Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts

Abstract Background Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin. Results Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus Herbaspirillum. Furthermore, the AU14040 strain cluster contained the neuABC genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system. Conclusions Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.https://deepblue.lib.umich.edu/bitstream/2027.42/152201/1/12864_2019_Article_5982.pd

Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

Nowadays defying homology relationships among sequences is essential for biological research. Within homology the analysis of orthologs sequences is of great importance for computational biology, annotation of genomes and for phylogenetic inference. Since 2007, with the increase in the number of new sequences being deposited in large biological databases, researchers have begun to analyse computerized methodologies and tools aimed at selecting the most promising ones in the prediction of orthologous groups. Literature in this field of research describes the problems that the majority of available tools show, such as those encountered in accuracy, time required for analysis (especially in light of the increasing volume of data being submitted, which require faster techniques) and the automatization of the process without requiring manual intervention. Conducting our search through BMC, Google Scholar, NCBI PubMed, and Expasy, we examined more than 600 articles pursuing the most recent techniques and tools developed to solve most the problems still existing in orthology detection. We listed the main computational tools created and developed between 2011 and 2017, taking into consideration the differences in the type of orthology analysis, outlining the main features of each tool and pointing to the problems that each one tries to address. We also observed that several tools still use as their main algorithm the BLAST “all-against-all” methodology, which entails some limitations, such as limited number of queries, computational cost, and high processing time to complete the analysis. However, new promising tools are being developed, like OrthoVenn (which uses the Venn diagram to show the relationship of ortholog groups generated by its algorithm); or proteinOrtho (which improves the accuracy of ortholog groups); or ReMark (tackling the integration of the pipeline to turn the entry process automatic); or OrthAgogue (using algorithms developed to minimize processing time); and proteinOrtho (developed for dealing with large amounts of biological data). We made a comparison among the main features of four tool and tested them using four for prokaryotic genomas. We hope that our review can be useful for researchers and will help them in selecting the most appropriate tool for their work in the field of orthology

Sugarcane: an unexpected habitat for black yeasts in Chaetothyriales

Abstract Sugarcane (Saccharum officinarum, Poaceae) is cultivated on a large scale in (sub)tropical regions such as Brazil and has considerable economic value for sugar and biofuel production. The plant is a rich substrate for endo- and epiphytic fungi. Black yeasts in the family Herpotrichiellaceae (Chaetothyriales) are colonizers of human-dominated habitats, particularly those rich in toxins and hydrocarbon pollutants, and may cause severe infections in susceptible human hosts. The present study assessed the diversity of Herpotrichiellaceae associated with sugarcane, using in silico identification and selective isolation. Using metagenomics, we identified 5833 fungal sequences, while 639 black yeast-like isolates were recovered in vitro. In both strategies, the latter fungi were identified as members of the genera Cladophialophora, Exophiala, and Rhinocladiella (Herpotrichiellaceae), Cyphellophora (Cyphellophoraceae), and Knufia (Trichomeriaceae). In addition, we discovered new species of Cladophialophora and Exophiala from sugarcane and its rhizosphere. The first environmental isolation of Cladophialophora bantiana is particularly noteworthy, because this species up to now is exclusively known from the human host where it mostly causes fatal brain disease in otherwise healthy patients

Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis

Submitted by Manoel Barata ([email protected]) on 2018-02-09T13:19:12Z No. of bitstreams: 1 FaoroComparativ.pdf: 5399928 bytes, checksum: af51deed6d3e60618950577e576e6aad (MD5)Approved for entry into archive by Manoel Barata ([email protected]) on 2018-05-03T19:30:23Z (GMT) No. of bitstreams: 1 FaoroComparativ.pdf: 5399928 bytes, checksum: af51deed6d3e60618950577e576e6aad (MD5)Made available in DSpace on 2018-05-03T19:30:23Z (GMT). No. of bitstreams: 1 FaoroComparativ.pdf: 5399928 bytes, checksum: af51deed6d3e60618950577e576e6aad (MD5) Previous issue date: 2017Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil / Universidade Federal do Paraná. Engenharia de Bioprocessos e Biotecnologia. Curitiba, PR, Brasil.Universidade Federal do Paraná. Setor de Educação Profissional e Tecnológica. Laboratório de Bioinformática. Curitiba, PR, Brasil / Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil / CBS-KNAW Fungal Biodiversity Centre. Utrecht, Netherlands / University of Amsterdam. Institute for Biodiversity and Ecosystem Dynamics. Amsterdam, Netherlands.Universidade Federal do Paraná. Engenharia de Bioprocessos e Biotecnologia. Curitiba, PR, Brasil.Universidade Federal do Paraná. Setor de Educação Profissional e Tecnológica. Laboratório de Bioinformática. Curitiba, PR, Brasil.Universidade Federal do Paraná. Engenharia de Bioprocessos e Biotecnologia. Curitiba, PR, Brasil / Universidade Federal do Paraná. Setor de Educação Profissional e Tecnológica. Laboratório de Bioinformática. Curitiba, PR, Brasil / Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil.Universidade de Brasília. Departamento de Biologia Celular. Brasilia, Brasil.Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil.Universidade de Brasília. Departamento de Biologia Celular. Brasilia, Brasil.Guangdong Provincial Center for Disease Control and Prevention. Guangdong Provincial Institute of Public Health, Guangzhou, China.Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade de São Paulo. Faculdade de Ciências Farmacêuticas. Departamento de Análises Clínicas e Toxicológicas. São Paulo, SP, Brasil.Universidade de São Paulo. Faculdade de Ciências Farmacêuticas. Departamento de Análises Clínicas e Toxicológicas. São Paulo, SP, Brasil.Universidade de Brasília. Departamento de Biologia Celular. Brasilia, Brasil / Northern Arizona University. Pathogen and Microbiome Institute. Flagstaff, United States.Universidade Católica de Brasília. Departamento de Ciências Genômicas e Biotecnologia. Brasília, DF, Brasil.Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade Federal do Paraná. Setor de Educação Profissional e Tecnológica. Laboratório de Bioinformática. Curitiba, PR, Brasil / Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade de Campinas. Divisão de Recursos Microbianos. Campinas, SP, Brasil.Mashhad University of Medical Sciences. School of Medicine. Department of Parasitology and Mycology. Mashhad, Iran.Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil / Universidade Federal do Paraná. Hospital das Clínicas. Curitiba, PR, Brasil.Universidade Federal do Paraná. Setor de Educação Profissional e Tecnológica. Laboratório de Bioinformática. Curitiba, PR, Brasil / Universidade Federal do Paraná. Departamento de Bioquímica. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Patologia Básica. Laboratório de Imunogenética e Histocompatibilidade. Curitiba, PR, Brasil / CBS-KNAW Fungal Biodiversity Centre. Utrecht, Netherlands / University of Amsterdam. Institute for Biodiversity and Ecosystem Dynamics. Amsterdam, Netherlands.Fonsecaea and Cladophialophora are genera of black yeast-like fungi harboring agents of a mutilating implantation disease in humans, along with strictly environmental species. The current hypothesis suggests that those species reside in somewhat adverse microhabitats, and pathogenic siblings share virulence factors enabling survival in mammal tissue after coincidental inoculation driven by pathogenic adaptation. A comparative genomic analysis of environmental and pathogenic siblings of Fonsecaea and Cladophialophora was undertaken, including de novo assembly of F. erecta from plant material. The genome size of Fonsecaea species varied between 33.39 and 35.23 Mb, and the core genomes of those species comprises almost 70% of the genes. Expansions of protein domains such as glyoxalases and peptidases suggested ability for pathogenicity in clinical agents, while the use of nitrogen and degradation of phenolic compounds was enriched in environmental species. The similarity of carbohydrate-active vs. protein-degrading enzymes associated with the occurrence of virulence factors suggested a general tolerance to extreme conditions, which might explain the opportunistic tendency of Fonsecaea sibling species. Virulence was tested in the Galleria mellonella model and immunological assays were performed in order to support this hypothesis. Larvae infected by environmental F. erecta had a lower survival. Fungal macrophage murine co-culture showed that F. erecta induced high levels of TNF-α contributing to macrophage activation that could increase the ability to control intracellular fungal growth although hyphal death were not observed, suggesting a higher level of extremotolerance of environmental species

