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Host plant physiological transformation and microbial population heterogeneity as important determinants of the Soft Rot Pectobacteriaceae-plant interactions. Semin Cell Dev Biol 2023; 148-149:33-41. [PMID: 36621443 DOI: 10.1016/j.semcdb.2023.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Pectobacterium and Dickeya species belonging to the Soft Rot Pectobacteriaceae (SRP) are one of the most devastating phytopathogens. They degrade plant tissues by producing an arsenal of plant cell wall degrading enzymes. However, SRP-plant interactions are not restricted to the production of these "brute force" weapons. Additionally, these bacteria apply stealth behavior related to (1) manipulation of the host plant via induction of susceptible responses and (2) formation of heterogeneous populations with functionally specialized cells. Our review aims to summarize current knowledge on SRP-induced plant susceptible responses and on the heterogeneity of SRP populations. The review shows that SRP are capable of adjusting the host's hormonal balance, inducing host-mediated plant cell wall modification, promoting iron assimilation by the host, stimulating the accumulation of reactive oxygen species and host cell death, and activating the synthesis of secondary metabolites that are ineffective in limiting disease progression. By this means, SRP facilitate host plant susceptibility. During host colonization, SRP populations produce various functionally specialized cells adapted for enhanced virulence, increased resistance, motility, vegetative growth, or colonization of the vascular system. This enables SRP to perform self-contradictory tasks, which benefits a population's overall fitness in various environments, including host plants. Such stealthy tactical actions facilitate plant-SRP interactions and disease progression.
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Gogoleva NE, Kataev VY, Balkin AS, Plotnikov AO, Shagimardanova EI, Subbot AM, Cherkasov SV, Gogolev YV. Dataset for transcriptome analysis of Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S response to starvation. Data Brief 2020; 31:106008. [PMID: 32695865 PMCID: PMC7364113 DOI: 10.1016/j.dib.2020.106008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica is an ubiquitous pathogen throughout the world causing gastroenteritis in humans and animals. Survival of pathogenic bacteria in the external environment may be associated with the ability to overcome the stress caused by starvation. The bacterial response to starvation is well understood in laboratory cultures with a sufficiently high cell density. However, bacterial populations often have a small size when facing this challenge in natural biotopes. The aim of this work was to find out if there are differences in the transcriptomes of S. enterica depending on the factor of cell density during starvation. Here we present transcriptome data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S grown in carbon rich or carbon deficient medium with high or low cell density. These data will help identify genes involved in adaptation of low-density bacterial populations to starvation conditions.
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Affiliation(s)
- Natalia E Gogoleva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky St., Kazan, 420111, Russian Federation.,Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, 11 Pionerskaya St., Orenburg, 460000, Russian Federation
| | - Vladimir Ya Kataev
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, 11 Pionerskaya St., Orenburg, 460000, Russian Federation
| | - Alexander S Balkin
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, 11 Pionerskaya St., Orenburg, 460000, Russian Federation
| | - Andrey O Plotnikov
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, 11 Pionerskaya St., Orenburg, 460000, Russian Federation
| | - Elena I Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18 Kremlyovskaya St., Kazan, 420111, Russian Federation
| | - Anastasia M Subbot
- Research Institute of Eye Diseases, 11 Rossolimo St., Moscow, 119021, Russian Federation
| | - Sergey V Cherkasov
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, 11 Pionerskaya St., Orenburg, 460000, Russian Federation
| | - Yuri V Gogolev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky St., Kazan, 420111, Russian Federation.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18 Kremlyovskaya St., Kazan, 420111, Russian Federation
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Gorshkov V, Islamov B, Mikshina P, Petrova O, Burygin G, Sigida E, Shashkov A, Daminova A, Ageeva M, Idiyatullin B, Salnikov V, Zuev Y, Gorshkova T, Gogolev Y. Pectobacterium atrosepticum exopolysaccharides: identification, molecular structure, formation under stress and in planta conditions. Glycobiology 2017; 27:1016-1026. [DOI: 10.1093/glycob/cwx069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/28/2017] [Indexed: 01/19/2023] Open
Affiliation(s)
- Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
- Kazan Federal University, Kremlyovskaya Street,18, 420008 Kazan, Russia
| | - Bakhtiyar Islamov
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
- Kazan Federal University, Kremlyovskaya Street,18, 420008 Kazan, Russia
| | - Polina Mikshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
| | - Gennady Burygin
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov, 13, 410049 Saratov, Russia
| | - Elena Sigida
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Prospekt Entuziastov, 13, 410049 Saratov, Russia
| | - Alexander Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Pr., 47, 119991 Moscow, Russia
| | - Amina Daminova
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
| | - Marina Ageeva
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
| | - Bulat Idiyatullin
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
| | - Vadim Salnikov
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
- Kazan Federal University, Kremlyovskaya Street,18, 420008 Kazan, Russia
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
- Kazan Federal University, Kremlyovskaya Street,18, 420008 Kazan, Russia
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Kazan Science Centre, Russian Academy of Sciences, Lobachevsky Str. 2/31, P.O. Box 30, 420111 Kazan, Russia
- Kazan Federal University, Kremlyovskaya Street,18, 420008 Kazan, Russia
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Gorshkov V, Kwenda S, Petrova O, Osipova E, Gogolev Y, Moleleki LN. Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum. PLoS One 2017; 12:e0169536. [PMID: 28081189 PMCID: PMC5230779 DOI: 10.1371/journal.pone.0169536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022] Open
Abstract
The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, Pectobacterium atrosepticum (Pba) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed Pba to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected Pba phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features that distinguish cross-protected phenotype from the growing cells.
