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Aim: To unveil a putative correlation between phage genome flexibility and virion morphogenesis yield. Materials & methods: A deeper analysis of the mechanical properties of three Pseudomonas aeruginosa lytic phage genomes was undertaken, together with full genome cyclizability calculations. Results & conclusion: A putative correlation was established among phage genome flexibility, eclipse timeframe and virion particle morphogenesis yield, with a more flexible phage genome leading to a higher burst size and a more rigid phage genome leading to lower burst sizes. The results obtained are highly relevant to understand the influence of the phage genome plasticity on the virion morphogenesis yield inside the infected bacterial host cells and assumes particular relevance in the actual context of bacterial resistance to antibiotics.

Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenome data. In the last few years, many thousands of MAGs have been reported in the literature, for a variety of environments and host-associated microbiota, including humans. MAGs have helped us better understand microbial populations and their interactions with the environment where they live; moreover most MAGs belong to novel species, therefore helping to decrease the so-called microbial dark matter. However, questions about the biological reality of MAGs have not, in general, been properly addressed. In this review, I define the notions of hypothetical MAGs and conserved hypothetical MAGs. These notions should help with the understanding of the biological reality of MAGs, their worldwide occurrence, and the efforts to improve MAG recovery processes.

Despite advances in therapeutics, the progression of melanoma to metastasis still confers a poor outcome to patients. Nevertheless, there is a scarcity of biological models to understand cellular and molecular changes taking place along disease progression. Here, we characterized the transcriptome profiles of a multi-stage murine model of melanoma progression comprising a nontumorigenic melanocyte lineage (melan-a), premalignant melanocytes (4C), nonmetastatic (4C11-) and metastasis-prone (4C11+) melanoma cells. Clustering analyses have grouped the 4 cell lines according to their differentiated (melan-a and 4C11+) or undifferentiated/“mesenchymal-like” (4C and 4C11-) morphologies, suggesting dynamic gene expression patterns associated with the transition between these phenotypes. The cell plasticity observed in the murine melanoma progression model was corroborated by molecular markers described during stepwise human melanoma differentiation, as the differentiated cell lines in our model exhibit upregulation of transitory and melanocytic markers, whereas “mesenchymal-like” cells show increased expression of undifferentiated and neural crest-like markers. Sets of differentially expressed genes (DEGs) were detected at each transition step of tumor progression, and transcriptional signatures related to malignancy, metastasis and epithelial-to-mesenchymal transition were identified. Finally, DEGs were mapped to their human orthologs and evaluated in uni- and multivariate survival analyses using gene expression and clinical data of 703 drug-naïve primary melanoma patients, revealing several independent candidate prognostic markers. Altogether, these results provide novel insights into the molecular mechanisms underlying the phenotypic switch taking place during melanoma progression, reveal potential drug targets and prognostic biomarkers, and corroborate the translational relevance of this unique sequential model of melanoma progression.

Made available in DSpace on 2022-04-29T08:46:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-05-05 Plant natriuretic peptide-like (PNP) are signaling molecules related to adaptive responses to stress. The Arabidopsis thaliana PNP (AtPNP-A) is capable of modulating catalase 2 (CAT2) and rubisco activase (RCA) activity in some circumstances. Interestingly, many plant-pathogens co-opted PNP-like molecules to their benefit. For instance, the citrus pathogen Xanthomonas citri carries a PNP-like (XacPNP) that can mimic and regulate plant homeostasis, and many phytopathogenic fungi carry effectors (e.g., Ave1 and AvrLm6) that are indeed PNP-like homologs. This work investigates the PNP-like evolution across the tree of life, revealing many parallel gains and duplications in plant and fungi kingdoms. All PNP-like proteins in the final dataset are structurally similar, containing the AtPNP-A active domains modulating CAT2 activity and RCA interaction. Comparative genomics evinced that XacPNP is a lysogenic conversion factor associated with a Myoviridae-like prophage identified in many Xanthomonas species. Surprisingly, a PNP-like homolog was identified in Bemisia tabaci, an important agricultural pest, being to date the second example of lateral gene transfer (LGT) from plant to the whitefly. Moreover, the Bemisia PNP-like homolog can also be considered a potential new effector of this phloem-feeding insect. Noteworthy, the whiteflies infest many plants carrying PNP-like copies and interact with some of their bacterial and fungal pathogens, strongly suggesting complex recipient/donor traits of PNP by LGT and bringing new insights into the evolution of host-pathogen arms race across the tree of life. Departamento de Bioquímica Instituto de Química Universidade de São Paulo, SP Departamento de Ciências Biológicas e Núcleo de Pesquisas em Ciências Biológicas Universidade Federal de Ouro Preto, MG Faculdade de Medicina Universidade de Brasília-DF Universidade Estadual Paulista (UNESP) Faculdade de Ciências Agrárias e Veterinárias, SP Universidade Estadual Paulista (UNESP) Faculdade de Ciências Agrárias e Veterinárias, SP

