Phylogenomics of plant-associated Botryosphaeriaceae species

AbstractThe Botryosphaeriaceae is a fungal family that includes many destructive vascular pathogens of woody plants (e.g., Botryosphaeria dieback of grape, Panicle blight of pistachio). Species in the genera Botryosphaeria, Diplodia, Dothiorella, Lasiodiplodia, Neofusicoccum, and Neoscytalidium attack a range of horticultural crops, but they vary in virulence and in their abilities to infect their hosts via different infection courts (flowers, green shoots, woody twigs). Isolates of seventeen species, originating from symptomatic apricot, grape, pistachio, and walnut were tested for pathogenicity to grapevine wood after four months of incubation in potted plants in the greenhouse. Results revealed significant variation in virulence in terms of the length of the internal wood lesions caused by these seventeen species. Phylogenomic comparisons of the seventeen species of wood-colonizing fungi revealed clade-specific expansion of gene families representing putative virulence factors involved in toxin production and mobilization, wood degradation, and nutrient uptake. Statistical analyses of the evolution of the size of gene families revealed expansions of secondary metabolism and transporter gene families in Lasiodiplodia and of secreted cell wall degrading enzymes (CAZymes) in Botryosphaeria and Neofusicoccum genomes. In contrast, Diplodia, Dothiorella, and Neoscytalidium generally showed a contraction in the number of members of these gene families. Overall, species with expansions of gene families, such as secreted CAZymes, secondary metabolism, and transporters, were the most virulent (i.e., were associated with the largest lesions), based on our pathogenicity tests and published reports. This study represents the first comparative phylogenomic investigation into the evolution of possible virulence factors from diverse, cosmopolitan members of the Botryosphaeriaceae.

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Phylogenomics of Plant-Associated Botryosphaeriaceae Species

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652802 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jadran F. Garcia ◽

Daniel P. Lawrence ◽

Abraham Morales-Cruz ◽

Renaud Travadon ◽

Andrea Minio ◽

...

Keyword(s):

Secondary Metabolism ◽

Virulence Factors ◽

Gene Families ◽

Toxin Production ◽

Cell Wall Degrading Enzymes ◽

Horticultural Crops ◽

Potted Plants ◽

Specific Expansion ◽

Pathogenicity Tests ◽

Vascular Pathogens

The Botryosphaeriaceae is a fungal family that includes many destructive vascular pathogens of woody plants (e.g., Botryosphaeria dieback of grape, Panicle blight of pistachio). Species in the genera Botryosphaeria, Diplodia, Dothiorella, Lasiodiplodia, Neofusicoccum, and Neoscytalidium attack a range of horticultural crops, but they vary in virulence and their abilities to infect their hosts via different infection courts (flowers, green shoots, woody twigs). Isolates of seventeen species, originating from symptomatic apricot, grape, pistachio, and walnut were tested for pathogenicity on grapevine wood after 4 months of incubation in potted plants in the greenhouse. Results revealed significant variation in virulence in terms of the length of the internal wood lesions caused by these seventeen species. Phylogenomic comparisons of the seventeen species of wood-colonizing fungi revealed clade-specific expansion of gene families representing putative virulence factors involved in toxin production and mobilization, wood degradation, and nutrient uptake. Statistical analyses of the evolution of the size of gene families revealed expansions of secondary metabolism and transporter gene families in Lasiodiplodia and of secreted cell wall degrading enzymes (CAZymes) in Botryosphaeria and Neofusicoccum genomes. In contrast, Diplodia, Dothiorella, and Neoscytalidium generally showed a contraction in the number of members of these gene families. Overall, species with expansions of gene families, such as secreted CAZymes, secondary metabolism, and transporters, were the most virulent (i.e., were associated with the largest lesions), based on our pathogenicity tests and published reports. This study represents the first comparative phylogenomic investigation into the evolution of possible virulence factors from diverse, cosmopolitan members of the Botryosphaeriaceae.

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Global Aspects of pacC Regulation of Pathogenicity Genes in Colletotrichum gloeosporioides as Revealed by Transcriptome Analysis

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-13-0080-r ◽

2013 ◽

Vol 26 (11) ◽

pp. 1345-1358 ◽

Cited By ~ 61

Author(s):

Noam Alkan ◽

Xiangchun Meng ◽

Gilgi Friedlander ◽

Eli Reuveni ◽

Serenella Sukno ◽

...

