Identification of a Gene Involved in the Control of the Root System Development in Arabidopsis thaliana

Genetic and molecular genetic analysis of a lethal root mutant of Arabidopsis thaliana was carried out. The mutant was obtained from a collection created earlier by means of insertion mutagenesis. The mutation was found to be recessive. It was caused by an insertion of the T region of vector pLD3 used for transformation of germinating seeds when creating the collection of insertion mutants. A 118-bp DNA fragment flanking the left border of the insertion was isolated using the TAIL PCR technique, and its nucleotide sequence was determined. Computer analysis of this DNA region demonstrated that it was located in exon 32 of the YUP8H12R.44 gene in chromosome 1.     

Identification of mutant gene responsible for cotyledons necrosis in developing seedlings of Arabidopsis thaliana]

Genetic and molecular analyses of an Arabidopsis thaliana mutant with necrotic cotyledons from the collection of insertion mutants obtained earlier were conducted. The mutation under study showed incomplete dominance and represented a single insertion of the T region of pLD3 vector used for transformation of germinating seeds to the plant genome during the creation of the collection. Using TAIL-PCR, a fragment of the mutant DNA adjacent to the left border of the T-DNA insertion was isolated and sequenced. Computer r-aided analysis showed that the insertion was located on the left arm of chromosome 1. The open reading frame containing the insertion has one exon and encodes a protein of 446 amino acids, whose functions are unknown.     

Identification of the gene whose mutation leads to hypocotyl tropism in Arabidopsis thaliana

Genetic and molecular analysis of a mutant of Arabidopsis thaliana with bended hypocotyl from a previously obtained collection of insertion mutants is presented. The examined mutation was shown to be recessive and based on a single insertion of pLD3 vector T-region into the A. thaliana genome. Computer-aided analysis of a DNA region adjacent to the left border of the insertion revealed a putative site of T-DNA insertion, the At1g15760 gene from 609-bp chromosome 1 represented by a single exon.     

Identification of a Mutant Gene Controlling Necrotic Cotyledons in Developing Seedlings of Arabidopsis thaliana

Genetic and molecular analyses of an Arabidopsis thalianamutant with necrotic cotyledons from the collection of insertion mutants obtained earlier were conducted. The mutation under study showed incomplete dominance and represented a single insertion of the T region of pLD3 vector used for transformation of germinating seeds to the plant genome during the creation of the collection. Using TAIL–PCR, a fragment of the mutant DNA adjacent to the left border of the T-DNA insertion was isolated and sequenced. Computer r-aided analysis showed that the insertion was located on the left arm of chromosome 1. The open reading frame containing the insertion has one exon and encodes a protein of 446 amino acids, whose function is unknown.     

Identification of the gene whose mutation leads to the appearance of recessive lethal germlings in Arabidopsis thaliana

The data are presented on genetic and molecular-genetic analysis of a mutant from the collection of morphological insertion mutants of Arabidopsis thaliana we obtained earlier, which belongs to the phenotypic class of recessive lethal germlings. A nucleotide DNA sequence, 147 bp in size, was identified, which adheres to the left border area of T-DNA insertion. The site of localization of the insertion was determined using computer analysis.     

Identification of the gene whose mutation leads to hypocoptyl tropism in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Genetic and molecular analysis of a mutant of Arabidopsis thaliana with bended hypocoptyl from a previously obtained collection of insertion mutants is presented. The examined mutation was shown to be recessive and based on a single insertion of pLD3 vector T-region into the A. thaliana genome. Computer-aided TAIL-PCR analysis of a DNA region adjacent to the left border of the insertion revealed a putative site of T-DNA insertion, the 609-bp At1g15760 gene from chromosome 1 represented by a single exon.Translated from Genetika, Vol. 41, No. 3, 2005, pp. 427–429.Original Russian Text Copyright © 2005 by Ogarkova, Tomilov, Tomilova, Tarasov.     

Identification of the Gene Whose Mutation Leads to the Appearance of Recessive Lethal Germlings in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

The data are presented on genetic and molecular-genetic analysis of a mutant from the collection of morphological insertion mutants of Arabidopsis thaliana we obtained earlier, which belongs to the phenotypic class of recessive lethal germlings. A nucleotide DNA sequence, 147 bp in size, was identified, which adheres to the left border area of T-DNA insertion. The site of localization of the insertion was determined using computer analysis.__________Translated from Ontogenez, Vol. 36, No. 3, 2005, pp. 222–224.Original Russian Text Copyright © 2005 by Ogarkova, Tomilov, Tomilova, Tarasov.     

