Heterogenicity within the LPS Structure in Relation to the Chosen Genomic and Physiological Features of the Plant Pathogen Pectobacterium parmentieri.

Agata Motyka-Pomagruk,Wojciech Sledz,Zbigniew Kaczyński,Ewa Lojkowska,Natalia Kaczyńska,Karolina Ossowska,Agnieszka Kowalczyk

doi:10.3390/ijms23042077

Agata Motyka-Pomagruk, Wojciech Sledz + Show 5 more

Open Access

https://doi.org/10.3390/ijms23042077

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Abstract

Pectobacterium parmentieri is a pectinolytic plant pathogenic bacterium causing high economic losses of cultivated plants. The highly devastating potential of this phytopathogen results from the efficient production of plant cell wall-degrading enzymes, i.e., pectinases, cellulases and proteases, in addition to the impact of accessory virulence factors such as motility, siderophores, biofilm and lipopolysaccharide (LPS). LPS belongs to pathogen-associated molecular patterns (PAMPs) and plays an important role in plant colonization and interaction with the defense systems of the host. Therefore, we decided to investigate the heterogeneity of O-polysaccharides (OPS) of LPS of different strains of P. parmentieri, in search of an association between the selected genomic and phenotypic features of the strains that share an identical structure of the OPS molecule. In the current study, OPS were isolated from the LPS of two P. parmentieri strains obtained either in Finland in the 1980s (SCC3193) or in Poland in 2013 (IFB5432). The purified polysaccharides were analyzed by utilizing 1D and 2D NMR spectroscopy (1H, DQF-COSY, TOCSY, ROESY, HSQC, HSQC-TOCSY and HMBC) in addition to chemical methods. Sugar and methylation analyses of native polysaccharides, absolute configuration assignment of constituent monosaccharides and NMR spectroscopy data revealed that these two P. parmentieri strains isolated in different countries possess the same structure of OPS with a very rare residue of 5,7-diamino-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (pseudaminic acid) substituted in the position C-8: →3)-β-d-Galf-(1→3)-α-d-Galp-(1→8)-β-Pse4Ac5Ac7Ac-(2→6)-α-d-Glcp-(1→6)-β-d-Glcp-(1→. The previous study indicated that three other P. parmentieri strains, namely IFB5427, IFB5408 and IFB5443, exhibit a different OPS molecule than SCC3193 and IFB5432. The conducted biodiversity-oriented assays revealed that the P. parmentieri IFB5427 and IFB5408 strains possessing the same OPS structure yielded the highest genome-wide similarity, according to average nucleotide identity analyses, in addition to the greatest ability to macerate chicory tissue among the studied P. parmentieri strains. The current research demonstrated a novel OPS structure, characteristic of at least two P. parmentieri strains (SCC3193 and IFB5432), and discussed the observed heterogenicity in the OPS of P. parmentieri in a broad genomic and phenotype-related context.

Highlights

Pectobacterium parmentieri is a Gram-negative phytopathogenic bacterium from the family Pectobacteriaceae [1]. This species used to be known as Erwinia carotovora subsp. carotovora, Pectobacterium carotovorum subsp. carotovorum or Pectobacterium wasabiae [2–4]
During pangenome-oriented studies performed on 15 P. parmentieri strains, Zoledowska et al [10] observed that the core genome fraction barely exceeded 50%, and suggested that the extended accessory (20.9%) and unique (26.3%) partitions may explain the notable plasticity of this species in adapting to different environmental niches
The LPS was isolated from P. parmentieri SCC3193 cells using phenol-water extraction, purified by ethanol precipitation and hydrolyzed to cleave lipid A

Summary

Introduction

Pectobacterium parmentieri is a Gram-negative phytopathogenic bacterium from the family Pectobacteriaceae [1]. During pangenome-oriented studies performed on 15 P. parmentieri strains, Zoledowska et al [10] observed that the core genome fraction barely exceeded 50%, and suggested that the extended accessory (20.9%) and unique (26.3%) partitions may explain the notable plasticity of this species in adapting to different environmental niches. This fact is confirmed by the ubiquitous presence of P. parmentieri under the diverse environmental conditions of, e.g., Finland, Canada, Poland, South Africa, China, New Zealand and Turkey [11–16]. Due to the above-mentioned progress in genome-based classification methods, the SCC3193 strain underwent notable taxonomic rearrangements At first, it adhered to the P. wasabiae species [2], went on to be reclassified to a newly established P. parmentieri species [4]. This study aimed to elucidate the relationship between the structure of the OPS molecule and the chosen genomic and physiological features of P. parmentieri

Results and Discussion

Analysis of the Phenotypic Features and

Materials and Methods

Determination of the OPS

Isolation of OPS

Chemical Analysis

GLC and GLC-MS Analyses

NMR Spectroscopy

Whole-Genome Comparisons

Phenotypic Assays

Statistical Analyses