Four Ubiquitously Expressed Genes,RD(D6S45)–SKI2W(SKIV2L)–DOM3Z–RP1(D6S60E), Are Present between Complement Component Genes FactorBandC4in the Class III Region of the HLA

The association of the HLA class III region with many diseases motivates the investigation of unidentified genes in the 30-kb segment between complement component genesBfandC4. RD,which codes for a putative RNA binding protein, is 205 bp downstream ofBf. SKI2W(HGMW-approved symbol SKIV2L), a DEVH-box gene probably involved in RNA turnover, is 171 bp downstream ofRD(HGMW-approved symbol D6S45).RP1(HGMW-approved symbol D6S60E) is located 611 bp upstream ofC4.The DNA sequence between humanRDandRP1was determined and the exon–intron structure ofSKI2Welucidated.SKI2Wconsists of 28 exons. The putative RNA helicase domain of Ski2w is encoded by 9 exons. Further analysis of the 2.5-kb intergenic sequence betweenSKI2WandRP1led to the discovery ofDOM3Z.The full-length cDNA sequence ofDOM3Zencodes 396 amino acids with a leucine zipper motif. Dom3z-related proteins are present in simple and complex eukaryotes. InCaenorhabditis elegans,Dom3z-related protein could be involved in the development of germ cells. HumanRD–SKI2WandDOM3Z–RP1are arranged as two head-to-head oriented gene pairs with unmethylated CpG sequences at the common 5′ regulatory region of each gene pair. The ubiquitous expression pattern suggests that these four genes are probably housekeeping genes.     

Nucleotide Sequencing Analysis of the 146-Kilobase Segment around theIkBLandMICAGenes at the Centromeric End of the HLA Class I Region

To elucidate the complete gene structure and to identify new genes involved in the development ofHLAclass I antigen-associated diseases in the class I region of the human major histocompatibility complex on chromosome 6, a YAC clone (745D12) covering the 146-kb segment around theIkBLandMICAloci was isolated from a YAC library constructed from the B-cell line, BOLETH. A physical map of this region was constructed by isolation of overlapping cosmid clones derived from 745D12. Of these, five contiguous cosmids were chosen for DNA sequencing by the shotgun strategy to give a single contig of 146,601 bp from 2.8 kb telomeric of theIkBLgene to exon 6 ofMICA.This region was confirmed to contain five known genes,IkBL, BAT1, MICB, P5-1,andHLA-X(class I fragment), from centromere to telomere, and their exon–intron organizations were determined. The3.8-1homologue gene (3.8-1-hom) showing 99.7% identity with the3.8-1cDNA clone, which was originally isolated using the 3.8-kbEcoRI fragment between theHLA-54/Hand theHLA-Ggenes, was detected betweenMICAandMICBand was suggested to represent the cognate3.8-1genomic sequence from which the cDNA clone was derived. No evidence for the presence of expressed new genes could be obtained in this region by homology and EST searches or coding and exon prediction analyses. One TA microsatellite repeat spanning 2545 bases with as many as 913 repetitions was found on the centromeric side of theMICAgene and was indicated to be a potential hot spot for genetic recombination. The two segments of approximately 35 kb upstream of theMICAandMICBgenes showed high sequence homology (about 85%) to each other, suggesting that segmental genome duplication including theMICAandMICBgenes must have occurred during the evolution of the humanMHC.     

Genetics and expression of two pectinesterase genes in Valencia orange

The genetics and expression of pectinesterase (PE) genes were examined in Valencia orange. Degenerate primers based on partial amino acid sequence of a 36 kDa PE protein isolated from juice vesicles were used to amplify a 350 bp DNA fragment from cDNA prepared from juice vesicle total RNA. Two groups of 350 bp PE clones with 66% sequence identity were isolated. A clone from each group was used to screen a Valencia orange genomic DNA λ library. Two different lambda clones that contained complete PE coding sequence (CsPME1 and CsPME3) and a third lambda clone that contained partial PE sequence (CsPME2) were characterized. The CsPME1 gene contained two exons (1063 and 689 bp) interrupted by a 1452 bp intron, whereas the CsPME3 gene had two exons (844 and 686 bp) interrupted by a 771 bp intron. CsPME1 shared significant sequence similarity with the partial clone CsPME2, including the entire cloned region of the first exon, a large region in the 5′ portion of the intron and the 3′ portion of the second exon, but the 3′ portion of the intron and the 5′ portion of the second exon were dissimilar. Southern blots suggested that Valencia orange has two genes within each PE group. Full-length cDNA clones that shared 99% sequence identity with CsPME1 and CsPME3 were isolated. Both groups of PE genes were differentially expressed in tissues of Valencia orange, and in addition CsPME3 appeared to be ethylene-regulated. The deduced proteins of PE cDNA clones CsPME1 (63.5 kDa) and CsPME3 (56.3 kDa) were considerably larger than the PE protein we isolated from Valencia orange juice vesicles and also other mature plant PE proteins. The estimated size of group I (2.2 kb) and group II (2.0 kb) PE mRNAs also predicted a larger protein than was isolated from juice vesicles. Alignment of the mature tomato and mung bean PE proteins, the most N-terminal sequence we obtained from polypeptides derived from the 36 kDa PE isolated from juice vesicles and the deduced amino acid sequences of plant PE cDNA clones suggest that a post-translational cleavage event separates the variable N-terminus from the more conserved C-terminal domain of the mature PE protein.     

