Multiple Forms and Distribution of Calcium/Calmodulin-Stimulated Protein Kinase II in Brain

In recent years, the enzyme Ca²⁺/calmodulin-stimulated protein kinase II¹ (CaM-PK II) as attracted a great deal of interest. CaM-PK II is the most abundant calmodulin-stimulated protein kinase in brain, where it is particularly enriched in neurons (Ouimet et al., 1984; Erondu and Kennedy, 1985; Lin et al., 1987; Scholz et al., 1988). Neuronal CaM-PK II has been suggested to be involved in several phenomena associated with synaptic plasticity (Lisman and Goldring, 1988; Kelly, 1992), including long-term potentiation (Malinow et al., 1988; Malenka et al.,1989), neurotransmission (Nichols et al., 1990; Siekevitz, 1991), and learning (for review, see Rostas, 1991). This enzyme has also been postulated to be selectively vulnerable in several pathological condition, including epilepsy/kindling (Bronstein et al.,1990; Wu et al., 1990), cerebral ischemia (Taft et al., 1988), and organophosphorus toxicity (Abou-Donia and Lapadula, 1990).     

The murine MHC encodes a mammalian homolog of bacterial ribosomal protein S13

The mouse major histocompatibility complex (MHC) contains many genes in addition to the classical immune response genes. We have screened overlapping cosmid clones covering 170 kb of the H-2K region for genes expressed in embryonal carcinoma (EC) cells. The Ke-3 gene (Abe et al. 1988) found in this region was further studied by Southern, Northern, and sequence analysis. It is an expressed, intron-containing locus encoding a mouse homolog of the bacterial ribosomal protein S13. This is the first nonorganelle S13 homolog identified in metazoans, and its genomic location has been determined precisely.     

Regional localization of th human EGF-like growth factor CRIPTO gene (TDGF-1) to chromosome 3p21

The CRIPTO gene encodes a novel human growth factor structurally related to epidermal growth factor. We localized the CRIPTO gene to chromosome 3p21 by fluorescence in situ hybridization with a cosmid clone containing 40 kb of the CRIPTO genomic region (TDGF-1). To suppress hybridization to CRIPTO-related sequences, present in multiple copies in the human genome, hybridization was carried out in the presence of unlabeled CRIPTO cDNA in excess over the probe. Our finding confirms the provisional mapping of the CRIPTO gene to chromosome 3, and assigns it precisely to a chromosomal region involved in several rearrangements occurring in malignancy.CRIPTO-specific sequences are present in multiple copies in the human genome (Dono et al. 1991). Two genomic CRIPTO-encoding sequences, TDGF-1 and TDGF-3, have been isolated and characterized. TDGF-1 corresponds to the structural gene encoding the protein expressed in teratocarcinoma cells (Ciccodicola et al. 1989). TDGF-3, possibly a functional pseudogene, corresponds to a complete copy of the TDGF-1 mRNA that contains seven base changes representing both silent and replacement substitutions in the coding region (Dono et al. 1991). By somatic cell hybrid analysis TDGF-1 has been assigned to chromosome 3, and TDGF-3 to the Xq21–22 region (Dono et al. 1991).     

(Brady)Rhizobium-plant communications involved in infection and nodulation

Conclusion The interactions between(Brady)Rhizobium and legume plants involves many interesting problems. In the last ten years, there were remarkable experiments which have detected excreted flavonoid compounds at pmol levels from plant roots, which induce(Brady)Rhizobium nod gene expression (Long 1989, Nap and Bisseling 1990, Dénariéet al. 1992, Schlamanet al. 1992). The responses of rhizobial genes to the various kinds of chemical compound are different (Maxwellet al. 1989, Zaatet al. 1989, Davis and Johnston 1990, Hartwiget al. 1990, Hungriaet al. 1992). The resolution of pSym genes controlling those mechanisms makes way for the long-term goal of introducing nitrogen fixation ability into nonlegume plants. Recently, some experiments have shown thatRhizobium and other nitrogen fixing bacteria form nodule-like strutures on rice, barley or wheat (Al-Mallah 1989, Jinget al. 1990, Rolfe and Bender 1991). Some O₂ protection mechanism instead of leghemoglobin must be needed for nitrogen fixation byRhizobium or other N₂-fixing bacteria which have invaded in the nonlegume root tissue. The isolation of the plant mutants or preparation of transgenic plants capable of hyper-nodule formation having efficient nitrogen fixation ability may be major goals. For the attainment of these goals, transformation of a foreign genome (nif-ornod gene cassette) into the plant cell might be a good way to proceed (Barkeret al. 1990). It is also necessary to clarify the relationships between the level of relative endogenous plant hormones and the exchange of the differentiation of the root tissue to the nodule tissue. This phenomenon of redifferentiation of plant tissue by the results from(Brady)Rhizobium and legume communications will be an important approach likely to lead to solve the molecular basis of plant having “TOTIPOTENCY”.     