Keyword(s):

Colletotrichum Gloeosporioides ◽

Global Analysis ◽

Gene Families ◽

Polymerase Chain Reaction Analysis ◽

Fungal Genome ◽

Cell Wall Degrading Enzymes ◽

Ph Change ◽

Global Regulation ◽

Knock Out ◽

Pathogenicity Genes

Colletotrichum gloeosporioides alkalinizes its surroundings during colonization of host tissue. The transcription factor pacC is a regulator of pH-controlled genes and is essential for successful colonization. We present here the sequence assembly of the Colletotrichum fruit pathogen and use it to explore the global regulation of pathogenicity by ambient pH. The assembled genome size was 54 Mb, encoding 18,456 genes. Transcriptomes of the wild type and ΔpacC mutant were established by RNA-seq and explored for their global pH-dependent gene regulation. The analysis showed that pacC upregulates 478 genes and downregulates 483 genes, comprising 5% of the fungal genome, including transporters, antioxidants, and cell-wall-degrading enzymes. Interestingly, gene families with similar functionality are both up- and downregulated by pacC. Global analysis of secreted genes showed significant pacC activation of degradative enzymes at alkaline pH and during fruit infection. Select genes from alkalizing-type pathogen C. gloeosporioides and from acidifying-type pathogen Sclerotinia sclerotiorum were verified by quantitative reverse-transcription polymerase chain reaction analysis at different pH values. Knock out of several pacC-activated genes confirmed their involvement in pathogenic colonization of alkalinized surroundings. The results suggest a global regulation by pacC of key pathogenicity genes during pH change in alkalinizing and acidifying pathogens.

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Toxin production by Campylobacter spp.

Clinical Microbiology Reviews ◽

10.1128/cmr.10.3.466 ◽

1997 ◽

Vol 10 (3) ◽

pp. 466-476 ◽

Cited By ~ 97

Author(s):

T M Wassenaar

Keyword(s):

Animal Model ◽

Campylobacter Jejuni ◽

Virulence Factors ◽

Clinical Data ◽

Related Species ◽

Toxin Production ◽

Biochemical Properties ◽

Future Directions ◽

Model Studies ◽

Campylobacter Spp

Of all the virulence factors that were proposed for Campylobacter jejuni and related species to cause disease in humans, the discovery of toxin production was the most promising but led to a rather confusing and even disappointing stream of data. The discussion of whether proteinaceous exotoxins are relevant in disease remains open. One important reason for this lack of consensus is the anecdotal nature of the literature reports. To provide a basis for an unbiased opinion, this review compiles all described exotoxins, compares their reported properties, and provides a summary of animal model studies and clinical data. The toxins are divided into enterotoxins and cytotoxins and are sorted according to their biochemical properties. Since many Campylobacter toxins have been compared with toxins of other species, some key examples of the latter are also discussed. Future directions of toxin research that appear promising are defined.

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Biochemical and molecular effects of yeast extract applications on anthocyanin accumulation in cv. Sangiovese.

BIO Web of Conferences ◽

10.1051/bioconf/20191303005 ◽

2019 ◽

Vol 13 ◽

pp. 03005

Author(s):

Chiara Pastore ◽

Gianluca Allegro ◽

Gabriele Valentini ◽

Emilia Colucci ◽

Fabrizio Battista ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Phenolic Compounds ◽

Secondary Metabolism ◽

Yeast Extract ◽

Anthocyanin Accumulation ◽

Yeast Saccharomyces Cerevisiae ◽

Potted Plants ◽

Expression Of Genes ◽

Anthocyanin Concentration ◽

Molecular Effects

The effect of biotic and abiotic elicitors on the secondary metabolism in grapevine is gaining a lot of interest, as it has been shown that they can increase the accumulation of phenolic compounds and anthocyanins in particular. The aim of this research was to verify the biochemical and molecular effects of the application of LalVigne™ MATURE (Lallemand, St. Simon, France), 100% inactivated natural yeast (Saccharomyces cerevisiae) on the anthocyanin accumulation in potted plants of Sangiovese. In both years, LVM plants did not differ from C in technological ripening at harvest. A significant increase in anthocyanin concentration and the expression of genes involved in their biosynthesis was found in 2016 in LVM grapes compared to C, while in 2017, a year with extremely warm temperatures, the anthocyanins of C and LVM were comparable, despite a slight increase in LVM after the second treatment.

