Biology Direct

Mitochondrial pyruvate carrier (MPC) inhibition was found protective in models of neurodegenerative diseases, such as Alzheimers and Parkinsons. However, little is known about MPC as a potential therapeutic target in Huntingtons disease (HD), a neurodegenerative disorder with dysregulation of the pro-survival pathway integrated stress response (ISR). Here, we investigate if MPC inhibition modulates the ISR and mitigates mutant huntingtin (mut-Htt) proteotoxicity in a cellular HD model. We treated cells expressing N-terminal fragments of wild-type- (wt-) or mut-Htt with two MPC inhibitors (mitoglitazone and UK5099) or solvent control. Metabolism was assessed analysing resazurin reduction, oxygen consumption, extracellular acidification, and ATP levels. ISR activation and huntingtin proteostasis were assessed using western-blot and filter-trap assays. Mut-Htt-expressing cells showed decreased resazurin reduction and ATP levels, and increased eIF2 phosphorylation, indicating metabolic stress and ISR activation. MPC inhibitors (100 {micro}M) increased resazurin reduction and decreased respiration. The latter was rescued by the membrane-permeant methyl pyruvate, which bypasses MPC inhibition. In wt-Htt-expressing cells, MPC inhibitors increased levels of ATP and ISR markers, suggesting metabolic adaptation and ISR activation. In mut-Htt-expressing cells, MPC inhibitors preserved ATP levels and attenuated mut-Htt-induced eIF2 phosphorylation but without changing soluble or aggregated mut-Htt levels. This work showed that MPC inhibition differentially modulates the ISR: it activates ISR in control cells and attenuates overactive ISR in mut-Htt-expressing cells. However, MPC inhibition did not impact the proteostasis of N-terminal fragment mut-Htt. Further studies are essential to explore MPC inhibition in less severe full-length mut-Htt-expressing models to better understand its therapeutic potential in HD.

Cyanobacteria utilize type IV pili for many behavioural responses, such as phototaxis, aggregation, floating, and DNA uptake. Type IV pilus-dependent functions are regulated by the nucleotide second messengers, c-di-GMP and cAMP. In this study, we investigated the role of a recently identified c-di-GMP receptor (CdgR) in cyanobacteria that harbours a ComFB domain. ComFB-domain proteins are widespread in cyanobacteria and are also present in heterotrophic bacteria. We demonstrated that the CdgR homolog from the cyanobacterium Synechocystis sp. PCC 6803, a model organism for studying type IV pilus-dependent functions, specifically binds to c-di-GMP. Genetic and phenotypic analyses revealed that Synechocystis CdgR is involved in phototactic motility and natural competence. Inactivation of cdgR resulted in altered expression of specific sets of minor pilins, which are essential for motility or natural competence. We identified interactions between CdgR and the CRP-family transcription factors, SyCRP1 and SyCRP2. Disruption of these CdgR-SyCRP1 and CdgR/SyCRP2 complexes is initiated by elevated c-di-GMP levels. Moreover, the assembly and stability of these complexes are influenced by other cyclic nucleotides, such as cAMP and c-di-AMP. These observed interactions imply a complex regulatory mechanism by which CdgR influences gene expression in response to cyclic nucleotide messenger signalling, particularly c-di-GMP. The present findings highlight the importance of CdgR in c-di-GMP signalling and its role in regulating type IV pilus-dependent functions in Synechocystis. The modulation of the expression of specific minor pilin genes by CdgR, through interactions with the transcription factors SyCRP1 and SyCRP2, contributes to the establishment of multiple type IV pilus functions and adaptive behaviours of cyanobacteria.

