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REPAIRtoire--a database of DNA repair pathways.
Get PDFREPAIRtoire is the first comprehensive database resource for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. REPAIRtoire provides also links to publications and external databases. REPAIRtoire contains information about eight main DNA damage checkpoint, repair and tolerance pathways: DNA damage signaling, direct reversal repair, base excision repair, nucleotide excision repair, mismatch repair, homologous recombination repair, nonhomologous end-joining and translesion synthesis. The pathway/protein dataset is currently limited to three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The DNA repair and tolerance pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. REPAIRtoire can be queried by the name of pathway, protein, enzymatic complex, damage and disease. In addition, a tool for drawing custom DNA-protein complexes is available online. REPAIRtoire is freely available and can be accessed at http://repairtoire.genesilico.pl/
The role of AlkB protein in repair of 1,N6-ethenoadenine in Escherichia coli cells
Get PDFEtheno () DNA adducts, including 1,N6-ethenoadenine (A), are formed by various bifunctional agents of exogenous and endogenous origin. The AT→TA transversion, the most frequent mutation provoked by the presence of A in DNA, is very common in critical codons of the TP53 and RAS genes in tumors induced by exposure to carcinogenic vinyl compounds. Here, using a method that allows examination of the mutagenic potency of a metabolite of vinyl chloride, chloroacetaldehyde (CAA), but eliminates its cytotoxicity, we studied the participation of alkA, alkB and mug gene products in the repair of A in E. coli cells. The test system used comprised the pIF105 plasmid bearing the lactose operon of CC105 origin which allowed monitoring of Lac+ revertants that arose by ATTA substitutions due to the modification of adenine by CAA. The plasmid was CAA-modified in vitro and replicated in E. coli of various genetic backgrounds (wt, alkA, alkB, mug, alkAalkB, alkAmug and alkBmug). To modify the levels of the AlkA and AlkB proteins, mutagenesis was studied in E. coli cells induced or not in adaptive response to alkylating agents. Considering the levels of CAA-induced Lac+ revertants in strains harboring the CAA-modified pIF105 plasmid and induced or not in adaptive response, we conclude that the AlkB dioxygenase plays a major role in decreasing the level of ATTA mutations, thus in the repair of A in E. coli cells. The observed differences of mutation frequencies in the various mutant strains assayed indicate that Mug glycosylase is also engaged in the repair of A, whereas the role the AlkA glycosylase in this repair is negligible
Configuration of polyisoprenoids affects the permeability and thermotropic properties of phospholipid/polyisoprenoid model membranes.
Get PDFThe influence of α-cis- and α-trans-polyprenols on the structure and properties of model membranes was analyzed. The interaction of Ficaprenol-12 (α-cis-Prenol-12, α-Z-Prenol-12) and Alloprenol-12 (α-trans-Prenol-12, α-E-Prenol-12) with model membranes was compared using high performance liquid chromatography (HPLC), differential scanning calorimetry (DSC) and fluorescent methods. L-α-phosphatidylcholine from egg yolk (EYPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) as the main lipid components of unilamellar (SUVs) and multilamellar (MLVs) vesicles were used. The two-step extraction procedure (n-pentane and hexane, respectively) allowed to separately analyze the fractions of polyprenol as non-incorporated (PrenolNonInc) and incorporated (PrenolInc) into liposomes. Consequently, distribution coefficients, P', describing the equilibrium of prenol content between phospholipid (EYPC) membrane and the aqueous phase gave different logP' for α-cis- and α-trans-Prenol-12, indicating that the configuration of the α-terminal residue significantly alters the hydrophobicity of the polyisoprenoid molecule and consequently the affinity of polyprenols for EYPC membrane. In fluorescence experiments α-trans-Pren-12 increased up to 1.7-fold the permeability of EYPC bilayer for glucose while the effect of α-cis-Pren-12 was almost negligible. Considerable changes of thermotropic behavior of DPPC membranes in the presence of both prenol isomers were observed. α-trans-Pren-12 completely abolished the pretransition while in the case of α-cis-Pren-12 it was noticeably reduced. Furthermore, for both prenol isomers, the temperature of the main phase transition (Tm) was shifted by about 1ºC to lower values and the height of the peak was significantly reduced. The DSC analysis profiles also showed a new peak at 38.7°C, which may suggest the concomitant presence of more that one phase within the membrane.
Results of these experiments and the concomitant occurrence of alloprenols and ficaprenols in plant tissues suggest that cis/trans isomerization of the α-residue of polyisoprenoid molecule might comprise a putative mechanism responsible for modulation of the permeability of cellular membranes
Genome sequence and analysis of the tuber crop potato.
Get PDFPotato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop
LTR retrotransposons in fungi.
