Genomes and Genes
Experts and Doctors on molecular sequence data in Warsaw, Masovian Voivodeship, Poland
Locale: Warsaw, Masovian Voivodeship, Poland
Topic: molecular sequence data
Publications182 found, 100 shown here
- Sadowy E, Kuch A, Gniadkowski M, Hryniewicz W. Expansion and evolution of the Streptococcus pneumoniae Spain9V-ST156 clonal complex in Poland. Antimicrob Agents Chemother. 2010;54:1720-7 pubmed publisher..The Spain(9V)-ST156 clonal complex has been largely responsible for a decreasing susceptibility to penicillin among pneumococci in Poland in recent years, in spite of a relatively moderate antimicrobial use. ..
- Szolajska E, Burmeister W, Zochowska M, Nerlo B, Andreev I, Schoehn G, et al. The structural basis for the integrity of adenovirus Ad3 dodecahedron. PLoS ONE. 2012;7:e46075 pubmed publisher..We also provide evidence that the distal N-terminal residues are externally exposed and available for attaching cargo. ..
- Ganguly K, Rejmak E, Mikosz M, Nikolaev E, Knapska E, Kaczmarek L. Matrix metalloproteinase (MMP) 9 transcription in mouse brain induced by fear learning. J Biol Chem. 2013;288:20978-91 pubmed publisher..Hence, our results suggest that AP-1 acts as a positive regulator of MMP-9 transcription in the brain following fear learning. ..
- Koprowski P, Kubalski A. C termini of the Escherichia coli mechanosensitive ion channel (MscS) move apart upon the channel opening. J Biol Chem. 2003;278:11237-45 pubmed..We propose that the as yet undefined C-terminal region may form a cytoplasmic gate of the channel. The results are discussed and interpreted based on the recently released quaternary structure of the channel. ..
- Szymanik M, Welc Faleciak R, Bartosik D, Włodarczyk M. Replication system of plasmid pMTH4 of Paracoccus methylutens DM12 contains an enhancer. Pol J Microbiol. 2006;55:261-70 pubmed..We speculate that this region might constitute a site of binding of plasmid or host-encoded proteins that are able to interact with the origin, which positively regulates the initiation of replication...
- Podsiadly E, Chmielewski T, Sochon E, Tylewska Wierzbanowska S. Bartonella henselae in Ixodes ricinus ticks removed from dogs. Vector Borne Zoonotic Dis. 2007;7:189-92 pubmed..This is the first report about the existence of B. henselae in ticks removed from dogs. It is, however, an open issue that needs further investigation if ticks consist a new competent vector involved in transmission of bartonellosis...
- Obarska Kosinska A, Taylor J, Callow P, Orlowski J, Bujnicki J, Kneale G. HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling. J Mol Biol. 2008;376:438-52 pubmed publisher..The model reveals an ellipsoidal shape of the enzymatic core comprising the N-terminal and central domains, and suggests conformational heterogeneity of the C-terminal region implicated in binding of HsdR to the HsdS-HsdM complex. ..
- Szaflik J, Ołdak M, Maksym R, Kaminska A, Pollak A, Udziela M, et al. Genetics of Meesmann corneal dystrophy: a novel mutation in the keratin 3 gene in an asymptomatic family suggests genotype-phenotype correlation. Mol Vis. 2008;14:1713-8 pubmed..Location of the E498V mutation emphasizes the functional relevance of the highly conserved boundary motifs at the COOH-terminus of the alpha-helical rod domain in keratin 3 (K3). ..
- Szuplewska M, Bartosik D. Identification of a mosaic transposable element of Paracoccus marcusii composed of insertion sequence ISPmar4 (ISAs1 family) and an IS1247a-driven transposable module (TMo). FEMS Microbiol Lett. 2009;292:216-21 pubmed publisher..The identification of this novel TE provides evidence that transposition of TMos may change an IS into a more complex element resembling noncomposite transposons...
- Kloch M, Milewski M, Nurowska E, Dworakowska B, Cutting G, Dołowy K. The H-loop in the second nucleotide-binding domain of the cystic fibrosis transmembrane conductance regulator is required for efficient chloride channel closing. Cell Physiol Biochem. 2010;25:169-80 pubmed publisher..These results suggest that the H-loop of NBD2, apart from being required for CFTR channel closing, may be involved in regulating CFTR trafficking to the cell surface. ..
