PLoS Biology最新文献

Brain aging can cause cognitive and motor disabilities which often correlate with changes in dendritic branch, axon collateral, and synapse numbers. However, from invertebrates to mammals, age-related decline is typically restricted to specific neuron types or brain parts, indicating differential vulnerability. The rules to pinpoint the susceptibility of distinct brain elements to aging remain largely unknown. Here, we combine longitudinal studies with neuroanatomical, electrophysiological, and optophysiological analyses in the Drosophila genetic model to identify aging-susceptible and aging-resilient elements in a sensorimotor circuit that underlies escape. Young and mid-aged flies escape predator-like visual stimuli with a jump followed by flight, but behavioral performance declines with age. Mapping the underlying functional decline into the brain shows that most circuit components are robust against aging and remain functional even in old flies that have lost the behavior. By contrast, behavioral decline is caused by the selective decay of synaptic transmission between one specific visual projection neuron type (LC4) and the dendrite of one identified descending neuron (GF). Structurally, presynaptic active zone marker density is reduced whereas postsynaptic marker density remains normal. Other central synapses in this circuit as well as neuromuscular synapses are robust to aging. The synaptic connection susceptible to aging is also the circuit element most vulnerable to starvation or oxidative stress. Moreover, the vulnerable circuit element is also required for habituation, and thus, underlying circuit plasticity. In conjunction with data from mammalian brains our data suggest that a trade-off for functional neural circuit plasticity might be vulnerability to aging.

Single-cell RNA sequencing (scRNA-seq) requires high sensitivity, throughput, and broad compatibility across specimens. Current high-capacity methods lack sensitivity compared to low-capacity counterparts. Moreover, tissue-specific methods for collecting cells/nuclei limit unbiased comparisons across samples. Here, we propose a Unified framework by Split-Pool barcoding with optimal-efficiency PolydeoxyAdenylation for scRNA detection (USPPAR). Using short and long dsDNA substrates, low Co²⁺ concentration, while eliminating all other metal-ion components, enabled terminal deoxynucleotide transferase to efficiently polydeoxyadenylate intractable blunt and 3' recessed dsDNA ends, which was unattainable with other systems. By benchmarking against six state-of-the-art technologies using HEK293, the efficient addition of PCR handles for cDNA amplification made USPPAR's gene detection sensitivity comparable to high-sensitivity methods and significantly higher than existing high-cell-capacity platforms. In primary PBMCs, USPPAR enabled high-sensitivity, high-resolution scRNA-seq, and lysine conjugation improved sensitivity as an RNase inactivator. Based on nuclease reporter and mRNA protection assays, partially chelated Cu²⁺ served as a potent, non-precipitating, broad-spectrum nuclease inhibitor across various pH levels. Beyond demonstrating high sensitivity in liver tissue, an organ with low nuclease activity, single-nucleus RNA sequencing (snRNA-seq) with this inhibitor enabled one-pot extraction of RNA-stable nuclei from nuclease-rich tissues, such as the pancreas. Finally, comparisons with reference datasets from the 10× platform using mouse spleen and maize tissues showed that USPPAR matched cell-type coverage while achieving higher gene-detection efficiency. With five key enzymes available and quality-controlled, USPPAR provides a unified, cost-effective, sensitive method for high-cell-capacity scRNA profiling of diverse specimens without special equipment.

Despite early assumptions of neutrality, numerous mechanisms are now thought to cause selection on synonymous mutations, commonly supported by a low evolutionary rate at synonymous sites (Ks). This has been best evidenced in the first ~10 codons of genes in E. coli, where Ks is less than around half that of the gene body. Diverse lines of evidence support the hypothesis that these first ~10 codons are under selection for high AT content which causes low mRNA stability that in turn enables ribosomal initiation. There remains one enigmatic discrepancy, however, namely that the low Ks domain extends far beyond the first 10 codons. Here we ask why this is. As we see no evidence that the zone influencing protein levels has been misestimated, we consider three further hypotheses: that reduced Ks is a) owing to overlapping genes, b) reflects an extended slow translational "ramp," and c) is mutational. We reject the first two as in both E. coli and Bacillus sp. the extended low Ks domain persists on analysis of non-overlapping genes and in Bacillus, where fast optimal codons tend to be A/T-ending, a fast-to-slow codon trend is seen. We fail to falsify the third hypothesis. Employing mutation accumulation data for E. coli we show that the 5' end has a lower mutation rate, with the first 10 codons having a rate around half that of the gene body, this then steadily increasing following the trend seen for Ks. Compositional variation is likely to explain some of the difference, the 5' end lacking GC-rich runs while these are most mutagenic. We conclude that even a highly reduced Ks is not always adequate to substantiate selection on synonymous mutations. This result has broad implications for inference of the causes of evolutionary rate variation.

