Biology subjects

Lipzen, A.

Publications and source records attributed to Lipzen, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Plasticity of the mutation rate and spectrum in eukaryotic marine phytoplankton

The ability to adapt shapes the future of any species or population. Adaptive potential is primarily determined by the spontaneous mutation rate {micro} and the mutation spectrum, which define the new genetic variation available to selection. Increasing evidence points to the plasticity of the mutation rate and spectrum, which vary according to environment. However, data is lacking for marine phytoplankton, an essential group for marine ecosystems as well as a major player in biogeochemical cycles. Here, we measure the plasticity of mutation rates and spectra in the chlorophyte Ostreococcus tauri by mutation accumulation experiments in 4 different conditions: low salinity, high salinity, low temperature, and high temperature. {micro}SNM is lowest under low salinity, doubles under high salinity and low temperature and quadruples under high temperature. SNM spectra become increasingly biased towards C:G[->]T:A transitions with increasing {micro}SNM. While {micro}ID does not change with the environment, the structural mutation rate {micro}SM is higher at low temperature, likely due to transposon activity. Given the rapid environmental changes associated with global climate change, mutation rates and spectra plasticity may critically influence the adaptive potential of marine primary producers.

evolutionary biology↗

bioRxiv2026

From tiny to massive: exploring genome evolution in the model 1 grass genus Brachypodium

Brachypodium is a powerful model system for investigating grass genome evolution, yet genomic resources remain concentrated in the three annual species, whereas perennial species are less sampled. Here, we present chromosome-level assemblies for two perennial species, Brachypodium mexicanum and B. arbuscula, which represent the earliest-diverging lineages of the genus and the earliest-diverging lineage of the core perennial clade, respectively. Synteny-based phylogenomics indicate that B. mexicanum is a meso-allotetraploid composed of two closely related but temporally distinct x=10 subgenomes, here designed as P and U, each carrying subgenome-specific chromosome rearrangements. We further show that the unusually large B. mexicanum genome, in contrast to the reduced genomes of most other Brachypodium species, is primarily due to transposable elements distributed across all chromosomal regions. By contrast, the diploid genome of the earliest-diverging core perennial, B. arbuscula, contains few transposable elements, whereas the most recent diverged diploid perennial B. sylvaticum shows evidence of a secondary TEs proliferation. Comparisons of lineage-specific and functionally enriched orthogroups among B. mexicanum, core perennial species and annual species suggest that ancestral hybridization between annual and perennial lineages may have contributed to the origin of allotetraploid B. mexicanum. These assemblies provide a framework for testing how polyploidy, descending dysploidy, transposable-element turnover, and life-history evolution jointly shaped genome architecture in Brachypodium.

evolutionary biology↗

bioRxiv2026

Spliceosome loss in the red tide ciliate Mesodinium rubrum presents a symbiotic cul-de-sac

Mesodinium rubrum, a marine microbial eukaryote associated with some of the largest red tides on Earth, has the remarkable ability to commandeer the plastids, mitochondria and nuclei from the alga Teleaulax amphioxeia for photosynthesis. Here we report analyses of assemblies of M. rubrums two nuclear genomes. Unexpectedly, M. rubrum appears to have completely lost its spliceosomal introns, most spliceosomal molecules, and the key genes for an intron splicing-associated process, Nonsense-mediated mRNA Decay (NMD). In contrast, non-spliceosomal tRNA introns have been retained, as have thousands of intron analogs spliced out of DNA during ciliate somatic genome development (internal eliminated sequences - IESs). Intron-containing genes, especially from intron-rich species like T. amphioxeia, would likely be defunct if horizontally transferred to a host without a spliceosome like M. rubrum, and thus we propose that introns can be a roadblock to progressive endosymbiotic genomic integration.

genomics↗

bioRxiv2026

Genic Position and Methylation Context Shape DNA Methylation-Expression Relationships in Rice Internode Development

