Genomes and Genes
Experts and Doctors on escherichia coli in Warsaw, Masovian Voivodeship, Poland
Locale: Warsaw, Masovian Voivodeship, Poland
Topic: escherichia coli
- Tudek B, van Zeeland A, Kusmierek J, Laval J. Activity of Escherichia coli DNA-glycosylases on DNA damaged by methylating and ethylating agents and influence of 3-substituted adenine derivatives. Mutat Res. 1998;407:169-76 pubmed..Taken together, these results suggest that hydrophobic interactions are involved in the mechanism of inhibition and/or recognition and excision of alkylated purines by TagA protein. ..
- Zaleski P, Wawrzyniak P, Sobolewska A, Mikiewicz D, Wójtowicz Krawiec A, Chojnacka Puchta L, et al. New cloning and expression vector derived from Escherichia coli plasmid pIGWZ12; a potential vector for a two-plasmid expression system. Plasmid. 2012;67:264-71 pubmed publisher..NM_006900.3) or ubi-human growth hormone (ubi-hGH; patent No. WO 2005/066208 A2) cloned in another plasmid. In this system, both ubi-interferon alpha and ubi-human growth hormone were deubiquitinated efficiently in E. coli cells. ..
- Bujnicki J, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA. 2004;10:1236-42 pubmed..We have cloned, expressed, and purified the YfcK protein and demonstrated that it catalyzes the formation of mnm5s2U in tRNA. Thus, we suggest to rename YfcK as MnmC. ..
- Bykowski T, van der Ploeg J, Iwanicka Nowicka R, Hryniewicz M. The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5'-phosphosulphate (APS) as a signalling molecule for sulphate excess. Mol Microbiol. 2002;43:1347-58 pubmed..Our data comprise the first evidence that APS may act as the negative cofactor of the transcriptional regulator Cbl, and that APS, and not sulphate itself, serves as the signalling molecule for sulphate excess. ..
- Janowska B, Kurpios Piec D, Prorok P, Szparecki G, Komisarski M, Kowalczyk P, et al. Role of damage-specific DNA polymerases in M13 phage mutagenesis induced by a major lipid peroxidation product trans-4-hydroxy-2-nonenal. Mutat Res. 2012;729:41-51 pubmed publisher..The results suggest that Pol V can infrequently bypass HNE-DNA adducts inducing mutations at G, C and A sites, while bypass by Pol IV and Pol II is error-free, but for Pol II infrequent. ..
- Nowosielska A, Janion C, Grzesiuk E. Effect of deletion of SOS-induced polymerases, pol II, IV, and V, on spontaneous mutagenesis in Escherichia coli mutD5. Environ Mol Mutagen. 2004;43:226-34 pubmed..We postulate that the proofreading activity of pol II excises DNA lesions in exponentially growing cells, whereas pol V and pol IV are more active in stationary-phase cultures. ..
- Łobocka M, Rose D, Plunkett G, Rusin M, Samojedny A, Lehnherr H, et al. Genome of bacteriophage P1. J Bacteriol. 2004;186:7032-68 pubmed..The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication...
- Wyszyńska A, Zycka J, Godlewska R, Jagusztyn Krynicka E. The Campylobacter jejuni/coli cjaA (cj0982c) gene encodes an N-glycosylated lipoprotein localized in the inner membrane. Curr Microbiol. 2008;57:181-8 pubmed publisher..Site-directed mutagenesis of the Asn residues of two putative N-linked glycosylation sites (NIS and NFT) showed that CjaA is glycosylated and that only the first N-X-S/T sequeon serves as a glycan acceptor...
- Orlowski J, Mebrhatu M, Michiels C, Bujnicki J, Aertsen A. Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr. Biochem Biophys Res Commun. 2008;377:862-6 pubmed publisher..The activity of a number of spontaneous and strategically constructed Mrr mutants is discussed in the light of this model, providing a first insight into the structure-function relationships of the Mrr enzyme. ..
- Sirko A, Zatyka M, Sadowy E, Hulanicka D. Sulfate and thiosulfate transport in Escherichia coli K-12: evidence for a functional overlapping of sulfate- and thiosulfate-binding proteins. J Bacteriol. 1995;177:4134-6 pubmed..The single cysP and sbp mutants are able to utilize both sulfate and thiosulfate as a sole sulfur source, while the inactivation of both genes leads to cysteine auxotrophy resulting from the block in the transport of both ions. ..