- Geremek M, Bruinenberg M, Zietkiewicz E, Pogorzelski A, Witt M, Wijmenga C. Gene expression studies in cells from primary ciliary dyskinesia patients identify 208 potential ciliary genes. Hum Genet. 2011;129:283-93 pubmed publisher..Our predictions are based directly on the human material and not on model organisms. This list of genes provides candidate genes for PCD and other ciliopathies. ..
- Sousa S, Jenkins D, Chanudet E, Tasseva G, Ishida M, Anderson G, et al. Gain-of-function mutations in the phosphatidylserine synthase 1 (PTDSS1) gene cause Lenz-Majewski syndrome. Nat Genet. 2014;46:70-6 pubmed publisher..We have identified LMS as the first human disease, to our knowledge, caused by disrupted phosphatidylserine metabolism. Our results point to an unexplored link between phosphatidylserine synthesis and bone metabolism. ..
- Jagielski T, Rup E, Ziółkowska A, Roeske K, Macura A, Bielecki J. Distribution of Malassezia species on the skin of patients with atopic dermatitis, psoriasis, and healthy volunteers assessed by conventional and molecular identification methods. BMC Dermatol. 2014;14:3 pubmed publisher..The predominance of M. sympodialis in both normal and pathologic skin, contrasts with other European countries, reporting M. globosa and M. restricta as the most frequently isolated Malassezia species. ..
- Wielgus Kutrowska B, Modrak Wójcik A, Dyzma A, Breer K, Zolkiewski M, Bzowska A. Purine nucleoside phosphorylase activity decline is linked to the decay of the trimeric form of the enzyme. Arch Biochem Biophys. 2014;549:40-8 pubmed publisher..These results suggest that the biological role of packing of the PNP monomers into a trimeric structure is to provide the stability of the enzyme since the monomers are not stable in solution. ..
- Aleksandrzak Piekarczyk T, Koryszewska BagiÅ„ska A, Grynberg M, Nowak A, Cukrowska B, Kozakova H, et al. Genomic and Functional Characterization of the Unusual pLOCK 0919 Plasmid Harboring the spaCBA Pili Cluster in Lactobacillus casei LOCK 0919. Genome Biol Evol. 2015;8:202-17 pubmed publisher..casei LOCK 0919 became the dominant strain and persisted there for at least 48 days. ..
- Dobrowolska G, Boldyreff B, Issinger O. Cloning and sequencing of the casein kinase 2 alpha subunit from Zea mays. Biochim Biophys Acta. 1991;1129:139-40 pubmed..The primary amino acid sequence exhibits 75% identity to the alpha subunit and 71% identity to the alpha' subunit of human casein kinase 2. ..
- Gniadkowski M, Schneider I, Pa ucha A, Jungwirth R, Mikiewicz B, Bauernfeind A. Cefotaxime-resistant Enterobacteriaceae isolates from a hospital in Warsaw, Poland: identification of a new CTX-M-3 cefotaxime-hydrolyzing beta-lactamase that is closely related to the CTX-M-1/MEN-1 enzyme. Antimicrob Agents Chemother. 1998;42:827-32 pubmed..freundii strain causing routine urinary tract infections has been maintained for a relatively long time in the hospital environment...
- Dzikowska A, Swianiewicz M, Talarczyk A, Wisniewska M, Goras M, Scazzocchio C, et al. Cloning, characterisation and regulation of the ornithine transaminase (otaA) gene of Aspergillus nidulans. Curr Genet. 1999;35:118-26 pubmed..AREA binding-sites are composed of GATT sequences which are not typical binding sites for the GATA - binding family of transcription factors. ..
- 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. ..
- Piekarowicz A, Kłyz A, Kwiatek A, Stein D. Analysis of type I restriction modification systems in the Neisseriaceae: genetic organization and properties of the gene products. Mol Microbiol. 2001;41:1199-210 pubmed..However, significant differences in the organization and structure of the hsdS genes in both these systems suggests that, if functional, they would possess recognition sites that differ from the gonococcus and from themselves. ..
- Bujnicki J, Rychlewski L. In silico identification, structure prediction and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses. Protein Eng. 2002;15:101-8 pubmed..e. the cap 1 MTase). Evolutionary relationships between these proteins are also discussed. ..
