bluuebunny/crossref_metadata_2025_split huggingface dataset:
GPCRome-wide structural analysis of G-protein-coupling selectivity
Authors: Matic Marin , Miglionico Pasquale , Inoue Asuka , Raimondi Francesco 
Published: September 2022

AbstractWe present a comprehensive computational analysis of available 3D GPCR-G-protein complexes to inspect the structural determinants of G-protein-coupling selectivity.Analysis of the residue contacts at interaction interfaces has revealed a network of secondary structure elements recapitulating known structural hallmarks determining G-protein-coupling specificity, including TM5, TM6 and ICLs. We coded interface contacts into generic-number fingerprints to reveal specific coupling-determinant positions. Clustering of Gs vs Gi complexes is best achieved when considering both GPCR and G-protein contacting residues rather than separated representations of the interaction partners, suggesting that coupling specificity emerges as contextual residue interactions at the interface. Interestingly, Gs-GPCR complexes contain a higher number of contacts than Gi/o-GPCR complexes, likely caused by overall higher conservation and structural constraint on the Gs interface. In contrast, Gi/o proteins adopt a wider number of alternative docking poses on cognate receptors, as assessed via structural alignments of representative 3D complexes.Furthermore, binding energy calculations demonstrate that distinct structural properties of the complexes contribute to higher stability of Gs than Gi/o complexes. AlphaFold2 predictions of experimental binary complexes confirmed several of these structural features and allowed us to augment the structural coverage of poorly characterized complexes (e.g. G12/13).We propose that the structural properties of different G-protein complexes, such as structural restraining of Gs compared to Gi/o ones, could be instrumental in fine-tuning their activation and downstream signaling mechanisms.Highlights-Comprehensive structural bioinformatics analysis of available GPCR-G-protein complexes captures common as well as group-specific structural features responsible of receptor-G-protein recognition-Distinct contact patterns explain different docking modes of Gi/o vs Gs complexes, the latter being characterized by higher enrichment of characteristic contacts and lower structural variability suggestive of higher interface conservation.-Structural hallmarks are associated with different estimated binding energies, which mainly discriminates Gs versus Gi/o couplings, but which also point to class-dependent differences (e.g. Class A vs Class B) in binding the same transducer (Gs)
High-accuracy protein model quality assessment using attention graph neural networks
Authors: Zhang Peidong , Xia Chunqiu , Shen Hong-Bin 
Published: September 2022

AbstractGreat improvement has been brought to protein tertiary structure prediction through deep learning. It is important but very challenging to accurately rank and score decoy structures predicted by different models. CASP14 results show that existing quality assessment (QA) approaches lag behind the development of protein structure prediction methods, where almost all existing QA models degrade in accuracy when the target is a decoy of high quality. How to give an accurate assessment to high-accuracy decoys is particularly useful with the available of accurate structure prediction methods. Here we propose a fast and effective single-model QA method, QATEN, which can evaluate decoys only by their topological characteristics and atomic types. Our model uses graph neural networks and attention mechanisms to evaluate global and amino acid level scores, and uses specific loss functions to constrain the network to focus more on high-precision decoys and high-precision protein domains. On the CASP14 evaluation decoys, QATEN performs better than other QA models under all correlation coefficients when targeting averageLDDT. QATEN shows promising performance when considering only high-accuracy decoys. Compared to the embedded evaluation modules of predictedCα-RMSD(pRMSD) in RosettaFold and predictedLDDT(pLDDT) in AlphaFold2, QATEN is complementary and capable of achieving better evaluation on some decoy structures generated by AlphaFold2 and RosettaFold themselves. These results suggest that the new QATEN approach can be used as a reliable independent assessment algorithm for high-accuracy protein structure decoys.
Gills, growth, and activity across fishes
Authors: Bigman Jennifer S. , Wegner Nicholas C. , Dulvy Nicholas K. 
Published: September 2022

