Draft Genome of the Entomopathogenic Fungus Metarhizium robertsii DSM 1490

Metarhizium robertsii DSM 1490 is a generalist entomopathogenic fungus. The mechanisms of pathogenesis of such fungi in insects like termites are not completely understood. Here, we report the draft genome sequence, as sequenced on the Oxford Nanopore platform. The genome has a GC% of 47.82 and a size of 45,688,865 bp

Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa

IntroductionEvery year, millions of deaths are associated with the increased spread of antimicrobial resistance genes (ARGs) in bacteria. With the increasing urbanization of the global population, the spread of ARGs in urban bacteria has become a more severe threat to human health.MethodsIn this study, we used metagenome-assembled genomes (MAGs) recovered from 1,153 urban metagenomes in multiple urban locations to investigate the fate and occurrence of ARGs in urban bacteria. Additionally, we analyzed the occurrence of these ARGs on plasmids and estimated the virulence of the bacterial species.ResultsOur results showed that multidrug and glycopeptide ARGs are ubiquitous among urban bacteria. Additionally, we analyzed the deterministic effects of phylogeny on the spread of these ARGs and found ARG classes that have a non-random distribution within the phylogeny of our recovered MAGs. However, few ARGs were found on plasmids and most of the recovered MAGs contained few virulence factors.DiscussionOur results suggest that the observed non-random spreads of ARGs are not due to the transfer of plasmids and that most of the bacteria observed in the study are unlikely to be virulent. Additional research is needed to evaluate whether the ubiquitous and widespread ARG classes will become entirely prevalent among urban bacteria and how they spread among phylogenetically distinct species

Microbial impact on initial soil formation in arid and semiarid environments under simulated climate change

The microbiota is attributed to be important for initial soil formation under extreme climate conditions, but experimental evidence for its relevance is scarce. To fill this gap, we investigated the impact of in situ microbial communities and their interrelationship with biocrust and plants compared to abiotic controls on soil formation in initial arid and semiarid soils. Additionally, we assessed the response of bacterial communities to climate change. Topsoil and subsoil samples from arid and semiarid sites in the Chilean Coastal Cordillera were incubated for 16 weeks under diurnal temperature and moisture variations to simulate humid climate conditions as part of a climate change scenario. Our findings indicate that microorganism-plant interaction intensified aggregate formation and stabilized soil structure, facilitating initial soil formation. Interestingly, microorganisms alone or in conjunction with biocrust showed no discernible patterns compared to abiotic controls, potentially due to water-masking effects. Arid soils displayed reduced bacterial diversity and developed a new community structure dominated by Proteobacteria, Actinobacteriota, and Planctomycetota, while semiarid soils maintained a consistently dominant community of Acidobacteriota and Proteobacteria. This highlighted a sensitive and specialized bacterial community in arid soils, while semiarid soils exhibited a more complex and stable community. We conclude that microorganism-plant interaction has measurable impacts on initial soil formation in arid and semiarid regions on short time scales under climate change. Additionally, we propose that soil and climate legacies are decisive for the present soil microbial community structure and interactions, future soil development, and microbial responses

Nicotinic acid adenine dinucleotide phosphate-mediated calcium signalling in effector T cells regulates autoimmunity of the central nervous system

Nicotinic acid adenine dinucleotide phosphate represents a newly identified second messenger in T cells involved in antigen receptor-mediated calcium signalling. Its function in vivo is, however, unknown due to the lack of biocompatible inhibitors. Using a recently developed inhibitor, we explored the role of nicotinic acid adenine dinucleotide phosphate in autoreactive effector T cells during experimental autoimmune encephalomyelitis, the animal model for multiple sclerosis. We provide in vitro and in vivo evidence that calcium signalling controlled by nicotinic acid adenine dinucleotide phosphate is relevant for the pathogenic potential of autoimmune effector T cells. Live two photon imaging and molecular analyses revealed that nicotinic acid adenine dinucleotide phosphate signalling regulates T cell motility and re-activation upon arrival in the nervous tissues. Treatment with the nicotinic acid adenine dinucleotide phosphate inhibitor significantly reduced both the number of stable arrests of effector T cells and their invasive capacity. The levels of pro-inflammatory cytokines interferon-gamma and interleukin-17 were strongly diminished. Consecutively, the clinical symptoms of experimental autoimmune encephalomyelitis were ameliorated. In vitro, antigen-triggered T cell proliferation and cytokine production were evenly suppressed. These inhibitory effects were reversible: after wash-out of the nicotinic acid adenine dinucleotide phosphate antagonist, the effector T cells fully regained their functions. The nicotinic acid derivative BZ194 induced this transient state of non-responsiveness specifically in post-activated effector T cells. Naïve and long-lived memory T cells, which express lower levels of the putative nicotinic acid adenine dinucleotide phosphate receptor, type 1 ryanodine receptor, were not targeted. T cell priming and recall responses in vivo were not reduced. These data indicate that the nicotinic acid adenine dinucleotide phosphate/calcium signalling pathway is essential for the recruitment and the activation of autoaggressive effector T cells within their target organ. Interference with this signalling pathway suppresses the formation of autoimmune inflammatory lesions and thus might qualify as a novel strategy for the treatment of T cell mediated autoimmune diseases

