eLife: latest articles by subject

Global transcription factors analyses reveal hierarchy and synergism of regulatory networks and master virulence regulators in Pseudomonas aeruginosa

xindeng@cityu.edu.hk (Beifang Lu) — Thu, 16 Apr 2026 00:00:00 +0000

The transcription factor (TF) regulatory network in Pseudomonas aeruginosa is complex and involves multiple regulators that respond to various environmental signals and physiological cues by regulating gene expression. However, the biological functions of at least half of its 373 putative TFs remain uncharacterised. Herein, chromatin immunoprecipitation sequencing (ChIP-seq) was used to investigate the binding sites of 172 TFs in the P. aeruginosa PAO1 strain. The results revealed 81,009 significant binding peaks in the genome, more than half of which were located in the promoter regions. To further decode the diverse regulatory relationships among TFs, a hierarchical network was assembled into three levels: top, middle, and bottom. Thirteen ternary regulatory motifs revealed flexible relationships among TFs in small hubs, and a comprehensive co-association atlas was established, showing the enrichment of seven core associated clusters. Twenty-four TFs were identified as the master regulators of virulence-related pathways. The pan-genome analysis revealed the conservation and evolution of TFs in P. aeruginosa complex and other species. A web-based database combining existing and new data from ChIP-seq and the high-throughput systematic evolution of ligands by exponential enrichment was established for searching TF-binding sites. This study provides important insights into the pathogenic mechanisms of P. aeruginosa and related bacteria and is expected to contribute to the development of effective therapies for infectious diseases caused by this pathogen.

Epigenetics and chromatin structure regulate var2csa expression and the placental-binding phenotype in Plasmodium falciparum

karine.leroch@ucr.edu (Hannes Hoppe) — Wed, 15 Apr 2026 00:00:00 +0000

Plasmodium falciparum is responsible for what appears to be a never-ending public health issue in the developing world. With repeated infections, a gradual semi-immunity to severe malaria can be acquired, but this is disrupted when women become pregnant as the parasite cytoadheres in the placenta to prevent splenic clearance. This change in tissue tropism is due to specific transcription of the antigenically variable adhesin VAR2CSA. To better understand the molecular mechanisms activating var2csa and antigenic variation overall, we used a combination of phenotypic and systems biology assays. We first established phenotypically homogenous populations of VAR2CSA-expressing and placenta-binding parasites that were shown to exclusively transcribe var2csa while all other var genes remained silenced. We also confirmed that the transcriptional activation was strongly associated with distinct depletion of repressive H3K9me3 marks. Further, we used chromatin conformation capture as a high-resolution approach to determine interchromosomal interactions and established that transcriptional activation is linked to a small yet significant repositioning of var2csa relative to heterochromatic telomeric clusters. Lastly, we demonstrated that occupancy of 5-methylcytosine was present in all var genes but independent of transcriptional repression and switching. All together, these findings provide insights at high resolution into the potential role of 5-methylcytosine in P. falciparum and increase our understanding of the mechanisms regulating antigenic variation at the epigenetics and chromatin structure level.

Synaptotagmin 1 and Synaptotagmin 7 promote MR1-mediated presentation of Mycobacterium tuberculosis antigens

karamooz@ohsu.edu (Andrew J Olive) — Tue, 14 Apr 2026 00:00:00 +0000

Mycobacterium tuberculosis (Mtb) is an intracellular pathogen that can be sensed by T cells, which are essential for the control of infection. In comparison to viral infections, Mtb antigens are relatively limited and hence, challenging to sample. Specialized antigen presentation pathways enable the presentation of such scarce antigens to CD8⁺ T cells, which are, thus, uniquely poised to survey intracellular environments. A subset of CD8⁺ T cells prevalent in the airways, known as mucosal-associated invariant T (MAIT) cells, can be activated through the presentation of Mtb antigens via the major histocompatibility complex class I-related protein 1 (MR1) molecule. Prior work demonstrates that endosomal calcium signaling is critical for MR1-mediated presentation of Mtb-derived antigens. Here, we show that the calcium-sensing trafficking proteins Synaptotagmin (Syt) 1 and Syt7 specifically promote MAIT cell activation in response to Mtb-infected cells. In bronchial epithelial cells, Syt1 and Syt7 localize to late endo-lysosomes and MR1 vesicles. Loss of Syt1 and Syt7 results in enlarged MR1 vesicles and an increased number of MR1 vesicles in close proximity to Mtb-containing vacuoles during infection. This study identifies a specialized pathway in which Syt1 and Syt7 facilitate the translocation of MR1 from Mtb-containing vacuoles, potentially to the cell surface for antigen presentation.