The unicellular green alga Chlamydomonas reinhardtii provides a tractable model for investigating how carbon availability influences metabolic organization and cell-cycle control in photosynthetic eukaryotes. Its capacity for autotrophic (light, CO2), mixotrophic (light, CO2, acetate), and heterotrophic (acetate, dark) growth enables systematic analysis of trophic-state-dependent regulation. We performed comparative transcriptomic analyses of strain 21gr grown under these three regimes at 30 {degrees}C. Mixotrophy resulted in the highest biomass accumulation and was associated with earlier cell-cycle commitment compared with autotrophy, whereas heterotrophy displayed delayed commitment and reduced growth. Transcriptomic profiling revealed coordinated upregulation of central carbon metabolic pathways under mixotrophy, including photorespiration, glycolysis, the oxidative pentose phosphate pathway, and tricarboxylic acid cycle functions, consistent with enhanced carbon flux and biosynthetic capacity. In contrast, heterotrophy preferentially induced acetate assimilation and glyoxylate cycle genes and was accompanied by elevated expression of cell-cycle regulators, including the CDK-inhibitory kinase WEE1. Together, these findings indicate that trophic mode modulates the coupling between carbon metabolism and cell-cycle progression, with mixotrophy supporting integrated metabolic and proliferative activity, whereas heterotrophy is associated with delayed cell-cycle timing and transcriptional signatures of metabolic adjustment.

Cyanobacteria are important primary producers and are used in biotechnology as microbial cell factories due to their ability to use solar light for oxygenic photosynthesis. Synechocystis sp. PCC 6803 is a popular model cyanobacterium, yet there are ambiguities in the precise coding regions of many genes, and numerous genes encoding small proteins have remained undetected. Here we present the results of a ribosome profiling (Ribo-seq) analysis involving inhibitors that stall ribosomes at translation initiation and termination sites (TIS- and TTS-Ribo-seq), combined with a proteogenomic reevaluation and reannotation of its entire genome. We report evidence for the translation of 3,050 annotated genes based on proteogenomics (83%), of 3,492 based on Ribo-seq (95.2%), and of 3,009 supported by both methods (82%). The data suggested both novel protein-coding genes and corrections for annotated ones. We validated 15 novel small proteins translated from antisense RNAs, from intergenic and intragenic regions and identified 69 novel, mostly small proteins based on proteogenomics. With slr0489, slr1079 and slr1082 we identified three genes with [~]300 nt long intragenic out-of-frame coding regions and show that both the internal and host reading frames are translated. The resulting proteins interact with each other, resembling certain defense or toxin-antitoxin systems. Our data illustrate the enormous value of consolidating genome annotations in the context of integrated experimental data and suggest that genome annotations in general need to be extended and revised. All of our data can be accessed via an intuitive and interactive genome browser platform at https://www.bioinf.uni-freiburg.de/~ribobase/.

Age-related macular degeneration (AMD) is the leading cause of irreversible visual loss in elderly individuals for which no effective treatments are currently available. The photoreceptor loss in dry AMD is secondary to the demise of the retinal pigment epithelium (RPE) cells. The accumulation of extracellular deposits, known as drusen, resulting in part from deficient lysosomal and autophagosomal degradation, is a key feature of dry AMD pathogenesis. Chaperone-mediated autophagy (CMA) is a selective lysosomal degradation pathway that maintains proteostasis by targeting specific cytosolic proteins for lysosomal translocation and degradation. LAMP2A (lysosome-associated membrane protein 2A) functions as the key lysosomal receptor required for CMA. Using Lamp2a knockout mouse, we show that selective CMA dysfunction recapitulates AMD-like pathologies, including sub-RPE lipid and protein deposits, RPE atrophy, Bruchs membrane thickening, and impaired autophagic activity. Furthermore, we identify large-conductance Ca{superscript 2}-activated K (BK) channels as a therapeutic target for restoring autophagic activity. Mechanistically, pharmacological activation of BK channels with the small-molecule agonist GLA-1-1 enhances macroautophagy and stimulates autophagic flux by promoting autophagosome-lysosome fusion. Importantly, oral administration of GLA-1-1 in markedly attenuates structural, functional, and molecular retinal abnormalities in Lamp2a-deficient mice, suggesting that pharmacological activation of macroautophagy through facilitating autophagosome-lysosome fusion can partially compensate for CMA deficiency. Together, these findings demonstrate that pharmacological activation of macroautophagy can ameliorate the retinal phenotype resulting from CMA dysfunction and support BK channel activation by GLA-1-1 as a promising therapeutic strategy for dry AMD.

