Biology subjects

Anderson, M. Z.

Publications and source records attributed to Anderson, M. Z..

10 recordsLinked to original sources

bioRxiv2026

Paralogs of the Candida albicans TLO gene family form interconnected functional networks with incomplete redundancy

Gene duplication typically fails to confer a selective advantage to an organism, prompting their removal from a population. In the rare instance that duplication either does not incur a fitness cost or it enhances fitness, gene families can form through repeating the duplication process. While the function of gene duplicates has been studied in detail, little work has explored how repeated duplication impacts paralog redundancy and may restrict the emergence of new paralogs or novel function. Here, we constructed a panel of single deletion mutants for each of the 14 members of the Candida albicans telomere-associated (TLO) gene family to test the redundancy in molecular and biological function among paralogs from a lineage-specific expansion. Tlo proteins function as interchangeable subunits of the Mediator transcriptional regulatory complex and have the potential to alter gene expression and an array of cellular responses. Redundancy was the most common outcome, being observed for approximately 80% of the phenotypic assays in strains lacking single TLO genes. However, mutants for all 14 paralogs displayed non-redundant functions in phenotypes ranging from carbon utilization to in vivo virulence. Analysis of gene expression in single TLO mutants found similar trends in redundancy, and loss of single TLOs disproportionately affected genes involved in filamentation, adhesion, redox reactions, and transporter activity at the cell surface. Importantly, sequence divergence between paralogs positively correlated with the frequency of altered phenotypes in single TLO mutants, indicating the acquisition of non-redundant function with increased evolutionary distance. Double mutants lacking two TLO genes produced both positive and negative synergistic phenotypes, suggesting that crosstalk or coordinated regulation is common among paralogs. Together, this study demonstrates that recently emergent paralogs acquire non-redundant functions despite often retaining redundancy with other gene family members to form a highly interconnected functional network.

genetics↗

bioRxiv2025

Candida albicans infiltrates colon and rectal cancers causing therapeutic resistance and decreased survival

The microbiome is increasingly recognized as a modifier of cancer progression and therapy response, yet the role of intratumoral fungi remains poorly defined. Here, we identify Candida albicans colonization within human colorectal tumors as a predictor of reduced survival and impaired radiation response. Leveraging the Oncology Research Information Exchange Network (ORIEN) cohort, we show that high intratumoral Candida burden is associated with decreased survival across multiple gastrointestinal cancers, with the strongest treatment-specific effect in rectal cancer patients receiving radiotherapy. This observation was validated in independent rectal cancer cohorts using RNA sequencing and quantitative PCR. In immune-competent murine colorectal cancer models, oral gavage of C. albicans resulted in intratumoral colonization, accelerated tumor growth, and radiation resistance, effects not observed with Saccharomyces cerevisiae or PBS controls. Colonized tumors exhibited increased hypoxia, altered metabolic and transcriptional programs, and distinct expression of genes linked to cytokine signaling and cell survival. Hypoxia conditioned C. albicans secreted metabolites that directly conferred radiation resistance to colorectal cancer cells in vitro, implicating a cancer cell intrinsic mechanism independent of immune signaling. Untargeted metabolomics revealed enrichment of nucleosides and lipid oxidation intermediates under hypoxia, suggesting that C. albicans metabolites may provide substrates facilitating tumor recovery after irradiation. These findings establish C. albicans as a causal modifier of tumor biology and radiation response, highlighting intratumoral fungi as future potential therapeutic targets. Modulating fungal colonization or metabolism may improve radiotherapy outcomes and broaden our understanding of interactions between microbes and tumors.

cancer biology↗

bioRxiv2025

Strain background interacts with chromosome 7 aneuploidy to determine commensal and virulence phenotypes in Candida albicans