- Bartosik D, Sochacka M, Baj J. Identification and characterization of transposable elements of Paracoccus pantotrophus. J Bacteriol. 2003;185:3753-63 pubmed..These elements will be of a great value in the design of new genetic tools for paracocci, since only one element (IS1248 of P. denitrificans) has been described so far in this genus...
- Towpik J, Chacinska A, Ciesla M, Ginalski K, Boguta M. Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes. J Biol Chem. 2004;279:14096-103 pubmed
- Karkusiewicz I, Rempola B, Gromadka R, Grynberg M, Rytka J. Functional and physical interactions of Faf1p, a Saccharomyces cerevisiae nucleolar protein. Biochem Biophys Res Commun. 2004;319:349-57 pubmed..The primary defect is apparently due to inefficient processing of 35S rRNA at the A(0), A(1), and A(2) cleavage sites. ..
- Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, et al. Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length. Biochim Biophys Acta. 2006;1764:299-306 pubmed..Mass spectrometry of K protein isolated from proliferating cells and from cells under oxidative stress revealed the same pattern of phosphopeptides. The structural implications of phosphorylation are discussed. ..
- Bochtler M, Szczepanowski R, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, et al. Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J. 2006;25:2219-29 pubmed publisher..Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site...
- Szczesny P, Iacovache I, Muszewska A, Ginalski K, van der Goot F, Grynberg M. Extending the aerolysin family: from bacteria to vertebrates. PLoS ONE. 2011;6:e20349 pubmed publisher..Its putative role in the virulence of B. anthracis and its three dimensional model are discussed. ..
- Grzybowska E, Zayat V, Konopinski R, Trebinska A, Szwarc M, Sarnowska E, et al. HAX-1 is a nucleocytoplasmic shuttling protein with a possible role in mRNA processing. FEBS J. 2013;280:256-72 pubmed publisher..These results suggest that HAX-1 may be involved in the regulation of expression of bound transcripts, possibly as part of the stress response. ..
- Dybicz M, Gierczak A, Dabrowska J, Rdzanek Ł, Michałowicz B. Molecular diagnosis of cystic echinococcosis in humans from central Poland. Parasitol Int. 2013;62:364-7 pubmed publisher..These data demonstrate that the pig strain of this parasite is the most frequent causative agent of human cystic echinococcosis in central Poland...
- Drozak J, Chrobok L, Poleszak O, Jagielski A, Derlacz R. Molecular identification of carnosine N-methyltransferase as chicken histamine N-methyltransferase-like protein (hnmt-like). PLoS ONE. 2013;8:e64805 pubmed publisher..The identification of the gene encoding carnosine N-methyltransferase might be beneficial for estimation of the biological functions of anserine...
- Blackford A, Nieminuszczy J, Schwab R, Galanty Y, Jackson S, Niedzwiedz W. TopBP1 interacts with BLM to maintain genome stability but is dispensable for preventing BLM degradation. Mol Cell. 2015;57:1133-1141 pubmed publisher..Taken together, our findings provide molecular insights into a key tumor suppressor and genome stability network. ..
- 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. ..
- Gromadka R, Kaniak A, Slonimski P, Rytka J. A novel cross-phylum family of proteins comprises a KRR1 (YCL059c) gene which is essential for viability of Saccharomyces cerevisiae cells. Gene. 1996;171:27-32 pubmed..We propose to call this essential gene KRR1. ..
- Piotrowska M, Natorff R, Paszewski A. sconC, a gene involved in the regulation of sulphur metabolism in Aspergillus nidulans, belongs to the SKP1 gene family. Mol Gen Genet. 2000;264:276-82 pubmed..sconC mRNA is present in the sconC3 and sconB2 mutants and the level of the sconC transcript seems not to be significantly regulated by supplementation of the medium with sulphur. ..
- Nowotny M, Spiechowicz M, Jastrzebska B, Filipek A, Kitagawa K, Kuznicki J. Calcium-regulated interaction of Sgt1 with S100A6 (calcyclin) and other S100 proteins. J Biol Chem. 2003;278:26923-8 pubmed..These findings suggest that protein ubiquitination via Sgt1-dependent pathway can be regulated by S100 proteins. ..
