Lars Rask

Mutations and selection in the generation of class II histocompatibility antigen polymorphism.

A comparison of seven human DR and DC class II histocompatibility antigen beta‐chain amino acid sequences indicates that the allelic variation is of comparable magnitude within the DR and DC beta‐chain genes. Silent and replacement nucleotide substitutions in six DR and DC beta‐chain sequences, as well as in seven murine class II sequences (three I‐A beta and four I‐A alpha alleles) were analyzed. The results suggest that the mutation rates are of a comparable magnitude in the nucleotide sequences encoding the first and second external domains of the class II molecules. Nevertheless, the allelic amino acid replacements are predominantly located in the first domains. We conclude that a conservative selective pressure acts on the second domains, whereas in many positions in the first domains replacement substitutions are selectively neutral or maybe even favoured. Thus, the difference between the first and second domains as regards the number of amino acid replacements is mainly due to selection.

Both alpha and beta chains of HLA-DC class II histocompatibility antigens display extensive polymorphism in their amino-terminal domains.

At least three class II antigens, all composed of an alpha and a beta subunit, are encoded in the human major histocompatibility complex, i.e., DR, DC and SB. Two cDNA clones, encoding a DC alpha and a DC beta chain, respectively, were isolated from a cDNA library of the lymphoblastoid cell line Raji (DR3,w6). The two polypeptides predicted from the nucleotide sequences of these clones are each composed of a signal peptide, two extracellular domains, a hydrophobic transmembrane region and a short cytoplasmic tail. Comparison of the DC alpha sequence with two previously published partial sequences shows that the majority of the differences is located in the amino‐terminal domain. The differences are not randomly distributed; a cluster of replacements is present in the central portion of the amino‐terminal domain. Likewise, the allelic polymorphism of the DC beta chains occurs preferentially in the amino‐terminal domain, where three minor clusters of replacements can be discerned. The non‐random distribution of the variability of DC alpha and beta chains may be due to phenotypic selection against replacement substitutions in the second domains of the polypeptides.

Disruption of an overlapping E-box/ABRE motif abolished high transcription of the napA storage-protein promoter in transgenic Brassica napus seeds

The storage protein napin is one of the major protein components of Brassica napus L. (oilseed rape) seeds. To investigate the transcriptional regulation of the napin promoter, different constructs of the napin gene napA promoter were fused to the Escherichia coli uidA gene and transformed into B. napus. A -152-bp promoter construct directed a strong expression of the marker gene in mature seeds. The 5′ deletion of an additional 8 completely abolished this activity. This deletion disrupted sequence motifs that are similar to an E-box, (CA↓ NNTG) and an ABRE (CGCCA↓CGTGTCC) element (identity is indicated by bold face). Further, internal deletion of a segment corresponding to -133 to -121 caused an eightfold reduction in the activity of the -152 construct. This region contains an element, CAAACAC, conserved in many storage-protein gene promoters. These results imply that the E-box/ABRE-like sequence is a major motif of the napA promoter and suggest that the CAAACAC sequence is important for high activity of the napA promoter. Similar results have been obtained by analysing some of the constructs in transgenic tobacco, suggesting that many of the cis-elements in the napA promoter are conserved, at least in dicotyledonous species.

Functional dissection of a napin gene promoter: identification of promoter elements required for embryo and endosperm-specific transcription

The promoter region (−309 to +44) of the Brassica napus storage protein gene napA was studied in transgenic tobacco by successive 5′ as well as internal deletions fused to the reporter gene GUS (β-glucuronidase). The expression in the two main tissues of the seed, the endosperm and the embryo, was shown to be differentially regulated. This tissue-specific regulation within the seed was found to affect the developmental expression during seed development. The region between −309 to −152, which has a large effect on quantitative expression, was shown to harbour four elements regulating embryo and one regulating endosperm expression. This region also displayed enhancer activity. Deletion of eight bp from position −152 to position −144 totally abolished the activity of the napA promoter. This deletion disrupted a cis element with similarity to an ABA-responsive element (ABRE) overlapping with an E-box, demonstrating its crucial importance for quantitative expression. An internal deletion of the region −133 to −120, resulted in increased activity in both leaves and endosperm and a decreased activity in the embryo. Within this region, a cis element similar to the (CA)n element, found in other storage protein promoters, was identified. This suggest that the (CA)n element is important for conferring seed specificity by serving both as an activator and a repressor element.

