Characterization of CRISPR‐Cas systems in the <i>Ralstonia solanacearum</i> species complex

Xavier, André da Silva; Almeida, Juliana Cristina Fraleon de; Melo, Alessandra Gonçalves de; Rousseau, Geneviève M.; Tremblay, Denise M.; Rezende, Rafael Reis de; Moineau, Sylvain; Alfenas‐Zerbini, Poliane

doi:10.1111/mpp.12750

Cited by 17 publications

(18 citation statements)

References 123 publications

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“…O. S. Gonçalves et al (28) reported that in the presence of CRISPR arrays, 27.9% of CRISPR spacers from Ralstonia genomes targeted prophage elements. In our study, two Ralstonia MAGs from a low temperature environment were devoid of CRISPR systems, implying that representatives of this genus have alternative strategies for defense against mobile genetic elements (43). However, analyses on more Ralstonia genomes are necessary to corroborate this statement.…”

Section: Discussionmentioning

confidence: 74%

“…Upon exposure to a virulent phage under laboratory conditions, the CRISPR array of Ralstonia solanacearum strain CFBP2957 did not acquire new spacers from viral protospacers. This demonstrates the CRISPR system's inefficiency in viral eradication and suggests alternative antiviral mechanisms in this Ralstonia strain (43). More recently, a publication reported that in the presence of CRISPR arrays, 27.9% of spacers from Ralstonia genomes targeted prophage elements (28).…”

Section: Discussionmentioning

confidence: 97%

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Host-associated phages disperse across the extraterrestrial analogue Antarctica

Rahlff

Bornemann

Lopatina

et al. 2021

Preprint

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Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples especially from polar regions yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating or prophages) across the Antarctic continent can be tracked via their genetic signatures and benefits our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria including Ralstonia spp. Betaproteobacteria of this genus have been found in Antarctic snow as well as on space-related equipment. We reconstructed the complete genome of a temperate phage with near-complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which appeared in seawater from the Western Antarctic Peninsula with up to 5538 km to the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp. disperse over long distances despite harsh conditions of the Antarctic continent. Due to the additional identification of 14 phages associated with two R. pickettii draft genomes isolated from space equipment, we conclude implications for the spread of biological contaminants in extraterrestrial settings.ImportanceHost-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to presence of this bacterial strain including genome-integrated prophages on space-related equipment, and the here demonstrated potential for dispersal of host-associated phages, our work has implications for Planetary Protection, a discipline in Astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.

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Section: Discussionmentioning

confidence: 74%

Section: Discussionmentioning

confidence: 97%

Host-associated phages disperse across the extraterrestrial analogue Antarctica

Rahlff

Bornemann

Lopatina

et al. 2021

Preprint

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“…This system utilizes numerous Cas proteins for the recognition and cleavage of targeted nucleic acids, therefore the genome of the RSSC strains contains the following Cas proteins: Cas1_0_IE, Cas2_0_IE, Cas3_0_IE, Cas5_0_IE, Cas6_0_IE, Cas7_0_IE, Cse1_0_IE, and Cse2_0_IE. Besides the mentioned strains, other strains from phylotypes I and IV not included in Table 2 show the presence of CRISPR-Cas system as da Silva, Xavier et al (2019) reported. This result indicates that the CRISPR-Cas system is present in all phylotypes although it is not widely distributed across strains.…”

Section: Clustered Regularly Interspaced Short Palindromic Repeats (Cmentioning

confidence: 89%

“…The CRISPR-Cas system in RSSC was first described by da Silva, Xavier et al (2019). They found this system in 31% of RSSC genomes present in public databases.…”

Section: Discussionmentioning

confidence: 99%

“…This competitive interaction has created an evolutionary arms race that has driven the production of the extraordinary diversity of bacterial defense mechanisms in RSSC to hinder phage aggressions. However, the relative abundance, diversity, and evolution of the defense systems that RSSC possesses are unknown, with the exception of the CRISPR system reported by da Silva, Xavier et al (2019). Therefore, in this study, we present a detailed study of the arsenal of defense systems that RSSC harbors and their evolutionary dynamics.…”

Section: Introductionmentioning

confidence: 95%

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Diversity and Evolutionary Dynamics of Antiphage Defense Systems in Ralstonia solanacearum Species Complex

et al. 2020

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Over the years, many researchers have reported a great diversity of bacteriophages infecting members of the Ralstonia solanacearum species complex (RSSC). This diversity has driven bacterial evolution by leading the emergence and maintenance of bacterial defense systems to combat phage infection. In this work, we present an in silico study of the arsenal of defense systems that RSSC harbors and their evolutionary history. For this purpose, we used a combination of genomic, phylogenetic and associative methods. We found that in addition to the CRISPR-Cas system already reported, there are eight other antiphage defense systems including the well-known Restriction-Modification and Toxin-Antitoxin systems. Furthermore, we found a tenth defense system, which is dedicated to reducing the incidence of plasmid transformation in bacteria. We undertook an analysis of the gene gain and loss patterns of the defense systems in 15 genomes of RSSC. Results indicate that the dynamics are inclined toward the gain of defense genes as opposed to the rest of the genes that were preferably lost throughout evolution. This was confirmed by evidence on independent gene acquisition that has occurred by profuse horizontal transfer. The mutation and recombination rates were calculated as a proxy of evolutionary rates. Again, genes encoding the defense systems follow different rates of evolution respect to the rest of the genes. These results lead us to conclude that the evolution of RSSC defense systems is highly dynamic and responds to a different evolutionary regime than the rest of the genes in the genomes of RSSC.

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