- Dolowy P, Mondzelewski J, Zawadzka R, Baj J, Bartosik D. Cloning and characterization of a region responsible for the maintenance of megaplasmid pTAV3 of Paracoccus versutus UW1. Plasmid. 2005;53:239-50 pubmed..pantotrophus. Basic replicons of the pTAV3-type are able to maintain large bacterial genomes, therefore they appear to be good candidates for the construction of vectors specific for Alphaproteobacteria...
- Obarska A, Blundell A, Feder M, Vejsadová S, Sisáková E, Weiserová M, et al. Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Nucleic Acids Res. 2006;34:1992-2005 pubmed..The model structure, together with location of the mutant residues, provides a better background on which to study protein-protein and protein-DNA interactions in Type I R-M systems. ..
- Tkaczuk K, Dunin Horkawicz S, Purta E, Bujnicki J. Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics. 2007;8:73 pubmed..The results of our analysis provide a comprehensive 'roadmap' for experimental characterization of SPOUT MTases and interpretation of functional studies in the light of sequence-structure relationships. ..
- Kaba J, Rola M, Materniak M, Kuzmak J, Nowicki M. Isolation and characterization of caprine arthritis encephalitis virus in goats from Poland. Pol J Vet Sci. 2009;12:183-8 pubmed..5) and 10(2.5) TCID50 per ml. New CAEV isolates are suitable candidates for further analysis of their genetic and biological properties...
- Zdanowski M, Weglenski P, Golik P, Sasin J, Borsuk P, Zmuda M, et al. Bacterial diversity in Adélie penguin, Pygoscelis adeliae, guano: molecular and morpho-physiological approaches. FEMS Microbiol Ecol. 2004;50:163-73 pubmed publisher..The results indicate that the bacterial community in penguin guano is not only one of the richest in Antarctica, but is extremely diverse, both phylogenetically and morpho-physiologically...
- Sadowy E, Matynia B, Hryniewicz W. Population structure, virulence factors and resistance determinants of invasive, non-invasive and colonizing Streptococcus agalactiae in Poland. J Antimicrob Chemother. 2010;65:1907-14 pubmed publisher..Analysis of bacterial serotypes, alp genes and antimicrobial resistance determinants in the background of MLST-based population structure strengthened evidence of the importance of horizontal gene transfer in GBS evolution. ..
- Surmacz L, Swiezewska E. Polyisoprenoids - Secondary metabolites or physiologically important superlipids?. Biochem Biophys Res Commun. 2011;407:627-32 pubmed publisher..These discoveries highlighting the cellular significance of polyisoprenoids simultaneously establish the background for future pharmacological interventions. Our mini-review summarizes the results of recent studies on polyisoprenoids. ..
- Szawłowska U, Grabowska A, Zdunek Zastocka E, Bielawski W. TsPAP1 encodes a novel plant prolyl aminopeptidase whose expression is induced in response to suboptimal growth conditions. Biochem Biophys Res Commun. 2012;419:104-9 pubmed publisher..This paper is the first report describing changes in the transcript levels of any plant PAP in response to suboptimal growth conditions. ..
- Sarnowski T, Swiezewski S, Pawlikowska K, Kaczanowski S, Jerzmanowski A. AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time. Nucleic Acids Res. 2002;30:3412-21 pubmed..This interaction is through the C-terminal region of FCA, located outside the conserved RNA- and protein-binding domains of this protein. ..
- Bebas P, Kotwica J, Joachimiak E, Giebultowicz J. Yolk protein is expressed in the insect testis and interacts with sperm. BMC Dev Biol. 2008;8:64 pubmed publisher..It is produced in the testes and released into the seminal fluid where it interacts with sperm. These data reveal unexpected common factor in the maturation of insect eggs and sperm. ..
- Dudkiewicz M, Lenart A, Pawłowski K. A novel predicted calcium-regulated kinase family implicated in neurological disorders. PLoS ONE. 2013;8:e66427 pubmed publisher..Unusually high cysteine content and presence of signal peptides in some of the family members suggest that FAM69 proteins may be involved in phosphorylation of proteins in the secretory pathway and/or of extracellular proteins. ..
- 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. ..
