Prediction of NB‐LRR resistance genes based on full‐length sequence homology

The activation of plant immunity is mediated by resistance (R)‐gene receptors, also known as nucleotide‐binding leucine‐rich repeat (NB‐LRR) genes, which in turn trigger the authentic defense response. R‐gene identification is a crucial goal for both classic and modern plant breeding strategies for disease resistance. The conventional method identifies NB‐LRR genes using a protein motif/domain‐based search (PDS) within an automatically predicted gene set of the respective genome assembly. PDS proved to be imprecise since repeat masking prior to automatic genome annotation unwittingly prevented comprehensive NB‐LRR gene detection. Furthermore, R‐genes have diversified in a species‐specific manner, so that NB‐LRR gene identification cannot be universally standardized. Here, we present the full‐length Homology‐based R‐gene Prediction (HRP) method for the comprehensive identification and annotation of a genome's R‐gene repertoire. Our method has substantially addressed the complex genomic organization of tomato (Solanum lycopersicum) NB‐LRR gene loci, proving to be more performant than the well‐established RenSeq approach. HRP efficiency was also tested on three differently assembled and annotated Beta sp. genomes. Indeed, HRP identified up to 45% more full‐length NB‐LRR genes compared to previous approaches. HRP also turned out to be a more refined strategy for R‐gene allele mining, testified by the identification of hitherto undiscovered Fom‐2 homologs in five Cucurbita sp. genomes. In summary, our high‐performance method for full‐length NB‐LRR gene discovery will propel the identification of novel R‐genes towards development of improved cultivars

Multilevel evolution shapes the function of NB-LRR encoding genes in plant innate immunity

A sophisticated innate immune system based on diverse pathogen receptor genes (PRGs) evolved in the history of plant life. To reconstruct the direction and magnitude of evolutionary trajectories of a given gene family, it is critical to detect the ancestral signatures. The rearrangement of functional domains made up the diversification found in PRG repertoires. Structural rearrangement of ancient domains mediated the NB-LRR evolutionary path from an initial set of modular proteins. Events such as domain acquisition, sequence modification and temporary or stable associations are prominent among rapidly evolving innate immune receptors. Over time PRGs are continuously shaped by different forces to find their optimal arrangement along the genome. The immune system is controlled by a robust regulatory system that works at different scales. It is important to understand how the PRG interaction network can be adjusted to meet specific needs. The high plasticity of the innate immune system is based on a sophisticated functional architecture and multi-level control. Due to the complexity of interacting with diverse pathogens, multiple defense lines have been organized into interconnected groups. Genomic architecture, gene expression regulation and functional arrangement of PRGs allow the deployment of an appropriate innate immunity response

Genome-wide identification and analysis of candidate genes for disease resistance in tomato

Tomato (Solanum lycopersicum L.) has served as an important model system for studying the genetics and molecular basis of resistance mecha- nisms in plants. An unprecedented challenge is now to capitalize on the genetic and genomic achievements obtained in this species. In this study, we show that information on the tomato genome can be used predictively to link resistance function with specific sequences. An integrated genomic approach for identifying new resistance (R) gene candidates was developed. An R gene functional map was created by co-localization of candidate pathogen recognition genes and anchoring molecular markers associated with resistance phenotypes. In-depth characterization of the identified pathogen recognition genes was performed. Finally, in order to highlight expressed pathogen recognition genes and to provide a first step in validation, the tomato transcriptome was explored and basic molecular analyses were conducted. Such methodology can help to better direct positional cloning, reducing the amount of effort required to identify a functional gene. The resulting candidate loci selected are available for exploiting their specific function

Seed storage allergens tackled via next-generation research assistant

The expanding consumption of plant proteins in the diet to overcome the environmental issues associated with animal proteins is increasing the incidence of food-induced allergic reactions. One of the 21st-century research drivers in agriculture sciences is the development and validation of concrete approaches for modulating the expression of allergenic proteins in crops before harvesting. The increasing incidence of plant food allergies is primarily induced by seed storage proteins that clinicians are experiencing recently because of the more predominant use of plant-derived proteins in the food industry. Increased availability of high-throughput technologies has generated an ever-growing number of omics data, allowing us to have better structural knowledge of SSPs and molecular properties that can inform the allergenicity assessment. The recent systems for targeted genome engineering, without double-strand DNA breaks, allow the introduction of precise modifications directly into commercial plant species. Artificial intelligence is significantly transforming scientific research across every stage, assisting scientists, processing large-scale data, making predictions, automating tasks. During this epochal change, marked by the encounter between artificial intelligence and synthetic biology, a next-generation research assistant (NGA) is coming alive. Here, we propose a new conceptual vision to facilitate and speed up the editing of cross-reactivity sites to obtain hypoallergenic cultivars and avoid pleiotropic effects. Finally, we discuss the potential applications of this new way to conceive the research. NGA may be undoubtedly capable of managing the evolution of SPP allergies through the prediction of novel epitopes, as well as the prediction of immunological response mechanisms