Summary: The question of whether host genetics plays a role in the development of the infant gut microbiota does not, as yet, have a clear answer. In order to throw additional light on this question, we have analyzed 16S rRNA amplicon sequences from 99 valid fecal samples of five sets of dichorionic triplet babies born by C-section from 1 to 36 months of age. Beta diversity analysis showed that monozygotic twins were more similar to each other than their dizygotic siblings. Monozygotic twins also tended to share more amplicon sequence variants between them. Heritability analysis showed that the genera Bacteroides and Veillonella are particularly susceptible to host genetics. We conclude that infant gut microbiota development is influenced by host genetics, but this effect is subtle and may affect only certain bacterial taxa during a limited time period early in life.

Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.

The experimental determination of a bacteriophage host is a laborious procedure. For this reason, there is a pressing need for reliable computational predictions of bacteriophage hosts in phage research in general and in phage therapy in particular. Here, we present a new program called vHULK for phage host prediction based on 9,504 phage genome features. These features take into account alignment significance scores between predicted-protein sequences in the phage genomes and a curated database of viral protein families. The features were fed to a deep neural network, and four distinct models were trained to predict 61 different host genera and 52 host species. In random controlled test sets, the program obtained 99% and 98% accuracy values at the genus and species levels, respectively. On a validation dataset with 2,178 phage genomes, mean accuracies were 82% and 52% at the genus and species levels, respectively. When compared against other phage host prediction programs on the same validation dataset, vHULK achieved substantially better performance, therefore demonstrating that the program is an advance on the state-of-art in phage host prediction. vHULK is freely available at https://github.com/LaboratorioBioinformatica/vHULK.

The Gram-negative bacterium Xylella fastidiosa colonizes plant xylem vessels and is obligately vectored by xylem sap-feeding hemipteran insects. X. fastidiosa causes diseases in many plant species but in a variety of its plant hosts this bacterium behaves as a commensal endophyte. Originally confined to the Americas, infecting mainly grapevine, citrus and coffee plants, X. fastidiosa has spread to several plant species in Europe, causing devastating crop diseases. Although many pathogenicity and virulence factors have been identified in X. fastidiosa which enable the bacterium to successfully establish in the xylem tissue, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in specific plant hosts have not been fully elucidated. Here we present comparative analyses of 94 publicly available whole-genome sequences of X. fastidiosa strains with the goal of providing insights into plant host specificity determinants for this phytopathogen as well as of expanding the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results revealed a pangenome of 4,549 protein coding sequences (CDSs) which is still open. The core- and accessory genomes comprise 954 and 2,219 CDSs, respectively. Phylogenetic tree construction using all core genome CDSs grouped the strains in three major clades of subspecies fastidiosa, multiplex and pauca, with subclades related to the strains’ sequence type (ST) obtained from multi-locus sequence typing (MLST). The geographic region where the strains were collected showed stronger association with the clades of X. fastidiosa strains rather than the plant species from which they were isolated. Among the CDS related to virulence and pathogenicity found in the core genome, those related to lipopolysaccharide (LPS) synthesis and trimeric autotransporter adhesins (TAA) are somewhat related with the plant host of a given strain according to phylogenetic inference. The X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, which includes a diversity of prophage regions. In summary, the genome comparisons reported here will enable a better understanding of the diversity of phylogenetically close genomes and warrant further investigation of LPS and TAAs as potential X. fastidiosa host-specificity determinants.Impact statementThe bacterium Xylella fastidiosa is a pathogen that infects many plant species and has caused devastating diseases in grapevine, citrus, coffee, and olive plants. This phytopathogen X. fastidiosa is original from the Americas and has emerged in Europe where it is causing severe economic losses for olive producers, mainly in Italy. Although many pathogenicity and virulence factors have been identified in X. fastidiosa, which enable this bacterium to successfully establish in the xylem vessels network, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in the different plant host species have not been fully elucidated. The comparative analyses of 94 whole-genome sequences from X. fastidiosa strains from diverse hosts and geographic regions provide insights into host specificity determinants for this phytopathogen as well as expand the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results contribute for a better understanding of the diversity of phylogenetically close genomes and warrant further experimental investigation of lipopolysaccharide and trimeric autotransporter adhesins as potential host-specificity determinants for X. fastidiosa.Data summaryAll genomic sequences were accessed from publicly available GenBank RefSeq database at NCBI (National Center for Biotechnology Information). A full listing of NCBI accession numbers for X. fastidiosa strains described in this paper is available in Table S1 (available in the online version of this article).

