Bacterial small RNAs (sRNAs) derived from mRNA 3' untranslated regions (3' UTRs) have emerged as important regulators of gene expression, yet their evolutionary origins and functional diversification remain poorly understood compared to the protein-coding sequences of the same transcripts. In this study, we present a comparative analysis of the biogenesis and regulatory functions of UhpU, a 3' UTR-derived sRNA from the hexose phosphate transporter gene , in and . We show that UhpU likely originated as a processed sRNA generated by RNase E cleavage in Enterobacteriaceae, enabling repression of genes in the hexose phosphotransferase system, thereby contributing to hexose phosphate homeostasis in coordination with its parental gene. In , UhpU subsequently evolved the ability to repress , a transcriptional repressor, via a UhpU-binding site introduced by a horizontally acquired DNA fragment that extended the 5' UTR. After divergence from the most recent common ancestor with , the lineage comprising , , and acquired a FliA-dependent promoter within the coding region, allowing independent transcription of UhpU and establishing it as a dual-biogenesis sRNA. Together, our results outline a stepwise trajectory in which UhpU evolved from a processing-derived metabolic regulator to an sRNA with expanded regulatory connections and a lineage-specific FliA-dependent transcriptional program in .

IMP dehydrogenase (IMPDH) controls a key regulatory node in purine biosynthesis. Gain-of-function mutations in human IMPDH2 are associated with neurodevelopmental disorders and neuromuscular symptoms including dystonia, but the developmental mechanisms underlying these defects are unknown. We previously showed that these mutants are insensitive to GTP inhibition and hypothesized that their hyperactivity would affect nucleotide metabolism in vivo. Here, we characterize the metabolic and developmental consequences of the neurodevelopmental disorder-associated IMPDH2 mutant, S160del, in . We show that expressing S160del but not WT human IMPDH2 disrupts purine pools and somite organization in the developing tadpole. We also show that S160del disrupts in vivo IMPDH filament assembly, a well-described IMPDH regulatory mechanism. Cryo-EM structures show that S160del disrupts filament assembly by destabilizing the dimerization of regulatory Bateman domains. Dimerization of Bateman domains and subsequent filament formation can be restored with a high affinity ligand, but this does not restore sensitivity to GTP inhibition, suggesting S160del also disrupts allostery of IMPDH2 filaments. This work demonstrates that the structural effects of patient IMPDH2 variants can cause disruptions both to nucleotide levels and to the normal development of sensorimotor structures, helping us better understand the physiological basis of disease in these patients.

Phosphate is often a limiting resource, directly affecting the availability of key biomolecules such as nucleotides. To cope with phosphate scarcity, bacteria have evolved enzymes that utilize alternative phosphorus compounds, including phosphite (Pt). Although a few enzymes oxidize Pt to produce phosphate, the enzymes responsible for Pt oxidation in many environmental bacteria remain unidentified, and the role of microbial Pt oxidation in the global phosphorus cycle is not yet fully understood. In this study, we performed bioinformatic analyses of three Pt-oxidizing enzymes: the native Pt oxidase, phosphite dehydrogenase (PtxD), and two promiscuous Pt oxidases, alkaline phosphatase (PhoA) and carbon-phosphorus lyase. Among these, PhoA was found to be widely distributed across bacteria since the early stages of their evolution. In contrast, PtxD emerged later in a limited number of bacterial lineages that had lost PhoA. Our biochemical characterizations revealed that most extant and reconstructed ancestral PhoAs tested exhibited Pt oxidation activity. Moreover, disruption of active-site residues diminished Pt oxidase activity in PhoA, while only partially affecting its native function. This promiscuous function of PhoA reveals an overlooked mechanism in bacterial phosphate metabolism and underscores the role of Pt in the cycling of bioavailable phosphorus in ecosystems.