Single-cell RNA-seq reveals trans-sialidase-like superfamily gene expression heterogeneity in Trypanosoma cruzi populations

psmircich@fcien.edu.uy (Gabriel Rinaldi) — Tue, 07 Apr 2026 00:00:00 +0000

Trypanosoma cruzi, the causative agent of Chagas disease, presents a major public health challenge in Central and South America, affecting approximately 8 million people and placing millions more at risk. The T. cruzi life cycle includes transitions between epimastigote, metacyclic trypomastigote, amastigote, and blood trypomastigote stages, each marked by distinct morphological and molecular adaptations to different hosts and environments. Unlike other trypanosomatids such as Trypanosoma brucei, T. cruzi does not employ a monoallelic model of antigenic variation; instead, it relies on a diverse repertoire of cell-surface associated proteins encoded by large multigene families, which are essential for infectivity and immune evasion. This study analyzes cell-specific transcriptomes using single-cell RNA sequencing of amastigote and trypomastigote cells to characterize stage-specific surface protein expression during mammalian infection. Through clustering and identification of cell-specific markers, we assigned cells to distinct parasite developmental forms. Analysis of individual cells revealed that surface protein-coding genes, especially members of the trans-sialidase-like superfamily (TcS), are expressed with greater heterogeneity than single-copy genes. Moreover, no recurrent combinations of TcS genes were observed between individual cells in the population. Remarkably, a small subset of TcS mRNAs, encoded by genes preferentially located in the core genomic compartment, are frequently detected across the cell population, whereas the vast majority of TcS mRNAs show low detection frequencies and are mainly encoded in the disruptive compartment. Our findings thus reveal transcriptomic heterogeneity within trypomastigote populations where each cell displays unique TcS expression profiles. Focusing on the diversity of surface protein expression, this research aims to deepen our understanding of T. cruzi cellular biology and infection strategies.

Peptidoglycan recycling is critical for cell division, cell wall integrity, and β-lactam resistance in Caulobacter crescentus

thanbichler@uni-marburg.de (Anna Merz) — Thu, 02 Apr 2026 00:00:00 +0000

Most bacteria possess a peptidoglycan (PG) sacculus, which is continuously remodeled during cell growth and division. The turnover products generated in this process are typically imported into the cell and reused for PG biosynthesis. While the underlying pathways have been studied intensively in gammaproteobacteria, knowledge of their presence and physiological roles in other bacterial lineages remains limited. Here, we comprehensively investigate PG recycling in the alphaproteobacterial model organism Caulobacter crescentus. Characterizing the activities of key enzymes in vitro and in vivo, we show that this species contains a functional PG recycling pathway, including the MurU shunt. Our results reveal that PG recycling is critical for C. crescentus cell morphology and division and is dynamically regulated to balance the flux of metabolic intermediates toward PG biosynthesis and central carbon metabolism. Importantly, defects in PG recycling strongly impair the intrinsic ampicillin resistance of C. crescentus without changing the activity of its β-lactamase BlaA, likely by limiting PG precursor biosynthesis and thereby decreasing the activity of the cell wall biosynthetic machinery in the presence of residual antibiotic. These findings underscore the central role of PG recycling in bacterial fitness and suggest that inhibiting this process could provide a promising strategy to combat β-lactam-resistant pathogens.

A conserved mycobacterial nucleomodulin hijacks the host COMPASS complex to reprogram pro-inflammatory transcription and promote intracellular survival

zhanglei2023@mail.hzau.edu.cn (Aizhen Guo) — Tue, 31 Mar 2026 00:00:00 +0000

Nucleomodulins are a class of effector proteins secreted by bacterial pathogens that translocate into the host cell nucleus to modulate nuclear processes. However, their target proteins and underlying molecular mechanisms remain poorly understood in mycobacteria. Herein, we identified a conserved hypothetical protein Rv1075c, designated MgdE, as a nucleomodulin that enhances mycobacterial intracellular survival. MgdE undergoes nuclear translocation via two nuclear localization signals, KRIR^108-111 and RLRRPR^300-305, and interacts with ASH2L and WDR5, two subunits of the host histone methyltransferase COMPASS complex. This interaction suppresses histone H3 lysine 4 (H3K4) methylation-mediated transcription of pro-inflammatory genes, including IL6 and IL1Β, thereby promoting mycobacterial survival in both macrophages and mice. Our study provides the first experimental evidence that a bacterial nucleomodulin facilitates intracellular survival by directly targeting the host COMPASS complex. These findings advance our understanding of mycobacterial pathogenesis by revealing a novel mechanism that contributes to its intracellular survival strategy.