The expression of a new HD-Zip II gene, MSHB1, involving the inhibitory effect of thidiazuron on somatic embryogenic competence in alfalfa (Medicago sativa L. cv. Jinnan) callus

Homeodomain leucine zipper (HD-Zip) proteins play important roles in plant development. In this study, we not only identified and characterized a new HD-Zip II gene, designated as MSHB1 (HM114227), from alfalfa (Medicago sativa L. cv. Jinnan) callus treated with thidiazuron (TDZ) which reduced the embryogenic competence of the callus, but also presented the first evidence that MSHB1 is involved in the inhibitory effect of TDZ on somatic embryogenic competence in alfalfa callus. The full-length cDNA was 1,578 bp with an open reading frame of 1,023 bp, encoding a predicted protein of 340 amino acid residues, plus three introns. MSHB1 was strongly expressed in the callus treated with TDZ, but was only slightly detected in the leaf and petiole. TDZ treatment significantly decreased the frequency of somatic embryogenesis in the callus, but up-regulated MSHB1 expression during callus induction, callus maintenance and somatic embryo induction. These results suggest that the inhibitory effect of TDZ on embryogenic competence of alfalfa callus might be mediated by the regulation of MSHB1 expression.     

Application of suppression subtractive hybridization (SSH) to cloning differentially expressed cDNA inDunaliella salina (chlorophyta) under hyperosmotic shock

Two subtracted cDNA libraries ofDunaliella salina (Volvocales, Chlorophyceae) under different hyperosmotic shock were constructed using the suppression subtractive hybridization (SSH) method. The mRNA isolated from algae grown without stress was used as a “driver”, and the mRNAs isolated from algae 16 h (short-term treatment) or 7 d (long-term treatment) after salt stress were used as “testers”. The differentially expressed cDNA fragments inD. salina under salt stress were identified by screening these 2 libraries. Two cDNA fragments,D27 andD114, were identified from clones pL27 and pL114 after the long-term treatment. Three cDNA fragments,D21, D39, andD88, were identified from clones pSh21, pSh39, and pSh88 after the short-term treatment. The homology analysis revealed that D27 was highly similar (91%) to the subunit V of PS I reaction center inChlamydomonas reinhardtii. D21 was similar to fructose-1,6-diphosphate aldolase (78.4%). After searching GenBank with the sequences ofD39, D88, andD114, no similar sequences were found. Northern analysis revealed that the expression levels of all 5 cDNAs were increased significantly after salt stress. This means that SSH can be used in cloning differentially expressed cDNAs inD. salina under salt stress. The expression ofD27, D21, andD88 wasde novo induced by salt stress, and the expression ofD114 andD39 was increased from a relatively lower level; this indicates that all 5 cDNAs might exert an influence on the alga under hyperosmotic shock.     

Strategy for comprehensive identification of human N‐myristoylated proteins using an insect cell‐free protein synthesis system

To establish a strategy for the comprehensive identification of human N‐myristoylated proteins, the susceptibility of human cDNA clones to protein N‐myristoylation was evaluated by metabolic labeling and MS analyses of proteins expressed in an insect cell‐free protein synthesis system. One‐hundred‐and‐forty‐one cDNA clones with N‐terminal Met‐Gly motifs were selected as potential candidates from ～2000 Kazusa ORFeome project human cDNA clones, and their susceptibility to protein N‐myristoylation was evaluated using fusion proteins, in which the N‐terminal ten amino acid residues were fused to an epitope‐tagged model protein. As a result, the products of 29 out of 141 cDNA clones were found to be effectively N‐myristoylated. The metabolic labeling experiments both in an insect cell‐free protein synthesis system and in the transfected COS‐1 cells using full‐length cDNA revealed that 27 out of 29 proteins were in fact N‐myristoylated. Database searches with these 27 cDNA clones revealed that 18 out of 27 proteins are novel N‐myristoylated proteins that have not been reported previously to be N‐myristoylated, indicating that this strategy is useful for the comprehensive identification of human N‐myristoylated proteins from human cDNA resources.     

cDNA cloning and function analysis of two novel erythroid differentiation related genes

