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1.
Adrianna Nowicka Magdalena Kanabus Ewa Sledziewska-Gójska Zygmunt Ciesla 《Molecular genetics and genomics : MGG》1994,243(5):584-592
An Escherichia coli strain bearing the dnaQ49 mutation, which results in a defective s subunit of DNA polymerase III, and carrying the lexA71 mutation, which causes derepression of the SOS regulon, is totally unable to maintain high-copy-number plasmids containing the umuDC operon. The strain is also unable to maintain the pAN4 plasmid containing a partial deletion of the umuD gene but retaining the wild-type umuC gene. These results suggest that a high cellular level of UmuC is exceptionally harmful to the defective DNA polymerase III of the dnaQ49 mutant. We have used this finding as a basis for selection of new plasmid umuC mutants. The properties of two such mutants, bearing the umuC61 or umuC95 mutation, are described in detail. In the umuC122:: Tn 5 strain harbouring the mutant plasmids, UV-induced mutagenesis is severely decreased compared to that observed with the parental umuDC + plasmid. Interestingly, while the frequency of UV-induced GC → AT transitions is greatly reduced, the frequency of AT → TA transversions is not affected. Both mutant plasmids bear frameshift mutations within the same run of seven A residues present in umuC +; in umuC61 the run is shortened to six A whereas in umuC95 is lengthened to eight A. We have found in both umuC61 and umuC95 that translation is partially restored to the proper reading frame. We propose that under conditions of limiting amounts of UmuC, the protein preferentially facilitates processing of only some kinds of UV-induced lesions. 相似文献
2.
Magdalena Kanabus Adrianna Nowicka Ewa Sledziewska-Gójska Piotr Jonczyk Zygmunt Ciesla 《Molecular & general genetics : MGG》1995,247(2):216-221
It has previously been suggested that inhibition of the proofreading 3-5 exonuclease activity of DNA polymerase may play an important role in generation of UV-induced mutations inEscherichia coli. Our previous work showing that overproduction of , the proofreading subunit of DNA polymerase III, counteracts the SOS mutagenic response ofE. coli seemed to be consistent with this hypothesis. To explore further the nature of the antimutagenic effect of we constructed plasmid pMK17, which encodes only two of the three highly conserved segments of — Exol and ExoII; the third segment, ExoIII, which is essential for 3–5 exonuclease activity, is deleted. We show that at 40°C, over-production of the truncated e subunit significantly delays production of M13 phage, suggesting that the protein retains its capacity to bind to DNA. On the other hand, the presence of pMK17 in atrpE65 strain growing at 40°C causes a 10-fold decrease in the frequency of UV-induced Trp+ mutations. This antimutagenic effect of the truncated s is effectively relieved by excess UmuD,C proteins. We also show that the presence of plasmid pIP21, which contains thednaQ49 allele encoding an subunit that is defective in proofreading activity, almost completely prevents generation of UV-induced mutations in thetrpE65 strain. We propose that the DNA binding ability of free , rather than its 3–5 exonuclease activity, affects processing of premutagenic UV-induced lesions, possibly by interfering with the interaction between the UmuC-UmuD-RecA complex and Pol III holoenzyme. This interaction is probably a necessary condition for translesion synthesis. 相似文献
3.
Lukasz Lebioda Marcos H. Hatada A. Tulinsky Irene M. Mavridis 《Journal of molecular biology》1982,162(2):445-458
The 8-fold α/β barrel conformation of 2-keto-3-deoxy-6-phosphogluconate aldolase has been compared to that of triosephosphate isomerase and the A-domain of pyruvate kinase. There are eight supersecondary structure units (α/β) in each of these proteins, and the comparisons were carried out in orientations corresponding to each of the possible congruences, i.e. first to first, first to second,… of the supersecondary structure units. The comparison of the Cα structure of the main chain folding of the three enzymes indicated about 150 equivalences with rootmean-square differences of about 3.1 Å, with no orientational preference, including the aldolase with itself. In addition, there is no sequence homology between the aldolase and the isomerase, and no indication of gene duplication in the former. The lack of orientational preference among the three enzymes suggests convergence to a fold of exceptional stability. However, all three enzymes activate a CH bond adjacent to a carbonyl, and their active sites correspond to the f strand, F helix region of the α/β barrel, thus contradicting the foregoing and suggesting divergent evolution from a common precursor. Other and similar arguments are also presented for and against convergent evolution of these three strikingly similar enzymes. 相似文献
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PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma 相似文献
6.
