PubMed Health⌕ Search

Biomedical subjects

Andreas Bachmair

Publications and source records attributed to Andreas Bachmair.

13 recordsLinked to original sources

Expression of the ubiquitin variant ubR48 decreases proteolytic activity in Arabidopsis and induces cell death.

The ubiquitin-proteasome pathway is the major route for protein degradation in eukaryotes. We show here that this pathway can be inhibited in Arabidopsis thaliana by expression of a ubiquitin variant that contains Arg instead of Lys at position 48 (ubR48). A major consequence of ubR48 expression is the induction of cell death. Cell death induction coincides with the appearance of reactive oxygen intermediates, but is independent of salicylic acid. We found changes in expression of some defense-related genes, but these changes are apparently insufficient to cause alterations in the response to a bacterial pathogen. Expression of ubR48 from an inducible gene allowed investigation of kinetic parameters of cell death induction. In the absence of additional stress factors, slow death processes dominate if the transgene is induced in seedlings older than 2 weeks. The inducible gene also allowed isolation of suppressor mutants. Expression of ubR48 may cause changes similar to inhibition of the proteasome, which also induces various forms of cell death. Thus, ubR48 is a tool to manipulate protein turnover and to probe cell death programs in plants.

Apoptosis↗

Lotus burttii takes a position of the third corner in the lotus molecular genetics triangle.

In order to consolidate molecular genetic system in Lotus japonicus and to further access the biological diversity in Lotea, we introduce here Lotus burttii B-303 derived from West Pakistan as the third crossing partner of the Gifu ecotype (B-129-S9) for a genetic analysis. L. burttii is a relatively small and early flowering plant with non-shattering behavior. The general chromosome morphology is very similar to Gifu, and fluorescence in situ hybridization (FISH) analysis revealed that the short arm of chromosome 1 in L. burttii is comparable to that of Gifu, indicating that the translocation event involving chromosomes 1 and 2, which was observed in L. japonicus Miyakojima MG-20, is not present in L. burttii. In addition L. burttii has a higher level of DNA polymorphism compared to Gifu and MG-20 enabling design of codominant markers such as SSR, CAPS and dCAPS. Using an F2 population from a cross between Gifu and L. burttii, codominant makers that co-segregated at the translocation site could be expanded. In order to normalize the genetic background, L. burttii was inbred for nine generations and the germplasm L. burttii B-303-S9 was established.

Base Sequence↗

Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family.

BACKGROUND: Post-translational modification by Small Ubiquitin-like Modifiers (SUMO) has been implicated in protein targeting, in the maintenance of genomic integrity and in transcriptional control. But the specific molecular effects of SUMO modification on many target proteins remain to be elucidated. Recent findings point at the importance of SUMO-mediated histone NAD-dependent deacetylase (HDAC) recruitment in transcriptional regulation. RESULTS: We describe the RENi family of SUMO-like domain proteins (SDP) with the unique feature of typically containing two carboxy-terminal SUMO-like domains. Using sequence analytic evidence, we collect family members from animals, fungi and plants, most prominent being yeast Rad60, Esc2 and mouse NIP45 http://mendel.imp.univie.ac.at/SEQUENCES/reni/. Different proteins of the novel family are known to interact directly with histone NAD-dependent deacetylases (HDACs), structural maintenance of chromosomes (SMC) proteins, and transcription factors. In particular, the highly non-trivial designation of the first of the two successive SUMO-domains in non-plant RENi provides a rationale for previously published functionally impaired mutant variants. CONCLUSIONS: Till now, SUMO-like proteins have been studied exclusively in the context of their covalent conjugation to target proteins. Here, we present the exciting possibility that SUMO domain proteins, similarly to ubiquitin modifiers, have also evolved in a second line - namely as multi-domain proteins that are non-covalently attached to their target proteins. We suggest that the SUMO stable fusion proteins of the RENi family, which we introduce in this work, might mimic SUMO and share its interaction motifs (in analogy to the way that ubiquitin-like domains mimic ubiquitin). This presumption is supported by parallels in the spectrum of modified or bound proteins e.g. transcription factors and chromatin-associated proteins and in the recruitment of HDAC-activity.

