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Article ; Online: The structure of O-polysaccharide isolated from the type strain of Pectobacterium versatile CFBP6051

Kowalczyk, Agnieszka / Babińska-Wensierska, Weronika / Lojkowska, Ewa / Kaczyński, Zbigniew

2023 Volume 524, Page(s) 108743

Abstract: Utilizing sugar, methylation, and absolute configurations analyses as well as NMR spectroscopy, the chemical repeating unit of the O-specific polysaccharide of Pectobacteriumversatile ... ...

Abstract	Utilizing sugar, methylation, and absolute configurations analyses as well as NMR spectroscopy, the chemical repeating unit of the O-specific polysaccharide of Pectobacteriumversatile CFBP6051
MeSH term(s)	Carbohydrate Sequence ; Monosaccharides ; Pectobacterium/chemistry ; O Antigens/chemistry ; Magnetic Resonance Spectroscopy
Chemical Substances	Monosaccharides ; O Antigens
Language	English
Publishing date	2023-01-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1435-7
ISSN	1873-426X ; 0008-6215
ISSN (online)	1873-426X
ISSN	0008-6215
DOI	10.1016/j.carres.2023.108743
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Article ; Online: Genome-Wide Analyses of the Temperature-Responsive Genetic Loci of the Pectinolytic Plant Pathogenic

Kaczynska, Natalia / Lojkowska, Ewa / Narajczyk, Magdalena / Czajkowski, Robert

International journal of molecular sciences

2021 Volume 22, Issue 9

Abstract: Temperature is one of the critical factors affecting gene expression in bacteria. Despite the general interest in the link between bacterial phenotypes and environmental temperature, little is known about temperature-dependent gene expression in plant ... ...

Abstract	Temperature is one of the critical factors affecting gene expression in bacteria. Despite the general interest in the link between bacterial phenotypes and environmental temperature, little is known about temperature-dependent gene expression in plant pathogenic
MeSH term(s)	DNA Transposable Elements/genetics ; Disease Resistance/genetics ; Gene Expression Regulation, Bacterial/genetics ; Genome-Wide Association Study ; Pectins/chemistry ; Pectins/genetics ; Pectobacterium/genetics ; Pectobacterium/pathogenicity ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Solanum tuberosum/genetics ; Solanum tuberosum/microbiology ; Temperature ; Transposases/genetics
Chemical Substances	DNA Transposable Elements ; Tn5 transposase ; Pectins (89NA02M4RX) ; Transposases (EC 2.7.7.-)
Language	English
Publishing date	2021-05-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22094839
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Article ; Online: Phyloproteomic study by MALDI-TOF MS in view of intraspecies variation in a significant homogenous phytopathogen Dickeya solani.

Motyka-Pomagruk, Agata / Babinska-Wensierska, Weronika / Sledz, Wojciech / Kaczorowska, Anna-Karina / Lojkowska, Ewa

Scientific reports

2023 Volume 13, Issue 1, Page(s) 18863

Abstract: Dickeya solani is an economically significant pectinolytic phytopathogen belonging to the Pectobacteriaceae family, which causes soft rot and blackleg diseases. Despite its notable impact on global potato production, there are no effective methods to ... ...

Abstract	Dickeya solani is an economically significant pectinolytic phytopathogen belonging to the Pectobacteriaceae family, which causes soft rot and blackleg diseases. Despite its notable impact on global potato production, there are no effective methods to control this pest. Here, we undertook a phyloproteomic study on 20 D. solani strains, of various origin and year of isolation, with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) supported by an in-depth characterization of the strains in terms of the virulence-associated phenotype. In spite of high homogeneity in this species, we herein revealed for the first time intraspecies variation in the MALDI-TOF MS protein profiles among the studied D. solani isolates. Finally, representative mass spectra for the four delineated clades are presented. A majority of the analysed D. solani strains showed high virulence potential, while two strains stood out in their growth dynamics, virulence factors production and ability to macerate plant tissue. Nonetheless, the metabolic profiles of D. solani strains turned out to be uniform, except for gelatinase activity. Given that all D. solani isolates distinctly grouped from the other Dickeya species in the MALDI-TOF MS analysis, there is strong evidence supporting the potential routine use of this method for fast and reliable to-species identification of D. solani isolates of environmental origin.
MeSH term(s)	Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Enterobacteriaceae/genetics ; Dickeya ; Gammaproteobacteria
Language	English
Publishing date	2023-11-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-46012-3
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Article ; Online: The chemical structure of the O-antigen and enterobacterial common antigen of Pectobacterium brasiliense NCPPB 4609

