Regulation of Heterogenous LexA Expression in Staphylococcus aureus by an Antisense RNA Originating from Transcriptional Read-Through upon Natural Mispairings in the sbrB Intrinsic Terminator

Bacterial genomes are pervasively transcribed, generating a wide variety of antisense RNAs (asRNAs). Many of them originate from transcriptional read-through events (TREs) during the transcription termination process. Previous transcriptome analyses revealed that the lexA gene from Staphylococcus aureus, which encodes the main SOS response regulator, is affected by the presence of an asRNA. Here, we show that the lexA antisense RNA (lexA-asRNA) is generated by a TRE on the intrinsic terminator (TTsbrB) of the sbrB gene, which is located downstream of lexA, in the opposite strand. Transcriptional read-through occurs by a natural mutation that destabilizes the TTsbrB structure and modifies the efficiency of the intrinsic terminator. Restoring the mispairing mutation in the hairpin of TTsbrB prevented lexA-asRNA transcription. The level of lexA-asRNA directly correlated with cellular stress since the expressions of sbrB and lexA-asRNA depend on the stress transcription factor SigB. Comparative analyses revealed strain-specific nucleotide polymorphisms within TTsbrB, suggesting that this TT could be prone to accumulating natural mutations. A genome-wide analysis of TREs suggested that mispairings in TT hairpins might provide wider transcriptional connections with downstream genes and, ultimately, transcriptomic variability among S. aureus strains.

Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes

All-flesh tomato cultivars are devoid of locular gel and exhibit enhanced firmness and improved postharvest storage. Here, we show that SlMBP3 is a master regulator of locular tissue in tomato fruit and that a deletion at the gene locus underpins the All-flesh trait. Intriguingly, All-flesh varieties lack the deleterious phenotypes reported previously for SlMBP3 under-expressing lines and which preclude any potential commercial use. We resolve the causal factor for this phenotypic divergence through the discovery of a natural mutation at the SlAGL11 locus, a close homolog of SlMBP3. Misexpressing SlMBP3 impairs locular gel formation through massive transcriptomic reprogramming at initial phases of fruit development. SlMBP3 influences locule gel formation by controlling cell cycle and cell expansion genes, indicating that important components of fruit softening are determined at early pre-ripening stages. Our findings define potential breeding targets for improved texture in tomato and possibly other fleshy fruits.

Mutation saturation for fitness effects at human CpG sites

Whole exome sequences have now been collected for millions of humans, with the related goals of identifying pathogenic mutations in patients and establishing reference repositories of data from unaffected individuals. As a result, we are approaching an important limit, in which datasets are large enough that, in the absence of natural selection, every highly mutable site will have experienced at least one mutation in the genealogical history of the sample. Here, we focus on CpG sites that are methylated in the germline and experience mutations to T at an elevated rate of ~10-7 per site per generation; considering synonymous mutations in a sample of 390,000 individuals, ~99% of such CpG sites harbor a C/T polymorphism. Methylated CpG sites provide a natural mutation saturation experiment for fitness effects: as we show, at current sample sizes, not seeing a non-synonymous polymorphism is indicative of strong selection against that mutation. We rely on this idea in order to directly identify a subset of CpG transitions that are likely to be highly deleterious, including ~27% of possible loss-of-function mutations, and up to 20% of possible missense mutations, depending on the type of functional site in which they occur. Unlike methylated CpGs, most mutation types, with rates on the order of 10-8 or 10-9, remain very far from saturation. We discuss what these findings imply for interpreting the potential clinical relevance of mutations from their presence or absence in reference databases and for inferences about the fitness effects of new mutations.

Study of Wine Volatile Composition of Tempranillo versus Tempranillo Blanco, a New White Grape Variety

The aim of this work was to analyze and compare the concentration of higher alcohols, esters, and acids in wines from Tempranillo and Tempranillo Blanco. Tempranillo Blanco is a new and little-studied white variety that originated from Tempranillo by a natural mutation. During three seasons, grapevines of both varieties were harvested, and nine wines were made from each. The volatile composition of the wines was determined by GC-MS. In the wines of both varieties, the content of higher alcohols was higher than those of esters and acids. Wines from Tempranillo Blanco had lower content of 2-phenylethanol, methionol, 1-hexanol, benzyl alcohol, and total higher alcohols, but higher hexyl acetate and ethyl decanoate than Tempranillo wines. Total ethyl esters and total esters were higher in Tempranillo wines due to the higher ethyl lactate and ethyl succinate content derivate from the malolactic fermentation that was not made in Tempranillo Blanco. The content of hexanoic and octanoic acids and total acids was also higher in Tempranillo Blanco wines than in Tempranillo. This is one of the first studies carried out on the wine volatile composition of Tempranillo Blanco and therefore contributes to a better understanding of the oenological characteristics of this white variety.

Structural Analysis And Molecular Characteristics of SARSCoV-2 Spike Protein Following S494P Point Mutation: Molecular Dynamics Study

The emergence of some mutations in the SARS-CoV-2 receptor binding domain (RBD) can increase the spread and pathogenicity due to the conformational changes and increase the stability of Spike protein. Due to the formation of different strains of SARS-CoV-2 by mutations, and their catastrophic effect on public health, the study of the effect of mutations by scientists and researchers around the world is inevitable. According to available evidence, the S494P variant is observed in several SARS-CoV-2 strains from Michigan, USA. To investigate how the S494P natural mutation alters receptor binding affinity in RBD, we performed structural analysis of wild-type and mutant spike proteins using some bioinformatics and computational tools. The results show that S494P mutation increases the spike protein stability. Also, applying docking by HADDOCK displayed higher binding affinity to hACE2 for mutant spike than wild type possibly due to the increased β-strand and Turn secondary structures which increases surface accessibly surface area (SASA) and chance of interaction. The analysis of S494P as a critical RBD mutation may provide the continuing surveillance of spike mutations to aid in the development of COVID-19 drugs and vaccines.

Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2

Neutralizing antibodies (nAbs) to SARS-CoV-2 hold powerful potentials for clinical interventions against COVID-19 disease. However, their common genetic and biologic features remain elusive. Here we interrogate a total of 165 antibodies from eight COVID-19 patients, and find that potent nAbs from different patients have disproportionally high representation of IGHV3-53/3-66 usage, and therefore termed as public antibodies. Crystal structural comparison of these antibodies reveals they share similar angle of approach to RBD, overlap in buried surface and binding residues on RBD, and have substantial spatial clash with receptor angiotensin-converting enzyme-2 (ACE2) in binding to RBD. Site-directed mutagenesis confirms these common binding features although some minor differences are found. One representative antibody, P5A-3C8, demonstrates extraordinarily protective efficacy in a golden Syrian hamster model against SARS-CoV-2 infection. However, virus escape analysis identifies a single natural mutation in RBD, namely K417N found in B.1.351 variant from South Africa, abolished the neutralizing activity of these public antibodies. The discovery of public antibodies and shared escape mutation highlight the intricate relationship between antibody response and SARS-CoV-2, and provide critical reference for the development of antibody and vaccine strategies to overcome the antigenic variation of SARS-CoV-2.

Screening Cotoneaster sp. for Resistance to Fire Blight Using Foliar Inoculation with Two Strains of Erwinia amylovora

The genus Cotoneaster is composed of ≈400 species with a wide variety of growth habits and forms. These hardy landscape shrubs used to be commonplace because of their low maintenance and landscape functionality. However, the interest in and sales of cotoneaster have decreased for a variety of reasons, with the greatest being its susceptibility to a bacterial disease fire blight caused by Erwinia amylovora. The resistances of 15 different genotypes of Cotoneaster to a wild-type strain of Erwinia amylovora (Ea153) and a strain LA635 that has a natural mutation in avrRpt2 that encodes for a type III secretion effector were tested separately by inoculating leaves. Fire blight resistance was assessed by calculating the percent shoot necrosis (PSN) [PSN = 100 × (lesion length ÷ total branch length)] at 6 to 8 weeks after inoculation. Across all experiments, Cotoneaster genotypes H2011-01-002 and C. ×suecicus ‘Emerald Sprite’ consistently had the lowest PSN values when inoculated with either strain. Cotoneaster ×suecicus ‘Emerald Beauty’ was significantly more resistant to Ea153 than to LA635, whereas C. splendens was significantly more susceptible to Ea153 than to LA635.

Mutation saturation for fitness effects at human CpG sites

Whole exome sequences have now been collected for millions of humans, with the related goals of identifying pathogenic mutations in patients and establishing reference repositories of data from unaffected individuals. As a result, we are approaching an important limit, in which datasets are large enough that, in the absence of natural selection, every highly mutable site will have experienced at least one mutation in the genealogical history of the sample. Here, we focus on putatively-neutral, synonymous CpG sites that are methylated in the germline and experience mutations to T at an elevated rate of ~10-7 per site per generation; in a sample of 390,000 individuals, ~99% of such CpG sites harbor a C/T polymorphism. These CpG sites provide a natural mutation saturation experiment for fitness effects: as we show, at current sample sizes, not seeing a polymorphism is indicative of strong selection against that mutation. We rely on this idea in order to directly identify a subset of highly deleterious CpG transitions, including ~27% of possible loss-of-function mutations, and up to 21% of possible missense mutations, depending on the type of site in which they occur. Unlike methylated CpGs, most mutation types, with rates on the order of 10-8 or 10-9, remain very far from saturation. We discuss what this contrast implies about interpreting the potential clinical relevance of mutations from their presence or absence in reference databases and for inferences about the fitness effects of new mutations.

Social Acceptance for Commercialization of Genetically Modified Food Animals

Genetically modified food animals (GMFAs) are needed to address early the cumulative effects of livestock production on the environment and to accommodate future food demands. In 2020 China and the U.S., the world's two largest economies, embarked on regulatory reforms to boost the commercialization of such animals. However, gaining social acceptance of GMFAs for commercialization remains a global challenge. We propose a framework that focuses on social license for commercialization of GMFAs by defining four classes of improvement using precision genetics: 1) animals equivalent to natural variation to obtain the improved effect of cross-breeding (ENV); 2) animals with an inactivated gene that could occur via natural mutation (ENC-); 3) animals harboring a natural genetic sequence isolated from another species (ENC+); and 4) animals with synthetic sequences encoding novel genes (BNE). Our approach can guide regulators and the public to support orderly commercialization of genetically modified food animals.

COVID-19 New variant and air pollution relationship: how airborne mutagens agent can act on genoma viruses expression: Hypothesis of work

Before actual COVID-19 pandemia coronavirus was not so dangerous like now. In December 2019 - January 2020 in Wuhan first and then in other places this coronavirus was responsible of a first wave of severe pulmonitis responsible of many deaths. Wuhan and other region involved first was high level air polluted and industrial area. New COVID-19 variant in last part of 2020 and in first month of 2021 was responsible of great diffusion of this pandemic disease. UK, South Africa and brasilian new variant show higher diffusion then the first wave of COVID-19. Aim of this work is to analyze relationship with air pollution and the possibility that mutagen substantia inside of this microenvironment can produce new variant trough an genetic pressure process. RNA viruses are normally subjected by natural mutation but some phenomena can contribute to accelerate this process and their airborne – aeresols microenvironment is relevant. Some air pollutants are recognized as mutagen factors by literature.