Human genetic ancestry, Mycobacterium tuberculosis diversity, and tuberculosis disease severity in Dar es Salaam, Tanzania

sebastien.gagneux@swisstph.ch (Amanda Ross) — Tue, 24 Mar 2026 00:00:00 +0000

Infectious diseases have affected humanity for millennia and are among the strongest selective forces. Tuberculosis (TB) is an ancient disease, caused by the human-adapted members of the Mycobacterium tuberculosis complex (MTBC). The outcome of TB infection and disease is highly variable, and co-evolution between human populations and MTBC strains may account for some of this variability. Particular human genetic ancestries have been associated with higher susceptibility to TB, but sociodemographic aspects of the disease can confound such associations. Here, we studied 1000 TB patients from Dar es Salaam, Tanzania, together with their respective MTBC isolates, by combining human and bacterial genomics with clinical data. We found that the genetic background of the TB patient population was strongly influenced by migrations of Bantu-speaking populations from West Africa, which contrasts with the corresponding MTBC genotypes that were mainly introduced from outside Africa. These findings suggest a recent evolutionary history of co-existence between the human and MTBC populations in Dar es Salaam. We detected no evidence of an effect of human genetic ancestry, or MTBC phylogenetic diversity alone, nor their interaction, on TB disease severity. There was also no evidence of an association between human variation genome-wide and TB disease severity. Treatment-seeking, social, and environmental factors are likely to be the main determinants of disease severity at the point of care in this patient population.

Bacteria weigh up costs and benefits of mobile weapons

fuy@sustech.edu.cn (Yang Fu) — Mon, 23 Mar 2026 00:00:00 +0000

Gaining the ability to kill rival microbes is not always an advantage for bacteria in complex gut microbiomes.

4-Aminoquinolines block heme iron reactivity and interfere with artemisinin action

dgoldberg@wustl.edu (Daniel E Goldberg) — Mon, 23 Mar 2026 00:00:00 +0000

Artemisinin-based combination therapies (ACTs) remain the mainstay of treatment for Plasmodium falciparum malaria, despite reports of ACT treatment failure. ACTs consist of an artemisinin and a longer-lived partner drug, which is often a quinoline. Given that heme is central to the mechanism of action of artemisinins and some quinolines, we hypothesized that these antimalarials would exhibit strong drug-drug interactions. Previous studies using standard 48 hr or 72 hr assays identified additive to mildly antagonistic interactions between artemisinins and quinolines. Here, we sought to re-evaluate these interactions using a pulsing assay that better mimics the short in vivo half-life of artemisinins. We found that chloroquine (CQ), piperaquine (PPQ), and amodiaquine substantially antagonize dihydroartemisinin (DHA), the active metabolite of artemisinins. CQ-DHA antagonism was notably exacerbated in CQ-resistant parasites, resulting in a superantagonistic phenotype in isobolograms. Further, we found that CQ co-treatment conferred artemisinin resistance to Kelch 13 wild-type parasites in the ring-stage survival assay. Using a small molecule probe (Ac-H-FluNox) to measure chemically reactive heme in live parasites, we determined that quinolines block artemisinin activation by rendering cytosolic heme inert. Finally, we probed beyond traditional ACTs, evaluating interactions of the proposed triple ACT, DHA-PPQ-mefloquine, as well as OZ439-quinoline combinations, which were all found to be antagonistic. Collectively, these in vitro data suggest that peroxide-quinolines may have liabilities as combination therapies.

Mycobacterial metallophosphatase MmpE acts as a nucleomodulin to regulate host gene expression and promote intracellular survival

zhanglei2023@mail.hzau.edu.cn (Aizhen Guo) — Wed, 18 Mar 2026 00:00:00 +0000

Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a major global health challenge. Nucleomodulins, bacterial effectors that target the host cell nuclei, are increasingly recognized as key virulence factors, but their roles in mycobacterial pathogenesis remain incompletely elucidated. Here, we characterize a hypothetical protein Rv2577 (designated MmpE) not only as a Fe³⁺/Zn²⁺-dependent metallophosphatase but also as a critical nucleomodulin involved in immune evasion and intracellular persistence. MmpE utilizes two nuclear localization signals, RRR^20-22 and RRK^460-462, to enter the host cell nucleus, where it binds to the promoter region of the vitamin D receptor (VDR) gene, thereby inhibiting host inflammatory gene expression. Additionally, MmpE regulates the PI3K-Akt-mTOR signaling pathway, thereby arresting lysosome maturation. These actions collectively facilitate immune suppression and promote mycobacterial survival in macrophages and in mice. Our findings identify MmpE as a conserved nucleomodulin in mycobacteria and reveal a novel mechanism of MmpE-mediated intracellular survival.

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

nadine.ziemert@uni-tuebingen.de (Alison Butler) — Mon, 09 Mar 2026 00:00:00 +0000

Microbial competition for trace metals shapes their communities and interactions with humans and plants. Many bacteria scavenge trace metals with metallophores, small molecules that chelate environmental metal ions. Metallophore production may be predicted by genome mining, where genomes are scanned for homologs of known biosynthetic gene clusters (BGCs). However, accurately detecting non-ribosomal peptide (NRP) metallophore biosynthesis requires expert manual inspection, stymieing large-scale investigations. Here, we introduce automated identification of NRP metallophore BGCs through a comprehensive algorithm, implemented in antiSMASH, that detects chelator biosynthesis genes with 97% precision and 78% recall against manual curation. We showcase the utility of the detection algorithm by experimentally characterizing metallophores from several taxa. High-throughput NRP metallophore BGC detection enabled metallophore detection across 69,929 genomes spanning the bacterial kingdom. We predict that 25% of all bacterial non-ribosomal peptide synthetases encode metallophore production and that significant chemical diversity remains undiscovered. A reconstructed evolutionary history of NRP metallophores supports that some chelating groups may predate the Great Oxygenation Event. The inclusion of NRP metallophore detection in antiSMASH will aid non-expert researchers and continue to facilitate large-scale investigations into metallophore biology.

