Search

Intravascular nematodes were considered the cause of death of 14 captive callitrichids. All animals were captive born at zoos in France and died with little or no premonitory signs of disease. No consistent gross lesions were observed at necropsy, although in certain cases intracardiac adult parasites were noted. The most significant histologic findings were verminous pneumonia and pulmonary endarteritis. In all cases except one, intravascular adult nematodes were observed with eggs and larvae in the lungs. Adult nematodes were obtained from 8 animals and in all cases were identified as Parastrongylus dujardini. To the authors’ knowledge, this is the first report of intravascular angiostrongylosis with primary cardiopulmonary location in callitrichids in France. [ABSTRACT FROM PUBLISHER]

Abstract: Ribose-5-phosphate isomerase A has an important role in sugar metabolism by interconverting ribose-5-phosphate and ribulose-5-phosphate. This enzyme is ubiquitous and highly conserved among the three kingdoms of life. We have solved the 2.1 Å resolution crystal structure of the Saccharomyces cerevisiae enzyme by molecular replacement. This protein adopts the same fold as its archaeal and bacterial orthologs with two α/β domains tightly packed together. Mapping of conserved residues at the surface of the protein reveals strong invariability of the active site pocket, suggesting a common ligand binding mode and a similar catalytic mechanism. The yeast enzyme associates as a homotetramer similarly to the archaeal protein. The effect of an inactivating mutation (Arg189 to Lys) is discussed in view of the information brought by this structure. [Copyright &y& Elsevier]

In many cases, antibody and their complexes can be crystallized and their structure determined without major difficulties. The remaining problematic cases may be approached through techniques such as of combinatorial complex crystallization which uses immunoglobulin binding proteins (IBP). The range of lattices that can be made using this method can be expanded by engineering mutants of IBP domains. We have designed Peptostreptococcus magnus protein L (PpL) mutants with altered immunoglobulin light chain binding characteristics. While the wild type PpL has two binding sites, some of the mutants contact the light chain via only one site. Other mutants have combinations of weakened first and second binding sites that modify their crystallization properties and their packing mode. In this study, we have selected PpL mutants with different behavior and that are most useful for crystallization and we present the various packing modes obtained so far. [ABSTRACT FROM AUTHOR]

Polychlorinated dibenzo- p -dioxins and dibenzofurans (PCDD/Fs) are ubiquitous in the environment. The main route of human exposure is through food consumption. Soil contamination can be problematic for sanitary safety depending on the usage of the soil, such as farming. In case of environmental soil contamination with PCDD/Fs, hen's eggs may be contaminated due to soil ingestion by hens. For this reason, it is important to understand the parameters that influence eggs' contamination when hens are raised in contaminated areas. After the discovery of a contaminated area in Lausanne (Switzerland), we collected hens' eggs from ten domestic-produced eggs and one farm. Based on PCDD/F measurements of eggs and soil, and a toxicokinetic model, we estimated individual hen's soil intake levels and highlighted appropriate parameters to predict the dose ingested. Recommended weekly consumption for home-produced eggs was calculated based on the tolerable weekly intake proposed by EFSA in 2018. The most important parameter to assess the soil ingestion does not seem to be the soil coverage by vegetation but rather the hen's pecking behaviour, the latter being difficult to estimate objectively. For this reason, we recommend using a realistic soil ingestion interval to assess the distribution of egg PCDD/F concentration from free-range hens reared on contaminated soil. The addition of soil contamination in the toxicokinetic model can then be used to recommend to the general population weekly consumption of eggs. The consumption by adults of free-range eggs produced on land with soil containing >90 ng toxic-equivalent (TEQ)/kg dry soil should be avoided. Even with a low level of soil contamination (1-5 ng TEQ/kg dry soil), we would recommend consuming not more than 5 eggs per week for adults and no more than 2 eggs for children below 4 years old.