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Protein moonlighting in parasitic protists

Biochemical Society Transactions ◽

10.1042/bst20140215 ◽

2014 ◽

Vol 42 (6) ◽

pp. 1734-1739 ◽

Cited By ~ 8

Author(s):

Michael L. Ginger

Keyword(s):

Animal Models ◽

Virulence Factors ◽

Gene Families ◽

Evolutionary Divergence ◽

Reductive Evolution ◽

Niche Adaptation ◽

Moonlighting Proteins ◽

Parasite Biology

Reductive evolution during the adaptation to obligate parasitism and expansions of gene families encoding virulence factors are characteristics evident to greater or lesser degrees in all parasitic protists studied to date. Large evolutionary distances separate many parasitic protists from the yeast and animal models upon which classic views of eukaryotic biochemistry are often based. Thus a combination of evolutionary divergence, niche adaptation and reductive evolution means the biochemistry of parasitic protists is often very different from their hosts and to other eukaryotes generally, making parasites intriguing subjects for those interested in the phenomenon of moonlighting proteins. In common with other organisms, the contribution of protein moonlighting to parasite biology is only just emerging, and it is not without controversy. Here, an overview of recently identified moonlighting proteins in parasitic protists is provided, together with discussion of some of the controversies.

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Genome wide identification of bacterial genes required for plant infection by Tn-seq

10.1101/126896 ◽

2017 ◽

Author(s):

Kevin Royet ◽

Nicolas Parisot ◽

Agnès Rodrigue ◽

Erwan Gueguen ◽

Guy Condemine

Keyword(s):

Virulence Factors ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Plant Cell Wall ◽

Infection Process ◽

Cell Wall Degrading Enzymes ◽

Plant Pathogenic Bacteria ◽

Regulatory Cascade ◽

Plant Infection ◽

Genome Wide

ABSTRACTSoft rot enterobacteria (DickeyaandPectobacterium) are major pathogens that cause diseases on plants of agricultural importance such as potato and ornamentals. Long term studies to identify virulence factors of these bacteria focused mostly on plant cell wall degrading enzymes secreted by the type II secretion system and the regulation of their expression. To identify new virulence factors we performed a Tn-seq genome-wide screen of a transposon mutant library during chicory infection followed by high-throughput sequencing. This allowed the detection of mutants with reduced but also increased fitness in the plant. Virulence factors identified differed from those previously known since diffusible ones (secreted enzymes, siderophores or metabolites) were not detected by this screen. In addition to genes encoding proteins of unknown function that could be new virulence factors, others could be assigned to known biological functions. The central role of the FlhDC regulatory cascade in the control of virulence was highlighted with the identification of new members of this pathway. Scarcity of the plant in certain amino acids and nucleic acids required presence of the corresponding biosynthetic genes in the bacteria. Their products could be targets for the development of antibacterial compounds. Among the genes required for full development in chicory we also identified six genes involved in the glycosylation of the flagellin FliC, glycosylation, which in other plant pathogenic bacteria contributes to virulence.Author summaryIdentification of virulence factors of plant pathogenic bacteria has relied on the test of individual mutants on plants, a time-consuming method. New methods like transcriptomic or proteomic can now be used but they only allow the identification of genes induced during the infection process and non-induced genes may be missed. Tn-seq is a very powerful method to identify genes required for bacterial growth in their host. We used for the first time this method in a plant pathogenic bacteria to identify genes required for the multiplication ofDickeya dadantiiin chicory. We identified about 100 genes with decreased or increased fitness in the plant. Most of them had no previously described role in bacterial virulence. We unveiled important metabolic genes and regulators of motility and virulence. We showed thatD. dadantiiflagellin is glycosylated and that this modification confers fitness to the bacteria during plant infection. Our work opens the way to the use of Tn-seq with bacterial phytopathogens. Assay by this method of large collections of environmental pathogenic strains now available will allow an easy and rapid identification of new virulence factors.

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Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?

10.1101/2021.02.23.432530 ◽

2021 ◽

Author(s):

Brian Looney ◽

Shingo Miyauchi ◽

Emmanuelle Morin ◽

Elodie Drula ◽

Pierre Emmanuel Courty ◽

...