Genetic and Mapping Analysis of Arabidopsis thaliana Male Sterile Mutant filament no elongation

To identify new genes important for anther development, we screened for male sterile mutants among a population of Arabidopsis ecotype Columbia (Col) mutagenized by T DNA insertion (provided by ARBC). A male sterile mutant line with normal vegetative and flora development but no seed yield was isolated from Salk_118481 line. T DNA insertion site identification showed that there were no T DNA sequences in the genome of the mutants. Genetic analysis indicated that the mutant was controlled by a single recessive nuclear gene named filament no elongation because the filament of the mutant remains very short at the 13-14 stage of anther development. The fne gene was mapped to a region of 97kb between the molecular makers MBD2 and MMG4 on chromosome 5 using map based cloning technique. No genes involved filament elongation were reported in this region, so we believe that FNE gene could be a new gene controlling filament elongation in Arabidopsis.     

拟南芥雄性不育突变体fne的遗传与定位分析

在T-DNA插入突变体Salk_118481株系的群体中,筛选到一株雄性不育突变体,用T-DNA序列上的一对引物进行PCR鉴定表明其基因组中没有T DNA插入。通过背景纯化与遗传分析发现该雄性不育突变体是由单个隐性基因控制的,引起不育的主要原因是在花药发育的第13~14期,花丝不能伸长以完成授粉,故该突变体命名为fne （filament no elongation）。利用图位克隆的方法对FNE基因进行了定位,结果表明FNE基因位于第五条染色体上分子标记MBD2和MMG4之间的97kb区间内。目前该区间内尚未见到控制花丝伸长基因的报道,因此,FNE基因是一个控制花丝伸长的新基因。     

Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes

To assist in the analysis of plant gene functions we have generated a new Arabidopsis insertion mutant collection of 90 000 lines that carry the T-DNA of Agrobacterium gene fusion vector pPCV6NFHyg. Segregation analysis indicates that the average frequency of insertion sites is 1.29 per line, predicting about 116 100 independent tagged loci in the collection. The average T-DNA copy number estimated by Southern DNA hybridization is 2.4, as over 50% of the insertion loci contain tandem T-DNA copies. The collection is pooled in two arrays providing 40 PCR templates, each containing DNA from either 4000 or 5000 individual plants. A rapid and sensitive PCR technique using high-quality template DNA accelerates the identification of T-DNA tagged genes without DNA hybridization. The PCR screening is performed by agarose gel electrophoresis followed by isolation and direct sequencing of DNA fragments of amplified T-DNA insert junctions. To estimate the mutation recovery rate, 39 700 lines have been screened for T-DNA tags in 154 genes yielding 87 confirmed mutations in 73 target genes. Screening the whole collection with both T-DNA border primers requires 170 PCR reactions that are expected to detect a mutation in a gene with at least twofold redundancy and an estimated probability of 77%. Using this technique, an M2 family segregating a characterized gene mutation can be identified within 4 weeks.     

A new wc-1 mutant of Neurospora crassa shows unique light sensitivity in the circadian conidiation rhythm

A new clock mutant ( rhy-2) was isolated by DNA insertion mutagenesis using a plasmid that contains a region located upstream of the cmd gene in the genome of Neurospora crassa. This mutant is arrhythmic with regard to conidiation in continuous darkness but rhythmic under a light-dark cycle. After plasmid rescue from genomic DNA of the rhy-2 strain, the insertion was localized to the gene white collar-1 ( wc-1). Plasmid DNA was inserted 3' to the sequence encoding the polyglutamine region of the WC-1 gene product, and an mRNA encoding a truncated WC-1 protein must be synthesized under the control of the cmd promoter. The new wc-1 mutant, rhy-2, is still sensitive to light, although only weakly. Since the circadian rhythm of conidiation in continuous darkness is eliminated in the mutant, the polyglutamine region in WC-1 may be essential for both clock function and light-induced carotenogenesis in Neurospora.     

