bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outer surface lipoproteins from the Lyme disease spirochete exploit the molecular switch mechanism of the complement protease C1s
Authors: Garrigues Ryan J. , Thomas Sheila , Leong John M. , Garcia Brandon L. 
Published: August 2022

AbstractProteolytic cascades comprise several important physiological systems, including a primary arm of innate immunity called the complement cascade. To safeguard against complement-mediated attack, the etiologic agent of Lyme disease, Borreliella burgdorferi, produces numerous outer surface-localized lipoproteins that contribute to successful complement evasion. Recently, we discovered a pair of B. burgdorferi surface lipoproteins of the OspEF-related protein family – termed ElpB and ElpQ – that inhibit antibody-mediated complement activation. In this study, we investigate the molecular mechanism of ElpB and ElpQ complement inhibition using an array of biochemical and biophysical approaches. In vitro assays of complement activation show that an independently folded homologous C-terminal domain of each Elp protein maintains full complement inhibitory activity and selectively inhibits the classical pathway. Using surface plasmon resonance, Alpha bead-based technology, and C1s enzyme assays, we show that binding of Elp proteins to activated C1s blocks C4 cleavage by competing with C1s/C4 binding without occluding the active site. C1s-mediated C4 cleavage is dependent on activation-induced binding sites, termed exosites. To test whether these exosites are involved in Elp/C1s binding, we performed site-directed mutagenesis which showed that ElpB– and ElpQ-binding require C1s residues in the anion-binding exosite located on the serine protease domain of C1s. Based on these results, we propose a model whereby ElpB and ElpQ exploit activation-induced conformational changes that are normally important for C1s-mediated C4 cleavage. Our study expands the known complement evasion mechanisms of microbial pathogens and reveals a novel molecular mechanism for selective C1s inhibition by Lyme disease spirochetes.
Evolutionary analysis in Enterobacterales of the Rcs-repressor protein IgaA unveils two cytoplasmic small β-barrel domains central for function
Authors: Rodríguez Leticia , Peñalver Marcos , Casino Patricia , García-del Portillo Francisco 
Published: August 2022

ABSTRACTThe Rcs sensor system, comprised by the proteins RcsB/RcsC/RcsD and RcsF, is used by bacteria of the order Enterobacterales to withstand envelope damage. Under non-stress conditions, the system is repressed by the membrane protein IgaA. How IgaA has evolved within Enterobacterales in concert with the Rcs system has not been explored. Here, we report phylogenetic data supporting co-evolution of IgaA with the inner membrane proteins RcsC and RcsD. Functional assays showed that IgaA from representative genera as Shigella and Dickeya, but not those from Yersinia or the endosymbionts Photorhabdus and Sodalis, repress the Rcs system when expressed in a heterogenous host like Salmonella enterica serovar Typhimurium. IgaA structural features have therefore diverged among Enterobacterales. Modelling of IgaA structure unveiled one periplasmic and two cytoplasmic β-rich architectures forming partially-closed small β-barrel (SBB) domains related to OB (oligonucleotide/oligosaccharide binding motif) fold domains. Interactions among conserved residues were mapped in a connector linking SBB-1 domain of cytoplasmic region cyt1 to SBB-2 domain of region cyt2 (residues E180-R265); the C-terminus of cyt1 facing cyt2 (R188-E194-D309 and T191-H326); and, between cyt2-cyt3 regions (H293-E328-R686). These interactions identify a previously unnoticed "hybrid" SBB-2 domain. We also identified interactions absent in the IgaA variants not functional in S. Typhimurium, including H192-P249, which links cyt1 to cyt2, R255-D313 and D287-R314. A short α-helix (α6) located in the SSB-1 domain is also missing in the non-complementing IgaA tested. Taken together, our data support a central role of the two cytoplasmic SBB domains in IgaA function and evolution.SIGNIFICANCEThe "intracellular growth attenuator A" protein (IgaA) was first reported as repressor of the Rcs system in S. enterica serovar Typhimurium. IgaA orthologs were later studied in other genera and families of the Enterobacterales order, mainly in Escherichia coli. Despite intense investigation about the mechanism by which IgaA controls the Rcs system, the extent at which IgaA evolved within families of the Enterobacterales order has not been investigated. Using a combination of functional assays and in silico structural analyses, our work provides a detail map of conserved and divergent residues in IgaA representing interactions occurring in all Enterobacterales and others that may have diverged concomitantly to interacting proteins, probably for responding to specific environments. Future studies involving mutagenesis of these residues in IgaA of Enterobacterales families and genera of interest will certainly provide valuable insights into the regulation acting in the IgaA-Rcs axis.
Hypoxia truncates and constitutively activates the key cholesterol synthesis enzyme squalene monooxygenase
Authors: Coates Hudson W. , Olzomer Ellen M. , Du Ximing , Farrell Rhonda , Yang Hongyuan , Byrne Frances L. , Brown Andrew J. 
Published: August 2022