Songbird Genomics: Analysis of 45 kb Upstream of a Polymorphic Mhc Class II Gene in Red-Winged Blackbirds (Agelaius phoeniceus)

Here we present the sequence of a 45 kb cosmid containing a previously characterized poly-morphic Mhc class II B gene (Agph-DAB1) from the red-winged blackbird (Agelaius phoeniceus). We compared it with a previously sequenced cosmid from this species, revealing two regions of 7.5 kb and 13.0 kb that averaged greater than 97% similarity to each another, indicating a very recent shared duplication. We found 12 retroelements, including two chicken repeat 1 (CR1) elements, constituting 6.4% of the sequence and indicating a lower frequency of retroelements than that found in mammalian genomic DNA. Agph-DAB3, a new class II B gene discovered in the cosmid, showed a low rate of polymorphism and may be functional. In addition, we found a Mhc class II B gene fragment and three genes likely to be functional (encoding activin receptor type II, a zinc finger, and a putative γ-filamin). Phylogenetic analysis of exon 2 alleles of all three known blackbird Mhc genes indicated strong clustering of alleles by locus, implying that large amounts of interlocus gene conversion have not occurred since these genes have been diverging. Despite this, interspecific comparisons indicate that all three blackbird Mhc genes diverged from one another less than 35 million years ago and are subject to concerted evolution in the long term. Comparison of blackbird and chicken Mhc promoter regions revealed songbird promoter elements for the first time. The high gene density of this cosmid confirms similar findings for the chicken Mhc, but the segment duplications and diversity of retroelements resembles mammalian sequences.     

CFTR: Domains, Structure, and Function

Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis (CF) (Collins, 1992). Over 500 naturally occurring mutations have been identified in CF gene which are located in all of the domains of the protein (Kerem et al., 1990; Mercier et al., 1993; Ghanem et al., 1994; Fanen et al., 1992; Ferec et al., 1992; Cutting et al., 1990). Early studies by several investigators characterized CFTR as a chloride channel (Anderson et al.; 1991b,c; Bear et al., 1991). The complex secondary structure of the protein suggested that CFTR might possess other functions in addition to being a chloride channel. Studies have established that the CFTR functions not only as a chloride channel but is indeed a regulator of sodium channels (Stutts et al., 1995), outwardly rectifying chloride channels (ORCC) (Gray et al., 1989; Garber et al., 1992; Egan et al., 1992; Hwang et al., 1989; Schwiebert et al., 1995) and also the transport of ATP (Schwiebert et al., 1995; Reisin et al., 1994). This mini-review deals with the studies which elucidate the functions of the various domains of CFTR, namely the transmembrane domains, TMD1 and TMD2, the two cytoplasmic nucleotide binding domains, NBD1 and NBD2, and the regulatory, R, domain.     

New Phytologist 140 (1998), 363–383

In the November 1998 issue of New Phytologist , we published the Tansley review 'Gibberellins: regulating genes and germination' by Sian Ritchie and Simon Gilroy ( New Phytol. (1998) 140 , 363–383). Since its publication, it has come to our attention that text associated with Fig. 4 was omitted during production. The correct figure is reprinted here in full.
We apologise to the author and to our readers for this mistake.
Figure 4. Promoter sequences of various genes expressed in the cereal aleurone and shown to be regulated by GA. The position of each sequence is indicated relative to the start codon. Regions identified as being involved in regulation of the genes are highlighted, as are similar regions in other genes. Sites at which protein has been shown to bind are also indicated. ( a ) Barley Amy 32b (Sutcliff et al ., 1993; Whittier et al ., 1987); wheat Amy 2/54 (Huttley et al ., 1992; Rushton et al ., 1992; Rushton et al ., 1995); barley Amy 46 (Khursheed & Rogers, 1988); barley Amy 2/p155 (Knox et al ., 1987); barley aleurain (Whittier et al ., 1987); barley β-glucanase II (Wolf, 1992); wheat cathepsin B-like (Cejudo et al ., 1992); rice ubiquitin-conjugating enzyme (Chen et al ., 1995). ( b ). Wheat Amy 1/18 (Rushton et al ., 1992); barley Amy pHV 19 (Jacobsen & Close, 1991; Gubler & Jacobsen, 1992)/ Amy 1 / 6-4 (Khursheed & Rogers, 1988; Rogers, Lanahan & Rogers 1994); rice OSamy-a / Amy 3c (Ou-Lee et al ., 1988; Sutcliff et al ., 1991; Yu et al ., 1992; Goldman et al ., 1994); rice Amy 3B (Sutcliffe et al ., 1991); rice OSamy-c (Kim et al ., 1992; Kim & Wu, 1992; Tanida et al ., 1994); rice Amy 1A (Huang et al ., 1990; Itoh et al ., 1995).
Figure 4 ( b ). For legend see facing page.     