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Affiliation(s)
- Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
- Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan, Russia
| | - Stanford Kwenda
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
| | - Elena Osipova
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics of Kazan Science Centre of Russian Academy of Sciences, Kazan, Russia
- Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan, Russia
| | - Lucy N. Moleleki
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PRJ, Moleleki LN. Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. BMC Genomics 2016; 17:47. [PMID: 26753530 PMCID: PMC4710047 DOI: 10.1186/s12864-016-2376-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/06/2016] [Indexed: 12/15/2022] Open
Abstract
Background Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. Results In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. Conclusions Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2376-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stanford Kwenda
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia. .,Department of Botany and Plant Physiology, Kazan Federal University, Kazan, Russia.
| | - Aadi Moolam Ramesh
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology (FABI), University of Pretoria, Pretoria, South Africa.
| | - Enrico Rubagotti
- Genomics Research Institute, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa.
| | - Paul R J Birch
- Division of Plant Sciences, College of Life Sciences, University of Dundee (at The James Hutton Institute), Errol Road, Invergowrie, Dundee, DD25DA, Scotland, UK.
| | - Lucy N Moleleki
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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Czajkowski R, Pérombelon MCM, Jafra S, Lojkowska E, Potrykus M, van der Wolf JM, Sledz W. Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review. THE ANNALS OF APPLIED BIOLOGY 2015; 166:18-38. [PMID: 25684775 PMCID: PMC4320782 DOI: 10.1111/aab.12166] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/05/2014] [Indexed: 05/10/2023]
Abstract
The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. Efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the SRE as well as in seed certification programmes. The aim of this review was to collect all existing information on methods available for SRE detection. The review reports on the sampling and preparation of plant material for testing and on over thirty methods to detect, identify and differentiate the soft rot and blackleg causing bacteria to species and subspecies level. These include methods based on biochemical characters, serology, molecular techniques which rely on DNA sequence amplification as well as several less-investigated ones.
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Affiliation(s)
- R Czajkowski
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | | | - S Jafra
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | - E Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | - M Potrykus
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
| | | | - W Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of GdanskGdansk, Poland
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Mascher F, Hase C, Bouffaud ML, Défago G, Moënne-Loccoz Y. Cell culturability of Pseudomonas protegens CHA0 depends on soil pH. FEMS Microbiol Ecol 2013; 87:441-50. [PMID: 24224494 DOI: 10.1111/1574-6941.12234] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas inoculants may lose colony-forming ability in soil, but soil properties involved are poorly documented. Here, we tested the hypothesis that soil acidity could reduce persistence and cell culturability of Pseudomonas protegens CHA0. At 1 week in vitro, strain CHA0 was found as culturable cells at pH 7, whereas most cells at pH 4 and all cells at pH 3 were noncultured. In 21 natural soils of contrasted pH, cell culturability loss of P. protegens CHA0 took place in all six very acidic soils (pH < 5.0) and in three of five acidic soils (5.0 < pH < 6.5), whereas it was negligible in the neutral and alkaline soils at 2 weeks and 2 months. No correlation was found between total cell counts of P. protegens CHA0 and soil composition data, whereas colony counts of the strain correlated with soil pH. Maintenance of cell culturability in soils coincided with a reduction in inoculant cell size. Some of the noncultured CHA0 cells were nutrient responsive in Kogure's viability test, both in vitro and in soil. Thus, this shows for the first time that the sole intrinsic soil composition factor triggering cell culturability loss in P. protegens CHA0 is soil acidity.
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Affiliation(s)
- Fabio Mascher
- Plant Pathology, Institute of Integrative Biology, Swiss Federal Institute of Technology, Zürich, Switzerland; Agroscope Changins-Wädenswil research station ACW, Nyon, Switzerland
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Tashyreva D, Elster J. Production of Dormant Stages and Stress Resistance of Polar Cyanobacteria. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/978-94-007-4966-5_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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Gorshkov V, Petrova O, Gogoleva N, Gogolev Y. Cell-to-cell communication in the populations of enterobacteriumErwinia carotovorassp.atrosepticaSCRI1043 during adaptation to stress conditions. ACTA ACUST UNITED AC 2010; 59:378-85. [DOI: 10.1111/j.1574-695x.2010.00684.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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