Nat Commun. 2023 Apr 19;14(1):2233. doi: 10.1038/s41467-023-37839-5.

ABSTRACT

Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the D-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arabinogalactan-degrading activities and identified four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using one of these isolates with exo-D-galactofuranosidase activity, we generated enriched D-arabinan and used it to identify a strain of Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan, including members of the DUF2961 family (GH172) and a family of glycoside hydrolases (DUF4185/GH183) that display endo-D-arabinofuranase activity and are conserved in mycobacteria and other microbes. Mycobacterial genomes encode two conserved endo-D-arabinanases with different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.

PMID:37076525 | DOI:10.1038/s41467-023-37839-5

Nat Commun. 2023 Apr 19;14(1):2222. doi: 10.1038/s41467-023-37958-z.

ABSTRACT

Variational autoencoders are unsupervised learning models with generative capabilities, when applied to protein data, they classify sequences by phylogeny and generate de novo sequences which preserve statistical properties of protein composition. While previous studies focus on clustering and generative features, here, we evaluate the underlying latent manifold in which sequence information is embedded. To investigate properties of the latent manifold, we utilize direct coupling analysis and a Potts Hamiltonian model to construct a latent generative landscape. We showcase how this landscape captures phylogenetic groupings, functional and fitness properties of several systems including Globins, β-lactamases, ion channels, and transcription factors. We provide support on how the landscape helps us understand the effects of sequence variability observed in experimental data and provides insights on directed and natural protein evolution. We propose that combining generative properties and functional predictive power of variational autoencoders and coevolutionary analysis could be beneficial in applications for protein engineering and design.

PMID:37076519 | DOI:10.1038/s41467-023-37958-z

Nat Commun. 2023 Apr 19;14(1):2230. doi: 10.1038/s41467-023-37661-z.

ABSTRACT

Despite the increasing use of genomic sequencing in clinical practice, the interpretation of rare genetic variants remains challenging even in well-studied disease genes, resulting in many patients with Variants of Uncertain Significance (VUSs). Computational Variant Effect Predictors (VEPs) provide valuable evidence in variant assessment, but they are prone to misclassifying benign variants, contributing to false positives. Here, we develop Deciphering Mutations in Actionable Genes (DeMAG), a supervised classifier for missense variants trained using extensive diagnostic data available in 59 actionable disease genes (American College of Medical Genetics and Genomics Secondary Findings v2.0, ACMG SF v2.0). DeMAG improves performance over existing VEPs by reaching balanced specificity (82%) and sensitivity (94%) on clinical data, and includes a novel epistatic feature, the 'partners score', which leverages evolutionary and structural partnerships of residues. The 'partners score' provides a general framework for modeling epistatic interactions, integrating both clinical and functional information. We provide our tool and predictions for all missense variants in 316 clinically actionable disease genes (demag.org) to facilitate the interpretation of variants and improve clinical decision-making.

PMID:37076482 | DOI:10.1038/s41467-023-37661-z

Nat Commun. 2023 Apr 19;14(1):2245. doi: 10.1038/s41467-023-37621-7.

ABSTRACT

Bacterial pathogens often make use of post-translational modifications to manipulate host cells. Legionella pneumophila, the causative agent of Legionnaires disease, secretes the enzyme AnkX that uses cytidine diphosphate-choline to post-translationally modify the human small G-Protein Rab1 with a phosphocholine moiety at Ser76. Later in the infection, the Legionella enzyme Lem3 acts as a dephosphocholinase, hydrolytically removing the phosphocholine. While the molecular mechanism for Rab1 phosphocholination by AnkX has recently been resolved, structural insights into the activity of Lem3 remained elusive. Here, we stabilise the transient Lem3:Rab1b complex by substrate mediated covalent capture. Through crystal structures of Lem3 in the apo form and in complex with Rab1b, we reveal Lem3's catalytic mechanism, showing that it acts on Rab1 by locally unfolding it. Since Lem3 shares high structural similarity with metal-dependent protein phosphatases, our Lem3:Rab1b complex structure also sheds light on how these phosphatases recognise protein substrates.

PMID:37076474 | DOI:10.1038/s41467-023-37621-7

J Hum Lact. 2023 May;39(2):191-193. doi: 10.1177/08903344231156919.

NO ABSTRACT

PMID:37073878 | DOI:10.1177/08903344231156919

Genes Cells. 2023 Apr 19. doi: 10.1111/gtc.13028. Online ahead of print.