Gut microbiota-derived short-chain fatty-acid (SFCA) acetate protects mice against RSV A2 strain infection by increasing interferon-β production and expression of interferon-stimulated genes (ISGs). However, the role of SFCA in RSV infection using strains isolated from patients is unknown.We first used RSV clinical strains isolated from infants hospitalized with RSV bronchiolitis to investigate the effects of in vitro SCFA-acetate treatment of human pulmonary epithelial cells. We next examined whether SCFA-acetate treatment is beneficial in a mouse model of RSV infection using clinical isolates. We sought to investigate the relationship of gut microbiota and fecal acetate with disease severity among infants hospitalized with RSV bronchiolitis, and whether treating their respiratory epithelial cells with SCFA-acetate ex-vivo impacts viral load and ISG expression. We further treated epithelial cells from SARS-CoV-2 infected patients with SCFA-acetate.In vitro pre-treatment of A549 cells with SCFA-acetate reduced RSV infection with clinical isolates and increased the expression of RIG-I and ISG15. Animals treated with SCFA-acetate intranasally recovered significantly faster, with reduction in the RSV clinical isolates viral load, and increased lung expression of IFNB1 and the RIG-I. Experiments in RIG-I knockout A549 cells demonstrated that the protection relies on RIG-I presence. Gut microbial profile was associated with bronchiolitis severity and with acetate in stool. Increased SCFA-acetate levels were associated with increasing oxygen saturation at admission, and shorter duration of fever. Ex-vivo treatment of patients' respiratory cells with SCFA-acetate reduced RSV load and increased expression of ISGs OAS1 and ISG15, and virus recognition receptors MAVS and RIG-I, but not IFNB1. These SCFA-acetate effects were not found on cells from SARS-CoV-2 infected patients.SCFA-acetate reduces the severity of RSV infection and RSV viral load through modulation of RIG-I expression.FAPERGS (FAPERGS/MS/CNPq/SESRS no. 03/2017 - PPSUS 17/2551-0001380-8 and COVID-19 20/2551-0000258-6); CNPq 312504/2017-9; CAPES) - Finance Code 001.

Background Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. Results Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. Conclusions The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.

Assessing the compatibility between gene family phylogenies is a crucial and often computationally demanding step in many phylogenomic analyses. Here, we describe the Evolutionary Similarity Index (IES), a means to assess shared evolution between gene families using a weighted orthogonal distance regression model applied to sequence distances. The utilization of pairwise distance matrices circumvents comparisons between gene tree topologies, which are inherently uncertain and sensitive to evolutionary model choice, phylogenetic reconstruction artifacts, and other sources of error. Furthermore, IES enables the many-to-many pairing of multiple copies between similarly evolving gene families. This is done by selecting non-overlapping pairs of copies, one from each assessed family, and yielding the least sum of squared residuals. Analyses of simulated gene family data sets show that IES’s accuracy is on par with popular tree-based methods while also less susceptible to noise introduced by sequence alignment and evolutionary model fitting. Applying IES to an empirical data set of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. The most cohesive cluster consisted of 62 genes with compatible evolutionary signal, which occur as both single-copy and multiple homologs per genome; phylogenetic analysis of concatenated alignments from this cluster produced a tree closely matching previously published species trees for Archaea. Four other clusters are mainly composed of accessory genes with limited distribution among Archaea and enriched toward specific metabolic functions. Pairwise evolutionary distances obtained from these accessory gene clusters suggest patterns of interphyla horizontal gene transfer. An IES implementation is available at https://github.com/lthiberiol/evolSimIndex.

