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At least 631 records · Page 35

Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis

Dark-induced senescence provokes profound metabolic shifts to recycle nutrients and to guarantee plant survival. To date, research on these processes has largely focused on characterizing mutants deficient in individual pathways. Here, we adopted a time-resolved genome-wide association-based approach to characterize dark-induced senescence by evaluating the photochemical efficiency and content of primary and lipid metabolites at the beginning, or after 3 or 6 days in darkness. We discovered six patterns of metabolic shifts and identified 215 associations with 81 candidate genes being involved in this process. Among these associations, we validated the roles of four genes associated with glycine, galactinol, threonine, and ornithine levels. We also demonstrated the function of threonine and galactinol catabolism during dark-induced senescence. Intriguingly, we determined that the association between tyrosine contents and TYROSINE AMINOTRANSFERASE 1 influences enzyme activity of the encoded protein and transcriptional activity of the gene under normal and dark conditions, respectively. Moreover, the single-nucleotide polymorphisms affecting the expression of THREONINE ALDOLASE 1 and the amino acid transporter gene AVT 1 B, respectively, only underlie the variation in threonine and glycine levels in the dark. Taken together, these results allow us to present a very detailed model of the metabolic aspects of dark-induced senescence, as well as the process itself.

59 BASIC BIOLOGICAL SCIENCES↗

Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain

The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.

59 BASIC BIOLOGICAL SCIENCES↗

A charge transfer framework that describes supramolecular interactions governing structure and properties of 2D perovskites

The elucidation of structure-to-function relationships for two-dimensional (2D) hybrid perovskites remains a primary challenge for engineering efficient perovskite-based devices. By combining insights from theory and experiment, we describe the introduction of bifunctional ligands that are capable of making strong hydrogen bonds within the organic bilayer. We find that stronger intermolecular interactions draw charge away from the perovskite layers, and we have formulated a simple and intuitive computational descriptor, the charge separation descriptor (CSD), that accurately describes the relationship between the Pb-I-Pb angle, band gap, and in-plane charge transport with the strength of these interactions. A higher CSD value correlates to less distortion of the Pb-I-Pb angle, a reduced band gap, and higher in-plane mobility of the perovskite. These improved material properties result in improved device characteristics of the resulting solar cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Observation of site-selective chemical bond changes via ultrafast chemical shifts

The concomitant motion of electrons and nuclei on the femtosecond time scale marks the fate of chemical and biological processes. Here we demonstrate the ability to initiate and track the ultrafast electron rearrangement and chemical bond breaking site-specifically in real time for the carbon monoxide diatomic molecule. We employ a local resonant x-ray pump at the oxygen atom and probe the chemical shifts of the carbon core-electron binding energy. We observe charge redistribution accompanying core-excitation followed by Auger decay, eventually leading to dissociation and hole trapping at one site of the molecule. The presented technique is general in nature with sensitivity to chemical environment changes including transient electronic excited state dynamics. This work provides a route to investigate energy and charge transport processes in more complex systems by tracking selective chemical bond changes on their natural timescale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rhizobial Secretion of Truncated Exopolysaccharides Severely Impairs the Mesorhizobium-Lotus Symbiosis

The symbiosis between Mesorhizobium japonicum R7A and Lotus japonicus Gifu is an important model system for investigating the role of bacterial exopolysaccharides (EPS) in plant-microbe interactions. Previously, we showed that R7A exoB mutants that are affected at an early stage of EPS synthesis and in lipopolysaccharide (LPS) synthesis induce effective nodules on L. japonicus Gifu after a delay, whereas exoU mutants affected in the biosynthesis of the EPS side chain induce small uninfected nodule primordia and are impaired in infection. The presence of a halo around the exoU mutant when grown on Calcofluor-containing media suggested the mutant secreted a truncated version of R7A EPS. A nonpolar ΔexoA mutant defective in the addition of the first glucose residue to the EPS backbone was also severely impaired symbiotically. Here, we used a suppressor screen to show that the severe symbiotic phenotype of the exoU mutant was due to the secretion of an acetylated pentasaccharide, as both monomers and oligomers, by the same Wzx/Wzy system that transports wild-type exopolysaccharide. We also present evidence that the ΔexoA mutant secretes an oligosaccharide by the same transport system, contributing to its symbiotic phenotype. In contrast, ΔexoYF and polar exoA and exoL mutants have a similar phenotype to exoB mutants, forming effective nodules after a delay. These studies provide substantial evidence that secreted incompatible EPS is perceived by the plant, leading to abrogation of the infection process.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial production of advanced biofuels

Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced by engineered microorganisms that use a renewable carbon source. Two biofuels, ethanol and biodiesel, have made inroads in displacing petroleum-based fuels, but their uptake has been limited by the amounts that can be used in conventional engines and by their cost. Further, advanced biofuels that mimic petroleum-based fuels are not limited by the amounts that can be used in existing transportation infrastructure but have had limited uptake due to costs. In this Review, we discuss engineering metabolic pathways to produce advanced biofuels, challenges with substrate and product toxicity with regard to host microorganisms and methods to engineer tolerance, and the use of functional genomics and machine learning approaches to produce advanced biofuels and prospects for reducing their costs.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis

We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named "pre-op" isolates) and then 6 days later from the anastomotic site (herein named "post-op" isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown.

59 BASIC BIOLOGICAL SCIENCES↗

Electron Transport in Polymerized Cytochrome Appendages

This project has been aimed at understanding the mechanism of long-range electron transport in extracellular cytochrome polymers. Starting with the initial discovery of OmcS filaments in Geobacter sulfurreducens, the three laboratories supported by this award characterized the extracellular polymers of two other cytochromes, OmcE and OmcZ. The overall work showed that the predominant view that existed, that these extracellular filaments were type IV pili, was completely wrong.

59 BASIC BIOLOGICAL SCIENCES↗

Analytical Modeling of Biomass Transport and Feeding Systems

The processing of biomass solids in a biorefinery consists of pretreatment, enzyme hydrolysis / concurrent fermentation of sugars to ethanol, product recovery, and drying. Sustainable operation requires a front end that transforms wet solids into a pumpable slurry. Otherwise the biorefinery will suffer unscheduled shut-downs and inefficient operation due to solids that obstruct pumps and other equipment and resist mixing in a bioreactor. Downtime in pioneer biorefineries due to interruptions from materials handling problems has been 50% or more, leading to unsustainable manufacturing processes. This work addresses new technology, predictive computational models, and definition of operational conditions that result in formation of slurries of corn stover at up to 300 g/L using low enzyme loadings (1 to 3 FPU cellulase/g) before the biomass (corn stover) enters the pretreatment step. A team of researchers from Purdue University, Idaho National Laboratory (INL), Forest Concepts, AdvanceBio, Argonne National Laboratory, and DOE BETO have combined their knowledge in agricultural and biological engineering, bioprocess engineering, mechanical engineering, chemical engineering, agricultural economics, materials engineering and enzyme and microbial technology to address the challenge of making lignocellulose flow. This team effort has resulted in the development and validation of conditions that employ low levels of commercial enzyme in an agitated bioreactor to which corn stover pellets are added resulting in formation of slurries at high solids loadings, before pretreatment. This approach overcomes challenges caused by handling of dry, particulate biomass materials at the front end of the biorefinery. The subsequent materials handling issues cause obstruction at pumps, pipes and valves. Formation of high loadings slurries with low yield stress, as reported here, significantly decreases the potential for process interruption and enhances plant operability. Key advances in the knowledge of how slurry formation occurs is reported here and in recently published journal papers. We found that pellets are needed to achieve high solids loading, and that commercial enzymes are effective in forming slurries of corn stover particles from pellets that have not been pretreated. Our work has resulted in models that predict solids behavior for formation of compressed solids and pellets that in turn facilitate slurries made of high concentrations of corn stover particles. A computational model was developed that gives mechanistic insights into properties of particles and mixing process that gives the slurry rheology needed to facilitate pumping. Hence, the corn stover may be pumped into a pretreatment reactor in place of auguring in solids against high pressure which is a root cause of interruptions at the front end of a biorefinery. Subsequent mixing in enzyme and microbial bioreactors results in conversion of lignocellulose to sugars in a biorefinery in agitated bioreactors, with flows in and out of the vessels being less likely to be interrupted due to plugging or materials handling problems. The obtained data coupled to process models, techno-economic assessment (TEA) and Life Cycle Analysis (LCA) were used to assess whether this approach is practical. These results are based on a foundation of laboratory characterization and pilot runs. The NREL biochemical sugar model was utilized to carry out techno-economic analysis of enzyme catalyzed liquefaction followed by enzyme hydrolysis. The minimum sugar selling price was between 17.5 and 18.3 ¢/pound or about the same as calculated by the NREL model for dilute acid pretreatment followed by enzyme hydrolysis. Life cycle analysis (LCA) based on Argonne’s Greet Model showed the enzyme catalyzed route had the lowest greenhouse gas emissions of the three combinations studied (i.e., enzyme, enzyme mimetic, and enzyme + mimetic combined). GHG emissions for enzyme-based corn stover liquefaction step, alone, were about 21 g CO 2 -equivalent/kg of liquefied slurry. We believe this approach will further enhance operability of a pioneer biorefinery, and bring large-scale conversion of lignocellulosic biomass to low carbon footprint biofuels closer to implementation.

