Targeting these mediators may be a novel therapeutic strategy for anti-fibrosis and anti-tumor treatment. Many small molecules suppress EMT by targeting these mediators, including commercial drugs and compounds derived from natural products. In addition, these compounds that target EMT have shown anticancer effects on multiple types of cancer. For example, luteolin not only attenuated gastric cancer but also showed a therapeutic effect in lung cancer cells. Therefore, we concluded that compounds targeting EMT exerted anticancer effect in one type of cancer may be effective in other types of cancer. Moreover, curcumin targeted EMT and exhibited both anticancer and anti-fibrotic properties, which suggests that drugs targeting EMT may exhibit both anti-fibrotic and anticancer effects. Taken together, these data suggest that drugs targeting EMT not only have both anti-fibrotic and anticancer effects but also are active against multiple types of organ fibrosis and cancer, which may assist in discovering therapeutic drugs against fibrosis and cancer. Small molecules are a huge resource for bio-active leading compounds, and it is important to discover novel bio-active compounds effectively and quickly. Here, we summarized several methods to investigate the prospect of natural products as drug candidates. First, molecular docking is used to predict the interaction between a ligand and target protein, and molecular docking‐based virtual screening is helpful to discriminate active compounds from inactive ones. In addition, during lead optimization,tower garden calculations can quickly test modifications to the structures of known active compounds before synthesis.
Therefore, computational methodologies can accelerate the discovery of bio-active compounds. Second, reverse pharmacokinetics is used for drug discovery from natural products with defined clinical benefits. Reverse pharmacokinetics can be used to guide potential target tissues/organs/molecules, and then further physiologically relevant pharmacological models are designed to discover bio-active compounds and reveal their corresponding mechanisms. It is worth noting that many compounds show low solubility, which limits their clinical efficiency and restricts their clinical use. Fortunately, there are multiple ways to enhance the bio-availability, such as cocrystallization and the formation of phospholipid complexes and nanoemulsions.Finally, based on the hypothesis that drugs targeting EMT have both anti-fibrotic and anticancer effects, many important mediators contributing to EMT have been discovered. Additionally, a great number of compounds suppress EMT in tumor and fibrosis by targeting these mediators. It is hoped that many new drugs are designed and developed in the future based on the aforementioned mediators to treat tumors and fibrosis.Modern plant trade disturbs historical ecological relationships and creates opportunities for the development of novel pathogenic interactions , often with correlated genetic changes . However, pathogens must be adapted to the environment of the novel host before they meet, or they will not be able to survive and reproduce . That does not mean pathogens necessarily preadapted to the exact same host, but they could have adapted to a similar host earlier and retained that adaptation until encountering a novel host. Convergent evolution in diverse pathogen populations can allow for divergent strains to have the ability to infect the same hosts. Three potential mechanisms of genetic change that can accompany host shifts are nucleotide changes leading to different alleles in the core genome of a pathogen , whole-gene gain and loss in the pan-genome, leading to unique sets of genes in individual strains, or regulatory/epigenetic changes.
Due to the recent increase in whole-genome sequencing of plant pathogens, we can now more effectively use phylogenetic analyses to investigate their genetic associations to both novel and historical host plants . Understanding the phylogenetic relationships between specific hosts and pathogens should allow the development of preemptive plans to protect natural ecosystems as well as agriculture from the emergence of novel pathogens. Xylella fastidiosa is an insect-transmitted, xylem-limited bacterial plant pathogen found across the Americas and, as of recently, globally. X. fastidiosa is considered to be a generalist pathogen because, as a species, it reportedly infects at least 563 species belonging to 82 botanical families . The lack of host specificity that X. fastidiosa exhibits as a species contrasts with increased plant host specificity in smaller clades and strains . It is still debated whether a pathogen like X. fastidiosa should be considered a generalist species that “leaps” between phylogenetically distant hosts or, alternatively, a crawler at shallower clades . The difference is biological, as there are unique implications for either evolutionary path. X. fastidiosa could be repeatedly evolving specialization, or it could have biological and genetic traits as a species that make particular hosts of disparate plant taxa suitable. From an applied perspective, there have been recent calls from government agencies for increased focus on understanding the host range of X. fastidiosa. This is because the pathogen has been deemed likely to spread and to be of extremely high risk to crops of agricultural value . Xylella fastidiosa causes disease in a range of high-value crops, including Pierce’s disease of grapevines , citrus variegated chlorosis disease in sweet oranges, almond leaf scorch, leaf scorch of coffee, and olive quick decline syndrome , spanning North and South America, Europe, the Middle East, and Taiwan . While there are three distinctive subspecies of X. fastidiosa and it would be desirable to be able to use those subspecies for management decisions, so far, the subspecies have not been found to have sufficient resolution to define host range or to infer risk . Understanding the molecular basis of plant host specificity in X. fastidiosa is vital for predicting and acting upon host shifts, but these are processes yet to be described . Xylella fastidiosa is a member of the group Xanthomonadaceae and phylogenetically clusters sister to Xanthomonas albilineans, technically within the paraphyletic genus Xanthomonas, although Xylella is considered a separate genus . Xylella spp. and Xanthomonas albilineans are the only xylem-limited Xanthomonadaceae and have convergently reduced genomes compared to the rest of the genus.