HLA class II nucleotide sequences, 1991

The HLA class II sequences included in this compilation are taken from publications listed in the accompanying paper, Nomenclature for factors of the HLA system, 1990 (Bodmer et al. 1991) and Nomenclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Where discrepancies have arisen between reported sequences the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identity between residues is indicated by a hyphen (-). Unavailable sequence is indicated by an asterisk (*). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.     

Gene organization of the quail major histocompatibility complex (MhcCoja) class I gene region

 Class I genomic clones of the quail (Coturnix japonica) major histocompatibility complex (MhcCoja) were isolated and characterized. Two clusters spanning the 90.8 kilobase (kb) and 78.2 kb class I gene regions were defined by overlapping cosmid clones and found to contain at least twelve class I loci. However, unlike in the chicken Mhc, no evidence for the existence of any Coja class II gene was obtained in these two clusters. Based on comparative analysis of the genomic sequences with those of the cDNA clones, Coja-A, Coja-B, Coja-C, and Coja-D (Shiina et al. 1999), these twelve loci were assigned to represent one Coja-A gene, two Coja-B genes (Coja-B1 and -B2), four Coja-C genes (Coja-C1-C4), four Coja-D genes (Coja-D1-D4), and one new Coja-E gene. A class I gene-rich segment of 24.6 kb in which five of these genes (Coja-B1, -B2, -D1, -D2 and -E) are densely packed were sequenced by the shotgun strategy. All of these five class I genes are very compact in size [2089 base pairs (bp)–2732 bp] and contain no apparent genetic defect for functional expression. A transporter associated with the antigen processing (TAP) gene was identified in this class I gene-rich segment. These results suggest that the quail class I region is physically separated from the class II region and characterized by a large number of the expressible class I loci (at least seven) in contrast to the chicken Mhc, where the class I and class II regions are not clearly differentiated and only at most three expressed class I loci so far have been recognized. Received: 9 March 1998 / Revised: 12 October 1998     

Interspecific transfer and expression of melanin gene(s) on cosmids in Streptomyces strains

Summary Cosmid pR4C1 has been constructed from a multicopy plasmid pIJ365 and the cohesive ends site of an actinophage R4 (Morino et al. 1985). The cosmid can be transferred to various Streptomyces strains by R4 phage-mediated transduction. Melanin-synthesizing gene(s) originated from Streptomyces antibioticus was inserted into the cosmid and succesfully transferred by tranduction to 7 different strains out of 10 strains examined. The features of melanin-gene(s) expresion were examined in those cells. Tyrosinase activities from the melanin-gene(s) were detected in culture media and/or cell extracts although the extents of mel gene expression and tyrosinase excretion vary strain to strain. The cosmid transfer system described in this paper will be promising to survey suitable hosts for the maximum expression of cloned genes among Streptomyces strains.     

HLA class I nucleotide sequences, 1992

The HLA class I sequences included in this compilation are taken from publications listed in the papers: Nomenclature for factors of the HLA system, 1991 (Bodmer et al. 1992); Nomenclature for factors of the HLA system, 1990 (Bodmer et al. 1991); and Nomenclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Due to the increased number of sequences we have only included sequences for exons 2, 3, and 4 in this compilation. Where discrepancies have arisen between reported sequences, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments, identify between nucleotides is indicated by a hyphen (-). An unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number. *** DIRECT SUPPORT *** A4903038 00002     

Antigens similar to major histocompatibility complex B-G are expressed in the intestinal epithelium in the chicken

A monoclonal antibody directed against the erythrocytic B-G antigens of the major histocompatibility complex (MHC) of the chicken, an antiserum raised against purified erythrocytic B-G protein, and a cDNA probe from the BeckmanB-G subregion were used to look for evidence of the expression ofB-G genes in tissues other than blood. Evidence has been found in northern hybridizations, in immunoblots, and in immunolabeled cryosections for the presence of B-G-like antigens in the duodenal and caecal epithelia. Additional B-G-like molecules may be expressed in the liver as well. The BG-like molecules in these tissues appear larger and somewhat more heterogeneous than the B-G antigens expressed on erythrocytes. Further characterization of these newly recognized B-G-like molecules may help to define a function for the enigmatic B-G antigens of the MHC. al. 1977; Miller et al. 1982, 1984; Salomonsen et al. 1987; Kline et al. 1988), and in the multiplicity of B-G restriction fragment patterns found in genomic DNA from different haplotypes (Goto et al. 1988; Miller et al. 1988; Chaussé et al. 1989). The B-G antigens have contributed, together with the B-F (class I) and B-L (class II) antigens, to the definition of over 27 B system haplotypes in experimental flocks (Briles et al. 1982). Yet the function of the B-G antigens remains entirely unknown. No mammalian counterparts have been identified, although the possibility remains that there may be similar antigens among the blood group systems of mammals. In an effort to define a function of the B-G antigens, a recently cloned B-G sequence (Miller et al. 1988; Goto et al. 1988) and antibodies to the B-G polypeptides (Miller et al. 1982, 1984) were used to examine other tissues for evidence of B-G expression.     

