Genetic mapping and characteristics of the actinophage phi C31 deletion mutants of Streptomyces coelicolor A3(2) incapable of lysogenization

Actinophage phi C31 deletion c mutants with impaired ability to make repressor were genetically studied. Genetic crosses indicate that the c28 deletion mutant is situated with the c-region of the phi C31 genetic map. Based on the results of a qualitive test for recombination between several c mutants, a scheme of their order relative to deletion mutants was presented. The approximate distances between eight c mutants have been represented in units of the physical DNA map estimation. Genetic studies of actinophage lyg deletion mutants which cannot lysogenize sensitive cultures were carried out. Mutants failed to lysogenize upon mixed infection with lyg+ phages. The absence of the effect of lyg+ gene in trans suggests that lyg deletions cause a structural defect in an integration site of the phage. Preliminary data on alignment of lyg positions on physical and genetic maps of phi C31 phage have been obtained. According to evidence from genetic crosses, lyg mutation has been located in the right half of the phi C31 genome.     

Association of the Late Cornified Envelope-3 Genes with Psoriasis and Psoriatic Arthritis:A Systematic Review

Psoriasis(Ps)and psoriatic arthritis(Ps A)are genetically complex diseases with strong genetic evidence.Recently,susceptibility genes for Ps and Ps A have been identified within the late cornified envelop(LCE)gene cluster,especially the cluster 3(LCE3)genes.It is noteworthy that the deletion of LCE3B and LCE3C(LCE3C_LCE3B-del)is significantly associated with these two diseases.Gene-gene interactions between LCE3 genes and other genes are associated with Ps and Ps A.LCE3 genes also have pleiotropic effect on some autoimmune diseases,such as rheumatoid arthritis,atopic dermatitis and systemic lupus erythematosus.Further studies need to focus on the potential function of LCE3 genes in the pathogenesis of Ps and Ps A in the future.     

与胎儿珠蛋白基因持续表达有关的(A_γδβ)°—地贫纯合子及杂合子的分子鉴别

我们分子鉴别了一个缺失型中国(A_γδβ)°-地贫家系。先证者为这一缺失的纯合子,具有中度贫血症状。家系的另五个成员均为这一缺失的杂合子,其胎儿血红蛋白(HbF)为16—21％,接近或达到HPFH杂合子的HbF水平,并且几乎不表现贫血症状。限制性内切酶图谱分析证明了β-珠蛋白基因簇内的DNA顺序缺失,缺失的5′端点位于Aγ基因IVSⅡ内,3′端点在β-珠蛋白基因下游区远端,距HPFH-2的3′缺失端点上游区约11kb。缺失的总长度约为80kb。本文讨论了这一缺失导致胎儿血红蛋白在成人中持续活跃表达的可能机制。     

Extensive variation in the O-antigen gene cluster within one Salmonella enterica serogroup reveals an unexpected complex history

The 46 serogroups of Salmonella enterica have different O-antigens, and each is thought to have a specific form of the O-antigen cluster. Comparison of the 145 serovars of serogroup B revealed much more intraserogroup genetic diversity than expected. The O27 factor, due to an alpha 1-6 linkage between O units in place of the more common alpha 1-2 linkage and previously thought to be due to a converting bacteriophage, is now shown to be due to a wzy(alpha(1-6)) gene located within the major gene cluster. Surprisingly a remnant of this gene in all O27(-) serovars shows that the ancestor was O27(+). There are six distinct gene cluster forms, five apparently derived by a series of deletions and one by an insertion from an ancestral O27(+) form present in 57 serovars. The history of the gene cluster and movement between subspecies I and II can be traced. Two of the derivative forms still have a functional wzy(alpha(1-6)) gene, while in three it has been inactivated by deletion or insertion. Two of the forms lacking a functional wzy(alpha(1-6)) gene have the wzy(alpha(1-2)) gene first described for strain LT2 as rfc, whereas for the third the wzy gene has not been located.     

Genetic aspects of the organization of legumin genes in pea

We have compared physical and genetic maps of the region around the legJ gene in pea. In this vicinity there are four B-type legumin genes, arranged as two close pairs. The detection of a recombination event within this gene cluster allows the orientation of this group of genes within the surrounding linkage group to be determined. The relationship between physical and genetic distances in this region is discussed, as are the implications of this for relating physical and genetic maps elsewhere in the pea genome.     