Chromosome spatial organization plays critical roles in transcriptional regulation and DNA protection. In cyanobacteria--oxygenic photosynthetic bacteria that experience dramatic fluctuations in light intensity--chromosome reorganization may facilitate rapid transcriptional reprogramming and protect DNA from photodamage. However, direct observation of chromosome organization in these polyploid organisms has remained technically challenging, leaving light-dependent chromosomal responses unexplored. Here we show that local chromosome organization in Synechocystis sp. PCC 6803 is reorganized in response to high-light stress. We established fluorescence in situ hybridization (FISH) methods for this model cyanobacterium carrying multi-copy genomes, together with a computational pipeline for optimal same-genome-copy probe pairing. Under standard conditions, spatial distance between paired signals increased with genomic distance (slope {beta} = 0.972 nm/kbp, R{superscript 2} = 0.12), demonstrating that linear genome organization is reflected in three-dimensional chromosome structure at the 25-124 kbp scale. This genomic-spatial distance relationship substantially weakened under high-light conditions ({beta} = 0.450 nm/kbp, R{superscript 2} = 0.02), indicating that local chromosome organization is disrupted by elevated light intensity. Same-color nearest-neighbor distances further revealed that the spatial distribution of genome copies differed between conditions, independently supporting condition-dependent chromosome reorganization. Hi-C analysis corroborated these findings, revealing reduced short-range interactions within the 10-100 kbp genomic range under high-light conditions. Our integrative single-cell and population-level approach provides a framework for investigating how environmental signals modulate higher-order chromosome structure in polyploid bacteria.

Matrix metalloproteinase (MMP) expression and function are highly context dependent, varying across physiological and pathological conditions. We previously documented the expression profiles of select MMPs in the ischemic brains of young male rodents. However, aging is a major risk factor for stroke in humans and is associated with vasculature alterations, increased oxidative stress, and elevated inflammation. In addition, sex differences have been reported in stroke incidence and severity. Despite this, the effects of age, sex, and species on brain MMP gene expression after cerebral ischemia/reperfusion (I/R) has not been systematically examined. Therefore, we investigated how age, sex, and species influence the mRNA expression of all known MMPs (22 total) in the brain following cerebral I/R. Moderate-to-severe neurological deficits were induced by transient middle cerebral artery occlusion (MCAO) followed by reperfusion in young and aged male and female C57BL/6 mice and in young male Sprague-Dawley rats. Brain tissue from the ipsilateral (ischemic) hemisphere was collected on post-MCAO day 1, and MMP mRNA levels were quantified by real-time PCR and expressed as fold change relative to the sham control group. Across species, MMP-3, MMP-8, MMP-12, MMP-13, MMP-19, MMP-20, and MMP-27 were upregulated in both rats and mice. Species-specific increases were also observed: MMP-1, MMP-7, MMP-9, MMP-14, MMP-21, and MMP-25 were upregulated only in rats, whereas MMP-10 was upregulated only in mice. The most strongly upregulated MMPs were MMP-12 in rats and MMP-3, MMP-10, and MMP-12 in mice. By contrast, MMP-15 and MMP-17 were downregulated in both species, whereas MMP-23 and MMP-24 were downregulated only in rats and mice, respectively. Within mice, MMP-3, MMP-10, MMP-12, MMP-19, MMP-20, and MMP-21 increased in both sexes and age groups, except for MMP-19 in aged males and MMP-21 in young males. MMP-14 increased only in females (young and aged), whereas MMP-27 increased only in males (young and aged). Notably, MMP-3, MMP-10, and MMP-12 were the three most highly upregulated MMPs in both male and female mice regardless of age. Overall MMP mRNA expression levels were higher in aged male mice and lower in aged female mice relative to sex-matched young mice. Among all MMPs examined, MMP-12 showed the most marked upregulation across species and, within mice, across age groups and sexes. Collectively, these findings demonstrate that brain MMP gene expression after cerebral I/R is modulated by age, sex, and species, underscoring the importance of incorporating these biological variables when targeting MMPs individually or in combination in preclinical rodent stroke models.