- Janion C. Mechanisms of action of methyl methanesulfonate on Escherichia coli: mutagenesis, DNA damage and repair. Postepy Biochem. 1995;41:308-13 pubmed
- Gniadkowski M, Schneider I, Jungwirth R, Hryniewicz W, Bauernfeind A. Ceftazidime-resistant Enterobacteriaceae isolates from three Polish hospitals: identification of three novel TEM- and SHV-5-type extended-spectrum beta-lactamases. Antimicrob Agents Chemother. 1998;42:514-20 pubmed..The new TEM derivatives probably document the already advanced microevolution of ESBLs ongoing in Polish hospitals, in a majority of which no monitoring of ESBL producers was performed before 1996...
- Lochowska A, Iwanicka Nowicka R, Plochocka D, Hryniewicz M. Functional dissection of the LysR-type CysB transcriptional regulator. Regions important for DNA binding, inducer response, oligomerization, and positive control. J Biol Chem. 2001;276:2098-107 pubmed..The single substitution Y27G resulted in the CysBpc variant, able to bind DNA and to respond to the inducer by a qualitative change in the DNA-protein complex, but defective in the positive control of the cysP promoter. ..
- Skowronek K, Kasprzak A. A two-plasmid system for independent genetic manipulation of subunits of homodimeric proteins and selective isolation of chimeric dimers. Anal Biochem. 2002;300:185-91 pubmed..The system is a powerful tool in studies of different aspects of interactions between subunits of the homodimeric proteins since it makes possible separate genetic manipulations on each subunit of the dimer. ..
- Zienkiewicz M, Ferenc A, Wasilewska W, Romanowska E. High light stimulates Deg1-dependent cleavage of the minor LHCII antenna proteins CP26 and CP29 and the PsbS protein in Arabidopsis thaliana. Planta. 2012;235:279-88 pubmed publisher..The interaction of Deg1 with the PsbS protein and the minor LHCII subunits implies its involvement in the regulation of both excess energy dissipation and state transition adaptation processes. ..
- Grudniak A, Kurek A, Szarlak J, Wolska K. Oleanolic and ursolic acids influence affect the expression of the cysteine regulon and the stress response in Escherichia coli. Curr Microbiol. 2011;62:1331-6 pubmed publisher..In addition, oleanolic acid, but not ursolic acid, caused a weak increase in DnaK synthesis, suggesting moderate ability of inducing heat-shock response. ..
- Wegleńska A, Jacob B, Sirko A. Transcriptional pattern of Escherichia coli ihfB (himD) gene expression. Gene. 1996;181:85-8 pubmed..The observed growth rate-dependent regulation of the transcription of these transcripts is in agreement with the previously published data about the regulation of the rpsA and ihfB promoters (Pedersen et al., 1984; Aviv et al., 1994). ..
- Mikiewicz D, Wrobel B, Wegrzyn G, Płucienniczak A. Isolation and characterization of a ColE1-like plasmid from Enterobacter agglomerans with a novel variant of rom gene. Plasmid. 1997;38:210-9 pubmed..Moreover, this plasmid may serve as a source of the new rom-like gene coding for a protein useful in investigation of RNA-protein interactions. A role for the pPIGDM1 plasmid in the host strain is not known. ..
- Stypulkowska Misiurewicz H, Pancer K, Roszkowiak A. Two unrelated cases of septicaemia due to Vibrio cholerae non-O1, non-O139 in Poland, July and August 2006. Euro Surveill. 2006;11:E061130.2 pubmed
- Wlodarczyk J, Kierdaszuk B. A new approach to interpretation of heterogeneity of fluorescence decay: effect of induced tautomeric shift and enzyme-->ligand fluorescence resonance energy transfer. Biophys Chem. 2006;123:146-53 pubmed..Moreover, proposed model is simple, and objectively describes heterogeneous nature of studied systems. ..
- Banach Orlowska M, Fijalkowska I, Schaaper R, Jonczyk P. DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli. Mol Microbiol. 2005;58:61-70 pubmed..A second role of Pol II is to protect mismatched 3' termini against the mutagenic action of polymerase IV (dinB product). Overall, Pol II may be considered a main player in the polymerase trafficking at the replication fork. ..
- Fijalkowska I, Jonczyk P, Tkaczyk M, Bialoskorska M, Schaaper R. Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc Natl Acad Sci U S A. 1998;95:10020-5 pubmed..Analysis of the possible mispairs underlying each specific base pair substitution suggests that the lagging strand replication on the E. coli chromosome may be more accurate than leading strand replication. ..