ABSTRACT

Histone methylation plays a vital role in retinal development. However, the role of histone H3K36 methylation in retinal development is not clear. We examined the role of H3K36 methylation by loss-of-function analysis of H3K36me1/2 demethylases, Fbxl10, and Fbxl11. We analyzed the effect of knockout of these genes in the developing and mature retina on retinal development. Knockout of Fbxl10 specifically in the developing retina did not result in gross developmental abnormalities. Although adult rod photoreceptor-specific knockout of Fbxl11 in mature retinas did not result in morphological abnormalities, Fbxl11 knockout in developing retinas increased apoptosis, suppressed the proliferation of retinal progenitor cells, and resulted in microphthalmia. Morphological analysis revealed perturbed differentiation of rod photoreceptor and bipolar cells. RNA-seq of retinas at P7 showed markedly decreased expression of genes characterizing rod photoreceptor and bipolar cells in Fbxl11-knockout retinas. In addition, perturbation of alternative splicing increased intron retention in Fbxl11-knockout retinas. Genome-wide evaluation of the H3K36 methylation status revealed that Fbxl11 knockout altered the distribution of H3K36me2/3 in genes important for rod photoreceptor development. Taken together, we show that Fbxl11 plays pivotal roles in the development of retinal late-born cell types and may contribute to tight control of H3K36 methylation during retinal development.

PMID:37073980 | DOI:10.1111/gtc.13028

Elife. 2023 Apr 19;12:e83792. doi: 10.7554/eLife.83792. Online ahead of print.

ABSTRACT

Collective cell migration plays an essential role in vertebrate development, yet the extent to which dynamically changing microenvironments influence this phenomenon remains unclear. Observations of the distribution of the extracellular matrix (ECM) component fibronectin during the migration of loosely connected neural crest cells (NCCs) lead us to hypothesize that NCC remodeling of an initially punctate ECM creates a scaffold for trailing cells, enabling them to form robust and coherent stream patterns. We evaluate this idea in a theoretical setting by developing an individual-based computational model that incorporates reciprocal interactions between NCCs and their ECM. ECM remodeling, haptotaxis, contact guidance, and cell-cell repulsion are sufficient for cells to establish streams in silico, however additional mechanisms, such as chemotaxis, are required to consistently guide cells along the correct target corridor. Further model investigations imply that contact guidance and differential cell-cell repulsion between leader and follower cells are key contributors to robust collective cell migration by preventing stream breakage. Global sensitivity analysis and simulated gain- and loss-of-function experiments suggest that long-distance migration without jamming is most likely to occur when leading cells specialize in creating ECM fibers, and trailing cells specialize in responding to environmental cues by upregulating mechanisms such as contact guidance.

PMID:37073859 | DOI:10.7554/eLife.83792

J Infect Dis. 2023 Apr 19:jiad105. doi: 10.1093/infdis/jiad105. Online ahead of print.

ABSTRACT

People with human immunodeficiency virus (HIV) (PWH) have an increased risk of developing cardiovascular disease (CVD). RNA-Seq was performed on hearts from simian immunodeficiency virus (SIV)-infected rhesus macaques with or without antiretroviral therapy (ART). SIV infection led to high plasma viral load with very little myocardial viral RNA. SIV infection promoted an inflammatory environment in the heart through interferon and pathogen signaling, in the absence of myocardial viral RNA. While ART dampened interferon and cytokine response in the heart, SIV-infected animals receiving ART had deficits in expression of genes directly involved in fatty acid (FA) metabolism relative to uninfected animals.

PMID:37073617 | DOI:10.1093/infdis/jiad105

NAR Genom Bioinform. 2023 Apr 18;5(2):lqad036. doi: 10.1093/nargab/lqad036. eCollection 2023 Jun.

ABSTRACT

Satellites such as phage-induced chromosomal islands (PICIs) are mobile genetic elements relying on helper phages for their mobilization, through trans-regulatory interactions. We discovered a PICI with a more intimate cis-regulatory configuration, integrated within a late gene of its helper prophage. This helper-embedded PICI (HE-PICI) configuration delays expression of the interrupted helper late gene until the satellite excises and provides passive helper-driven components to both HE-PICI replication and late transcription. Upon induction of a helper-satellite composite, precise excision of the entire composite was observed, followed by composite replication, then satellite excision. We mapped 491 additional HE-PICIs to one of 14 sites in cognates of phage lambda late genes. Associated integrases form a single phylogenetic clade with subclades respecting the 14 site groups, exhibiting repeated tropism for prophage late genes as new integration sites evolve. Four ordered zones in a general gram-negative PICI genome organization are: an integration zone encoding integrase and AlpA, a dynamic zone encoding members of the Bro-N network of domain-swapping DNA-interactive proteins and immunity repressor RNAs, a replication zone, and a dynamic late zone in which clusters as large as 17 consecutive helper prophage late genes have been captured. Helper-embedded satellites present new dimensions in satellite/helper relationships.