A spontaneous insertion in the agrocin sensitivity region of the Ti-plasmid of Agrobacterium tumefaciens C58

A spontaneous agrocin-resistant mutant of Agrobacterium tumefaciens strain C58 was shown to have an insertion of 1.2 kb in the agrocin-sensitivity region of pTiC58. The insertion was cloned from the Ti-plasmid, and a subclone containing only DNA internal to the insertion was used to probe the Ti-plasmid and chromosomal DNA of the wild-type strain C58. The probe showed homology to chromosomal sequences but showed no homology to wild-type pTiC58. Homology was also detected with chromosomal sequences of A. tumefaciens strains, B6, K24, and T37. These results suggest that an indigenous insertion sequence of 1.2 kb transposed from the chromosome to the agrocin-sensitivity region of the Ti-plasmid in this spontaneous mutant of C58.     

Identification of the gene whose mutation leads to the morphological changes in the hypocotyl of Arabidopsis thaliana

The results of genetic and molecular genetic analysis of line 176 of Arabidopsis thaliana with reduced hypocotyls obtained from a previously obtained collection of insertion mutants, are presented. The examined mutation proved to be recessive and based on a single insertion of the T-DNA vector pLD3 into the A. thaliana genome. Computer-aided analysis of the DNA region adjacent to the left border of the insertion revealed a putative site of T-DNA insertion, the 2.5-kb At2g09920 gene located in the long arm of chromosome 2, near the centromere.     

Structural alterations of the aprt locus induced by deoxyribonucleoside triphosphate pool imbalances in Chinese hamster ovary cells.

Mutants induced at the adenine phosphoribosyl transferase (aprt) locus by dTTP or dCTP pool imbalances were examined for alterations in genomic DNA sequences. No observable changes were detected by Southern blot analysis of most mutant DNAs, suggesting induction of base pair alterations or other events below our level of detection (approximately 30 base pairs). However, in a few strains (11 from a total collection of 125 mutant cell strains), we were able to localize these events to restriction endonuclease recognition sequences when the mutations resulted in the loss or gain of a particular site. The distribution of lost or gained sites in aprt-deficient mutants induced by the two types of pool imbalances clearly varied, with those occurring in a mutator strain with increased dCTP clustering at one end of the aprt gene. Mutants induced by dTTP also revealed novel events: multiple restriction site modifications in a small region of the aprt gene in one mutant and a small (approximately 50 base pairs) insertion or duplication of DNA sequences. As in previous studies, very few deletion or insertion mutants were detected at the aprt locus. The significance of these findings in terms of the known biochemical and genetic consequences of these pool imbalances is discussed.     

Identification of a locus involved in meningococcal lipopolysaccharide biosynthesis by deletion mutagenesis

A novel method for insertion/deletion mutagenesis in meningococci was devised. This consisted of ligating a digest of total chromosomal DNA to a 1.1 kb restriction fragment containing an erythromycin-resistance marker ( ermC ), and subsequent transformation of the ligation mixture into the homologous meningococcal strain H44/76. Southern blotting of a number of the resulting erythromycin-resistant transformants demonstrated that all carried the ermC gene inserted at different positions in the chromosome. Mutants with a specific phenotype were identified by screening with the anti-lipopolysaccharide (LPS) monoclonal antibody MN4A8B2, which is specific for immunotype L3. In this way, two independent L3-negative mutant strains were isolated. In transformation experiments with chromosomal DNA from these mutants, erythromycin-resistance and lack of MN4A8B2 reactivity were always linked, showing that the insertion/deletion was in a locus involved in LPS biosynthesis. On SDS–PAGE, the mutant LPS displayed an electrophoretic mobility intermediate between that produced by the previously isolated galE and rfaF mutant strains. Chemical analysis of the mutant LPS revealed that the structure was probably lipid A–(KDO)₂–(Hep)₂. Chromosomal DNA flanking the ermC insertion in these two mutant strains was cloned, and used as probe for the isolation of the corresponding region of the wild-type strain. From hybridization and polymerase chain reaction (PCR) analysis, it could be concluded that both mutations map to the same locus. The affected gene probably encodes the glycosyltransferase necessary for adding N -acetylglucosamine to heptose.     