Kowalczyk, Agnieszka / Kaczyńska, Natalia / Motyka-Pomagruk, Agata / Śledź, Wojciech / Łojkowska, Ewa / Kaczyński, Zbigniew

Carbohydrate research

2023 Volume 534, Page(s) 108983

Abstract: Pectobacterium brasiliense is a widely distributed phytopathogenic bacterium that causes diseases such as soft rot and blackleg, leading to significant yield losses in potatoes as well as other vegetables and ornamental plants. Lipopolysaccharide (LPS) ... ...

Abstract	Pectobacterium brasiliense is a widely distributed phytopathogenic bacterium that causes diseases such as soft rot and blackleg, leading to significant yield losses in potatoes as well as other vegetables and ornamental plants. Lipopolysaccharide (LPS) is an important virulence factor that plays an essential role in colonisation of plant tissues and overcoming the host defence mechanisms. The O-polysaccharide from the LPS of P. brasiliense strain NCPPB 4609
MeSH term(s)	O Antigens/chemistry ; Lipopolysaccharides/chemistry ; Pectobacterium
Chemical Substances	O Antigens ; Lipopolysaccharides ; enterobacterial common antigen
Language	English
Publishing date	2023-11-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1435-7
ISSN	1873-426X ; 0008-6215
ISSN (online)	1873-426X
ISSN	0008-6215
DOI	10.1016/j.carres.2023.108983
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Article ; Online: The chemical structure of the O-polysaccharide isolated from the lipopolysaccharide of Pectobacterium brasiliense IFB5527, a phytopathogenic bacterium of high economic importance

Szulta, Sylwia / Kowalczyk, Agnieszka / Czerwicka-Pach, Małgorzata / Motyka-Pomagruk, Agata / Śledź, Wojciech / Kaczyńska, Natalia / Łojkowska, Ewa / Kaczyński, Zbigniew

Carbohydrate Research. 2023 May, v. 527 p.108806-

2023

Abstract: Pectobacterium brasiliense is a widespread plant pathogenic bacterium classified to the Pectobacteriaceae family, which causes significant economic losses because of the developed soft rot and blackleg symptoms on potatoes and a wide spectrum of crops, ... ...

Abstract	Pectobacterium brasiliense is a widespread plant pathogenic bacterium classified to the Pectobacteriaceae family, which causes significant economic losses because of the developed soft rot and blackleg symptoms on potatoes and a wide spectrum of crops, vegetables, and ornamentals. One of the key virulence factors is a lipopolysaccharide due to its involvement in efficient colonisation of plant tissues and overcoming the host defence mechanisms. Thus, we structurally characterised the O-polysaccharide from the LPS of P. brasiliense strain IFB5527 (HAFL05) using chemical methods followed by GLC and GLC-MS as well as 1D and 2D NMR spectroscopy. The analyses revealed that the polysaccharide repeating unit consists of Fuc, Glc, GlcN and an unusual N-formylated 6-deoxy amino sugar, Qui3NFo, and has the structure shown below: [Display omitted]
Keywords	Pectobacterium ; chemical structure ; lipopolysaccharides ; nuclear magnetic resonance spectroscopy ; ornamental plants ; plant pathogenic bacteria ; research ; sugars ; virulence ; Lipopolysaccharide ; O-polysaccharide structure ; Pectobacterium brasiliense ; Soft rot
Language	English
Dates of publication	2023-05
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	1435-7
ISSN	1873-426X ; 0008-6215
ISSN (online)	1873-426X
ISSN	0008-6215
DOI	10.1016/j.carres.2023.108806
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Article ; Online: PacBio-Based Protocol for Bacterial Genome Assembly.

Motyka-Pomagruk, Agata / Zoledowska, Sabina / Kabza, Michal / Lojkowska, Ewa

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2242, Page(s) 3–14

Abstract: Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this ... ...