Comparative genomics of sibling species of Fonsecaea associated with Human Chromoblastomycosis

Fonsecaea and Cladophialophora are genera of black yeast-like fungi harboring agents of a mutilating implantation disease in humans, along with strictly environmental species. The current hypothesis suggests that those species reside in somewhat adverse microhabitats, and pathogenic siblings share virulence factors enabling survival in mammal tissue after coincidental inoculation driven by pathogenic adaptation. A comparative genomic analysis of environmental and pathogenic siblings of Fonsecaea and Cladophialophora was undertaken, including de novo assembly of F. erecta from plant material. The genome size of Fonsecaea species varied between 33.39 and 35.23Mb, and the core genomes of those species comprises almost 70% of the genes. Expansions of protein domains such as glyoxalases and peptidases suggested ability for pathogenicity in clinical agents, while the use of nitrogen and degradation of phenolic compounds was enriched in environmental species. The similarity of carbohydrate-active vs. protein-degrading enzymes associated with the occurrence of virulence factors suggested a general tolerance to extreme conditions, which might explain the opportunistic tendency of Fonsecaea sibling species. Virulence was tested in the Galleria mellonella model and immunological assays were performed in order to support this hypothesis. Larvae infected by environmental F. erecta had a lower survival. Fungal macrophage murine co-culture showed that F. erecta induced high levels of TNF-alpha contributing to macrophage activation that could increase the ability to control intracellular fungal growth although hyphal death were not observed, suggesting a higher level of extremotolerance of environmental species8CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPES573828/2008-3059201

Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis

Fonsecaea and Cladophialophora are genera of black yeast-like fungi harboring agents of a mutilating implantation disease in humans, along with strictly environmental species. The current hypothesis suggests that those species reside in somewhat adverse microhabitats, and pathogenic siblings share virulence factors enabling survival in mammal tissue after coincidental inoculation driven by pathogenic adaptation. A comparative genomic analysis of environmental and pathogenic siblings of Fonsecaea and Cladophialophora was undertaken, including de novo assembly of F. erecta from plant material. The genome size of Fonsecaea species varied between 33.39 and 35.23 Mb, and the core genomes of those species comprises almost 70% of the genes. Expansions of protein domains such as glyoxalases and peptidases suggested ability for pathogenicity in clinical agents, while the use of nitrogen and degradation of phenolic compounds was enriched in environmental species. The similarity of carbohydrate-active vs. protein-degrading enzymes associated with the occurrence of virulence factors suggested a general tolerance to extreme conditions, which might explain the opportunistic tendency of Fonsecaea sibling species. Virulence was tested in the Galleria mellonella model and immunological assays were performed in order to support this hypothesis. Larvae infected by environmental F. erecta had a lower survival. Fungal macrophage murine co-culture showed that F. erecta induced high levels of TNF-α contributing to macrophage activation that could increase the ability to control intracellular fungal growth although hyphal death were not observed, suggesting a higher level of extremotolerance of environmental species

Proposed pathways for aromatic compounds metabolism in <i>H. seropedicae</i> SmR1.

<p>Proposed pathways for aromatic compounds metabolism in <i>H. seropedicae</i> SmR1.</p

General features of the genome of <i>Herbaspirillum seropedicae</i> SmR1.

<p>General features of the genome of <i>Herbaspirillum seropedicae</i> SmR1.</p

Molecular mechanisms probably involved in plant colonization and plant growth promotion identified in the <i>H. seropedicae</i> SmR1 genome.

<p>Plant signals can modulate the expression of bacterial genes coding for adhesins, type IV <i>pili</i> and enzymes of lipopolysaccharide (LPS) synthesis, triggering bacterial attachment to root surfaces. The molecular communication involves bacterial protein secretion and phytohormones to stimulate plant growth and modulate plant defense response. In addition, modulation of plant ethylene levels by ACC deaminase may contribute to plant growth promotion. The success of the endophytic association depends on a compatible genetic background that leads to benefits for both organisms.</p