The human fungal pathobiont Candida albicans displays extensive genomic plasticity, including large-scale chromosomal changes such as aneuploidy. Chromosome trisomy appears frequently in natural and laboratory strains of C. albicans. Trisomy of specific chromosomes has been linked to large phenotypic effects, such as increased murine gut colonization by strains trisomic for chromosome 7 (Chr7). However, studies of whole-chromosome aneuploidy are generally limited to the SC5314 genome reference strain, making it unclear whether the imparted phenotypes are conserved across C. albicans genetic backgrounds. Here, we report the presence of a Chr7 trisomy in the "commensal-like" oral candidiasis strain, 529L, and dissect the contribution of Chr7 trisomy to colonization and virulence in 529L and SC5314. These experiments show that strain background and homolog identity (i.e., AAB vs ABB) interact with Chr7 trisomy to alter commensal and virulence phenotypes in multiple host niches. In vitro filamentation was the only phenotype altered by Chr7 trisomy in similar ways across the two strain backgrounds. Oral colonization of mice was increased by the presence of a Chr7 trisomy in 529L but not SC5314; conversely, virulence during systemic infection was reduced by Chr7 trisomy in SC5314 but not 529L. Strikingly, the AAB Chr7 trisomy in the SC5314 background rendered this strain avirulent in murine systemic infection. Increased dosage of NRG1 failed to reproduce most of the Chr7 trisomy phenotypes. Our results demonstrate that aneuploidy interacts with background genetic variation to produce complex phenotypic patterns that deviate from our current understanding in the genome reference strain. AUTHOR SUMMARYCandida albicans is a clinically important fungus of humans that is also part of the microbiota that typically colonizes our bodies. Changes in the number of copies of chromosome 7 (Chr7) in the genome of the reference strain of C. albicans enhances host colonization. We identified a third copy of Chr7 in a strain classified as a good colonizer of humans that doesnt cause disease, mimicking the increased colonization of the reference strain. Here, we demonstrate that the number of copies of Chr7 alters phenotypes differently between these strains, and three copies of Chr7 does not universally produce a strain that is only a better commensal strain. Additionally, which copy of Chr7 in this diploid species exists as the third copy influences commensal and pathogen phenotypes. Therefore, trisomic changes of the same chromosome in different C. albicans strains have substantially different effects.

genetics↗

bioRxiv2024

Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity

Phosphorus is essential in all cells structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. In this process, initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity were eventually lost as populations presumably gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations fitness recovery in Pi scarcity, while that of others like membrane stress responses diverged from these fitness phenotypes. C. albicans therefore has diverse options to reconfigure Pi management during prolonged scarcity. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth and virulence. Author SummaryFungi must be able to access enough phosphate in order to invade the human body. Virulence of Candida albicans, the most common invasive human fungal pathogen, is known to decrease when one of the proteins that brings phosphate into the fungal cell, called Pho84, is disabled. We identified three more proteins in C. albicans that transport phosphate into the cell. We found that Pho84 plays the largest role among them across the broadest range of environmental conditions. After eliminating all 4 of these transporters, we let two resulting mutants evolve for two months in limited phosphate and analyzed the growth and stress resistance of the resulting populations. We analyzed genomes of representative populations and found that early adaptations to phosphate scarcity occurred together with major changes to chromosome configurations. In later stages of the adaptation process, these large-scale changes disappeared as populations presumably gained small-scale mutations that increased cells ability to grow in limited phosphate. Some but not all of these favorable mutations improved resistance of evolving populations to stressors like membrane- and cell wall stress. Pinpointing distinct mutation combinations that affect stress resistance differently in populations adapting to scarce phosphate, may identify useful antifungal drug targets.

microbiology↗

bioRxiv2023

A metagenomics approach to identification of eukaryotes in metazoan-associated microbiomes

BackgroundMicrobial eukaryotes are integral components of the microbiome where they shape community composition and ecological interactions. However, the abundance and diversity of eukaryotic species within the microbiome, the eukaryome, remains poorly defined. These deficiencies arise from unresolved technical limitations in recovering DNA from microbial eukaryotes due to their relatively low abundance in most samples and resilience to extraction. To overcome these limitations, we developed an extraction protocol that specifically targets recovery of eukaryotic microbes from microbiome samples and allows for metagenomics sequencing of eukaryotic species. MethodsMicrobes were seeded in synthetic stool prior to DNA extraction to mimic microbiome samples from the gastrointestinal tract. Assessment of cell disruption was performed using intracellular staining with the azo dye trypan blue or quantification of DNA recovery. A mock microbial community of five bacteria and five eukaryotes was built to test the effectiveness of the full protocol by seeding stool with defined numbers of cells from each species. ResultsMechanical disruption efficiently released DNA from bacterial, fungal, and protozoan species where standard microbiome DNA extraction kits did not. Optimization of the bead beating parameters lysed >95% of fungal cells within synthetic stool samples. In a mixed bacteria- eukaryote sample, eukaryotic DNA could be further enriched by targeting methylated DNA for destruction with methyl-specific restriction endonucleases. Application of this approach to a defined community of 10 different microbes, five eukaryotes and five bacteria, seeded in synthetic stool demonstrated the success of this strategy by enriching for eukaryotes approximately 72-fold and producing a eukaryote-dominated DNA pool. ConclusionsOverall, development of a microbiome sample protocol that includes DNA extraction and enrichment from eukaryotic species will facilitate exploration of the eukaryome and its impact on human health.