- Mieczkowski P, Fikus M, Ciesla Z. Characterization of a novel DNA damage-inducible gene of Saccharomyces cerevisiae, DIN7, which is a structural homolog of the RAD2 and RAD27 DNA repair genes. Mol Gen Genet. 1997;253:655-65 pubmed..Surprisingly, a high basal level of DIN7 expression was found in strains in which the DUN1 gene was inactivated by transposon insertion. We suggest that a form of Dun1 may be a negative regulator of the DIN7 gene expression. ..
- Bartosik D, Szymanik M, Baj J. Identification and distribution of insertion sequences of Paracoccus solventivorans. Appl Environ Microbiol. 2003;69:7002-8 pubmed..Phylogenetic analysis of Tnps of the novel ISs and their closest relatives showed their evolutionary relationships and possible directions of lateral transfer between various bacterial hosts...
- Minczuk M, Lilpop J, Boros J, Stepien P. The 5' region of the human hSUV3 gene encoding mitochondrial DNA and RNA helicase: promoter characterization and alternative pre-mRNA splicing. Biochim Biophys Acta. 2005;1729:81-7 pubmed..Furthermore, we show that the 5' region of the hSUV3 pre-mRNA can be alternatively spliced. ..
- Rzepecka J, Lucius R, Doligalska M, Beck S, Rausch S, Hartmann S. Screening for immunomodulatory proteins of the intestinal parasitic nematode Heligmosomoides polygyrus. Parasite Immunol. 2006;28:463-72 pubmed..Single proteins of fraction 9 were analysed by mass spectrometry. These data suggest that antigens that are recognised by IgE antibodies might play an important role in immunomodulation exerted by nematode infections. ..
- Iwanicka Nowicka R, Zielak A, Cook A, Thomas M, Hryniewicz M. Regulation of sulfur assimilation pathways in Burkholderia cenocepacia: identification of transcription factors CysB and SsuR and their role in control of target genes. J Bacteriol. 2007;189:1675-88 pubmed..The phylogenetic relationships among members of the "CysB family" in the gamma and beta subphyla are presented. ..
- Kosinski J, Kubareva E, Bujnicki J. A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering. Proteins. 2007;68:324-36 pubmed..The model is in good agreement with the available experimental data and will serve as a template for further analyses of R.MvaI, R.BcnI, R.ScrFI and other related enzymes. ..
- Schneider G, Nieznanski K, Kilanczyk E, Bieganowski P, Kuznicki J, Filipek A. CacyBP/SIP interacts with tubulin in neuroblastoma NB2a cells and induces formation of globular tubulin assemblies. Biochim Biophys Acta. 2007;1773:1628-36 pubmed..Altogether, our results suggest that CacyBP/SIP, via its interaction with tubulin, might contribute to the differentiation of neuroblastoma NB2a cells. ..
- Lukasik A, Uniewicz K, Kulis M, Kozlowski P. Ciz1, a p21 cip1/Waf1-interacting zinc finger protein and DNA replication factor, is a novel molecular partner for human enhancer of rudimentary homolog. FEBS J. 2008;275:332-40 pubmed..When ERH and Ciz1 are coexpressed in HeLa cells, Ciz1 recruits ERH to DNA replication foci. ..
- Tabaka M, Cybulski O, Hołyst R. Accurate genetic switch in Escherichia coli: novel mechanism of regulation by co-repressor. J Mol Biol. 2008;377:1002-14 pubmed publisher..This genetic switch responds accurately to fast consumption of Trp from the interior of a cell. It switches with minimal dispersion when the concentration of Trp drops below a thousand molecules per cell. ..
- Kabzinska D, Saifi G, Drac H, Rowinska Marcinska K, Hausmanowa Petrusewicz I, Kochanski A, et al. Charcot-Marie-Tooth disease type 4C4 caused by a novel Pro153Leu substitution in the GDAP1 gene. Acta Myol. 2007;26:108-11 pubmed..Herein, a novel Pro153Leu mutation in the GDAP1 gene identified in a consanguineous Polish family is described and longitudinal clinical and electrophysiological studies as well as morphological findings are presented. ..
- Kokoszynska K, Ostrowski J, Rychlewski L, Wyrwicz L. The fold recognition of CP2 transcription factors gives new insights into the function and evolution of tumor suppressor protein p53. Cell Cycle. 2008;7:2907-15 pubmed..Finally, the identification of distant homologs of TP53 allowed performing a phylogenetic footprinting analysis explaining the role of the specific amino acids important for both - the protein folding and the binding of DNA. ..