Red blood cell production is one of the most dynamic processes, yet the underlying mechanisms responsible are only partially understood. A new study in PLOS Biology suggests a broadly applicable mechanism able to balance the maintenance of the steady-state and effective stress response.

The liver's regenerative capacity is underscored by the plasticity potential of adult hepatocytes. In this context, hepatocyte-to-cholangiocyte transdifferentiation (HCT) has been ascribed with pro-regenerative functions in animal models and is a feature of end-stage human chronic liver diseases. While dampened activities of hepatocyte identity transcription factors (TFs) underlay HCT, how the cholangiocyte transcriptional program is implemented is poorly defined. Here, we identify that HCT does not involve transitioning through a hepatoblast-like transcriptional program. Furthermore, we show that HCT primarily involves induction of the archetypal transcriptional program of monopolarized epithelial cells initially repressed in hepatocytes. Indeed, HCT requires relieving H3K27me3-mediated and polycomb-dependent epigenetic silencing of epithelial TF encoding genes including Grainyhead Like Transcription Factor 2 (GRHL2). Ectopic expression of GRHL2 in hepatocytes, including in vivo in the adult mouse liver, induces epithelial genes reminiscent of those activated during HCT. Finally, GRHL2 is detected in human hepatocytes undergoing HCT as evidenced using samples from end-stage chronic liver diseases. Hence, HCT is a process chiefly characterized by induction of a conventional epithelial transcriptional program originally lacking in hepatocytes promoted by derepression of the master epithelial TF GRHL2.

Variants in the protein kinase CDKL5 cause CDKL5 Deficiency Disorder (CDD), a severe neurodevelopmental condition characterized by seizures, developmental delay, and intellectual disability. The Chlamydomonas homolog of CDKL5, LF5, is a flagellar protein whose loss leads to elongated flagella. Here, we combine live-cell imaging, immunofluorescence, and biochemical approaches including mass spectrometry to define how CDKL5 activity is regulated and how its loss alters ciliary function. We find that Chlamydomonas CDKL5 is activated by LF2, a cyclin-dependent kinase, through phosphorylation of its activation loop. This activation controls CDKL5 localization in steady-state cilia, down-regulates its IFT-mediated transport as flagella reach steady-state, controls ciliary abundance of IFT proteins, and controls phosphorylation of the tubulin-binding domain of IFT74, thereby influencing flagellar length. Mouse Cdkl5 shows similar properties: it localizes within cilia, its loss leads to ciliary elongation, and its localization depends on both its kinase activity and Cdk20, the mammalian ortholog of LF2. These results extend our understanding of ciliary length control, challenge the prevailing model that CDKL5 is activated by autophosphorylation, and suggest that CDD pathogenesis arises, at least in part, from disruption of this conserved ciliary regulatory pathway.

The Klebsiella pneumoniae species complex inhabits a wide variety of hosts and environments, and is a major cause of antimicrobial resistant infections. Genomics has revealed the population comprises multiple species/sub-species and hundreds of distinct co-circulating sub-lineage (SLs) that are associated with distinct gene complements. A substantial fraction of the pan-genome is predicted to be involved in metabolic functions and hence these data are consistent with metabolic differentiation at the SL level. However, this has so far remained unsubstantiated because in the past it was not possible to explore metabolic variation at scale. Here, we used a combination of comparative genomics and high-throughput genome-scale metabolic modeling to systematically explore metabolic diversity across the K. pneumoniae species complex (n = 7,835 genomes). We simulated growth outcomes for each isolate using carbon, nitrogen, phosphorus, and sulfur sources under aerobic and anaerobic conditions (n = 1,278 conditions per isolate). We showed that the distributions of metabolic genes and growth capabilities are structured in the population, and confirmed that SLs exhibit unique metabolic profiles. In vitro co-culture experiments demonstrated reciprocal commensalistic cross-feeding between SLs, effectively extending the range of conditions supporting individual growth. We propose that these substrate specializations may promote the existence and persistence of co-circulating SLs by reducing nutrient competition and facilitating commensal interactions. Our findings have implications for understanding the eco-evolutionary dynamics of K. pneumoniae and for the design of novel strategies to prevent opportunistic infections caused by this World Health Organization priority antimicrobial resistant pathogen.

