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Department of Microbial Biochemistry

 

Research activity of the Department includes the following topics:

  1. Physiological, biochemical and genomic analyses of Lactococcus lactis focused on: regulation of lactose and beta-glucosides catabolism, characterization of a plasmidic gene pools, identification and characterization of bacteriophages infecting L. lactis and identification of antibiotic resistance mechanisms in lactic acid bacteria
    (PI prof. J. Bardowski).
  2. Postgenomic analyses of broad-host range plasmids, in particular - functional characterization of replication, stable maintenance mechanisms, conjugation systems and regulatory network integrating plasmid functions
    (PI G. prof. Jagura-Burdzy and PI dr. I. Kern-Zdanowicz).
  3. Mechanisms governing segregation of bacterial chromosomes focused on characterization of the role of Par proteins and their cellular counterparts in the opportunistic pathogen Pseudomonas aeruginosa (PI prof. G. Jagura Burdzy).
  4. Structural and functional genomics of bacteriophages, biology of host-phage interactions, mechanisms of active partition of plasmid-prophages (PI assoc. prof. M. Łobocka).
  5. Genetics, biochemistry and regulation of bacterial sulfur assimilation process, in particular molecular mechanisms governing transcriptional control of genes involved in this process in E. coli and Burkholderia cenocepacia
    (PI  prof. M. Hryniewicz).
  6. Structure and microorganic biodiversity of biofilms naturally occurring in arsenic-polluted environments (PI dr. U. Zielenkiewicz). 

 

Functional analysis of genes from selected plasmids originating from bacteria of clinical importance

Group leader: Dr. Izabela Kern-Zdanowicz
Staff: Dr. Michał Dmowski

 

Our work is focused on the functional analysis of genes from plasmids found in clinical isolates (T27).

Plasmid pSM19035 (ca. 29kb), isolated from Streptococcus pyogenes confers erythromycine resistance (ermB) and replicates in Gram-positive bacteria which have low G+C content in the chromosomal DNA. It occurs in 5-8 copies per cell. Plasmid pSM19035 is stably maintained in bacterial population. The better than random plasmid segregation to daughter cells is ensured by the active partition (genes δ and ω) and postesegregational killing (genes ω-ε-ζ) systems studied in our group. Their genetic organization differ from similar systems characterized so far.

We are also interested in plasmids isolated from bacteria of family Enterobacteriaceae of clinical origin. Up till now we have determined the nucleotide sequence of two plasmids: pCTX-M-3 (Acc. No. AF550415) and p1658/97 (Acc. No. AF550679).

Plasmid pCTX-M3 (89kb) isolated from Citrobacter freundii can replicated in the broad range of hosts (IncL/M group). It is responsible for dissemination of the blaCTX-M-3, the gene coding for CTX-M-3, the most common in Poland variant of an extended spectrum β-lactamase (ESBL). This plasmid also harbors the very efficient conjugal system.

Plasmid p1658/97 (125kb) was isolated from Escherichia coli clinical strain; it possesses two replicons IncFII and IncFIB, and bears a gene encoding ESBL SHV-5 type as well as the resistances for practically all therapeutically used aminoglycoside antibiotics. The plasmid region of 8.8kb in size, bordered by two IS26 copies covering also blaSHV-5 gene, undergoes multiplication even up to 11 copies. This results in increased β-lactam resistance of the plasmid host.

Other plasmids interesting for us have been chosen after screening of Enterobacteriaceae strain collection gathered in the National Institute of Medicines (Warsaw) - we look for replicons of new types, correlated with dissemination of β-lactamase genes in the clinical environment.