We report the microbial 16S rRNA gene and internal transcribed spacer (ITS) sequencing data of maize and soybean plants and field soil from eight locations in Brazil. Enterobacter and Pseudomonas were among the most abundant genera. The data suggest the presence of several species that have not been documented for Brazil.

Serratia liquefaciens strain FG3 (SlFG3), isolated from the flower of Stachytarpheta glabra in the Brazilian ferruginous fields, has distinctive genomic, adaptive, and biotechnological potential. Herein, using a combination of genomics and molecular approaches, we unlocked the evolution of the adaptive traits acquired by S1FG3, which exhibits the second largest chromosome containing the largest conjugative plasmids described for Serratia. Comparative analysis revealed the presence of 18 genomic islands and 311 unique protein families involved in distinct adaptive features. S1FG3 has a diversified repertoire of genes associated with Nonribosomal peptides (NRPs/PKS), a complete and functional cluster related to cellulose synthesis, and an extensive and functional repertoire of oxidative metabolism genes. In addition, S1FG3 possesses a complete pathway related to protocatecuate and chloroaromatic degradation, and a complete repertoire of genes related to DNA repair and protection that includes mechanisms related to UV light tolerance, redox process resistance, and a laterally acquired capacity to protect DNA using phosphorothioation. These findings summarize that SlFG3 is well-adapted to different biotic and abiotic stress situations imposed by extreme conditions associated with ferruginous fields, unlocking the impact of the lateral gene transfer to adjust the genome for extreme environments, and providing insight into the evolution of prokaryotes. Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior -Brazil (CAPES)CAPES [001, CFP 51/2013, 3385/2013]; National Council of Technological and Scientific Development (CNPq)National Council for Scientific and Technological Development (CNPq) [481226/2013-3]; Foundation of Protection to Research of the State of Minas Gerais - FAPEMIG [APQ-02387-14, APQ-02357-17]; CNPqNational Council for Scientific and Technological Development (CNPq); Fundect-MS [TO 141/2016, TO 007/2015, 007/2015 SIAFEM 025139]; UFOP grants; Laboratory of Biochemistry and Molecular Biology of the Faculty of Agrarian and Veterinary Sciences UNESP, Jaboticabal campus Thanks to all members of the Laboratory of Biochemistry and Molecular Biology (LBBM, Federal University of Ouro Preto, UFOP) and to the Laboratory of Biochemistry and Molecular Biology of the Faculty of Agrarian and Veterinary Sciences UNESP, Jaboticabal campus, for their support. This study was financed in part by the Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior -Brazil (CAPES) - Finance Code 001 - (the BIGA Project, CFP 51/2013, process 3385/2013), National Council of Technological and Scientific Development (CNPq Process 481226/2013-3), and Foundation of Protection to Research of the State of Minas Gerais - FAPEMIG (process APQ-02387-14 and process APQ-02357-17). LMM, JCS, AMV, NFA and JAF have a research fellowship from CNPq. NFA has grants from Fundect-MS (TO 141/2016 and TO 007/2015) and Fundect-MS (007/2015 SIAFEM 025139). LAGM and LMM have UFOP grants. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Made available in DSpace on 2021-06-25T11:01:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-01 Xanthomonas arboricola pv. juglandis (Xaj) is the most significant aboveground walnut bacterial pathogen. Disease management uses copper-based pesticides which induce pathogen resistance. We examined the genetic repertoire associated with adaptation and virulence evolution in Xaj. Comparative genomics of 32 Xaj strains reveal the possible acquisition and propagation of virulence factors via insertion sequences (IS). Fine-scale annotation revealed a Tn3 transposon (TnXaj417) encoding copper resistance genes acquired by horizontal gene transfer and associated with adaptation and tolerance to metal-based pesticides commonly used to manage pathogens in orchard ecosystems. Phylogenomic analysis reveals IS involvement in acquisition and diversification of type III effector proteins ranging from two to eight in non-pathogenic strains, 16 to 20 in pathogenic strains, besides six other putative effectors with a reduced identity degree found mostly among pathogenic strains. Yersiniabactin, xopK, xopAI, and antibiotic resistance genes are also located near ISs or inside genomic islands and structures resembling composite transposons. Center of Research in Biological Science Federal University of Ouro Preto Department of Plant Sciences University of California Faculty of Agricultural and Veterinary Sciences of Jaboticabal (FCAV) Universidade Estadual Paulista (UNESP) Department of Technology Cell Cycle Laboratory Butantan Institute Department of Biochemistry Chemistry Institute University of Sao Paulo School of Computing Federal University of Mato Grosso do Sul Department of Biological Science Institute of Exact and Biological Science Federal University of Ouro Preto Faculty of Agricultural and Veterinary Sciences of Jaboticabal (FCAV) Universidade Estadual Paulista (UNESP) Department of Technology

