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Members of the family 4-oxalocrotonate tautomerase are small monomers with a structural motif α-β-α and a length between 61 to 84 amino acids. These peptides o mini-proteins catalyze a wide range of chemical reactions, but their chemical capabilities and participation in biological functions remain unknown. We have identified a region that codes for a tautomerase from that family in the endophytic bacteria Caulobacter from the coralloid root of Dioon edule. This tautomerase is encoded in a biosynthetic gene cluster (BGC) between the protein pseudouridine-5 ́-phosphate glucosidase (PsiMP) and the non-ribosomal peptide synthase (NRPS) module. Using genome mining and phylogenetic analysis, we observed that the tautomerase-encoding region and PsiMP are present in several BGCs between various actinomycetes and our Caulobacter strains. In 2019, Kong and co-workers (2019) reported the BGC of C-nucleoside minimycin in Streptomyces hygroscopicus JCM 4712 where the tautomerase-encoding region was fused to the NRPS module. The S. hygroscopicus tautomerase was critical to metabolic divergence in the biosynthesis of two natural products: the alkaloid indigoidine and the minimycin. The role of tautomerase in endophytic Caulobacter strains is unclear. We hypothesize that this enzyme is involved in the substrate selection to initiate the biosynthesis of natural products; indigoidine-like alkaloids and C-nucleosides. Using AlphaFold2, we built the 3D protein structure of endophytic Caulobacter tautomerase with high confidence that we submitted to docking experiments to discover potential enzymatic modulators. We identified a unique protein binding pocket promiscuous to several substrates (i.e., amino acids) and potential inhibitors such as indigoidine.

The Kemp’s ridley is the most endangered of the seven sea turtles. Long-term binational efforts between Mexico and the U.S. have contributed to the preservation of this critically endangered species. The Kemp’s ridley experienced a severe bottleneck, but the population has grown and it is in the path to recovery. Thus, it is important to obtain information on the genomic variability of this sea turtle to determine its evolutionary potential and whether genomic erosion occurred as consequence of the past bottleneck. A fraction of the Kemp’s ridley genome was recently analyzed with a genotyping by sequencing technique known as ddRAD-seq (Double digest restriction-site associated DNA). However, this technique has some limitations, including the presence of artifacts due to batch effect and low sequencing coverage. To improve SNPs recovery rates, a reference genome can be used. In this study, we aim to 1) compare the SNPs recovered with and without using the Kemp's ridley genome draft as reference, 2) validate SNPs using Kemp’s ridley sequenced genomes, and 3) assembly the kemp’s ridley mitochondrial genomes.

The SARS-CoV-2 coronavirus has acquired mutations that underlie multiple evolutionary and epidemiological advantages. Although most of the mutations detected are due to the deletion, substitution or addition of a nucleotide, genomic analyses have found that there are long deletions in SARS-CoV-2 appearing frequently. One of the regions where large deletions have been detected multiple times is in the ORFs 7a/8, but the genomic and/or phenotypic consequences of these deletions are still unknown.

In Mexico, the Mexican Genomic Surveillance Consortium (CoViGen-Mex) found that large deletions were not correctly detected by standard software, since possible deletions could be confused with sequencing errors. For this, it was necessary to create a pipeline that could detect deletions from alignments of raw data to the SARS-CoV-2 reference genome. Using bioinformatic methods, we corroborated a 411 nt deletion in the B.1.243 lineage circulating in Mexico, which was first identified and verified in México by means of PCR and by long read sequencing of amplicons at the INER. We also identified more deletions in virus circulating in Mexico, including a possible 222 nt deletion in SARS-CoV-2 samples assigned to the B.1.243 lineage. The analysis of the alignments of 3805 samples allowed us to detect 97 samples with deletions between ORF7a and ORF8 that circulated in the year 2021. These deletions appear to be unrelated to a particular size or lineage, and they do not have common origin. We now know that multiple deletions of ORFs 7a/8 have been spreading and have emerged in the year 2021. Long deletions could keep appearing in the coming years of the pandemic, for this reason, Indel-Mex will search for large deletions in other regions of the SARS-CoV-2 genome. Determining the frequency, length and metadata correlates of long deletions is the first step towards understanding the functional significance of these deletions in the virus and their implications for human health.