 

Research grants:
2009-2012 "Functional analysis of centromeric regions and the host range of the partition system of pSM19035 plasmid
                  from Steptococcus pyogenes", (Ministry of Science and Higher Education)
2007-2010 "Mobile genetic elements in bacteria- molecular analysis and tools construction applied in biotechnology",
                 (Ministry of Science and Higher Education)
2007-2008 "Molecular analysis of interactions of Delta and Omega, the partition proteins from the streptococcal plasmid
                  pSM19035", (Ministry of Science and Higher Education)

 

Selected publications:

  1. Baraniak A., Izdebski R., Herda M., Fiett J., Hryniewicz W., Gniadkowski M., Kern-Zdanowicz I., Filczak K., Łopaciuk U., 2009. Emergence of Klebsiella pneumoniae ST258 with KPC-2 in Poland. Antimicrob Agents Chemother., 53:4565-4567.
  2. Hrabák J., Empel J., Bergerová T., Fajfrlík K., Urbásková P., Kern-Zdanowicz I., Hryniewicz W., Gniadkowski M., 2009. International clones of Klebsiella pneumoniae and Escherichia coli with extended-spectrum beta-lactamases in a Czech hospital. J Clin Microbiol., 47:3353-3357.
  3. Gołębiewski M., Kern-Zdanowicz I., Zienkiewicz M., Adamczyk M., Żylińska J., Baraniak A., Gniadkowski M., Bardowski J.and Cegłowski P. 2007. Complete nucleotide sequence of the pCTX-M3 plasmid and its involvement in spread of the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-3. Antimicrob. Agents Chemother. 51: 3789-3795.
  4. Zienkiewicz M., Kern-Zdanowicz I., Gołębiewski M., Żylińska J., Mieczkowski P., Gniadkowski M., Bardowski J. and Cegłowski P. 2007. Mosaic structure of p1658/97, a 125- kilobase plasmid harbouring an active amplicon with the extended-spectrum β-lactamase gene blaSHV-5. Antimicrob. Agents Chemother. 51:1164-1171.
  5. Livermore D.M., Canton R., Gniadkowski M., Nordmann P., Rossolini G.M., Arlet G., Ayala J., Coque T.M., Kern-Zdanowicz I., Luzzaro F., Poirel L., Woodford N. 2007. CTX-M: changing the face of ESBLs in Europe. J Antimicrob Chemother. 59:165-74.
  6. Dmowski M., Sitkiewicz I., Ceglowski P., 2006. Characterization of a novel partition system encoded by the delta and omega genes from the streptococcal plasmid pSM19035. J Bacteriol. 188:4362-72.
  7. Nowakowska B., Kern-Zdanowicz I., Zielenkiewicz U. and Cegłowski P. 2005. Characterization of Bacillus subtilis clones surviving overproduction of Zeta, a pSM19035 plasmid-encoded toxin. Acta Biochim. Polon., 52: 99–107. 

Mechanisms of active segregation of low copy number P1 plasmid to daughter cells at cell division

Group leader: Assoc. Prof. Małgorzata Łobocka
Staff: Dr. Agnieszka Gozdek, Dr. Monika Hejnowicz, Dr. Jarosław Kosakowski, M.Sc. Kamil Dąbrowski, M.Sc. Małgorzata Kołacz, M.Sc. Patrycja Litwicka, M.Sc. Katarzyna Poławska, M.Sc. Magdalena Ulatowska, M.Sc. Magdalena Witkowska

 

P1 is a temperate bacteriophage. In lysogens, it is maintained as a large unit copy plasmid which is stably inherited. Active segregation (partition) of P1 copies at cell division depends on two P1 proteins, ParA and ParB. They mediate translocation of newly replicated plasmids from the center of the mother cell to the centers of future daughters. A cis-acting site in P1 DNA, parS, serves as a handle for plasmid DNA in these interactions. It binds ParB protein and facilitates ParB spreading along flanking DNA, but it is unclear to what extent this spreading contributes to partitioning. ParA is a Walker-type ATPase that is required for the proper positioning of plasmids in partition. We used sources of independently regulated par genes and fusions of Par proteins with fluorescent proteins to study P1 partition reactions. Partitioning of mini-P1 (parS+) plasmid occurred efficiently only at a certain ratio of ParB to ParA. Differential expression of partition genes depended on transcription of parB from internal par promoters in the parA gene. ParA-Egfp, at concentrations permissive for partitioning, translocated within the nucleoid region and could form helical filaments, independently of ParB and parS. ParB-Gfp was also associated with the nucleoid region but its localization in this region depended on ParA, both in the presence and in the absence of parS. Localization of mutant ParB-Gfp proteins that have the decreased ability to bind parS-flanking DNA was only slightly influenced by ParA. These results suggest that the ParA-mediated translocation of mini-P1-ParB complexes depends on ParB molecules bound to parS as well as ParB molecules bound to parS-flanking DNA of P1.