PMID:37081865 | PMC:PMC10111431 | DOI:10.1093/nargab/lqad036

Trends Endocrinol Metab. 2023 Apr 18:S1043-2760(23)00055-3. doi: 10.1016/j.tem.2023.03.002. Online ahead of print.

ABSTRACT

Acute COVID-19 infection is followed by prolonged symptoms in approximately one in ten cases: known as Long COVID. The disease affects ~65 million individuals worldwide. Many pathophysiological processes appear to underlie Long COVID, including viral factors (persistence, reactivation, and bacteriophagic action of SARS CoV-2); host factors (chronic inflammation, metabolic and endocrine dysregulation, immune dysregulation, and autoimmunity); and downstream impacts (tissue damage from the initial infection, tissue hypoxia, host dysbiosis, and autonomic nervous system dysfunction). These mechanisms culminate in the long-term persistence of the disorder characterized by a thrombotic endothelialitis, endothelial inflammation, hyperactivated platelets, and fibrinaloid microclots. These abnormalities of blood vessels and coagulation affect every organ system and represent a unifying pathway for the various symptoms of Long COVID.

PMID:37080828 | DOI:10.1016/j.tem.2023.03.002

Sci Rep. 2023 Apr 18;13(1):6279. doi: 10.1038/s41598-023-33398-3.

ABSTRACT

Chickpea is an important food legume cultivated in several countries. A sudden drop in autumn temperature, freezing winter temperature, and late spring cold events result in significant losses in chickpea production. The current study used RNA sequencing of two cold tolerant (Saral) and sensitive (ILC533) Kabuli chickpea genotypes to identify cold tolerance-associated genes/pathways. A total of 200.85 million raw reads were acquired from the leaf samples by Illumina sequencing, and around 86% of the clean reads (199 million) were mapped to the chickpea reference genome. The results indicated that 3710 (1980 up- and 1730 down-regulated) and 3473 (1972 up- and 1501 down-regulated) genes were expressed differentially under cold stress in the tolerant and sensitive genotypes, respectively. According to the GO enrichment analysis of uniquely down-regulated genes under cold stress in ILC533, photosynthetic membrane, photosystem II, chloroplast part, and photosystem processes were enriched, revealing that the photosynthesis is severely sensitive to cold stress in this sensitive genotype. Many remarkable transcription factors (CaDREB1E, CaMYB4, CaNAC47, CaTCP4, and CaWRKY33), signaling/regulatory genes (CaCDPK4, CaPP2C6, CaMKK2, and CaHSFA3), and protective genes (CaCOR47, CaLEA3, and CaGST) were identified among the cold-responsive genes of the tolerant genotype. These findings would help improve cold tolerance across chickpea genotypes by molecular breeding or genetic engineering.

PMID:37072529 | DOI:10.1038/s41598-023-33398-3

Commun Biol. 2023 Apr 18;6(1):427. doi: 10.1038/s42003-023-04785-3.

ABSTRACT

Ectopic ATP synthase complex (eATP synthase), located on cancer cell surface, has been reported to possess catalytic activity that facilitates the generation of ATP in the extracellular environment to establish a suitable microenvironment and to be a potential target for cancer therapy. However, the mechanism of intracellular ATP synthase complex transport remains unclear. Using a combination of spatial proteomics, interaction proteomics, and transcriptomics analyses, we find ATP synthase complex is first assembled in the mitochondria and subsequently delivered to the cell surface along the microtubule via the interplay of dynamin-related protein 1 (DRP1) and kinesin family member 5B (KIF5B). We further demonstrate that the mitochondrial membrane fuses to the plasma membrane in turn to anchor ATP syntheses on the cell surface using super-resolution imaging and real-time fusion assay in live cells. Our results provide a blueprint of eATP synthase trafficking and contribute to the understanding of the dynamics of tumor progression.

PMID:37072500 | DOI:10.1038/s42003-023-04785-3

Stroke Vasc Neurol. 2023 Apr 18:svn-2022-002227. doi: 10.1136/svn-2022-002227. Online ahead of print.

