Publications

4865

Peptidyl-tRNA hydrolase (Pth2) hydrolyzes peptidyl-tRNA, an immature product of aborted translation, into peptide and tRNA, thereby maintaining cellular protein synthesis through peptide release and tRNA recycling. Here, we present the crystal structure of Pth2 from Candidatus Lokiarchaeum sp. GC14_75 ( Loki Pth2) at 2.12 Å resolution. This is the first structure of Pth2 from a lineage within Promethearchaeati, a kingdom of archaea closely related to eukaryotes. The structure reveals that Loki Pth2 forms a homodimer and closely resembles Pth2 structures from other species. However, Loki Pth2 exhibits two prominent structural differences: a short helix around the catalytic center, which is absent in other Pth2s, and a distinct orientation of the C-terminal helix. Detailed comparative structural analysis suggests that these regions may regulate enzymatic activity and substrate binding, respectively. Furthermore, the corresponding regions in other Pth2s also exhibit high flexibility, suggesting that similar mechanisms may be conserved among Pth2s. To gain insights into the growth environment of Candidatus Lokiarchaeum sp. GC14_75, we assess the optimal temperature for the catalytic reaction of Loki Pth2, which suggests that Candidatus Lokiarchaeum sp. GC14_75 inhabits moderately thermophilic environments.

“Candidatus Sarcina troglodytae” (“Ca. S. troglodytae”), a proposed bacterial species in the family Clostridiaceae, has been epidemiologically associated with a lethal disease in sanctuary chimpanzees in Sierra Leone, epizootic neurologic and gastroenteric syndrome (ENGS). As sarcinae are known to be difficult to culture, a lack of viable in vitro growth conditions has limited further characterization of this bacterium. Such studies are critical to elucidating the relationship between “Ca. S. troglodytae” and ENGS.  Here, we isolate a Gram-stain-positive, endospore-forming, coccus and anaerobic bacterial strain, designated JB3T, from brain tissue of a western chimpanzee (Pan troglodytes verus) using a reinforced clostridial medium. We describe the growth of strain JB3T at a pH range of 6 to 9 (optimum 6) at 37°C in an atmosphere composed of 5% H2, 5% CO2, and 90% N2 and demonstrate endospore production under alkaline conditions, suggesting the possibility of an environmental reservoir. We identify ethanol as the primary non-gaseous fermentation byproduct which we hypothesize to have relevance for ENGS. Antibiotic susceptibility testing shows susceptibility to common antimicrobial agents with notable resistance to ceftriaxone. By establishing in vitro conditions for the viable culture, propagation, and storage of “Ca. S. troglodytae”, this study lays the groundwork for future infection studies to test hypotheses about pathogenic mechanisms and prevention/treatment measures for ENGS.

Candidatus (Ca.) Allocryptoplasma is a newly identified, genetically diverse genus of vector-borne bacteria closely related to established blood-borne zoonotic pathogens, including Anaplasma, Ehrlichia, and Neoehrlichia species. Ca. Allocryptoplasma is a globally distributed pathogen detected across taxonomically diverse tick species and varied ecological niches. It maintains a complex enzootic circulation involving multiple vertebrate classes, including birds, small mammals, primates, and particularly reptiles, which serve as reservoir hosts. Methods: To characterize this emerging agent, multi-locus genetic DNA sequence analyses using the maximum likelihood method were performed on 16S rRNA, sucA, and rpoB genes amplified from the blood and vectors of marine iguanas and lizard species sampled across multiple islands in the Galápagos archipelago. Results: The compiled genomic data demonstrate that the Ca. Allocryptoplasma detected in the Galápagos lizards and marine iguanas represents a distinct lineage and a novel Ca. Allocryptoplasma species. Conclusions: Given its broad host plasticity, widespread geographic footprint, and vector-mediated transmission, the potential of Ca. Allocryptoplasma as a hidden, emerging zoonotic blood pathogen warrants intensive further evaluation.

Objective. To evaluate the effectiveness of eradicating HLB-symptomatic trees in reducing the spread of CLas. Materials and methods. The study was conducted from January to December 2019 in three phytosanitary epidemiological management areas (AMEFIs in Spanish) located in the municipalities of Güémez, Hidalgo, Llera de Canales, and Padilla, in the state of Tamaulipas, Mexico. In each AMEFI, a post-eradication sampling route was established around a tree confirmed to be symptomatic of CLas via q-PCR. Sampling sites were defined at distances of 6.7 km (S1), 13.4 km (S2), and 20.1 km (S3) from the eradicated tree, where leaf samples were randomly collected from asymptomatic trees to determine the presence or absence of CLas. The data were analyzed using chi-square tests to compare the frequency of positive and negative trees among AMEFIs and sampling sites. Results. The frequency of asymptomatic trees that were positive and negative for CLas differed significantly among the evaluated AMEFIs; at the site level, only AMEFI 3 showed significant differences. Conclusion. The eradication of trees with HLB symptoms was not sufficient to prevent the persistence of CLas, as asymptomatic infected trees were detected after the removal of symptomatic trees.

Introduction Huanglongbing (HLB) is a devastating disease impacting citrus orchards worldwide. Identifying candidate genes and/or genomic regions that significantly influence plants' response to HLB is essential for breeding programs. Nevertheless, this remains a challenge, especially during the early stages of the citrus-pathogen interaction, when phenotypically distinguishing tolerant genotypes is not trivial. This work focused on identifying genomic regions and candidate genes associated with citrus response to Candidatus Liberibacter asiaticus ( C Las). Methods Quantitative trait loci (QTL) mapping was performed in a citrandarin population (278 individuals) derived from a fullsib cross between susceptible Citrus sunki (CS) and tolerant Poncirus trifoliata (PT). The mapping population was genotyped using DArTseq markers and the SNPs obtained from them (DArTseq-derived SNPs), as well as the EMBRAPA Multispecies 65K Illumina Infinium® chip. Phenotyping was based on four individual trials (two in a greenhouse and two in field conditions). QTL mapping was based on composite interval mapping implemented in the fullsibQTL software, with the cycle threshold (Ct) of quantitative PCR (qPCR) as the trait of interest for assessing C Las quantification in infected tissues, which can be evaluated in plants at any developmental stage. The biological function of QTLs was investigated by gene annotation using the chromosome-level phased Citrus sinensis genome (assembly DVS_A1.0) as the reference. The candidate genes were functionally annotated using Blast2Go software. Results A predominance of markers in a 1:1 ratio was observed, resulting in two maps, one for each parent. The linkage map had 5464 cM (1872 markers) for CS and 4794 cM (1340 markers) for PT. A total of 44 QTLs were mapped: 25 for the CS map (13 for field and 12 for greenhouse conditions), of which 17 were located at gene sites; and 19 were mapped for the PT (nine for field and 10 for greenhouse conditions), of which 16 were located at gene sites. Discussion Several genes associated with the identified QTLs are involved in stress responses, making them potential targets for further functional validation. These genomic regions and candidate genes provide valuable targets for future incorporation into citrus breeding programs aimed at developing HLB tolerance.

ABSTRACT We present the complete de novo assembly of a Candidatus Walczuchella monophlebidarum genome (286,606 bp), a flavobacterial endosymbiont of the giant-scale insect Icerya purchasi . The genome was assembled from metagenomic short read Illumina sequences obtained from DNA of citrus leaves collected in Carinthia, Austria in November 2024.