Bacteriophage biology and applications

Bacterial viruses (bacteriophages) are the most abundant, most diversified and the most dynamically evolving group of "organisms" on earth.  They infect only bacteria and are harmless to eukaryotic cells.  Obligatory virulent phages can develop in bacteria only lytically, leading to cell death and the release of phage progeny. Temperate phages can also exist in cells in the form of chromosomally integrated DNA or of plasmids. They may encode adaptative functions that help their hosts to invade new environments. Over 95% of phages have virions that consist of a head and a tail, and hence are called tailed phages. Their diversity is remarkable. Sizes of their genomes range from under 20 to about 700 kb, and hence the huge differences in the number of encoded functions. Studies on selected model phages of different life-styles and specifities can help to understand these functions.

P1 and P7 are temperate phages of large genomes that infect enteric bacteria. They lysogenize cells as unit-copy plasmids and in their genomes they contain several conserved plasmid-specific genes.  A complex regulatory system controls lysis/lysogeny decision and a switch to lytic development in lysogens. We determined the complete DNA sequences of P1 and P7 and analysed their genomes in a search for functions that could be responsible for a relatively wide host range of these phages. Contribution of multiple lytic genes of P1 and P7 to phage specificity is currently under study.

A5W is an obligatory virulent phage that belongs to the order Caudovirales (tailed phages). Its virion consists of a head and a tail which contains a contractile sheath. A5W infects cells of different Staphylococcal strains and is used at the Ludwik Hirszfeld Institute of Immunology and Experimental Therapy in Wrocław for phage therapy studies. Within a collaborative project of Bacteriophage Biology and Biotechnology Network we determined the genomic sequence of A5W (GenBank acc. no. EU418428) and identified functions of selected A5W genes. Functional analysis of A5W genes encoding lytic and proteolytic functions is in progress.

 

More information: http://fagoland.ibb.waw.pl:8080/Phagen/english

 

Research grants:
2009-2012 "Optimization of characteristic and production of phage preparations for therapeutic purposes ",
                 (POIG Ministry of Science and Higher Education)

2007-2010 "Bacterial mobile genetic elements - molecular analysis and employment for construction of tools for
                  the biotechnological industry" (Ministry of Science and Higher Education)

2006-2008 "Bacteriophage Biology and Biotechnology" (Ministry of Science and Higher Education)

 

Selected publications:

  1. Górski, A., Międzybrodzki, R., Borysowski J., Weber-Dąbrowska, B., Łobocka, M., Letkiewicz, S., Zimecki, M., Filby, G. Bacteriophage therapy for the treatment of infections. Curr. Opin. Investig. Drugs (2009) 10: 766-774.
  2. Łobocka, M. B., Rose, D.J., Plunkett, 3rd, G., Rusin, M., Samojedny, A., Lehnherr, H., Yarmolinsky, M. B., Blattner, F. R. Genome of bacteriophage P1. J. Bacteriol. (2004) 186: 7032-7068.
  3. Grigoriev, P. S., Łobocka, M. B. Determinants of segregational stability of the linear plasmid prophage N15 of Escherichia coli. Mol. Microbiol. (2001) 42: 355-368.
  4. Rodionov, O., Łobocka, M., Yarmolinsky, M. Silencing of genes flanking the P1 plasmid centromere. Science (1999) 283: 546-549.

Group leader: Prof. Grażyna Jagura-Burdzy
Staff: Dr. Aneta Bartosik, Dr. Anna Kulińska, Dr. Jolanta Mierzejewska, M.Sc. Krzysztof Głąbski (Ph.D. student), M.Sc. Magda Kusiak (Ph.D. student), M.Sc. Jolanta Szarlak (Ph.D. student), M.Sc. Marta Warsińska (Ph.D. student), Aleksandra Markowska (research technician)

 

The group is interested in two somehow related topics.