Elongating rice internodes present a developmental gradient from dividing meristem to mature cells, providing an elegant pseudo-time course for study of plant vegetative development. We tested the hypothesis that DNA methylation regulates gene expression during rice internode development by integrating RNA-seq and bisulfite DNA sequencing across eight internode segments. Previously described topologically associated chromatin domain borders aligned with transcription start sites of constitutive expressed genes. CpG and CHG differential methylation was enriched in young segments, consistent with maintenance methylation; whereas CHH methylation showed similar differential abundance in young and old segments. CHH and CHG methylation in upstream regions, CpG methylation within gene bodies, and any methylation in 5' and 3' untranslated regions were permissive of moderate to high gene expression. Very low expression was associated with CpG methylation upstream, CHG and CHH methylation within gene bodies, and CpG and CHG methylation downstream. A nonrandom subset of genes, including cell wall-related glycoside hydrolases, lignin and tricin biosynthesis enzymes, and WD40 proteins, showed methylation-expression correlations, with expression changes enriched in triple-marked elements. These results suggest that internode phenotypes of DNA methylation machinery mutants relate to alteration of specific target genes, opening approaches for grass culm improvement for lodging resistance and biomass production. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/737558v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@b726eaorg.highwire.dtl.DTLVardef@5bd017org.highwire.dtl.DTLVardef@1bac873org.highwire.dtl.DTLVardef@1be3474_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance statementStems of cereals and other grasses have an important function in supporting grain production and serving as a source of carbon for the bioeconomy. This study supports methylation of the cytosine bases of DNA as a regulator of chromatin structure and gene expression in the stems of rice. Different methylation contexts are implicated in specific roles in both positive and negative gene expression regulation that might be leveraged to improve stem properties.

plant biology↗

bioRxiv2026

Comparative genomics reveals shared accessory regions between members of two Fusarium species complexes virulent on garden pea

The contribution of accessory or conditionally dispensable chromosomes to host-specific virulence was first demonstrated in members of the Fusarium solani species complex (FSSC) that are pathogens of garden pea, Pisum sativum L. The phenomenon has since been shown to exist in many fungal plant pathogens, including the closely related F. oxysporum species complex (FOSC). Genome analysis of members of the FSSC and FOSC pathogenic on pea revealed a diverse size range of the accessory genome of these fungi. Despite the [~]65 million years of diverging time, regions on a chromosome known to carry host-specific virulence factors for pea, including the cytochrome P450 pisatin demethylase (PDA) and other pea pathogenicity (PEP) genes, were present in all genomes of these pea pathogens. Genes directly involved in virulence on pea - PEP2, PDA, and PEP5- were the most frequently clustered together. Transcriptome analysis of fungal mycelia treated with the pea phytoalexin pisatin, identified 1,155 differentially expressed genes where many were involved in cellular stress responses. As wilt pathogens that invade host xylem, members of the FOSC encode more putative effectors, when compared to those in the FSSC, and several FOSC effectors were identified to confer race specificity. The conservation of part of the accessory genomes across two evolutionarily diverged species complexes suggests a common origin. Horizontal transfer of accessory chromosomes containing genetic loci involved in pathogenesis for garden pea offers a parsimonious explanation of the polyphyletic origin of host specificity.

genomics↗

bioRxiv2026

Prediction of Lignocellulose Degradation Potential of Wood Decay Fungi using Comparative Genomic Analysis

The Agaricomycotina accounts for roughly a third of all described fungi. They are important due to their wide range of lifestyles and economic and environmental relevance. Certain agaricomycetes act as lignocellulose degraders, playing a significant role in forest ecosystems and bioremediation processes. These wood-decaying fungi have historically been classified as mostly white- or brown-rot based on their ability to degrade lignin, with white-rot fungi possessing a collection of lignocellulose-degrading enzymes, which are reduced or absent in brown-rot fungi. Here, we sequenced and annotated the genome of the agaricomycete Crepidotus cesatii CBS 511.95 and explored its genome and predicted enzymatic content in a comparative context. The 36.04 Mbp genome is in 235 scaffolds, with 3.34% repeat content and 12,891 predicted genes. We found that the PFAM distributions of identified orthogroups suggested that C. cesatii shows patterns more similar to white-rot fungi compared to brown-rot fungi. Additionally, C. cesatii contained multiple copies of CAZymes CBM1 and AA9 involved in hydrolysis of lignocellulose, similar to white-rot fungi. On the other hand, according to the Conserved Unique Peptide Patterns (CUPP) data for AA2 peroxidases, the key enzymes in lignin degradation, C. cesatii is more similar to brown-rot fungi. Based on our analyses we predict that C. cesatii is another representation of the continuum of wood decaying modes between white and brown rot fungi combining genetic features of both types of fungi.