The molecular basis of endospore formation in the model gram-positive bacterium Bacillus subtilis has been investigated for over half a century. Here, using high throughput and classical genetic approaches, we performed a comparative analysis of sporulation in the human pathogen Bacillus anthracis. A transposon-sequencing screen identified >150 genes required for B. anthracis sporulation. As anticipated, many of the genes that are critical for sporulation in B. subtilis were also required for B. anthracis sporulation. However, we identified >50 genes that are important for sporulation in B. anthracis but not in B. subtilis, and 22 B. anthracis sporulation genes that are absent from the B. subtilis genome. To validate the hits from our screen, we generated an ordered transposon-mutant library using Knockout Sudoku. Cytological analysis of a subset of the canonical sporulation-defective mutants revealed similar but not identical phenotypes in the pathogen compared to the model. We investigated several of the newly identified sporulation genes, with an in-depth analysis of one, ORF 04167, renamed ipdA. Sporulating cells lacking ipdA are blocked in the morphological process of engulfment, generating septal bulges. An AlphaFold-Multimer screen and a classical genetic enrichment revealed that IpdA is a secreted inhibitor of the polysaccharide deacetylase PdaN. Our data support a model in which induction of IpdA at the onset of sporulation inhibits deacetylation of the cell wall peptidoglycan (PG), enabling the sporulation-specific PG hydrolases to catalyze engulfment. Altogether, our studies reveal that B. subtilis is an excellent model for endospore formation in B. anthracis, while underscoring the importance of direct analysis in B. anthracis. The suite of tools that we have generated will catalyze the molecular dissection of sporulation and other cell biological processes in this important human pathogen.

Red blood cell production is regulated by erythropoietin (Epo), maintaining tissue oxygen tension in the steady state and in response to stress. To date, only a handful of factors other than Epo are known to stimulate erythropoiesis, limiting therapeutic options. We recently found that IL-17, a pleiotropic pro-inflammatory cytokine, interacts synergistically with Epo to increase formation of erythroid colonies in vitro. Here, we administered IL-17 to mice to determine whether it accelerates erythropoiesis in vivo. We found that while IL-17 alone had little effect on erythroid and other hematopoietic lineages, combined treatment with both IL-17 and Epo generated a specific and strong synergistic response in erythroid progenitors that significantly increased erythropoietic rate. IL-17 administration also accelerated the erythropoietic response of mice to hypoxia. Single-cell transcriptomic analysis showed that IL-17 acts by sensitizing erythroid progenitors to Epo, rather than through a distinct transcriptional response. Using a dynamical model, we propose that this mechanism optimizes conflicting requirements in the regulation of erythropoiesis, balancing the need for low-cost maintenance of the steady state, with a sufficiently fast stress response. Further, our findings suggest a potentially broadly applicable mechanism whereby pleiotropic cytokines are able to exert lineage-specific effects when their actions are dependent on synergism with lineage-specific factors.

Introgression between species has the potential to shape evolutionary trajectories in important ways, but uncovering complex introgression dynamics has only recently been made possible by advances in genomics. Warblers of the avian family Parulidae exemplify rapid diversification and sexual trait divergence, and we endeavored to study historical introgression in the family. We sequenced multiple genomes of nearly every species, constructed a phylogeny for the family, and investigated gene flow across the genome and at genes known for controlling feather color. We found that DNA haplotypes including the gene BCO2, which encodes an enzyme that degrades yellow carotenoids, have spread among genera multiple times-from Vermivora to Geothlypis and from Leiothlypis to multiple Cardellina and Setophaga species. Patterns of inheritance in the latter case point to introgression that occurred 0.5 to 2 million years ago, and the shared haplotype among recipient species is less than 100 nucleotides long. Separately, we found evidence of introgression from red Cardellina species to both of the two red Myioborus species at BDH1L and from one red Myioborus species to the other at CYP2J19; both are key genes in the pathway that converts yellow carotenoids to red ketocarotenoids. Our results show that introgression is a common mechanism for the evolution of colorful plumage in parulid warblers and hint at complex histories of gene flow behind some of the Western Hemisphere's most colorful birds.