Deletion analysis of a 2S seed storage protein promoter of Brassica napus in transgenic tobacco

The promoter and upstream region of the Brassica napus 2S storage protein napA gene were studied to identify cis-acting sequences involved in developmental seed-specific expression. Fragments generated by successive deletions of the 5′ control region of the napA gene were fused to the reporter gene β-glucuronidase (GUS). These constructs were used to transform tobacco leaf discs. Analyses of GUS activities in mature seeds from the transformed plants indicated that there were both negatively and positively acting sequences in the napin gene promoter. Deletion of sequences between −1101 and −309 resulted in increased GUS activity. In contrast, deletion of sequences between −309 and −211 decreased the expression. The minimum sequence required for seed-specific expression was a 196 bp fragment between −152 and +44. Further 5′ deletion of the fragment to −126 abolished this activity. Sequence comparison showed that a G box-like sequence and two sequence motifs conserved between 2S storage protein genes are located between −148 to −120. Histochemical and fluorometric analysis of tobacco seeds showed that the spatial and developmental expression pattern was retained in the deletion fragments down to −152. However, the expression in tobacco seeds differed from the spatial and temporal expression in B. napus. In tobacco, the napA promoter directed GUS activity early in the endosperm before any visible activity could be seen in the heart-shaped embryo. Later, during the transition from heart to torpedo stages, the main expression of GUS was localized to the embryo. No significant GUS activity was found in either root or leaf.

Structure of the murine immune response I-Aβ locus: Sequence of the I-Aβ gene and an adjacent β-chain second domain exon

Abstract The murine major histocompatibility complex I region encodes two class II antigens, I-A and I-E. From a mouse spleen DNA cosmid library of the b haplotype, we isolated a clone containing the entire I-A β gene and a separate exon encoding a β-chain second domain (A β2 ). The A β gene, encompassing more than 6 kb, is encoded by six exons corresponding to the different domains of the A β polypeptide. The translated A β amino acid sequence displays 73% homology to human DC β chains; homologies to other subsets of human β-chains are lower, establishing that I-A corresponds structurally to DC. The A β2 exon is about 20 kb centromeric to the A β gene. Its translated amino acid sequence includes all the conserved amino acids of other class II β-chain second domains. It shows about 60% homology to each of three subsets of human β-chains available for comparison, and to the A β chain. No A β2 first domain exon has been detected with A β or DC β probes.

Characterization of the MHC class II region in cattle. The number of DQ genes varies between haplotypes

The organization of the major histocompatibility complex (MHC) class II region in cattle was investigated by Southern blot analysis using human probes corresponding to DO, DP, DQ, and DR genes. Exon-specific probes were also employed to facilitate the assessment of the number of different bovine class II genes. The results indicated the presence of single DOβand DRαgenes, at least three DRβgenes, while the number of DQ genes was found to vary between MHC haplotypes. Four DQ haplotypes, DQα1β1 to DQα2β4, possessed a single DQα and a single DQβgene whereas both these genes were duplicated in eight other haplotypes, DQα3β5 to DQα9β12. No firm evidence for the presence of bovine DP genes was obtained. The same human probes were also used to investigate the genetic polymorphism of bovine class II genes. DQα DQβ, DRα DRβ, and DOβ restriction fragment length polymorphisms (RFLPs) were resolved and in particular the DQ restriction fragment patterns were highly polymorphic. Comparison of the present result with the current knowledge of the class II region in other mammalian species suggested that the DO, DP, DQ, DR, and DZ subdivision of the class II region was established already in the ancestor of mammals. The DP genes appear to be the least conserved class II genes among mammalian species and may have been lost in cattle. The degree of polymorphism of different class II genes, as revealed by RFLP analyses, shows striking similarities between species.

