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Błaszczyk E, Płociński P, Lechowicz E, Brzostek A, Dziadek B, Korycka-Machała M, Słomka M, Dziadek J. Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs. Sci Rep 2023; 13:20717. [PMID: 38001315 PMCID: PMC10673834 DOI: 10.1038/s41598-023-47944-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
In reference to gene annotation, more than half of the tRNA species synthesized by Mycobacterium tuberculosis require the enzymatic addition of the cytosine-cytosine-adenine (CCA) tail, which is indispensable for amino acid charging and tRNA functionality. It makes the mycobacterial CCA-adding enzyme essential for survival of the bacterium and a potential target for novel pipelines in drug discovery avenues. Here, we described the rv3907c gene product, originally annotated as poly(A)polymerase (rv3907c, PcnA) as a functional CCA-adding enzyme (CCAMtb) essential for viability of M. tuberculosis. The depletion of the enzyme affected tRNAs maturation, inhibited bacilli growth, and resulted in abundant accumulation of polyadenylated RNAs. We determined the enzymatic activities displayed by the mycobacterial CCAMtb in vitro and studied the effects of inhibiting of its transcription in bacterial cells. We are the first to properly confirm the existence of RNA polyadenylation in mycobacteria, a previously controversial phenomenon, which we found promoted upon CCA-adding enzyme downexpression.
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Affiliation(s)
- Ewelina Błaszczyk
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Przemysław Płociński
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Ewelina Lechowicz
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | | | - Marcin Słomka
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 139, 90-235, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland.
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Żukowska L, Zygała-Pytlos D, Struś K, Zabost A, Kozińska M, Augustynowicz-Kopeć E, Dziadek J, Minias A. Correction: An overview of Tuberculosis outbreaks reported in the years 2011-2020. BMC Infect Dis 2023; 23:754. [PMID: 37919653 PMCID: PMC10621217 DOI: 10.1186/s12879-023-08751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Affiliation(s)
- Lidia Żukowska
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- The Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Lodz, Poland
| | - Daria Zygała-Pytlos
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- The Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Lodz, Poland
| | - Katarzyna Struś
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzesz?w, Rzesz?w, Poland
| | - Anna Zabost
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Monika Kozińska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Alina Minias
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
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3
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Kawka M, Płocińska R, Płociński P, Pawełczyk J, Słomka M, Gatkowska J, Dzitko K, Dziadek B, Dziadek J. The functional response of human monocyte-derived macrophages to serum amyloid A and Mycobacterium tuberculosis infection. Front Immunol 2023; 14:1238132. [PMID: 37781389 PMCID: PMC10540855 DOI: 10.3389/fimmu.2023.1238132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction In the course of tuberculosis (TB), the level of major acute phase protein, namely serum amyloid A (hSAA-1), increases up to a hundredfold in the pleural fluids of infected individuals. Tubercle bacilli infecting the human host can be opsonized by hSAA-1, which affects bacterial entry into human macrophages and their intracellular multiplication. Methods We applied global RNA sequencing to evaluate the functional response of human monocyte-derived macrophages (MDMs), isolated from healthy blood donors, under elevated hSAA-1 conditions and during infection with nonopsonized and hSAA-1-opsonized Mycobacterium tuberculosis (Mtb). In the same infection model, we also examined the functional response of mycobacteria to the intracellular environment of macrophages in the presence and absence of hSAA-1. The RNASeq analysis was validated using qPCR. The functional response of MDMs to hSAA-1 and/or tubercle bacilli was also evaluated for selected cytokines at the protein level by applying the Milliplex system. Findings Transcriptomes of MDMs cultured in the presence of hSAA-1 or infected with Mtb showed a high degree of similarity for both upregulated and downregulated genes involved mainly in processes related to cell division and immune response, respectively. Among the most induced genes, across both hSAA-1 and Mtb infection conditions, CXCL8, CCL15, CCL5, IL-1β, and receptors for IL-7 and IL-2 were identified. We also observed the same pattern of upregulated pro-inflammatory cytokines (TNFα, IL-6, IL-12, IL-18, IL-23, and IL-1) and downregulated anti-inflammatory cytokines (IL-10, TGFβ, and antimicrobial peptide cathelicidin) in the hSAA-1 treated-MDMs or the phagocytes infected with tubercle bacilli. At this early stage of infection, Mtb genes affected by the inside microenvironment of MDMs are strictly involved in iron scavenging, adaptation to hypoxia, low pH, and increasing levels of CO2. The genes for the synthesis and transport of virulence lipids, but not cholesterol/fatty acid degradation, were also upregulated. Conclusion Elevated serum hSAA-1 levels in tuberculosis enhance the response of host phagocytes to infection, including macrophages that have not yet been in contact with mycobacteria. SAA induces antigen processing and presentation processes by professional phagocytes reversing the inhibition caused by Mtb infection.
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Affiliation(s)
- Malwina Kawka
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Renata Płocińska
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | | | - Jakub Pawełczyk
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Justyna Gatkowska
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Katarzyna Dzitko
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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Żukowska L, Zygała-Pytlos D, Struś K, Zabost A, Kozińska M, Augustynowicz-Kopeć E, Dziadek J, Minias A. An overview of tuberculosis outbreaks reported in the years 2011-2020. BMC Infect Dis 2023; 23:253. [PMID: 37081448 PMCID: PMC10116450 DOI: 10.1186/s12879-023-08197-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND In many countries tuberculosis (TB) remains a highly prevalent disease and a major contributor to infectious disease mortality. The fight against TB requires surveillance of the population of strains circulating worldwide and the analysis of the prevalence of certain strains in populations. Nowadays, whole genome sequencing (WGS) allows for accurate tracking of TB transmission. Currently, there is a lack of a comprehensive summary of the characteristics of TB outbreaks. METHODS We systematically analyzed studies reporting TB outbreaks worldwide, monitored through WGS of Mycobacterium tuberculosis. We 1) mapped the reported outbreaks from 2011- 2020, 2) estimated the average size of the outbreaks, 3) indicated genetic lineages causing the outbreaks, and 4) determined drug-resistance patterns of M. tuberculosis strains involved in the outbreaks. RESULTS Most data originated from Europe, Asia, and North America. We found that TB outbreaks were reported throughout the globe, on all continents, and in countries with both high and low incidences. The detected outbreaks contained a median of five M. tuberculosis isolates. Most strains causing the outbreaks belonged to lineage four, more rarely to lineage two. Reported outbreak isolates were often drug resistant. CONCLUSIONS We conclude that more WGS surveillance of M. tuberculosis outbreaks is needed. Globally standardized procedures might improve the control of M. tuberculosis infections.
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Affiliation(s)
- Lidia Żukowska
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- The Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Lodz, Poland
| | - Daria Zygała-Pytlos
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- The Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Lodz, Poland
| | - Katarzyna Struś
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszów, Rzeszów, Poland
| | - Anna Zabost
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Monika Kozińska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Alina Minias
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
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Korycka-Machała M, Kawka M, Lach J, Płocińska R, Bekier A, Dziadek B, Brzostek A, Płociński P, Strapagiel D, Szczesio M, Gobis K, Dziadek J. 2,4-Disubstituted pyridine derivatives are effective against intracellular and biofilm-forming tubercle bacilli. Front Pharmacol 2022; 13:1004632. [DOI: 10.3389/fphar.2022.1004632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/26/2022] [Indexed: 11/12/2022] Open
Abstract
It was recently reported that 4-substituted picolinohydrazonamides carrying hydrophilic cyclic amines, such as morpholine and pyrrolidine, at the end of their thiosemicarbazide chain have potent antimycobacterial activity in vitro at concentrations below 1 μg/ml. Here, two selected compounds, 2,4-disubstituted pyridine derivatives 11 and 15, revealed significant bactericidal activity against Mycobacterium tuberculosis localized intracellularly within human macrophages, as well as against biofilm-forming tubercle bacilli. Mutants were selected that were resistant to the investigated compounds at an efficiency similar to that identified in the presence of the first line antituberculosis drug rifampicin. The resistant mutants were viable in the presence of the tested compounds exclusively on solid media. Genome-wide sequencing of the mutants selected in the presence of compound 11 revealed the accumulation of nonsynonymous mutations in the mmpR5 gene encoding a transcriptional repressor of the MmpS5-MmpL5 efflux pump, whose upregulation has been associated with bedaquiline resistance. The depletion of MmpR5 in wild-type M. tuberculosis using CRISPR–Cas9 technology increased the resistance of this strain to compound 11. Mass spectrometry-based proteomics (LC–MS/MS) of wild-type tubercle bacilli growing in subinhibitory concentrations of compounds 11 or 15 revealed 15 overproduced proteins not detectable in the control cells, including virulence-related proteins.
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Płocińska R, Wasik K, Płociński P, Lechowicz E, Antczak M, Błaszczyk E, Dziadek B, Słomka M, Rumijowska-Galewicz A, Dziadek J. The Orphan Response Regulator Rv3143 Modulates the Activity of the NADH Dehydrogenase Complex (Nuo) in Mycobacterium tuberculosis via Protein–Protein Interactions. Front Cell Infect Microbiol 2022; 12:909507. [PMID: 35837472 PMCID: PMC9274095 DOI: 10.3389/fcimb.2022.909507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Two-component signal transduction systems enable mycobacterial cells to quickly adapt and adequately respond to adverse environmental conditions encountered at various stages of host infection. We attempted to determine the role of the Rv3143 “orphan” response regulator in the physiology of Mycobacterium tuberculosis and its orthologue Msmeg_2064 in Mycobacterium smegmatis. We identified the Rv3143 protein as an interaction partner for NuoD, a member of the type I NADH dehydrogenase complex involved in oxidative phosphorylation. The mutants Δrv3143 and Δmsmeg_2064 were engineered in M. tuberculosis and M. smegmatis cells, respectively. The Δmsmeg_2064 strain exhibited a significant reduction in growth and viability in the presence of reactive nitrogen species. The Rv3143-deficient strain was sensitive to valinomycin, which is known to reduce the electrochemical potential of the cell and overexpressed genes required for nitrate respiration. An increased level of reduction of the 2,3,5-triphenyltetrazolium chloride (TTC) electron acceptor in Δrv3143 and Δmsmeg_2064 cells was also evident. The silencing of ndh expression using CRISPRi/dCas9 affected cell survival under limited oxygen conditions. Oxygen consumption during entry to hypoxia was most severely affected in the double-mutant Δmsmeg_2064 ndhCRISPRi/dCas9. We propose that the regulatory protein Rv3143 is a component of the Nuo complex and modulates its activity.
