure of the human annexin VI gene

We report the structure of the human annexin VI gene and compare the intron-exon organization with the known structures of the human annexin I and II genes. The gene is approximately 60 kbp long and contains 26 exons. Consistent with the published annexin VI cDNA sequence, the genomic sequence at the 3' end does not contain a canonical polyadenylation signal. The genomic sequence upstream of the transcription start site contains TATAA and CAAT motifs. The spatial organization of the exons does not reveal any obvious similarities between the two halves of the annexin VI gene. Comparison of the intron-exon boundary positions of the annexin VI gene with those of annexins I and II reveals that within the repeated domains the break points are perfectly conserved except for exon 8, which is one codon smaller in annexin II. The corresponding point in the second half of annexin VI is represented by two exons, exons 20 and 21. The latter exon is alternatively spliced, giving rise to two annexin VI isoforms that differ with respect to a 6-amino acid insertion at the start of repeat 7.

Z-DNA-forming sequences at a putative duplication site in the human annexin VI-encoding gene

We report here the presence of five stretches of alternating purine/pyrimidine (APP) intronic sequence close to the 5' end of the first exon in the C-terminal half of the human annexin VI-encoding gene (ANX VI). ANX VI, which comprises eight conserved repeats, is considered to have arisen by duplication of a hypothetical four repeat Anx; the location of the duplication would be predicted to occur within the intron where the APP sequences have been identified. The APP sequences have, by computer prediction, been identified as having significant potential to form Z-DNA. We discuss the significance of these potential Z-DNA-forming sequences being located in a region predicted to be the site of duplication which gave rise to the human ANX VI gene.

Organisation of the chicken annexin V gene and its correlation with the tertiary structure of the protein

Chicken annexin V (anchorin CII) is a collagen binding, membrane-associated molecule with Ca2+ channel activity. Here we report on the coding sequences, promoter region, size and distribution of exons, and exon-intron junctions of the chicken annexin V gene. It is about 25 kb long and codes for 13 short exons between 50 and 581 bp length. Exon sizes and locations of splice sites are almost completely homologous to those of the human and mouse annexin II or pigeon annexin I genes, although there is only 50-60% homology in the sequence of the corresponding proteins. The four repeat structure and symmetry of the annexin V as evident from sequence and X-ray analysis studies is only partially reflected in this highly conserved exon distribution. In the first two repeats of chicken annexin V the exons correlate with protein domains containing one, two, or three alpha-helices, while in the repeats 3 and 4 exon junctions and alpha-helical domains do not correlate. The analysis of the promoter structure revealed the absence of a typical TATA-box, but a GC-rich region which may possibly promote transcription from several start sites.

Gene expression in cells of the central nervous system

This review summarized a part of our studies over a long period of time, relating them to the literature on the same topics. We aimed our research toward an understanding of the genetic origin of brain specific proteins, identified by B. W. Moore and of the high complexity of the nucleotide sequence of brain mRNA, originally investigated by W. E. Hahn, but have not completely achieved the projected goal. According to our studies, the reason for the high complexity in the RNA of brain nuclei might be the high complexity in neuronal nuclear RNA as described in the Introduction. Although one possible explanation is that it results from the summation of RNA complexities of several neuronal types, our saturation hybridization study with RNA from the isolated nuclei of granule cells showed an equally high sequence complexity as that of brain. It is likely that this type of neuron also contains numerous rare proteins and peptides, perhaps as many as 20,000 species which were not detectable even by two-dimensional PAGE. I was possible to gain insight into the reasons for the high sequence complexity of brain RNA by cloning the cDNA and genomic DNA of the brain-specific proteins as described in the previous sections. These data provided evidence for the long 3'-noncoding regions in the cDNA of the brain-specific proteins which caused the mRNA of brain to be larger than that from other tissues. During isolation of such large mRNAs, a molecule might be split into a 3'-poly(A)+RNA and 5'-poly(A)-RNA. In the studies on genomic DNA, genes with multiple transcription initiation sites were found in brain, such as CCK, CNP and MAG, in addition to NSE which was a housekeeping gene, and this may contribute to the high sequence complexity of brain RNA. Our studies also indicated the presence of genes with alternative splicing in brain, such as those for CNP, MAG and NGF, suggesting a further basis for greater RNA nucleotide sequence complexity. It is noteworthy that alternative splicing of the genes for MBP and PLP also produced multiple mRNAs. Such a mechanism may be a general characteristic of the genes for the myelin-specific proteins produced by oligodendrocytes. In considering the high nucleotide sequence complexity, it is interesting that MAG and S-100 beta genes etc. possess two additional sites for poly(A).(ABSTRACT TRUNCATED AT 400 WORDS)