- Tkaczuk K. Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site. J Mol Model. 2010;16:599-606 pubmed publisher..A molecular model of the Trm13p structure has been constructed and evaluated for potential accuracy using model quality assessment methods. The predicted structure will facilitate experimental analyses of the Trm13p mechanism of action. ..
- Naskalska A, Szolajska E, Chaperot L, Angel J, Plumas J, Chroboczek J. Influenza recombinant vaccine: matrix protein M1 on the platform of the adenovirus dodecahedron. Vaccine. 2009;27:7385-93 pubmed publisher..These results show that proposed vaccine model is feasible and that adenovirus dodecahedron is a potent delivery platform for foreign antigens to human cells. ..
- 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...
- Steczkiewicz K, Zimmermann M, Kurcinski M, Lewis B, Dobbs D, Kloczkowski A, et al. Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step. Proc Natl Acad Sci U S A. 2011;108:9443-8 pubmed publisher..This first structural model of the human telomerase enzyme provides many details of the molecular mechanism of telomerase and immediately provides an important target for rational drug design. ..
- Dziewit L, Kuczkowska K, Adamczuk M, Radlinska M, Bartosik D. Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686. FEMS Microbiol Lett. 2011;324:56-63 pubmed publisher..This indicates the crucial role of the analyzed R-M system in the stable maintenance of pAMI7, which is, to our knowledge, the first report of 'symbiosis' between a R-M system and a plasmid in the Alphaproteobacteria...
- Ciok A, Dziewit L, Grzesiak J, Budzik K, Górniak D, Zdanowski M, et al. Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax. FEMS Microbiol Ecol. 2016;92:fiw043 pubmed publisher..The miniature plasmids share no similarity with known sequences present in the databases. In silico and experimental analyses identified conserved DNA regions essential for the initiation of replication of these replicons. ..
- Gora Sochacka A, Kierzek A, Candresse T, Zagorski W. The genetic stability of potato spindle tuber viroid (PSTVd) molecular variants. RNA. 1997;3:68-74 pubmed..Although it has been observed previously that artificially mutated PSTVd molecules may revert rapidly to the wild-type sequence, this study presents direct evidence for the rapid evolution of naturally occurring PSTVd sequence variants. ..
- Boguta M, Czerska K, Zoładek T. Mutation in a new gene MAF1 affects tRNA suppressor efficiency in Saccharomyces cerevisiae. Gene. 1997;185:291-6 pubmed..Maf1p may play a role in the tRNA biosynthetic pathway since a fragment of the RPO31/RPC160 gene encoding the largest subunit of RNA polymerase III was cloned as a multicopy suppressor of mafl-1. ..
- 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. ..
- 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
- Bujnicki J, Rychlewski L. Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs. Acta Microbiol Pol. 2000;49:253-60 pubmed..The N-terminal region of YgdE, which has no counterpart in RrmJ, is predicted to form an independent domain, possibly involved in target recognition. ..
- Bujnicki J, Feder M, Radlinska M, Rychlewski L. mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinformatics. 2001;2:2 pubmed
- Dobrzanska M, Szurmak B, Wyslouch Cieszynska A, Kraszewska E. Cloning and characterization of the first member of the Nudix family from Arabidopsis thaliana. J Biol Chem. 2002;277:50482-6 pubmed..The recombinant AtNUDT1 migrated as a dimer on a gel filtration column. Biochemical analysis of recombinant AtNUDT1 indicated that the first characterized member of the Nudix family from A. thaliana is a NADH pyrophosphatase. ..
- Grynberg M, Jaroszewski L, Godzik A. Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. BMC Bioinformatics. 2003;4:46 pubmed..Distant homology searches allowed the identification of unknown regions of cofactors as self-reliant domains and allow us to present a detailed hypothesis of how a cofactor complex performs its function. ..
- 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. ..
- Leśniak W, Szczepańska A, Kuznicki J. Calcyclin (S100A6) expression is stimulated by agents evoking oxidative stress via the antioxidant response element. Biochim Biophys Acta. 2005;1744:29-37 pubmed..The results indicate that agents evoking oxidative stress activate calcyclin gene via the ARE sequence in its promoter. ..