  1. Postgenomic analysis of broad-host range conjugative plasmids, in particular - characterization of stable maintenance mechanisms and regulatory network integrating plasmid functions
    Our studies on broad-host-range IncP-1 plasmids demonstrated the existence of extremely complicated regulatory network controlling their replication, stability mechanisms and conjugation system. It was postulated that multivalent regulatory network with multiple repressors (global and specialized) and overlapping regulons is mainly responsible for extremely adaptive nature of these group of plasmids. Recently we demonstrated that conjugative RA3 plasmid of IncU group (isolated from the fish pathogen Aeromonas hydrophila) also represents very broad host range (α-, β-, γ-proteobacteria). Sequencing of its genome (45.9 kb, DQ401103) initiated post-genomic analysis of replication, partitioning, conjugation and regulatory systems of RA3 plasmid. Promiscuous replication, stability and conjugation mechanisms are coordinated by the simple regulatory network (in contrary to IncP-1 plasmids) that also seems to provide a “switch” between horizontal transfer and vertical inheritance functions.
  2. Mechanisms governing segregation (partition) of bacterial chromosomes, molecular characterization of Par proteins and identification of their cellular partners
    Our previous studies demonstrated the important role ParA and ParB proteins (homologues of low-copy-number plasmid partitioning proteins) play in chromosome segregation of Pseudomonas aeruginosa, facultative pathogen of immuno-suppressed patients. Par proteins also participate in other cell processes in P. aeruginosa like growth, cell division and motilities required to form biofilms. Proteomic analysis (2D gels and iTRAQ) confirmed pleiotropic character of par mutants of P. aeruginosa. The complex phenotype of deficiency or excess of Par proteins is presumably due to the interactions of Par proteins with various cell components.

Current projects:

  1. Search for counterparts of ParA and ParB proteins in proteome of P. aeruginosa.
    Different approaches are undertaken. Firstly, the library of Pseudomonas genes is constructed to screen for interactions with Par proteins by use of bacterial two-hybrid system BACTH. Secondly, co-purification with Par proteins on affinity columns as well as cross-linking with formaldehyde in vivo and immunoprecipitation with the use of anti-ParB/anti-ParA antibodies are applied. Thirdly, the selected putative counterparts will be analyzed in vitro for interactions with Par proteins and in vivo for their role in chromosome partitioning, cell motilities and defects in the cell growth and division
  2. Post-genomic analysis of broad-host-range RA3 plasmid from IncU group.
    Dissection of replication and stabilization systems will be continued. Molecular analysis of the replication system reveals the regulatory circuit combined of autorepression by protein products and antisense RNA. Extremely stable minireplicon of RA3 (3.4 kb) has been genetically modified to become a perfect tool for biotechnology needs: low-copy number, stably inherited, broad-host-range vector. The analysis of conjugation mechanisms has been initiated. The interlocking regulatory circuits will be analyzed at the level of the whole plasmid. Biotechnological application of the vector and its functional cassettes (replication, stabilization and conjugation modules) will be exploited.
  3. Analysis of new plasmid replicons from clinical Pseudomonas strains.
    Screening of the collections of clinical Pseudomonas strains will be continued. The search for new replicons and stabilization cassettes has been initiated. The replicons applicable for biotechnology will be sequenced and studied in details.

Research projects:
2008-2011 "Chromosome segregation in Pseudomonas aeruginosa - the role of ParA, ParB and selected host proteins
                   in this process", (Ministry of Science and Higher Education)

2007-2010 "Mobile genetic elements in bacteria- molecular analysis and tools construction applied in biotechnology",
                  (Ministry of Science and Higher Education)

2007-2009 "Search for counterparts of ParA and ParB proteins in Pseudomonas aeruginosa", (Ministry of Science
                   and Higher Education)


Selected publications:

