Genomes and Genes
Experts and Doctors on bacterial proteins in Warsaw, Masovian Voivodeship, Poland
Locale: Warsaw, Masovian Voivodeship, Poland
Topic: bacterial proteins
- Patzer J, Walsh T, Weeks J, Dzierzanowska D, Toleman M. Emergence and persistence of integron structures harbouring VIM genes in the Children's Memorial Health Institute, Warsaw, Poland, 1998-2006. J Antimicrob Chemother. 2009;63:269-73 pubmed publisher..There is also compelling evidence of the persistence of individual strains in the hospital throughout the study period. This suggests that once MBL genes have emerged in a hospital environment, they are difficult to remove. ..
- Kosinski J, Plotz G, Guarné A, Bujnicki J, Friedhoff P. The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol. 2008;382:610-27 pubmed publisher..Finally, we demonstrate that the conserved residues of the metal ion binding domain are crucial for MMR activity of MutLalpha in vitro. ..
- Lasocki K, Bartosik A, Mierzejewska J, Thomas C, Jagura Burdzy G. Deletion of the parA (soj) homologue in Pseudomonas aeruginosa causes ParB instability and affects growth rate, chromosome segregation, and motility. J Bacteriol. 2007;189:5762-72 pubmed publisher..Inactivation of parA also increases the turnover rate (degradation) of ParB. This may provide a mechanism for controlling the level of ParB in response to the growth rate and expression of the parAB operon...
- Mierzejewska J, Kulinska A, Jagura Burdzy G. Functional analysis of replication and stability regions of broad-host-range conjugative plasmid CTX-M3 from the IncL/M incompatibility group. Plasmid. 2007;57:95-107 pubmed..Deletion of the par operon strongly destabilized pCTX-M3 despite the presence of the pemIK toxin-antidote system identical to that on NR1(R100) plasmids. Deletion of the pemIK operon had no effect on plasmid stability...
- Adamczyk Poplawska M, Lower M, Piekarowicz A. Deletion of one nucleotide within the homonucleotide tract present in the hsdS gene alters the DNA sequence specificity of type I restriction-modification system NgoAV. J Bacteriol. 2011;193:6750-9 pubmed publisher..NgoAV? recognizes DNA sequences 5'-GCA(N(7))GTCA-3' and 5'-GCA(N(7))CTCA-3', although the latter sequence is methylated only on the complementary strand within the 5'-CTCA-3' region of the second recognition target sequence...
- Sikora M, Cieplak M. Cystine plug and other novel mechanisms of large mechanical stability in dimeric proteins. Phys Rev Lett. 2012;109:208101 pubmed..The latter two mechanisms are topological in nature; the cystine plug mechanism has not yet been discussed but it turns out to provide the largest resistance to stretching. Its possible applications in elastomers are discussed...
- Dzierzanowska D, Kamińska W, Semczuk K, Borowiec D, Matysiak M, Szumała Kakol A, et al. Carriage of genes for various extended-spectrum beta-lactamases: a novel resistance strategy of Klebsiella pneumoniae in Poland. Int J Antimicrob Agents. 2010;35:392-5 pubmed publisher..pneumoniae isolates by pulsed-field gel electrophoresis (PFGE) revealed a relatively high genetic diversity between isolates producing the same combination of enzymes. Clonally related strains were uncommon. ..
- Wysocka M, Rytka J, Kurlandzka A. Saccharomyces cerevisiae CSM1 gene encoding a protein influencing chromosome segregation in meiosis I interacts with elements of the DNA replication complex. Exp Cell Res. 2004;294:592-602 pubmed..We propose that, besides its other functions, Csm1p may be involved in premeiotic DNA replication. ..
- Figiel M, Chon H, Cerritelli S, Cybulska M, Crouch R, Nowotny M. The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-GoutiÃ¨res syndrome defects. J Biol Chem. 2011;286:10540-50 pubmed publisher..Our model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition. ..
- Bzowska A, Tebbe J, Luic M, Wielgus Kutrowska B, Schroder W, Shugar D, et al. Crystallization and preliminary X-ray studies of purine nucleoside phosphorylase from Cellulomonas sp. Acta Crystallogr D Biol Crystallogr. 1998;54:1061-3 pubmed..5 A. Crystal form B appears as thick plates in the space group P212121 with unit-cell dimensions a = 63.2, b = 108.3 and c = 117.4 A. Both crystal forms contain three monomers (one trimer) in the asymmetric unit...
- Gruszczynska Biegala J, Pomorski P, Wisniewska M, Kuznicki J. Differential roles for STIM1 and STIM2 in store-operated calcium entry in rat neurons. PLoS ONE. 2011;6:e19285 pubmed publisher..Our data indicate that both STIM proteins are involved in calcium homeostasis in neurons. STIM1 mainly activates SOCE, whereas STIM2 regulates resting Ca(2+) levels in the ER and Ca(2+) leakage with the additional involvement of STIM1. ..