HOXB13 is a lineage-specific transcription factor that plays a critical role in initiation and progression of prostate cancer (PCa). While most research has focused on the role of HOXB13 on androgen receptor (AR) activity, here we demonstrate that HOXB13 is frequently expressed in AR-negative tumors and is essential for the proliferation of both AR-positive and -negative PCa models. Strikingly, HOXB13 is remarkably selective and has almost no effect on nonprostatic tissues. Despite this common essentiality in PCa, HOXB13 activity is markedly different in AR-negative stem cell-like tumors, where interactions with the AP-1 change the HOXB13 cistrome and interactome. Yet despite these distinct activities, HOXB13 activity is commonly mediated by SMARCD2, a member of the mSWI/SNF chromatin remodeling complex. The HOXB13/SMARCD2 interaction alters chromatin accessibility at HOXB13-binding sites, causing increased proliferation in AR-negative PCa. Overall, this work demonstrates a distinct mechanism of action for HOXB13 and highlights its critical role in AR-negative castration-resistant PCa.

Guanidine is well known as a denaturing agent. However, recent studies have demonstrated both the widespread synthesis of guanidine, e.g., in plants and mammals, as well as the widespread occurrence of guanidine metabolism in bacteria, suggesting a broader biological role. Here, we provide insights into guanidine assimilation via guanidine hydrolases (GdmH) in cyanobacteria. The gene is widespread among cyanobacteria and enables growth on guanidine as the sole nitrogen source. Consistent with this, gene expression increased under nitrogen limitation, regulated by the transcription factor NtcA. However, guanidine is toxic above 5 mM, necessitating GdmH activity and adaptive mutations activating the multidrug efflux system PrqA. The gene is frequently colocalized with ABC transporter genes (named ), which are driven by an additional NtcA-regulated promoter. The corresponding substrate-binding protein GimA showed high affinity to guanidine. Consistent with a high affinity import system, disruption of genes or impaired guanidine-dependent growth of sp. PCC 6803 at low concentrations. However, in presence of >1 mM guanidine, these mutants grew like wildtype, suggesting the existence of additional uptake mechanisms for guanidine. We also demonstrate the high-affinity binding of guanidine to a previously described, conserved RNA motif located within the 5'-untranslated region, validating it as a guanidine-I riboswitch. By combining it with various promoters, we achieved precise, titratable control of heterologous gene expression in cyanobacteria in vivo. Our findings establish guanidine assimilation as an integral element of cyanobacterial nitrogen metabolism and highlight guanidine riboswitches as valuable tools for synthetic biology.

Despite significant advances in characterizing the highly nonconvex landscapes of constraint satisfaction problems, the good performance of certain algorithms in solving hard combinatorial optimization tasks remains poorly understood. This gap in understanding stems largely from the lack of theoretical tools for analyzing their out-of-equilibrium dynamics. To address this challenge, we develop a system of approximate master equations that capture the behavior of local search algorithms in constraint satisfaction problems. Our framework shows excellent qualitative agreement with the phase diagrams of two paradigmatic algorithms: Focused Metropolis Search (FMS) and greedy-WalkSAT (G-WalkSAT) for random 3-SAT. The equations not only confirm the numerical observation that G-WalkSAT's algorithmic threshold is nearly parameter-independent but also successfully predict FMS's threshold beyond the clustering transition. We also exploit these equations in a decimation scheme, demonstrating that the computed marginals encode valuable information about the local structure of the solution space explored by stochastic algorithms. Notably, our decimation approach achieves a threshold that surpasses the clustering transition, outperforming conventional methods like Belief Propagation-guided decimation. These results challenge the prevailing assumption that long-range correlations are always necessary to describe efficient local search dynamics and open a path to designing efficient algorithms to solve combinatorial optimization problems.

This study reanalyzed endothelial cell (EC) gene expression in the mouse aorta utilizing eight single-cell RNA-sequencing datasets. Contrary to the assumption that all ECs originated from the luminal surface, we identified two distinct sites of origin: aortic lumen (-positive ECs) and peri-aortic microvascular (-positive ECs). The proportions of these EC subtypes varied extensively across the eight datasets, likely due to differing experimental procedures. We deduced complete transcriptomes for each EC subtype, revealing differential gene expression and predicted functional properties. We provide marker lists and an accessible online database for gene-by-gene analysis to aid in correct cell identification and in gauging the impact of patho/physiological parameters on aortic EC gene expression.