- Purta E, van Vliet F, Tricot C, De Bie L, Feder M, Skowronek K, et al. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins. 2005;59:482-8 pubmed
- Grudniak A, Nowicka Sans B, Maciag M, Wolska K. Influence of Escherichia coli DnaK and DnaJ molecular chaperones on tryptophanase (TnaA) amount and GreA, GreB stability. Folia Microbiol (Praha). 2004;49:507-12 pubmed..The half-life of GreA and GreB proteins (being activators of transcription elongation of the tna operon) are diminished in both mutants suggesting the involvement of DnaK and DnaJ in the stability of these proteins. ..
- Bujnicki J, Blumenthal R, Rychlewski L. Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus. J Mol Microbiol Biotechnol. 2002;4:93-9 pubmed
- Lochowska A, Iwanicka Nowicka R, Zaim J, Witkowska Zimny M, Bolewska K, Hryniewicz M. Identification of activating region (AR) of Escherichia coli LysR-type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the cysP promoter. Mol Microbiol. 2004;53:791-806 pubmed
- Maciejewska A, Poznanski J, Kaczmarska Z, Krowisz B, Nieminuszczy J, Polkowska Nowakowska A, et al. AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action. J Biol Chem. 2013;288:432-41 pubmed publisher..Molecular modeling of these adducts bound by AlkB allowed evaluation of the participation of their possible conformational states in the enzymatic reaction...
- Adamczyk Popławska M, Kondrzycka A, Urbanek K, Piekarowicz A. Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems. Microbiology. 2003;149:3311-9 pubmed..The authors propose that the type IC family of R-M systems could consist of several complementation subgroups whose specificity would depend on differences in the conserved regions of the HsdS polypeptide. ..
- Popowska M, Markiewicz Z. Murein-hydrolyzing activity of flagellin FlaA of Listeria monocytogenes. Pol J Microbiol. 2004;53:237-41 pubmed..Peptidoglycan hydrolysing activity of FlaA purified by FPLC on Mono-S Sepharose against labelled Escherichia coli murein was demonstrated. ..
- Gawel D, Maliszewska Tkaczyk M, Jonczyk P, Schaaper R, Fijalkowska I. Lack of strand bias in UV-induced mutagenesis in Escherichia coli. J Bacteriol. 2002;184:4449-54 pubmed..These data suggest that SOS-mediated mutagenic translesion synthesis on the Escherichia coli chromosome may occur with equal or similar probability on leading and lagging strands. ..
- Minczuk M, Piwowarski J, Papworth M, Awiszus K, Schalinski S, Dziembowski A, et al. Localisation of the human hSuv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA. Nucleic Acids Res. 2002;30:5074-86 pubmed..The presented analysis of the hSuv3p NTPase/helicase suggests that new functions of the protein have been acquired in the course of evolution. ..
- Maciejewska A, Sokołowska B, Nowicki A, Kuśmierek J. The role of AlkB protein in repair of 1,N?-ethenoadenine in Escherichia coli cells. Mutagenesis. 2011;26:401-6 pubmed publisher..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. ..
- Lobocka M, Hennig J, Wild J, Kłopotowski T. Organization and expression of the Escherichia coli K-12 dad operon encoding the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase. J Bacteriol. 1994;176:1500-10 pubmed..We propose that the high-affinity site, centered 59.5 bp upstream of the main transcription start point, plays a role in cAMP-CRP-mediated activation of dad operon expression in the absence of glucose. ..
- Bujnicki J. Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases. FASEB J. 2000;14:2365-8 pubmed
- Wypijewska A, Bojarska E, Lukaszewicz M, Stepinski J, Jemielity J, Davis R, et al. 7-methylguanosine diphosphate (m(7)GDP) is not hydrolyzed but strongly bound by decapping scavenger (DcpS) enzymes and potently inhibits their activity. Biochemistry. 2012;51:8003-13 pubmed publisher..Our data have important implications for the regulatory role of m(7)GDP in mRNA metabolic pathways due to its possible interactions with different cap-binding proteins, such as DcpS or eIF4E...
- Mielecki D, Saumaa S, Wrzesiński M, Maciejewska A, Zuchniewicz K, Sikora A, et al. Pseudomonas putida AlkA and AlkB proteins comprise different defense systems for the repair of alkylation damage to DNA - in vivo, in vitro, and in silico studies. PLoS ONE. 2013;8:e76198 pubmed publisher..It probably creates a backup system that protects P. putida strains defective in other DNA repair systems against alkylating agents of exo- and endogenous origin. ..
- Kesik M, Jedlina Panasiuk L, Kozak Cieszczyk M, Płucienniczak A, Wedrychowicz H. Enteral vaccination of rats against Fasciola hepatica using recombinant cysteine proteinase (cathepsin L1). Vaccine. 2007;25:3619-28 pubmed..However, CD8+ and CD4+ lymphocytes appeared in significantly higher numbers in the peritoneal fluid of vaccinated rats than in controls. ..