Scaling up efforts to target evolving viruses

hs743@cam.ac.uk (Henrik Salje) — Mon, 23 Feb 2026 00:00:00 +0000

High-throughput neutralisation tests could lead to a better understanding of the evolution of human influenza.

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

jbloom@fredhutch.org (Andrea N Loes) — Mon, 23 Feb 2026 00:00:00 +0000

Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neutralization titers for 78 recent H3N2 HA strains against a large set of children and adult sera, measuring ~10,000 total titers. There is substantial person-to-person heterogeneity in the titers against different viral strains, both within and across age cohorts. The growth rates of H3N2 strains in the human population in 2023 are highly correlated with the fraction of sera with low titers against each strain. Notably, strain growth rates are less correlated with neutralization titers against pools of human sera, demonstrating the importance of population heterogeneity in shaping viral evolution. Overall, these results suggest that high-throughput neutralization measurements of human sera against many different viral strains can help explain the evolution of human influenza.

Neutralizing human monoclonal antibodies that target the PcrV component of the type III secretion system of Pseudomonas aeruginosa act through distinct mechanisms

ina.attree@ibs.fr (Andrea Dessen) — Tue, 17 Feb 2026 00:00:00 +0000

Pseudomonas aeruginosa is a major human opportunistic pathogen associated with a high incidence of multi-drug resistance. The antibody-based blockade of P. aeruginosa virulence factors represents a promising alternative strategy to mitigate its infectivity. In this study, we employed single B cell sorting from cystic fibrosis patients to isolate human monoclonal antibodies (mAbs) targeting proteins from the P. aeruginosa Type 3 Secretion System (T3SS) and characterized a panel of mAbs directed at PscF and PcrV. Among those, two mAbs, P5B3 and P3D6, that bind to the injectisome tip protein PcrV, exhibited T3SS blocking activity. We solved the crystal structure of the P3D6 Fab-PcrV complex, which revealed that the Ab binds to the C-terminal region of PcrV. In addition, we compared the T3SS-blocking activity of three PcrV-targeting mAbs, including two from previous independent studies, using two distinct assays to evaluate pore formation and toxin injection. We conducted a mechanistic and structural analysis of their modes of action through modeling based on the known structure of a functional homolog, SipD from Salmonella typhimurium. The analysis suggests that anti-PcrV mAbs may act through different mechanisms, ranging from preventing PcrV oligomerization to disrupting PcrV’s scaffolding function, thereby inhibiting the assembly and function of the translocon pore. Our findings provide additional evidence that T3SS-targeting Abs, some capable of inhibiting virulence, are elicited in P. aeruginosa-infected patients. The results offer deeper insights into PcrV recognition by mAbs and their associated mechanisms of action, helping to identify which Abs are more likely to be therapeutically useful based on their mode of action and potency. This paves the way for the development of effective alternatives to traditional antibiotics in the fight against this resilient pathogen.

Glycolysis-dependent sulfur metabolism orchestrates morphological plasticity and virulence in fungi

sriram.ccmb@csir.res.in (Adishree M) — Fri, 06 Feb 2026 00:00:00 +0000

Fungi exhibit remarkable morphological plasticity, which allows them to undergo reversible transitions between distinct cellular states in response to changes in their environment. This phenomenon, termed fungal morphogenesis, is critical for fungi to survive and colonize diverse ecological niches and establish infections in a variety of hosts. Despite significant advancements in the field with respect to understanding the gene regulatory networks that control these transitions, the metabolic determinants of fungal morphogenesis remain poorly characterized. In this study, we uncover a previously uncharacterized, conserved dependency between central carbon metabolism and de novo biosynthesis of sulfur-containing amino acids that is critical for fungal morphogenesis in two key fungal species. Using a multidisciplinary approach, we demonstrate that glycolytic flux is crucial to drive fungal morphogenesis in a cAMP-independent manner and perturbation of this pathway leads to a significant downregulation in the expression of genes involved in de novo biosynthesis of sulfur-containing amino acids. Remarkably, exogenous supplementation of sulfur-containing amino acids robustly rescues the morphogenesis defect induced by the perturbation of glycolysis in both Saccharomyces cerevisiae and Candida albicans, underscoring the pivotal role of de novo biosynthesis of sulfur-containing amino acids as a downstream effector of morphogenesis. Furthermore, a C. albicans mutant lacking the glycolytic enzyme, phosphofructokinase-1 (Pfk1), exhibited significantly reduced survival within murine macrophages and attenuated virulence in a murine model of systemic candidiasis. Overall, our work elucidates a previously uncharacterized coupling between glycolysis and sulfur metabolism that is critical for driving fungal morphogenesis, contributing to our understanding of this conserved phenomenon.