The competition-colonization trade-off is a possible explanation for coexistence of species in a metacommunity context that has been intensively studied for decades. Nonetheless, questions about the ubiquity and generality of the mechanism remain. The outcome of the model, equilibrium species abundances, are relatively easy to measure. However, the input into the basic model, the competitive hierarchy and the colonization rates, are not easy to measure in the field. We propose an approach that starts with an observed equilibrium configuration. We show that for any assumed competitive hierarchy we can find a corresponding set of colonization rates that would produce the observed equilibrium. We also find a simple formula for the colonization rates in terms of the observed abundances. This approach both shows that any observed set of abundances can result from a competition-colonization trade-off, and provides a method for future analyses. Additionally, generalizations of our approach can apply to generalizations of the basic competition-colonization model that avoid any biologically questionable assumptions.

During vertebrate embryogenesis, hematopoietic stem and progenitor cells (HSPCs) originate from hemogenic endothelium (HE) in the dorsal aorta through endothelial-to-hematopoietic transition (EHT). While basal inflammation is essential for this process, excessive immune activation disrupts HSPC emergence. Here, we identify angiotensin-converting enzyme 2 (Ace2), a key component of renin-angiotensin system, as a crucial anti-inflammatory regulator of embryonic hematopoiesis in zebrafish and mice. Loss of Ace2 impairs HE specification and reduces nascent HSPC production. Mechanistically, transcriptomic profiling reveals that deficiency leads to aberrant activation of NLR family pyrin domain containing 3 (Nlrp3) signaling and pyroptosis in vascular endothelial cells. Importantly, pharmacological inhibition of Nlrp3 or Caspase-1 restores HSPC emergence upon deficiency, consistent with treatment with exogenous angiotensin-(1-7) [Ang-(1-7)], a downstream product of Ace2 enzymatic activity. Moreover, Ace2 knockdown in mouse embryos phenocopies the defects in zebrafish, demonstrating evolutionary conservation of ACE2 in developmental hematopoiesis in mammals. Together, our findings uncover an essential role for ACE2 in maintaining a permissive inflammatory environment for HSPC development and suggest therapeutic potential for targeting the ACE2/Ang-(1-7)/Nlrp3-pyroptosis axis in inflammatory hematopoietic disorders.

In the United States, people of color are disproportionately and unjustly exposed to air pollution. Historically, environmental policy has emphasized aggregate emission reductions, yet major emission reduction scenarios do not sufficiently mitigate relative exposure disparities. Here, we show that without focusing on relative disparity (percent difference) in exposure, the only way to improve air quality and eliminate absolute exposure disparity is to eliminate all emissions (an unlikely outcome). We demonstrate that the relative disparity metric is ethically important and also a controllable societal feature that can reduce absolute disparity in exposure. We illustrate a range of approaches to air pollution policy that go beyond traditional emission reductions to meaningfully address exposure disparities. These strategies should be at the center of the future US environmental policy.

The brain is a metabolically vulnerable organ as neurons have both high resting metabolic rates and the need for local rapid conversion of carbon sources to ATP during activity. Midbrain dopamine neurons are thought to be particularly vulnerable to metabolic perturbations, as a subset of these are the first to undergo degeneration in Parkinson's disease, a neurodegenerative disorder long suspected to be in part driven by deficits in mid-brain bioenergetics. In skeletal muscle, energy homeostasis under varying demands is achieved in part by its ability to rely on glycogen as a fuel store, whose conversion to ATP is under hormonal regulatory control. In neurons, however, the absence of easily observable glycogen granules has cast doubt on whether this fuel store is operational, even though brain neurons express the key regulatory enzymes associated with building or burning glycogen. We show here that in primary mid-brain dopaminergic neurons, glycogen availability is under the control of dopamine autoreceptors, such that dopamine itself provides a signal to store glycogen. We find that when glycogen stores are present, they provide remarkable resilience to dopamine nerve terminal function under extreme hypometabolic conditions, but loss of this dopamine-derived signal, or impairment of access to glycogen, makes them hypersensitive to fuel deprivation. These data show that neurons can use an extracellular cue to regulate local metabolism and suggest that loss of dopamine secretion might make dopamine neurons particularly subject to neurodegeneration driven by metabolic stress.