09 BIOMASS FUELS↗

Investigating biological nitrogen fixation via single-cell transcriptomics

The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.

Lotus japonicus↗

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 A resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. Here, we propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling methane dynamics in three wetlands in Northeastern China by using the CLM-Microbe model

Wetlands account for up to 70% of the natural source of methane (CH 4 ) in terrestrial ecosystems on a global scale. Soil microbes are the ultimate producers and biological consumers of CH 4 in wetlands. Therefore, simulating microbial mechanisms of CH 4 production and consumptionwould improve the predictability of CH 4 flux in wetland ecosystems. In this study, we applied a microbial-explicit model, the CLM-Microbe, to simulate CH 4 flux in three major natural wetlands in northeastern China. The CLM-Microbe model was able to capture the seasonal variation of gross primary productivity (GPP), dissolved organic carbon (DOC), and CH 4 flux. The CLM-Microbe model explained more than 40% of the variation in GPP and CH 4 flux across sites. Marsh wetlands had higher CH 4 flux than mountain peatlands. Ebullition dominated the CH 4 transport pathway in all three wetlands. The methanogenesis dominates while methanotroph makes a minor contribution to the CH 4 flux, making all wetlands a CH 4 source. Sensitivity analysis indicated that microbial growth and death rates are the key factors governing CH 4 emission and vegetation physiological properties (flnr) and maintenance respiration predominate GPP variation. Explicitly simulating microbial processes allows genomic information to be incorporated, laying a foundation for better predicting CH 4 dynamics under the changing environment.