AbstractLife history theory argues that an organism’s maximum size and its corresponding growth rate have evolved to maximize lifetime reproductive output. The Gill Oxygen Limitation Theory suggests that in aquatic organisms, maximum size is instead constrained by the surface area of the gills, the primary site of gas exchange with the environment. A central prediction of this theory is a tight relationship among maximum size, growth, and gill surface area. Yet since this idea was first tested in the early 1980s, data availability has increased and analytical methods have advanced considerably. Here, we revisit this relationship with new data and a novel phylogenetic Bayesian multilevel modeling framework that allows us to understand how individual variation in gill surface area confers relationships of maximum size, growth, and gills across species. Specifically, we bring gill surface area into an allometric context and examine whether the gill surface area for a given body size (intercept) and the rate at which gill surface changes with size (slope), for a given species, explains growth performance -- an index integrating the life history tradeoff between growth and maximum size -- across fish species. Additionally, we assess whether variation in von Bertalanffy growth coefficients across species can be explained by gill surface area. Finally, we explore whether additional factors – here, activity and evolutionary history -- explain variation in maximum size and growth across species. Overall, we find that although a positive relationship exists among maximum size, growth, and gill surface area across fishes, it is weak. Additionally, gill surface area does not explain much variation in growth coefficients across species, especially for those that reach the same maximum size. However, we find that the activity level of a fish explains more variation in maximum size and growth across species compared to gill surface area. Our results support the idea that in fishes, growth and maximum size are not simply related to gill surface area, and that other covariates—both tractable (e.g., activity, metabolic rate, temperature) and less tractable (e.g., predation risk, resource availability, and variation)—appear to explain more variation in life history traits across species.
Mapping of the Classical Mutation rosette Highlights a Role for Calcium in Wound-induced Rooting
Authors: Modrego Abelardo , Pasternak Taras , Omary Moutasem , Albacete Alfonso , Cano Antonio , Pérez-Pérez José Manuel , Efroni Idan 
Published: September 2022

AbstractRemoval of the root system induces the formation of new roots from the remaining shoot. This process is primarily controlled by the phytohormone auxin which interacts with other signals in a yet unresolved manner. Here, we study the classical tomato mutation rosette (ro) which lacks shoot-borne roots. ro plants were severely inhibited in the formation of wound-induced roots and have reduced rates of auxin transport. We mapped ro to the tomato ortholog of the Arabidopsis thaliana BIG and the mammalians UBR4/p600. RO/BIG is a large protein of unknown biochemical function. In A. thaliana, BIG was implicated in the regulation of auxin transport and calcium homeostasis. We show that exogenous calcium inhibits wound-induced root formation in both tomato and A. thaliana ro/big mutants. Exogenous calcium antagonized the root-promoting effects of the auxin IAA, but not of 2,4-D, an auxin analog that is not recognized by the polar transport machinery, and accumulation of the auxin transporter PIN1 was sensitive to calcium levels in the ro/big mutants. Consistent with a role for calcium in mediating auxin transport, both ro/big mutants and calcium-treated wild-type plants were hypersensitive to treatment with polar auxin transport inhibitors. Subcellular localization of BIG suggests that like its mammalian ortholog, it is associated with the endoplasmic reticulum (ER). Analysis of subcellular morphology revealed that ro/big mutants exhibited disruption in cytoplasmic streaming. We suggest that RO/BIG maintain auxin flow by stabilizing PIN membrane localization, possibly by attenuating the inhibitory effect of Ca2+ on cytoplasmic streaming.
On the Geometry of Elementary Flux Modes
Authors: Wieder Frederik , Henk Martin , Bockmayr Alexander 
Published: September 2022

AbstractElementary flux modes (EFMs) play a prominent role in the constraint-based analysis of metabolic networks. They correspond to minimal functional units of the metabolic network at steady-state and as such have been studied for almost 30 years. The set of all EFMs in a metabolic network tends to be very large and may have exponential size in the number of reactions. Hence, there is a need to elucidate the structure of this set. Here we focus on geometric properties of EFMs. We analyze the distribution of EFMs in the face lattice of the steady-state flux cone of the metabolic network and show that EFMs in the relative interior of the cone occur only in very special cases. As a measure of complexity, we introduce the concept of the degree of an EFM, which is the dimension of the inclusionwise minimal face containing it. Geometric analysis can help to better understand the structure of the set of EFMs, which is important from both the mathematical and the biological viewpoint.
RNA cytometry of single-cells using semi-permeable microcapsules
Authors: Leonaviciene Greta , Mazutis Linas 
Published: September 2022

ABSTRACTAnalytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, bacteria, or other biological species. The microcapsules support sequential multi-step enzymatic reactions, and remain intact under different biochemical conditions, freezing, thawing and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.
Mechanical stimuli activate gene expression via a cell envelope stress sensing pathway
Authors: Harper Christine E. , Zhang Wenyao , Shin Jung-Ho , van Wijngaarden Ellen , Chou Emily , Lee Junsung , Wang Zhaohong , Dörr Tobias , Chen Peng , Hernandez Christopher J. 
Published: September 2022