ABSTRACT

OBJECTIVE: Extra-axial cavernous hemangiomas (ECHs) are sporadic and rare intracranial occupational lesions that usually occur within the cavernous sinus. The aetiology of ECHs remains unknown.

METHODS: Whole-exome sequencing was performed on ECH lesions from 12 patients (discovery cohort) and droplet digital polymerase-chain-reaction (ddPCR) was used to confirm the identified mutation in 46 additional cases (validation cohort). Laser capture microdissection (LCM) was carried out to capture and characterise subgroups of tissue cells. Mechanistic and functional investigations were carried out in human umbilical vein endothelial cells and a newly established mouse model.

RESULTS: We detected somatic GJA4 mutation (c.121G>T, p.G41C) in 5/12 patients with ECH in the discovery cohort and confirmed the finding in the validation cohort (16/46). LCM followed by ddPCR revealed that the mutation was enriched in lesional endothelium. In vitro experiments in endothelial cells demonstrated that the GJA4 mutation activated SGK-1 signalling that in turn upregulated key genes involved in cell hyperproliferation and the loss of arterial specification. Compared with wild-type littermates, mice overexpressing the GJA4 mutation developed ECH-like pathological morphological characteristics (dilated venous lumen and elevated vascular density) in the retinal superficial vascular plexus at the postnatal 3 weeks, which were reversed by an SGK1 inhibitor, EMD638683.

CONCLUSIONS: We identified a somatic GJA4 mutation that presents in over one-third of ECH lesions and proposed that ECHs are vascular malformations due to GJA4-induced activation of the SGK1 signalling pathway in brain endothelial cells.

PMID:37072338 | DOI:10.1136/svn-2022-002227

Proc Natl Acad Sci U S A. 2023 Apr 25;120(17):e2219418120. doi: 10.1073/pnas.2219418120. Epub 2023 Apr 18.

ABSTRACT

Significant recent advances in structural biology, particularly in the field of cryoelectron microscopy, have dramatically expanded our ability to create structural models of proteins and protein complexes. However, many proteins remain refractory to these approaches because of their low abundance, low stability, or-in the case of complexes-simply not having yet been analyzed. Here, we demonstrate the power of using cross-linking mass spectrometry (XL-MS) for the high-throughput experimental assessment of the structures of proteins and protein complexes. This included those produced by high-resolution but in vitro experimental data, as well as in silico predictions based on amino acid sequence alone. We present the largest XL-MS dataset to date, describing 28,910 unique residue pairs captured across 4,084 unique human proteins and 2,110 unique protein-protein interactions. We show that models of proteins and their complexes predicted by AlphaFold2, and inspired and corroborated by the XL-MS data, offer opportunities to deeply mine the structural proteome and interactome and reveal mechanisms underlying protein structure and function.

PMID:37071682 | DOI:10.1073/pnas.2219418120

Annu Rev Virol. 2023 Apr 18. doi: 10.1146/annurev-virology-111821-115754. Online ahead of print.

ABSTRACT

The mammalian gastrointestinal tract (GIT) hosts a diverse and highly active microbiota composed of bacteria, eukaryotes, archaea, and viruses. Studies of the GIT microbiota date back more than a century, although modern techniques, including mouse models, sequencing technology, and novel therapeutics in humans, have been foundational to our understanding of the roles of commensal microbes in health and disease. Here, we review the impacts of the GIT microbiota on viral infection, both within the GIT and systemically. GIT-associated microbes and their metabolites alter the course of viral infection through a variety of mechanisms, including direct interactions with virions, alteration of the GIT landscape, and extensive regulation of innate and adaptive immunity. Mechanistic understanding of the full breadth of interactions between the GIT microbiota and the host is still lacking in many ways but will be vital for the development of novel therapeutics for viral and nonviral diseases alike. Expected final online publication date for the Annual Review of Virology, Volume 10 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

PMID:37071931 | DOI:10.1146/annurev-virology-111821-115754

Mol Biol Evol. 2023 Apr 18:msad092. doi: 10.1093/molbev/msad092. Online ahead of print.

ABSTRACT

Horizontal transfer of transposable elements is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of transposable elements at what appears to be a high rate compared to other mammals. We investigated the occurrence of horizontally transferred DNA transposons involving bats. We found over 200 putative horizontally transferred elements within bats; sixteen transposons were shared across distantly related mammalian clades and two other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.

PMID:37071810 | DOI:10.1093/molbev/msad092

J Enzyme Inhib Med Chem. 2023 Dec;38(1):2201410. doi: 10.1080/14756366.2023.2201410.

