Biology subjects

Narajczyk, M.

Publications and source records attributed to Narajczyk, M..

6 recordsLinked to original sources

bioRxiv2025

Beyond kin killing: Dickeya-derived phage-tail-like bacteriocin P2D1 targets phylogenetically distant Pseudomonas spp.

Tailocins, phage-tail-derived bacteriocins, are increasingly recognized as potent mediators of microbial antagonism, yet their ecological scope beyond kin-targeting remains poorly understood. Here, we investigated whether P2D1, a tailocin produced by the plant pathogen Dickeya dadantii 3937, can act against environmental bacteria phylogenetically distant from Dickeya spp. Screening 480 soil and rhizosphere isolates from three distinct plant-associated habitats in Poland, we identified nine Pseudomonas spp. strains susceptible to tailocin P2D1. Whole-genome sequencing and phenotype profiling revealed that these isolates spanned multiple clades, including taxa related to P. germanica, P. tensinigenes, and P. parakoreensis. The D. dadantii mutant lacking genes encoding tailocin sheath and tube proteins lost antagonistic activity against Pseudomonas isolates, confirming that tailocins alone mediate the observed killing. Plant tissue assays revealed that six of the P2D1-susceptible strains were non-pathogenic and could mitigate D. dadantii-induced soft rot on potato. In contrast, three isolates related to P. tensinigenes were able to cause rot on their own under permissive conditions. Together, these findings demonstrate that P2D1 tailocin extends its activity to ecologically co-occurring but taxonomically distant Pseudomonas, suggesting that conserved receptors underline cross-genus targeting. More broadly, our results add to the limited evidence for tailocin activity beyond kin killing and therefore challenge the prevailing paradigm of kin-restricted tailocin specificity. They further suggest that tailocins may influence microbial community assembly across taxonomic boundaries, while their in vivo roles remain understudied.

microbiology↗

bioRxiv2024

Tailocin-mediated interactions in Soft Rot Pectobacteriaceae

Bacteria carry phage-derived elements within their genomes, some of which can produce phage-like particles (tailocins) used as weapons to kill kin strains in response to environmental conditions. This study investigates the production and activity of tailocins by plant pathogenic bacteria: Pectobacterium, Dickeya, and Musicola genera, which compete for niche, providing an attractive model to study the ecological role of tailocins. Microscopy revealed that most analyzed strains (88%) produced tailocins. Tailocin-mediated killing interactions were assessed across 351 strain pairs, showing that Dickeya spp. had a higher likelihood of killing neighbors (57.1%) than Pectobacterium spp. (21.6%). Additionally, Dickeya spp. strains exhibited broader phylogenetic killing, targeting both Pectobacterium spp. and Musicola sp., while Pectobacterium spp. tailocins were genus-specific. Mutual killing was observed in 33.9% of interactions, predominantly within Dickeya spp. Although tailocins were morphologically indistinguishable between producers, genomic analyses identified conserved clusters having distinct differences between Pectobacterium spp. and Dickeya spp tailocins. This suggests different origins of these particles. Induction experiments demonstrated that tailocin production was boosted by hydrogen peroxide, supporting the role of these particles in bacteria-bacteria competition during infection. Tailocins were detectable in infected potato tissue but not in river water, highlighting the particular ecological relevance of tailocins in plant environments.

microbiology↗

bioRxiv2024

Inner membrane protein OutB is covalently attached to peptidoglycan in the γ-proteobacterium Dickeya dadantii

Gram-negative bacteria possess a multilayered envelope comprising an inner membrane (IM), a thin peptidoglycan (PG) layer, and an outer membrane (OM). In Escherichia coli and certain other {gamma}-proteobacteria, Braun lipoprotein (Lpp) covalently tethers the OM to PG. Only a few other OM proteins have been found to be covalently linked to PG in Gram-negative bacteria. Here, we showed that in the phytopathogenic {gamma}-proteobacterium Dickeya dadantii, an IM protein, OutB, is covalently attached to PG, thereby tethering itself and the associated type 2 secretion system to the cell wall. In contrast to Lpp, OutB reaches the PG layer from the IM side. By modifying the length of Lpp, which would displace the PG layer in the periplasm, we found that the elongated Lpp+21 improved OutB attachment to PG, whereas the shortened Lpp{Delta}21 reduced it. We showed that two L,D-transpeptidases, Ldt03 and Ldt84, tether Lpp and OutB to PG by the same catalytic mechanism involving the formation of an amide bond between their C-terminal lysine and the stem peptide. Ldt03 and Ldt84, each display substrate specificity for the type of peptide stem and preferentially cross-link Lpp to monomeric and dimeric muropeptide, respectively. The C-terminal Lpp-like box of OutB is almost identical to that of Lpp; it tolerates substantial amino acid substitutions and allows PG-tethering of a bona fide periplasmic protein. Thus, it seems possible that the repertoire of periplasmic and membrane proteins tethered to PG may be more extensive than currently assumed.