Foxp3 regulatory T cells (Tregs) heavily infiltrate malignant tumors and restrict antitumor immunity. These tumor-infiltrating Tregs (TI-Tregs) adopt a distinct phenotype by expressing a unique set of genes. This TI-Treg gene expression signature is conserved in TI-Tregs across species and tumor types and stages, suggesting the presence of a common inducing mechanism in the tumor microenvironment (TME). However, identity of such a mechanism remains elusive. Here, we show that prostaglandin E (PGE) produced in TME directly acts on its receptor EP2/EP4 on Tregs to induce the TI-Treg phenotype. PGE added to TCR-activated Tregs induces a set of genes, many of which are included in the TI-Treg signature, in both induced Tregs (iTregs) and naturally occurring Tregs (nTregs) via EP2/EP4- cAMP-PKA pathway. Concomitantly, PGE-treated Tregs exhibit potent suppressive activity to CD8 T cells and strongly inhibit their proliferation in an EP4 dependent manner. Consistently, selective loss of EP2 and EP4 in mouse Tregs reduces expression of those genes in Tregs infiltrating Lewis lung carcinoma 1 (LLC1) mouse tumor and significantly delays the tumor progression. In human FOXP3iTregs, PGE-EP4 signaling upregulated the expression of Treg signature genes, FOXP3, CD25, and CTLA-4 as well as a typical TI-Treg signature gene, 4-1BB, and enhanced suppressive activity. Furthermore, analysis of single-cell RNA sequencing of nasopharyngeal cancer patients demonstrates preferential expression of the TI-Treg signature genes in Tregs infiltrating the tumor group compared to the tumor group. These findings suggest that PGE-EP2/EP4 signaling is one of the core mechanisms inducing the TI-Treg phenotype in TME for tumor growth.

Subduction zones transport significant amounts of water into Earth's mantle, primarily through hydrous minerals such as lawsonite. However, the seismic detectability of lawsonite-bearing oceanic crust at mantle depths remains uncertain. To address this issue, we measured sound velocities of lawsonite up to 7.4 GPa and 600 °C. Both P- and S-wave velocities exhibited unexpected increases with temperature under high-pressure conditions. Our result suggest that hydrous oceanic crust exhibits higher seismic velocities than the surrounding mantle at depths of 150 to 250 km, resulting in high-velocity anomalies rather than the previously assumed low-velocity anomalies. Furthermore, the seismic velocity difference between hydrous and dry oceanic crust is less than 2%, making it challenging to distinguish between them using seismic velocities. This limitation may hinder the detection of the hydration state in subducted crust. In addition, lawsonite remains stable in 90% of subduction zones, and thus, such "seismically invisible water" may exist in most subducted slabs around the world.

Signal transduction by histidine kinases (HKs) is nearly ubiquitous in bacterial species. HKs can either sense ligands directly or indirectly via a cognate solute-binding protein (SBP). The molecular basis for SBP-dependent signal reception, however, remains poorly understood in most cases. CBP and ChiS are the SBP-HK pair that activate the chitin utilization program of . Here, we elucidate the molecular basis for allosteric regulation of CBP-ChiS by generating structural models of this complex in the unliganded and liganded states, which we support with extensive genetic, biochemical, and cell biological analysis. Our results reveal that ligand-binding induces a large conformational interface switch that is distinct from previously described SBP-HKs. Structural modeling suggests that similar interface switches may also regulate other uncharacterized SBP-HKs. Together, these results extend our understanding of signal transduction in bacterial species and highlight an approach for uncovering the molecular basis of allostery in protein complexes.

