Transcriptome profiling helps to identify potential and true molecular switches of stealth to brute force behavior in Pectobacterium atrosepticum during systemic colonization of tobacco plants

Gorshkov, Vladimir; Gubaev, Rim; Petrova, Olga; Daminova, Amina; Gogoleva, Natalia; Ageeva, Marina; Parfirova, Olga; Prokchorchik, Maxim; Nikolaichik, Yevgeny; Kamnev, Alexander A.

doi:10.1007/s10658-018-1496-6

Cited by 27 publications

(41 citation statements)

References 67 publications

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“…Within the vessel, RG serves as an extracellular matrix for bacterial emboli assemblage. The release of RG could not be explained by the action of bacterial enzymes, and, therefore, was attributed to the host plant ones [ 11 , 35 ]. The performed transcriptome profiling distinctly points to the mechanism of RG release.…”

Section: Resultsmentioning

confidence: 99%

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Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Tsers

Gorshkov

Gogoleva

et al. 2020

Plants

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Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular “players” in plant–Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by “missed” genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease’s development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters.

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Section: Resultsmentioning

confidence: 99%

“…Thus, the induction of the lipoxygenase pathway, as well as ethylene-regulated responses, is a typical hallmark of Pba -caused disease. This is supported by the fact that the inability of Pba to produce coranafacic acid (a functional analog of JA) leads to a reduction in the pathogen’s virulence [ 35 ].…”

Section: Resultsmentioning

confidence: 99%

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Tsers

Gorshkov

Gogoleva

et al. 2020

Plants

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“…We have previously noticed decreased phoP expression in another example of Pectobacterium-plant interaction. A 3.5-and 5.2-fold phoP repression was observed for P. atrosepticum strain SCRI 1043 in asymptomatic and necrotic zones of infected tobacco stems (27). This reduction of phoP expression correlated well with expression level changes of PhoP controlled genes: e.g.…”

Section: Phop Regulon Expression In Plantamentioning

confidence: 72%

“…Although no differential expression was registered in vitro for any of the two loci encoding secreted arabinogalactanases, both arabinogalactanase genes could be expected to be induced by galactose in planta via GalR. Indeed, our recent transcriptome profiling of P. atrosepticum has shown 4-and 24fold in planta induction of OA04_08560 and ganA orthologues ECA0852 and ECA3128 (27).…”

Section: Arabinose Transport and Utilisationmentioning

confidence: 94%

The PhoPQ two-component system is the major regulator of cell surface properties, stress responses and plant-derived substrate utilisation during development ofPectobacterium versatile-host plant pathosystem

Kravchenko

Gogoleva

Kolubako

et al. 2020

Preprint

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The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile, we demonstrate that PhoP controls a regulon of at least 116 genes with a large fraction of regulon members specific for pectobacteria. The functions performed by the PhoP controlled genes include transport and metabolism of plant-derived carbon sources (polygalacturonate, arabinose and citrate), modification of bacterial cell envelope and stress resistance. High concentrations of calcium and magnesium ions were found to abolish the PhoPQdependent transcription activation. Reduced PhoP expression and minimisation of PhoP dependence of regulon members' expression in the cells isolated from rotten potato tuber tissues suggest that PhoPQ system may adjust expression levels of multiple virulence-related genes during the course of P. versatile-host plant pathosystem development.PehR was originally described as a transcriptional activator of the pehA gene encoding endopolygalacturonase, a major virulence factor in soft rot bacteria (16). PehR is a response regulator that forms a two-component sensory system (TCS) with the membrane histidine kinase PehS. In the SCC3193 strain, which is currently classified as Pectobacterium parmentieri, inactivation of either pehR or pehS resulted in reduced virulence and Ca 2+ was reported as the ligand detected by the PehS sensor (16,17). It was also suggested that the PehRS system is responsible for the decrease of the polygalacturonase and increase of the pectate lyase activities in response to Ca 2+ released from the degraded cell walls (17).The pectobacterial PehRS two-component system received very little attention since its discovery two decades ago. However, much information has been accumulated about the orthologous system called PhoPQ in other bacteria from the order Enterobacetrales. In Dickeya dadantii, which belongs to the Pectobacteriaceae family together with Pve, PhoPQ TCS was shown to control pellicle formation, motility, resistance to cationic antimicrobial peptides and expression of pectate lyases in response to Mg 2+ concentration (18,19). The PhoPQ system has been thoroughly characterised in Salmonella and to a lesser extent in few more Enterobacteriaceae species including Escherichia coli and Yersinia spp. (see (20) for a review). The PhoQ sensor histidine kinase activates PhoP by phosphorylation in response to several stimuli, including low Mg 2+ concentration (21), cationic peptides (22), acidity (23) and high osmolarity (24). PhoP binds to direct repeats with a consensus gGTTTA which seems to be well conserved in enterobacteria (25,26). The regulon composition nevertheless varies widely even between closely related bacteria. In Salmonella enterica, over a hundred genes are regulated by PhoP, but only three of them (phoP, phoQ and slyB) are always under PhoP control in other enterobacteria. Some regulon members are shared by several species, but most PhoP controlled gene...