AbstractCholesterol synthesis is both energy- and oxygen-intensive, yet relatively little is known of the regulatory effects of hypoxia on pathway enzymes. We previously showed that the rate-limiting and first oxygen-requiring enzyme of the committed cholesterol synthesis pathway, squalene monooxygenase (SM), can undergo partial proteasomal degradation that renders it constitutively active. Here, we show that hypoxia is the physiological trigger for this truncation, which occurs through a two-part mechanism: (1) increased targeting of SM to the proteasomeviastabilization of the E3 ubiquitin ligase MARCHF6, and (2) accumulation of the SM substrate, squalene, which impedes the complete degradation of SM and liberates its truncated form. Truncation of SM is also increased in endometrial cancer tissues, where it correlates with levels of hypoxia-inducible factor−1α. These results uncover a feedforward mechanism that enables SM to accommodate fluctuations in substrate levels yet is also a likely contributor to its widely reported oncogenic properties.
Using developmental rules to align microevolution with macroevolution
Authors: Machado Fabio Andrade , Mongle Carrie S. , Slater Graham , Penna Anna , Wisniewski Anna , Soffin Anna , Dutra Vitor , Uyeda Josef C. 
Published: August 2022

ABSTRACTMacroevolutionary biologists have classically rejected the notion that higher level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behavior of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here, we reframe this issue by asking if using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically-informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro and macro scales, while biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor-like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution.
The CD103-XCR1 axis mediates the recruitment of immunoregulatory dendritic cells after traumatic injury
Authors: Lokwani Ravi , Ngo Tran B , DeStefano Sabrina , Adusei Kenneth M , Bhuiyan Minhaj , Josyula Aditya , Faust Mondreakest , Lin Aaron , Karkanitsa Maria , Fathi Parinaz , Sadtler Kaitlyn 
Published: August 2022

ABSTRACTDuring wounding and material implantation there is a disturbance in tissue homeostasis and release of self-antigen, and regulation between tolerance and auto-inflammation in injury is not well understood. Here, we analyzed antigen-presenting cells in biomaterial-treated muscle injury and found that pro-regenerative materials enrich Batf3-dependent CD103+XCR1+CD301b+ dendritic cells associated with cross-presentation and self-tolerance. Muscle trauma was accompanied by CD8+ iTregs and expansion of CD103+XCR1+CD62L- adaptive immune cells. Up-regulation of E-Cadherin (the ligand for CD103) and XCL-1 in injured tissue suggests a mechanism for cell recruitment to trauma. Without cross-presenting cells T cell activation increases, pro-regenerative macrophage polarization decreases, and muscle healing is impaired. These data describe a regulatory communication network through CD103+XCR1+ immune cells resulting in downstream effects on tissue regeneration.
Evaluation of tumor antigen-specific antibody responses in patients with metastatic triple negative breast cancer treated with cyclophosphamide and pembrolizumab
Authors: Routh Eric D. , Woodcock Mark G. , Serody Jonathan S. , Vincent Benjamin G. 
Published: August 2022