AbstractIn tissues with mechanical function, the regulation of remodeling and repair processes is often controlled by mechanosensitive mechanisms; damage to the tissue structure is detected by changes in mechanical stress and strain, stimulating matrix synthesis and repair. While this mechanoregulatory feedback process is well recognized in animals and plants, it is not known whether such a process occurs in bacteria. InVibrio cholerae, antibiotic-induced damage to the load-bearing cell wall promotes increased signaling by the two-component system VxrAB, which stimulates cell wall synthesis. Here we show that changes in mechanical stress and strain within the cell envelope are sufficient to stimulate VxrAB signaling in the absence of antibiotics. We applied mechanical forces to individual bacteria using three distinct loading modalities: extrusion loading within a microfluidic device, compression, and hydrostatic pressure. In all three cases, VxrAB signaling, as indicated by a fluorescent protein reporter, was increased in cells submitted to greater magnitudes of mechanical loading, hence diverse forms of mechanical stimuli activate VxrAB signaling. Mechanosensitivity of VxrAB signaling was lost following removal of the VxrAB stimulating endopeptidase ShyA, suggesting that VxrAB may not be directly sensing mechanical forces, but instead relies on other factors including lytic enzymes in the periplasmic space. Our findings suggest that mechanical signals play an important role in regulating cell wall homeostasis in bacteria.Significance StatementBiological materials with mechanical function (bones, muscle, etc.) are often maintained through mechanosensitive mechanisms, in which damage-induced reductions in stiffness stimulate remodeling and repair processes that restore mechanical function. Here we show that a similar process can occur in bacteria. We find that mechanical stresses in the bacterial cell envelope (the primary load-bearing structure in bacteria) regulate signaling of a two-component system involved in cell wall synthesis. These findings suggest that the mechanical stress state within the cell envelope can contribute to cell wall homeostasis. Furthermore, these findings demonstrate the potential to use mechanical stimuli to regulate gene expression in bacteria.
Nicotinamide-N-methyltransferase is essential for SAM and 1-methylnicotinamide homeostasis in the AML12 hepatocyte cell line
Authors: Yoda Mayuko , Mizuno Rin , Izumi Yoshihiro , Takahashi Masatomo , Bamba Takeshi , Kawaoka Shinpei 
Published: September 2022

AbstractNicotinamide-N-methyltransferase (NNMT) is an enzyme that consumes S-adenosyl-methionine (SAM) and nicotinamide (NAM) to produce S-adenosyl-homocysteine (SAH) and 1-methylnicotinamide (MNAM). How much NNMT contributes to the quantity regulation of these four metabolites depends on whether NNMT is a major consumer or producer of these metabolites, which varies among various cellular contexts. Yet, whether NNMT critically regulates these metabolites in the AML12 hepatocyte cell line has been unexplored. To address this, we knock down Nnmt in AML12 cells and investigate the effects of Nnmt RNAi on metabolism and gene expression. We find that Nnmt RNAi accumulates SAM and SAH, whereas it reduces MNAM with NAM being unaltered. These results indicate that NNMT is a significant consumer of SAM and critical for MNAM production in this cell line. Moreover, transcriptome analyses reveal that altered SAM and MNAM homeostasis is accompanied by various detrimental molecular phenotypes, as exemplified by the down-regulations of lipogenic genes such as Srebf1. Consistent with this, oil-red O-staining experiments demonstrate the decrease of total lipids upon Nnmt RNAi. These results suggest that NNMT maintains proper SAM and MNAM homeostasis, providing an additional example where NNMT plays a critical role in regulating SAM and MNAM metabolism.
Physiological state matching in a pair bonded poison frog
Authors: Nowicki Jessica P. , Rodríguez Camilo , Lee Julia C. , Goolsby Billie C. , Yang Chen , Cleland Thomas A. , O’Connell Lauren A. 
Published: September 2022

AbstractMore than a century ago, Charles Darwin hypothesized that the empathy-like phenotype is a phylogenetically widespread phenomenon. This idea remains contentious, due to the challenges of empirically examining emotions, and few investigations among non-mammalian vertebrates. We provide support for Darwin’s hypothesis by discovering partial evidence for the most ancestral form of empathy, emotional contagion (i.e., matching another individual’s emotional state), in the pair bonding mimetic poison frog,Ranitomeya imitator. We found that male corticosterone, a physiological biomarker of stress, positively correlates with female partners in experimental and semi-natural conditions. This does not appear to coincide with behavioral state-matching. However, it is specific to female partners relative to familiar female non-partners, and is independent of effects that commonly confound studies on emotional contagion. Furthermore, this physiological state-matching is irrespective of partnership longevity or lifetime reproductive output. These results physiologically indicate socially selective emotional contagion in a monogamous amphibian, and paradigms that elicit coinciding neural and behavioral indicators and morphogenic co-variation are needed for further corroboration. Further studies on ancestral forms of empathy in non-mammalian vertebrates are warranted.
Dysregulation of Acid Ceramidase-mediated Sphingolipid Metabolism Contributes to Tumor Progression in Tuberous Sclerosis Complex
Authors: Astrinidis Aristotelis , Li Chenggang , Zhang Erik Y. , Zhao Xueheng , Zhao Shuyang , Guo Minzhe , Huang Rong , Zhang Alan G. , Kopras Elizabeth , Gupta Nishant , Smith Eric , Fugate Elizabeth , Lindquist Diana , Wikenheiser-Brokamp Kathryn , Setchell Kenneth D. , McCormack Francis x. , Xu Yan , Yu Jane J. 
Published: September 2022