Abstract	Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000 bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline based on open-source software that might be handled also by non-bioinformaticians interested in transformation of sequencing data into reliable biological information. With the use of this method, we successfully closed six Dickeya solani genomes, while the assembly process was run just on a slightly improved desktop computer.
MeSH term(s)	DNA, Bacterial/genetics ; Databases, Genetic ; Dickeya/genetics ; Genome, Bacterial ; Genomics ; High-Throughput Nucleotide Sequencing ; Research Design ; Single Molecule Imaging ; Whole Genome Sequencing ; Workflow
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2021-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1099-2_1
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Article ; Online: Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study.

Zoledowska, Sabina / Motyka-Pomagruk, Agata / Misztak, Agnieszka / Lojkowska, Ewa

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2242, Page(s) 91–112

Abstract: High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from ...

Abstract	High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. All of them were applied in the studies focused on revealing inter- and intraspecies variation in pectinolytic plant pathogenic bacteria classified to Dickeya solani and Pectobacterium parmentieri. As the described software performed well on the species within the Pectobacteriaceae family, it presumably may be readily utilized on some closely related taxa from the Enterobacteriaceae family. First of all, implementation of various annotation software is discussed and compared. Then, tools computing whole genome comparisons including generation of circular juxtapositions of multiple sequences, revealing the order of synteny blocks or calculation of ANI or Tetra values are presented. Besides, web servers intended either for functional annotation of the genes of interest or for detection of genomic islands, plasmids, prophages, CRISPR/Cas are described. Last but not least, utilization of the software designed for pangenome studies and the further downstream analyses is explained. The presented work not only summarizes broad possibilities assured by the comparative genomic approach but also provides a user-friendly guide that might be easily followed by nonbioinformaticians interested in undertaking similar studies.
MeSH term(s)	DNA, Bacterial/genetics ; Databases, Genetic ; Dickeya/genetics ; Genome, Bacterial ; Genomics ; High-Throughput Nucleotide Sequencing ; Pectobacterium/genetics ; Research Design ; Sequence Analysis, DNA ; Software Design ; Workflow
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2021-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1099-2_7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The chemical structure of the O-polysaccharide isolated from the lipopolysaccharide of Pectobacterium brasiliense IFB5527, a phytopathogenic bacterium of high economic importance.

Szulta, Sylwia / Kowalczyk, Agnieszka / Czerwicka-Pach, Małgorzata / Motyka-Pomagruk, Agata / Śledź, Wojciech / Kaczyńska, Natalia / Łojkowska, Ewa / Kaczyński, Zbigniew

Carbohydrate research

2023 Volume 527, Page(s) 108806

Abstract	Pectobacterium brasiliense is a widespread plant pathogenic bacterium classified to the Pectobacteriaceae family, which causes significant economic losses because of the developed soft rot and blackleg symptoms on potatoes and a wide spectrum of crops, vegetables, and ornamentals. One of the key virulence factors is a lipopolysaccharide due to its involvement in efficient colonisation of plant tissues and overcoming the host defence mechanisms. Thus, we structurally characterised the O-polysaccharide from the LPS of P. brasiliense strain IFB5527 (HAFL05) using chemical methods followed by GLC and GLC-MS as well as 1D and 2D NMR spectroscopy. The analyses revealed that the polysaccharide repeating unit consists of Fuc, Glc, GlcN and an unusual N-formylated 6-deoxy amino sugar, Qui3NFo, and has the structure shown below.
MeSH term(s)	Lipopolysaccharides ; Pectobacterium/chemistry ; Polysaccharides/chemistry
Chemical Substances	Lipopolysaccharides ; Polysaccharides
Language	English
Publishing date	2023-04-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1435-7
ISSN	1873-426X ; 0008-6215
ISSN (online)	1873-426X
ISSN	0008-6215
DOI	10.1016/j.carres.2023.108806
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Plumbagin Increases Paclitaxel-Induced Cell Death and Overcomes Paclitaxel Resistance in Breast Cancer Cells through ERK-Mediated Apoptosis Induction.

Kawiak, Anna / Domachowska, Anna / Lojkowska, Ewa

Journal of natural products

2019 Volume 82, Issue 4, Page(s) 878–885

Abstract: ERK is a component of mitogen-activated protein kinases that controls a range of cellular processes including cell proliferation and survival. The upregulation of ERK has been associated with apoptosis inhibition in response to various stimuli including ... ...