ZFT is the major iron and zinc transporter in Toxoplasma gondii

clare.harding@glasgow.ac.uk (Augustin Pouzache) — Thu, 05 Feb 2026 00:00:00 +0000

Transition metals, such as iron and zinc, are indispensable trace elements for eukaryotic life, acting as co-factors in essential processes ranging from metabolism to DNA replication. These metals can be transported into cells by an evolutionary-conserved family of metal transporters; however, how the ubiquitous mammalian parasite Toxoplasma gondii acquires essential metals has been unknown. Here, we have identified and characterised the first iron and zinc importer in T. gondii. This transporter, named ZFT, localised to the parasite plasma membrane and is essential for the parasite’s life cycle. We find ZFT is regulated by iron availability and overexpression sensitises cells to excess iron and zinc. Using a conditional knockdown system, we find that knockdown of ZFT leads to reduction in mitochondrial respiration and a switch to a more quiescent lifecycle stage. To confirm transport activity, we find that knockdown of ZFT leads to a reduction in parasite-associated zinc and iron, and ZFT expression complements loss of zinc transporter activity in a yeast model. Further, expression of ZFT in Xenopus oocytes demonstrates direct uptake of iron, which is outcompeted in the presence of zinc. Overall, we have identified the first metal uptake transporter in T. gondii and demonstrated the importance of iron and zinc to the parasite. This finding advances our understanding of how this obligate intracellular parasite acquires nutrients from its host.

Mast cells promote pathology and susceptibility in tuberculosis

khader@uchicago.edu (Abhimanyu) — Wed, 28 Jan 2026 00:00:00 +0000

Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis (Mtb), infects approximately one-fourth of the world’s population. We reported an increased accumulation of mast cells (MCs) in the lungs of macaques with active pulmonary TB (PTB), compared with those with latent TB infection (LTBI). MCs respond in vitro to Mtb exposure via degranulation and by inducing proinflammatory cytokines. In the current study, we demonstrate an increased production of chymase by MCs in granulomas of humans and macaques with PTB. Single-cell (sc) RNA sequencing analysis revealed distinct MC transcriptional programs between LTBI and PTB, with PTB-associated MCs enriched in interferon gamma, oxidative phosphorylation, and MYC signaling. In a mouse model, MC deficiency led to improved control of Mtb infection that coincided with reduced accumulation of lung myeloid cells and diminished lung inflammation at chronic stages of infection. Airway transfer of MCs into wild-type Mtb-infected mice showed increased neutrophils, decreased recruited macrophages, and elevated Mtb dissemination to the spleen. Together, these findings highlight MCs as active drivers of TB pathogenesis and potential targets for host-directed therapies for TB.

Doubling dolutegravir dosage reduces the viral reservoir in ART-treated people with HIV

a.o.pasternak@amsterdamumc.nl (Alexander O Pasternak) — Fri, 23 Jan 2026 00:00:00 +0000

Whether antiretroviral therapy (ART) is always completely suppressive, or HIV might continue to replicate at low levels despite ART in some people with HIV (PWH), is still debated. Here, we intensified the ART regimen by doubling dolutegravir (DTG) dosage and investigated the impact of this strategy on HIV blood and tissue reservoirs, immune activation, and inflammation. Twenty HIV-infected adults, who had received a triple ART consisting of 50 mg DTG/600 mg abacavir/300 mg lamivudine pre-intensification and had been suppressed on ART for at least 2 years, were enrolled in a phase 2 randomized clinical trial (https://clinicaltrials.gov/ identifier: NCT05351684). Half of them received an additional 50 mg of DTG for a period of 84 days. As expected, plasma and tissue DTG concentrations significantly increased during the study period in the intensified group but not in the control group. Accordingly, significant decreases in total HIV DNA, intact HIV DNA, and cell-associated unspliced (US) HIV RNA in peripheral blood mononuclear cells, as well as in the US RNA/total DNA ratio, were observed in the intensified group but not in the control group. Intensification also modestly reduced markers of immune activation and exhaustion but had no measurable impact on systemic or tissue inflammation. Together with this, intensification resulted in a temporary decrease in the CD4/CD8 ratio that returned to baseline by day 84. Our results strongly suggest that the pre-intensification ART regimen was not completely suppressive. If confirmed in larger clinical trials, these results could have an impact on the clinical management of PWH and HIV curative strategies.