ABSTRACTBackgroundThe role of B cells in antitumor immunity is becoming increasingly appreciated, as B cell populations have been associated with response to immune checkpoint blockade (ICB) in breast cancer patients and murine models of breast cancer. Deeper understanding of antibody responses to tumor antigens is needed to clarify the function of B cells in determining response to immunotherapy.MethodsWe evaluated tumor antigen-specific antibody responses in patients with metastatic triple negative breast cancer treated with pembrolizumab following low dose cyclophosphamide therapy using computational linear epitope prediction and custom peptide microarrays.ResultsWe found that a minority of predicted linear epitopes were associated with antibody signal, and signal was associated with both neoepitopes and self-peptides. No association was observed between signal presence and subcellular localization or RNA expression of parent proteins. Patient-specific patterns of antibody signal boostability were observed that were independent of clinical response. Intriguingly, measures of cumulative antibody signal intensity relative to immunotherapy treatment showed that the one complete responder in the trial had the greatest increase in total antibody signal, which supports a potential association between ICB-dependent antibody boosting and clinical response. The antibody boost in the complete responder was largely driven by increased levels of IgG specific to a sequence of N-terminal residues in native Epidermal Growth Factor Receptor Pathway Substrate 8 (EPS8) protein, a known oncogene in several cancer types including breast cancer. Structural protein prediction showed that the targeted epitope of EPS8 was in a region of the protein with mixed linear/helical structure, and that this region was solvent-exposed and not predicted to bind to interacting macromolecules.ConclusionsThis study highlights the potential importance of the humoral immune response targeting neoepitopes as well as self epitopes in shaping clinical response to immunotherapy.
NBR1-mediated selective autophagy of ARF7 modulates root branching
Authors: Ebstrup E , Ansbøl J , Paez-Garcia A , Culp H , Chevalier J , Clemmens P , Coll NS , Moreno-Risueno M A , Rodriguez E 
Published: August 2022

AbstractAuxin dictates root architecture via the Auxin Response Factor (ARF) family of transcription factors, which control lateral root (LR) formation. InArabidopsis, ARF7 regulates the specification of prebranch sites (PBS) generating LRs through gene expression oscillations and plays a pivotal role during LR initiation. Despite the importance of ARF7 in this process, there is a surprising lack of knowledge about how ARF7 turnover is regulated and how this impacts root architecture. Here, we show that ARF7 accumulates in autophagy mutants and is degraded through NBR1-dependent selective autophagy. We demonstrate that the previously reported rhythmic changes to ARF7 abundance in roots are modulated via autophagy and might occur in other tissues. Additionally, we prove that the level of co- localization between ARF7 and autophagy markers oscillates and can be modulated by auxin to trigger ARF7 turnover. Furthermore, we observed that autophagy impairment prevents ARF7 oscillation and reduces both PBS establishment and LR formation. In conclusion we report a novel role for autophagy during development, namely by enacting auxin-induced selective degradation of ARF7 to optimize periodic root branching.
The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition
Authors: Subbalakshmi Ayalur Raghu , Sahoo Sarthak , Manjunatha Prakruthi , Goyal Shaurya , Kasiviswanathan Vignesh A , Yeshwanth M , Soundharya R , McMullen Isabelle , Somarelli Jason A. , Jolly Mohit Kumar 
Published: August 2022

