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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes’ innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.

Science & Technology - Other Topics↗
DOE OSTI2023

Enumerating soil biodiversity

Soil is an immense habitat for diverse organisms across the tree of life, but just how many organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity consider only certain types of organisms (e.g., animals) or report values for diverse groups without partitioning species that live in soil versus other habitats. Here, we reviewed the biodiversity literature to show that soil is likely home to 59 ± 15% of the species on Earth. We therefore estimate an approximately two times greater soil biodiversity than previous estimates, and we include representatives from the simplest (microbial) to most complex (mammals) organisms. Enchytraeidae have the greatest percentage of species in soil (98.6%), followed by fungi (90%), Plantae (85.5%), and Isoptera (84.2%). Our results demonstrate that soil is the most biodiverse singular habitat. By using this estimate of soil biodiversity, we can more accurately and quantitatively advocate for soil organismal conservation and restoration as a central goal of the Anthropocene.

Science & Technology - Other Topics↗
DOE OSTI2025

The GRAS protein RAM1 interacts with WRI transcription factors to regulate plant genes required for arbuscule development and function

During arbuscular mycorrhiza (AM) symbiosis AM fungi form tree-shaped structures called arbuscules in root cortex cells of host plants. Arbuscules and their host cells are central for reciprocal nutrient exchange between the symbionts.REQUIRED FOR ARBUSCULAR MYCORRHIZATION1(RAM1) encodes a GRAS protein crucial for transcriptionally regulating plant genes needed for arbuscule development and nutrient exchange. Similar to other GRAS proteins, RAM1 likely does not bind to DNA and how RAM1 activates its target promoters remained elusive. Here, we demonstrate that RAM1 interacts with five AM-induced APETALA 2 (AP2) transcription factors of the WRINKLED1-like family called CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), WRI3, WRI5a, WRI5b, and WRI5c via a C-terminal domain containing the M2/M2a motif. This motif is conserved and enriched in WRI proteins encoded by genomes of AM-competent plants. RAM1 together with any of these WRI proteins activates the promoters of genes required for symbiotic nutrient exchange, namelyRAM2,STUNTED ARBUSCULES (STR),andPHOSPHATE TRANSPORTER 4 (PT4), inNicotiana benthamianaleaves. This activation as well as target promoter induction inLotus japonicushairy roots depends onMYCS(MYCORRHIZA SEQUENCE)-elements andAW-boxes, previously identified as WRI-binding sites. TheWRIgenes are activated in two waves: Transcription ofRAM1,CBX1,andWRI3is coregulated by calcium- and calmodulin-dependent protein kinase-activated CYCLOPS, through theAMCYC-REin their promoter, and DELLA, whileWRI5a,b,andcpromoters containMYCS-elements andAW-boxes and can be activated by RAM1 heterocomplexes with CBX1 or WRI3. We propose that RAM1 provides an activation domain to DNA-binding WRI proteins to activate genes with central roles in AM development and function.

Science & Technology - Other Topics↗
DOE OSTI2021

Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin

The siderophore rhizoferrin (N 1 ,N 4 -dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in Escherichia coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli. Rhizoferrin is also synthesized by Francisella tularensis and Francisella novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways because of genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase homolog FslC/FigC, required for rhizoferrin biosynthesis. Ornithine decarboxylase produces putrescine from ornithine, but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli and produced rhizoferrin. A 2.1 Å X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Niche Partitioning of Microbial Communities at an Ancient Vitrified Hillfort: Implications for Vitrified Radioactive Waste Disposal

A pre-Viking era vitrified hillfort, Broborg, provides a habitat analogue for disposed radioactive waste glass and shows strong niche partitioning among the organisms involved in glass alteration. Microbes cannot be eliminated from radioactive waste disposal facilities and the consequences of bio-colonization must be understood. We use Broborg as a model system to inform what microbial processes might influence long-term radioactive waste glass durability by examining anthropogenic glass that has been subjected to bio-colonization for over 1,500 years. Scanning electron microscopy (SEM) images reveal the surficial biofilm structure, and chemical/mineralogy analysis in combination with deoxyribonucleic acid (DNA) sequencing of samples from the vitrified substrate, the adjacent soil, and the general topsoil provide insight into niche partitioning. The ancient glass niche supports a unique microbial community of bacteria, fungi, and protists that manifests the species response to local geochemical and mineralogical conditions. Communities from the geochemical niche associated with the glass are distinct and less diverse than soil communities. The microbiome of the glass and adjacent soil are dominated by lichens, lichen-associated microorganisms, and other epilithic, endolithic, and epigeic organisms. Pseudomonads dominate the prokaryotic communities on the vitrified material, but not the adjacent soil. In contrast, the general topsoil communities are enriched in plant rhizosphere organisms. Taxa associated with vitrification have bio-corrosive properties that could be detrimental to glass durability, including silicate mineral dissolution, extraction of essential elements, secretion of geochemically reactive organic acids, and dissolution induced by improved water retention. However, these stable long-term biofilms also possess a homeostatic function that could limit glass alteration. Overall, this study demonstrates the potential impacts that microbial colonization and niche partitioning can have on glass alteration and subsequent release of radionuclides from a disposal facility for vitrified radioactive waste.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metabolic engineering strategies for sesquiterpene production in microorganism