Keyword(s):

Secondary Metabolism ◽

Plant Cell Wall ◽

Gene Evolution ◽

Plant Root ◽

Gene Clusters ◽

Sister Group ◽

Cell Wall Degrading Enzymes ◽

Ectomycorrhizal Symbiosis ◽

Forested Ecosystems ◽

High Degree

AbstractThe ectomycorrhizal symbiosis is an essential guild of many forested ecosystems and has a dynamic evolutionary history across kingdom Fungi, having independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic features of the transition to the ectomycorrhizal habit within the Russulaceae, one of the most diverse lineages of ectomycorrhizal fungi. We present comparative analyses of the pangenome and gene repertoires of 21 species across the order Russulales, including a closely related saprotrophic member of Russulaceae. The ectomycorrhizal Russulaceae is inferred to have originated around the Cretaceous-Paleogene extinction event (73.6-60.1 million years ago (MY)). The genomes of the ectomycorrhizal Russulaceae are characterized by a loss of genes for plant cell-wall degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of genes coding for certain secreted proteins with TE “nests”. The saprotrophic sister group of the ectomycorrhizal Russulaceae, Gloeopeniophorella convolvens, possesses some of these aspects (e.g., loss of some PCWDE and protease orthologs, TE expansion, reduction in secondary metabolism clusters), resulting from an accelerated rate of gene evolution in the shared ancestor of Russulaceae that predates the evolution of the ectomycorrhizal habit. Genomes of Russulaceae possess a high degree of synteny, including a conserved set of terpene secondary metabolite gene clusters. We hypothesize that the evolution of the ectomycorrhizal habit requires premodification of the genome for plant root association followed by an accelerated rate of gene evolution within the secretome for host-defense circumvention and symbiosis establishment.

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Genotypic and phenotypic diversity of Staphylococcus aureus from cystic fibrosis lung infections and their interactions with Pseudomonas aeruginosa

10.1101/814152 ◽

2019 ◽

Author(s):

Eryn E. Bernardy ◽

Robert A. Petit ◽

Vishnu Raghuram ◽

Ashley M. Alexander ◽

Timothy D. Read ◽

...

Keyword(s):

Cystic Fibrosis ◽

Staphylococcus Aureus ◽

Pseudomonas Aeruginosa ◽

Virulence Factors ◽

Phenotypic Diversity ◽

Laboratory Strain ◽

Toxin Production ◽

Reference Isolate ◽

Patient Health ◽

Lung Infections

AbstractPseudomonas aeruginosa and Staphylococcus aureus are the most common bacteria that infect the respiratory tract of individuals with the genetic disease cystic fibrosis (CF); in fact, S. aureus has recently overtaken P. aeruginosa to become the most common. Substantial research has been performed on the epidemiology of S. aureus in CF; however, there appears to be a gap in knowledge in regard to the pathogenesis of S. aureus in the context of CF lung infections. Most studies have focused on a few S. aureus isolates, often exclusively laboratory adapted strains, and how they are killed by P. aeruginosa. Because of this, little is known about the diversity of S. aureus CF lung isolates in both virulence and interaction with P. aeruginosa. To begin to address this gap in knowledge, we recently sequenced 65 clinical S. aureus isolates from the Emory CF Biospecimen Registry and Boston Children’s Hospital, including the reference isolate JE2, a USA300 strain. Here, we analyzed antibiotic resistance genotypes, sequence type, clonal complex, spa type, and agr type of these isolates. We hypothesized that major virulence phenotypes of S. aureus that may be associated with CF lung infections, namely toxin production and mucoid phenotype, would be retained in these isolates. To test our hypothesis, we plated on specific agars and found that most isolates can hemolyze both rabbit and sheep blood (67.7%) and produce polysaccharide (69.2%), consistent with virulence retention in CF lung isolates. We also identified three distinct phenotypic groups of S. aureus based on their survival in the presence of nonmucoid P. aeruginosa laboratory strain PAO1 and its mucoid derivative. Altogether, our work provides greater insight into the diversity of S. aureus CF isolates, specifically the distribution of important virulence factors and their interaction with P. aeruginosa, all of which have implications in patient health.Author SummaryStaphylococcus aureus is now the most frequently detected pathogen in the lungs of individuals who have cystic fibrosis (CF), followed closely by Pseudomonas aeruginosa. When these two pathogens are found to coinfect the CF lung, patients have a significantly worse prognosis. While P. aeruginosa has been rigorously studied in the context of bacterial pathogenesis in CF, less is known about S. aureus. Here we present an in-depth study of 64 S. aureus CF clinical isolates where we investigated genetic diversity utilizing whole genome sequencing, virulence phenotypes, and interactions with P. aeruginosa. We have found that S. aureus isolated from the CF lung are phylogenetically diverse, most retain known virulence factors, and they vary in interactions with P. aeruginosa from highly sensitive to completely tolerant. Deepening our understanding of how S. aureus responds to its environment and other microbes in the CF lung will enable future development of effective treatments and preventative measures against these formidable infections.