Yunnanese(~Aγδβ)~0-地贫缺失桥片段的克隆及缺失连接区的序列测定

为研究导致Ｙｕｎｎａｎｅｓｅ（Ａγδβ）０－地贫缺失事件的分子机制,并从３′并入序列中搜寻增强子类序列,使用ＥＭＢＬ３为载体构建了一例缺失杂合子的基因组文库,筛选到来源于异常染色体１１并包含Ｇγ珠蛋白基因区６．７ｋｂ序列以及１１．５ｋｂ３′并入序列（即缺失桥片段）的克隆．此１１．５ｋｂ序列在正常染色体中位于β珠蛋白基因约下游６６～７８ｋｂ区域．详细分析了这一区域的限制性内切酶图谱．分析了围绕缺失连接区的ＤＮＡ序列,精确定位缺失的５′端点发生在Ａγ珠蛋白基因上游－１１６～－１１７碱基之间．确定缺失的３′端点处于一个Ｌ１序列内,位于β珠蛋白基因下游～６６ｋｂ,距离Ｃｈｉｎｅｓｅ（Ａγδβ）０－地贫缺失３′端点上游～１２．２ｋｂ的一个ＥｃｏＲⅠ位点上游４１３ｂｐ．围绕５′和３′端点的序列之间无明显同源性,说明这一缺失代表了体内的非同源重组事件．这一重组事件可能由Ｌ１序列介导．缺失３′端点下游序列的克隆分离也为进一步从中搜寻加强子类序列奠定了基础     

A genetic mechanism for deletion of the ser2 gene cluster and formation of rough morphological variants of Mycobacterium avium

A major phenotypic trait of the Mycobacterium avium complex is the ability to produce rough and smooth colony variants. The chemical basis of this morphological variation is the loss of an antigenic surface structure, termed glycopeptidolipid (GPL), by rough variants. Using M. avium serovar 2 strain 2151 as a model system, this laboratory previously reported that rough variants arise via the deletion of large genomic regions encoding GPL biosynthesis. One such deletion encompasses the gene cluster (ser2) responsible for production of the serovar 2 GPL haptenic oligosaccharide. In this study, nucleotide sequencing revealed that both ends of the ser2 gene cluster are flanked by a novel insertion sequence (IS1601) oriented as direct repeats. Detailed analyses of the site of deletion in the genome of M. avium 2151 Rg-1 demonstrated that a single copy of IS1601 remained and that the ser2 gene cluster was deleted by homologous recombination. This same deletion pattern was observed for 10 out of 15 rough colony variants tested. Additionally, these studies revealed that IS1601 contains portions of three independent insertion sequences. This report is the first to define the precise genetic basis of colony variation in Mycobacterium spp. and provides further evidence that homologous recombination between insertion sequence elements can be a primary determinant of genome plasticity in these bacteria.     

Mapping of the human complement factor I gene to 4q25

A detailed genetic and physical map of human complement factor I (IF) using somatic cell hybrids, in situ hybridization, and genetic linkage is reported. The gene has been localized to band 4q25. The order GC-INP10-ADH3-EGF-IF-IL2-MNS is proposed for genes on 4q on the basis of genetic and physical mapping techniques. A BclI polymorphism found with the IF probe demonstrated a maternal origin for a de novo deletion of chromosome 4 that was used in physically mapping the gene. The genetic and physical distances around band 4q24 suggest that 1 cM is approximately 1.2 million bp of DNA. This work provides a useful addition to the map of 4q.     

A genetic,deletion, physical,and human homology map of the long fin region on zebrafish linkage group 2

Mutation of the gene long fin causes overgrowth of zebrafish fins. Thus, molecular identification of the gene long fin may reveal the mechanisms involved in normal growth control. We have therefore developed genetic and physical maps of the corresponding region on linkage group 2 (LG2). A single deletion allele (lof(jg)(61)) of the long fin gene was also generated. Examination of this deletion for the presence or absence of ESTs independently mapped to LG2 revealed a contiguous deletion of SSLP, STS, and gene-based markers spanning a physical distance of approximately 500 kb, including at least 10 zebrafish genes. Human orthologs of the zebrafish genes in the long fin region were identified and revealed two synteny segments from human chromosome 1 (Hsa1) and Hsa19. Homology searching for additional genes linked to the human orthologs revealed one additional gene in the long fin deletion region. Thus, our development of the genetic, physical, deletion, and human homology maps of the long fin region provides one of the first high-resolution comparisons of a zebrafish region with a homologous human region, and facilitates the molecular identification of the long fin gene.     