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“…Согласно аннотации, представленной в базах данных CAZy и Uni-Prot, в геноме P. atrosepticum SCRI1043 присутствует 8 генов, кодирующих ферменты, которые разрушают РГУ I. Экспрессия этих генов повышается при колонизации пектобактериями растений-хозяев (23). Для нокаута генов, кодирующих ферменты деградации РГУ I, были выбраны геномные локусы eca3749 и eca0852 P. atrosepticum, один из которых кодирует фермент, расщепляющий остов РГУ I, а второй -боковые цепи.…”

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ФЕРМЕНТЫ ДЕГРАДАЦИИ РАМНОГАЛАКТУРОНАНА I КАК ФАКТОРЫ ВИРУЛЕНТНОСТИ ФИТОПАТОГЕННОЙ БАКТЕРИИ Pectobacterium atrosepticum

КОВТУНОВ¹,

ГОРШКОВ²,

Gogoleva³

et al. 2019

s-h. biol.

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Фитопатогенные пектобактерии (род Pectobacterium) известны как возбудители мягких (мокрых) гнилей. Симптомы мягких гнилей связаны с обширной мацерацией растительных тканей вследствие продукции микроорганизмами ферментов, разрушающих компоненты растительных клеточных стенок. Большинство ферментов, секретируемых пектобактериями, катализируют расщепление гомогалактуронана. Этот полисахарид, представляющий собой линейный гомополимер, состоит из остатков галактуроновой кислоты и является основным (по массе) пектиновым полисахаридом растительных клеточных стенок. Известно, что нокаут генов ферментов деградации гомогалактуронана приводит к снижению вирулентности пектобактерий. В то же время при инфекции, вызываемой пектобактериями, происходит модификация другого типа пектинов-рамногалактуронана I. Это разветвленный гетерополимер, остов которого построен из чередующихся остатков рамнозы и галактуроновой кислоты, а боковые цепи-из остатков галактозы или арабинозы. Однако роль пектобактериальных ферментов, разрушающих рамногалактуронан I, в развитии мягких гнилей не выявлена. Цель настоящей работы заключалась в проверке необходимости ферментов P. atrosepticum SCRI1043, разрушающих рамногалактуронан I, для полноценного развития мягких гнилей в растениях, инфицированных пектобактериями. С помощью направленного мутагенеза мы получили мутантные формы P. atrosepticum SCRI1043 по генам, кодирующим ферменты, расщепляющие рамногалактуронан I. В качестве целевых для нокаута были выбраны гены, кодирующие рамногалактуронил гидролазу (геномный локус eca3749), расщепляющую остов рамногалактуронана I, и галактаназу (геномный локус eca0852), отщепляющую боковые цепи этого полимера. Для нокаута целевых генов конструировали мутантные локусы с помощью ПЦР по методу перекрывающегося сплайсинг-расширения. Большую часть кодирующей области гена удаляли, а на ее место встраивали кассету устойчивости к канамицину. Полученную конструкцию лигировали в суицидный мобилизуемый вектор pKNG101, и сконструированную таким образом плазмиду переносили в клетки донорного штамма Escherichia coli СС118. Рекомбинантную плазмиду с мутантным локусом вводили в клетки P. atrosepticum SCRI1043, используя трехродительское скрещивание. Клоны P. atrosepticum SCRI1043, в которых проходила замена исходного локуса на мутантный и элиминация донорной плазмиды, отбирали на селективных средах. Мутантные по локусам ECA3749 и ECA0852 штаммы P. atrosepticum приводили к значительно менее интенсивному повреждению тканей растений пекинской капусты (Brassica rapa spp. pekinensis) сорта Cha Cha по сравнению с родительским штаммом дикого типа. При этом наименьшую вирулентность проявлял штамм, мутантный по локусу eca0852, кодирующему галактаназуфермент, расщепляющий боковые цепи рамногалактуронана I. Снижение вирулентности при этом не было связано с подавлением активности ферментов, расщепляющих гомогалактуронан, или с меньшей подвижностью бактерий. Таким образом, ферменты деградации рамногалактуронана I могут быть отнесены к факторам вирулентности фитопатогенных пектобактерий, а гидро...

show abstract

Transcriptome profiling helps to identify potential and true molecular switches of stealth to brute force behavior in Pectobacterium atrosepticum during systemic colonization of tobacco plants

Cited by 27 publications

References 67 publications

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

The PhoPQ two-component system is the major regulator of cell surface properties, stress responses and plant-derived substrate utilisation during development ofPectobacterium versatile-host plant pathosystem

ФЕРМЕНТЫ ДЕГРАДАЦИИ РАМНОГАЛАКТУРОНАНА I КАК ФАКТОРЫ ВИРУЛЕНТНОСТИ ФИТОПАТОГЕННОЙ БАКТЕРИИ Pectobacterium atrosepticum

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