Some microbes externalize costly biosynthetic precursors in sufficient quantities to sustain a recipient population through cross-feeding. However, it is unclear whether metabolites are externalized purely for a reciprocal benefit or if metabolite externalization also plays a physiological role for the producer. Here we focus on adenine, a metabolite externalized by some strains of the phototrophic bacterium Rhodopseudomonas palustris at sufficient levels to support Escherichia coli growth. In 10 long-term monocultures and 22 cocultures pairing R. palustris with E. coli, extracellular adenine externalized by all 140 isolates screened was 1.7 - 3.4-fold higher than that by the ancestor, suggesting that there was selective pressure for adenine externalization. We hypothesized that adenine is toxic to R. palustris. The CGA0092 growth rate decreased by half in the presence of about 0.3 mM external adenine. This inhibitory effect increased by an order of magnitude when we over-expressed adenine phosphoribosyltransferase to overcome a bottleneck in the purine salvage pathway, suggesting that toxicity stems from a metabolite derived from adenine. To assess whether adenine tolerance is connected to adenine externalization, we surveyed 12 evolved isolates and 49 environmental strains that externalized different levels of adenine, revealing a significant positive correlation. Our data suggests a physiological role for externalization of costly-metabolites like adenine at the origin of cross-feeding. In addition to cross-feeding, resulting metabolic interactions could be negative, considering that even a biosynthetic precursor like adenine can be inhibitory.

Marine picocyanobacteria, including the genera Prochlorococcus and Synechococcus, are major contributors to oceanic photosynthesis and global primary production. Their populations are influenced by T4-like cyanophages, which frequently encode auxiliary metabolic genes (AMGs) capable of altering host metabolism during infection. One such AMG, pebS, encodes a ferredoxin-dependent bilin reductase (FDBR) phycoerythrobilin (PEB) synthase, which converts biliverdin IX to PEB. In contrast, cyanobacteria perform a two-step reaction using the FDBR enzymes PebA (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and PebB (PEB:ferredoxin oxidoreductase), whereas pebS has not been reported in cyanobacterial genomes. Here, we re-evaluated whether pebS is truly restricted to cyanophages by searching the Ocean Gene Atlas and all available cyanobacterial genomes at NCBI using a cyanophage-derived PebS sequence as query. Using protein phylogenies, we find that most search hits group with PebA or PebB, while few sequences from cyanobacterial genome assemblies were confirmed to belong to PebS based on phylogenetic placement. However, genomic context analysis of these pebS sequences revealed that they are phage-derived, consistent with cyanophage infection at the time of sampling. In conclusion, our results support that pebS is absent in cyanobacterial genomes, raising questions about the evolutionary and biochemical rationale for the two-step reduction of biliverdin IX to PEB in these organisms.