Sesquiterpenes are a large variety of terpene natural products, widely existing in plants, fungi, marine organisms, insects, and microbes. Value-added sesquiterpenes are extensively used in industries such as: food, drugs, fragrances, and fuels. With an increase in market demands and the price of sesquiterpenes, the biosynthesis of sesquiterpenes by microbial fermentation methods from renewable feedstocks is acquiring increasing attention. Synthetic biology provides robust tools of sesquiterpene production in microorganisms. This review presents a summary of metabolic engineering strategies on the hosts and pathway engineering for sesquiterpene production. Advances in synthetic biology provide new strategies on the creation of desired hosts for sesquiterpene production. Especially, metabolic engineering strategies for the production of sesquiterpenes such as: amorphadiene, farnesene, bisabolene, and caryophyllene are emphasized in: Escherichia coli , Saccharomyces cerevisiae , and other microorganisms. Herein, challenges and future perspectives of the bioprocess for translating sesquiterpene production into practical industrial work are also discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fungal social barriers: to fuse, or not to fuse, that is the question

Cell fusion takes place in all domains of life and contributes greatly to the formation of complex multicellular structures. In particular, many fungi, such as the filamentous Neurospora crassa, rely on conspecific somatic cell fusion to drive the unicellular-to-multicellular transition and formation of the interconnected mycelial syncytium. This can, however, lead to the transmission of infectious elements and deleterious genotypes that have a negative impact on the organismal fitness. Accumulating evidence obtained from natural populations suggests that N. crassa has evolved various self/non-self or allorecognition systems to avoid fusion between genetically non-identical spores or hyphae at all costs. Here we present an overview of the recent advances made in the field of fungal allorecognition, describe its genetic basis, and comment on its evolutionary meaning. These data pinpoint the multilayered complexity of the cooperative social behaviors undertaken by a model eukaryotic microbe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Exploring the environmental drivers of human blastomycosis cases in the Midwestern United States

Blastomycosis is a fungal infection endemic to the eastern United States (US) and Canada caused by the inhalation of the fungi Blastomyces spp. Currently, the environmental drivers of disease dynamics are poorly understood. The goal of our work was to explore what environmental conditions are associated with the annual presence of blastomycosis cases, and therefore are potentially explanatory of the ecological niche of Blastomyces. We examined the relationships between reported cases of blastomycosis in three Midwestern US states (Michigan, Minnesota, and Wisconsin) from 2007–2017 in relation to eleven hypothesized environmental conditions, including climate, stream and soil mineral content, and land cover variables. Then, we fit logistic regression models to explore the relationships between the environmental variables and yearly blastomycosis case occurrence. Mean soil moisture, stream sediment mercury content, percent of water within the county, and woody wetlands land cover were all positively associated with the presence of annual cases, with woody wetlands having the most consistent signal across the three states. We also found significant differences in the likelihood of case presence between US states that were not explained by the variables in our model, suggesting state-level differences in case reporting and disease awareness. Our results provide a perspective on potential biological hypotheses to further test regarding environmental controls on the life cycle and ecological niche of Blastomyces.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H 2 O 2 -producing enzymes with H 2 O 2 -consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Viral infections likely mediate microbial controls on ecosystem responses to global warming

Abstract Climate change is affecting how energy and matter flow through ecosystems, thereby altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses: viral infections within complex microbial food webs. We show how understanding and predicting ecosystem responses to warming could be challenging—if not impossible—without accounting for the direct and indirect effects of viral infections on different microbes (bacteria, archaea, fungi, protists) that together perform diverse ecosystem functions. Importantly, understanding how rising temperatures associated with climate change influence viruses and virus-host dynamics is crucial to this task, yet is severely understudied. In this perspective, we (i) synthesize existing knowledge about virus-microbe-temperature interactions and (ii) identify important gaps to guide future investigations regarding how climate change might alter microbial food web effects on ecosystem functioning. To provide real-world context, we consider how these processes may operate in peatlands—globally significant carbon sinks that are threatened by climate change. We stress that understanding how warming affects biogeochemical cycles in any ecosystem hinges on disentangling complex interactions and temperature responses within microbial food webs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Metagenomic investigation of African dust events in the Caribbean

