VapD in Xylella fastidiosa Is a Thermostable Protein with Ribonuclease Activity

Mendes, Juliano S.; Santiago, André da Silva; Toledo, Marcelo Augusto Szymanski de; Rosselli‐Murai, Luciana K.; Favaro, Marianna T.P.; Santos, Clelton A.; Horta, Maria Augusta Crivelente; Crucello, Aline; Beloti, Lilian L.; Romero, Fabian; Tasić, Ljubica; Souza, Alessandra Alves de; Souza, Anete Pereira de

doi:10.1371/journal.pone.0145765

Cited by 8 publications

(7 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to confirm the ribonuclease activity of SF216 is not ascribed to nuclease contamination, we boiled the purified SF216 and carried out fluorescence quenching assay. RNase A, B, and C have been known to be thermostable which is demonstrated by that those RNases maintain their activity even after autoclave [32,33], and we confirmed that RNase A at 60°C and after boiling retained the ribonuclease activity (Fig. S5).…”

Section: Ribonuclease Activity Of Sf216supporting

confidence: 79%

Crystal structure and functional characterization of SF216 from Shigella flexneri

et al. 2017

View full text Add to dashboard Cite

Shigella flexneri is a Gram-negative anaerobic bacterium that causes highly infectious bacterial dysentery in humans. Here, we solved the crystal structure of SF216, a hypothetical protein from the S. flexneri 5a strain M90T, at 1.7 Å resolution. The crystal structure of SF216 represents a homotrimer stabilized by intersubunit interactions and ion-mediated electrostatic interactions. Each subunit consists of three β-strands and five α-helices with the β-β-β-α-α-α-α-α topology. Based on the structural information, we also demonstrate that SF216 shows weak ribonuclease activity by a fluorescence quenching assay. Furthermore, we identify potential druggable pockets (putative hot spots) on the surface of the SF216 structure by computational mapping.

show abstract

Section: Ribonuclease Activity Of Sf216supporting

confidence: 79%

Crystal structure and functional characterization of SF216 from Shigella flexneri

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Moreover, it was observed that sequences of pXF51 were found integrated in the bacterium chromosome (Marques et al 2001). This plasmid encodes the virulence related protein VapD, a thermostable ribonuclease predicted to belong to CRISPR/Cas2 family (Mendes et al 2015). However, the contribution of VapD to X. fastidiosa virulence remains undetermined.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Xylella fastidiosa Plasmids Assessed by Comparative Genomics

Pierry

Uceda-Campos

Feitosa-Junior

et al. 2020

Trop. plant pathol.

View full text Add to dashboard Cite

Plasmids are a major source of horizontal gene transfer among bacteria contributing to their evolution and ecology. The known collection of plasmids carried by the plant pathogen Xylella fastidiosa increases as new strains from different origins and hosts are sampled and sequenced. Here we performed an extensive comparison of 61 publicly available sequences annotated as plasmids belonging to 38 X. fastidiosa strains isolated from different plant species and distinct geographical locations. Twenty-six strains exhibited at least one plasmid and up to four plasmids were found in a single strain. Plasmids sizes varied widely from 1.3 kbp to 64.3 kbp, ranging from 1 to 70 protein-coding sequences (CDS) encompassing 324 orthologs. Based on the presence of specific mobility proteins such as relaxases and type 4 secretion system-related genes, respectively 40 and 8 of the X. fastidiosa plasmids were classified as conjugative and mobilizable, while 13 were classified as non-mobilizable. X. fastidiosa plasmids did not carry known antibiotic resistance or virulence genes, and their stability seems to take advantage of toxin/antitoxin systems. The comparative analyses described here revealed similarity among plasmids of X. fastidiosa from different subspecies, geographical regions, and hosts, as well as with sequences found in plasmids from other bacterial species. Altogether, our results provide an in silico analysis of X. fastidiosa plasmid content and their main features, with applications in future studies of epidemiology, ecology, and evolution of this phytopathogen.

show abstract

“…2). The plasmid also contained a virulence-associated protein D (VapD) that has not been extensively characterized but has been previously associated with biofilm growth in other bacterial species (27).…”

Section: Resultsmentioning

confidence: 99%

Genomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States

Smith

Miller

Weber

et al. 2020

Appl Environ Microbiol

View full text Add to dashboard Cite

Ornithobacterium rhinotracheale is a causative agent of respiratory tract infections in avian hosts worldwide but is a particular problem for commercial turkey production. Little is known about the ecologic and evolutionary dynamics of O. rhinotracheale, which makes prevention and control of this pathogen a challenge. The purpose of this study was to gain insight into the genetic relationships between O. rhinotracheale populations through comparative genomics of clinical isolates from different U.S. turkey producers. O. rhinotracheale clinical isolates were collected from four major U.S. turkey producers and several independent turkey growers from the upper Midwest and Southeast, and whole-genome sequencing was performed. Genomes were compared phylogenetically using single nucleotide polymorphism (SNP)-based analysis, and then assembly and annotations were performed to identify genes encoding putative virulence factors and antimicrobial resistance determinants. A pangenome approach was also used to establish a core set of genes consistently present in O. rhinotracheale and to highlight differences in gene content between phylogenetic clades. A total of 1,457 nonrecombinant SNPs were identified from 157 O. rhinotracheale genomes, and four distinct phylogenetic clades were identified. Isolates clustered by company on the phylogenetic tree, however, and each company had isolates in multiple clades with similar collection dates, indicating that there are multiple O. rhinotracheale strains circulating within each of the companies examined. Additionally, several antimicrobial resistance proteins, putative virulence factors, and the pOR1 plasmid were associated with particular clades and multilocus sequence types, which may explain why the same strains seem to have persisted in the same turkey operations for decades. IMPORTANCE The whole-genome approach enhances our understanding of evolutionary relationships between clinical Ornithobacterium rhinotracheale isolates from different commercial turkey producers and allows for identification of genes associated with virulence, antimicrobial resistance, or mobile genetic elements that are often excluded using traditional typing methods. Additionally, differentiating O. rhinotracheale isolates at the whole-genome level may provide insight into selection of the most appropriate autogenous vaccine strain, or groups of strains, for a given population of clinical isolates.

show abstract

VapD in Xylella fastidiosa Is a Thermostable Protein with Ribonuclease Activity

Cited by 8 publications

References 57 publications

Crystal structure and functional characterization of SF216 from Shigella flexneri

Crystal structure and functional characterization of SF216 from Shigella flexneri

Genetic Diversity of Xylella fastidiosa Plasmids Assessed by Comparative Genomics

Genomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States

Contact Info

Product

Resources

About