The genus Ostreococcus, comprising picoeukaryotic unicellular algae, plays a key role in many coastal marine ecosystems. These phytoplankton are infected by lytic double-stranded DNA prasinoviruses against whom they have the capacity to reliably evolve stable antiviral resistance. Regulation of virus resistance and susceptibility is hypothesized to arise through a phenotypic switch, as resistant cell lines can be isolated from susceptible lines after viral exposure and vice versa. To elucidate the molecular mechanisms underlying this resistance, we integrated untargeted metabolomic analyses and transcriptomics in virus-resistant and virus-susceptible lines of O. mediterraneus. Transcriptomic analyses corroborated previous findings in O. tauri, revealing that most gene expression changes were concentrated on a single chromosome. Specifically, a [~]530 kb region was over-transcribed in virus-resistant lines, while a distinct [~]110 kb region was over-expressed in virus-susceptible lines. Comparative metabolomics identified several oxidized galactolipids and oxidized sterols as biomarkers of the susceptible phenotype, while fewer biomarkers were identified for the resistant phenotype. By integrating transcriptomic and metabolomic signatures--focusing on the expression of genes within biosynthetic pathways linked to these metabolite biomarkers--we uncovered candidate molecular mechanisms underlying the cellular physiology of susceptible versus resistant phenotypes. Authors SummaryViruses are the most abundant biological entities in the ocean, shaping the dynamics of phytoplankton communities that underpin marine food webs. Ostreococcus, one of the smallest photosynthetic eukaryotes, is frequently infected by highly abundant prasinoviruses in its natural environment. In this study, we aimed to understand the physiological bases of virus-resistant and susceptible Ostreococcus mediterraneus lines. We compared gene expression and untargeted metabolite profiles between a resistant line and a susceptible line derived from it. The metabolic profiles were much more variable between replicates than the transcriptomic profiles and the most differentially expressed genes did not include those involved in the biosynthetic pathways of the metabolite biomarkers identified. We estimated the congruence between the metabolomes and transcriptomes as the percent of relative expression changes fitting to the relative change in the metabolite. This study provides evidence of the subtle links between gene expression and metabolomic signatures and the importance of integrating multiple levels of cellular processes.

BACKGROUND AND PURPOSEThe role of immune checkpoint B7-H3 in acute ischemic stroke prognosis and post-stroke immunosuppression remains uninvestigated, despite the clinical significance of immune checkpoints with inflammaging and post-stroke infections. We recently reported the neuroprotective effects of acute B7-H3 inhibition after stroke in adult and aged mice. In this study, we investigated the mechnsistic association of regulating the cerebral induction of B7-H3 after acute ischemic stroke on brain damage, neuroinflammation, vascular integrity, host defense gene regulation, and functional outcomes. METHODSC57BL/6 mice were subjected to transient middle cerebral artery occlusion and injected (i.v.) with either B7-H3 siRNA or a negative (non-targeting) siRNA at 5 min after reperfusion. At 24 hours of reperfusion, magnetic resonance imaging (MRI) of the mouse brain was performed using a 9.4 T scanner to assess brain damage (T2, ADC, and Kurtosis). Real-time qPCR and NanoString nCounter(R) Neuroinflammation Panels were used to determine the acute changes in overall neuroinflammatory functions that are mediated by B7-H3. Motor function (beam walk, rotarod tests, and grip strength) was assessed between days 1 and 7 of reperfusion. RESULTSEarly inhibition of B7-H3 after stroke significantly reduced the brain damage and promoted the functional outcomes. Post-stroke neuroinflammation was reprogrammed with B7-H3 inhibition towards balancing of neuroprotective anti-inflammatory mechanisms without compromising the immune response that is crucial for preventing post-stroke infections. CONCLUSIONSOur results demonstrate that the induction of B7-H3 during the acute period after stroke is a mediator of post-stroke neuroinflammation and secondary brain damage.