The nonsense-mediated mRNA decay (NMD) pathway clears eukaryotic cells of mRNAs containing premature termination codons (PTCs) or normal stop codons located in specific contexts. It therefore plays an important role in gene expression regulation. The precise molecular mechanism of the NMD pathway has long been considered to differ substantially from yeast to metazoa, despite the involvement of universally conserved factors such as the central ATP-dependent RNA-helicase Upf1. Here, we describe the crystal structure of the yeast Upf1 bound to its recently identified but yet uncharacterized partner Nmd4, show that Nmd4 stimulates Upf1 ATPase activity and that this interaction contributes to the elimination of NMD substrates. We also demonstrate that a region of Nmd4 critical for the interaction with Upf1 in yeast is conserved in the metazoan SMG6 protein, another major NMD factor. We show that this conserved region is involved in the interaction of SMG6 with UPF1 and that mutations in this region affect the levels of endogenous human NMD substrates. Our results support the universal conservation of the NMD mechanism in eukaryotes., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Barbarin-Bocahu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and translation. Dysregulation of such modifications and the enzymes installing them have been linked to various human pathologies including neurodevelopmental disorders and cancers. Several methyltransferases (MTases) are regulated allosterically by human TRMT112 (Trm112 in Saccharomyces cerevisiae), but the interactome of this regulator and targets of its interacting MTases remain incompletely characterized. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMPD2) as direct partners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. For THUMPD2, we discovered that it directly associates with the U6 snRNA, a core component of the catalytic spliceosome, and is required for the formation of m2G, the last 'orphan' modification in U6 snRNA. Furthermore, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The recent breakthrough made in the field of three-dimensional (3D) structure prediction by artificial intelligence softwares, such as initially AlphaFold2 (AF2) and RosettaFold (RF) and more recently large Language Models (LLM), has revolutionized the field of structural biology in particular and also biology as a whole. These models have clearly generated great enthusiasm within the scientific community, and different applications of these 3D predictions are regularly described in scientific articles, demonstrating the impact of these high-quality models. Despite the acknowledged high accuracy of these models in general, it seems important to make users of these models aware of the wealth of information they offer and to encourage them to make the best use of them. Here, we focus on the impact of these models in a specific application by structural biologists using X-ray crystallography. We propose guidelines to prepare models to be used for molecular replacement trials to solve the phase problem. We also encourage colleagues to share as much detail as possible about how they use these models in their research, where the models did not yield correct molecular replacement solutions, and how these predictions fit with their experimental 3D structure. We feel this is important to improve the pipelines using these models and also to get feedback on their overall quality.

In metazoans, most proteins have pleiotropic cellular functions and have the ability to interact with several factors to accomplish these different functions. This is the case of eukaryotic ERH proteins, a family of homodimeric proteins involved in DNA replication and cell cycle control as well as in gene silencing by contributing either to the biogenesis of small interference RNAs (miRNAs, piRNAs) or to the recruitment of RNA decay machineries. Very recently, several crystal structures describing complexes formed by eukaryotic ERH proteins and several small peptides from various partners have highlighted the existence of different binding sites on the surface of ERH proteins. In this issue of The FEBS Journal, Wang et al. present the crystal structure of the complex formed between the human ERH protein and a short peptide of the CIZ1 protein, one of its partners. Altogether, this information will be particularly important for future studies aimed at dissecting the different biological functions governed by this family of highly conserved proteins. Comment on: https://doi.org/10.1111/febs.16611., (© 2022 Federation of European Biochemical Societies.)