Deletion of the Escherichia coli O14:K7 O antigen gene cluster

Escherichia coli O14:K7 is a rough strain, lacking a typical O antigen, in which the enterobacterial common antigen is attached to the lipopolysaccharide core. The rough phenotype was previously mapped to the O antigen gene cluster; however, the nature of the nonfunctional locus was not defined. In this study, we have shown that the O antigen gene cluster of an O14:K7 type strain (Su4411/41) was most likely deleted via homologous recombination between the GDP-mannose pathway genes (manB and manC) of the colanic acid and O antigen gene clusters. A similar recombination event has previously been inferred for the deletion of E. coli Sonnei chromosomal O antigen genes. Therefore, recombination between the GDP-mannose pathway genes provides a convenient mechanism for the deletion of O antigen genes, which may occur if the typical O antigen becomes redundant.     

Reduction in the DAZ gene copy number in two infertile men with impaired spermatogenesis.

Microdeletions of Yq are associated with azoospermia and severe oligozoospermia. Recently, we described a new molecular genetic strategy based on the denaturing gradient gel electrophoresis (DGGE) to rapidly identify deletions of the Y chromosome that include the DAZ locus. Using this approach, we have shown not a complete deletion but only a reduction in the number of copies of the DAZ gene by PCR-DGGE in two oligozoospermic patients. These results have been confirmed by Southern blot analysis. This finding suggests that partial deletion of the DAZ cluster could be cause of impaired spermatogenesis.     

Detecting high-resolution polymorphisms in human coding loci by combining PCR and single-strand conformation polymorphism (SSCP) analysis.

A strategy is described that allows the development of polymorphic genetic markers to be characterized in individual genes. Segments of the 3' untranslated regions are amplified, and polymorphisms are detected by digestion with frequently cutting enzymes and with the detection of single-stranded conformation polymorphisms. This allows these genes, or DNA segments, to be placed on the linkage maps of human chromosomes. Polymorphisms in two genes have been identified using this approach. A HaeIII polymorphism was detected in the KIT proto-oncogene, physically assigned to chromosome 4q11-12. This polymorphism is linked to other chromosome 4p markers and is in linkage disequilibrium with a HindIII polymorphism previously described at this locus. We have also identified in the insulin-like growth factor1 receptor gene (IGF1R) a 2-bp deletion that is present at a frequency of .25 in the Caucasian population. Pedigree analysis with this insertion/deletion polymorphism placed the IGF1R gene at the end of the current linkage map of chromosome 15q, consistent with the physical assignment of 15q2526. Thus, polymorphisms in specific genes can be used to related the physical, genetic, and comparative maps of mammalian genomes and to simplify the testing of candidate genes for human diseases.     

Genomic map of Clostridium perfringens strain 13

A physical and genetic map of Clostridium perfringens strain 13 was constructed. C. perfringens strain 13 was found to have a 3.1-Mb chromosome and a large 50-kb plasmid, indicating that strain 13 has a relatively small genome among C. perfringens strains. A total of 313 genetic markers were mapped on the chromosome of strain 13. Compared with the physical and genetic map of C. perfringens CPN50, strain 13 had a quite similar genome organization, but with a large deletion (approximately 400 kb) in a particular segment of the chromosome. Among several toxin genes, a beta2 toxin gene that is a novel virulence gene in C. perfringens was found to be located on the 50-kb plasmid.     

Physical mapping of the Vrn-A1 and Fr1 genes on chromosome 5A of wheat using deletion lines

 Homozygous deletion lines of wheat for 5AL, generated in the variety ‘Chinese Spring’, were tested for flowering time without vernalization and for frost resistance after cold hardening. It was found that the Vrn-A1 gene for vernalization requirement mapped between breakpoints 0.68 and 0.78, whilst the frost resistance gene Fr1 was flanked by deletion breakpoints 0.67 and 0.68. This confirms previous evidence that these genes are linked but are not the pleiotropic effect of a single gene. A comparison between the physical and genetic maps for Vrn-A1 and Fr1 shows that the linear order is identical. These results indicate that cytogenetically based physical maps of Vrn-A1 and Fr1 loci, together with genetic maps, could be useful in the further study of genome synteny and in elaborating a gene cloning strategy. Received: 16 November 1998 / Accepted: 28 November 1998     

