Covering: up to 2019
Fungi produce a remarkable diversity of secondary metabolites: small, bioactive molecules not required for growth but which are essential to their ecological interactions with ...other organisms. Genes that participate in the same secondary metabolic pathway typically reside next to each other in fungal genomes and form biosynthetic gene clusters (BGCs). By synthesizing state-of-the-art knowledge on the evolution of BGCs in fungi, we propose that fungal chemodiversity stems from three molecular evolutionary processes involving BGCs: functional divergence, horizontal transfer, and
de novo
assembly. We provide examples of how these processes have contributed to the generation of fungal chemodiversity, discuss their relative importance, and outline major, outstanding questions in the field.
This highlight synthesizes knowledge of the molecular evolutionary processes - functional divergence, horizontal transfer, and
de novo
assembly - that govern biosynthetic gene cluster diversification and the generation of chemodiversity in fungi.
About the Authors: Antonis Rokas * E-mail: antonis.rokas@vanderbilt.edu Affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America ORCID ...logo http://orcid.org/0000-0002-7248-6551 Matthew E. Mead Affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America ORCID logo http://orcid.org/0000-0001-9195-7585 Jacob L. Steenwyk Affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America ORCID logo http://orcid.org/0000-0002-8436-595X Nicholas H. Oberlies Affiliation: Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America ORCID logo http://orcid.org/0000-0002-0354-8464 Gustavo H. Goldman Affiliation: Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil ORCID logo http://orcid.org/0000-0002-2986-350X Introduction Species in the genus Aspergillus are saprophytic filamentous fungi that are most commonly found in soil and litter environments of subtropical and warm temperate latitudes 1. The most severe form of aspergillosis is invasive aspergillosis, which primarily affects individuals with compromised immune systems or preexisting lung conditions 3. Since drugs targeting invasive aspergillosis are not always effective due to our lack of understanding of how they function inside the human host 4 and the evolution of drug resistance 5, 6, infected individuals suffer high morbidity and mortality 7. Addressing this question requires that we consider the fact that pathogenic Aspergillus species are not dependent on their hosts for survival and their pathogenic effects are entirely accidental or opportunistic. ...understanding the evolution of pathogenicity in the genus requires that we understand how variation in the traits that enable Aspergillus species to survive in their natural soil and litter environments has rendered a few of these species capable to establish infections inside human hosts. More broadly, given that the ability to cause human disease has repeatedly evolved across the fungal tree of life, and that the vast majority of human fungal pathogens have non-pathogenic close relatives 22, understanding the evolution of Aspergillus pathogenicity can serve as a model for studying fungal pathogenicity in general.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Aspergillus fumigatus is a major fungal pathogen of humans but its two closest relatives, Aspergillus fischeri and Aspergillus oerlinghausenensis, are not. Steenwyk et al. examined ...whether...
Abstract
Aspergillus fumigatus is a major human pathogen. In contrast, Aspergillus fischeri and the recently described Aspergillus oerlinghausenensis, the two species most closely related to A. fumigatus, are not known to be pathogenic. Some of the genetic determinants of virulence (or “cards of virulence”) that A. fumigatus possesses are secondary metabolites that impair the host immune system, protect from host immune cell attacks, or acquire key nutrients. To examine whether secondary metabolism-associated cards of virulence vary between these species, we conducted extensive genomic and secondary metabolite profiling analyses of multiple A. fumigatus, one A. oerlinghausenensis, and multiple A. fischeri strains. We identified two cards of virulence (gliotoxin and fumitremorgin) shared by all three species and three cards of virulence (trypacidin, pseurotin, and fumagillin) that are variable. For example, we found that all species and strains examined biosynthesized gliotoxin, which is known to contribute to virulence, consistent with the conservation of the gliotoxin biosynthetic gene cluster (BGC) across genomes. For other secondary metabolites, such as fumitremorgin, a modulator of host biology, we found that all species produced the metabolite but that there was strain heterogeneity in its production within species. Finally, species differed in their biosynthesis of fumagillin and pseurotin, both contributors to host tissue damage during invasive aspergillosis. A. fumigatus biosynthesized fumagillin and pseurotin, while A. oerlinghausenensis biosynthesized fumagillin and A. fischeri biosynthesized neither. These biochemical differences were reflected in sequence divergence of the intertwined fumagillin/pseurotin BGCs across genomes. These results delineate the similarities and differences in secondary metabolism-associated cards of virulence between a major fungal pathogen and its nonpathogenic closest relatives, shedding light onto the genetic and phenotypic changes associated with the evolution of fungal pathogenicity.