  1. Bartosik, A. A., Mierzejewska J., Thomas, C.M. and Jagura-Burdzy, G. 2009. ParB deficiency in Pseudomonas aeruginosa destabilises ParA partner and affects a variety of physiological parameters. Microbiology, 155: 1080-1092.
  2. Kulińska A., Czeredys M., Hayes F. and Jagura-Burdzy G. 2008. Genomic and functional characterization of the modular broad-host-range RA3 plasmid, the archetype of the IncU group. Appl. Environ. Microbiol. 74:4119-32.
  3. Lasocki K., Bartosik A.A., Mierzejewska J., Thomas C.M., Jagura-Burdzy G. 2007. Deletion of the parA (soj) homologue in Pseudomonas aeruginosa causes ParB instability and affects growth rate, chromosome segregation, and motility. J. Bacteriol. 189:5762-72.
  4. Mierzejewska J., Kulińska A. and Jagura-Burdzy G. 2007. Functional analysis of replication and stability regions of broad-host-range conjugative plasmid CTX-M3 from the IncL/M incompatibility group. Plasmid 57:95-107.
  5. Adamczyk M., Dolowy P., Jonczyk M., Thomas C.M. and Jagura-Burdzy, G. 2006. The kfrA gene is the first in a tricistronic operon required for survival of IncP-1 plasmid R751. Microbiology 152: 1621-1637.
  6. Bartosik, A.A. and Jagura-Burdzy, G. (2005) Bacterial chromosome segregation. Acta Biochimica Polonica, 52, 1-34
  7. Bartosik A.A., Lasocki K., Mierzejewska J., Thomas C.M.and Jagura-Burdzy G. (2004) ParB of Pseudomonas aeruginosa: interactions with its partner ParA, its target parS and specific effects on bacterial growth. J. Bacteriol. 186, 6983-6998 

Group leader: Assoc. Prof. Jacek Bardowski
Staff:
Post-doctoral Researchers:
Dr. Tamara Aleksandrzak-Piekarczyk (Ph.D. Biochemistry), Dr. Magdalena Kowalczyk (Ph.D. Biochemistry), Dr. Agnieszka Szczepańska (Ph.D. Biochemistry), Dr. Katarzyna Szatraj (Ph.D. Veterinary Medicine)
Ph.D. students:
Roman Krzysztof Górecki (MSc Biotechnology), Anna Koryszewska-Bagińska (MSc Biotechnology), Joanna Życka-Krzesińska (MSc Microbiology), Wiktoria Łabudzka (MSc Biology)
Research Assistants:
Joanna Żylińska (MSc Food Technology)

 

Our group is currently doing research on lactic acid bacteria (LAB) with the main focus on lactococci and on such topics like: sugar catabolism, plasmidic gene pool in survival of different stresses, biology of bacteriophages, LAB as producers of heterologous proteins of biotechnological interest and biological diversity of natural bacterial strains and bacteriophages.

In respect to sugar catabolism, we investigate molecular mechanisms of coupling of lactose and β-glucoside catabolism in Lactococcus lactis. This work led us to discover the role of the CcpA protein in lactose metabolism induced by cellobiose, which is a plant sugar.

We are also interested in enzymatic potential of Lactococcus lactis to degrade starch, which is one of the most abundant carbon and energy sources in nature. Among strains from our own collection (natural isolates) a few demonstrating amylolytic features were identified and one of them was further characterized showing that the amylolytic enzyme is secreted to the medium, is plasmid encoded and its biosynthesis is regulated by glucose repression. DNA sequencing of the plasmid showed that the amylolytic enzyme is homologous to a pullulanase and is located in a gene-adaptation cassette.

Another branch of our research deals with biological diversity of natural bacterial strains and bacteriophages. We isolated a number of wild type strains from their natural environment, that is samples of milk collected at farms and part of them was already identified and characterized with RAPD method.

We explore technological, microbiological, nutritional and health-promoting functions of complex and mixed microbial populations in kefir grains and traditional Polish cheese - Oscypek by using physiological, biochemical, genetic and bioinformatic research tools.

Plasmid DNA isolation, analysis and sequencing approach was applied to characterize the lactococcal plasmidic gene pool important for environmental adaptation, as well as for plasmid evolution. Restriction enzyme analysis and PCR techniques are being used for molecular characterization of isolated bacteriophages. Bacteriocins, anti-bacterial substances produced by lactococci, were also a subject of our research, some years ago, and have become our new interest. Lastly, we became involved in research on probiotics.