BackgroundTraumatic brain injury (TBI) together with non-cerebral injuries characterizes the TBI-polytrauma (P-TBI) constellation, which is associated with acute neurological deterioration, delirium and unfavourable prognosis. It is hypothesized that systemic inflammatory mediators my enhances the focal, cerebral neuroimmune reaction with overall detrimental consequences, in particular in terms of acute microglial reactivity. MethodsWe explored the role of the Complement factor 3 (C3) and of the TLR-co receptor cluster of differentiation (CD14) in a murine polytrauma model that involves a mild TBI together with femur fracture, blunt thorax trauma and resuscitated haemorrhagic shock, making use of mice genetically lacking either C3, CD14 or both. ResultsWe show that P-TBI results in a rapid (4h) and brain-wide induction of inflammatory cytokines, although with distinct profiles (TNF and CCL2 having brain-wide involvement and IL-1{beta} restricted to ipsilateral cortex and striatum). TNF and CCL2 mRNA as well as protein synthesis were upregulated in microglia upon P-TBI in cortex, hippocampus and striatum which was fully abolished in the C3-/-CD14-/-animals. The analysis of single-KO animals revealed that induction of TNF and CCL2 was prevented in animals lacking C3, but not CD14, in the contralateral cortex and striatum, with an abolishment in hippocampus in mice lacking both C3 and CD14. In the cortical area of focal lesion neither C3 nor CD14 affected the induction of pro-inflammatory cytokines. ConclusionThus, C3 and CD14 are dispensable for the acute cytokine response to P-TBI in the site of injury but play differential roles across the cortex, hippocampus and striatum for the induction of cytokines in the non-injured parenchyma and in particular in microglia. Thus, interventions on C3 (mainly) and/or CD14 may reduce the encephalopathy risk associated with P-TBI but not the acute response in the injury site, where additional DAMP signalling may offer redundant activation pathways.

APOBEC cytidine deaminases can convert cytosines to uracils in DNA as well as in RNA. The knowledge of DNA deamination motifs preferred by individual APOBECs revealed APOBEC3A as a major source of hypermutation in cancer. However, the extent and relative contribution of specific APOBECs into RNA editing remains unclear as their preferred RNA-editing motifs have not been defined. Here, using a parallel DNA and RNA sequencing strategy, coupled with motif-centered statistical analyses, we sought to identify mRNA edits and diagnostic editing motifs in yeast and human cells overexpressing individual APOBEC enzymes. This approach revealed a prevailing global enrichment for the uCg trinucleotide motif with even greater preference to the motifs cytosines located in 3 base of a loop within a hairpin-loop secondary structure when APOBEC3A, but not any other tested APOBEC, was overexpressed. Further analysis revealed the APOBEC3A-like diagnostic motif enrichment in editing calls from human cancers and blood cells. The APOBEC3A-like editing motif also prevailed in the RNA genomes of SARS-CoV-2 pandemic isolates, as well as in infectious persistent rubella viruses, and in polioviruses emerging from live-attenuated vaccine strains. Together, our results indicate that APOBEC3A is the predominant global APOBEC RNA editor with a potential to impact cell physiology and viral evolution.

One of the key uncertainties in climate change models is how microbes will adapt to rising temperatures. Large-scale comparisons of bacterial thermal performances show a clear boundary between mesophiles and thermophiles. Here, we investigated whether phylogenetic constraints limit the adaptive potential of bacteria to warming soils. Focusing on copiotrophs within Gammaproteobacteria, we found that both thermal optima and upper thermal limits are constrained; variation in these traits decreases above 42{degrees}C across the phylogeny, with minimal influence of present-day bioclimatic variables. This, along with the reduced thermal safety margins found in fluctuating hot climates, suggests that many isolates may already be maladapted to local temperature variability. Our findings indicate that these constraints interact with the geometry of thermal performance curves, imposing a trade-off between high-temperature performance and the risk of substantial fitness losses above Topt. Overall, this work underscores potential limits to thermal adaptation and their implications for bacterial fitness.