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Affiliation(s)
- Renata Płocińska
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Karolina Wasik
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Przemysław Płociński
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Ewelina Lechowicz
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Magdalena Antczak
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Ewelina Błaszczyk
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Anna Rumijowska-Galewicz
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
| | - Jarosław Dziadek
- Department of Genetics and Physiology of Mycobacteria, Institute of Medical Biology of the Polish Academy of Sciences, Łódź, Poland
- *Correspondence: Jarosław Dziadek,
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7
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Horetski M, Gorlova A, Płocińska R, Brzostek A, Faletrov Y, Dziadek J, Shkumatov V. Synthesis, Optical Properties, Preliminary Antimycobacterial Evaluation and Docking Studies of Trifluoroacetylated 3‐Pyrrolyl Boron‐Dipyrromethene. ChemistrySelect 2022. [DOI: 10.1002/slct.202200506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Matvey Horetski
- Department of Macromolecular Compounds Belarusian State University 14 Leningradskaya Street. Minsk 220030 Belarus
| | - Anna Gorlova
- Department of Natural Sciences Novosibirsk State University 1 Pirogova Street. Novosibirsk 630090 Russia
| | - Renata Płocińska
- The Institute of Medical Biology Polish Academy of Sciences 106 Lodowa Street. Lodz 93-232 Poland
| | - Anna Brzostek
- The Institute of Medical Biology Polish Academy of Sciences 106 Lodowa Street. Lodz 93-232 Poland
| | - Yaroslav Faletrov
- Department of Macromolecular Compounds Belarusian State University 14 Leningradskaya Street. Minsk 220030 Belarus
| | - Jarosław Dziadek
- The Institute of Medical Biology Polish Academy of Sciences 106 Lodowa Street. Lodz 93-232 Poland
| | - Vladimir Shkumatov
- Department of Macromolecular Compounds Belarusian State University 14 Leningradskaya Street. Minsk 220030 Belarus
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Różański M, Walczak-Drzewiecka A, Witaszewska J, Wójcik E, Guziński A, Zimoń B, Matusiak R, Kazimierczak J, Borowiec M, Kania K, Paradowska E, Pawełczyk J, Dziadek J, Dastych J. RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics. Sci Rep 2022; 12:8082. [PMID: 35577836 PMCID: PMC9109753 DOI: 10.1038/s41598-022-12179-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/28/2022] [Indexed: 01/09/2023] Open
Abstract
Swab, RT-qPCR tests remain the gold standard of diagnostics of SARS-CoV-2 infections. These tests are costly and have limited throughput. We developed a 3-gene, seminested RT-qPCR test with SYBR green-based detection designed to be oversensitive rather than overspecific for high-throughput diagnostics of populations. This two-tier approach depends on decentralized self-collection of saliva samples, pooling, 1st-tier testing with highly sensitive screening test and subsequent 2nd-tier testing of individual samples from positive pools with the IVD test. The screening test was able to detect five copies of the viral genome in 10 µl of isolated RNA with 50% probability and 18.8 copies with 95% probability and reached Ct values that were highly linearly RNA concentration-dependent. In the side-by-side comparison, the screening test attained slightly better results than the commercially available IVD-certified RT-qPCR diagnostic test DiaPlexQ (100% specificity and 89.8% sensitivity vs. 100% and 73.5%, respectively). Testing of 1475 individual clinical samples pooled in 374 pools of four revealed 0.8% false positive pools and no false negative pools. In weekly prophylactic testing of 113 people within 6 months, a two-tier testing approach enabled the detection of 18 infected individuals, including several asymptomatic individuals, with substantially lower cost than individual RT-PCR testing.
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Affiliation(s)
- Michał Różański
- Laboratory of Cellular Immunology, Institute of Medical Biology of PAS, Lodz, Poland
| | | | | | - Ewelina Wójcik
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland
| | | | - Bogumił Zimoń
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland
| | - Rafał Matusiak
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland
| | | | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Kania
- Laboratory of Virology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Jakub Pawełczyk
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology of PAS, Lodz, Poland
| | - Jarosław Dastych
- Laboratory of Cellular Immunology, Institute of Medical Biology of PAS, Lodz, Poland.
- Proteon Pharmaceuticals S.A., Tylna 3A, 90-364, Lodz, Poland.
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9
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Bekier A, Brzostek A, Paneth A, Dziadek B, Dziadek J, Gatkowska J, Dzitko K. 4-Arylthiosemicarbazide Derivatives as Toxoplasmic Aromatic Amino Acid Hydroxylase Inhibitors and Anti-inflammatory Agents. Int J Mol Sci 2022; 23:ijms23063213. [PMID: 35328634 PMCID: PMC8955734 DOI: 10.3390/ijms23063213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/12/2022] Open
Abstract
Approximately one-third of the human population is infected with the intracellular cosmopolitan protozoan Toxoplasma gondii (Tg), and a specific treatment for this parasite is still needed. Additionally, the increasing resistance of Tg to drugs has become a challenge for numerous research centers. The high selectivity of a compound toward the protozoan, along with low cytotoxicity toward the host cells, form the basis for further research, which aims at determining the molecular targets of the active compounds. Thiosemicarbazide derivatives are biologically active organic compounds. Previous studies on the initial preselection of 58 new 4-arylthiosemicarbazide derivatives in terms of their anti-Tg activity and selectivity made it possible to select two promising derivatives for further research. One of the important amino acids involved in the proliferation of Tg and the formation of parasitophorous vacuoles is tyrosine, which is converted by two unique aromatic amino acid hydroxylases to levodopa. Enzymatic studies with two derivatives (R: para-nitro and meta-iodo) and recombinant aromatic amino acid hydroxylase (AAHs) obtained in the E. coli expression system were performed, and the results indicated that toxoplasmic AAHs are a molecular target for 4-arylthiosemicarbazide derivatives. Moreover, the drug affinity responsive target stability assay also confirmed that the selected compounds bind to AAHs. Additionally, the anti-inflammatory activity of these derivatives was tested using THP1-Blue™ NF-κB reporter cells due to the similarity of the thiosemicarbazide scaffold to thiosemicarbazone, both of which are known NF-κB pathway inhibitors.
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Affiliation(s)
- Adrian Bekier
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (A.B.); (B.D.); (J.G.)
| | - Anna Brzostek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (A.B.); (J.D.)
| | - Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (A.B.); (B.D.); (J.G.)
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (A.B.); (J.D.)
| | - Justyna Gatkowska
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (A.B.); (B.D.); (J.G.)
| | - Katarzyna Dzitko
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (A.B.); (B.D.); (J.G.)
- Correspondence:
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10
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Pawełczyk J, Brzostek A, Minias A, Płociński P, Rumijowska-Galewicz A, Strapagiel D, Zakrzewska-Czerwińska J, Dziadek J. Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis. Sci Rep 2021; 11:12396. [PMID: 34117327 PMCID: PMC8196197 DOI: 10.1038/s41598-021-91812-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an obligate human pathogen that can adapt to the various nutrients available during its life cycle. However, in the nutritionally stringent environment of the macrophage phagolysosome, Mtb relies mainly on cholesterol. In previous studies, we demonstrated that Mtb can accumulate and utilize cholesterol as the sole carbon source. However, a growing body of evidence suggests that a lipid-rich environment may have a much broader impact on the pathogenesis of Mtb infection than previously thought. Therefore, we applied high-resolution transcriptome profiling and the construction of various mutants to explore in detail the global effect of cholesterol on the tubercle bacillus metabolism. The results allow re-establishing the complete list of genes potentially involved in cholesterol breakdown. Moreover, we identified the modulatory effect of vitamin B12 on Mtb transcriptome and the novel function of cobalamin in cholesterol metabolite dissipation which explains the probable role of B12 in Mtb virulence. Finally, we demonstrate that a key role of cholesterol in mycobacterial metabolism is not only providing carbon and energy but involves also a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment far before specific stress-inducing phagosomal signals occur.