genetics↗

bioRxiv2026

Uncovering genetic mechanisms underlying trait variation in switchgrass using explainable artificial intelligence

Uncovering the genetic architecture of quantitative traits is challenging because polygenic control yields small individual gene effects and because gene-gene and genotype-by-environment interactions add further complexity. To understand the genetic basis of polygenic traits and their plasticity across environments, we integrated genome-wide SNPs and RNA-seq transcript data with interpretable statistical and machine learning models in a switchgrass (Panicum virgatum) diversity panel grown at contrasting field sites in Michigan and Texas. Notably, in addition to single environments, our trait prediction models were able to predict phenotypic differences, across environments i.e., plasticity. By interpreting trait prediction models with explainable machine learning methods, we identified genes that are the most predictive of flowering time and annual biomass production across environments, based on their associated gene expression levels and nearby SNPs. This approach recovered canonical flowering regulators and revealed novel, environment-specific candidate flowering genes. Further, transcriptome models consistently recovered more switchgrass genes homologous to experimentally validated genes in Arabidopsis and rice than SNP-based models. Feature interaction scores from the models also allow the identification of trait and environment-dependent gene-gene interactions, where flowering time showed stronger and more abundant interactions than biomass. While some of the interactions identified are consistent with the link between flowering time and yield, most are novel predictors that need to be further evaluated. These findings provide insight into the genetic basis of trait variation and plasticity across environments and help prioritize candidate genes for functional validation and cultivar improvement.

genetics↗

bioRxiv2026

Ancient eukaryotic immunity through genome editing of viral sequences

Mutations provide the raw material for evolution, but mutation rates are not uniform across genomes. Using a mutation accumulation experiment in the marine phytoplankton Bigelowiella natans, we discovered extreme local variation in mutation rate: over 1000-fold differences across its nuclear genome. While the baseline single-nucleotide mutation rate is approximately 3.5x10-10 per site per generation, a common value for unicellular species, two genomic regions derived from integrated viruses exhibit strikingly elevated rates of about 6x10-7. These two regions show a distinctive mutational signature with almost exclusively T/A[->]C/G transitions, a pattern also found in other non-eukaryote derived sequences in B. natans, contrary to the usual GC to AT mutation bias. Notably, hypermutation occurs only on TpA dinucleotides, and only in a subset of experimental lines, suggesting a regulated process rather than random genomic instability. We propose that B. natans targets invading DNA through localized hypermutation, reminiscent of deamination-based antiviral defense systems in animals, prompting the idea of genome editing as a conserved immune system in eukaryotes. Significance StatementDe novo mutations provide the raw material for adaptation, but at high frequencies they can compromise genome integrity. Here, we describe a hypermutable process targeting two integrated viral genomes in a chlorarachniophyte alga, resulting in a mutation rate 1000 times higher than in other regions and a very particular mutation spectrum. These observations are reminiscent of hypermutation-based antiviral defenses described in humans against HIV and influenza; whereby host-mediated deamination of the viral genome increases its mutation rate such that the virus loses its infectivity.

genomics↗

bioRxiv2025

The origins and adaptive consequences of polyploidy in a dominant prairie grass

Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species Andropogon gerardi, a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 popula-tions and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9x A. gerardi cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9x cy-totype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9x A. gerardi, the establishment of 9x may lower overall population fitness due to the lower reproductive viability of 9x individuals. Significance statementPolyploid species are abundant in North American prairies and make up many of the dominant species in the ecosystem. This prominence could be a result of whole genome duplication conferring an advantage that increases the frequency of polyploids or could simply indicate that the opportunity for whole genome duplication is higher in this ecosystem, or both. Through examining three polyploidization events in A. gerardi, the dominant species in endangered tallgrass North American prairies, we found whole genome duplication is both surprisingly common and confers traits that are beneficial in some environments.

plant biology↗

bioRxiv2025

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

O_LIEukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity. C_LIO_LIHere, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the speciess current genetic diversity to catalogue variation in genome structure and content. C_LIO_LIAcross this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained. C_LIO_LIOur findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop. C_LI

genomics↗

bioRxiv2025

Engineering anaerobic fungal-bacterial consortia for medium-chain fatty acid production from lignocellulosic biomass

