BIOCHEMISTRY
Mapping proteolytic neo-N termini at the surface of living cells
Fluorescence image of HEK293T cells expressing subtiligase-TM. Subtiligase-TM expression is shown in red, cell surface labeling activity is shown in green, and the overlap between the two is shown in yellow.
Proteolysis of cell surface proteins is an important regulatory mechanism that remodels cells during differentiation and proliferation and is dysregulated in diseases such as cancer. To help uncover targets of proteolysis and identify their specific cleavage sites, Amy Weeks et al. developed a technique for N terminomics that uses an engineered peptide ligase—subtiligase—to specifically biotinylate N termini for enrichment and analysis by mass spectrometry. Noting that the low abundance of plasma membrane proteins limits N terminomics at the cell surface, the authors developed a strategy that tethers subtiligase to the membranes of living cells by fusing it to a transmembrane helix called subtiligase-TM. Using the technique, the authors identified 807 cell-surface N termini, most of which had not been previously described, and quantified changes in events during proteolytic remodeling of the cell surface proteome. The authors shared the data via an online atlas termed Atlas of Subtiligase-Captured Extracellular N Termini (ASCENT) to enable data access for the research community. Identifying neoepitopes created by cell surface proteolysis can help reveal new biomarkers and therapeutic targets for cancer and other diseases, according to the authors. — T.J.
PNAS e2018809118 (2021)
BIOCHEMISTRY
Mobile interface between monomers in dimeric ATP synthase
Rows of dimeric ATP synthase complexes (orange), actively making adenosine triphosphate to sustain life, mold themselves to the tips of the folds of the cristae (in grey) in the inner membranes of mitochondria by adjusting the way that the dimeric enzyme complexes are in contact with each other.
Lodged in the inner membranes of mitochondria, molecular machines known as ATP synthase work like rotary motors to synthesize ATP. These dimeric complexes comprise long rows of paired, V-shaped monomers that protrude at an angle relative to one another into the mitochondrial matrix. Tobias Spikes et al. used cryo-electron microscopy to analyze purified, dimeric bovine ATP synthase and report that the angle between the central rotatory axes of the monomeric complexes ranges between approximately 76° and 95°. The analysis also reveals that the protein-lipid monomer-to-monomer connections in dimeric ATP synthase are not static, but change to accommodate rocking motions associated with rotary ATP catalysis as well as noncatalytic structural changes. This dynamic structural malleability suggests that ATP synthases can mold themselves to accommodate a variety of oligomeric arrangements while maintaining their critical ability to synthesize ATP, the primary energy source for most cellular functions. According to the authors, the study demonstrates that tomography can reveal valuable molecular details about how dimers of ATP synthases interact in mammalian mitochondria as well as in other species. — T.J.
PNAS e2021012118 (2021)
SOCIAL SCIENCES
COVID-19 and socioeconomic inequality
The Great Recession of 2007–2009 exacerbated socioeconomic inequities experienced by racial and ethnic minorities and those without college degrees. Given the high unemployment levels reported during the early stages of the COVID-19 pandemic, concern about the pandemic’s potential to similarly widen socioeconomic inequality exists. Brea Perry et al. used data from a representative survey of nearly 1,000 Indiana residents, conducted before and during the pandemic, to assess the pandemic’s impact on economic precarity. The authors measured four self-reported indicators of economic precarity: housing insecurity, food insecurity, general financial insecurity, and unemployment or job loss. After controlling for prepandemic status, Black respondents reported significantly higher rates of food and financial insecurity and unemployment due to the pandemic, compared with White respondents. Respondents without a college degree reported significantly higher rates of all economic precarity measures than respondents with at least a bachelor’s degree. Women were more likely to report housing and financial insecurity than men, whereas younger respondents were more likely than older respondents to report food and financial insecurity and unemployment. The results are consistent with the aftermath of other disasters, suggesting that vulnerable groups disproportionately bear the burden of such disasters, leading to long-term inequalities, according to the authors. — B.D.
PNAS e2020685118 (2021)
AGRICULTURAL SCIENCES
Targeting gene network that controls flowering time could improve soybean yield
Soybean is a major global crop, providing more than 25% of the world’s protein to humans and livestock. Similar to other plants, soybean has a circadian clock that controls flowering time—one of the most important determinants of crop yield—but the underlying molecular mechanisms are not completely understood. Tiantian Bu, Sijia Lu, Kai Wang, Lidong Dong, et al. addressed this knowledge gap, showing that proteins called LUX1, LUX2, and J interact with one another in the nucleus of soybean cells to form a circadian evening complex that regulates flowering time. Specifically, this protein complex inhibits the transcription of a flowering-repressor gene called E1. Compared to wild-type soybean, mutants with inactivated LUX1 and LUX2 genes began to flower 11 weeks later and had an extended growth period under natural short-day conditions. Taken together, the findings suggest that the J–LUX protein complex suppresses E1 expression, leading to undesirably early flowering and reduced overall yield potential in short-day environments. According to the authors, plant breeding or gene-editing techniques targeting this pathway could be leveraged to develop high-yielding soybean varieties that can better adapt to different latitudes. — J.W.
PNAS e2010241118 (2021)
CELL BIOLOGY
Reprogramming stem cell-derived epithelial cells into a suitable BBB model
hPSC-derived epithelial cells misidentified as brain microvascular endothelial cells reprogram to an endothelial fate and acquire vascular markers (PECAM1 and CDH5) upon overexpression of ETS transcription factors.