Asexual sporulation is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In
, the production of asexual spores is primarily governed by ...the BrlA→AbaA→WetA regulatory cascade. The final step in this cascade is controlled by the WetA protein and governs not only the morphological differentiation of spores but also the production and deposition of diverse metabolites into spores. While WetA is conserved across the genus
, the structure and degree of conservation of the
gene regulatory network (GRN) remain largely unknown. We carried out comparative transcriptome analyses of comparisons between
null mutant and wild-type asexual spores in three representative species spanning the diversity of the genus
:
,
, and
We discovered that WetA regulates asexual sporulation in all three species via a negative-feedback loop that represses BrlA, the cascade's first step. Furthermore, data from chromatin immunoprecipitation sequencing (ChIP-seq) experiments in
asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory motif. Several global regulators known to bridge spore production and the production of secondary metabolites show species-specific regulatory patterns in our data. These results suggest that the BrlA→AbaA→WetA cascade's regulatory role in cellular and chemical asexual spore development is functionally conserved but that the
-associated GRN has diverged during
evolution.
The formation of resilient spores is a key factor contributing to the survival and fitness of many microorganisms, including fungi. In the fungal genus
, spore formation is controlled by a complex gene regulatory network that also impacts a variety of other processes, including secondary metabolism. To gain mechanistic insights into how fungal spore formation is controlled across
, we dissected the gene regulatory network downstream of a major regulator of spore maturation (WetA) in three species that span the diversity of the genus: the genetic model
, the human pathogen
, and the aflatoxin producer
Our data show that WetA regulates asexual sporulation in all three species via a negative-feedback loop and likely binds a novel regulatory element that we term the WetA response element (WRE). These results shed light on how gene regulatory networks in microorganisms control important biological processes and evolve across diverse species.
Bridging cellular reproduction and survival is essential for all life forms. Aspergillus fungi primarily reproduce by forming asexual spores called conidia, whose formation and maturation is governed ...by the central genetic regulatory circuit BrlA→AbaA→WetA. Here, we report that WetA is a multi-functional regulator that couples spore differentiation and survival, and governs proper chemical development in Aspergillus flavus. The deletion of wetA results in the formation of conidia with defective cell walls and no intra-cellular trehalose, leading to reduced stress tolerance, a rapid loss of viability, and disintegration of spores. WetA is also required for normal vegetative growth, hyphal branching, and production of aflatoxins. Targeted and genome-wide expression analyses reveal that WetA exerts feedback control of brlA and that 5,700 genes show altered mRNA levels in the mutant conidia. Functional category analyses of differentially expressed genes in ΔwetA RNA-seq data indicate that WetA contributes to spore integrity and maturity by properly regulating the metabolic pathways of trehalose, chitin, α-(1,3)-glucan, β-(1,3)-glucan, melanin, hydrophobins, and secondary metabolism more generally. Moreover, 160 genes predicted to encode transcription factors are differentially expressed by the absence of wetA, suggesting that WetA may play a global regulatory role in conidial development. Collectively, we present a comprehensive model for developmental control that bridges spore differentiation and survival in A. flavus.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In filamentous fungi, asexual development involves cellular differentiation and metabolic remodeling leading to the formation of intact asexual spores. The development of asexual spores (conidia) in
...is precisely coordinated by multiple transcription factors (TFs), including VosA, VelB, and WetA. Notably, these three TFs are essential for the structural and metabolic integrity, i.e., proper maturation, of conidia in the model fungus
To gain mechanistic insight into the complex regulatory and interdependent roles of these TFs in asexual sporogenesis, we carried out multi-omics studies on the transcriptome, protein-DNA interactions, and primary and secondary metabolism employing
conidia. RNA sequencing and chromatin immunoprecipitation sequencing analyses have revealed that the three TFs directly or indirectly regulate the expression of genes associated with heterotrimeric G-protein signal transduction, mitogen-activated protein (MAP) kinases, spore wall formation and structural integrity, asexual development, and primary/secondary metabolism. In addition, metabolomics analyses of wild-type and individual mutant conidia indicate that these three TFs regulate a diverse array of primary metabolites, including those in the tricarboxylic acid (TCA) cycle, certain amino acids, and trehalose, and secondary metabolites such as sterigmatocystin, emericellamide, austinol, and dehydroaustinol. In summary, WetA, VosA, and VelB play interdependent, overlapping, and distinct roles in governing morphological development and primary/secondary metabolic remodeling in
conidia, leading to the production of vital conidia suitable for fungal proliferation and dissemination.