Cellular mobile genetic elements in the regulatory region of the pneumotropic mouse polyomavirus genome: structure and function in viral gene expression and DNA replication

DNA from the murine pneumotropic virus was extracted from virus in lung tissue of infected mice, and the regulatory region of the genome was amplified by PCR. The regulatory region of individual plasmid cloned DNA molecules appeared to have heterogeneous enhancer segments, whereas the protein-coding part of the genome had a uniform length. Nucleotide sequence analysis revealed that the majority of the DNA molecules had a structure differing from the standard type. A 220-bp insertion at nucleotide position 142 with a concomitant deletion of nucleotides 143 to 148 was prominent. There were two variants of the 220-bp insertion, differing at two nucleotide positions at one of the termini. Other DNA molecules had complete or partial deletions of these structures and surrounding sequences in the viral enhancer. However, the end of the insertion at nucleotide 142 was frequently preserved. The viral early and late promoter activity of the variant regulatory regions was tested in a luciferase reporter assay by using transfected NIH 3T3 cells. In relation to the standard-type DNA, all variants, including a G272T mutant, had much stronger late promoters. In contrast, the early promoter activity was influenced in a positive or negative direction by individual mutations. Also, the activity of the viral origin of DNA replication was affected by the sequence variation of the regulatory region, although the effects were smaller than for the late promoter. Analysis by Southern blotting and quantification using dot blots showed that approximately 10(3) copies of material related to the 220-bp insert in murine pneumotropic virus DNA was present in mouse and human DNA but not in Escherichia coli DNA. Moreover, analysis by PCR indicated that there were multiple copies in the mouse genome of sequences that were identical or closely related to the 220-bp viral DNA segment. These data together with the nucleotide sequence analysis suggest that the 220-bp insertion is related to a transposable element of a novel type.     

Study of the mechanism of mutagenesis directed by phosphotriester analogs of oligonucleotides. The role of repair in mutagenesis

The mutation system has been suggested in an effort to test insertion and deletion mutants by changing the Lac-phenotype of bacterial colonies transformed by mutant DNA. This system also makes possible to determine heterozygotes and homozygotes among the mutants. The yield of mutants in shown to depend on the structure of the DNA heteroduplex region. The yield of deletion mutants is greater than that of insertion mutants. Heterozygotes prevail in mutant colonies (greater than 90%).     

Analysis of mutant Moloney murine leukemia viruses containing linker insertion mutations in the 3'' region of pol.

Twelve linker insertion mutations have been constructed in the 3' part of the pol gene of Moloney murine leukemia virus. This region of the Moloney murine leukemia virus genome encodes IN or p46pol, which is required for integration of the retroviral DNA into the host cell chromosome. Viral proteins synthesized by these mutants were used to pseudotype a neo-containing retroviral vector. Ten of twelve linker insertion mutant pseudotypes were unable to generate stable proviruses in infected mouse cells, as measured by the formation of G418-resistant colonies. Two mutants mapping at the 3' terminus of the IN-encoding region were competent for the formation of stable vector proviruses (hundreds of G418-resistant colonies per mutant pseudotype-infected plate). Representative linker insertion mutants were also tested for the ability to synthesize viral unintegrated DNA in newly infected cells. All assayed mutants were capable of synthesizing all normal forms of viral unintegrated DNA. The structure of integrated vector proviruses generated by defective and nondefective linker insertion mutants was also analyzed. All replication-competent mutants generated normal proviruses, while the few obtainable proviruses generated by replication-defective mutants were sometimes aberrant in structure. These results argue strongly (and confirm previous data) that the IN-encoding region of pol does not play a significant role in DNA synthesis, but is absolutely required for the formation of normal proviral DNA.     

Analysis of two gene regions involved in the expression of the imipenem-specific, outer membrane porin protein OprD of Pseudomonas aeruginosa

A Tn501 mutant of Pseudomonas aeruginosa resistant to imipenem and lacking the imipenem-specific outer membrane porin protein OprD was isolated. The mutation could be complemented to imipenem susceptibility and OprD-sufficiency by a cloned 6-kb EcoRI-PstI fragment of DNA from the region of chromosome of the wild-type strain surrounding the site of Tn501 insertion. However, this fragment did not contain the oprD structural gene as judged by its inability to hybridize with an oligonucleotide corresponding to the N-terminal amino acid sequence of OprD. DNA sequencing of 3.9 kb of the region surrounding the Tn501 insertion site revealed three large open reading frames, one of which would be interrupted by the Tn501 insertion in the mutant. This latter open reading frame, named opdE (for putative regulator of oprD expression), predicted a hydrophobic protein of M(r) 41,592. Using the above-mentioned oligonucleotide, the oprD structural gene was cloned and expressed in Escherichia coli on a 2.1-kb Bam HI-KpnI fragment. DNA sequencing predicted a 420 amino acid mature OprD protein with a 23 amino acid signal sequence.