- Kalwarczyk T, Tabaka M, Holyst R. Biologistics--diffusion coefficients for complete proteome of Escherichia coli. Bioinformatics. 2012;28:2971-8 pubmed publisher..Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo. email@example.com. Supplementary data are available at Bioinformatics Online. ..
- Firczuk M, Bochtler M. Mutational analysis of peptidoglycan amidase MepA. Biochemistry. 2007;46:120-8 pubmed..Mutation of residue W203 to aspartate impairs substrate binding. ..
- Plochocka D, Kierzek A, Obtulowicz T, Tudek B, Zielenkiewicz P. 3-Methyladenine-DNA glycosylase I from Escherichia coli-computer modeling and supporting experimental evidence. Biochem Biophys Res Commun. 2000;268:724-7 pubmed..None of the eight cysteines present in the TagA sequence forms a disulfide bridge in the model structure, which has also been experimentally verified with the use of Ellman method. ..
- Sirko A, Hryniewicz M, Hulanicka D, Bock A. Sulfate and thiosulfate transport in Escherichia coli K-12: nucleotide sequence and expression of the cysTWAM gene cluster. J Bacteriol. 1990;172:3351-7 pubmed..Expression of the four genes was analyzed in the T7 promoter-polymerase system. ..
- Smorawinska M, Szuplewska M, Zaleski P, Wawrzyniak P, Maj A, Plucienniczak A, et al. Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species. FEMS Microbiol Lett. 2012;326:76-82 pubmed publisher..g. resistance transposons) among evolutionarily distinct bacterial species. Thus, mobilizable NHR plasmids may play a much more important role in horizontal gene transfer than previously thought...
- Korza H, Bochtler M. Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. J Biol Chem. 2005;280:40802-12 pubmed publisher..We conclude that ld-carboxypeptidases are serine peptidases with Ser-His-Glu catalytic triads...
- Olejnik K, Kraszewska E. Cloning and characterization of an Arabidopsis thaliana Nudix hydrolase homologous to the mammalian GFG protein. Biochim Biophys Acta. 2005;1752:133-41 pubmed..2 mM and 2.7 s(-1) respectively. The products of ADP-ribose hydrolysis were AMP and ribose-5-phosphate. The optimal activity was at alkaline pH (8.5) with Mg2+ (5 mM) ions as the cofactor. The protein exists as a dimmer in solution. ..
- Speina E, Kierzek A, Tudek B. Chemical rearrangement and repair pathways of 1,N6-ethenoadenine. Mutat Res. 2003;531:205-17 pubmed..This may explain the previously reported 20-fold higher mutagenic potency of product C in comparison to epsilon A in E. coli [Biochemistry 32 (1993) 12793]. ..
- Filipek R, Rzychon M, Oleksy A, Gruca M, Dubin A, Potempa J, et al. The Staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease. J Biol Chem. 2003;278:40959-66 pubmed publisher..Mutations in this residue lead to a loss of affinity of the inhibitor for protease and convert the inhibitor into a substrate...
- Maliszewska Tkaczyk M, Jonczyk P, Bialoskorska M, Schaaper R, Fijalkowska I. SOS mutator activity: unequal mutagenesis on leading and lagging strands. Proc Natl Acad Sci U S A. 2000;97:12678-83 pubmed..Specifically, the lagging strand of replication appears most susceptible to the SOS mutator effect. ..
- Jonczyk P, Nowicka A, Fijałkowska I, Schaaper R, Ciesla Z. In vivo protein interactions within the Escherichia coli DNA polymerase III core. J Bacteriol. 1998;180:1563-6 pubmed..Thus, the mutator phenotype of dnaQ49 may be the result of an altered conformation of the epsilon protein, which leads to altered interactions within the Pol III core. ..
- Leszczynska K, Bolhuis A, Leenhouts K, Venema G, Cegłowski P. Cloning and molecular analysis of the dihydrofolate reductase gene from Lactococcus lactis. Appl Environ Microbiol. 1995;61:561-6 pubmed..Results of these experiments indicate that in L. lactis the dhfr gene represents part of a larger transcription unit. ..
- Hryniewicz M, Sirko A, Pałucha A, Bock A, Hulanicka D. Sulfate and thiosulfate transport in Escherichia coli K-12: identification of a gene encoding a novel protein involved in thiosulfate binding. J Bacteriol. 1990;172:3358-66 pubmed..Preliminary sequence data from the corresponding region of the Salmonella typhimurium chromosome showed strictly homologous counterparts of the E. coli cysP and cysT genes. ..