- Dziewit L, Dmowski M, Baj J, Bartosik D. Plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries N,N-dimethylformamide degradation-related genes whose expression is activated by a LuxR family regulator. Appl Environ Microbiol. 2010;76:1861-9 pubmed publisher..To our knowledge, this is the first study to provide insights into the genetic organization and regulation as well as the dissemination in bacteria of genes involved in the enzymatic breakdown of DMF...
- Kowalczyk M, Cocaign Bousquet M, Loubiere P, Bardowski J. Identification and functional characterisation of cellobiose and lactose transport systems in Lactococcus lactis IL1403. Arch Microbiol. 2008;189:187-96 pubmed..These data could indicate that lactose and cellobiose are transported by a unique system-a PTS carrier induced by the presence of cellobiose, and negatively controlled by the CcpA regulator. ..
- Zaim J, Kierzek A. The structure of full-length LysR-type transcriptional regulators. Modeling of the full-length OxyR transcription factor dimer. Nucleic Acids Res. 2003;31:1444-54 pubmed..A comparison of the LTTR DBD model with the structures of other HTH proteins also provides insights into the interaction of LTTRs with the C-terminal domain of the RNA polymerase alpha subunit. ..
- Wyszyńska A, Pawłowski M, Bujnicki J, Pawelec D, van Putten J, Brzuszkiewicz E, et al. Genetic characterisation of the cjaAB operon of Campylobacter coli. Pol J Microbiol. 2006;55:85-94 pubmed..Notably, no CjaB family members were identified in epsilon-Proteobacteria from different ecological niches, such as H. hepaticus and Wolinella succinogenes...
- Odintsov S, Sabala I, Marcyjaniak M, Bochtler M. Latent LytM at 1.3A resolution. J Mol Biol. 2004;335:775-85 pubmed..aureus supernatant. The "asparagine switch" in LytM is analogous to the "cysteine switch" in pro-matrix metalloproteases...
- Gladki A, Kaczanowski S, Szczesny P, Zielenkiewicz P. The evolutionary rate of antibacterial drug targets. BMC Bioinformatics. 2013;14:36 pubmed publisher..As a proof of concept, we analyzed GO enrichment among the slowest evolving genes. These may become the starting point in the search for antibiotics with a novel mechanism. ..
- 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...
- Pawłowski K, Muszewska A, Lenart A, Szczepińska T, Godzik A, Grynberg M. A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins. BMC Genomics. 2010;11:590 pubmed publisher..The new protein structural domain, now with a broad enzymatic function predicted, may become a drug target once its detailed molecular mechanism of action is understood in detail. ..
- 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. ..
- Bartosik D, Szymanik M, Wysocka E. Identification of the partitioning site within the repABC-type replicon of the composite Paracoccus versutus plasmid pTAV1. J Bacteriol. 2001;183:6234-43 pubmed..versutus when RepA and RepB were delivered in trans, proving that this region has centromere-like activity. Thus, it was demonstrated that repA, repB, and inc2 constitute a functional system for active partitioning of pTAV320...
- Knapska E, Macias M, Mikosz M, Nowak A, Owczarek D, Wawrzyniak M, et al. Functional anatomy of neural circuits regulating fear and extinction. Proc Natl Acad Sci U S A. 2012;109:17093-8 pubmed publisher..Our data show functional anatomy of neural circuits regulating fear and extinction, providing a framework for therapeutic manipulations of these circuits. ..
- Dunin Horkawicz S, Feder M, Bujnicki J. Phylogenomic analysis of the GIY-YIG nuclease superfamily. BMC Genomics. 2006;7:98 pubmed
- Bielak Zmijewska A, Kolano A, Szczepanska K, Maleszewski M, Borsuk E. Cdc42 protein acts upstream of IQGAP1 and regulates cytokinesis in mouse oocytes and embryos. Dev Biol. 2008;322:21-32 pubmed publisher..Our results indicate that Cdc42 acts upstream of IQGAP1 and is involved in regulation of cytokinesis in mouse oocytes and cleaving embryos, rather than in establishing the polarity of the oocyte. ..
- Krajewska J, Modrak Wójcik A, Arent Z, Więckowski D, Zolkiewski M, Bzowska A, et al. Characterization of the molecular chaperone ClpB from the pathogenic spirochaete Leptospira interrogans. PLoS ONE. 2017;12:e0181118 pubmed publisher..Our results indicate that ClpB's importance during infection might be due to its role as a molecular chaperone involved in reactivation of protein aggregates. ..