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Affiliation(s)
- Jakub Pawełczyk
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Anna Brzostek
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Alina Minias
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Przemysław Płociński
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland ,grid.10789.370000 0000 9730 2769Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódz, Łódź, Poland
| | - Anna Rumijowska-Galewicz
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- grid.10789.370000 0000 9730 2769Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- grid.8505.80000 0001 1010 5103Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Jarosław Dziadek
- grid.413454.30000 0001 1958 0162Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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11
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Minias A, Żukowska L, Lechowicz E, Gąsior F, Knast A, Podlewska S, Zygała D, Dziadek J. Early Drug Development and Evaluation of Putative Antitubercular Compounds in the -Omics Era. Front Microbiol 2021; 11:618168. [PMID: 33603720 PMCID: PMC7884339 DOI: 10.3389/fmicb.2020.618168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, the disease is one of the top 10 causes of death of people worldwide. Mycobacterium tuberculosis is an intracellular pathogen with an unusually thick, waxy cell wall and a complex life cycle. These factors, combined with M. tuberculosis ability to enter prolonged periods of latency, make the bacterium very difficult to eradicate. The standard treatment of TB requires 6-20months, depending on the drug susceptibility of the infecting strain. The need to take cocktails of antibiotics to treat tuberculosis effectively and the emergence of drug-resistant strains prompts the need to search for new antitubercular compounds. This review provides a perspective on how modern -omic technologies facilitate the drug discovery process for tuberculosis treatment. We discuss how methods of DNA and RNA sequencing, proteomics, and genetic manipulation of organisms increase our understanding of mechanisms of action of antibiotics and allow the evaluation of drugs. We explore the utility of mathematical modeling and modern computational analysis for the drug discovery process. Finally, we summarize how -omic technologies contribute to our understanding of the emergence of drug resistance.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Lidia Żukowska
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Ewelina Lechowicz
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Filip Gąsior
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Agnieszka Knast
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Krakow, Poland
- Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - Daria Zygała
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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12
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Różycka D, Korycka-Machała M, Żaczek A, Dziadek J, Gurda D, Orlicka-Płocka M, Wyszko E, Biniek-Antosiak K, Rypniewski W, Olejniczak AB. Novel Isoniazid-Carborane Hybrids Active in Vitro Against Mycobacterium tuberculosis. Pharmaceuticals (Basel) 2020; 13:ph13120465. [PMID: 33333865 PMCID: PMC7765321 DOI: 10.3390/ph13120465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/27/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) is a severe infectious disease with high mortality and morbidity. The emergence of drug-resistant TB has increased the challenge to eliminate this disease. Isoniazid (INH) remains the key and effective component in the therapeutic regimen recommended by World Health Organization (WHO). A series of isoniazid-carborane derivatives containing 1,2-dicarba-closo-dodecaborane, 1,7-dicarba-closo-dodecaborane, 1,12-dicarba-closo-dodecaborane, or 7,8-dicarba-nido-undecaborate anion were synthesized for the first time. The compounds were tested in vitro against the Mycobacterium tuberculosis (Mtb) H37Rv strain and its mutant (DkatG) defective in the synthesis of catalase-peroxidase (KatG). N'-((7,8-dicarba-nido-undecaboranyl)methylidene)isonicotinohydrazide (16) showed the highest activity against the wild-type Mtb strain. All hybrids could inhibit the growth of the ΔkatG mutant in lower concentrations than INH. N'-([(1,12-dicarba-closo-dodecaboran-1yl)ethyl)isonicotinohydrazide (25) exhibited more than 60-fold increase in activity against Mtb DkatG as compared to INH. This compound was also found to be noncytotoxic up to a concentration four times higher than the minimum inhibitory concentration 99% (MIC99) value.
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Affiliation(s)
- Daria Różycka
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland; (D.R.); (M.K.-M.); (J.D.)
| | - Małgorzata Korycka-Machała
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland; (D.R.); (M.K.-M.); (J.D.)
| | - Anna Żaczek
- Institute of Medical Sciences, Medical College, University of Rzeszow, 2A Kopisto Avenue, 35-959 Rzeszow, Poland;
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland; (D.R.); (M.K.-M.); (J.D.)
| | - Dorota Gurda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14Z. Noskowskiego St., 61-704 Poznan, Poland; (D.G.); (M.O.-P.); (E.W.); (K.B.-A.); (W.R.)
| | - Marta Orlicka-Płocka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14Z. Noskowskiego St., 61-704 Poznan, Poland; (D.G.); (M.O.-P.); (E.W.); (K.B.-A.); (W.R.)
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14Z. Noskowskiego St., 61-704 Poznan, Poland; (D.G.); (M.O.-P.); (E.W.); (K.B.-A.); (W.R.)
| | - Katarzyna Biniek-Antosiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14Z. Noskowskiego St., 61-704 Poznan, Poland; (D.G.); (M.O.-P.); (E.W.); (K.B.-A.); (W.R.)
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14Z. Noskowskiego St., 61-704 Poznan, Poland; (D.G.); (M.O.-P.); (E.W.); (K.B.-A.); (W.R.)
| | - Agnieszka B. Olejniczak
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland; (D.R.); (M.K.-M.); (J.D.)
- Correspondence: ; Tel.: +48-42-272-36-37
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13
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Minias A, Żukowska L, Lach J, Jagielski T, Strapagiel D, Kim SY, Koh WJ, Adam H, Bittner R, Truden S, Žolnir-Dovč M, Dziadek J. Subspecies-specific sequence detection for differentiation of Mycobacterium abscessus complex. Sci Rep 2020; 10:16415. [PMID: 33009494 PMCID: PMC7532137 DOI: 10.1038/s41598-020-73607-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium abscessus complex (MABC) is a taxonomic group of rapidly growing, nontuberculous mycobacteria that are found as etiologic agents of various types of infections. They are considered as emerging human pathogens. MABC consists of 3 subspecies—M. abscessus subsp. bolletti, M. abscessus subsp. massiliense and M. abscessus subsp. abscessus. Here we present a novel method for subspecies differentiation of M. abscessus named Subspecies-Specific Sequence Detection (SSSD). This method is based on the presence of signature sequences present within the genomes of each subspecies of MABC. We tested this method against a virtual database of 1505 genome sequences of MABC. Further, we detected signature sequences of MABC in 45 microbiological samples through DNA hybridization. SSSD showed high levels of sensitivity and specificity for differentiation of subspecies of MABC, comparable to those obtained by rpoB sequence typing.
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Affiliation(s)
- Alina Minias
- Institute of Medical Biology, Polish Academy of Sciences, ul. Lodowa 106, 93-232, Lodz, Poland.
| | - Lidia Żukowska
- BioMedChem Doctoral School of the University of Lodz, The Institutes of the Polish Academy of Sciences, Lodz, Poland
| | - Jakub Lach
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Heather Adam
- Diagnostic Services, Shared Health, Winnipeg, MB, Canada
| | - Ruth Bittner
- Diagnostic Services, Shared Health, Winnipeg, MB, Canada
| | - Sara Truden
- National Reference Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Manca Žolnir-Dovč
- National Reference Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, ul. Lodowa 106, 93-232, Lodz, Poland
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14
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Brissett NC, Zabrady K, Płociński P, Bianchi J, Korycka-Machała M, Brzostek A, Dziadek J, Doherty AJ. Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C. Nat Commun 2020; 11:4196. [PMID: 32826907 PMCID: PMC7442782 DOI: 10.1038/s41467-020-18012-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 07/30/2020] [Indexed: 02/03/2023] Open
Abstract
Cells utilise specialized polymerases from the Primase-Polymerase (Prim-Pol) superfamily to maintain genome stability. Prim-Pol's function in genome maintenance pathways including replication, repair and damage tolerance. Mycobacteria contain multiple Prim-Pols required for lesion repair, including Prim-PolC that performs short gap repair synthesis during excision repair. To understand the molecular basis of Prim-PolC's gap recognition and synthesis activities, we elucidated crystal structures of pre- and post-catalytic complexes bound to gapped DNA substrates. These intermediates explain its binding preference for short gaps and reveal a distinctive modus operandi called Synthesis-dependent Template Displacement (STD). This mechanism enables Prim-PolC to couple primer extension with template base dislocation, ensuring that the unpaired templating bases in the gap are ushered into the active site in an ordered manner. Insights provided by these structures establishes the molecular basis of Prim-PolC's gap recognition and extension activities, while also illuminating the mechanisms of primer extension utilised by closely related Prim-Pols.
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Affiliation(s)
- Nigel C Brissett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.,School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK
| | - Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Przemysław Płociński
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.,Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Lodz, Poland
| | - Julie Bianchi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.,Department of Oncology-Pathology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | | | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Lodz, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Lodz, Poland
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.
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15
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Czubat B, Minias A, Brzostek A, Żaczek A, Struś K, Zakrzewska-Czerwińska J, Dziadek J. Functional Disassociation Between the Protein Domains of MSMEG_4305 of Mycolicibacterium smegmatis ( Mycobacterium smegmatis) in vivo. Front Microbiol 2020; 11:2008. [PMID: 32973726 PMCID: PMC7466739 DOI: 10.3389/fmicb.2020.02008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/29/2020] [Indexed: 12/02/2022] Open
Abstract
MSMEG_4305 is a two-domain protein of Mycolicibacterium smegmatis (Mycobacterium smegmatis) (Mycolicibacterium smegmatis). The N-terminal domain of MSMEG_4305 encodes an RNase H type I. The C-terminal domain is a presumed CobC, predicted to be involved in the aerobic synthesis of vitamin B12. Both domains reach their maximum at distinct pH, approximately 8.5 and 4.5, respectively. The presence of the CobC domain influenced RNase activity in vitro in homolog Rv2228c. Here, we analyzed the role of MSMEG_4305 in vitamin B12 synthesis and the functional association between both domains in vivo in M. smegmatis. We used knock-out mutant of M. smegmatis, deficient in MSMEG_4305. Whole-cell lysates of the mutants strain contained a lower concentration of vitamin B12, as it determined with immunoenzimatic assay. We observed growth deficits, related to vitamin B12 production, on media containing sulfamethazine and propionate. Removal of the CobC domain of MSMEG_4305 in ΔrnhA background hardly affected the growth rate of M. smegmatis in vivo. The strain carrying truncation showed no fitness deficit in the competitive assay and it did not show increased level of RNA/DNA hybrids in its genome. We show that homologs of MSMEG_4305 are present only in the Actinomycetales phylogenetic branch (according to the old classification system). The domains of MSMEG_4305 homologs accumulate mutations at a different rate, while the linker region is highly variable. We conclude that MSMEG_4305 is a multidomain protein that most probably was fixed in the phylogenetic tree of life due to genetic drift.