There is an urgent need for a molecular understanding of how SARS-CoV-2 influences the machineries of the host cell. Herein, we focused our attention on the capacity of the SARS-CoV-2 protein NSP2 to bind the human 4EHP-GIGYF2 complex, a key factor involved in microRNA-mediated silencing of gene expression. Using in vitro interaction assays, our data demonstrate that NSP2 physically associates with both 4EHP and a central segment in GIGYF2 in the cytoplasm. We also provide functional evidence showing that NSP2 impairs the function of GIGYF2 in mediating translation repression using reporter-based assays. Collectively, these data reveal the potential impact of NSP2 on the post-transcriptional silencing of gene expression in human cells, pointing out 4EHP-GIGYF2 targeting as a possible strategy of SARS-CoV-2 to take over the silencing machinery and to suppress host defenses., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)

The breakthrough recently made in protein structure prediction by deep-learning programs such as AlphaFold and RoseTTAFold will certainly revolutionize biology over the coming decades. The scientific community is only starting to appreciate the various applications, benefits and limitations of these protein models. Yet, after the first thrills due to this revolution, it is important to evaluate the impact of the proposed models and their overall quality to avoid the misinterpretation or overinterpretation of these models by biologists. One of the first applications of these models is in solving the `phase problem' encountered in X-ray crystallography in calculating electron-density maps from diffraction data. Indeed, the most frequently used technique to derive electron-density maps is molecular replacement. As this technique relies on knowledge of the structure of a protein that shares strong structural similarity with the studied protein, the availability of high-accuracy models is then definitely critical for successful structure solution. After the collection of a 2.45 Å resolution data set, we struggled for two years in trying to solve the crystal structure of a protein involved in the nonsense-mediated mRNA decay pathway, an mRNA quality-control pathway dedicated to the elimination of eukaryotic mRNAs harboring premature stop codons. We used different methods (isomorphous replacement, anomalous diffraction and molecular replacement) to determine this structure, but all failed until we straightforwardly succeeded thanks to both AlphaFold and RoseTTAFold models. Here, we describe how these new models helped us to solve this structure and conclude that in our case the AlphaFold model largely outcompetes the other models. We also discuss the importance of search-model generation for successful molecular replacement.

Mycolic acids are key components of the complex cell envelope of Corynebacteriales . These fatty acids, conjugated to trehalose or to arabinogalactan form the backbone of the mycomembrane. While mycolic acids are essential to the survival of some species, such as Mycobacterium tuberculosis , their absence is not lethal for Corynebacterium glutamicum, which has been extensively used as a model to depict their biosynthesis. Mycolic acids are first synthesized on the cytoplasmic side of the inner membrane and transferred onto trehalose to give trehalose monomycolate (TMM). TMM is subsequently transported to the periplasm by dedicated transporters and used by mycoloyltransferase enzymes to synthesize all the other mycolate-containing compounds. Using a random transposition mutagenesis, we recently identified a new uncharacterized protein (Cg1246) involved in mycolic acid metabolism. Cg1246 belongs to the DUF402 protein family that contains some previously characterized nucleoside phosphatases. In this study, we performed a functional and structural characterization of Cg1246. We showed that absence of the protein led to a significant reduction in the pool of TMM in C. glutamicum , resulting in a decrease in all other mycolate-containing compounds. We found that, in vitro , Cg1246 has phosphatase activity on organic pyrophosphate substrates but is most likely not a nucleoside phosphatase. Using a computational approach, we identified important residues for phosphatase activity and constructed the corresponding variants in C. glutamicum . Surprisingly complementation with these non-functional proteins fully restored the defect in TMM of the Δ cg1246 mutant strain, suggesting that in vivo , the phosphatase activity is not involved in mycolic acid biosynthesis.