 

Current projects:

  • Identification of the ccpA regulatory gene and demonstration of its role in the catabolism of lactose and β-glucosides in L. lactis;
  • Demonstration of the role of  CelB protein in the catabolism of lactose and cellobiose in L. lactis;
  • Demonstration of an amylolytic potential of L. lactis and molecular characterisation of the gene coding for pullulanase;
  • Complete nucleotide sequence of the bacteriophage bIBB29 genome;
  • Molecular characterization of  7 plasmids of L. lactis IL594

 

Research grants:

2008-2011 „Center of Biotechnology of therapeutics. A package of innovative biopharmaceutics for therapy and
                 prophylaxes of humans and animals”, (POIG Ministry of Science and Higher Education),

2007-2010 „Mobile genetic elements in bacteria - molecular analysis and tools construction applied in biotechnology”,
                 (Ministry of Science and Higher Education),

2007-2010 „Identification of metabolic systems encoded on 7 plasmids in Lactococcus lactis IL594”,
                (Ministry of Science and Higher Education),

2007-2010 „Searching for the influence of the inactivation of ccpA and yebF regulatory genes and acquisition of genes
                 localized on pIL7 plasmid on the metabolism of Lactococcus lactis in proteomic approach”,
                 (Ministry of Science and Higher Education),

2007-2010 „Application of lactic acid bacteria as bioreactors for synthesis of neuropeptides and induction of oral tolerance
                 in rats with EAE”, (Ministry of Science and Higher Education),

2008-2009 „Functional characterization of restriction and modification systems encoded by plasmidic genes in Lactococcus
                 lactis
IL594(Ministry of Science and Higher Education),

2007-2009 „Identification and characterization of proteins participating in adsorption of bacteriophage bIBB29 to
                 Lactococcus lactis bacteria”, (Ministry of Science and Higher Education),

2006-2009 „Anti-Campylobacter immunoprofilaxis – identification of new antigens, potential candidates for vaccine
                 construction and analysis of their efficiency in modulating the mucosal immune system”, 
                 (Ministry of Science and Higher Education),

2006-2009 „Identification of biodiversity of genes, proteins and antibiotic substances produced by kefir grains”,
                 (Ministry of Science and Higher Education),

2006-2008 "Bacteriophage Biology and Biotechnology Network", (Ministry of Science and Higher Education),

2005-2008 „Functional analysis of ccpA and yebF regulatory genes and identification of other genes engaged in lactose
                 and β-glucosides catabolism in Lactococcus lactis”,  (Ministry of Science and Higher Education),

2006-2008 „Express Fingerprints – Expression profiles as fingerprints for the safety evaluation of new strains, including
                 GMOs used in bioprocessed food”;  EU 6FP (Ministry of Science and Higher Education),

2004-2006 FOOD 2002 – AREA 5.4.6- (T28) “Assessment and Critical Evaluation of Antibiotic Resistance Transferability
                 in Food Chain”, Proposal 506214 (ACE-ART), EU 6FP

2002-2005 „Identification and molecular characterisation of Lactococcus lactis bacteriophages in Polish dairy environment”;
                 (Ministry of Science and Higher Education),

 

Selected publications:

