Publications by authors named "Michał Burmistrz"

12 Publications

  • Page 1 of 1

RNA-Mediated Control in : Insights Into Regulatory Mechanisms and Roles in Metabolism and Virulence.

Front Microbiol 2021 14;12:622829. Epub 2021 Apr 14.

Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.

is an intracellular pathogen that is well known for its adaptability to life in a broad spectrum of different niches. RNA-mediated regulatory mechanisms in play important roles in successful adaptation providing fast and versatile responses to a changing environment. Recent findings indicate that non-coding RNAs (ncRNAs) regulate a variety of processes in this bacterium, such as environmental sensing, metabolism and virulence, as well as immune responses in eukaryotic cells. In this review, the current knowledge on RNA-mediated regulation in is presented, with special focus on the roles and mechanisms underlying modulation of metabolism and virulence. Collectively, these findings point to ncRNAs as important gene regulatory elements in , both outside and inside an infected host. However, the involvement of regulatory ncRNAs in bacterial physiology and virulence is still underestimated and probably will be better assessed in the coming years, especially in relation to discovering the regulatory functions of 5' and 3' untranslated regions and excludons, and by exploring the role of ncRNAs in interaction with both bacterial and host proteins.
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http://dx.doi.org/10.3389/fmicb.2021.622829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8079631PMC
April 2021

A short overview of CRISPR-Cas technology and its application in viral disease control.

Transgenic Res 2021 06 8;30(3):221-238. Epub 2021 Apr 8.

Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW, 2006, Australia.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) together with CRISPR-associated (Cas) proteins have catalysed a revolution in genetic engineering. Native CRISPR-Cas systems exist in many bacteria and archaea where they provide an adaptive immune response through sequence-specific degradation of an invading pathogen's genome. This system has been reconfigured for use in genome editing, drug development, gene expression regulation, diagnostics, the prevention and treatment of cancers, and the treatment of genetic and infectious diseases. In recent years, CRISPR-Cas systems have been used in the diagnosis and control of viral diseases, for example, CRISPR-Cas12/13 coupled with new amplification techniques to improve the specificity of sequence-specific fluorescent probe detection. Importantly, CRISPR applications are both sensitive and specific and usually only require commonly available lab equipment. Unlike the canonical Cas9 which is guided to double-stranded DNA sites of interest, Cas13 systems target RNA sequences and thus can be employed in strategies directed against RNA viruses or for transcriptional silencing. Many challenges remain for these approach, including issues with specificity and the requirement for better mammalian delivery systems. In this review, we summarize the applications of CRISPR-Cas systems in controlling mammalian viral infections. Following necessary improvements, it is expected that CRISPR-Cas systems will be used effectively for such applications in the future.
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http://dx.doi.org/10.1007/s11248-021-00247-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027712PMC
June 2021

RNA-Targeting CRISPR-Cas Systems and Their Applications.

Int J Mol Sci 2020 Feb 7;21(3). Epub 2020 Feb 7.

Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-089 Warsaw, Poland.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems have revolutionized modern molecular biology. Numerous types of these systems have been discovered to date. Many CRISPR-Cas systems have been used as a backbone for the development of potent research tools, with Cas9 being the most widespread. While most of the utilized systems are DNA-targeting, recently more and more attention is being gained by those that target RNA. Their ability to specifically recognize a given RNA sequence in an easily programmable way makes them ideal candidates for developing new research tools. In this review we summarize current knowledge on CRISPR-Cas systems which have been shown to target RNA molecules, that is type III (Csm/Cmr), type VI (Cas13), and type II (Cas9). We also present a list of available technologies based on these systems.
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http://dx.doi.org/10.3390/ijms21031122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036953PMC
February 2020

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System.

J Bacteriol 2017 12 31;199(23). Epub 2017 Oct 31.

Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland

The CRISPR-Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated protein) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. CRISPR RNAs (crRNAs) are the key element of this system, since they are responsible for its selectivity and effectiveness. Typical crRNAs consist of a spacer sequence flanked with 5' and 3' handles originating from repeat sequences that are important for recognition of these small RNAs by the Cas machinery. In this investigation, we studied the type I-C CRISPR-Cas system in , a human pathogen associated with periodontitis, rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. We demonstrated the importance of the 5' handle for crRNA recognition by the effector complex and consequently activity, as well as secondary trimming of the 3' handle, which was not affected by modifications of the repeat sequence., a clinically relevant Gram-negative, anaerobic bacterium, is one of the major etiologic agents of periodontitis and has been linked with the development of other clinical conditions, including rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. The presented results on the biogenesis and functions of crRNAs expand our understanding of CRISPR-Cas cellular defenses in and of horizontal gene transfer in bacteria.
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http://dx.doi.org/10.1128/JB.00275-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5686588PMC
December 2017

Structural Characterization of Human Coronavirus NL63 N Protein.

J Virol 2017 06 12;91(11). Epub 2017 May 12.

Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland

Coronaviruses are responsible for upper and lower respiratory tract infections in humans. It is estimated that 1 to 10% of the population suffers annually from cold-like symptoms related to infection with human coronavirus NL63 (HCoV-NL63), an alphacoronavirus. The nucleocapsid (N) protein, the major structural component of the capsid, facilitates RNA packing, links the capsid to the envelope, and is also involved in multiple other processes, including viral replication and evasion of the immune system. Although the role of N protein in viral replication is relatively well described, no structural data are currently available regarding the N proteins of alphacoronaviruses. Moreover, our understanding of the mechanisms of RNA binding and nucleocapsid formation remains incomplete. In this study, we solved the crystal structures of the N- and C-terminal domains (NTD, residues 10 to 140, and CTD, residues 221 to 340, respectively) of the N protein of HCoV-NL63, both at a 1.5-Å resolution. Based on our structure of NTD solved here, we proposed and experimentally evaluated a model of RNA binding. The structure of the CTD reveals the mode of N protein dimerization. Overall, this study expands our understanding of the initial steps of N protein-nucleic acid interaction and may facilitate future efforts to control the associated infections. Coronaviruses are responsible for the common cold and other respiratory tract infections in humans. According to multiple studies, 1 to 10% of the population is infected each year with HCoV-NL63. Viruses are relatively simple organisms composed of a few proteins and the nucleic acids that carry the information determining their composition. The nucleocapsid (N) protein studied in this work protects the nucleic acid from the environmental factors during virus transmission. This study investigated the structural arrangement of N protein, explaining the first steps of its interaction with nucleic acid at the initial stages of virus structure assembly. The results expand our understanding of coronavirus physiology and may facilitate future efforts to control the associated infections.
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http://dx.doi.org/10.1128/JVI.02503-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432860PMC
June 2017

Substrate profiling of Zika virus NS2B-NS3 protease.

FEBS Lett 2016 Oct 18;590(20):3459-3468. Epub 2016 Oct 18.

Department of Microbiology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.

Zika virus (ZIKV), isolated from macaques in Uganda in 1947, was not considered to be a dangerous human pathogen. However, this view has recently changed as ZIKV infections are now associated with serious pathological disorders including microcephaly and Guillain-Barré syndrome. Similar to other viruses in the Flaviviridae family, ZIKV expresses the serine protease NS3 which is responsible for viral protein processing and replication. Herein, we report the expression of an active NS3 domain fused with the NS2B cofactor (NS2B NS3 ) in a prokaryotic expression system and profile its specificity for synthesized FRET-type substrate libraries. Our findings pave way for screening potential intracellular substrates of NS3 and for developing specific inhibitors of this ZIKV protease.
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http://dx.doi.org/10.1002/1873-3468.12443DOI Listing
October 2016

CRISPR-Cas Systems in Prokaryotes.

Pol J Microbiol 2015 ;64(3):193-202

Prokaryotic organisms possess numerous strategies that enable survival in hostile conditions. Among others, these conditions include the invasion of foreign nucleic acids such as bacteriophages and plasmids. The clustered regularly interspaced palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) system provides the majority of bacteria and archaea with adaptive and hereditary immunity against this threat. This mechanism of immunity is based on short fragments of foreign DNA incorporated within the hosts genome. After transcription, these fragments guide protein complexes that target foreign nucleic acids and promote their degradation. The aim of this review is to summarize the current status of CRISPR-Cas research, including the mechanisms of action, the classification of different types and subtypes of these systems, and the development of new CRISPR-Cas-based molecular biology tools.
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February 2016

Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems.

J Bacteriol 2015 Aug 26;197(16):2631-41. Epub 2015 May 26.

Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Cracow, Poland Malopolska Center of Biotechnology, Jagiellonian University, Cracow, Poland

Unlabelled: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system provides prokaryotic cells with an adaptive and heritable immune response to foreign genetic elements, such as viruses, plasmids, and transposons. It is present in the majority of Archaea and almost half of species of Bacteria. Porphyromonas gingivalis is an important human pathogen that has been proven to be an etiological agent of periodontitis and has been linked to systemic conditions, such as rheumatoid arthritis and cardiovascular disease. At least 95% of clinical strains of P. gingivalis carry CRISPR arrays, suggesting that these arrays play an important function in vivo. Here we show that all four CRISPR arrays present in the P. gingivalis W83 genome are transcribed. For one of the arrays, we demonstrate in vivo activity against double-stranded DNA constructs containing protospacer sequences accompanied at the 3' end by an NGG protospacer-adjacent motif (PAM). Most of the 44 spacers present in the genome of P. gingivalis W83 share no significant similarity with any known sequences, although 4 spacers are similar to sequences from bacteria found in the oral cavity and the gastrointestinal tract. Four spacers match genomic sequences of the host; however, none of these is flanked at its 3' terminus by the appropriate PAM element.