An 800-kb region of deletion at 13q14 in human prostate and other carcinomas

Deletions of regions at 13q14 have been detected by various genetic approaches in human cancers including prostate cancer. Several studies have defined one region of loss of heterozygosity (LOH) at 13q14 that seems to reside in a DNA segment of 7.1 cM between genetic markers D13S263 and D13S153. To define the smallest region of overlap (SRO) for deletion at 13q14, we first applied tissue microdissection and multiplex PCR to detect homozygous deletion and/or hemizygous deletion at 13q14 in 134 prostate cancer specimens from 114 patients. We detected deletions at markers D13S1227, D13S1272, and A005O48 in 13 (10%) of these tumor specimens. Of the 13 tumors with deletions, 12 were either poorly differentiated primary tumors or metastases of prostate cancer. To fine-map the deletion region, we then constructed a high-resolution YAC/BAC/STS/EST physical map based on experimental and database analyses. Several markers encompassing the deletion region were analyzed for homozygous deletion and/or hemizygous deletion in 61 cell lines/xenografts derived from human cancers of the prostate, breast, ovary, endometrium, cervix, and bladder, and a region of deletion was defined by duplex PCR assay between markers A005X38 and WI-7773. We also analyzed LOH at 13q14 in the 61 cell lines/xenografts using the homozygosity mapping of deletion approach and 26 microsatellite markers. We found 24 (39%) of the cell lines/xenografts to show LOH at 13q14 and defined a region of LOH by markers M1 and M5. Combination of homozygous or hemizygous deletion and LOH results defined the SRO for deletion to be an 800-kb DNA interval between A005X38 and M5. There are six known genes located in or close to the SRO for deletion. This region of deletion is at least 2 Mb centromeric to the RB1 tumor-suppressor gene and the leukemia-associated genes 1 and 2, each of which is located at 13q14. These data suggest that the 800-kb DNA segment with deletion contains a gene whose deletion may be important for the development of prostate and other cancers. This study also provides a framework for the fine-mapping, cloning, and identification of a novel tumor-suppressor gene at 13q14.     

Fine Structure Genetic and Physical Map of the Phage P22 Tail Protein Gene

Bacteriophage P22 which are incapable of making functional tail protein can be propagated by the addition of purified mature tail protein trimers to either liquid or solidified medium. This unique in vitro complementation condition has allowed us to isolate 74 absolute lethal tail protein mutants of P22 after hydroxylamine mutagenesis. These phage mutants have an absolute requirement for purified P22 tail protein to be present in a soft agar overlay in order to form plaques and do not grow on any nonsense suppressing strains of Salmonella typhimurium. In order to genetically map and physically locate these mutations we have constructed two complementary sets of fine structure deletion mapping strains using a collection of Tn1 insertions in gene 9, the structural gene for the tail protein. Fourteen bacteriophage P22 strains carrying unique Tn1 transposon insertions (Ap phage) in gene 9 have been crossed with Ap phage carrying Tn1 insertions in gene 20. Phage carrying deletions that arose from homologous recombination between the Tn1 elements were isolated as P22 lysogens. The deletion prophage were shown to be missing all genetic information bracketed by the parental Tn1 elements and thus form a set of deletions into gene 9 from the 5' end of the gene. From the frequency of production of these deletion phage the orientation of the Tn1 insertions in gene 9 could be deduced. The genetic end points of the deletions in gene 9 and thus the order of Tn1 insertions were determined by marker rescue experiments using the original Ap phage. The genetic end points of the deletions in gene 20 were determined in similar experiments using nonsense mutations in gene 20. To locate the physical end points of these deletions in gene 9, DNA containing the Tn1 element has been cloned from each of the original Ap phage into plasmids. The precise point of insertion of Tn1 into gene 9 was determined by restriction enzyme mapping and DNA sequencing of the relevant portions of each of these plasmids. In vitro deletion of different 3' gene 9 sequences in the plasmid clones was accomplished through the use of unique restriction endonuclease sites in Tn1. The resulting plasmids form a set of deletions extending into the 3' end of the gene which are complementary compared to the deletion lysogens.(ABSTRACT TRUNCATED AT 400 WORDS)