Mapping and characterization of the DQ subregion of the ovine MHC

A map of the ovine MHC class II DQ subregion has been constructed from overlapping cosmid clones. This region consists of two loci linked on a linear tract of 130 kb DNA. Each locus consists of a DQA and a DQB gene in a tail-to-tail orientation. The genes in each locus are transcribed but only those designated DQ1 express class II molecules at the surface of mouse L cells following DNA-mediated gene transfection. The DQA1 and DQB1 genes are separated by 11kb while the DQA2 and B2 genes are 25 kb apart. The loci are separated by 22 kb.     

Linkage of a new member of the lectin supergene family to chicken Mhc genes

With the use of tissue-specific cDNA probes, several genes, which do not correspond to the class I (B-F), class II (B-L), or class IV (B-G) genes, were detected within the cosmid clusters containing the chicken major histocompatibility genes. We isolated cDNA clones with a probe corresponding to one of them, the 17.5 gene, located between two class I genes. The 17.5.3 cDNA, isolated from a chicken spleen cDNA library, encodes a 257-residue-long protein. This sequence shows significant similarity with several members of the C-type animal lectin superfamily and is probably a type II transmembrane protein. Analysis of several cDNA clones, together with Southern blot experiments, strongly suggest that this gene belongs to a multigene family, with at least some of its members being polymorphic. Several arguments lend support to the possibility that, together with the linked Mhc genes, the 17.5 gene is part of the recently described Rfp-Y system.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M88072.     

HLA class I nucleotide sequences, 1991

The HLA class I sequences included in this compilation are taken from publications listed in the accompanying paper, Nomenclature for factors of the HLA system, 1990 (Bodmer et al. 1991) and Nomeclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Where discrepancies have arisen between reported sequences the original authors have been contavted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identify between residues is indicated by a hyphen (-). Unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.     

Two types of aminoacyl-trna synthetases could be originally encoded by complementary strands of the same nucleic ACID

The lack of even a marginal similarity between the two aminoacyl-tRNA synthetase (aaRS) classes suggests their independent origins (Erianiet al., 1990; Nagel and Doolittle, 1991). Yet, this independence is a puzzle inconsistent with the common origin of transfer RNAs, the coevolutionary theory of the genetic code (Wong, 1975, 1981) and other associated data and ideas. We present here the results of antiparallel class I versus class II comparisons of aaRSs within their signature sequences. The two main HIGH- and KMSKS-containing motifs of class I appeared to be complementary to the class II motifs 2 and 1, respectively. The above sequence complementarity along with the mirror-image between crystal structures of complexes formed by the opposite aaRSs and their cognate tRNAs (Ruffet al., 1991), and the generally mirror (head-to-tail ) mapping of the basic functional sites in the sequences of aaRSs from the opposite two classes led us to conclude that these two synthetases emerged synchronously as complementary strands of the same primordial nucleic acid. This conclusion, combined with the hypothesis of tRNA concerted origin (Rodinet al., 1993a,b), may explain many intriguing features of aaRSs and favor the elucidation of the origin of the genetic code.     

The nucleotide sequence of the bovine MHC class II alpha genes:DRA,DQA, andDYA

The nucleotide sequence of the exons 2, 3, and 4, and parts of the intervening sequences of aBoLA-DRA and-DQA gene and one other class IIBoLA-A gene have been determined. The structure of theBoLA-DRA and-DQA gene was found to be very similar to that of the corresponding human HLA class II genes. An analysis of the structure of the other class IIBoLA-A gene showed that thisA gene was clearly very different from both the humanA genes and the bovineDRA andDQA genes. The results indicate that this other type of class IIA gene probably represents the class II gene that has already been identified in restriction fragment length polymorphism (RFLP) studies asBoLA-DYA. Since no clear homologue of this presumedBoLA-DYA gene was found among the human HLA class II genes, these results indicate that, at least as far as theA genes are concerned, a distinct class II gene is present in cattle.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M30117–M30120. Address correspondence and offprint requests to: J. van der Poel.