ABSTRACT African dust from the Sahara and Sahel regions of Northern Africa is blown intercontinental distances and is the highest portion of atmospheric dust generated each year. During the Northern Hemisphere summer months (boreal summer), these dust events travel into the Caribbean and southern United States. While viability assays, microscopy and bacterial amplicon analyses have shown that dust-associated microbes may be diverse, the specific microbial taxa that are transported intercontinental distances with these dust events remain poorly characterized. To provide new insights into these issues, five metagenomes of Saharan dust events occurring in the Caribbean, collected in the summer months of 2002 and 2008, were analyzed. The data revealed that similar microbial composition existed between three out of the five of the distinct dust events and that fungi were a prominent feature of the metagenomes compared to other environmental samples. These results have implications for better understanding of microbial transport through the atmosphere and may implicate that the dust-associated microbial load transiting the Atlantic with Saharan dust is similar from year to year.

Waters, Samantha Marie↗
DOE OSTI2023

The cell morphological diversity of Saccharomycotina yeasts

The ~1 200 known species in subphylum Saccharomycotina are a highly diverse clade of unicellular fungi. During its lifecycle, a typical yeast exhibits multiple cell types with various morphologies; these morphologies vary across Saccharomycotina species. Here, we synthesize the evolutionary dimensions of variation in cellular morphology of yeasts across the subphylum, focusing on variation in cell shape, cell size, type of budding, and filament production. Examination of 332 representative species across the subphylum revealed that the most common budding cell shapes are ovoid, spherical, and ellipsoidal, and that their average length and width is 5.6 µm and 3.6 µm, respectively. 58.4% of yeast species examined can produce filamentous cells, and 87.3% of species reproduce asexually by multilateral budding, which does not require utilization of cell polarity for mitosis. Interestingly, ~1.8% of species examined have not been observed to produce budding cells, but rather only produce filaments of septate hyphae and/or pseudohyphae. 76.9% of yeast species examined have sexual cycle descriptions, with most producing one to four ascospores that are most commonly hat-shaped (37.4%). Systematic description of yeast cellular morphological diversity and reconstruction of its evolution promises to enrich our understanding of the evolutionary cell biology of this major fungal lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The macroevolution of filamentation morphology across the Saccharomycotina yeast subphylum

Saccharomycotina is a subphylum of ascomycete fungi with diverse asexual growth morphologies. Filamentous growth can comprise linear and branched budding cells that do not undergo cell separation, termed pseudohyphae, or tubular filaments with septa that perforate allowing movement of organelles, termed true hyphae. We integrated phenotypic, genomic, metabolic, and environmental data on isolation sources from 1051 species to examine the variation and evolutionary history of filamentation across Saccharomycotina and determine whether these data could predict filamentation types. We found that 63.37% of strains can form filaments; 6.56% true hyphae, 42.40% pseudohyphae, and 14.39% both true hyphae and pseudohyphae. The distributions of species that can produce true hyphae or filament were more strongly correlated with the yeast phylogeny than the distribution of species with pseudohyphae. Ancestral state reconstruction suggested that true hyphal and pseudohyphal morphologies evolved several times, that most yeast ancestors likely produced pseudohyphae or lacked filaments, and that the Saccharomycotina last common ancestor likely produced pseudohyphae but not true hyphae. Machine learning models trained on genomic and metabolic features predicted filament morphologies with ∼70% accuracy. Connecting the evolution of morphologies to their genomic, physiological, and ecological characteristics will enrich our understanding of how the diversity of lifestyles evolved in Saccharomycotina.

Saccharomycotina↗
DOE OSTI2021

Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme

The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis—the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)—were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ~20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.

Cenococcum geophilum↗
DOE OSTI2022

Complex genetics cause and constrain fungal persistence in different parts of the mammalian body

Determining how genetic polymorphisms enable certain fungi to persist in mammalian hosts can improve understanding of opportunistic fungal pathogenesis, a source of substantial human morbidity and mortality. We examined the genetic basis of fungal persistence in mice using a cross between a clinical isolate and the lab reference strain of the budding yeast Saccharomyces cerevisiae. Employing chromosomally encoded DNA barcodes, we tracked the relative abundances of 822 genotyped, haploid segregants in multiple organs over time and performed linkage mapping of their persistence in hosts. Detected loci showed a mix of general and antagonistically pleiotropic effects across organs. General loci showed similar effects across all organs, while antagonistically pleiotropic loci showed contrasting effects in the brain vs the kidneys, liver, and spleen. Persistence in an organ required both generally beneficial alleles and organ-appropriate pleiotropic alleles. This genetic architecture resulted in many segregants persisting in the brain or in nonbrain organs, but few segregants persisting in all organs. These results show complex combinations of genetic polymorphisms collectively cause and constrain fungal persistence in different parts of the mammalian body.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