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Affiliation(s)
- Bożena Czubat
- Department of Experimental and Clinical Pharmacology, University of Rzeszów, Rzeszów, Poland.,Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Anna Brzostek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
| | - Anna Żaczek
- Institute of Medical Sciences, Medical College of Rzeszów University, Rzeszów, Poland
| | - Katarzyna Struś
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszów, Rzeszów, Poland
| | | | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, łLódź, Poland
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16
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Sokołowska A, Świerzko AS, Szala-Poździej A, Augustynowicz-Kopeć E, Kozińska M, Niemiec T, Błachnio M, Borkowska-Tatar D, Jensenius JC, Thiel S, Dziadek J, Cedzyński M. Selected factors of the innate immunity in Polish patients suffering from pulmonary tuberculosis. Immunobiology 2020; 225:151905. [PMID: 32007302 DOI: 10.1016/j.imbio.2020.151905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 02/01/2023]
Abstract
We conducted a prospective study of 453 Polish patients suffering from pulmonary tuberculosis and 267 healthy controls. Selected polymorphisms of the genes encoding for collectins, ficolins and MBL-associated serine protease 2 were investigated as were serum concentrations of mannose-binding lectin, surfactant protein D, ficolin-1 and ficolin-3. The number of MBL2 gene exon 1 variant allele carriers was significantly higher in patients, compared with controls. The homozygosity for SFTPA2 +26 C > A SNP variant allele occurred less commonly within TB, while homozygosity for the FCN1 -542 G > A major allele was less frequent within the control group. Two patients were found MASP-2-deficient. Serum concentrations of MBL, SP-D and ficolin-1 were higher amongst patients while the converse was found for ficolin-3. Ficolin-1 had high specificity to differentiate between individuals with tuberculosis and healthy persons and therefore may be considered potential disease marker.
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Affiliation(s)
- Anna Sokołowska
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Anna S Świerzko
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Agnieszka Szala-Poździej
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | | | - Monika Kozińska
- Institute of Tuberculosis and Lung Diseases, Plocka 26, 01-138, Warsaw, Poland
| | - Tomasz Niemiec
- The Voivodeship Hospital of Lung Diseases in Jaroszowiec, Kolejowa 1a, 32-312, Jaroszowiec, Poland
| | - Maria Błachnio
- Masovian Center of Lung Diseases and Tuberculosis Treatment, Narutowicza 80, 05-400, Otwock, Poland
| | | | - Jens C Jensenius
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus, Denmark
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus, Denmark
| | - Jarosław Dziadek
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Maciej Cedzyński
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland.
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17
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Jagielski T, Borówka P, Bakuła Z, Lach J, Marciniak B, Brzostek A, Dziadek J, Dziurzyński M, Pennings L, van Ingen J, Žolnir-Dovč M, Strapagiel D. Genomic Insights Into the Mycobacterium kansasii Complex: An Update. Front Microbiol 2020; 10:2918. [PMID: 32010067 PMCID: PMC6974680 DOI: 10.3389/fmicb.2019.02918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022] Open
Abstract
Only very recently, has it been proposed that the hitherto existing Mycobacterium kansasii subtypes (I-VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each M. kansasii subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., Mycobacterium ostraviense sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, a monophyletic origin, and overlapping phenotypes, our findings support the recognition of the M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the M. kansasii-derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug.
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Affiliation(s)
- Tomasz Jagielski
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Paulina Borówka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Zofia Bakuła
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Jakub Lach
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
| | - Błażej Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Mikołaj Dziurzyński
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Lian Pennings
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manca Žolnir-Dovč
- Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wroclaw, Poland
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18
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Płociński P, Macios M, Houghton J, Niemiec E, Płocińska R, Brzostek A, Słomka M, Dziadek J, Young D, Dziembowski A. Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis. Nucleic Acids Res 2019; 47:5892-5905. [PMID: 30957850 PMCID: PMC6582357 DOI: 10.1093/nar/gkz251] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/25/2019] [Accepted: 04/02/2019] [Indexed: 12/28/2022] Open
Abstract
The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim of the present study is to identify the core components of the RNA degradosome of M. tuberculosis and to analyse their function in RNA metabolism. Using an approach involving cross-linking to 4-thiouridine-labelled RNA, we mapped the mycobacterial RNA-bound proteome and identified degradosome-related enzymes polynucleotide phosphorylase (PNPase), ATP-dependent RNA helicase (RhlE), ribonuclease E (RNase E) and ribonuclease J (RNase J) as major components. We then carried out affinity purification of eGFP-tagged recombinant constructs to identify protein-protein interactions. This identified further interactions with cold-shock proteins and novel KH-domain proteins. Engineering and transcriptional profiling of strains with a reduced level of expression of core degradosome ribonucleases provided evidence of important pleiotropic roles of the enzymes in mycobacterial RNA metabolism highlighting their potential vulnerability as drug targets.
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Affiliation(s)
- Przemysław Płociński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland.,Mill Hill Laboratory, Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK.,Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź 93-232, Poland
| | - Maria Macios
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Joanna Houghton
- Mill Hill Laboratory, Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Emilia Niemiec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Renata Płocińska
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź 93-232, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź 93-232, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, Łódź 90-231, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź 93-232, Poland
| | - Douglas Young
- Mill Hill Laboratory, Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland.,Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5A, Warsaw 02-106, Poland
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19
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Minias A, Minias P, Czubat B, Dziadek J. Purifying Selective Pressure Suggests the Functionality of a Vitamin B12 Biosynthesis Pathway in a Global Population of Mycobacterium tuberculosis. Genome Biol Evol 2019; 10:2326-2337. [PMID: 30060031 PMCID: PMC6363050 DOI: 10.1093/gbe/evy153] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium tuberculosis is one of the deadliest and most challenging pathogens to study in current microbiological research. One of the issues that remains to be resolved is the importance of cobalamin in the metabolism of M. tuberculosis. The functionality of a vitamin B12 biosynthesis pathway in M. tuberculosis is under dispute, and the ability of this pathogen to scavenge vitamin B12 from the host is unknown. Here, we quantified the ratios of nonsynonymous and synonymous nucleotide substitution rates (dN/dS) in the genes involved in vitamin B12 biosynthesis and transport and in genes encoding cobalamin-dependent enzymes in nearly four thousand strains of M. tuberculosis. We showed that purifying selection is the dominant force acting on cobalamin-related genes at the levels of individual codons, genes and groups of genes. We conclude that cobalamin-related genes may not be essential but are adaptive for M. tuberculosis in clinical settings. Furthermore, the cobalamin biosynthesis pathway is likely to be functional in this species.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection University of Łódź, Łódź, Poland
| | - Bożena Czubat
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland.,Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Rzeszów, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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20
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Borówka P, Pułaski Ł, Marciniak B, Borowska-Strugińska B, Dziadek J, Żądzińska E, Lorkiewicz W, Strapagiel D. Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples. Gigascience 2019; 8:5521156. [PMID: 31220249 PMCID: PMC6586198 DOI: 10.1093/gigascience/giz065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/07/2019] [Accepted: 05/10/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results. RESULTS Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (∼20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases. CONCLUSIONS Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy.
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Affiliation(s)
- Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Łukasz Pułaski
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland.,Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland
| | - Błażej Marciniak
- Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland.,BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland
| | - Beata Borowska-Strugińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland
| | - Elżbieta Żądzińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland.,BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland
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21
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Minias A, Brzostek A, Dziadek J. Targeting DNA Repair Systems in Antitubercular Drug Development. Curr Med Chem 2019; 26:1494-1505. [DOI: 10.2174/0929867325666180129093546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/01/2017] [Accepted: 11/01/2017] [Indexed: 11/22/2022]
Abstract
Infections with Mycobacterium tuberculosis, the causative agent of tuberculosis, are difficult to treat using currently available chemotherapeutics. Clinicians agree on the urgent need for novel drugs to treat tuberculosis. In this mini review, we summarize data that prompts the consideration of DNA repair-associated proteins as targets for the development of new antitubercular compounds. We discuss data, including gene expression data, that highlight the importance of DNA repair genes during the pathogenic cycle as well as after exposure to antimicrobials currently in use. Specifically, we report experiments on determining the essentiality of DNA repair-related genes. We report the availability of protein crystal structures and summarize discovered protein inhibitors. Further, we describe phenotypes of available gene mutants of M. tuberculosis and model organisms Mycobacterium bovis and Mycobacterium smegmatis. We summarize experiments regarding the role of DNA repair-related proteins in pathogenesis and virulence performed both in vitro and in vivo during the infection of macrophages and animals. We detail the role of DNA repair genes in acquiring mutations, which influence the rate of drug resistance acquisition.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Anna Brzostek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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22
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Masiewicz P, Brzostek A, Wolański M, Dziadek J, Zakrzewska-Czerwińska J. Correction: A Novel Role of the PrpR as a Transcription Factor Involved in the Regulation of Methylcitrate Pathway in Mycobacterium tuberculosis. PLoS One 2018; 13:e0208565. [PMID: 30507947 PMCID: PMC6277100 DOI: 10.1371/journal.pone.0208565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Antczak M, Płocińska R, Płociński P, Rumijowska-Galewicz A, Żaczek A, Strapagiel D, Dziadek J. The NnaR orphan response regulator is essential for the utilization of nitrate and nitrite as sole nitrogen sources in mycobacteria. Sci Rep 2018; 8:17552. [PMID: 30510199 PMCID: PMC6277429 DOI: 10.1038/s41598-018-35844-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/05/2018] [Indexed: 12/12/2022] Open
Abstract
Nitrogen is an essential component of biological molecules and an indispensable microelement required for the growth of cells. Nitrogen metabolism of Mycobacterium smegmatis is regulated by a number of transcription factors, with the glnR gene product playing a major role. Under nitrogen-depletion conditions, GlnR controls the expression of many genes involved in nitrogen assimilation, including the msmeg_0432 gene encoding NnaR, the homologue of a nitrite/nitrate transport regulator from Streptomyces coelicolor. In the present study, the role of NnaR in the nitrogen metabolism of M. smegmatis was evaluated. The ∆glnR and ∆nnaR mutant strains were generated and cultured under nitrogen-depletion conditions. Total RNA profiling was used to investigate the potential role of NnaR in the GlnR regulon under nitrogen-depletion and in nitrogen-rich media. We found that disruption of MSMEG_0432 affected the expression of genes involved in nitrite/nitrate uptake, and its removal rendered mycobacteria unable to assimilate nitrogen from those sources, leading to cell death. RNA-Seq results were validated using quantitative real-time polymerase chain reaction (qRT-PCR) and electrophoretic mobility shift assays (EMSAs). The ability of mutants to grow on various nitrogen sources was evaluated using the BIOLOG Phenotype screening platform and confirmed on minimal Sauton's medium containing various sources of nitrogen. The ∆glnR mutant was not able to convert nitrates to nitrites. Interestingly, NnaR required active GlnR to prevent nitrogen starvation, and both proteins cooperated in the regulation of gene expression associated with nitrate/nitrite assimilation. The ∆nnaR mutant was able to convert nitrates to nitrites, but it could not assimilate the products of this conversion. Importantly, NnaR was the key regulator of the expression of the truncated haemoglobin trHbN, which is required to improve the survival of bacteria under nitrosative stress.