microbiology↗

bioRxiv2023

Soft rot pathogen Dickeya dadantii 3937 produces tailocins resembling the tails of Enterobacteria bacteriophage P2

Tailocins are nanomolecular machines with bactericidal activity. They are produced by bacteria to contribute to fitness in mixed communities, and hence, they play a critical role in their ecology in a variety of habitats. Here, we characterized the new tailocin produced by Dickeya dadantii strain 3937, a well-characterized member of plant pathogenic Soft Rot Pectobacteriaceae (SRP). Tailocins induced in D. dadantii were ca. 166 nm long tubes surrounded by contractive sheaths with baseplates having tail fibers at one end. A 22-kb genomic cluster involved in their synthesis and having high homology to the cluster coding for the tail of the Enterobacteriophage P2 was identified. The D. dadantii tailocins, termed dickeyocin P2D1 (phage P2-like dickeyocin 1), were resistant to inactivation by pH (3.5 - 12), temperature (4 - 50 {degrees}C), and elevated osmolarity (NaCl concentration: 0.01 - 1 M). P2D1 could kill a variety of different Dickeya spp. but not any strain of Pectobacterium spp. tested and were not toxic to Caenorhabditis elegans. TeaserTailocins are nanomolecular entities similar to syringes that are produced by various bacteria to fight other microorganisms present in the same environment.

microbiology↗

bioRxiv2023

Being spontaneous has its costs! Characterization of the spontaneous phage ΦD5-resistant mutants of Dickeya solani strain IPO 2222

Lytic bacteriophages able to infect and kill Dickeya spp. can be readily isolated from virtually all Dickeya spp.-containing environments, yet little is known about the selective pressure those viruses exert on their hosts. Here, we identified two spontaneous D. solani IPO 2222 mutants (0.8% of all obtained mutants), DsR34 and DsR207, resistant to infection caused by lytic phage vB_Dsol_D5 ({Phi}D5) that expressed a reduced ability to macerate potato tuber tissues compared to the wild-type, phage-susceptible D. solani IPO 2222 strain. Genome sequencing revealed that genes encoding: secretion protein HlyD (mutant DsR34) and elongation factor Tu (EF-Tu) (mutant DsR207) were altered in these strains. Both mutations impacted the proteomes of cells grown in both rich and minimal media, including the abundance of the cell envelope and transmembrane transport-associated proteins. Furthermore, features essential for the ecological success of these mutants in a plant environment, including their ability to use various carbon and nitrogen sources, produce plant cell wall degrading enzymes, ability to form biofilms, siderophore production, swimming and swarming motility and virulence in planta were assessed. Compared to the wild-type strain, D. solani strain IPO 2222, mutants DsR34 and DsR207 had a reduced ability to macerate chicory leaves and to colonize and cause symptoms in growing potato plants. The implications of the {Phi}D5 resistance on driving traits affecting the ecological performance of D. solani are discussed.

microbiology↗

bioRxiv2022

Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage vB_Dsol_D5 ({Phi}D5) results in fitness tradeoffs for the bacterium during infection

Resistance to bacteriophage infections protects bacteria in phage-full environments, allowing them to survive and multiply in the presence of their viral predators. However, such resistance may cause direct costs for strains linked with the ecological fitness expressed as reduced competitiveness for resources or reduced virulence or both. Unfortunately, limited knowledge exists about such costs paid by phage-resistant plant pathogenic bacteria in their natural environments. This study analyzed the costs of phage resistance paid by broad host phytopathogenic pectinolytic bacterium Dickeya solani both in vitro and in potato (Solanum tuberosum L.) plants. Thirteen D. solani IPO 2222 Tn5 mutants were identified that exhibited resistance to infection caused by lytic bacteriophage vB_Dsol_D5 ({Phi}D5). The genes disrupted in these 13 mutants encoded proteins involved in the synthesis of the bacterial envelope components (viz. LPS, EPS and capsule). The ability of {Phi}D5-resistant D. solani mutants to colonize and cause symptoms on potato plants as well as other phenotypes that are known to contribute to the ecological fitness of D. solani in-plant environment, including growth rate, production of effectors, swimming and swarming motility, use of various carbon and nitrogen sources and biofilm formation were assessed. Although phage resistance did not affect most of the phenotypes of {Phi}D5-resistant D. solani evaluated in vitro, all phage resistant mutants were significantly compromised in their ability to survive on and colonize and cause disease symptoms in potato plants. This study is, to our knowledge, one of few to show the direct link between phage resistance and the fitness of plant pathogenic bacteria and the first one to assess phage-host associations for D. solani.

microbiology↗