AbstractEpithelial-mesenchymal plasticity (EMP) involves bidirectional transitions between epithelial, mesenchymal and multiple intermediary hybrid epithelial/mesenchymal phenotypes. While the process of epithelial-mesenchymal transition (EMT) and its associated transcription factors are well-characterised, the transcription factors that promote mesenchymal-epithelial transition (MET) and stabilise hybrid E/M phenotypes are less well understood. Here, we analyse multiple publicly-available transcriptomic datasets at bulk and single-cell level and pinpoint ELF3 as a factor that is strongly associated with an epithelial phenotype and is inhibited during EMT. Using mechanism-based mathematical modelling, we also show that ELF3 inhibits the progression of EMT, suggesting ELF3 may be able to counteract EMT induction, including in the presence of EMT-inducing factors, such as WT1. Our model predicts that the MET induction capacity of ELF3 is stronger than that of KLF4, but weaker than that of GRHL2. Finally, we show that ELF3 levels correlates with worse patient survival in a subset of solid tumor types, suggesting cell-of-origin or lineage specificity in the prognostic capacity of ELF3.
Inflation induced motility for long-distance vertical migration
Authors: Larson Adam G. , Chajwa Rahul , Li Hongquan , Prakash Manu 
Published: August 2022

AbstractThe daily vertical migrations of plankton play a crucial role in shaping marine ecosystems and influencing global biogeochemical cycles. They also form the foundation of the largest daily biomass movement on Earth. Surprisingly, amongst this diverse group of organisms, some single cell protists transit these depths exceeding 50 meters without employing flagella or cilia, and the underlying mechanisms remain poorly understood. It has been previously proposed that this capability relies on the cell’s ability to regulate its internal density relative to seawater. Here, usingPyrocystis noctilucaas a model system, we demonstrate the primary mechanism for this density control is a rapid cellular inflation event, during which a single plankton cell expands its volume six-fold in less than 10 minutes. This self-regulated cellular inflation selectively imports fluid less dense than surrounding seawater, and can effectively sling-shot a cell and reverse sedimentation within minutes. This ability is made possible by a reticulated cytoplasmic architecture inPyrocystis noctilucathat enables this rapid increase in overall cell volume without dilution of its cytoplasmic content. We further present a generalized mathematical framework that unifies cell cycle driven density regulation, stratified ecology, and associated cell behavior in the open ocean. Our study unveils an ingenious strategy employed by non-motile plankton to evade the gravitational sedimentation trap, highlighting how precise control of cell size was essential for survival in the ocean.
Structural analyses of the plant PRT6-UBR box in the Cys-Arg/N-degron pathway and insights into the plant submergence response
Authors: Kim Leehyeon , Lin Chih-Cheng , Lin Ting-Jhen , Cao Yan-Cih , Chen Min-Chun , Chou Mei-Yi , Lin Wen-Hsuan , Kim Minki , Wu Jian-Li , Shih Ming-Che , Song Hyun Kyu , Ho Meng-Chiao 
Published: August 2022

AbstractThe submergence response in higher plants is highly dependent on the protein stability of group VII ethylene response factors, which are primarily degraded through the oxygen-dependent Cys-Arg branch of the N-degron pathway of targeted proteolysis. Knockout of PRT6, an E3 ligase and a vital component of the N-degron pathway, improves submergence tolerance in Arabidopsis and barley but is associated with side effects such as germination deficiency. In this study, we determined structures of rice and Arabidopsis PRT6-UBR box in complex with various Arg/N-degron related peptides. We identified two highly conserved motifs in the plant PRT6-UBR box, which is responsible for Cys-Arg/N-degron recognition. Structural and mutagenesis studies revealed the importance of two conserved motifs for Cys-Arg/N-degron recognition. The phenotype of Arabidopsis seedlings with PRT6-UBR mutants in these newly identified conserved motifs showed superior submergence survival suggesting that rational manipulation of the PRT6-UBR box can improve flood tolerance. Our results provide an engineering platform for generating crops with improved submergence tolerance.
Dynamics and length distributions of microtubules with a multistep catastrophe mechanism
Authors: Schwietert Felix , Heydenreich Lina , Kierfeld Jan 
Published: August 2022