Importance: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system is a unique system that provides prokaryotic cells with an adaptive and heritable immunity. In this report, we show that the CRISPR-Cas system of P. gingivalis, an important human pathogen associated with periodontitis and possibly also other conditions, such as rheumatoid arthritis and cardiovascular disease, is active and provides protection from foreign genetic elements. Importantly, the data presented here may be useful for better understanding the communication between cells in larger bacterial communities and, consequently, the process of disease development and progression.
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http://dx.doi.org/10.1128/JB.00261-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507336PMC
August 2015

The nucleocapsid protein of human coronavirus NL63.

PLoS One 2015 20;10(2):e0117833. Epub 2015 Feb 20.

Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.

Human coronavirus (HCoV) NL63 was first described in 2004 and is associated with respiratory tract disease of varying severity. At the genetic and structural level, HCoV-NL63 is similar to other members of the Coronavirinae subfamily, especially human coronavirus 229E (HCoV-229E). Detailed analysis, however, reveals several unique features of the pathogen. The coronaviral nucleocapsid protein is abundantly present in infected cells. It is a multi-domain, multi-functional protein important for viral replication and a number of cellular processes. The aim of the present study was to characterize the HCoV-NL63 nucleocapsid protein. Biochemical analyses revealed that the protein shares characteristics with homologous proteins encoded in other coronaviral genomes, with the N-terminal domain responsible for nucleic acid binding and the C-terminal domain involved in protein oligomerization. Surprisingly, analysis of the subcellular localization of the N protein of HCoV-NL63 revealed that, differently than homologous proteins from other coronaviral species except for SARS-CoV, it is not present in the nucleus of infected or transfected cells. Furthermore, no significant alteration in cell cycle progression in cells expressing the protein was observed. This is in stark contrast with results obtained for other coronaviruses, except for the SARS-CoV.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117833PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336326PMC
December 2015

Coke dust enhances coke plant wastewater treatment.

Chemosphere 2014 Dec 12;117:278-84. Epub 2014 Aug 12.

AGH University of Science and Technology, Faculty of Energy & Fuels, Mickiewicz Avenue 30, 30-059 Krakow, Poland.

Coke plant wastewater contain many toxic pollutants. Despite physico-chemical and biological treatment this specific type of wastewater has a significant impact on environment and human health. This article presents results of research on industrial adsorptive coke plant wastewater treatment. As a sorbent the coke dust, dozen times less expensive than pulverized activated carbon, was used. Treatment was conducted in three scenarios: adsorptive after full treatment with coke dust at 15 g L(-1), biological treatment enhanced with coke dust at 0.3-0.5 g L(-1) and addition of coke dust at 0.3 g L(-1) prior to the biological treatment. The enhanced biological treatment proved the most effective. It allowed additional removal of 147-178 mg COD kg(-1) of coke dust.
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http://dx.doi.org/10.1016/j.chemosphere.2014.07.025DOI Listing
December 2014

Stability of infectious human coronavirus NL63.

J Virol Methods 2014 09 18;205:87-90. Epub 2014 Apr 18.

Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland. Electronic address:

The human coronavirus NL63 was identified in 2004 and subsequent studies showed its worldwide distribution. Infection with this pathogen is associated with upper and lower respiratory tract diseases of mild to moderate severity. Furthermore, HCoV-NL63 is the main cause of croup in children. Within this study an optimal protocol for freeze-drying that allows safe and effective preservation of HCoV-NL63 infectious material was developed. Lyophilized virus preparations can be stored either at ambient temperature or at +4°C. In the latter case samples may be stored for at least two months. Surprisingly, conducted analysis showed that HCoV-NL63 virions are exquisitely stable in liquid media and can be stored also without preservatives at ambient temperature for up to 14 days.
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http://dx.doi.org/10.1016/j.jviromet.2014.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7113654PMC
September 2014

Distribution of polycyclic aromatic hydrocarbons in coke plant wastewater.

Water Sci Technol 2013 ;68(11):2414-20

Microbiology Department, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.

The subject of examinations presented in this paper is the distribution of polycyclic aromatic hydrocarbons (PAHs) between solid and liquid phases in samples of raw wastewater and wastewater after treatment. The content of 16 PAHs according to the US EPA was determined in the samples of coke plant wastewater from the Zdzieszowice Coke Plant, Poland. The samples contained raw wastewater, wastewater after physico-chemical treatment as well as after biological treatment. The ΣPHA16 content varied between 255.050 μg L(-1) and 311.907 μg L(-1) in raw wastewater and between 0.940 and 4.465 μg L(-1) in wastewater after full treatment. Investigation of the distribution of PAHs showed that 71-84% of these compounds is adsorbed on the surface of suspended solids and 16-29% is dissolved in water. Distribution of individual PAHs and ΣPHA16 between solid phase and liquid phase was described with the use of statistically significant, linear equations. The calculated values of the partitioning coefficient Kp changed from 0.99 to 7.90 for naphthalene in samples containing mineral-organic suspension and acenaphthylene in samples with biological activated sludge, respectively.
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http://dx.doi.org/10.2166/wst.2013.506DOI Listing
March 2014
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