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Affiliation(s)
- Magdalena Antczak
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Renata Płocińska
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | | | | | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland.
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24
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Żaczek A, Struś K, Sokołowska A, Parniewski P, Wojtasik A, Dziadek J. Differentiation of Clavibacter michiganensis subsp. sepedonicus using PCR melting profile and variable number of tandem repeat methods. Lett Appl Microbiol 2018; 68:24-30. [PMID: 30269341 DOI: 10.1111/lam.13081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/03/2018] [Accepted: 09/21/2018] [Indexed: 11/26/2022]
Abstract
The potato phytopathogen Clavibacter michiganensis subsp. sepedonicus (Cms) is a causative agent of bacterial ring rot, which is a serious threat to crops. In EU member countries, Cms is subject to quarantine and has to be combated. The knowledge about the transmission of C. michiganensis strains is limited due to a lack of methods which could be used for epidemiological analysis. In this study, PCR melting profile (PCR MP) and variable number tandem repeat methods were used in Cms epidemiological analysis for the first time. PCR MP was based on the melting temperature analysis of BamHI restriction fragments of chromosomal DNA. Respectively, for the variable number tandem repeat (VNTR) method, six loci were identified and used in the differentiation of Cms isolates. PCR MP was used for 93 Cms isolated in Poland. Both PCR MP and VNTR methods were used for the differentiation of 47 Cms strains in this collection. Both these methods were found to be useful for the epidemiological analysis of Cms. SIGNIFICANCE AND IMPACT OF THE STUDY: The potato phytopathogen, Clavibacter michiganensis subsp. sepedonicus (Cms), is a serious threat to crops and lead to significant economic losses. The only way to control and eliminate the disease caused by this pathogen is the use of certified seed potato and strict quarantine of infected fields. Here, for the first time, two molecular typing methods (PCR melting profile (PCR MP) and variable number tandem repeat (VNTR)) were evaluated in respect of their potential in differentiation of Cms isolates. As a result, we obtained characteristic profiles of DNA fragments (PCR MP) and numeric patterns (VNTR), which enable the intraspecies genotyping of Cms strains confirming the effectiveness of PCR MP and VNTR methods in differentiation of Cms strains.
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Affiliation(s)
- A Żaczek
- Department of Biochemistry and Cell Biology, Rzeszow University, Rzeszow, Poland
| | - K Struś
- Podkarpackie Center for Environmental Research and Development in Rzeszow, Rzeszow, Poland
| | - A Sokołowska
- Department of Biochemistry and Cell Biology, Rzeszow University, Rzeszow, Poland
| | - P Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - A Wojtasik
- Proteon Pharmaceuticals S.A., Lodz, Poland
| | - J Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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25
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Bakuła Z, Brzostek A, Borówka P, Żaczek A, Szulc-Kiełbik I, Podpora A, Parniewski P, Strapagiel D, Dziadek J, Proboszcz M, Bielecki J, van Ingen J, Jagielski T. Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis. Sci Rep 2018; 8:4462. [PMID: 29535391 PMCID: PMC5849605 DOI: 10.1038/s41598-018-21562-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/06/2018] [Indexed: 11/09/2022] Open
Abstract
Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston's discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.
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Affiliation(s)
- Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Paulina Borówka
- Department of Anthropology, University of Łódź, Łódź, Poland
| | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | | | - Agata Podpora
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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26
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Gatkowska J, Wieczorek M, Dziadek B, Dzitko K, Dziadek J, Długońska H. Assessment of the antigenic and neuroprotective activity of the subunit anti-Toxoplasma vaccine in T. gondii experimentally infected mice. Vet Parasitol 2018; 254:82-94. [PMID: 29657017 DOI: 10.1016/j.vetpar.2018.02.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 02/22/2018] [Accepted: 02/28/2018] [Indexed: 11/30/2022]
Abstract
The aim of this study was to evaluate the immunogenic and immunoprotective activities and to determine the neuroprotective capacity of the tetravalent vaccine containing selected recombinant T. gondii antigens (ROP2 + ROP4 + SAG1 + MAG1) administered with safe adjuvants (MPL and alum) using male and female inbred mice. The tested antigenic combination provided partial protection against brain cyst formation, especially in males (reduction in cyst burden by 72%). The decrease in cyst burden was observed for the whole brain as well as for specified brain regions associated with natural defensive behaviors, emotion processing and integration of motor and sensory stimuli. The vaccine triggered a strong, specific immune response, regardless of sex, which was characterized by the antigen-specific in vitro synthesis of cytokines (IL-2, IFN-γ and IL-10) and in vivo production of systemic IgG1 and IgG2a immunoglobulins. Immunization prior to the parasite challenge seemed to influence T. gondii - associated behavioral and neurochemical changes, although the impact of vaccination strongly depended on sex and time post-infection. Interestingly, in the vaccinated and T. gondii infected mice there was a significant delay in the parasite-induced loss of aversion toward cat smell (cats are the definitive hosts of the parasite). The regained attraction toward feline scent in vaccinated males, observed during chronic parasite invasion, correlated with the increase in the dopamine metabolism.
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Affiliation(s)
- Justyna Gatkowska
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Łódź, Banacha 12/16, Poland.
| | - Marek Wieczorek
- Department of Neurobiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Łódź, Pomorska 141/143, Poland.
| | - Bożena Dziadek
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Łódź, Banacha 12/16, Poland.
| | - Katarzyna Dzitko
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Łódź, Banacha 12/16, Poland.
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, 93-232 Łódź, Lodowa 106, Poland.
| | - Henryka Długońska
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Łódź, Banacha 12/16, Poland.
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27
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Dadura K, Płocińska R, Rumijowska-Galewicz A, Płociński P, Żaczek A, Dziadek B, Zaborowski A, Dziadek J. PdtaS Deficiency Affects Resistance of Mycobacteria to Ribosome Targeting Antibiotics. Front Microbiol 2017; 8:2145. [PMID: 29163430 PMCID: PMC5676007 DOI: 10.3389/fmicb.2017.02145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/19/2017] [Indexed: 11/13/2022] Open
Abstract
Two-component regulatory systems (TCSSs) are key regulatory elements responsible for the adaptation of bacteria to environmental stresses. A classical TCSS is typically comprised of a sensory histidine kinase and a corresponding response regulator. Here, we used homologous recombination to construct a Mycobacterium smegmatis mutant defective in the synthesis of cytosolic histidine kinase PdtaS (Msmeg_1918). The resulting ΔpdtaS mutant strain was tested in the Phenotype Microarray screening system, which allowed us to identify aminoglycoside antibiotic sensitivity, tetracyclines antibiotic resistance as well as membrane transport and respiration, as the main processes affected by removal of pdtaS. The antibiotic sensitivity profiles were confirmed by survival assessment and complementation studies. To gain insight into the molecular mechanisms responsible for the observed phenotype, we compared ribosomal RNA and protein profiles of the mutant and wild-type strains. We carried out Northern blotting and qRT-PCR to compare rRNA levels and analyzed ribosome sedimentation patterns of the wild-type and mutant strains on sucrose gradients. Isolated ribosomes were further used to estimate relative abundance of individual proteins in the ribosomal subunits using label free mass spectrometry analysis. Additionally, the ΔpdtaS mutant revealed lower activity of the respiratory chain as measured by the rate of TTC (triphenyltetrazolium chloride) reduction, while at the same time showing only insignificant changes in the uptake of aminoglycosides. We postulate that deficiency of PdtaS affects the oxidative respiration rates and ribosomal composition causing relevant changes to intrinsic resistance or susceptibility to antibiotics targeting ribosomes, which are commonly used to treat mycobacterial infections.
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Affiliation(s)
- Karolina Dadura
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Renata Płocińska
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | | | | | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | - Bożena Dziadek
- Department of Immunoparasitology, University of Łódź, Łódź, Poland
| | | | - Jarosław Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
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28
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Płociński P, Brissett NC, Bianchi J, Brzostek A, Korycka-Machała M, Dziembowski A, Dziadek J, Doherty AJ. DNA Ligase C and Prim-PolC participate in base excision repair in mycobacteria. Nat Commun 2017; 8:1251. [PMID: 29089537 PMCID: PMC5663958 DOI: 10.1038/s41467-017-01365-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 09/13/2017] [Indexed: 12/30/2022] Open
Abstract
Prokaryotic Ligase D is a conserved DNA repair apparatus processing DNA double-strand breaks in stationary phase. An orthologous Ligase C (LigC) complex also co-exists in many bacterial species but its function is unknown. Here we show that the LigC complex interacts with core BER enzymes in vivo and demonstrate that together these factors constitute an excision repair apparatus capable of repairing damaged bases and abasic sites. The polymerase component, which contains a conserved C-terminal structural loop, preferentially binds to and fills-in short gapped DNA intermediates with RNA and LigC ligates the resulting nicks to complete repair. Components of the LigC complex, like LigD, are expressed upon entry into stationary phase and cells lacking either of these pathways exhibit increased sensitivity to oxidising genotoxins. Together, these findings establish that the LigC complex is directly involved in an excision repair pathway(s) that repairs DNA damage with ribonucleotides during stationary phase. Ligase D is a conserved DNA repair protein complex that repairs double-strand breaks in stationary phase prokaryotes. Here the authors show that orthologous Ligase C has a role in base excision repair during stationary phase.