- Dominik M, Kłopocka W, Pomorski P, Kocik E, Redowicz M. Characterization of Amoeba proteus myosin VI immunoanalog. Cell Motil Cytoskeleton. 2005;61:172-88 pubmed..These results indicate that myosin VI immunoanalog is expressed in protist Amoeba proteus and may be involved in vesicle translocation and cell locomotion...
- 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...
- Kulinska A, Czeredys M, Hayes F, Jagura Burdzy G. Genomic and functional characterization of the modular broad-host-range RA3 plasmid, the archetype of the IncU group. Appl Environ Microbiol. 2008;74:4119-32 pubmed publisher..The putative conjugative-transfer module is highly similar in organization and in its products to transfer regions of certain broad-host-range environmental plasmids. ..
- Tomecki R, Kristiansen M, Lykke Andersen S, Chlebowski A, Larsen K, Szczesny R, et al. The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L. EMBO J. 2010;29:2342-57 pubmed publisher..Both hDIS3 and hDIS3L are active exonucleases; however, only hDIS3 has retained endonucleolytic activity. Our data suggest that three different ribonucleases can serve as catalytic subunits for the exosome in human cells. ..
- Mikula M, Gaj P, Dzwonek K, Rubel T, Karczmarski J, Paziewska A, et al. Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter. DNA Res. 2010;17:245-60 pubmed publisher..Our strategy of diverse approaches facilitated the direct characterization of various molecular properties of HNRNPK promoter bearing the palindromic motif TCTCGCGAGA, despite the obstacles that accompany in vitro methods. ..
- Sokolowska M, Czapinska H, Bochtler M. Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis. Nucleic Acids Res. 2011;39:1554-64 pubmed publisher..Taken together, our data reveal striking analogy in the absence of homology between GIY-YIG and ???-Me nucleases. ..
- Górecki R, Koryszewska Bagińska A, Gołebiewski M, Zylińska J, Grynberg M, Bardowski J. Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids. PLoS ONE. 2011;6:e22238 pubmed publisher..g. genes encoding citrate and lactose utilization, oligopeptide transport, restriction-modification system). Moreover, global gene analysis indicated cooperation between plasmid- and chromosome-encoded metabolic pathways. ..
- Drozdz M, Piekarowicz A, Bujnicki J, Radlinska M. Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res. 2012;40:2119-30 pubmed publisher..Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine methylation. ..
- Wolinowska R, Cegłowski P, Kok J, Venema G. Isolation, sequence and expression in Escherichia coli, Bacillus subtilis and Lactococcus lactis of the DNase (streptodornase)-encoding gene from Streptococcus equisimilis H46A. Gene. 1991;106:115-9 pubmed..The sdc gene was expressed in E. coli, Bacillus subtilis and Lactococcus lactis. As observed for S. equisimilis, in the heterologous Gram + hosts, at least part of the SDC protein was secreted into the medium. ..
- 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...
- Grzela R, Strokovska L, Andrieu J, Dublet B, Zagorski W, Chroboczek J. Potyvirus terminal protein VPg, effector of host eukaryotic initiation factor eIF4E. Biochimie. 2006;88:887-96 pubmed
- Kwiatkowska K. One lipid, multiple functions: how various pools of PI(4,5)P(2) are created in the plasma membrane. Cell Mol Life Sci. 2010;67:3927-46 pubmed publisher..In addition, PI(4,5)P(2) can accumulate at sphingolipid/cholesterol-based rafts following activation of distinct membrane receptors or be sequestered in a reversible manner due to electrostatic constrains posed by proteins like MARCKS. ..
- Babenko V, Dzwolak W. Amino acid sequence determinants in self-assembly of insulin chiral amyloid superstructures: role of C-terminus of B-chain in association of fibrils. FEBS Lett. 2013;587:625-30 pubmed publisher..Our study suggests that insulin's dimer-forming interface--specifically the B-chain's C-terminal fragment--may acquire the new role of a molecular velcro upon lateral alignment of individual fibrils into superstructures. ..
- Kucharczyk R, Zagulski M, Rytka J, Herbert C. The yeast gene YJR025c encodes a 3-hydroxyanthranilic acid dioxygenase and is involved in nicotinic acid biosynthesis. FEBS Lett. 1998;424:127-30 pubmed..As YJR025c encodes the yeast 3-hydroxyanthranilic acid dioxygenase, we have named this gene BNA1 for biosynthesis of nicotinic acid. ..