AbstractTuberous Sclerosis Complex (TSC) is disorder of multi-system benign neoplasia in the brain, heart, kidneys and lungs. Lymphangioleiomyomatosis (LAM) is a progressive pulmonary disease affecting exclusively women. Both are caused by mutations inTSC1andTSC2, resulting in mTORC1 hyperactivation. Single cell RNA sequencing of LAM lungs identified activation of genes in the sphingolipid pathway. Independent validation studies showed that acid ceramidase (ASAH1) and dihydroceramide desaturase (DEGS1), key enzyme for regulating sphingolipid and ceramide metabolism, were significantly increased in TSC2-null cells, and their expression and activity were rapamycin-insensitive. TSC2 negatively regulated the biosynthesis of tumorigenic sphingolipids. Suppression of ASAH1 by shRNA or the inhibitor ARN14976 (17a) markedly decreased the viability of TSC2-null cells.In vivo, 17a significantly decreased the growth of Tsc2-null cell derived mouse xenografts. When combined with rapamycin, 17a more strongly inhibited the progression of renal cystadenomas inTsc2+/-mice than either agent alone, evaluated by pathology and MRI. Collectively, our studies identify a rapamycin-insensitive disorder of sphingolipid metabolism in TSC2-null cells and tumors and validate the novel hypothesis that TSC2 regulates sphingolipid production and action via ASAH1. Targeting aberrant sphingolipid metabolism pathways may have therapeutic value in TSC and LAM, and possibly in mTORC1-hyperactive neoplasms.
Cuticular wax, but not the cutin matrix, is renewed during the lifespan of Clusia rosea leaves 13CO2 labelling and gas exchange study
Authors: Kubásek Jiří , Kalistová Tereza , Janová Jitka , Askanbayeva Balzhan , Bednář Jan , Šantrůček Jiří 
Published: September 2022

SummaryThe plant cuticle, which aided the water-to-land transition of plants, provides various services to the plant surface, and its synthesis and maintenance represent substantial metabolic costs. Nevertheless, only limited information regarding cuticle dynamics is available.We determined the composition and dynamics of Clusia rosea cuticular waxes and matrix using 13CO2 labelling, compound-specific and bulk isotope ratio mass spectrometry. Collodion was used for wax collection; gas exchange techniques were employed to test for any collodion effects on living leaves.Cutin matrix (MX) area density did not vary between young and mature leaves and between leaf sides. Only young leaves incorporated new carbon into their MX. Collodion-based sampling discriminated between epicuticular (EW) and intracuticular wax (IW) effectively. EW differed in composition from IW. The newly synthetized wax was deposited in IW first and later in EW. Both young and mature leaves synthetized IW and EW; the faster dynamics in young leaves was not due to a faster synthesis rate but was the result of lower wax coverage. Longer-chain alkanes were deposited preferentially on the abaxial, stomatous leaf side, producing differences between leaf sides in wax composition.We introduce a new, sensitive isotope labelling method and demonstrate that cuticular wax is renewed during leaf ontogeny of Clusia rosea. We discuss the ecophysiological significance of the new insights.
Structure of the Monkeypox virus profilin-like protein A42R reveals potential functional differences from cellular profilins
Authors: Minasov George , Inniss Nicole L. , Shuvalova Ludmilla , Anderson Wayne F. , Satchell Karla J. F. 
Published: September 2022

The infectious disease human monkeypox is spreading rapidly in 2022, causing a global health crisis. The genomics of Monkeypox virus (MPXV) have been extensively analyzed and reported, although little is known about the virus-encoded proteome. In particular, there are no reported experimental MPXV protein structures other than computational models. Here, a 1.52 Å resolution X-ray structure of the MPXV protein A42R, the first MPXV-encoded protein with a known structure, is reported. A42R shows structural similarity to profilins, which are cellular proteins that are known to function in the regulation of actin cytoskeletal assembly. However, structural comparison of A42R with known members of the profilin family reveals critical differences that support prior biochemical findings that A42R only weakly binds actin and does not bind poly(L-proline). In addition, the analysis suggests that A42R may make distinct interactions with phosphatidylinositol lipids. Overall, the data suggest that the role of A42R in the replication of orthopoxviruses may not be readily determined by comparison to cellular profilins. Furthermore, these findings support the need for increased efforts to determine high-resolution structures of other MPXV proteins to inform physiological studies of the poxvirus infection cycle and to reveal potential new strategies to combat human monkeypox should this emerging infectious disease with pandemic potential become more common in the future.