54 ENVIRONMENTAL SCIENCES↗

Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola

In warm and humid regions, the productivity of sorghum is significantly limited by the fungal hemibiotrophic pathogen Colletotrichum sublineola , the causal agent of anthracnose, a problematic disease of sorghum ( Sorghum bicolor (L.) Moench) that can result in grain and biomass yield losses of up to 50%. Despite available genomic resources of both the host and fungal pathogen, the molecular basis of sorghum− C. sublineola interactions are poorly understood. By employing a dual-RNA sequencing approach, the molecular crosstalk between sorghum and C. sublineola can be elucidated. In this study, we examined the transcriptomes of four resistant sorghum accessions from the sorghum association panel (SAP) at varying time points post-infection with C. sublineola . Approximately 0.3% and 93% of the reads mapped to the genomes of C. sublineola and Sorghum bicolor , respectively. Expression profiling of in vitro versus in planta C. sublineola at 1-, 3-, and 5-days post-infection (dpi) indicated that genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), and membrane transporters increased in expression during the transition from the biotrophic to the necrotrophic phase (3 dpi). The hallmark of the pathogen-associated molecular pattern (PAMP)-triggered immunity in sorghum includes the production of reactive oxygen species (ROS) and phytoalexins. The majority of effector candidates secreted by C. sublineola were predicted to be localized in the host apoplast, where they could interfere with the PAMP-triggered immunity response, specifically in the host ROS signaling pathway. The genes encoding critical molecular factors influencing pathogenicity identified in this study are a useful resource for subsequent genetic experiments aimed at validating their contributions to pathogen virulence. This comprehensive study not only provides a better understanding of the biology of C. sublineola but also supports the long-term goal of developing resistant sorghum cultivars.

Vela, Saddie↗

Chloroplast phosphate transporter CrPHT4-7 regulates phosphate homeostasis and photosynthesis in Chlamydomonas

Abstract In eukaryotic cells, phosphorus is assimilated and utilized primarily as phosphate (Pi). Pi homeostasis is mediated by transporters that have not yet been adequately characterized in green algae. This study reports on PHOSPHATE TRANSPORTER 4-7 (CrPHT4-7) from Chlamydomonas reinhardtii, a member of the PHT4 transporter family, which exhibits remarkable similarity to AtPHT4;4 from Arabidopsis (Arabidopsis thaliana), a chloroplastic ascorbate transporter. Using fluorescent protein tagging, we show that CrPHT4-7 resides in the chloroplast envelope membrane. Crpht4-7 mutants, generated by the CRISPR/Cas12a-mediated single-strand templated repair, show retarded growth, especially in high light, reduced ATP level, strong ascorbate accumulation, and diminished non-photochemical quenching in high light. On the other hand, total cellular phosphorous content was unaffected, and the phenotype of the Crpht4-7 mutants could not be alleviated by ample Pi supply. CrPHT4-7-overexpressing lines exhibit enhanced biomass accumulation under high light conditions in comparison with the wild-type strain. Expressing CrPHT4-7 in a yeast (Saccharomyces cerevisiae) strain lacking Pi transporters substantially recovered its slow growth phenotype, demonstrating that CrPHT4-7 transports Pi. Even though CrPHT4-7 shows a high degree of similarity to AtPHT4;4, it does not display any substantial ascorbate transport activity in yeast or intact algal cells. Thus, the results demonstrate that CrPHT4-7 functions as a chloroplastic Pi transporter essential for maintaining Pi homeostasis and photosynthesis in C. reinhardtii.

59 BASIC BIOLOGICAL SCIENCES↗

Illumination of serotonin transporter mechanism and role of the allosteric site

The serotonin transporter (SERT) terminates serotonin signaling by using sodium and chloride gradients to drive reuptake of serotonin into presynaptic neurons and is the target of widely used medications to treat neuropsychiatric disorders. Despite decades of study, the molecular mechanism of serotonin transport, the coupling to ion gradients, and the role of the allosteric site have remained elusive. Here, we present cryo–electron microscopy structures of SERT in serotonin-bound and serotonin-free states, in the presence of sodium or potassium, resolving all fundamental states of the transport cycle. From the SERT-serotonin complex, we localize the substrate-bound allosteric site, formed by an aromatic pocket positioned in the scaffold domain in the extracellular vestibule, connected to the central site via a short tunnel. Together with elucidation of multiple apo state conformations, we provide previously unseen structural understanding of allosteric modulation, demonstrating how SERT binds serotonin from synaptic volumes and promotes unbinding into the presynaptic neurons.