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Affiliation(s)
- Przemysław Płociński
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.,Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Lodz, Poland
| | - Nigel C Brissett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Julie Bianchi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.,Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet, R8:04, Karolinska Universitetssjukhuset Solna, 171 76, Stockholm, Sweden
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Lodz, Poland
| | | | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Lodz, Poland
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.
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Ratajewski M, Słomka M, Karaś K, Sobalska-Kwapis M, Korycka-Machała M, Sałkowska A, Dziadek J, Strapagiel D, Dastych J. Functional Analysis of the rs774872314, rs116171003, rs200231898 and rs201107751 Polymorphisms in the Human RORγT Gene Promoter Region. Genes (Basel) 2017; 8:genes8040126. [PMID: 28430123 PMCID: PMC5406873 DOI: 10.3390/genes8040126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 12/11/2022] Open
Abstract
RAR-related orphan receptor gamma RORγT, a tissue-specific isoform of the RORC gene, plays a critical role in the development of naive CD4+ cells into fully differentiated Th17 lymphocytes. Th17 lymphocytes are part of the host defense against numerous pathogens and are also involved in the pathogenesis of inflammatory diseases, including autoimmune disorders. In this study, we functionally examined four naturally occurring polymorphisms located within one of the previously identified GC-boxes in the promoter region of the gene. The single nucleotide polymorphisms (SNPs) rs774872314, rs116171003 and rs201107751 negatively influenced the activity of the RORγT promoter in a gene reporter system and eliminated or reduced Sp1 and Sp2 transcription factor binding, as evidenced by the electrophoretic mobility shift assay (EMSA) technique. Furthermore, we investigated the frequency of these SNPs in the Polish population and observed the presence of rs116171003 at a frequency of 3.42%. Thus, our results suggest that polymorphisms within the RORγT promoter occurring at significant rates in populations affect promoter activity. This might have phenotypic effects in immune systems, which is potentially significant for implicating pathogenetic mechanisms under certain pathological conditions, such as autoimmune diseases and/or primary immunodeficiencies (e.g., immunoglobulin E (IgE) syndrome).
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Affiliation(s)
- Marcin Ratajewski
- Laboratory of TranscriptionalRegulation, Institute of MedicalBiology, PolishAcademy of Sciences, 93-232 Lodz, Poland.
| | - Marcin Słomka
- BiobankLab, Department of MolecularBiophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland.
| | - Kaja Karaś
- Laboratory of TranscriptionalRegulation, Institute of MedicalBiology, PolishAcademy of Sciences, 93-232 Lodz, Poland.
| | - Marta Sobalska-Kwapis
- BiobankLab, Department of MolecularBiophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland.
| | - Małgorzata Korycka-Machała
- MycobacteriumGenetics and Physiology Unit, Institute of MedicalBiology, PolishAcademy of Sciences, 93-232 Lodz, Poland.
| | - Anna Sałkowska
- Laboratory of TranscriptionalRegulation, Institute of MedicalBiology, PolishAcademy of Sciences, 93-232 Lodz, Poland.
| | - Jarosław Dziadek
- MycobacteriumGenetics and Physiology Unit, Institute of MedicalBiology, PolishAcademy of Sciences, 93-232 Lodz, Poland.
| | - Dominik Strapagiel
- BiobankLab, Department of MolecularBiophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland.
| | - Jarosław Dastych
- Laboratory of Cellular Immunology, Institute of MedicalBiology, PolishAcademy of Sciences, 93-232 Lodz, Poland.
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Faletrov Y, Brzostek A, Plocinska R, Dziadek J, Rudaya E, Edimecheva I, Shkumatov V. Uptake and metabolism of fluorescent steroids by mycobacterial cells. Steroids 2017; 117:29-37. [PMID: 27718364 DOI: 10.1016/j.steroids.2016.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 09/29/2016] [Accepted: 10/01/2016] [Indexed: 11/26/2022]
Abstract
Fluorescent steroids BODIPY-cholesterol (BPCh) and 7-nitrobenzoxadiazole-4-amino-(NBD)-labeled 22-NBD-chelesterol (22NC) as well as synthesized 20-(NBD)-pregn-5-en-3β-ol (20NP) were found to undergo bioconversions by Mycobacterium tuberculosis H37Rv and M. smegmatis mc2 155. The major fluorescent products were determined to be 4-en-3-one derivatives of the compounds. Degradation of NBD fluorophore was also detected in the cases of 22NC and 20NP, but neither NBD degradation nor steroidal part modification were observed for the synthesized 3-(NBD)-cholestane. Mycobacterial 3β-hydroxysteroid dehydrogenases were concluded to be responsible for the formation of the 4-en-3-one derivatives. All the compounds tested were found to cause staining both membrane lipids and cytosolic lipid droplets when incubated with mycobacteria in different manner, demonstrating ability of the steroids to reside in the compartments. The findings reveal a potential of the compounds for monitoring of steroid interactions with mycobacteria and provide information for design of new probes for this purpose.
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Affiliation(s)
- Yaroslav Faletrov
- Research Institute for Physical Chemical Problems, Belarusian State University, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Minsk, Belarus.
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
| | - Renata Plocinska
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
| | - Elena Rudaya
- Research Institute for Physical Chemical Problems, Belarusian State University, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Minsk, Belarus.
| | - Irina Edimecheva
- Faculty of Chemistry, Belarusian State University, Minsk, Belarus.
| | - Vladimir Shkumatov
- Research Institute for Physical Chemical Problems, Belarusian State University, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Minsk, Belarus.
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Adamska A, Rumijowska-Galewicz A, Ruszczynska A, Studzińska M, Jabłońska A, Paradowska E, Bulska E, Munier-Lehmann H, Dziadek J, Leśnikowski ZJ, Olejniczak AB. Anti-mycobacterial activity of thymine derivatives bearing boron clusters. Eur J Med Chem 2016; 121:71-81. [DOI: 10.1016/j.ejmech.2016.05.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
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Mankiewicz-Boczek J, Bednarek A, Zaborowski A, Gągała I, Serwecińska L, Pawełczyk J, Dziadek J, Zalewski M. Microbiologically activated barriers for removal of nitrogen compounds from farm sewage. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2016.06.1174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Strapagiel D, Borówka P, Lorkiewicz W, Borowska-Strugińska B, Brzostek A, Dziadek J, Żądzińska E. Next generation sequencing in paleomicrobiology. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2016.06.948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Świerzko AS, Bartłomiejczyk MA, Brzostek A, Łukasiewicz J, Michalski M, Dziadek J, Cedzyński M. Mycobacterial antigen 85 complex (Ag85) as a target for ficolins and mannose-binding lectin. Int J Med Microbiol 2016; 306:212-21. [PMID: 27141819 DOI: 10.1016/j.ijmm.2016.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/07/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022] Open
Abstract
The pattern recognition molecules (PRMs) able to activate complement via the lectin pathway are suspected to be involved in the interaction between pathogenic Mycobacteria and the host immune response. Recently, we have found strong interactions between 25 and 35kDa mycobacterial cell fractions and mannose-binding lectin (MBL) and ficolins. Here we demonstrate that two biologically important mycobacterial structures, mannosylated lipoarabinomannan (ManLAM) and the antigen 85 (Ag85) complex, induce activation of the lectin pathway of complement. The strong interaction of recombinant MBL with purified ManLAM was confirmed, but no binding of recombinant ficolins (ficolin-1, -2, -3) with this structure was observed. Interestingly, all PRMs tested reacted with the mycobacterial antigen 85 (Ag85) complex. Based on the use of specific inhibitors (mannan for MBL, acetylated bovine serum albumin for ficolin-1 and -2, Hafnia alvei PCM 1200 lipopolysaccharide for ficolin-3), we concluded that carbohydrate-recognition (MBL) and fibrinogen-like domains (ficolins) were involved in these interactions. Our results indicate that the mycobacterial antigen 85 complex is a target for ficolins and MBL. Furthermore, those PRMs also bound to fibronectin and therefore might influence the Ag85 complex-dependent interaction of Mycobacterium with the extracellular matrix.
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Affiliation(s)
- Anna S Świerzko
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Marcin A Bartłomiejczyk
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Anna Brzostek
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Jolanta Łukasiewicz
- Department of Immunochemistry, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland
| | - Mateusz Michalski
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Maciej Cedzyński
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland.
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Wrońska N, Brzostek A, Szewczyk R, Soboń A, Dziadek J, Lisowska K. The Role of fadD19 and echA19 in Sterol Side Chain Degradation by Mycobacterium smegmatis. Molecules 2016; 21:molecules21050598. [PMID: 27164074 PMCID: PMC6273163 DOI: 10.3390/molecules21050598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/20/2016] [Accepted: 05/02/2016] [Indexed: 11/23/2022] Open
Abstract
Mycobacteria are able to degrade natural sterols and use them as a source of carbon and energy. Several genes which play an important role in cholesterol ring degradation have been described in Mycobacterium smegmatis. However, there are limited data describing the molecular mechanism of the aliphatic side chain degradation by Mycobacterium spp. In this paper, we analyzed the role of the echA19 and fadD19 genes in the degradation process of the side chain of cholesterol and β-sitosterol. We demonstrated that the M. smegmatis fadD19 and echA19 genes are not essential for viability. FadD19 is required in the initial step of the biodegradation of C-24 branched sterol side chains in Mycobacterium smegmatis mc2155, but not those carrying a straight chain like cholesterol. Additionally, we have shown that echA19 is not essential in the degradation of either substrate. This is the first report, to our knowledge, on the molecular characterization of the genes playing an essential role in C-24 branched side chain sterol degradation in M. smegmatis mc2155.