Chromosomal mapping of the human annexin IV (ANX4) gene

Annexin IV (placental anticoagulant protein II) is a member of the annexin or lipocortin family of calcium-dependent phospholipid-binding proteins. A cDNA for human annexin IV was isolated from a placental library that is 675 bases longer in the 3' untranslated region than previously reported, indicating the existence of alternative mRNA processing for this gene. Genomic Southern blotting with a cDNA probe indicated a gene size of 18-56 kb. Primers developed for polymerase chain reaction (PCR) allowed amplification of a 1.6-kb portion of the ANX4 gene. DNA sequence analysis showed that this PCR product contained a single intron with exon-intron boundaries in exactly the same position as in the mouse annexin I and annexin II genes. PCR analysis of a somatic cell hybrid panel mapped the ANX4 gene to chromosome 2, and in situ hybridization with a cDNA probe showed a unique locus for ANX4 at 2p13. This study provides further evidence that genes for the annexins are dispersed throughout the genome but are similar in size and exon-intron organization.

Correlation of gene and protein structure of rat and human lipocortin I

Lipocortins (annexins) are a family of calcium-dependent phospholipid-binding proteins with phospholipase A2 inhibitory activity. The characteristic primary structure of members of this family consists of a core structure of four or eight repeated domains, which have been implicated in calcium-dependent phospholipid binding. In two lipocortins (I and II) a short amino-terminal sequence distinct from the core structure has potential regulatory functions which are dependent on its phosphorylation state. We have isolated the rat and the human lipocortin I genes and found that they both consist of 13 exons with a striking conservation of their exon-intron structure and their promoter and amino acid sequences. Both lipocortin I genes are at least 19 kbp in length with exons ranging from 57 to 123 bp interrupted by introns as large as 5 kbp. Each of the four repeat units of lipocortin I are encoded by two consecutive exons while individual exons code for the highly conserved putative calcium-binding domains. The promoter sequences in the rat and in human genes are highly conserved and contain nucleotide sequences characterized as enhancer sequences in other genes. The structure of the lipocortin I gene lends support to the hypothesis that the lipocortin genes arose by a duplication of a single domain.

Structure of the gene encoding columbid annexin Icp35

The cp35 gene, encoding an annexin I (AnxI) cropsac 35-kDa protein (cp35) from the pigeon, consists of 13 exons and twelve introns. The borders of exons 2-13 were mapped by comparison with the known cDNA sequence. A 5-kb sequence containing exons 1, 2, and 3, and 1.4 kb of 5'-flanking DNA, is presented. The transcription start point was mapped by S1 nuclease protection. The region of the cp35 mRNA sequence, which we had previously shown to be profoundly different from mammalian anxI, is located in the first half of exon 3. Whereas human anxI is known to be single copy, Southern analysis of pigeon genomic DNA and genomic clones demonstrated multiple anxI genes in the pigeon, diverging significantly in their 5'-termini. Pigeon vimentin, on the other hand, is encoded by a single-copy gene as it is in other birds and mammals. These experiments have demonstrated that the cp35 mRNA is transcribed from its individual gene and is not a product of alternative processing of the pigeon homolog of mammalian anxI. We speculate that the diversification of anxI genes in Columbid birds allowed the recruitment of one of these genes (cp35) for unique regulation by prolactin in the absence of post-translational regulation via residues encoded by exons 2 and 3.