Human norovirus (HuNoV) is the leading cause of gastroenteritis. However, the lack of a reverse genetics system for infectious HuNoV has hindered the development of antivirals and vaccines. Herein, we established a reverse genetics system for infectious HuNoV using a robust HuNoV replication system based on zebrafish embryos. Transfection of a HuNoV cDNA clone into cultured cells, followed by microinjection of the supernatant into zebrafish embryos, produced infectious recombinant HuNoVs. The recombinant HuNoVs can replicate in human intestinal organoids, confirming their infectivity in a physiologically relevant system. Notably, we also recovered recombinant HuNoVs following direct HuNoV cDNA microinjection into zebrafish embryos without the use of cultured cells, which is a simpler and more efficient approach. Using the established systems, we recovered an infectious recombinant HuNoV carrying a reporter tag insertion, enabling rapid antiviral evaluation and virus inactivation assays. Furthermore, we generated recombinant HuNoVs of the GII.17 and GII.4 genotypes, as well as a chimeric virus carrying the GII.4 VP1 gene in a GII.17 backbone, demonstrating the utility of the systems for viral replication studies. These systems will accelerate research on HuNoV replication and enhance efforts to develop vaccines and antivirals.

The mechanisms of molecular processes can be characterized by following the minimum free energy pathway (MFEP) on the underlying multidimensional conformational landscapes. Despite recent advancements in enhanced sampling algorithms, obtaining a converged high-dimensional molecular free energy landscape remains a considerable challenge. To circumvent this issue, we employ a deep multitask learning algorithm that integrates deep neural networks with the established enhanced sampling method of well-tempered metadynamics to iteratively learn the MFEP between reactant and product conformations, without the knowledge of the underlying free energy landscape. Our approach improves upon existing pathway exploration algorithms by following a simpler protocol, thereby eliminating the need to identify intermediate structures along a guess path. From the learned pathway, an automatic reconstruction of a mechanistic fingerprint can be performed by following the sequence of events in the molecular process, allowing for a direct characterization of the molecular mechanism. We demonstrate applications of our algorithm to prototypical chemical reactions, protein folding, and ligand-receptor binding problems. Due to its low computational cost and overall simplicity, this framework is expected to find widespread applications in elucidating molecular mechanisms at all-atom resolution.

The long-term climate of Earth alternates between warmer and cooler periods, for which atmospheric CO content is often viewed as a primary control. Although silicate weathering feedback governs this long-term equilibrium, the partitioning of carbonate burial between neritic and pelagic environments can influence how rapidly the carbon cycle adjusts to perturbations. The impact of neritic carbonates accumulation on oceanic calcium and alkalinity fluxes, nannoplankton productivity, and carbon reservoirs is overlooked. To investigate this role, we combine plate-tectonic reconstructions with climatic and physiographic simulations and apply a macroecological model to estimate Meso-Cenozoic neritic warm-water carbonate habitats and productivity. We find that only during the Early Cretaceous and Cenozoic did geochemical influxes exceed the carbonate accumulation potential of neritic platforms, while for most of the interval they fell short. These alternating states define two regimes: i) habitability-limited periods, where environmental conditions restrict the development of neritic carbonate factories, and ii) alkalinity-limited periods, where ocean chemistry restricts carbonate precipitation. By alternating between these regimes, neritic platforms modulate the buffering capacity and the timescales (10 to 10 years) of carbon cycle recovery and regulate the development and productivity of nannoplankton, and therefore the biological pump. This framework highlights the role of shallow-water carbonate systems as important modulators of the Earth's climate system and pelagic ecosystems.

Cardiac calcification, often seen in age-related diseases, impairs heart function, yet its association with malignant tumors remains largely overlooked. Our study revealed that pericardial calcification (PC) occurs in up to 80% of breast cancer patients with pulmonary metastasis. We demonstrate a reciprocal relationship where breast cancer drives PC, which in turn accelerates cancer progression in humans and mice. Lung metastases increase monocyte-derived macrophage and mesenchymal stem cell (MSC)-derived osteoblast infiltration in the pericardial tissue, triggering inflammation and calcification. Mechanistically, metastatic cancer cells in the lungs highly express and secrete asparagine endopeptidase (AEP), which cleaves IGF2BP3 to free IGF2. AEP and IGF2 contribute to PC by promoting osteoblast differentiation in heart tissue through integrin αvβ5 and IGF1R activation, respectively. Pharmacological blockade of integrin αvβ5 and IGF1R, especially when combined, effectively inhibits ectopic osteogenesis and disrupts the feedback loop between PC and cancer progression. These findings elucidate the interplay between metastatic breast cancer and PC and suggest therapeutic strategies to hinder breast cancer progression.