Get PDFTransposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (8000 elements). The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other
Comprehensive Structural and Substrate Specificity Classification of the Saccharomyces cerevisiae Methyltransferome
Get PDFMethylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life
forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction,
transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation in S.
cerevisiae by conducting a comprehensive structural and functional survey of all the methyltransferases encoded in its
genome. Using distant homology detection and fold recognition, we found that the S. cerevisiae methyltransferome
comprises 86 MTases (53 well-known and 33 putative with unknown substrate specificity). Structural classification of their
catalytic domains shows that these enzymes may adopt nine different folds, the most common being the Rossmann-like.
We also analyzed the domain architecture of these proteins and identified several new domain contexts. Interestingly, we
found that the majority of MTase genes are periodically expressed during yeast metabolic cycle. This finding, together with
calculated isoelectric point, fold assignment and cellular localization, was used to develop a novel approach for predicting
substrate specificity. Using this approach, we predicted the general substrates for 24 of 33 putative MTases and confirmed
these predictions experimentally in both cases tested. Finally, we show that, in S. cerevisiae, methylation is carried out by 34
RNA MTases, 32 protein MTases, eight small molecule MTases, three lipid MTases, and nine MTases with still unknown
substrate specificity
[Letter to the editor] Ethylene emitted by nylon membrane filters questions their usefulness to transfer plant seedlings between media
Get PDFTransfer of seedlings between media is
a time-consuming process because the
traditional, widely used method involves
using forceps to transfer the plantlets one
by one. The previously reported solution
to avoid such a laborious procedure is
the use of nylon membrane filters
placed onto the surface of a medium.
Despite the increasing popularity of
this approach, justification for choosing
nylon membranes and their evaluation
as a tool for such methods have not
been performed yet. In this work we
have shown that wet nylon filters, when
placed on the surface of the medium,
emit significant amounts of ethylene,
a gaseous phytohormone which plays a
major role in many aspects of plant development
and their response to environmental
signals. Therefore, our results
indicate that the use of nylon membranes
as a material for seedling growth support
may be problematic due to the risk of
introducing an additional, uncontrolled
factor during experiments
Faithful chaperones
Get PDFThis review describes the properties of some rare eukaryotic chaperones that each assist in the folding of only one target protein. In particular, we describe a) the tubulin cofactors, b) p47, which assists in the folding of collagen, c) α-hemoglobin stabilizing protein (AHSP), d) the adenovirus L4-100K protein, which is a chaperone of the major structural viral protein, hexon, and e) HYPK, the huntingtin-interacting protein. These various sized proteins (102 to 1190 amino acids long) are all involved in the folding of oligomeric polypeptides but are otherwise functionally unique, as they each assist only one particular client. This raises a question regarding the biosynthetic cost of the high-level production of such chaperones. As the clients of faithful chaperones are all abundant proteins that are essential cellular or viral components, it is conceivable that this necessary metabolic expenditure withstood evolutionary pressure to minimize biosynthetic costs. Nevertheless, the complexity of the folding pathways in which these chaperones are involved results in error-prone processes. Several human disorders associated with these chaperones are discussed
Analysis of potyvirus terminal protein VPg-transgenic Arabidopsis thaliana plants.
Get PDFVirus-coded VPg protein of Potato virus Y (PVY) does not have homologs apart from other VPgs. Since VPg is indispensable for the potyvirus life cycle, it appeared a good candidate for eliciting pathogen-derived resistance to PVY. Following agroinfection used to obtain PVY VPg-transgenic Arabidopsis thaliana plants, only few transgenic seeds were recovered giving rise to six transgenic plants that contained the VPg gene with the correct sequence. They generated VPg mRNA, but VPg protein was not detected. Some plants were immune to PVY infection suggesting post-transcriptional gene silencing. However, the likely PVY VPg toxicity exerted at an early stage of transformed seeds development precludes its use for engineering pathogen-derived resistance
First ancient DNA sequences of the Late Pleistocene red deer (Cervus elaphus) from the Crimea, Ukraine
Get PDFThe Emine-Bair-Khosar Cave (EBK), situated on the northern edge of the Lower Plateau of the Chatyrdag Massif (Crimean Mountains) is rich in palaeontological material accumulated over most of the Pleistocene. mtDNA was isolated from bones of three specimens of red deer (Cervus elaphus) dated to the late Pleistocene (MIS 3). These are the first ancient DNA sequences obtained for this species. The position of the three red deer individuals on the phylogeographic tree is based on mtDNA sequences of contemporary representatives of the Cervinae inhabiting the Northern Hemisphere. The results confirm the notion that the Crimean Peninsula was the north-easternmost refugium in Europe, and that during and after the Late Pleistocene it played a major role in recolonisation and dispersal of temperate species in the whole Eurasian continent