Amino acid sequence analysis of the annexin super-gene family of proteins

The annexins are a widespread family of calcium-dependent membrane-binding proteins. No common function has been identified for the family and, until recently, no crystallographic data existed for an annexin. In this paper we draw together 22 available annexin sequences consisting of 88 similar repeat units, and apply the techniques of multiple sequence alignment, pattern matching, secondary structure prediction and conservation analysis to the characterisation of the molecules. The analysis clearly shows that the repeats cluster into four distinct families and that greatest variation occurs within the repeat 3 units. Multiple alignment of the 88 repeats shows amino acids with conserved physicochemical properties at 22 positions, with only Gly at position 23 being absolutely conserved in all repeats. Secondary structure prediction techniques identify five conserved helices in each repeat unit and patterns of conserved hydrophobic amino acids are consistent with one face of a helix packing against the protein core in predicted helices a, c, d, e. Helix b is generally hydrophobic in all repeats, but contains a striking pattern of repeat-specific residue conservation at position 31, with Arg in repeats 4 and Glu in repeats 2, but unconserved amino acids in repeats 1 and 3. This suggests repeats 2 and 4 may interact via a buried saltbridge. The loop between predicted helices a and b of repeat 3 shows features distinct from the equivalent loop in repeats 1, 2 and 4, suggesting an important structural and/or functional role for this region. No compelling evidence emerges from this study for uteroglobin and the annexins sharing similar tertiary structures, or for uteroglobin representing a derivative of a primordial one-repeat structure that underwent duplication to give the present day annexins. The analyses performed in this paper are re-evaluated in the Appendix, in the light of the recently published X-ray structure for human annexin V. The structure confirms most of the predictions and shows the power of techniques for the determination of tertiary structural information from the amino acid sequences of an aligned protein family.

Chromosomal localization of the human annexin III (ANX3) gene

The annexins or lipocortins are a new family of calcium-dependent phospholipid-binding proteins. Annexin III has been previously identified as inositol 1,2-cyclic phosphate 2-phosphohydrolase (EC 3.1.4.36), an enzyme of inositol phosphate metabolism, and also as placental anticoagulant protein III, lipocortin III, calcimedin 35-alpha, and an abundant neutrophil cytoplasmic protein. In this study, the gene (ANX3) encoding annexin III was localized to human chromosome 4 at band q21 (q13-q22) by (1) polymerase chain reaction analysis of a human-rodent hybrid cell panel, confirmed by genomic Southern blot analysis of the same panel with a cDNA probe and (2) in situ hybridization with a cDNA probe.

Mouse lipocortin I gene structure and chromosomal assignment: gene duplication and the origins of a gene family

Using cDNA probes obtained from library screening and anchored polymerase chain reaction, we have isolated and characterized three overlapping mouse genomic clones that contain the mouse lipocortin I (Lipo I) structural gene. Restriction enzyme mapping, Southern blotting, and DNA sequencing were carried out on the cloned genomic DNA. Lipo I spans about 17 kb and is divided into 13 exons encoding a protein of 346 amino acid residues. The promoter region of the gene has a TATA box and a CCAAT box located upstream of the transcription initiation site at -31 and -76 bp, respectively. Analysis of the strain distribution pattern of Lipo 1 in BXD and AKXD collections of recombinant inbred strains establishes that Lipo I is located on chromosome 19 in close proximity to Ea-4. While no striking relationship exists between the exon/intron structure of the gene and the four repeated 70-amino-acid domains of the protein, three of the four 17-amino-acid repeats believed to be responsible for Ca2+/phospholipid binding are encoded by the last codon of one exon and the first 16 codons of the following exon. This pattern supports the gene duplication theory, and the similarity in gene structure between mouse Lipo I and Lipo II suggests they have a recent evolutionary ancestor.

Characterization of the human lipocortin-2-encoding multigene family: its structure suggests the existence of a short amino acid unit undergoing duplication

Human genomic clones of the gene encoding lipocortin (LIP) 2 (p36) and of three pseudogenes have been isolated and characterized. The LIP2 gene is at least 40 kb long and consists of 13 exons. The three pseudogenes present typical features of retroposons and, together with the gene, probably represent the entire LIP2 multigene family. Chromosomal assignment of the four loci is proposed. The hypothesis that an ancestral unit coding for 15 to 20 amino acids may have been involved in the evolution of the gene is discussed.