Amino Acid Motifs↗

Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate.

Retroelement RNAs serve as templates for both translation and reverse transcription into extrachromosomal DNA. DNA copies may be inserted into the host genome to multiply element sequences. This transpositional activity of retroelements is usually restricted to specific conditions, particularly to conditions that impose stress on the host organism. In this work, we examined how the mRNA initiation point, and features of primary and secondary structure, of tobacco retrotransposon Tto1 RNA influence its transpositional activity. We found that the most abundant Tto1 RNA is not a substrate for reverse transcription. It is poorly translated, and its 5'-end does not contain a region of redundancy with the most prominent 3'-end. In contrast, expression of an mRNA with the 5'-end extended by 28 nucleotides allows translation and gives rise to transposition events in the heterologous host, Arabidopsis thaliana. In addition, the presence of extended hairpins and of two short open reading frames in the 5'-leader sequence of Tto1 mRNA suggests that translation does not involve ribosome scanning from the mRNA 5'-end to the translation initiation site.

3' Untranslated Regions↗

SUMO conjugation in plants.

Covalent attachment of small proteins to substrates can regulate protein activity in eukaryotes. SUMO, the small ubiquitin-related modifier, can be covalently linked to a broad spectrum of substrates. An understanding of SUMO's role in plant biology is still in its infancy. In this review, we briefly summarize the enzymology of SUMO conjugation (sumoylation), and the current knowledge of SUMO modification in Arabidopsis thaliana (L.) Heynh. and other plants, in comparison to animals and fungi. Furthermore, we assemble a list of potential pathway components in the genome of A. thaliana that have either been functionally defined, or are suggested by similarity to pathway components from other organisms.

Amino Acid Sequence↗

Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon.

Boudicca is a gypsy-like, long terminal repeat (LTR) retrotransposon that has colonized the genome of the human blood fluke, Schistosoma mansoni. Previous studies have indicated that more than 1000 copies of Boudicca reside within the S. mansoni genome, although many of them may be degenerate and inactive. Messenger RNAs transcribed from genomic copies of Boudicca were investigated by reverse transcription PCR. Overlapping RT-PCR products corresponding to the gag and pol polyproteins of Boudicca, along with relevant sequences of genomic fragments of Boudicca, were assembled into contigs. Consensus sequences from these contigs were used to predict the sequence and structure of transpositionally active copies of the Boudicca retrotransposon. They verified that Boudicca has a kabuki-like Cys-His box motif at the active site of its gag protein, a classic DTG motif as the active site of the protease domain of the pol ORF2, and indicated a contiguous integrase domain at the C-terminus of pol with strong identity to integrase from the LTR retrotransposons CsRn1 and kabuki, as well as to the conserved integrase core domain, GenBank rve (). Models of the secondary structure of the Boudicca transcript suggested that the first AUG was occluded by a stem loop structure, which in turn suggested a method of regulation of expression, at the level of translation, of Boudicca proteins. In addition, phylogenetic analysis targeting discrete domains of Boudicca revealed a generalized radiation in sequences among the multiple copies of Boudicca resident in the schistosome genome.

Amino Acid Sequence↗

Biochemical analysis of long terminal repeat retrotransposons.

A brief survey of the retrotransposition cycle is given with emphasis on intermediary steps and their identification by biochemical analysis. References include some older key publications that may not be easily accessible via electronic databases. Methods for enrichment of viruslike particles from plant material and from yeast are described.

DNA, Fungal↗

A single recessive mutation in the proteolytic machinery of Arabidopsis chloroplasts impairs photoprotection and photosynthesis upon cold stress.