Mansouri Borhan Błaszczyk Martyna Binkowski Lukasz J. Sayadi Mohammad Hossein Azadi Nammam Ali Amirabadizadeh Ali Reza Mehrpour Omid 《Biological trace element research》2020,195(1):63-70
Biological Trace Element Research - In low-income and middle-income countries such as Iran, smoking is becoming increasingly popular, especially among young people. This has led to additional... 相似文献
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8.
Edmond M. Linossi Indu R. Chandrashekaran Tatiana B. Kolesnik James M. Murphy Andrew I. Webb Tracy A. Willson Lukasz Kedzierski Alex N. Bullock Jeffrey J. Babon Raymond S. Norton Nicos A. Nicola Sandra E. Nicholson 《PloS one》2013,8(8)
Suppressor of Cytokine Signaling (SOCS)5 is thought to act as a tumour suppressor through negative regulation of JAK/STAT and epidermal growth factor (EGF) signaling. However, the mechanism/s by which SOCS5 acts on these two distinct pathways is unclear. We show for the first time that SOCS5 can interact directly with JAK via a unique, conserved region in its N-terminus, which we have termed the JAK interaction region (JIR). Co-expression of SOCS5 was able to specifically reduce JAK1 and JAK2 (but not JAK3 or TYK2) autophosphorylation and this function required both the conserved JIR and additional sequences within the long SOCS5 N-terminal region. We further demonstrate that SOCS5 can directly inhibit JAK1 kinase activity, although its mechanism of action appears distinct from that of SOCS1 and SOCS3. In addition, we identify phosphoTyr317 in Shc-1 as a high-affinity substrate for the SOCS5-SH2 domain and suggest that SOCS5 may negatively regulate EGF and growth factor-driven Shc-1 signaling by binding to this site. These findings suggest that different domains in SOCS5 contribute to two distinct mechanisms for regulation of cytokine and growth factor signaling. 相似文献
9.
Disordered nucleiome: Abundance of intrinsic disorder in the DNA‐ and RNA‐binding proteins in 1121 species from Eukaryota,Bacteria and Archaea
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Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty‐by‐association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (~548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA‐binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA‐binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation. 相似文献
10.
Andrzej Polanczyk Marek Podyma Lukasz Trebinski Jaroslaw Chrzastek Ireneusz Zbicinski Ludomir Stefanczyk 《PloS one》2016,11(4)
Currently, studies connected with Computational Fluid Dynamic (CFD) techniques focus on assessing hemodynamic of blood flow in vessels in different conditions e.g. after stent-graft’s placement. The paper propose a novel method of standardization of results obtained from calculations of stent-grafts'' “pushing forces” (cumulative WSS—Wall Shear Stress), and describes its usefulness in diagnostic process. AngioCT data from 27 patients were used to reconstruct 3D geometries of stent-grafts which next were used to create respective reference cylinders. We made an assumption that both the side surface and the height of a stent-graft and a reference cylinder were equal. The proposed algorithm in conjunction with a stent-graft “pushing forces” on an implant wall, allowed us to determine which spatial configuration of a stent-graft predispose to the higher risk of its migration. For stent-grafts close to cylindrical shape (shape factor φ close to 1) WSS value was about 267Pa, while for stent-grafts different from cylindrical shape (φ close to 2) WSS value was about 635Pa. It was also noticed that deformation in the stent-graft’s bifurcation part impaired blood flow hemodynamic. Concluding the proposed algorithm of standardization proved its usefulness in estimating the WSS values that may be useful in diagnostic process. Angular bends or tortuosity in bifurcations of an aortic implant should be considered in further studies of estimation of the risk of implantation failure. 相似文献