microbiology↗

bioRxiv2022

Architectural Groups of a Subtelomeric Gene Family Evolve Along Distinct Paths in Candida albicans

Subtelomeres are dynamic genomic regions shaped by elevated rates of recombination, mutation, and gene birth/death. These processes contribute to formation of lineage-specific gene family expansions that commonly occupy subtelomeres across eukaryotes. Investigating the evolution of subtelomeric gene families is complicated by the presence of repetitive DNA and high sequence similarity among gene family members that prevents accurate assembly from whole genome sequences. Here we investigated the evolution of the telomere-associated (TLO) gene family in Candida albicans using 189 complete coding sequences retrieved from 23 genetically diverse strains across the species. TLO genes conformed to the three major structural groups ( /{beta} /{gamma}) previously defined in the genome reference strain but significantly differed in the degree of within-group diversity and positional conservation. One group, TLO{beta}, was always found at the same chromosome arm with strong sequence similarity among all strains. In contrast, diverse Tlo sequences have proliferated among chromosome arms. Tlo{gamma} genes formed seven primary clades that included each of the previously identified Tlo{gamma} genes from the genome reference strain with limited mobility among chromosome arms. Structural groups displayed regions of high conservation that resolved newly identified functional motifs, providing insight into potential regulatory mechanisms that distinguish groups. Thus, by resolving intra-species subtelomeric gene variation, it is possible to identify previously unknown gene family complexity that may underpin adaptive functional variation.

genomics↗

bioRxiv2022

Genomic and Transcriptomic Profiling of Phoenix Colonies

Pseudomonas aeruginosa is a Gram-negative bacterium responsible for numerous human infections. Previously, novel antibiotic tolerant variants known as phoenix colonies as well as variants similar to viable but non-culturable (VBNC) colonies were identified in response to high concentrations of aminoglycosides. In this study, the mechanisms behind phoenix colony and VBNC-like colony emergence were further explored using both whole genome sequencing and RNA sequencing. Phoenix colonies were found to have a single nucleotide polymorphism (SNP) in the PA4673 gene, which is predicted to encode a GTP-binding protein. No SNPs were identified within VBNC-like colonies compared to the founder population. RNA sequencing did not detect change in expression of PA4673 but revealed multiple differentially expressed genes that may play a role in phoenix colony emergence. One of these differentially expressed genes, PA3626, encodes for a tRNA pseudouridine synthase which when knocked out led to a complete lack of phoenix colonies. Although not immediately clear whether the identified genes in this study may have interactions which have not yet been recognized, they may contribute to the understanding of how phoenix colonies are able to emerge and survive in the presence of antibiotic exposure.

microbiology↗

bioRxiv2021

Intra-species transcriptional profiling reveals key regulators of Candida albicans pathogenic traits

The human commensal and opportunistic fungal pathogen Candida albicans displays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences, and to link these differences to phenotypic traits. C. albicans adapts primarily through clonal evolution and yet hierarchical clustering of gene expression profiles in this set of isolates did not reproduce their phylogenetic relationship. Strikingly, strain-specific gene expression was prevalent in some strain backgrounds. Association of gene expression with phenotypic data by differential analysis, linear correlation, and assembly of gene networks connected both previously characterized and novel genes with 23 C. albicans traits. Construction of de novo gene modules produced a gene atlas incorporating 67% of C. albicans genes and revealed correlations between expression modules and important phenotypes such as systemic virulence. Furthermore, targeted investigation of two modules that have novel roles in growth and filamentation supported our bioinformatic predictions. Together, these studies reveal widespread transcriptional variation across C. albicans isolates and identify genetic and epigenetic links to phenotypic variation based on co-expression network analysis. ImportanceInfectious fungal species are often treated uniformly despite clear evidence of genotypic and phenotypic heterogeneity being widespread across strains. Identifying the genetic basis for this phenotypic diversity is extremely challenging because of the tens or hundreds of thousands of variants that may distinguish two strains. Here we use transcriptional profiling to determine differences in gene expression that can be linked to phenotypic variation among a set of 21 Candida albicans isolates. Analysis of this transcriptional dataset uncovered clear tends in gene expression characteristics for this species and new genes and pathways that associated with variation in pathogenic processes. Direct investigation confirmed functional predictions for a number of new regulators associated with growth and filamentation, demonstrating the utility of these approaches in linking genes to important phenotypes.

genomics↗

bioRxiv2020

Short chain fatty acid butyrate promotes virus infection by repressing interferon stimulated genes