Directed differentiation of human pluripotent stem cells (hPSCs) promises to improve disease modeling and facilitate drug discovery. Although stem cells produced from pluripotent sources in vitro must match their target in vivo cells as closely as possible, current comparisons often amount to simple qualitative analyses. Using a transcriptomic meta-analysis supported by physiological studies, Tyler Lu et al. detail the cellular identity of an established line of human pluripotent stem cell-derived induced Brain Microvascular Endothelial Cells (iBMECs), currently in use as a reliable model of the human blood–brain barrier (BBB) for drug screening and disease modeling. The authors reveal that the iBMECs lack key vascular lineage genes and functional attributes of brain microvascular endothelial cells that can form a BBB, corresponding instead to a homogenous epithelial cell population that is unsuitable as a model for the human BBB. However, the authors show that overexpressing three ETS transcription factors—ETV2, ERG, and FLI1—rescues the stems cells’ vascular fate by providing them with an endothelial transcriptomic signature and instilling key endothelial functions. According to the authors, the data suggest that the latest technologies should be used to characterize stem cell-derived products as a matter of course. — T.J.
PNAS e2016950118 (2021)
GENETICS
Fossil evidence for late arrival of modern humans to southern China
Geological dating techniques produce incorrect age estimates for human fossils.
Genetic studies suggest that anatomically modern humans migrated from Africa approximately 65,000 to 45,000 years ago, supporting the late dispersal hypothesis. Based on fossil evidence from caves in southern China, some paleoanthropologists have instead proposed that anatomically modern humans settled in the region between 120,000 and 70,000 years ago. To address this controversy, Xue-feng Sun, Shao-qing Wen, et al. took a comprehensive approach, combining ancient DNA analysis and multiple geological dating methods to estimate the age of human remains in five caves in southern China. Ancient DNA analysis and direct carbon-14 dating of teeth from two caves suggest that the remains date to later than 16,000 years ago, in contrast to the early dispersal hypothesis. On the other hand, uranium–thorium dating and optically stimulated luminescence dating of sediment samples from the same layer containing the human teeth produced incorrect estimates ranging from 302,000 to 90,000 years ago. According to the authors, the study highlights the importance of directly applying ancient DNA analysis and carbon-14 dating to human remains to accurately estimate their age and establish the timing of key events in human evolution. — J.W.
PNAS e2019158118 (2021)
PSYCHOLOGICAL AND COGNITIVE SCIENCES
Changing personality traits via digital interventions
Personality traits are malleable through adulthood. However, it is unclear whether personality traits can be changed through nonclinical psychological interventions. Mirjam Stieger et al. deployed a 3-month digital personality change intervention in a randomized, controlled trial of 1,523 participants aged 18 years or older. Accessible via a smartphone app, the intervention included elements of behavioral and resource activation—which targets increases in novel and desired behaviors and capitalizes on existing strengths and skills—psychoeducation, self-reflection, and progress feedback. The majority of participants indicated that they wanted to decrease their neuroticism, increase their conscientiousness, or increase their extraversion. Compared with participants on the control group who did not receive the intervention during the first month of the study, participants in the intervention group reported greater success in meeting their change goals. Close associates of the participants, such as friends and family members, detected trait changes for participants wanting to increase a trait but not for those wanting to decrease a trait. Trait changes reported by both participants and their close associates persisted 3 months after the intervention ended. The findings suggest that personality traits can be changed through interventions in nonclinical samples, according to the authors. — M.S.
PNAS e2017548118 (2021)
ENVIRONMENTAL SCIENCES
COVID-19 transmission on the Diamond Princess cruise ship
The Diamond Princess cruise ship was the site of a major COVID-19 outbreak in early 2020. Image credit: Wikimedia Commons/mstk east, licensed under CC BY 2.0.
Data on the relative importance of various pathways for COVID-19 transmission remain limited. However, several lines of evidence suggest the importance of transmission via small aerosols that can remain suspended in air and travel long distances. Parham Azimi et al. modeled COVID-19 transmission aboard the Diamond Princess cruise ship, which experienced a major COVID-19 outbreak in early 2020, to evaluate the relative contributions of various transmission pathways. Based on the model’s results, the authors estimated that short-range, long-range, and fomite transmission modes each contributed to 30–35% of overall disease transmission in this case study. Aerosols smaller than approximately 10 µm, which use all three modes of transmission, contributed to more than half of overall transmission. Both large droplets and small aerosols contributed equally to transmission before passengers were quarantined, whereas small aerosols dominated transmission postquarantine. The results underscore the importance of measures to control small-aerosol inhalation in addition to existing measures to control large-droplet and fomite transmission. According to the authors, similar methods could be applied to assess disease transmission risk in other indoor environments and for other airborne infectious diseases. — B.D.
PNAS e2015482118 (2021)
IMMUNOLOGY
Host defenses signal Salmonella to hijack immune cells, spur disease
Salmonella bacteria (red and green) invade a macrophage (blue nucleus and red cytoplasm). Recent work suggests the bacteria sense a cell’s defensive compounds as part of a key infection step. Image credit: Camilla Ciolli Mattioli.
Posted on February 12, 2021
Amy McDermott
Immune cells attack dangerous bacteria by engulfing them and then releasing a cascade of defense molecules. But some bacteria, known as intracellular pathogens, have evolved to survive this onslaught and replicate inside immune cells. The result can be Salmonella poisoning or even tuberculosis. A recent study in Science reveals that these sneaky intracellular bacteria know when to defend themselves, multiply, and cause disease by sensing the very compounds that the attacking immune cell releases. Accumulation of the molecule succinate in particular informs Salmonella enterica serovar Typhimurium that it’s inside an immune cell, explains senior author Roi Avraham, a host–pathogen biologist at the Weizmann Institute of Science, in Rehovot, Israel. Continue Reading⇒