AbstractRegarding the experimental observation that microtubule catastrophe can be described as a multistep process, we extend the Dogterom–Leibler model for dynamic instability in order to discuss the effect that such a multistep catastrophe mechanism has on the distribution of microtubule lengths in the two regimes of bounded and unbounded growth. We show that in the former case, the steady state length distribution is non-exponential and has a lighter tail if multiple steps are required to undergo a catastrophe. If rescue events are possible, we detect a maximum in the distribution, i.e., the microtubule has a most probable length greater than zero. In the regime of unbounded growth, the length distribution converges to a Gaussian distribution whose variance decreases with the number of catastrophe steps. We extend our work by applying the multistep catastrophe model to microtubules that grow against an opposing force and to microtubules that are confined between two rigid walls. We determine critical forces below which the microtubule is in the bounded regime, and show that the multistep characteristics of the length distribution are largely lost if the growth of a microtubule in the unbounded regime is restricted by a rigid wall. All results are verified by stochastic simulations.
Recombinant reporter phage rTUN1::nLuc enables rapid detection and real-time antibiotic susceptibility testing of Klebsiella pneumoniae K64 strains
Authors: Braun Peter , Raab Rene , Bugert Joachim J , Eckstein Simone 
Published: August 2022

AbstractThe emergence of multi drug resistant (MDR) Klebsiella pneumoniae (Kp) strains constitutes an enormous threat to global health as MDR associated treatment failure causes high mortality rates in nosocomial infections. Rapid pathogen detection and antibiotic resistance screening is therefore crucial for successful therapy and thus, patient survival. Reporter phage-based diagnostics offer a way to speed up pathogen identification and resistance testing, as integration of reporter genes into highly specific phages allow real-time detection of phage replication and thus, living host cells. Kp specific phages use the host’s capsule, a major virulence factor of Kp, as receptor for adsorption. To date, 80 different Kp capsule types (K-serotypes) have been described with predominant capsule types varying between different countries and continents. Therefore, reporter phages need to be customized according to the locally prevailing variants. Recently, we described the autographivirus vB_KpP_TUN1 (TUN1), which specifically infects Kp K64 strains, the most predominant capsule type at the military hospital in Tunis (MHT) that is also associated with high mortality rates. In this work, we developed the highly specific recombinant reporter phage rTUN1::nLuc, which produces Nanoluciferase (nLuc) upon host infection and thus, enables rapid detection of Kp K64 cells in clinical matrices such as blood and urine. At the same time, rTUN1::nLuc allows for rapid antibiotic susceptibility testing and therefore identification of suitable antibiotic treatment in less than 3 hours.
The pro-inflammatory response to influenza A virus infection is fueled by endothelial cells
Authors: Bauer Lisa , Rijsbergen Laurine C. , Leijten Lonneke , Benavides Feline F. W. , Noack Danny , Lamers Mart M. , Haagmans Bart. L. , de Vries Rory D. , de Swart Rik L. , van Riel Debby 
Published: August 2022

AbstractMorbidity and mortality from influenza are associated with high levels of systemic inflammation. Endothelial cells have been shown to play a key role in this systemic inflammatory response during severe influenza A virus (IAV) infections, despite the fact that these are rarely infected in humans. However, how endothelial cells contribute to these systemic inflammatory responses is unclear. To investigate this, we developed a transwell-system in which airway organoid-derived differentiated human lung epithelial cells at the apical side were co-cultured with primary human lung microvascular endothelial cells (LMEC) at the basolateral side. We compared the susceptibility of endothelial cells to pandemic H1N1 virus isolated in 2009 and seasonal H1N1 and H3N2 virus isolated in 2019, and assessed the associated immune responses. Despite the detection of IAV nucleoprotein in LMEC monocultures, there was no evidence for productive infection. In epithelial-endothelial co-cultures, abundant IAV infection of epithelial cells resulted in the breakdown of the epithelial barrier, but infection of LMECs was rarely detected. Furthermore, we observed a significantly higher secretion of pro-inflammatory cytokines in LMECs when co-cultured with IAV-infected epithelial cells, compared to LMEC monocultures exposed to IAV. Taken together, our data show that endothelial cells are abortively infected by IAV, but can fuel the inflammatory response. As endothelial cells are a prominent cell type in the lung, it is possible that they play an important role in the systemic inflammatory response during IAV infections.