  1. Bogusławska D.M., Życka-Krzesińska J., Wilcks A., Bardowski J.K. Intra- and interspecies conjugal transfer of Tn916-like elements from Lactococcus lactis in vitro and in vivo. Appl. Environ. Microbiol. (2009) 75: 6352-6360
  2. Hejnowicz M.S., Gołębiewski M., Bardowski J. Analysis of the complete genome sequence of the lactococcal bacteriophage bIBB29. Int. J. Food Microbiol. (2009) 131: 52-61
  3. Domig K.J., Mayrhofer S., Huys G., Tosi L., Danielsen M., Mayo B., Axelsson L., Korhonen J.M., Egervärn M., Bardowski J.K., Saarela M., Morelli L., Kneifel W. The ace-art database – antibiotic susceptibility of lactic acid bacteria and bifidobacteria in relation to their biological, geographical and chronological origin. International Journal of Probiotic and Prebiotics (2008) 3: 281-286
  4. Hoek van A.H.A.M., Margolles A., Domig K.J., Korhonen J.M., Życka-Krzesińska J., Bardowski J.K., Danielsen M., Huys G.,  Morelli L., Aarts H.J.M. Molecular assessment of erythromycin and tetracycline antibiotic resistance genes in lactic acid bacteria and bifidobacteria and their relation to the observed resistance. International Journal of Probiotic and Prebiotics (2008) 3: 271-280
  5. Flórez A.B., Tosi L., Danielsen M., von Wright A., Bardowski J., Morelli L., Mayo B. Resitance-susceptibility profiles of Lactococcus lactis and Streptococcus thermophilus strains to eight antibiotics and proposition of new cut-offs. International Journal of Probiotic and Prebiotics (2008) 3: 249-256
  6. JankowskaA., Wrzesinski M., Laubitz D., Kazimierczak W., Skrzypek H., Bardowski J., Zabielski R., Grzesiuk E. Intestinal MMC-related electric fields and pancreatic juice control the adhesion of Gram-positive and Gram-negative bacteria to the gut epithelium - in vitro study. J. Physiol. Pharmacol. (2008) 59: 795-810
  7. Lampkowska J., Feld L., Monaghan A., Toomey N., Schjørring S., Jacobsen B., van der Voet H., Andersen S.R., Bolton D., Aarts H., Krogfelt K.A., Wilcks A., Bardowski J. A standardized conjugation protocol to assess antibiotic resistance transfer between lactococcal species. Int J Food Microbiol. (2008) 127(1-2): 172-5
  8. Kowalczyk M., Cocaign-Bousquet M., Loubiere P., Bardowski J. Identification and Functional Characterization of Cellobiose and Lactose Transport Systems in Lactococcus lactis IL1403. Arch Microbiol. (2008) 189(3): 187-96
  9. Golebiewski M., Kern-Zdanowicz I., Zienkiewicz M., Adamczyk M., Zylinska J., Baraniak A., Gniadkowski M., Bardowski J., Ceglowski P. Complete nucleotide sequence of the pCTX-M3 plasmid and its involvement in spread of the extended-spectrum {beta}-lactamase (ESBL) gene blaCTX-M-3. Antimicrob Agents Chemother. (2007) 13:
  10. Florez A.B., Danielsen M., Korhonen J., Zycka J., von Wright A., Bardowski J., Mayo B. Antibiotic survey of Lactococcus lactis strains to six antibiotics by Etest, and establishment of new susceptibility-resistance cut-off values. J. Dairy Res. (2007) 30: 1-7
  11. Kowalczyk M., Bardowski J. Regulation of sugar catabolism in Lactococcus lactis. Critical Reviews in Microbiology (2007) 33: 1–13
  12. Loll B., Kowalczyk M., Alings C., Chieduch A., Bardowski J., Saenger W., Biesiadka J. Crystal structure of transcription regulator CcpA of Lactococcus lactis. Acta Crystallographica Section D (2007) 63: 431-436
  13. Kowalczyk M., Borcz B., Płochocka D., Bardowski J. Specific and unspecific binding of CcpA from Lactococcus lactis IL1403. Acta Biochimica Polonica (2007) 54: 71-78
  14. Szczepańska A., Bidnenko E., Płochocka D., McGovern S., Ehrlich S.D., Bardowski J., Polard P., Chopin M.-C. A distinct single-stranded DNA-binding protein encoded by the Lactococcus lactis bacteriophage bIL67. Virology (2007) 363: 104-112
  15. Szczepańska A., Hejnowicz M., Bardowski J. Biodiversity of Lactococcus lactis bacteriophages in Polish dairy environment. Acta Biochim. Polon. (2007) 54: 151-158
  16. Zienkiewicz M., Kern-Zdanowicz I., Golebiewski M., Zylinska J., Mieczkowski P., Gniadkowski M., Bardowski J., Ceglowski P. Mosaic structure of p1658/97, a 125-kilobase plasmid harbouring an active amplicon with the extended-spectrum {beta}-lactamase gene blaSHV-5. Antimicrob Agents Chemother. (2007) 51: 1164-1171
  17. Aleksandrzak-Piekarczyk T., Kok J., Renault P., Bardowski J. Alternative Lactose Catabolic Pathway in Lactococcus lactis IL1403. Appl. Environ. Microbiol. (2005) 71: 6060-6069
  18. Hejnowicz M.S., Bardowski J. Phage infections of mesophilic bacterial strains from the genus of Lactococcus in dairy industry. (in polish). Przegląd Mleczarski (2005) 7:4-7
  19. Doman-Pytka M., Bardowski J. Pullulan degrading enzymes of bacterial origin. Critical Reviews in Microbiology (2004) 30(2): 107-121
  20. Doman-Pytka M., Renault P., Bardowski J. Gene-cassette for adaptation of Lactococcus lactis to plant environment. Lait (2004) 84: 33-37
  21. Kowalczyk M., Bardowski J. Overproduction and purification of the CcpA protein from Lactococcus lactis. Acta Biochimica Polonica (2003) 50: 455-459
  22. Chopin A., Bardowski J., Raya R., Ehrlich S.D. La régulation génétique dans Lactococcus lactis: le modčle de la biosynthčse du tryptophane. Le Lait (1993) 73: 119‑126
  23. Godon J.‑J., Delorme C., Bardowski J., Chopin M.-C., Ehrlich S.D., Renault P. Gene inactivation in Lactococcus lactis: Branched‑chain amino acid biosynthesis. J. Bacteriol. (1993) 175: 4383‑4390
  24. Raya R.R., Bardowski J., Ehrlich S.D., Chopin A. Transcription of the trp biosythetic genes in Lactococcus lactis subsp. lactis. FEMS Microbiol. Rev. (1993) 12: P30
  25. Bardowski J., Ehrlich S.D., Chopin A. A regulatory protein in Lactococcus lactis subsp. lactis belongs to the BglG family of RNA‑binding transcription antiterminators. FEMS Microbiol. Rev. (1993) 12: P30
  26. Bardowski J., Ehrlich S.D., Chopin A. Tryptophan biosythesis genes in Lactococcus lactis subsp. lactis. J. Bacteriol. (1992) 174: 6563‑6570

