Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium

Abstract

The Pectobacterium genus comprises pectolytic enterobacteria defined as the causal agents of soft rot, blackleg, and aerial stem rot diseases of potato and economically important crops. In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. Bioinformatics approaches outlined a low nucleotide identity of P. parmentieri and P. wasabiae with other species, while P. carotovorum subsp. odoriferum was shown to harbor numerous pseudogenes, which suggests low coding capacity and genomic degradation. The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. The analyses unveiled a noteworthy heterogeneity in the pathogenicity determinants. Specifically, phytotoxins, polysaccharides, iron uptake systems, and the type secretion systems III–V were observed in just some species. Likewise, a comparison of gene clusters encoding antimicrobial compounds put in evidence for high conservation of carotovoricin, whereas a few species possessed the phenazine, carbapenem, and carocins. Moreover, three clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems: I-E, I-F, and III-A were identified. Surrounding some CRISPR-Cas regions, different toxin and antitoxin systems were found, which suggests bacterial suicide in the case of an immune system failure. Multiple whole-genome alignments shed light on to the presence of a novel cellobiose phosphotransferase system (PTS) exclusive to P. parmenteri, and an unreported T5SS conserved in almost all species. Several regions that were associated with virulence, microbe antagonism, and adaptive immune systems were predicted within genomic islands, which underscored the essential role that horizontal gene transfer has imparted in the dynamic evolution and speciation of Pectobacterium species. Overall, the results decipher the different strategies that each species has developed to infect their hosts, outcompete for food resources, and defend against bacteriophages. Our investigation provides novel genetic insights that will assist in understanding the pathogenic lifestyle of Pectobacterium, a genus that jeopardizes the agriculture sustainability of important crops worldwide.

Pectobacterium brasiliense: Genomics, Host Range and Disease Management

“…Therefore, some genomic comparisons have also allowed for delineating taxa, for identifying the core repertoire of virulence genes shared by related organisms and, for locating gene clusters or genome islands exclusive of species or even unique of a strain for developing molecular tools for identification and detection of pathogens [ 23 ]. To date, few comparative studies have also been conducted regarding Pectobacterium species [ 24 , 25 , 26 , 27 , 28 ]. Until now, six Pbr complete genome sequences are publicly available: Pbr PCC21 (misnamed as P. carotovorum PCC21 in NCBI) isolated from B. rapa ssp.…”

“…Comparative genomics revealed highly conserved virulence genes in the Pectobacterium [ 28 ]. Some of these virulence factors include, amongst other quorum-sensing (QS), secretion systems, adhesion, plant cell wall-degrading enzymes (PCWDEs), motility, chemotaxis, siderophores and biofilm formation [ 30 , 31 , 57 , 58 , 59 ].…”

Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide

“…carotovorum, syn: Erwinia carotovora) type strain. This strain, F160 = VKM 1247 = ATCC 15,713 = DSM 30,168 = LMG 5702 = CFBP 2046 = ICMP 5702 = NCPPB 312 T , was initially isolated in Denmark in the 1960s, and is used in international collections of microorganisms as a model representative of the species [5]. Draft genomes of this strain are available at NCBI GenBank as ICMP 5702 (NZ_AODT00000000.1) [28], NCPPB 312 (NZ_JQHJ00000000.1, directly submitted in 2014) and DSM30168 (NZ_FQWI00000000.1, directly submitted in 2016).…”

“…In recent years, the taxonomy of Pectobacterium and Dickeya genera comprising SRP have undergone numerous refinements and redistributions. Compared to the 1990s, when most SRP were considered to be representatives of the Erwinia genus (and some phytopathologists still use the term "pectolytic Erwinia" due to the similarity of symptoms), the current taxonomic situation with SRP is that there are almost 30 species, defined according to the plant host, severity of the resulting disease, adaptation to particular environmental conditions and, mostly, genomic features [3][4][5]. Most taxonomic alterations have been applied to the species Pectobacterium carotovorum (Pca), formerly Erwinia carotovora.…”

CRISPR/Cas9 high-throughput screening in cancer research

“…Finally, it was found that defects in IFN -γ signaling pathway led to resistance to immunotherapy. Marian et al found that cmtm6 protein is the key regulator of PD-L1 in a wide range of cancer cells by using the whole genome CRISPR / cas9 screening, which provides new insights for the biology of PD-L1 regulation, determines the main regulator that has not been recognized before in this immune checkpoint, and highlights the new potential therapeutic target to overcome the immune evasion of tumor cells [63]. random, size-matched samplings of sgRNAs present in the late tumor.…”