Oxidative stress has been associated with various inflammation-related human diseases. It is defined as an imbalance between the production and elimination of reactive oxygen species (ROS). ROS can oxidize proteins, lipids, and DNA, and some of these oxidized products are excreted in urine, such as malondialdehyde (MDA), which is considered a biomarker for oxidative damage of lipids. To interpret changes of this biomarker as a measure of oxidative species overproduction in humans, a background range for urinary MDA concentration in the general population is needed. We sought to establish urinary MDA concentration ranges for healthy adult populations based on reported values in the available scientific literature. We conducted a systematic review and meta-analysis using the standardized protocol registered in PROSPERO (CRD42020146623). EMBASE, PubMed, Web of Science, and Cochrane library databases were searched from journal inception up to October 2020. We included 35 studies (divided into 47 subgroups for the quantitative analysis). Only studies that measured creatinine-corrected urinary MDA with high-performance liquid chromatography (HPLC) with mass spectrometry (MS), fluorescence detection, or UV photometry were included. The geometric mean (GM) of urinary MDA concentration was 0.10 mg/g creatinine and 95% percentile confidence interval (CI) 0.07-0.12. Age, geographical location but not sex, and smoking status had a significant effect on urinary MDA concentrations. There was a significant increasing trend of urinary MDA concentrations with age. These urinary MDA values should be considered preliminary, as they are based on mostly moderate to some low-quality evidence studies. Although urinary MDA can reliably reflect excessive oxidative stress in a population, the influence of physiological parameters that affect its meaning needs to be addressed as well as harmonizing the chemical analytical methods.

The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications., (© 2021 Wiley Periodicals LLC.)

Long non-coding RNAs (lncRNAs) contribute to the regulation of gene expression in response to intra- or extracellular signals but the underlying molecular mechanisms remain largely unexplored. Here, we identify an uncharacterized lncRNA as a central player in shaping the meiotic gene expression program in fission yeast. We report that this regulatory RNA, termed mamRNA, scaffolds the antagonistic RNA-binding proteins Mmi1 and Mei2 to ensure their reciprocal inhibition and fine tune meiotic mRNA degradation during mitotic growth. Mechanistically, mamRNA allows Mmi1 to target Mei2 for ubiquitin-mediated downregulation, and conversely enables accumulating Mei2 to impede Mmi1 activity, thereby reinforcing the mitosis to meiosis switch. These regulations also occur within a unique Mmi1-containing nuclear body, positioning mamRNA as a spatially-confined sensor of Mei2 levels. Our results thus provide a mechanistic basis for the mutual control of gametogenesis effectors and further expand our vision of the regulatory potential of lncRNAs.

The Mtq2-Trm112 methyltransferase modifies the eukaryotic translation termination factor eRF1 on the glutamine side chain of a universally conserved GGQ motif that is essential for release of newly synthesized peptides. Although this modification is found in the three domains of life, its exact role in eukaryotes remains unknown. As the deletion of MTQ2 leads to severe growth impairment in yeast, we have investigated its role further and tested its putative involvement in ribosome biogenesis. We found that Mtq2 is associated with nuclear 60S subunit precursors, and we demonstrate that its catalytic activity is required for nucleolar release of pre-60S and for efficient production of mature 5.8S and 25S rRNAs. Thus, we identify Mtq2 as a novel ribosome assembly factor important for large ribosomal subunit formation. We propose that Mtq2-Trm112 might modify eRF1 in the nucleus as part of a quality control mechanism aimed at proof-reading the peptidyl transferase center, where it will subsequently bind during translation termination., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

tRNAs play a central role during the translation process and are heavily post-transcriptionally modified to ensure optimal and faithful mRNA decoding. These epitranscriptomics marks are added by largely conserved proteins and defects in the function of some of these enzymes are responsible for neurodevelopmental disorders and cancers. Here, we focus on the Trm11 enzyme, which forms N2-methylguanosine (m2G) at position 10 of several tRNAs in both archaea and eukaryotes. While eukaryotic Trm11 enzyme is only active as a complex with Trm112, an allosteric activator of methyltransferases modifying factors (RNAs and proteins) involved in mRNA translation, former studies have shown that some archaeal Trm11 proteins are active on their own. As these studies were performed on Trm11 enzymes originating from archaeal organisms lacking TRM112 gene, we have characterized Trm11 (AfTrm11) from the Archaeoglobus fulgidus archaeon, which genome encodes for a Trm112 protein (AfTrm112). We show that AfTrm11 interacts directly with AfTrm112 similarly to eukaryotic enzymes and that although AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. We finally describe the first crystal structures of the AfTrm11-Trm112 complex and of Trm11, alone or bound to the methyltransferase inhibitor sinefungin., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)