Filamentous fungi produce a vast number of asexual spores that act as efficient propagules. Due to their infectious and/or allergenic nature, fungal spores affect our daily life.
species produce asexual spores called conidia; their formation involves morphological development and metabolic changes, and the associated regulatory systems are coordinated by multiple transcription factors (TFs). To understand the underlying global regulatory programs and cellular outcomes associated with conidium formation, genomic and metabolomic analyses were performed in the model fungus
Our results show that the fungus-specific WetA/VosA/VelB TFs govern the coordination of morphological and chemical developments during sporogenesis. The results of this study provide insights into the interdependent, overlapping, or distinct genetic regulatory networks necessary to produce intact asexual spores. The findings are relevant for other
species such as the major human pathogen
and the aflatoxin producer
.
Fungal pathogens are a global threat to human health. For example, fungi from the genus
Aspergillus
cause a spectrum of diseases collectively known as aspergillosis. Most of the >200,000 ...life-threatening aspergillosis infections per year worldwide are caused by
Aspergillus fumigatus
. Recently, molecular typing techniques have revealed that aspergillosis can also be caused by organisms that are phenotypically similar to
A. fumigatus
but genetically distinct, such as
Aspergillus lentulus
and
Aspergillus fumigatiaffinis
. Importantly, some of these so-called cryptic species are thought to exhibit different virulence and drug susceptibility profiles than
A. fumigatus
, however, our understanding of their biology and pathogenic potential has been stymied by the lack of genome sequences and phenotypic profiling of multiple clinical strains. To fill this gap, we phenotypically characterized the virulence and drug susceptibility of 15 clinical strains of
A. fumigatus
,
A. lentulus
, and
A. fumigatiaffinis
from Spain and sequenced their genomes. We found heterogeneity in drug susceptibility across species and strains. We further found heterogeneity in virulence within each species but no significant differences in the virulence profiles between the three species. Genes known to influence drug susceptibility (
cyp51A
and
fks1
) vary in paralog number and sequence among these species and strains and correlate with differences in drug susceptibility. Similarly, genes known to be important for virulence in
A. fumigatus
showed variability in number of paralogs across strains and across species. Characterization of the genomic similarities and differences of clinical strains of
A. lentulus
,
A. fumigatiaffinis
,
and A. fumigatus
that vary in disease-relevant traits will advance our understanding of the variance in pathogenicity between
Aspergillus
species and strains that are collectively responsible for the vast majority of aspergillosis infections in humans.
Abstract
Bioinformatic analysis—such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, file format conversion, and processing and analysis—is ...integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses, but unified toolkits that conduct all these analyses are lacking. To address this gap, we introduce BioKIT, a versatile command line toolkit that has, upon publication, 42 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we conducted a comprehensive examination of relative synonymous codon usage across 171 fungal genomes that use alternative genetic codes, showed that the novel metric of gene-wise relative synonymous codon usage can accurately estimate gene-wise codon optimization, evaluated the quality and characteristics of 901 eukaryotic genome assemblies, and calculated alignment summary statistics for 10 phylogenomic data matrices. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwyk-biokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).
Abstract
Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest ...stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to nonpathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and nonpathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1700 genes whose evolutionary rate differed between pathogens and nonpathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and nonpathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.
PDF