HIV-specific CD8+ T-cell proliferative response 24 weeks after early antiretroviral therapy initiation is associated with the subsequent reduction in the viral reservoir

p.vanpaassen@amsterdamumc.nl (Ad C van Nuenen) — Fri, 23 Jan 2026 00:00:00 +0000

Antiretroviral therapy (ART) initiated in the acute phase of HIV infection (AHI) results in a smaller viral reservoir. However, the impact of early HIV-specific T-cell responses on long-term reservoir dynamics is less well characterized. Therefore, we measured the size of the viral reservoir and functionality of HIV-specific CD8+ T-cell responses after the acute phase at 24 and 156 weeks after ART initiation in people with HIV who started treatment during AHI. A significant reduction in total and defective HIV DNA and a trend toward a reduction in intact HIV DNA were observed between 24 and 156 weeks. Functional CD8+ T-cell responses against HIV peptides Env, Gag, Nef, and Pol were maintained over 3 years after treatment initiation. The proliferative capacity of HIV-specific CD8+ T-cells at 24 weeks of ART was predictive of the degree of reduction in total and defective HIV DNA between 24 and 156 weeks, suggesting HIV-specific CD8+ T-cells may at least partially drive the decline of the viral reservoir. Therefore, enforcing HIV-specific immune responses as early as possible after diagnosis of AHI should be a central focus of HIV cure strategies.

Stratification of viral shedding patterns in saliva of COVID-19 patients

iwamishingo@gmail.com (Christopher B Brooke) — Fri, 16 Jan 2026 00:00:00 +0000

Living with COVID-19 requires continued vigilance against the spread and emergence of variants of concern (VOCs). Rapid and accurate saliva diagnostic testing, alongside basic public health responses, is a viable option contributing to effective transmission control. Nevertheless, our knowledge regarding the dynamics of SARS-CoV-2 infection in saliva is not as advanced as our understanding of the respiratory tract. Here, we analyzed longitudinal viral load data of SARS-CoV-2 in saliva samples from 144 patients with mild COVID-19 (a combination of our collected data and published data). Using a mathematical model, we quantified individual-level viral dynamics and stratified them into three groups using a clustering approach. Notably, the three groups exhibited distinct differences in viral RNA detection durations: 11.5 days (95% CI: 10.6–12.4), 17.4 days (16.6–18.2), and 30.0 days (28.1–31.8), respectively. Surprisingly, this stratified grouping remained unexplained despite our analysis of 47 types of clinical data, including basic demographic information, clinical symptoms, results of blood tests, and vital signs. Additionally, we quantified the expression levels of 92 micro-RNAs in a subset of saliva samples, but these also failed to explain the observed stratification, although the mir-1846 level may have been weakly correlated with peak viral load. Our study provides insights into SARS-CoV-2 infection dynamics in saliva, highlighting the challenges in predicting the duration of viral RNA detection without indicators that directly reflect an individual’s immune response, such as antibody induction. Given the significant individual heterogeneity in the kinetics of saliva viral shedding, identifying biomarker(s) for viral shedding patterns will be crucial for improving public health interventions in the era of living with COVID-19.

Fish CDK2 recruits Dtx4 to degrade TBK1 through ubiquitination in the antiviral response

bob@ihb.ac.cn (Bao-Jie Cui) — Wed, 14 Jan 2026 00:00:00 +0000

Although the classical biological protein cell cycle protein kinase CDK2 has been extensively studied in higher vertebrates, its function in lower vertebrates beyond the regulation of mitosis remains unknown. In this study, we report a distinct mechanism whereby IFN expression is negatively regulated in fish by CDK2. After infection with the spring viremia of carp virus (SVCV), fish CDK2 expression significantly increased in tissues and cells. Moreover, antiviral resistance was improved in cdk2^-/- homozygotes, and the antiviral cytokine interferon (IFN) expression was significantly higher. At the cellular level, CDK2 overexpression reduced IFN expression, while cdk2 knockdown increased the ability of cells to produce IFN. Subsequently, it was discovered that fish CDK2 binds and degrades TBK1, resulting in reduced IFN. CDK2 increases the K48-linked ubiquitination of TBK1, causing its degradation, while E3 ubiquitin ligase Dtx4 was found to be involved in this process following the significant enhancement of TBK1 K48-linked ubiquitination. Protein mass spectrometry and immunoblot analysis confirmed that the K567 site on TBK1 is essential for CDK2 to engage with Dtx4 and degrade TBK1; thus, after mutating the K567 site, K48-linked ubiquitination of TBK1 was not enhanced by Dtx4, and TBK1 was not degraded by CDK2. Our data demonstrate that fish CDK2 recruits the E3 ubiquitin ligase Dtx4 to target the K567 site of TBK1 and promote its degradation. These results suggest that CDK2 in lower vertebrates is implicated in a specialized role for antiviral innate immunity.