Abstract	ERK is a component of mitogen-activated protein kinases that controls a range of cellular processes including cell proliferation and survival. The upregulation of ERK has been associated with apoptosis inhibition in response to various stimuli including chemotherapeutic agents. Research has suggested that the upregulation of ERK signaling by the anticancer agent paclitaxel leads to acquired resistance of cells to this compound. The presented research focused on determining the role of plumbagin, a naturally derived naphthoquinone, in the sensitization of breast cancer cells to paclitaxel-induced cell death and the involvement of ERK signaling in this process. The results of the study indicated that plumbagin increases the sensitivity of breast cancer cells to paclitaxel. Moreover, a synergistic effect between plumbagin and paclitaxel was observed. Plumbagin was shown to decrease levels of phosphorylated ERK in breast cancer cells and abrogated paclitaxel-induced ERK phosphorylation. The role of ERK in plumbagin-mediated sensitization of breast cancer cells to paclitaxel was shown through the enhancement of the synergistic effect between compounds in cells with decreased ERK expression. Furthermore, plumbagin reduced p-ERK levels in paclitaxel-resistant breast cancer cells and resensitized paclitaxel-resistant cells to this compound. These results imply that plumbagin inhibits ERK activation in breast cancer cells, which plays a role in the sensitization of cells to paclitaxel-induced cell death.
MeSH term(s)	Antineoplastic Agents, Phytogenic/administration & dosage ; Antineoplastic Agents, Phytogenic/pharmacology ; Apoptosis/drug effects ; Cell Line, Tumor ; Drug Resistance, Neoplasm/drug effects ; Drug Synergism ; Enzyme Activation ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Female ; Humans ; Naphthoquinones/administration & dosage ; Naphthoquinones/pharmacology ; Paclitaxel/administration & dosage ; Paclitaxel/pharmacology
Chemical Substances	Antineoplastic Agents, Phytogenic ; Naphthoquinones ; Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24) ; Paclitaxel (P88XT4IS4D) ; plumbagin (YAS4TBQ4OQ)
Language	English
Publishing date	2019-02-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	304325-3
ISSN	1520-6025 ; 0163-3864
ISSN (online)	1520-6025
ISSN	0163-3864
DOI	10.1021/acs.jnatprod.8b00964
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Article ; Online: Characterisation of Pectinolytic Bacillus pumilus and Paenibacillus amyloliticus Strains, New Pathogens of Potato in Tunisia

Yahyaoui, Anissa / Oueslati, Maroua / Motyka-Pomagruk, Agata / Kaczynska, Natalia / Sledz, Wojciech / Tarhouni, Belhassen / Hajlaoui, Mohamed Rabeh / Lojkowska, Ewa / Sadfi-Zouaoui, Najla

Agriculture. 2023 June 20, v. 13, no. 6

2023

Abstract: Soft rot disease in potato is a major problem in fields and warehouses all over the world. Although it is known that bacteria from the genera Pectobacterium and Dickeya are the main causative agents of soft rot diseases, recent studies indicate the ... ...

Abstract	Soft rot disease in potato is a major problem in fields and warehouses all over the world. Although it is known that bacteria from the genera Pectobacterium and Dickeya are the main causative agents of soft rot diseases, recent studies indicate the involvement of pectinolytic Bacillus and Paenibacillus in this disease. In the present research, samples of potato with soft rot symptoms were collected from eight governorates of Tunisia. Two hundred and seventy bacterial isolates were acquired from tubers. Twenty of the isolated strains indicted pectinolytic activity by forming deep cavities on crystal violet pectate medium. All pectinolytic isolates were able to macerate potato tuber tissue. Phenotypic characterisation showed that these isolates were Gram-positive bacilli, exhibiting pectinolytic, cellulolytic, proteolytic and amylolytic activity. The majority of the isolates indicated swimming and swarming motility. The application of API test, MALDI-TOF MS and 16S rDNA sequencing allowed for the assignment of nineteen of the tested isolates to the species Bacillus pumilus and one to the species Paenibacillus amyloliticus. To the best of our knowledge, this is the first report of soft rot in potato caused by pectinolytic B. pumilus in Tunisia.
Keywords	Bacillus pumilus ; Dickeya ; Paenibacillus ; Pectobacterium ; agriculture ; enzyme activity ; gentian violet ; phenotype ; potatoes ; proteolysis ; Tunisia
Language	English
Dates of publication	2023-0620
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2651678-0
ISSN	2077-0472
ISSN	2077-0472
DOI	10.3390/agriculture13061275
Database	NAL-Catalogue (AGRICOLA)

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