Our previous studies showed that some nuclear proteins that were expressed especially during terminal differentiation of erythroid cells might interact directly or indirectly with HS2 sequence to form the HS2-protein complexes and thus play an important role in the globin gene regulation and erythroid differentiation. Monoclonal antibodies against the nuclear proteins of terminal differentiated erythroid cells, including intermediate and late erythroblasts of human fetal liver and hemin induced K562 cells, were prepared by hybridoma technique. The monoclonal antibodies were used to screen λ-gtll human cDNA expression library of fetal liver in order to obtain the relevant cDNA clones. By the analysis of their cDNA clones and the identification of the proteins' functions, the regulation mechanism of the HS2 binding proteins might be better understood. Two cDNA clones (GenBank accession number AF040247 and AF040248 respectively) were obtained and one of them owns a full length and the other encodes a prote     

Molecular characterisation and expression of two venom allergen-like protein genes in Heterodera glycines

Secretory proteins encoded by genes expressed in the oesophageal gland cells of plant-parasitic nematodes have key roles in nematode parasitism of plants. Two venom allergen-like protein cDNAs (designated hg-vap-1 and hg-vap-2)were isolated from Heterodera glycines gland cell cDNA libraries. Both cDNAs hybridised to genomic DNA of H. glycines in Southern blots. The hg-vap-1 cDNA contained an open reading frame encoding 215 amino acids with the first 25 amino acids being a putative secretion signal. The hg-vap-2 cDNA contained an open reading frame encoding 212 amino acids with the first 19 amino acids being a putative secretion signal. Genes of hg-vap-1 and hg-vap-2 contained four introns, which ranged in size from 44 to 574 bp, and five exons ranging in size from 43 to 279 bp. In situ hybridisation analyses showed that mRNAs of both vap genes accumulated specifically in the subventral gland cells of H. glycines during parasitism. The gland cell-specific expression and presence of predicted secretion signal peptides in both VAPs suggest that these proteins are secreted from the nematode and may play a role in the infection of host plants by this parasite.     

The thioester and isotypic sites of complement component C4 in sheep and cattle

The region inclusive of the thioester and the isotype-determining sites of the sheep C4 genes from a single animal was amplified by polymerase chain reaction (PCR). Two bands, at 880 base pairs (bp) and 1000 bp, were resolved by agarose gel electrophoresis. Four different clones were obtained for the 880 bp (type 1) product and two from the 1000 bp (type 2) product. Two of the type 1 clones (type 1H) and both type 2 clones (type 2H) code for the PCPVIH sequence at the isotypic site whereas the other two type 1 clones (type 1D) code for the PFPVMD sequence. By restriction mapping and Southern blot analysis, there appears to be four C4 gene loci for the sheep: two type 1H, one type 1D, and one type 2H. The type 1H and type 2H genes are likely to code for proteins with C4B-like properties whereas the type 1D genes for proteins with C4A-like properties. The same region of the sheep C4 genes of nine other breeds of sheep are also amplified by PCR and analyzed by restriction mapping and Southern hybridization. Each of the sheep has type 1H, type 2H, and type 1D genes and appears to have four C4 gene loci except for the Orkney, which may have five. A single band of 880 bp was obtained from the PCR product from the genomic DNA of a single cow. Five different clones were identified, two of which code for the PFPVMD sequence and three for the PCPVIH sequence at the isotypic site, which is consistent with previous finding that C4 proteins with A- and B-like activities could be purified from the plasma of the same animal. Comparison of the nucleotide sequences of the isotype-determining region of the sheep and cattle C4 genes with those of the primates and mouse suggests that the C4A-like genes evolved independently in the primates and the ungulates. Correspondence to: S. K. A. Law.     

Molecular cloning of the lectin and a lectin-related protein from common Solomon's seal (Polygonatum multiflorum)

The most prominent protein ofPolygonatum multiflorum (common Solomon's seal) rhizomes has been identified as a mannose-binding lectin. Analysis of the purified lectin demonstrated that it is a tetramer of four identical subunits of 14 kDa. Molecular cloning further revealed that the lectin from this typical Liliaceae species belongs to the superfamily of monocot mannose-binding proteins. Screening of cDNA libraries constructed with RNA isolated from buds, leaves and flowers ofP. multiflorum also yielded cDNA clones encoding a protein, which contains two tandemly arranged domains with an obvious sequence homology to the mannose-binding lectins. Molecular modelling of thePolygonatum lectin and lectin-related protein indicated that the three-dimensional structure of both proteins strongly resembles that of the snowdrop lectin. In addition, this approach suggested that the presumed carbohydrate-binding sites of the lectin can accommodate a mannose residue whereas most of the carbohydratebinding sites of the lectin-related protein cannot.Abbreviations GNA Galanthus nivalis agglutinin - HCA hydrophobic cluster analysis - LECPMA cDNA clone encoding PMA - PM30 30 kDa protein isolated fromPolygonatum multiforum - PMA Polygonatum multiflorum agglutinin - PMLRP Polygonatum multiflorum lectin-related protein