Lignocellulosic biomass is a renewable feedstock for sustainable fuels and chemicals, yet industrial conversion remains constrained by carbohydrate solubilization. Inspired by herbivore rumen microbiomes, we engineered an anaerobic fungal-bacterial consortium converting native lignocellulose into medium-chain fatty acids (MCFAs) without pretreatment. Systematic screening identified a newly isolated anaerobic fungus, Neocallimastix sp. FC1, in co-culture with Megasphaera hexanoica as a top-performing pair, achieving a lignocellulose-to-MCFA yield of 21.0 % (carbon-to-carbon basis) through tight lactate cross-feeding without competition for soluble sugars. Because fungal lactate production rate constrained the growth of M. hexanoica, the bacterium reallocated protein from growth toward chain elongation, resulting in increased MCFAs production over butyrate. These results demonstrate that high lignocellulose-to-MCFA conversion by the consortium requires high lactate-producing capability and operating regimes sustaining low lactate concentrations at high flux. Technoeconomic analysis further identifies the cost and yield thresholds required for economically viable deployment, establishing quantitative design targets for pretreatment-free fungal-bacterial lignocellulose upgrading.

bioengineering↗

bioRxiv2025

The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelps accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of Nereocystis luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80x of coverage and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Mb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and M. pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPases enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

genomics↗

bioRxiv2025

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for desiccation tolerance. Here, we present a chromosome-level, haplotype-resolved reference genome for M. flabellifolia alongside transcriptomic profiling across a natural dehydration-rehydration cycle. The 1.28 Gb genome exhibits unusually consistent chromatin architecture with putative holocentric chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on chromosome 8. Transcriptomic changes during dehydration varied with the severity of water loss and pointed to early suppression of growth, progressive activation of protective mechanisms, and reversible changes in transcript abundance upon rehydration. Co-expression networks and targeted gene family analyses revealed dynamic regulation of LEA and ELIP genes, with evidence of transcriptome "priming" in hydrated plants, with transcript abundance shifting toward highly disordered proteins during desiccation. Enrichment of ABA and light-responsive cis-regulatory elements in key genes support the existence of conserved stress response pathways. M. flabellifolias rich profile of phenolics and antioxidant genes highlight the overlap between desiccation tolerance and medicinal potential. Together, this study provides foundational resources for understanding the genomic architecture and reproductive biology of M. flabellifolia while offering new insights into the mechanisms of desiccation tolerance.

plant biology↗

bioRxiv2025

Population and adaptation history of 739 Thlaspi arvense natural accessions

Pennycress (Thlaspi arvense) is a promising intermediate oilseed crop, producing oil suitable for conversion to biofuels--including aviation fuels. While domestication efforts are ongoing, a deeper understanding of the genetic architecture of traits is crucial for informing future breeding efforts. Here, we conducted the largest genomic and phenotypic survey of pennycress to date, analyzing 739 accessions collected across four continents. Leveraging whole-genome sequencing and field-collected phenotypes, we characterized the standing genetic variation underlying key agronomic traits and climate resilience. Our findings revealed multiple independent migration events to North America, with substantial genetic admixture. We identified homologs of Arabidopsis thaliana flowering-time genes that contribute to adaptation and demonstrated the agronomic benefits of winter-type pennycress. Furthermore, through multi-season field trials, we identified a genomic region containing a cluster of mTERF genes strongly associated with green canopy coverage, a critical trait for biomass retention and yield stability. These insights provide a genomic roadmap for accelerating pennycress domestication and improving its resilience to climate variability.

genomics↗

bioRxiv2025

A haplotype-resolved reference genome for Eucalyptus grandis

E. grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials and biorefinery products. The current v2.0 genome reference for the species (Bartholome et al., 2015; Myburg et al., 2014) served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The two haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70 to 90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8% to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4% and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pan-genome variation in the species. Paper summaryWe assembled a haplotype-phased genome for Eucalyptus grandis that will serve as reference for the most widely planted hardwood crop globally. It includes more than 430 new gene models with long introns and has 6% higher annotation completeness. The phased assembly provides a more accurate look at genome variation at DNA and transcript level and will better support future studies of genome structure and function. The improved assembly contains more tandem duplicate genes compared to the previous unphased reference. Finally, major genomic rearrangements between the two phased genomes provide a preview of pangenome and structural variation in E. grandis.