The malaria parasite Plasmodium falciparum possesses a unique Acetyl-CoA Synthetase (PfACS) which provides acetyl moieties for different metabolic and regulatory cellular pathways. We characterized PfACS and studied its role focusing on epigenetic modifications using the var gene family as reporter genes. For this, mutant lines to modulate plasmodial ACS expression by degron-mediated protein degradation or ribozyme induced transcript decay were created. Additionally, an ACS inhibitor was tested for its effectiveness and specificity in interfering with PfACS. The knockdown of PfACS or its inhibition led to impaired parasite growth. Decreased levels of PfACS also led to differential histone acetylation patterns, altered variant gene expression and concomitantly decreased cytoadherence of infected red blood cells containing knocked-down parasites. Further, ChIP analysis revealed the presence of PfACS in many loci in ring stage parasites, underscoring its involvement in the regulation of chromatin. Due to its significant differences to human ACS, PfACS seems an interesting target for drug development.

Summary Large-scale mapping of antigens and epitopes is pivotal for developing immunotherapies but challenging, especially for eukaryotic pathogens, owing to their large genomes. Here, we developed an integrated platform for genome phage display (gPhage) to show that unbiased libraries of the eukaryotic parasite Trypanosoma cruzi enable the identification of thousands of antigens recognized by serum samples from patients with Chagas disease. Because most of these antigens are hypothetical proteins, gPhage provides evidence of their expression during infection. We built and validated a comprehensive map of Chagas disease antibody response to show how linear and putative conformation epitopes, many rich in repetitive elements, allow the parasite to evade a buildup of neutralizing antibodies directed against protein domains that mediate infection pathogenesis. Thus, the gPhage platform is a reproducible and effective tool for rapid simultaneous identification of epitopes and antigens, not only in Chagas disease but perhaps also in globally emerging/reemerging acute pathogens., Graphical abstract, Highlights • Genomic shotgun phage display (gPhage) of eukaryotes is feasible and promising. • gPhage allows rapid antigen ID and epitope mapping, including 3D structures. • Conformation epitopes can be identified and validated by using the gPhage platform. • Most Chagas disease antigens are hypothetical proteins rich in repetitive elements., Parasitology; Sequence analysis; Systems biology

The phenotypes of allergic airway diseases are influenced by the interplay between host genetics and the gut microbiota, which may be modulated by probiotics. We investigated the probiotic effects on allergic inflammation in A/J and C57BL/6 mice. C57BL/6 mice had increased gut microbiota diversity compared to A/J mice at baseline. Acetate producer probiotics differentially modulated and altered the genus abundance of specific bacteria, such as Akkermansia and Allistipes, in mouse strains. We induced airway inflammation followed by probiotic treatment and found that only A/J mice exhibited decreased inflammation, and the beneficial effects of probiotics in A/J mice were partially due to acetate production. To understand the relevance of microbial composition colonization in the development of allergic diseases, we implanted female C57BL/6 mice with A/J embryos to naturally modulate the microbial composition of A/J mice, which increased gut microbiota diversity and reduced eosinophilic inflammation in A/J. These data demonstrate the central importance of microbiota to allergic phenotype severity. Video Abstract Supplementary Information The online version contains supplementary material available at 10.1186/s40168-021-01081-2.

International audience; Viruses are now recognized as important players in microbial dynamics and biogeochemical cycles in the oceans. Yet, compared with aquatic ecosystems, virus discovery in terrestrial ecosystems has been challenging partly due to the inherent complexity of soils. To expand our understanding of soil viruses and their putative contributions to soil microbial processes, we analysed metagenomes of community-level virus-enriched suspensions by tangential flow filtration obtained from two French agricultural soils. We found viral sequences representing a total of 239 viral operational taxonomic units that corresponded to 29.5% of the mapping reads in the metagenomic datasets. The analysis of their genomic sequences revealed novel virocell metabolic potential with implications to virus-host interactions, carbon cycling, plant-beneficial functions in the rhizosphere, horizontal gene transfer and other relevant microbial strategies applied to survive in soils.