Knocking at the brain’s door: intravital two-photon imaging of autoreactive T cell interactions with CNS structures

Since the first applications of two-photon microscopy in immunology 10 years ago, the number of studies using this advanced technology has increased dramatically. The two-photon microscope allows long-term visualization of cell motility in the living tissue with minimal phototoxicity. Using this technique, we examined brain autoantigen-specific T cell behavior in experimental autoimmune encephalitomyelitis, the animal model of human multiple sclerosis. Even before disease symptoms appear, the autoreactive T cells arrive at their target organ. There they crawl along the intraluminal surface of central nervous system (CNS) blood vessels before they extravasate. In the perivascular environment, the T cells meet phagocytes that present autoantigens. This contact activates the T cells to penetrate deep into the CNS parenchyma, where the infiltrated T cells again can find antigen, be further activated, and produce cytokines, resulting in massive immune cell recruitment and clinical disease

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function

<div><p>Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in <i>E</i>. <i>coli</i> mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the <i>E</i>. <i>coli</i> RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.</p></div

Ribosomal pausing induced by secondary structure in CDS.

<p><i>(</i>A) Globally, ribosomal pausing is not significantly affected by the presence of secondary structure in the CDS. Box plot analysis of the ratio of RPF upstream (L1) calculated from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005613#pgen.1005613.e002" target="_blank">Eq 2</a> and downstream (L2) calculated from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005613#pgen.1005613.e003" target="_blank">Eq 3</a> of detected secondary structures (<i>P</i> = 0.1209, Kolmogorov-Smirnov test). (B,C) Ribosomal pausing is observed within coding sequences above the 80^th percentile (panel A). Examples of <i>ompF</i> transcript with previously validated secondary structure [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005613#pgen.1005613.ref065" target="_blank">65</a>] (B) as well as newly detected genes (C) for which a local secondary structure causes non-uniform ribosomal distribution. Aligned PARS score (upper panel, gray) with the RPF counts (bottom panel, red) at each nucleotide.</p

The stop codon of operon genes is more structured than non-operon genes.

<p>(A) Average PARS score and GC content for each position of genes terminating with UAA (black), UAG (red) and UGA (green) stop codons. (B) RPF coverage around the stop codon region for genes terminated by UAA (black), UAG (dashed red) and UGA (green) stop codons. Only genes with coverage over 60 reads (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005613#pgen.1005613.s004" target="_blank">S4D Fig</a>) were used; overlapping operon genes were excluded. Note, that UAG-terminated genes are included only for comparison; their low number prevents performing any statistical analysis. The inset shows, for both UAA- and UAG-terminated genes, the ratio between the RPFs downstream of the stop codon (3 to27 nt) and a mean of the CDS. The readthrough value for the majority of the genes was zero; only genes with a value higher than zero are plotted.</p

mRNA structure correlates with mRNA abundance.

<p>(A) Distribution of transcript abundance, expressed in gene read counts normalized by the length of CDS per kilobase and the total mapped reads per million (rpkM). The 30% least (blue) and most (green) abundant genes from the reliably detected genes (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005613#pgen.1005613.s004" target="_blank">S4 Fig</a>) are highlighted. (B) Dependence of the mean PARS score on the mRNA abundance of the middle (black) and most (green) abundant transcripts as defined in panel A. R = 0.777, Pearson correlation coefficient. (C) Average PARS score (top) and GC content (bottom) for each position of all transcripts (black curve) as well as the 30% most (green) and least (blue) abundant. (D) Average PARS score (top) and GC content (bottom) for each position around the top 64 RNase E cleavage sites (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005613#pgen.1005613.s010" target="_blank">S2 Table</a>). Inset, the sequence logo of the aligned RNase E cleavage sites, spanning from -10 to +10 nt.</p

PARS analysis.

<p>(A) Overview of modified PARS approach. RNase V1 cleaves double-stranded RNA and combination of RNases A/T1 the single stranded RNA with optimal activities at physiological pH (7.0). RNAse A/T1 usage requires an additional phosphorylation step prior to library generation. (B) The PARS score of the <i>rpoS</i> leader sequence (inset) was overlaid with the experimentally determined structure [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005613#pgen.1005613.ref064" target="_blank">64</a>]. Double-stranded nucleotides with positive PARS score are colored red, single-stranded nucleotides with negative PARS score–blue, nucleotides with missing PARS score or equal to zero–green. The color intensity of the <i>rpoS</i> nucleotides reflects the PARS scores (rainbow legend). (C) Metagene analysis of protein-coding transcripts. Average PARS score for each nucleotide (top) and GC content (bottom) across the 5’UTRs, CDS and 3’UTRs of all protein-coding transcripts, aligned at the start or stop codon, respectively. For the shaded areas the average PARS scores or GC content is calculated; thus note the deviations from the total GC content of 51% in <i>E</i>. <i>coli</i>. Unstructured region upstream of the start codon and structured sequence preceding the stop codon are marked by arrows with filled and open arrow heads, respectively.</p