genomics↗

bioRxiv2025

Genomic and Transcriptomic Characterization of Carbohydrate-Active Enzymes in the Anaerobic Fungus Neocallimastix cameroonii var. constans

Anaerobic gut fungi effectively degrade lignocellulose in the guts of large herbivores, but there remains a limited number of isolated, publicly available, and sequenced strains that impede our understanding of the role of anaerobic fungi within microbial communities. We isolated and characterized a new fungal isolate, Neocallimastix cameroonii var. constans, providing a transcriptomic and genomic understanding of its ability to degrade diverse carbohydrates. This anaerobic fungal strain was stably cultivated for multiple years in vitro among members of an initial enrichment microbial community derived from goat feces, and it demonstrated the ability to pair with other microbial members, namely archaeal methanogens to produce methane from lignocellulose. Genomic analysis revealed a higher number of predicted carbohydrate-active enzymes encoded in the N. cameroonii var. constans genome compared to most other sequenced anaerobic fungi. The carbohydrate-active enzyme profile for this isolate contained 660 glycoside hydrolases, 160 carbohydrate esterases, 194 glycosyltrasferases, and 85 polysaccharide lyases. Differential gene expression analysis showed the upregulation of thousands of genes (including predicted carbohydrate-active enzymes) when N. cameroonii var. constans was grown on lignocellulose (reed canary grass) compared to less complex substrates, such as cellulose (filter paper), cellobiose, and glucose. AlphaFold was used to predict functions of transcriptionally active yet poorly annotated genes, revealing feruloyl esterases that likely play an important role in lignocellulose degradation by anaerobic fungi. The combination of this strains genomic and transcriptomic characterization, omics-informed structural prediction, and robustness in microbial co-culture make it a well-suited platform to conduct future investigations into bioprocessing and enzyme discovery.

microbiology↗

bioRxiv2024

Hydrophobins from Aspergillus mediate fungal interactions with microplastics

Microplastics present myriad ecological and human health risks including serving as a vector for pathogens in human and animal food chains. However, the specific mechanisms by which pathogenic fungi colonize these microplastics have yet to be explored. In this work, we examine the opportunistic fungal pathogen, Aspergillus fumigatus, and other common soil and marine Aspergilli, which we found bind microplastics tightly. Up to 3.85+/-1.48 g microplastic plastic/g fungi were bound and flocculated for polypropylene (PP), polyethylene (PE), and polyethylene terephthalate (PET) powders and particles ranging in size from 0.05 - 5 mm. Gene knockouts revealed hydrophobins as a key biomolecule driving microplastic-fungi binding. Moreover, purified hydrophobins were still able to flocculate microplastics independent of the fungus. Our work elucidates a role for hydrophobins in fungal colonization of microplastics and highlights a potential target for mitigating the harm of microplastics through engineered fungal-microplastic interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/622132v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@13eb679org.highwire.dtl.DTLVardef@3dc9c0org.highwire.dtl.DTLVardef@888c96org.highwire.dtl.DTLVardef@c5e1aa_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementMicroplastics pose serious ecological and human health effects by introducing pathogens and toxins into animal and human food chains. Many pathogenic microorganisms preferentially form biofilms on microplastic particles that are then ingested. Here, we demonstrate that hydrophobins, highly hydrophobic, cell surface proteins, enable microplastic binding and colonization by the opportunistic pathogen Aspergillus fumigatus and other fungi within the Aspergillus genus. Our work recognizes a novel role for hydrophobin proteins, identifying potential strategies for pathogen control and protein-based microplastics recovery.

molecular biology↗

bioRxiv2024

Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca

Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, as its emergence may depend on simple regulatory changes to deeply conserved metabolic pathways. Modern CAM research relies heavily on interpretation of transcriptomic data, though regulation occurs at multiple levels following transcription. Additionally, while most research to date has focused on a handful of genes and metabolites in the core CAM pathway, the co-option of conserved regulatory and functional genes is bound to have wide ranging effects on other aspects of primary metabolism. In this study, we integrate transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C3 species, Y. filamentosa. We observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. We also find evidence of shifts in gene expression and metabolite accumulation outside of the central CAM pathway suggesting that the shift to CAM has cascading effects across primary metabolism, especially nitrogen metabolism. Our findings provide insights into the metabolic shifts associated with CAM evolution and highlight the complexity of its regulation at multiple biological levels.

evolutionary biology↗