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Affiliation(s)
- Natalia Wrońska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Lodz, Poland.
| | - Rafał Szewczyk
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
| | - Adrian Soboń
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Lodz, Poland.
| | - Katarzyna Lisowska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Lodz, Poland.
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Mankiewicz-Boczek J, Jaskulska A, Pawełczyk J, Gągała I, Serwecińska L, Dziadek J. Cyanophages Infection of Microcystis Bloom in Lowland Dam Reservoir of Sulejów, Poland. Microb Ecol 2016; 71:315-25. [PMID: 26403721 DOI: 10.1007/s00248-015-0677-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/10/2015] [Indexed: 05/28/2023]
Abstract
An increased incidence of cyanobacterial blooms, which are largely composed of toxigenic cyanobacteria from the Microcystis genus, leads to a disruption of aquatic ecosystems worldwide. Therefore, a better understanding of the impact of environmental parameters on the development and collapse of blooms is important. The objectives of the present study were as follows: (1) to investigate the presence and identity of Microcystis-specific cyanophages capable of cyanobacterial cell lysis in a lowland dam reservoir in Central Europe; (2) to investigate Microcystis sensitivity to phage infections with regard to toxic genotypes; and (3) to identify key abiotic parameters influencing phage infections during the summer seasons between 2009 and 2013. Sequencing analysis of selected g91 gene amplification products confirmed that the identified cyanophages belonged to the family Myoviridae (95 % homology). Cyanophages and Microcystis hosts, including toxic genotypes, were positively correlated in 4 of the 5 years analyzed (r = 0.67-0.82). The average percentage of infected Microcystis cells varied between 0.1 and 32 %, and no particular sensitivity of the phages to toxigenic genotypes was recorded. The highest number of cyanophages (>10(4) gene copy number per microliter) was observed in the period preceded by the following: an increase of the water retention time, growth of the water temperature, optimum nutrient concentrations, and the predomination of Microcystis bloom.
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Affiliation(s)
- J Mankiewicz-Boczek
- Department of Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Łódź, Poland.
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland.
| | - A Jaskulska
- Department of Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Łódź, Poland
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
| | - J Pawełczyk
- Institute for Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - I Gągała
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
| | - L Serwecińska
- European Regional Centre for Ecohydrology, Polish Academy of Sciences, Tylna 3, 90-364, Łódź, Poland
| | - J Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
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Sarnik J, Czubatka-Bieńkowska A, Dziadek J, Witczak ZJ, Popławski T. [Thiosugars used as drugs]. Postepy Biochem 2016; 62:526-534. [PMID: 28132455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/07/2016] [Indexed: 06/06/2023]
Abstract
Thiosugars are carbohydrate analogs in which one or few of the oxygen atoms were replaced by sulfur. The sulfur atom which is present in the furan and pyran structures, changes biological properties of carbohydrates, as compared to their oxygen analogs. Among others, thiosugars are effective inhibitors of various cellular and enzymatic pathways and also have great therapeutic potential. They are used as a drugs in diabetes and infectious diseases treatment. Recent evidence suggests that these compounds may have therapeutic properties and be also used in the treatment of some pathological conditions, including cancer diseases. This research are aimed towards the development and improvement of the current methods of synthesis of new thiosugars through stabilization of sulfur bonds and in vitro and in vivo analysis of their potential therapeutic properties. In this work the summary of the latest reports about thiosugars and their application in the medicine is presented for the first time in the Polish language literature.
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Affiliation(s)
- Joanna Sarnik
- Department of Molecular Genetics, University of Lodz, Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
| | - Anna Czubatka-Bieńkowska
- Department of Molecular Genetics, University of Lodz, Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
| | - Jarosław Dziadek
- Mycobacterium Genetics and Physiology Unit, Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland
| | - Zbigniew J Witczak
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 West South St., Wilkes-Barre, PA 18766, USA
| | - Tomasz Popławski
- Department of Molecular Genetics, University of Lodz, Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
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38
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Słomka M, Sobalska-Kwapis M, Korycka-Machała M, Bartosz G, Dziadek J, Strapagiel D. Genetic variation of the ABC transporter gene ABCC1 (Multidrug resistance protein 1-MRP1) in the Polish population. BMC Genet 2015; 16:114. [PMID: 26395522 PMCID: PMC4579605 DOI: 10.1186/s12863-015-0271-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/11/2015] [Indexed: 11/12/2022] Open
Abstract
Background Multidrug resistance-associated protein 1 (MRP1), encoded by the ABCC1 gene, is an ATP-binding cassette transporter mediating efflux of organic anions and xenobiotics; its overexpression leads to multidrug resistance. In this study, 30 exons (from 31 in total) of the ABCC1 gene as well as and their flanking intron sequences were screened for genetic variation, using the High Resolution Melting (HRM) method, for 190 healthy volunteers representing the Polish population. Polymorphism screening is an indispensable step in personalized patient therapy. An additional targeted SNP verification study for ten variants was performed to verify sensitivity of the scanning method. Results During scanning, 46 polymorphisms, including seven novel ones, were found: one in 3’ UTR, 21 in exons (11 of them non-synonymous) and 24 in introns, including one deletion variant. These results revealed some ethnic differences in frequency of several polymorphisms when compared to literature data for other populations. Based on linkage disequilibrium analysis, 4 haplotype blocks were determined for 9 detected polymorphisms and 12 haplotypes were defined. To capture the common haplotypes, haplotype-tagging single nucleotide polymorphisms were identified. Conclusions Targeted genotyping results correlated well with scanning results; thus, HRM is a suitable method to study genetic variation in this model. HRM is an efficient and sensitive method for scanning and genotyping polymorphic variants. Ethnic differences were found for frequency of some variants in the Polish population compared to others. Thus, this study may be useful for pharmacogenetics of drugs affected by MRP1-mediated efflux. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0271-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231, Łódź, Poland.
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231, Łódź, Poland.
| | | | - Grzegorz Bartosz
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland.
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland.
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231, Łódź, Poland.
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Mankiewicz-Boczek J, Gągała I, Jurczak T, Jaskulska A, Pawełczyk J, Dziadek J. Bacteria homologus to Aeromonas capable of microcystin degradation. Open Life Sci 2015. [DOI: 10.1515/biol-2015-0012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractWater blooms dominated by cyanobacteria are capable of producing hepatotoxins known as microcystins. These toxins are dangerous to people and to the environment. Therefore, for a better understanding of the biological termination of this increasingly common phenomenon, bacteria with the potential to degrade cyanobacteria-derived hepatotoxins and the degradative activity of culturable bacteria were studied. Based on the presence of the mlrA gene, bacteria with a homology to the Sphingopyxis and Stenotrophomonas genera were identified as those presenting potential for microcystins degradation directly in the water samples from the Sulejów Reservoir (SU, Central Poland). However, this biodegrading potential has not been confirmed in in vitro experiments. The degrading activity of the culturable isolates from the water studied was determined in more than 30 bacterial mixes. An analysis of the biodegradation of the microcystin-LR (MC-LR) together with an analysis of the phylogenetic affiliation of bacteria demonstrated for the first time that bacteria homologous to the Aeromonas genus were able to degrade the mentioned hepatotoxin, although the mlrA gene was not amplified. The maximal removal efficiency of MC-LR was 48%. This study demonstrates a new aspect of interactions between the microcystin-containing cyanobacteria and bacteria from the Aeromonas genus.
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Affiliation(s)
- J. Mankiewicz-Boczek
- 1European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Łódź, 90-364, Poland
- 2Department of Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, 90-237, Poland
| | - I. Gągała
- 1European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Łódź, 90-364, Poland
| | - T. Jurczak
- 2Department of Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, 90-237, Poland
| | - A. Jaskulska
- 2Department of Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, 90-237, Poland
| | - J. Pawełczyk
- 3Institute for Medical Biology of the Polish Academy of Sciences, Łódź, 93-232, Poland
| | - J. Dziadek
- 3Institute for Medical Biology of the Polish Academy of Sciences, Łódź, 93-232, Poland
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40
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Grzybowski MM, Dziadek B, Dziadek J, Gatkowska J, Dzitko K, Długońska H. Toxoplasma gondii: cloning, expression and immunoreactivity of recombinant ROP5 and ROP18 antigens. Exp Parasitol 2015; 150:1-6. [PMID: 25592730 DOI: 10.1016/j.exppara.2015.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/19/2014] [Accepted: 01/07/2015] [Indexed: 11/17/2022]
Abstract
Early diagnosis and determining the infective stage are critical for effective therapy of toxoplasmosis. Owing to the progress in biotechnology, commonly used native, non-standardized diagnostic antigens should be replaced by genetically engineered antigens. The recombinant proteins are also promising components of subunit vaccines against Toxoplasma gondii infections. A strategic biological role of rhoptry proteins (ROP) in parasitophorous vacuole biogenesis and virulence of the parasite creates a necessity for an intensive study on the serological activity and immunogenicity of newly developed recombinant ROP antigens. Our findings indicate that all generated preparations of recombinant ROP5 and ROP18 antigens, expressed in Escherichia coli bacteria, are recognized by specific antibodies produced during acute and chronic infections in inbred laboratory mice. We noticed, for the first time, that ROP5 IgM antibodies are an early and sensitive marker of T. gondii infection. The proven immunoreactivity of the obtained preparations has become a premise for a further study on their utility in routine diagnosis of human and animal toxoplasmosis as well as in the immunoprevention of T. gondii infection (as the main or supplementary component of the vaccine).