Group leader: Dr. Urszula Zielenkiewicz
Staff: M.Sc. Karolina Tomczyk (Ph.D. student), M.Sc. Iwona Brzozowska (Ph.D. student)

The majority of microorganisms in nature grow in the form of biofilms- organized multicellular community of surface-adherent organisms, usually embedded in extracellular matrix. We focus on the structure and biodiversity of naturally occurring biofilms:
- in arsenic-polluted environment at Złoty Stok closed gold mine
- in continuous culture of H2 producing bacteria under anaerobic conditions at laboratory bioreactor

Metagenomic studies are based on culture-independent techniques: amplification and cloning of 16S rRNA gene sequences, multitemperature single-strand conformation polymorphism (MSSCP) and high-throughput shotgun sequencing followed by phylogenetic sequence analyses.

The physical structure, chemical composition and bacterial cells morphology of the biofilms are investigated with the use of SEM, light and fluorescent microscopy.

Current projects:

  1. Isolation and identification of microorganisms from Złoty Stok gold mine rock biofilms.
  2. Metagenomic analysis of the microbial diversity of the rock biofilms from Złoty Stok gold mine.
  3. Metagenomic analysis of the microbial diversity of the biofilm in long-term continuous culture in bioreactor favoring H2 production.
  4. Studies on the physical and chemical structure of biofilms.
  5. Application of FISH methodology in studies on bacterial composition of different biofilms.
  6. Analysis of mobile DNA pool of the biofilm bacteria consortium from Złoty Stok gold mine rock.

Research grants:
2009-2011 "Metagenomic analysis of the selected consortium of hydrogen-producing fermentative bacteria in a continuous
                 culture on waste substrates. Qualitative and quantitative determination of non-gaseous fermentation
                 end-products", (Ministry of Science and Higher Education)

2007-2010 "Mobile genetic elements in bacteria- molecular analysis and tools construction applied in biotechnology",
                 (Ministry of Science and Higher Education)

2005-2008 "Utilization of mineral production waste with biotechnological methods and creation of databank
                  of microorganisms potentially useful in biometallurgy", (Ministry of Science and Higher Education)

 

Selected publications:

  1. Zielenkiewicz U., M. Kowalewska, C. Kaczor and P. Ceglowski (2009) In Vivo Interactions between Toxin-Antitoxin Proteins Epsilon and Zeta of Streptococcal Plasmid pSM19035 in Saccharomyces cerevisiae J. Bacteriol., 191: 3677-3684.
  2. Zielenkiewicz U. and P. Cegłowski (2005) The toxin-antitoxin system of the streptococcal plasmid pSM19035. J. Bacteriol., 187: 6094–6105.