Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability

The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes 16 non-structural (Nsp) and 4 structural proteins. Among the Nsps, Nsp1 inhibits host gene expression and also evades the immune system. This protein has been proposed as a target for vaccine development and also for drug design. Owing to its important role, the current study aimed to identify mutations in Nsp1 and their effect on protein stability and flexibility. This is the first comprehensive study in which 295,000 complete genomes have been screened for mutations after alignment with the Wuhan-Hu-1 reference genome (Accession NC_045512), using the CoVsurver app. The sequences harbored 933 mutations in the entire coding region of Nsp1. The most frequently occurring mutation in the 180-amino-acid Nsp1 protein was R24C (n = 1122), followed by D75E (n = 890), D48G (n = 881), H110Y (n = 860), and D144A (n = 648). Among the 933 non-synonymous mutations, 529 exhibited a destabilizing effect. Similarly, a gain in flexibility was observed in 542 mutations. The majority of the most frequent mutations were detected in the loop regions. These findings imply that Nsp1 mutations might be useful to exploit SARS-CoV-2′s pathogenicity. Genomic sequencing of SARS-CoV-2 on a regular basis will further assist in analyzing variations among the drug targets and to test the diagnostic accuracy. This wide range of mutations and their effect on Nsp1’s stability may have some consequences for the host’s innate immune response to SARS-CoV-2 infection and also for the vaccines’ efficacy. Based on this mutational information, geographically strain-specific drugs, vaccines, and antibody combinations could be a useful strategy against SARS-CoV-2 infection.

Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon

Brachypodium distachyon is an established model for monocotyledonous plants. Numerous markers intended for gene discovery and population genetics have been designed. However to date, very few indel markers with larger and easily scored length polymorphism differences, that distinguish between the two morphologically similar and highly utilized B. distachyon accessions, Bd21, the reference genome accession, and Bd21-3, the transformation-optimal accession, are publically available. In this study, 22 indel markers were designed and utilized to produce length polymorphism differences of 150 bp or more, for easy discrimination between Bd21 and Bd21-3. When tested on four other B. distachyon accessions, one case of multiallelism was observed. It was also shown that the markers could be used to determine homozygosity and heterozygosity at specific loci in a Bd21 x Bd3-1 F2 population. The work done in this study allows researchers to maintain the fidelity of Bd21 and Bd21-3 stocks for both transgenic and nontransgenic studies. It also provides markers that can be utilized in conjunction with others already available for further research on population genetics, gene discovery and gene characterization, all of which are necessary for the relevance of B. distachyon as a model species.

Improved genome ofAgrobacterium radiobactertype strain provides new taxonomic insight intoAgrobacteriumgenomospecies 4

The reportedAgrobacterium radiobacterDSM 30174Tgenome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced theAgrobacterium radiobactertype strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome ofAgrobacterium tumefaciensB6T, enabling for the first time, a proper comparative genomics of these contentiousAgrobacteriumspecies. We provide concrete evidence that the previously reportedAgrobacterium radiobactertype strain genome (Accession Number:ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose thatAgrobacterium tumefaciensbe reclassified asAgrobacterium radiobactersubsp.tumefaciensand thatAgrobacterium radiobacterretains it species status with the proposed name ofAgrobacterium radiobactersubsp.radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of bothAgrobacterium radiobacterandAgrobacterium tumefaciensinto a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates thatAgrobacterium radiobacterNCPPB3001 is sufficiently divergent fromAgrobacterium tumefaciensto propose two independent sub-clades. Third,Agrobacterium tumefaciensdemonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively thanAgrobacterium radiobacter.