59 BASIC BIOLOGICAL SCIENCES↗

mTOR regulates aerobic glycolysis through NEAT1 and nuclear paraspeckle-mediated mechanism in hepatocellular carcinoma

Hepatocellular Carcinoma (HCC) is a major form of liver cancer and a leading cause of cancer-related death worldwide. New insights into HCC pathobiology and mechanism of drug actions are urgently needed to improve patient outcomes. HCC undergoes metabolic reprogramming of glucose metabolism from respiration to aerobic glycolysis, a phenomenon known as the ‘Warburg Effect’ that supports rapid cancer cell growth, survival, and invasion. mTOR is known to promote Warburg Effect, but the underlying mechanism(s) remains poorly defined. The aim of this study is to understand the mechanism(s) and significance of mTOR regulation of aerobic glycolysis in HCC. We profiled mTORC1-dependent long non-coding RNAs (lncRNAs) by RNA-seq of HCC cells treated with rapamycin. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were used to explore the transcriptional regulation of NEAT1 by mTORC1. [U- 13 C]-glucose labeling and metabolomic analysis, extracellular acidification Rate (ECAR) by Seahorse XF Analyzer, and glucose uptake assay were used to investigate the role of mTOR-NEAT1-NONO signaling in the regulation of aerobic glycolysis. RNA immunoprecipitation (RIP) and NONO-binding motif scanning were performed to identify the regulatory mechanism of pre-mRNA splicing by mTOR-NEAT1. Myristoylated AKT1 (mAKT1)/NRASV 12 -driven HCC model developed by hydrodynamic transfection (HDT) was employed to explore the significance of mTOR-NEAT1 signaling in HCC tumorigenesis and mTOR-targeted therapy. mTOR regulates lncRNA transcriptome in HCC and that NEAT1 is a major mTOR transcriptional target. Interestingly, although both NEAT1_1 and NEAT1_2 are down-regulated in HCC, only NEAT1_2 is significantly correlated with poor overall survival of HCC patients. NEAT1_2 is the organizer of nuclear paraspeckles that sequester the RNA-binding proteins NONO and SFPQ. We show that upon oncogenic activation, mTORC1 suppresses NEAT1_2 expression and paraspeckle biogenesis, liberating NONO/SFPQ, which in turn, binds to U5 within the spliceosome, stimulating mRNA splicing and expression of key glycolytic enzymes. This series of actions lead to enhanced glucose transport, aerobic glycolytic flux, lactate production, and HCC growth both in vitro and in vivo. Furthermore, the paraspeckle-mediated mechanism is important for the anticancer action of US FDA-approved drugs rapamycin/temsirolimus. These findings reveal a molecular mechanism by which mTOR promotes the ‘Warburg Effect’, which is important for the metabolism and development of HCC, and anticancer response of mTOR-targeted therapy.

59 BASIC BIOLOGICAL SCIENCES↗

Numerical investigation of microbial quorum sensing under various flow conditions

Microorganisms efficiently coordinate phenotype expressions through a decision-making process known as quorum sensing (QS). We investigated QS amongst distinct, spatially distributed microbial aggregates under various flow conditions using a process-driven numerical model. Model simulations assess the conditions suitable for QS induction and quantify the importance of advective transport of signaling molecules. In addition, advection dilutes signaling molecules so that faster flow conditions require higher microbial densities, faster signal production rates, or higher sensitivities to signaling molecules to induce QS. However, autoinduction of signal production can substantially increase the transport distance of signaling molecules in both upstream and downstream directions. We present empirical approximations to the solutions of the advection–diffusion–reaction equation that describe the concentration profiles of signaling molecules for a wide range of flow and reaction rates. These empirical relationships, which predict the distribution of dissolved solutes along pore channels, allow to quantitatively estimate the effective communication distances amongst multiple microbial aggregates without further numerical simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.

59 BASIC BIOLOGICAL SCIENCES↗