ABSTRACT

Among tyrosine kinase inhibitors, quinazoline-based compounds represent a large and well-known group of multi-target agents. Our previous studies have shown interesting kinases inhibition activity for a series of 4-aminostyrylquinazolines based on the CP-31398 scaffold. Here, we synthesised a new series of styrylquinazolines with a thioaryl moiety in the C4 position and evaluated in detail their biological activity. Our results showed high inhibition potential against non-receptor tyrosine kinases for several compounds. Molecular docking studies showed differential binding to the DFG conformational states of ABL kinase for two derivatives. The compounds showed sub-micromolar activity against leukaemia. Finally, in-depth cellular studies revealed the full landscape of the mechanism of action of the most active compounds. We conclude that S4-substituted styrylquinazolines can be considered as a promising scaffold for the development of multi-kinase inhibitors targeting a desired binding mode to kinases as effective anticancer drugs.

PMID:37070569 | DOI:10.1080/14756366.2023.2201410

Genetics. 2023 Apr 18:iyad065. doi: 10.1093/genetics/iyad065. Online ahead of print.

ABSTRACT

The evolution of gene expression is constrained by the topology of gene regulatory networks, as co-expressed genes are likely to have their expressions affected together by mutations. Conversely, co-expression can also be an advantage when genes are under joint selection. Here, we assessed theoretically whether correlated selection (selection for a combination of traits) was able to affect the pattern of correlated gene expressions and the underlying gene regulatory networks. We ran individual-based simulations, applying a stabilizing correlated fitness function to three genetic architectures: a quantitative genetics (multilinear) model featuring epistasis and pleiotropy, a quantitative genetics model where each genes has an independent mutational structure, and a gene regulatory network model, mimicking the mechanisms of gene expression regulation. Simulations showed that correlated mutational effects evolved in the three genetic architectures as a response to correlated selection, but the response in gene networks was specific. The intensity of gene co-expression was mostly explained by the regulatory distance between genes (largest correlations being associated to genes directly interacting with each other), and the sign of co-expression was associated with the nature of the regulation (transcription activation or inhibition). These results concur to the idea that gene network topologies could partly reflect past selection patterns on gene expression.

PMID:37070537 | DOI:10.1093/genetics/iyad065

Evol Dev. 2023 Apr 18. doi: 10.1111/ede.12436. Online ahead of print.

ABSTRACT

The development of an individual must be capable of resisting the harmful effects of internal and external perturbations. This capacity, called robustness, can make the difference between normal variation and disease. Some systems and organs are more resilient in their capacity to correct the effects of internal disturbances such as mutations. Similarly, organs and organisms differ in their capacity to be resilient against external disturbances, such as changes in temperature. Furthermore, all developmental systems must be somewhat flexible to permit evolutionary change, and understanding robustness requires a comparative framework. Over the last decades, most research on developmental robustness has been focusing on specific model systems and organs. Hence, we lack tools that would allow cross-species and cross-organ comparisons. Here, we emphasize the need for a uniform framework to experimentally test and quantify robustness across study systems and suggest that the analysis of fluctuating asymmetry might be a powerful proxy to do so. Such a comparative framework will ultimately help to resolve why and how organs of the same and different species differ in their sensitivity to internal (e.g., mutations) and external (e.g., temperature) perturbations and at what level of biological organization buffering capacities exist and therefore create robustness of the developmental system.

PMID:37070415 | DOI:10.1111/ede.12436

Nucleic Acids Res. 2023 Apr 18:gkad245. doi: 10.1093/nar/gkad245. Online ahead of print.

ABSTRACT

RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism Sacchromyces cerevisiae, the number of proteins identified as RBPs has greatly increased over the last decade. However, the cellular function of most of these novel RBPs remains largely unexplored. We used mass spectrometry-based quantitative proteomics to systematically identify protein-protein interactions (PPIs) and RNA-dependent interactions (RDIs) to create a novel dataset for 40 RBPs that are associated with the mRNA life cycle. Domain, functional and pathway enrichment analyses revealed an over-representation of RNA functionalities among the enriched interactors. Using our extensive PPI and RDI networks, we revealed putative new members of RNA-associated pathways, and highlighted potential new roles for several RBPs. Our RBP interactome resource is available through an online interactive platform as a community tool to guide further in-depth functional studies and RBP network analysis (https://www.butterlab.org/RINE).

PMID:37070168 | DOI:10.1093/nar/gkad245