BackgroundSpaceflight-associated neuro-ocular syndrome (SANS) poses significant risks to astronaut visual health during long-duration missions, yet its underlying molecular mechanisms remain incompletely understood. Oxidative stress and apoptosis are candidate molecular drivers, but their transcriptomic signatures in spaceflight-exposed retinal tissue have not been systematically characterized. MethodsWe applied a machine learning ensemble of linear regression models to predict two ocular phenotypes: 4-hydroxynonenal (4-HNE) immunostaining as a marker of lipid peroxidation-mediated oxidative damage; and TUNEL positivity as a marker of apoptotic cell death. In this observational study, we use bulk retinal gene expression data obtained from a controlled experiment with ground control and spaceflown mice to predict these phenotypes. Gene Ontology pathway enrichment was performed on the most predictive gene sets for each phenotype. ResultsThe 4-HNE phenotype was predicted by genes that converge on membrane-associated pathways, photoreceptor protein modification, synaptic dysfunction, and extracellular matrix dysregulation, including B2m, Tf, Cnga1, mt-Nd1, Snap25, and Efemp1. The genes predicting the TUNEL phenotype revealed a distinct signature emphasizing stress-induced apoptosis, rod photoreceptor degeneration, and endoplasmic reticulum dysfunction, with Ddit4, Nrl, Rom1, Reep6, and Gabarapl1 emerging as central regulators. ConclusionsOxidative lipid peroxidation and apoptotic cell death represent complementary and molecularly distinct pathological mechanisms in spaceflight-exposed murine retinal tissue. The gene signatures provide a putative molecular framework for developing noninvasive biomarkers and therapeutic targets to monitor and protect astronaut visual health during long-duration and deep-space missions.

Pathogenic organisms are typically thought to be constrained by a tradeoff between the rate and duration of transmission, an assumption that underpins a considerable body of evolutionary theory. Here we test for a transmission-duration tradeoff using detailed historical malaria infection data from an era prior to widespread use of antibiotics when humans were deliberately infected with malaria parasites as treatment for neurosyphilis (malariatherapy). These time series follow individual human infections until recovery or treatment with antimalarial drugs due to acute need (a proxy for virulence), and include data on the abundance of specialized transmission stages that can be used to project parasite fitness. We fit a model to estimate initial parasite multiplication rates (PMRs) and find that faster within-host multiplication extends infection duration (time until recovery) and enhances parasite fitness without a discernible cost, such as increased virulence. Initial PMRs exhibit strain-specific differences, a feature required for evolution by natural selection, but our results contradict the idea that the evolution of human malaria parasites is constrained by a transmission-duration tradeoff. Significance statementPathogenic organisms are usually assumed to face a tradeoff such that aggressively exploiting host resources enables more efficient transmission but at the cost of shorter infections. If such a classic transmission-duration tradeoff is not general, then it is not clear what prevents pathogenic organisms from evolving to exploit their hosts ever more aggressively. We use historical data from human malaria infections to show a remarkable lack of evidence for a transmission-duration tradeoff, since faster parasite multiplication tends to prolong infections and enable more efficient transmission. Therefore, classic predictions regarding the evolution of infection-induced harm to hosts may not apply to human malaria parasites, and efforts to locate general evolutionary constraints on pathogenic organisms should look beyond a classic tradeoff. FundingThis work was supported by the Cornell University College of Agriculture & Life Sciences (M.A.G.). L.M.C. was partially supported by the National Science Foundation Grant # 2144680. Data availabilityAll supporting data and code are provided as supplemental files. NoteFor ease of reviewing, this MS includes all elements (including figures) embedded in the text. If accepted, we would be happy to provide elements as separate files.

This study evaluates the impact of PFOA exposure on the metabolome and immune response to SARS-2 using a ferret model. Ferrets were separated into control or PFOA-exposed groups (10/mg/kg/day) and challenged with SARS-2. Longitudinal analyses encompassing clinical assessments, serological profiling, histopathology, and untargeted nuclear magnetic resonance (NMR) metabolomics revealed significant metabolic and immunological perturbations. We found prominent effects of PFOA exposure on metabolism, which resulted in altered metabolic responses to SARS-2 infection. PFOA exposure was also associated with impaired immune function, as evidenced by decreased serum IgG levels, increased viral loads, and prolonged peak infectivity. These findings underscore the consequences of PFOA exposure on host metabolism and immunity during infectious diseases.

