PLoS Biology最新文献

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.

Conjugative plasmids carrying antimicrobial resistance (AMR) genes are critical for the spread of AMR, due to their ability to transmit horizontally between bacterial hosts. We previously observed that during experimental evolution in the presence of abundant susceptible Escherichia coli hosts, the AMR plasmid R1 rapidly evolves variants with increased horizontal transmission due to mutations causing increased plasmid copy number. Yet AMR was progressively lost from the evolving populations. Here, we show that AMR loss was associated with evolution of streamlined plasmids in which the AMR region is spontaneously deleted, making plasmid carriage undetectable by plating on selective antibiotic-containing media. These plasmids transmit both vertically and horizontally more efficiently than the ancestral AMR plasmid, driving AMR extinction in bacterial populations and effectively acting as an intrinsic defence against AMR plasmids. A simple model of plasmid competition further shows that any horizontal or vertical transmission advantage conferred by plasmid streamlining would be enough to drive the displacement of competing AMR plasmids, with a given horizontal transmission advantage leading to faster replacement in conditions favoring horizontal transmission. Our results suggest that within-host plasmid evolution or engineered streamlined plasmids could be exploited to limit the spread of AMR in natural populations of bacteria.

The mammalian brain exhibits notable interspecies variation. Microanatomical and molecular differences in homologous neurons, those with similar locations and developmental origins across species, are best characterized in the neocortical mantle, the center of complex brain functions; however, the purpose of these differences remains unclear. We performed whole-cell microelectrode recordings along with microanatomical and molecular analyses of human fast-spiking parvalbumin (pvalb)-expressing interneurons in neocortical tissue resected during brain surgery, comparing them with similar data obtained from the mouse neocortex. The action potential (AP) firing threshold was lower in human neurons than in mouse neurons. This was due to a deficiency in low-voltage-activated inhibitory Kv1.1 and Kv1.2 potassium channels in the axon initial segment (AIS), a specialized axonal region that determines AP threshold and initiation, in human cells. In contrast, Kv1 ion channels were prominent in mouse neurons. The AIS was also moderately elongated in humans. Computational simulations of fast-spiking interneurons revealed that the human-type AIS lowers the AP threshold and shortens the time lag for AP initiation. We found that the low membrane AP firing threshold in pvalb neurons is closely linked to slow membrane potential kinetics in the soma. Thus, the human AIS supports fast in-fast out circuit function in human pvalb neurons, compensating for electrically slow somatic membrane responses. When formulating therapeutic strategies that involve fast-spiking neurons, it is crucial to take into account the molecular and functional species differences.

In most mammals, female sexual receptivity (estrus) closely coincides with ovulation, providing males with precise fertility signals. However, in some anthropoid primates living in multi-male societies, females display extended receptivity along with exaggerated sexual swellings that probabilistically indicate ovulation. This raises the question about how males successfully time mating, particularly when ovulation is difficult to predict from such signals. To address this question in bonobos, we combined daily variation in swelling size, hormonal profiles, and male mating behaviors. By estimating day-specific ovulation probabilities relative to the onset and subsidence (detumescence) of maximal swelling, we also examined how male efforts correlate with female fertility. Our results revealed that while ovulation probability was widely distributed and difficult to predict when aligned with the onset of the swelling phase, male behavior was closely aligned with the conception probability. Males concentrated mating efforts late in the phase and stopped after detumescence. High-ranking males intervened in copulations involving females with higher conception probabilities, specifically those with maximal swelling and older infants. When multiple females exhibited maximal swelling, males preferentially followed females whose maximal swelling started earlier and who had older infants. Male-male aggression increased when there were more females with maximal swelling. However, this tendency was reversed when male party size exceeded the average. Importantly, our results revealed that the low predictability of ovulation is best explained by inter- and intra-individual variation in the length of maximal swelling phase, rather than ovulation occurring randomly within that phase in bonobos. Males effectively manage such a noisy signal by prioritizing late-phase ovulatory cues and integrating reproductive history, thereby extracting usable timing information. This behavioral mechanism helps explain the persistence of conspicuous yet noisy ovulatory signals in bonobos. Since males are capable of inferring ovulation timing even under noisy conditions, selection may not favor highly precise female signals. Instead, it shifts more of the time and energy costs onto males, allowing conspicuous female traits to be maintained.