- Jaciuk M, Nowak E, Skowronek K, Tańska A, Nowotny M. Structure of UvrA nucleotide excision repair protein in complex with modified DNA. Nat Struct Mol Biol. 2011;18:191-7 pubmed publisher..The DNA region harboring the modification is deformed, with the double helix bent and unwound. UvrA uses damage-induced deformations of the DNA and a less rigid structure of the modified double helix for indirect readout of the lesion. ..
- Cieplak M, Filipek S, Janovjak H, Krzy ko K. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. Biochim Biophys Acta. 2006;1758:537-44 pubmed publisher..It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins...
- Krawczyk Balska A, Marchlewicz J, Dudek D, Wasiak K, Samluk A. Identification of a ferritin-like protein of Listeria monocytogenes as a mediator of ?-lactam tolerance and innate resistance to cephalosporins. BMC Microbiol. 2012;12:278 pubmed publisher..monocytogenes under ?-lactam pressure, but these regulators do not play a significant role in susceptibility and tolerance to this class of antibiotics...
- Bochtler M, Odintsov S, Marcyjaniak M, Sabala I. Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases. Protein Sci. 2004;13:854-61 pubmed
- Wardal E, Gawryszewska I, Hryniewicz W, Sadowy E. Abundance and diversity of plasmid-associated genes among clinical isolates of Enterococcus faecalis. Plasmid. 2013;70:329-42 pubmed publisher..In conclusion, there is a big and only partially characterized pool of diverse plasmids in clinical E. faecalis...
- 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...
- Daniluk P, Lesyng B. A novel method to compare protein structures using local descriptors. BMC Bioinformatics. 2011;12:344 pubmed publisher..It is well suited to improving automatic classification of structure domains, helping analyze protein fold space, or to improving protein classification schemes. DEDAL is available online at http://bioexploratorium.pl/EP/DEDAL. ..
- Jagusztyn Krynicka E, Godlewska R. New approaches for Helicobacter vaccine development--difficulties and progress. Pol J Microbiol. 2008;57:3-9 pubmed..The review presents also our knowledge concerning H. pylori interaction with immune system which might facilitate modulation of the host immune system by specific adjuvant included into vaccine. ..
- Dolka B, Chrobak Chmiel D, Czopowicz M, Szeleszczuk P. Characterization of pathogenic Enterococcus cecorum from different poultry groups: Broiler chickens, layers, turkeys, and waterfowl. PLoS ONE. 2017;12:e0185199 pubmed publisher..The study provides a new insight into EC as pathogen of different bird species. The obtained data may be useful in further studies on EC-infections more focused on a specific type of poultry...
- Adamczyk Poplawska M, Lower M, Piekarowicz A. Characterization of the NgoAXP: phase-variable type III restriction-modification system in Neisseria gonorrhoeae. FEMS Microbiol Lett. 2009;300:25-35 pubmed publisher..This phase variation was associated with the change in the number of pentanucleotide repeats (5'-CCAAC/G-3') present at the 5'-end of the coding region of the ngoAXPmod gene. ..
- 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. ..
- 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...
- Odintsov S, Sabała I, Bourenkov G, Rybin V, Bochtler M. Substrate access to the active sites in aminopeptidase T, a representative of a new metallopeptidase clan. J Mol Biol. 2005;354:403-12 pubmed..The different conformations indicate flexibility between the AmpT N and C-domains, and explain how AmpT can be active, although the unusual AmpS dimerization mode applies to AmpT as well. ..
- 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. ..
- 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. ..
- Koprowski P, Kubalski A. Bacterial ion channels and their eukaryotic homologues. Bioessays. 2001;23:1148-58 pubmed..The usefulness of bacterial mechanosensitive channels for the studies on general principles of mechanosensation is discussed. ..
- 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). ..
- Korsak D, Markiewicz Z, Gutkind G, Ayala J. Identification of the full set of Listeria monocytogenes penicillin-binding proteins and characterization of PBPD2 (Lmo2812). BMC Microbiol. 2010;10:239 pubmed publisher..Since Lmo2812 preferentially degrades low-molecular- mass substrates, this may indicate a role in cell wall turnover. ..
- 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. ..
- Kawalec M, Gniadkowski M, Kedzierska J, Skotnicki A, Fiett J, Hryniewicz W. Selection of a teicoplanin-resistant Enterococcus faecium mutant during an outbreak caused by vancomycin-resistant enterococci with the vanB phenotype. J Clin Microbiol. 2001;39:4274-82 pubmed..Expression of the resistance genes vanH(B), -B, and -X(B) was constitutive in the mutant, and this phenomenon was responsible for its unusual phenotype. ..
- 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
- 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. ..
- 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. ..
- 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