Translation reinitiation (REI) is one of the most important gene-specific regulatory mechanisms by which eukaryotic cells influence expression of main translons, for example during highly conserved integrated stress response (ISR). In S. cerevisiae, expression of the key stress response gene, GCN4, is controlled by an intricate interplay among four short upstream translons (uTranslons, formerly uORFs), resulting in high or low levels of REI at GCN4 depending on the growth conditions. Under nutrient rich conditions, GCN4 expression is repressed, but upon amino acid starvation, it is derepressed, despite of a general translational shut down. Capitalizing on our screening reporter system, we identified three new factors influencing efficiency of REI after translation of GCN4 uTranslons: Rai1p (an RNA quality control and processing factor), and Ssz1p and Zuo1p (members of the Ribosome Associated Complex [RAC]). Importantly, we showed that depletion of these factors deregulated derepression of Gcn4p synthesis under starvation. Furthermore, we found that similar to RAC, Rai1p associates with 40S subunits and actively translating ribosomes. We also explored interactomes of these proteins. Collectively, we present three previously unknown factors that co-regulate stress response to amino acid starvation in the budding yeast by unique mechanisms.

The size and diversity of bacterial gene repertoires, known as pangenomes, vary widely across species. The evolutionary forces driving the maintenance of pangenomes is an open topic of debate, with contradictory theories suggesting that pangenomes exist as a result of neutral evolution, with all genes gained and lost at random, or that all genes provide a fitness benefit to the host and are maintained by positive selection. Modelling of pangenome dynamics has provided insight into how gene exchange explains observed gene frequency distributions, and stands as the only means of jointly inferring contributions of individual gene selection effects and mobility on the maintenance of pangenomes. However, previous modelling studies have not included both gene-level selection and mobility, and do not consider broadly sampled genome datasets for many species. To differentiate neutral and selective forces maintaining pangenomes, we developed a mechanistic model of gene-level evolution, Pansim, and a scalable model fitting framework, PopPUNK-mod. Together, these tools leverage rapid genome distance calculation to fit models of pangenome dynamics to datasets containing hundreds of thousands of genomes. We used this framework to compare the pangenome dynamics of over 400 different bacterial species, using over 600,000 genomes. We find that diversity in pangenome characteristics between species is driven predominantly by variation in the number of rapidly exchanged genes, while the rate of exchange of remaining genes is conserved. We find that bacterial phylogeny, rather than ecology, correlates with pangenome dynamics. We express that pan-species gene-level analyses are now needed to understand selection across accessory genes. Our work highlights the importance of gene exchange rate differences in governing differences in pangenome characteristics between species.

DNA methylation plays a central role in the regulation of gene expression. In plants, methylation occurs in the CG, CHG and CHH contexts, via distinct DNA methyltransferases including MET1, CMT3 and the RNA-directed DNA Methylation (RdDM) pathway via DRM2. In interspecific hybrids, these epigenetic mechanisms are confronted to a mixed small RNA population and two subgenomes harbouring specific methylation patterns, therefore generating unique expression profiles. The aim of this work was to understand these regulations by analysing gene expression, DNA methylation and small RNAs in a Citrus hybrid resulting from the cross between C. reticulata (mandarin) and C. australasica (finger lime). Haplotype-resolved subgenomes assembly identified hundreds of allele-specifically expressed genes. Asymmetric reprogramming of methylation was observed, in particular an increase in CHH in C. australasica haplotype. Surprisingly, CHH methylation, usually associated with gene silencing, was correlated here with increased expression, but also 24nt small RNA populations at their promoter regions. Similar analyses of the parental lines and other citrus species suggest the correlation between CHH methylation-enriched promoter and high expression level is not due to the hybridization, but seem to be generally true for all citrus. These observations suggest that, in citrus fruit, RdDM could activate transcription. This work also provides a full pipeline to analyse the expression profiles and DNA methylation in complex hybrids, which could be crucial for anticipating varieties resistant to diseases and the current threats affecting citriculture such as the Huanglongbing disease.