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Deciphering the Dynamics of Signaling Cascades and Virulence Factors of B. cinerea during Tomato Cell Wall Degradation

Microorganisms ◽

10.3390/microorganisms9091837 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1837

Author(s):

Almudena Escobar-Niño ◽

Inés M. Morano Bermejo ◽

Rafael Carrasco Reinado ◽

Francisco Javier Fernandez-Acero

Keyword(s):

Signal Transduction ◽

Virulence Factors ◽

Plant Defenses ◽

Therapeutic Targets ◽

Pathogenic Fungi ◽

Toxin Production ◽

Infection Process ◽

Membrane Receptors ◽

Phenotypic Characterization ◽

Go Annotation

The ascomycete Botrytis cinerea is one of the most relevant plant pathogenic fungi, affecting fruits, flowers, and greenhouse-grown crops. The infection strategy used by the fungus comprises a magnificent set of tools to penetrate and overcome plant defenses. In this context, the plant-pathogen communication through membrane receptors and signal transduction cascades is essential to trigger specific routes and the final success of the infection. In previous reports, proteomics approaches to B. cinerea signal transduction cascades changes in response to different carbon source and plant-based elicitors have been performed. Analyzing the secretome, membranome, phosphoproteome, and the phosphomembranome. Moreover, phenotypic changes in fungal biology was analyzed, specifically toxin production. To obtain the whole picture of the process and reveal the network from a system biology approach, this proteomic information has been merged with the phenotypic characterization, to be analyzed using several bioinformatics algorithms (GO, STRING, MCODE) in order to unravel key points in the signal transduction regulation crucial to overcome plant defenses, as well as new virulence/pathogenicity factors that could be used as therapeutic targets in the control of the gray mold rot disease. A total of 1721 and 663 exclusive or overexpressed proteins were identified under glucose (GLU) and deproteinized tomato cell walls (TCW), summarizing all of the protein identifications under phenotypic characterized stages. Under GO analysis, there are more biological process and molecular functions described in GLU, highlighting the increase in signaling related categories. These results agree with the high number of total identified proteins in GLU, probably indicating a more varied and active metabolism of the fungus. When analyzing only GO annotations related with signal transduction, it was revealed that there were proteins related to TOR signaling, the phosphorelay signal transduction system, and inositol lipid-mediated signaling, only under GLU conditions. On the contrary, calcium-mediated signaling GO annotation is only present between the proteins identified under TCW conditions. To establish a potential relationship between expressed proteins, cluster analyses showed 41 and 14 clusters under GLU and TCW conditions, confirming an increase in biological activity in GLU, where we identified a larger number of clusters related to transcription, translation, and cell division, between others. From these analyses, clusters related to signal transduction and clusters related to mycotoxin production were found, which correlated with the phenotypic characterization. The identification of the proteins encompassed in each condition and signal transduction cascade would provide the research community with new information about the B. cinerea infection process and potential candidates of pathogenicity/virulence factors, overcoming plant defenses, and new therapeutic targets.

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Virulence Factors of Clostridioides (Clostridium) difficile Linked to Recurrent Infections

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2019/7127850 ◽

2019 ◽

Vol 2019 ◽

pp. 1-7

Author(s):

Laura Tijerina-Rodríguez ◽

Licet Villarreal-Treviño ◽

Rayo Morfín-Otero ◽

Adrián Camacho-Ortíz ◽

E. Garza-González

Keyword(s):

Virulence Factors ◽

Toxin Production ◽

Negative Regulator ◽

Binary Toxin ◽

Recurrent Infections ◽

Accessory Gene ◽

Accessory Gene Regulator ◽

Cell Internalization ◽

Adhesion Efficiency ◽

First Recurrence

From 20 to 30% of Clostridioides (Clostridium) difficile infection (CDI), patients might develop recurrence of the infection (RCDI) and, after the first recurrence, the risk of further episodes increases up to 60%. Several bacterial virulence factors have been associated with RCDI, including the elevated production of toxins A and B, the presence of a binary toxin CDT, and mutations in the negative regulator of toxin expression, tcdC. Additional factors have shown to regulate toxin production and virulence in C. difficile in RCDI, including the accessory-gene regulator agr, which acts as a positive switch for toxin transcription. Furthermore, adhesion and motility-associated factors, such as Cwp84, SlpA, and flagella, have shown to increase the adhesion efficiency to host epithelia, cell internalization, and the formation of biofilm. Finally, biofilm confers to C. difficile protection from antibiotics and acts as a reservoir for spores that allow the persistence of the infection in the host. In this review, we describe the key virulence factors of C. difficile that have been associated with recurrent infections.

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