ATP burst is the dominant driver of antibiotic lethality in Mycobacterium smegmatis

raju.mukherjee@iisertirupati.ac.in (Anjali Veeram) — Tue, 13 Jan 2026 00:00:00 +0000

Antibiotic-tolerant bacteria, due to their unique physiology, are refractory to antimicrobial killing and pose challenges for infection control. Incomplete knowledge of how bactericidal antibiotics work limits our understanding of partial resistance due to phenotypic tolerance in mycobacteria, a driver for developing genetic resistance. Using proteomics, ¹³C isotopomer analysis, genetic and biochemical assays, we investigated the physiological response of M. smegmatis challenged with aminoglycoside and fluoroquinolone antibiotics. Two distinct classes of antibiotics elicited remarkably similar responses and increased flux through the TCA cycle, causing enhanced respiration, ROS generation, and ATP burst. We observed that excessive ATP levels and not ROS dominantly contribute to cidality, which may in part be conferred by sequestration of divalent metal ions by ATP. Consequently, ¹³C isotope tracing indicated TCA cycle flux deviation from its oxidative arm as a bacterial adaptive mechanism, which also included activated intrinsic resistance and a higher propensity to develop antibiotic resistance. Our study provides a new understanding of the intricate mechanisms of antibiotic-induced cell death and expands the current paradigm for antibiotic action.

Heterogeneity of genetic sequence within quasi-species of influenza virus revealed by single-molecule sequencing

tabatak@g.ecc.u-tokyo.ac.jp (Hiroyuki Noji) — Tue, 06 Jan 2026 00:00:00 +0000

Influenza viruses exhibit high mutation rates and extensive genetic diversity, which hinder effective vaccine development and facilitate immune evasion (Taubenberger and Morens, 2006; Barr et al., 2010). These mutations arise from the error-prone viral RNA-dependent RNA polymerase, generating highly heterogeneous viral populations within individual hosts that conform to the quasi-species model of a cloud of related genomes evolving under selection (Domingo et al., 2012). Accurate characterization of this intra-host diversity is crucial for understanding viral evolution and improving vaccine design, yet conventional RNA sequencing often fails to detect low-frequency variants because of technical errors during sample preparation and sequencing. Here, we implement a single unique molecular identifier strategy that reduces sequencing artifacts and achieves an error rate of ~10⁻⁵, enabling single-particle–level quantification of quasi-species diversity. Mutation frequencies greatly exceeding background error confirm their biological origin, while information-theoretic metrics such as Shannon entropy and Jensen–Shannon divergence reveal non-random mutation distributions under selective constraints. This framework supports detailed studies of intra-host viral evolution and may inform artificial intelligence-driven prediction of mutational trajectories and more effective influenza vaccine strategies.

Decoding the biogenesis of HIV-induced CPSF6 puncta and their fusion with nuclear speckles

felipe.diaz-griffero@einsteinmed.edu (Bin Cui) — Tue, 06 Jan 2026 00:00:00 +0000

Viruses rely on host cellular machinery for replication. After entering the nucleus, the HIV genome accumulates in nuclear niches where it undergoes reverse transcription and integrates into neighbouring chromatin, promoting high transcription rates and new virus progeny. Despite antiretroviral treatment, viral genomes can persist in these nuclear niches and reactivate upon treatment interruption, raising the possibility that they could play a role in the establishment of viral reservoirs. The post-nuclear entry dynamics of HIV remain unclear, and understanding these steps is critical for revealing how viral reservoirs are established. In this study, we elucidate the formation of HIV-induced CPSF6 puncta and the domains of CPSF6 essential for this process. We also explore the roles of nuclear speckle (NS) scaffold factors, SON and SRRM2, in the biogenesis of these puncta. Through genetic manipulation and depletion experiments, we demonstrate the key role of the intrinsically disordered region of SRRM2 in enlarging NSs in the presence of the HIV capsid. We identify the FG domain of CPSF6 as essential for both puncta formation and binding to the viral core, which serves as the scaffold for CPSF6 puncta. While the low-complexity regions modulate CPSF6 binding to the viral capsid, they do not contribute to puncta formation, nor do the disordered mixed charge domains of CPSF6. Interestingly, the FG peptide facilitates viral replication. These results demonstrate how HIV evolved to hijack host nuclear factors, enabling its persistence in the host. Of note, this study provides new insights into the underlying interactions between host factors and viral components, advancing our understanding of HIV nuclear dynamics and offering potential therapeutic targets for preventing viral persistence.

Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism

aescdon94@gmail.com (Alexandre Campos) — Fri, 02 Jan 2026 00:00:00 +0000

Structural colors (SC), generated by light interacting with nano-structured materials, are responsible for the brightest and most vivid coloration in nature. Despite being widespread within the tree of life, there is little knowledge of the genes involved. Partial exceptions are some Flavobacteriia in which genes involved in a number of pathways, including gliding motility and polysaccharide metabolism, have been linked to SC. A previous genomic analysis of SC and non-SC bacteria suggested that the pterin pathway is involved in the organization of bacteria to form SC. Here, we focus on moeA, a molybdopterin molybdenum transferase. When this gene was deleted from Flavobacterium IR1, the knock-out mutant showed a strong blue shift in SC of the colony compared to the wild-type. The moeA mutant showed a particularly strong blue shift when grown on kappa-carrageenan and was upregulated for starch degradation. To further analyze the molecular changes, proteomic analysis was performed, showing the upregulation of various polysaccharide utilization loci, which supported the link between moeA and polysaccharide metabolism in SC. Overall, we demonstrated that a targeted approach, modifying a single gene identified by genomics, could change the optical properties of bacteria.

Neisseria gonorrhoeae LIN codes provide a robust, multi-resolution lineage nomenclature

odile.harrison@ndph.ox.ac.uk (Anastasia Unitt) — Wed, 31 Dec 2025 00:00:00 +0000

Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to consistently identify N. gonorrhoeae lineages is important for surveillance of this increasingly antimicrobial resistant organism, facilitating efficient communication regarding its epidemiology; however, conventional typing systems fail to reflect N. gonorrhoeae strain taxonomy in a reliable and stable manner. Here, a N. gonorrhoeae genomic lineage nomenclature, based on the barcoding system of Life Identification Number (LIN) codes, was developed using a refined 1430 core gene MLST (cgMLST). This hierarchical LIN code nomenclature conveys lineage information at multiple levels of resolution within one code, enabling it to provide immediate context to an isolate’s ancestry, and to relate to familiar, previously used typing schemes such as Ng cgMLST v1, 7-locus MLST, or NG-STAR clonal complex (CC). Clustering with LIN codes accurately reflects gonococcal diversity and population structure, providing insight into associations between genotype and phenotype for traits such as antibiotic resistance. These codes are automatically assigned and publicly accessible via the https://pubmlst.org/organisms/neisseria-spp database.

Evolution of a fuzzy ribonucleoprotein complex in viral assembly

schuckp@mail.nih.gov (Agata M Czaja) — Tue, 30 Dec 2025 00:00:00 +0000

Previously, we showed that the genetic diversity of SARS-CoV-2 nucleocapsid (N) protein explores a wide range of biophysical properties facilitated by non-local impact of point mutations to its intrinsically disordered regions (Nguyen et al., 2024). This includes modulation of self-association, such as the creation of a de novo binding interface through the P13L mutation characteristic of Omicron variants. In the present work, we focus on the key function of N condensing viral RNA into ribonucleoprotein particles (RNPs) for viral assembly. Lacking high-resolution structural information, biochemical and biophysical approaches have revealed architectural principles of RNPs, which involve cooperative interactions of several protein-protein and protein-RNA interfaces, initiated through oligomerization of conserved transient helices in the central disordered linker of N. Here, we study the impact of defining N-protein mutations in variants of concern on RNP formation, using biophysical tools, a virus-like particle assay, and reverse genetics experiments. We find convergent evolution in repeated, independent introduction of amino acid substitutions strengthening existing binding interfaces, compensating for other substitutions that promote viral replication but decrease RNP stability. Furthermore, we show that the P13L mutation of Omicron variants enhances RNP assembly and increases viral fitness. Overall, our data reveal RNP complexes to be highly variable not only in sequence and conformations but also in thermodynamic and kinetic stability, with its pleomorphism affecting basic architectural principles. We hypothesize that the formation of polydisperse, fuzzy N-RNA clusters with multiple distributed weak binding interfaces optimizes reversible RNA condensation, while supporting host adaptation and allowing for a large sequence space to be explored.

A system for functional studies of the major virulence factor of malaria parasites

bruchhaus@bnitm.de (Agnes Murk) — Mon, 29 Dec 2025 00:00:00 +0000

PfEMP1 is a variable antigen displayed on erythrocytes infected with the malaria parasite Plasmodium falciparum. PfEMP1 mediates binding of the infected cell to the endothelium of blood vessels, a cause of severe malaria. Each parasite encodes ~60 different PfEMP1 variants but only one is expressed at a time. Switching between variants underlies immune evasion in the host and variant-specific severity of disease. PfEMP1 is difficult to study due to expression heterogeneity between parasites which also renders genetic modification approaches ineffective. Here, we used selection-linked integration (SLI) to generate parasites all expressing the same PfEMP1 variant and genome edit the expressed locus. Moving this system from the reference strain 3D7 to IT4 resulted in PfEMP1 expressor parasites with effective receptor binding capacities. We also introduce a second version of SLI (SLI2) to introduce additional genome edits. Using these systems, we study PfEMP1 trafficking, generate cell lines binding to the most common endothelial receptors, survey the protein environment from functional PfEMP1 in the host cell, and identify new proteins needed for PfEMP1-mediated sequestration. These findings show the usefulness of the system to study the key virulence factor of malaria parasites.