Butyrate is an abundant metabolite produced by the gut microbiota and is known to modulate multiple immune system pathways and inflammatory diseases. However, studies of its effects on virus infection of cells are limited and enigmatic. We found that butyrate increases cellular infection and virus replication in influenza virus, reovirus, and human immunodeficiency virus infections. Further exploring this phenomenon, we found that addition of butyrate to cells deficient in type I interferon (IFN) signaling did not increase susceptibility to virus infection. Accordingly, we discovered that butyrate suppressed levels of specific IFN stimulated gene (ISG) products in human and mouse cells. Butyrate did not inhibit IFN-induced phosphorylation of transcription factors STAT1 and STAT2 or their translocation to the nucleus, indicating that IFN signaling was not disrupted. Rather, our data are suggestive of a role for inhibition of histone deacetylase activity by butyrate in limiting ISG induction. Global transcript analysis revealed that butyrate increases expression of more than 800 cellular genes, but represses IFN-induced expression of 60% of ISGs. Overall, we identify a new mechanism by which butyrate promotes virus infection via repression of ISGs. Our findings also add to the growing body of evidence showing that individual ISGs respond differently to type I IFN induction depending on the cellular environment, including the presence of butyrate. ImportanceButyrate is a lipid produced by intestinal bacteria that can regulate inflammation throughout the body. Here we show for the first time that butyrate influences the innate antiviral immune response mediated by type I IFNs. A majority of antiviral genes induced by type I IFNs were repressed in the presence of butyrate, resulting in increased virus infection and replication in cells. This suggests that butyrate could be broadly used as a tool to increase growth of virus stocks for research and for the generation of vaccines. Our research also indicates that metabolites produced by the gut microbiome can have complex effects on cellular physiology as demonstrated by the dampening of an inflammatory innate immune pathway by butyrate resulting in a pro-viral cellular environment.

microbiology↗

bioRxiv2018

The Genome of the Human Pathogen Candida albicans is Shaped by Mutation and Cryptic Sexual Recombination

The opportunistic fungal pathogen Candida albicans lacks a conventional sexual program and is thought to evolve, at least primarily, through the clonal acquisition of genetic changes. Here, we performed an analysis of heterozygous diploid genomes from 21 clinical isolates to determine the natural evolutionary processes acting on the C. albicans genome. Consistent with a model of inheritance by descent, most single nucleotide polymorphisms (SNPs) were shared between closely related strains. However, strain-specific SNPs and insertions/deletions (indels) were distributed non-randomly across the genome. For example, base substitution rates were higher in the immediate vicinity of indels, and heterozygous regions of the genome contained significantly more strain-specific polymorphisms than homozygous regions. Loss of heterozygosity (LOH) events also contributed substantially to genotypic variation, with most long-tract LOH events extending to the ends of the chromosomes suggestive of repair via break-induced replication. Importantly, some isolates contained highly mosaic genomes and failed to cluster closely with other isolates within their assigned clades. Mosaicism is consistent with strains having experienced inter-clade recombination during their evolutionary history and a detailed examination of nuclear and mitochondrial genomes revealed striking examples of recombination. Together, our analyses reveal that both (para)sexual recombination and mitotic mutational processes drive evolution of this important pathogen in nature. To further facilitate the study of genome differences we also introduce an online platform, SNPMap, to examine SNP patterns in sequenced C. albicans genomes.\n\nAUTHOR SUMMARYMutations introduce variation into the genome upon which selection can act. Defining the nature of these changes is critical for determining species evolution, as well as for understanding the genetic changes driving important cellular processes such as carcinogenesis. The fungus Candida albicans is a heterozygous diploid species that is both a frequent commensal organism and a prevalent opportunistic pathogen. Prevailing theory is that C. albicans evolves primarily through the gradual build-up of mutations, and a pressing question is whether sexual or parasexual processes also operate within natural populations. Here, we determine the evolutionary patterns of genetic change that have accompanied species evolution in nature by examining genomic differences between clinical isolates. We establish that the C. albicans genome evolves by a combination of base-substitution mutations, insertions/deletion events, and both short-tract and long-tract loss of heterozygosity (LOH) events. These mutations are unevenly distributed across the genome, and reveal that non-coding regions and heterozygous regions are evolving more quickly than coding regions and homozygous regions, respectively. Furthermore, we provide evidence that genetic exchange has occurred between isolates, establishing that sexual or parasexual processes have transpired in C. albicans populations and contribute to the diversity of both nuclear and mitochondrial genomes.

genomics↗