Intracellular proteases, together with molecular chaperones, are components of the cellular protein quality control system. Although the identity of chloroplast proteases has been revealed in recent years, little is known about their regulation. As a first step towards identifying unknown functional or regulatory components of the chloroplast proteolytic machinery, a genetic screen was devised with the aim of generating Arabidopsis thaliana (L.) Heynh. mutants impaired in chloroplast protein degradation. A streptomycin-resistance gene was fused to a cDNA construct that encodes an unstable mutant of the OE33 protein. This chimeric gene was used for transforming Arabidopsis plants. Analysis of transgenic plants revealed a correlation between streptomycin resistance and accumulation of the recombinant fusion protein. Seeds from transgenic plants that were sensitive to streptomycin were chemically mutagenized and screened for resistance to streptomycin. Such resistance could be due to stabilization of the protein caused by a mutation in the chloroplast proteolytic machinery. Genetic analysis of one of the mutants showed the mutation to be recessive, in a single nuclear gene. Further characterization of the mutant revealed that it was not a result of increased transcription of the transgene. Moreover, chloroplast lysates from the mutant plant showed decreased ATP-dependent degradation of a chloroplast protein substrate, consistent with the conclusion that the mutation impaired the proteolytic machinery. Physiological analysis revealed that upon cold stress, photoprotection and photosynthesis in the mutant was inhibited, suggesting that the chloroplast proteolytic machinery is involved in repairing damage incurred to the photosynthetic machinery upon exposure to cold temperatures.

Acclimatization↗

PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues.

The gene PRT1 of Arabidopsis, encoding a 45-kD protein with two RING finger domains, is essential for the degradation of F-dihydrofolate reductase, a model substrate of the N-end rule pathway of protein degradation. We have determined the function of PRT1 by expression in yeast (Saccharomyces cerevisiae). PRT1 can act as a ubiquitin protein ligase in the heterologous host. The identified substrates of PRT1 have an aromatic residue at their amino-terminus, indicating that PRT1 mediates degradation of N-end rule substrates with aromatic termini but not of those with aliphatic or basic amino-termini. Expression of model substrates in mutant and wild-type plants confirmed this substrate specificity. A ligase activity exclusively devoted to aromatic amino-termini of the N-end rule pathway is apparently unique to plants. The results presented also imply that other known substrates of the plant N-end rule pathway are ubiquitylated by one or more different ubiquitin protein ligases.

Amino Acids, Aromatic↗

The upstream Sal repeat-containing segment of Arabidopsis thaliana ribosomal DNA intergenic region (IGR) enhances the activity of adjacent protein-coding genes.

The sequence containing 'upstream Sal repeats' (USR) from the Arabidopsis thaliana ribosomal DNA intergenic region (IGR) was tested for its influence on the in vivo activity of nearby protein coding genes. On average, the presence of the IGR fragment leads to a four-fold increase in the expression of a reporter gene, beta-glucuronidase, under control of the strong CaMV 35S promoter. With the help of the site-specific cre-lox recombination system, we have also obtained pairs of transgenic lines with or without the USR-containing fragment, both integrated at the same chromosomal position. Results with these transgenic lines, which contain an NPT II (kanamycin resistance) gene under control of the nos promoter as a test gene, confirmed the results obtained with the CaMV 35S-driven GUS gene. Moreover, they show that the IGR sequence can oppose tendencies of gene silencing. We hypothesize that the described effect relates to features of the chromatin structure in the proximity of the upstream Sal repeats.

Arabidopsis↗

Chromosomal map of the model legume Lotus japonicus.

Lotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F(1) hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

Centromere↗

A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci.

A genetic map for the model legume Lotus japonicus has been developed. The F(2) mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framework of amplified fragment length polymorphism (AFLP) markers. Additional markers were generated by restriction fragment length polymorphism (RFLP) and sequence-specific PCR. A total of 524 AFLP markers, 3 RAPD markers, 39 gene-specific markers, 33 microsatellite markers, and six recessive symbiotic mutant loci were mapped. This genetic map consists of six linkage groups corresponding to the six chromosomes in L. japonicus. Fluorescent in situ hybridization (FISH) with selected markers aligned the linkage groups to chromosomes as described in the accompanying article by Pedrosa et al. 2002(this issue). The length of the linkage map is 367 cM and the average marker distance is 0.6 cM. Distorted segregation of markers was found in certain sections of the map and linkage group I could be assembled only by combining colormapping and cytogenetics (FISH). A fast method to position genetic loci employing three AFLP primer combinations yielding 89 markers was developed and evaluated by mapping three symbiotic loci, Ljsym1, Ljsym5, and Ljhar1-3.

Chromosome Mapping↗