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Background: Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results: The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions: The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control

PRGdb 2.0 : towards a community-based database model for the analysis of R-genes in plants

The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a comprehensive resource on resistance genes (R-genes), a major class of genes in plant genomes that convey disease resistance against pathogens. Initiated in 2009, the database has grown more than 6-fold to recently include annotation derived from recent plant genome sequencing projects. Release 2.0 currently hosts useful biological information on a set of 112 known and 104 310 putative R-genes present in 233 plant species and conferring resistance to 122 different pathogens. Moreover, the website has been completely redesigned with the implementation of Semantic MediaWiki technologies, which makes our repository freely accessed and easily edited by any scientists. To this purpose, we encourage plant biologist experts to join our annotation effort and share their knowledge on resistance-gene biology with the rest of the scientific community

Alien Domains Shaped the Modular Structure of Plant NLR Proteins

Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intracellular receptors to detect pathogen-derived molecules and to induce defense responses. A multitaxa reconstruction of NB-domain associations allowed us to identify the first NB-LRR arrangement in the Chlorophyta division of the Viridiplantae. Our analysis points out that the basic NOD-like receptor (NLR) unit emerged in Chlorophytes by horizontal transfer and its diversification started from Toll/interleukin receptor-NB-LRR members. The operon-based genomic structure of Chromochloris zofingiensis NLR copies suggests a functional origin of NLR clusters. Moreover, the transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis support the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system. Taken together, our findings suggest that NLRs originated in unicellular algae and may have a common origin with cell-surface LRR receptors

MicroRNA 199b-5p delivery through stable nucleic acid lipid particles (SNALPs) in tumorigenic cell lines

MicroRNA (miR)-199b-5p has been shown to regulate Hes-1, a downstream effector of the canonical Notch and noncanonical SHH pathways, whereby it impairs medulloblastoma (MB) cancer stem cells (CSCs) through a decrease in the CD133+/CD15+ cell population. Here, we have developed stable nucleic acid lipid particles (SNALPs) that encapsulate miR-199b-5p. The efficacy of the miR- 199b-5p delivery by these SNALPs is demonstrated by significant impairment of Hes-1 levels and CSC markers in a range of different tumorigenic cell lines: colon (HT- 29, CaCo-2, and SW480), breast (MDA-MB231T and MCF-7), prostate (PC-3), glioblastoma (U-87), and MB(Daoy, ONS-76, and UW-228). After treatment with SNALP miR-199b-5p, there is also impairment of cell pro- liferation and no signs of apoptosis, as measured by cas- pases 3/7 activity and annexin V fluorescence cell sorter analyses. These data strengthen the importance of such carriers for miRNA delivery, which show no cytotoxic effects and provide optimal uptake into cells. Thus, efficient target downregulation in different tumorigenic cell lines will be the basis for future preclinical studies

Correlation of NM23-H1 cytoplasmic expression with metastatic stage in human prostate cancer tissue

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Common variants at 21q22.3 locus influence MX1 and TMPRSS2 gene expression and susceptibility to severe COVID-19

The established risk factors of coronavirus disease 2019 (COVID-19) are advanced age, male sex and comorbidities, but they do not fully explain the wide spectrum of disease manifestations. Genetic factors implicated in the host antiviral response provide for novel insights into its pathogenesis. We performed an in-depth genetic analysis of chromosome 21 exploiting the genome-wide association study data, including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry from the COVID-19 Host Genetics Initiative. We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show associations with severe COVID-19. The minor alleles of the five SNPs correlated with a reduced risk of developing severe COVID-19 and high level of MX1 expression in blood. Our findings demonstrate that host genetic factors can influence the different clinical presentations of COVID-19 and that MX1 could be a potential therapeutic target