Xylella also lacks a type III secretion system , a loss compared to its higher-order taxonomic group. As the purpose of the T3SS in phytopathogens is to deliver effectors into living plant cells , the loss has been hypothesized to be due to X. fastidiosa primarily interacting with nonliving tissue, insect cuticle, and mature xylem vessels . While the molecular basis of host range is not understood, there are consistent patterns in the ability of particular X. fastidiosa isolates to infect specific plant hosts regardless of their environmental condition . This implies that genetics, as opposed to only environmental conditions, underlie the relationship between isolates and plant hosts that allow for colonization. Recurring pathogen specificity to a particular host can be either explained through phylogenetic signal, where members of a clade have shared traits that allow for pathogenesis in that host, or by pathological convergence,stacking flower pots tower where more distantly related strains have separately acquired mechanisms for virulence. Both processes have underlying genetics, but each shows different phylogenetic patterns . Last, we have seen that deletion of rpfF, which controls cell-cell signaling via a diffusible signal factor , can expand the host range of X. fastidiosa . Other insights into host range have been made in terms of plant immunological studies. For example, removing the O-antigen from the exterior ofX. fastidiosa cells allows the plant to quickly recognize X. fastidiosa and initiate immune responses, thus decreasing its likelihood of colonization of the plant . O-antigens are highly variable and evolve rapidly and often are shown to have coevolutionary histories between symbiotic organisms, as they are the first exposed part of any bacterium . In terms of phylogenetic methods, cophylogenies have shown no cospeciation between plant hosts and X. fastidiosa or any other congruence between the evolutionary histories of X. fastidiosa and its plant hosts . Based on the current data, it is not generally possible to tell if X. fastidiosa is undergoing host jumps or range expansions; however, the data available so far suggest that both are occurring given that, in certain situations, we see strains able to infect multiple hosts , while in other situations, we see multiple strains coexisting in nature but no cross infections of hosts . Using the influx of whole-genome data generated in the past several years, we searched the genomes of X. fastidiosa for correlations with plant host species. Ancestral state reconstructions use genetic data , with a known phenotype for each taxon, to characterize the most likely state that each ancestral node of the tree would have possessed for the phenotype of interest. This tool has been used to understand host-pathogen interactions via ancestral state reconstructions in fungi and trematodes parasite systems . Ideally, we would be able to ask: what was the most likely ancestral host of the ancestor of all X. fastidiosa? If we can understand patterns in the past, it can help us better build models to predict future hosts based on the genomic changes associated with historical host shifts. Following the ancestral state reconstructions, we looked further into the pan-genome by calculating correlations between plant host types and the presence/absence of each gene. This study aimed to compare the commonly used genetic data sets available for phylogenetic analyses of X. fastidiosa both to compare phylogenetic topologies as well as ancestral host states from each data set. We hypothesized that the pathogen phylogeny would be correlated with host history and that we could observe this trend through ancestral state reconstruction. If there is no relationship between host and the phylogeny, there should not be conclusive ancestral state reconstruction results.
We hypothesize that by using either the core genome of X. fastidiosa, pan-genome phylogenetic tree, or both, it would be possible to estimate the likelihood of hypothetical plant hosts for ancestral nodes of interest . This would show that the host is largely dependent and predictable based on the phylogeny of bacterial relationships and would lead to further pursuing allelic differences in core genome and/or gene gain/loss in the pan-genome and estimate how either or both are correlated with plant host identity. While not biologically meaningful, since multilocus sequence type data are still frequently used in X. fastidio sa management, we included that data type in our analysis for comparison as well.In this paper, we show that there is a genetic basis to the host range of X. fastidiosa. We demonstrate that both the phylogeny and gene gain and loss in the pan-genome are connected to plant host of the diverse species X. fastidiosa and that an Asterid of undetermined genus was the most likely ancestral plant host of X. fastidiosa. Ourresults indicate that the evolutionary trajectories of both the core and the pangenomes allow for a bacterial species with an extensive host range to specialize many times over a broad array of plant hosts. We see this system as an example of one that “leaps,” with host genera seemingly changing not via phylogenetic signal to related plant hosts but switching across large regions of plant host phylogenies . Prior to this study, we have not been able to trace a pattern of underlying genetic origins of host specificity in X. fastidiosa. In this way, our study shows that the phylogeny and gene gain/loss are connected to the adaptations that diversify host specificity in X. fastidiosa. Phylogenies for MLST, pan-genome, core genome, and non-recombinant core genome data were topologically similar, but not identical. While the subspecies relationships are not important to predicting host range, they are frequently used in management decisions and our ability to converse about outbreaks, so we are including our findings alongside our data on host use . In terms of taxonomic subspecies, there are differences between the four trees in whether the two debated subspecies, X.fastidiosa subsp. morus and X. fastidiosa subsp. sandyi, are contained within X. fastidiosa subsp. fastidiosa or X. fastidiosa subsp. multiplex or if they should be considered their own subspecies. While there are pairs of strains that are consistently close to each other, like the X. fastidiosa subsp. morus strains MulMD and Mul0034, the uncertainty in their position from phylogeny to phylogeny likely reflects large gaps in diversity that we have not yet sequenced or horizontal gene transfer more intensely affecting the pan-genome and particular genes used for MLST than the core genes, leading to issues recreating the vertical descent we aim for in a phylogeny . X. fastidiosa subsp. morus has been documented to have up to 15.30% of its core genome undergoing inter subspecies homologous recombination, which could account for its uncertain placement in the four phylogenies .