Linkage relationships in the bovine MHC region. High recombination frequency between class II subregions.

Class II genes of the bovine major histocompatibility complex (MHC) have been investigated by Southern blot analysis using human DNA probes. Previous studies revealed the presence of bovine DOβ, DQα, DQβ, DRαand DRβgenes, and restriction fragment length polymorphisms for each of these genes were documented. In the present study, the presence of three additional class II genes, designated DZα, DYα, and DYβ, are reported. DZαwas assumed to correspond to the human DZαgene while the other two were designated DY because their relationship to human class II genes could not be firmly established. The linkage relationships among bovine class II genes and two additional loci, TCP1B and C4, were investigated by family segregation analysis and analysis of linkage disequilibrium. The results clearly indicated that all these loci belong to the same linkage group. This linkage group is divided into two subregions separated by a fairly high recombination frequency. One region includes the C4, DQα, DQβ, DRαand DRβloci and the other one is composed of the DOβDYα, DYβ, and TCPIB loci. No recombinant was observed within any of these subregions and there was a strong or fairly strong linkage disequilibrium between loci within groups. In contrast, as many as five recombinants among three different families were detected in the interval between these subregions giving a recombination frequency estimate of 0.17 ± 0.07. The fairly high recombination frequency observed between class 11 genes in cattle is strikingly different from the corresponding recombination estimates in man and mouse. The finding implies either a much larger molecular distance between some of the bovine class II genes or alternatively the presence of a recombinational “hot spot” in the bovine class II region.

The glucosinolate-degrading enzyme myrosinase in Brassicaceae is encoded by a gene family.

A full-length cDNA clone (MB3) and three partial clones (MA1, MB1 and MB2) which encode myrosinase (thioglucoside glucohydrolase, EC 3.2.3.1) were isolated from a Sinapis alba (white mustard) cDNA library. Nucleotide sequence analysis of these clones revealed that they are encoded by a gene family. Southern blot analysis with gene-specific probes showed that the gene family consists of a least two subfamilies (MA and MB) each with several members both in S. alba and in Brassica napus (oilseed rape). In Arabidopsis thaliana (wall cress) only three myrosinase genes seem to be present. Northern blot analysis indicated that all the myrosinase mRNA species have the same size, approximately 1.95 kb.

The myrosinase gene family in Arabidopsis thaliana: gene organization, expression and evolution

Myrosinase (thioglucoside glucohydrolase, EC 3.2.3.1.) is in Brassicaceae species such as Brassica napus and Sinapis alba encoded by two differentially expressed gene families, MA and MB, consisting of about 4 and 10 genes, respectively. Southern blot analysis showed that Arabidopsis thaliana contains three myrosinase genes. These genes were isolated from a genomic library and two of them, TGG1 and TGG2, were sequenced. They were found to be located in an inverted mode with their 3′ ends 4.4 kb apart. Their organization was highly conserved with 12 exons and 11 short introns. Comparison of nucleotide sequences of TGG1 and TGG2 exons revealed an overall 75% similarity. In contrast, the overall nucleotide sequence similarity in introns was only 42%. In intron 1 the unusual 5′ splice border GC was used. Phylogenetic analyses using both distance matrix and parsimony programs suggested that the Arabidopsis genes could not be grouped with either MA or MB genes. Consequently, these two gene families arose only after Arabidopsis had diverged from the other Brassicaceae species. In situ hybridization experiments showed that TGG1 and TGG2 expressing cells are present in leaf, sepal, petal, and gynoecium. In developing seeds, a few cells reacting with the TGG1 probe, but not with the TGG2 probe, were found indicating a partly different expression of these genes.