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Affiliation(s)
- Marcin M Grzybowski
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - Bożena Dziadek
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Justyna Gatkowska
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Katarzyna Dzitko
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Henryka Długońska
- Department of Immunoparasitology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Zaczek A, Szwaja I, Skiba M, Brzostek A, Puchalski C, Lewandowska K, Dziadek J. Epidemiological Analysis of Mycobacterium tuberculosis Strains Isolated from Patients of Small Communities Living in the South-East of Poland. Pol J Microbiol 2015; 64:289-293. [PMID: 26638538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
The diversity of Mycobacterium tuberculosis clinical isolates, collected from a single hospital, was analyzed by ligation-mediated PCR techniques: FLiP and FLAP, and hybridization technique, IS6110-RFLP. The isolated strains were divided in terms of location (3 towns of Podkarpackie voivodeship differing in population size) and relationship (8 members of 4 families, each represented by 2 patients). Within each family identical DNA profiles, as well as drug resistance patterns were identified indicating a great chance of transmission of strains within the same family. Identical, or very similar patterns were also shared by strains isolated from unrelated patients living in a very small town (1 200 inhabitants) or hospitalized in the same place and time.
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Gatkowska JM, Dziadek B, Dziadek J, Dzitko K, Długońska H. Recombinant MAG1 Protein of Toxoplasma gondii as a Diagnostic Antigen. Pol J Microbiol 2015; 64:55-59. [PMID: 26094316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
The aim of this study was to evaluate the potential diagnostic usefulness of the full-length recombinant Toxoplasma gondii MAG1 protein by determining the levels of specific IgM and IgG antibodies in mouse and human sera obtained from individuals with acute and chronic toxoplasmosis. The obtained results revealed that IgG antibodies against MAG1 are a sensitive and specific marker of T. gondii infection since the protein was recognized by both mouse and human sera, 100% and 94.3%, respectively, rendering the full-length rMAG1 a prospective alternative for the polyvalent native antigen (TLA).
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Bartlomiejczyk MA, Swierzko AS, Brzostek A, Dziadek J, Cedzynski M. Interaction of lectin pathway of complement-activating pattern recognition molecules with mycobacteria. Clin Exp Immunol 2014; 178:310-9. [PMID: 25041480 DOI: 10.1111/cei.12416] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2014] [Indexed: 11/30/2022] Open
Abstract
We have demonstrated that mannose-binding lectin (MBL) recognizes various slow-growing, pathogenic mycobacteria [Mycobacterium tuberculosis (MTB), M. bovis, M. kansasii, M. gordonae] as well as non-pathogenic M. smegmatis. Recognition resulted in activation of the lectin pathway (LP) of complement and an enhancement of phagocytosis (shown for M. tuberculosis). Although MBL may be considered the main factor activating the LP upon recognition of mycobacteria, involvement of ficolins has also to be considered. Interaction of ficolin-3 with M. tuberculosis, M. bovis and M. kansasii, and ficolin-1 with M. tuberculosis and M. bovis was shown for the first time. Binding of recombinant MBL or ficolin-3 to MTB H37 Rv led to the agglutination of bacteria and promoted their phagocytosis, but little effect was apparent with ficolin-1 or ficolin-2. Data from Western blots suggest mannosylated lipoarabinomannan (ManLAM) to be one of the main cell components of slow-growing mycobacteria, involved in LP activation. However, the LP was also activated by other cell fractions. Results presented here supplement considerably the data concerning the ability of complement-activating lectins to interact with mycobacteria. Ficolins (especially ficolin-3) might influence host response to infection and thus have clinical significance, at least as disease modifiers.
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Affiliation(s)
- M A Bartlomiejczyk
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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Masiewicz P, Wolański M, Brzostek A, Dziadek J, Zakrzewska-Czerwińska J. Erratum to: Propionate represses the dnaA gene via the methylcitrate pathway-regulating transcription factor, PrpR, in Mycobacterium tuberculosis. Antonie Van Leeuwenhoek 2014. [PMCID: PMC4643565 DOI: 10.1007/s10482-014-0278-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paweł Masiewicz
- />Department of Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
- />Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marcin Wolański
- />Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Anna Brzostek
- />Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Jarosław Dziadek
- />Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- />Department of Microbiology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
- />Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Minias P, Minias A, Dziadek J. Heterozygosity correlates with body size, nest site quality and productivity in a colonial waterbird, the whiskered tern ( Chlidonias hybrida, Aves: Sternidae). J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Piotr Minias
- Department of Teacher Training and Biodiversity Studies; University of Łódź; Łódź Poland
| | - Alina Minias
- Institute of Medical Biology of the Polish Academy of Sciences; Łódź Poland
| | - Jarosław Dziadek
- Institute of Medical Biology of the Polish Academy of Sciences; Łódź Poland
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Żaczek A, Brzostek A, Kuroń A, Wojtasik A, Sajduda A, Dziadek J. Development of a new ligation-mediated PCR method for the differentiation of Mycobacterium tuberculosis strains. Int J Tuberc Lung Dis 2014; 18:302-9. [DOI: 10.5588/ijtld.13.0538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Gągała I, Izydorczyk K, Jurczak T, Pawełczyk J, Dziadek J, Wojtal-Frankiewicz A, Jóźwik A, Jaskulska A, Mankiewicz-Boczek J. Role of environmental factors and toxic genotypes in the regulation of microcystins-producing cyanobacterial blooms. Microb Ecol 2014; 67:465-79. [PMID: 24241584 DOI: 10.1007/s00248-013-0303-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 09/30/2013] [Indexed: 05/23/2023]
Abstract
The aim of this study was to understand: (1) how environmental conditions can contribute to formation of Microcystis-dominated blooms in lowland, dam reservoirs in temperate climate-with the use of quantitative molecular monitoring, and (2) what is the role of toxic Microcystis genotypes in the bloom functioning. Monitoring of the Sulejow Reservoir in 2009 and 2010 in two sites Tresta (TR) and Bronislawow BR), which have different morphometry, showed that physicochemical conditions were always favorable for cyanobacterial bloom formation. In 2009, the average biomass of cyanobacteria reached 13 mg L(-1) (TR) and 8 mg L(-1) (BR), and in the second year, it decreased to approximately 1 mg L(-1) (TR and BR). In turns, the mean number of toxic Microcystis genotypes in the total Microcystis reached 1% in 2009, both in TR and BR, and in 2010, the number increased to 70% in TR and 14 % in BR. Despite significant differences in the biomass of cyanobacteria in 2009 and 2010, the mean microcystins (MCs) concentration and toxicity stayed at a similar level of approximately 1 μg L(-1). Statistical analysis indicated that water retention time was a factor that provided a significant difference between the two monitoring seasons and was considered a driver of the changes occurring in the Sulejow Reservoir. Hydrologic differences, which occurred between two studied years due to heavy flooding in Poland in 2010, influenced the decrease in number of Microcystis biomass by causing water disturbances and by lowering water temperature. Statistical analysis showed that Microcystis aeruginosa biomass and 16S rRNA gene copy number representing Microcystis genotypes in both years of monitoring could be predicted on the basis of total and dissolved phosphorus concentrations and water temperature. In present study, the number of mcyA gene copies representing toxic Microcystis genotypes could be predicted based on the biomass of M. aeruginosa. Moreover, MCs toxicity and concentration could be predicted on the basic of mcyA gene copy number and M. aeruginosa (biomass, 16S rRNA), respectively. Present findings may indicate that Microcystis can regulate the number of toxic genotypes, and in this way adjust the whole bloom to be able to produce MCs at the level which is necessary for its maintenance in the Sulejow Reservoir under stressful hydrological conditions.
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Affiliation(s)
- Ilona Gągała
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364, Lodz, Poland,
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Bartlomiejczyk M, Swierzko A, Brzostek A, Dziadek J, Cedzynski M. The interaction of complement-activating lectins with Mycobacterium tuberculosis. Mol Immunol 2013. [DOI: 10.1016/j.molimm.2013.05.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sokolowska A, Swierzko A, Szala A, Michalski M, Augustynowcz-Kopec E, Niemiec T, Blachnio M, Dziadek J, Cedzynski M. Collectins and ficolins in Mycobacterium tuberculosis infections in Polish patients. Mol Immunol 2013. [DOI: 10.1016/j.molimm.2013.05.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Arranz SE, Avarre JC, Balasundaram C, Bouza C, Calcaterra NB, Cezilly F, Chen SL, Cipriani G, Cruz VP, D'Esposito D, Daniel C, Dejean A, Dharaneedharan S, Díaz J, Du M, Durand JD, Dziadek J, Foresti F, Peng-cheng F, Gao QB, García G, Gauffre-Autelin P, Giovino A, Goswami M, Guarino C, Guerra-Varela J, Gutiérrez V, Harris DJ, Heo MS, Khan G, Kim M, Lakra WS, Lauth J, Leclercq P, Lee J, Lee SH, Lee S, Lee T, Li YH, Liu H, Liu S, Malé PJG, Mandhan RP, Martinez P, Mayer VE, Mendel J, Mendes NJ, Mendonça FF, Minias A, Minias P, Oh KS, Oliveira C, Orivel J, Orsini L, Pardo BG, Perera A, Procaccini G, Rato C, Ríos N, Scibetta S, Sharma BS, Sierens T, Singh A, Terer T, Triest L, Urbánková S, Vera M, Villanova GV, Voglmayr H, Vyskočilová M, Wang H, Wang JL, Wattier RA, Xing R, Yadav K, Yin G, Yuan Y, Yun JC, Zhang FQ, Zhang JH, Zhuang Z. Permanent genetic resources added to molecular ecology resources database 1 December 2012-31 January 2013. Mol Ecol Resour 2013; 13:546-9. [PMID: 23521844 DOI: 10.1111/1755-0998.12095] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba.
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Affiliation(s)
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- Molecular Ecology Resources Editorial Office, Vancouver, BC, V6T 1Z4, Canada.
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