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Rodriguez-Cruz, U. E.

Publications and source records attributed to Rodriguez-Cruz, U. E..

2 recordsLinked to original sources

Role of VapBC4 toxin-antitoxin system of Sulfolobus acidocaldarius in heat stress adaptation

Toxin-antitoxin (TA) systems are important for stress adaptation in prokaryotes, including persistence, antibiotic resistance, pathogenicity, and biofilm formation. Toxins can cause cell death, reversible growth stasis, and direct inhibition of crucial cellular processes through various mechanisms, while antitoxins neutralize the effects of toxins. In bacteria, these systems have been studied in detail, whereas their function in archaea remains elusive. During heat stress, the thermoacidophilic archaeon Sulfolobus acidocaldarius exhibited an increase in the expression of several bicistronic type II vapBC TA systems, with the highest expression observed in the vapBC4 system. In the current study, we performed a comprehensive biochemical characterization of the VapBC4 TA system, establishing it as a bonafide type II toxin-antitoxin system. The VapC4 toxin is shown to have high-temperature catalyzed RNase activity specific for mRNA and rRNA, while the VapB4 antitoxin inhibits the toxic activity of VapC4 by interacting with it. VapC4 toxin expression led to heat-induced persister-like cell formation, allowing the cell to cope with the stress. Furthermore, this study explored the impact of vapBC4 deletion on biofilm formation, whereby deletion of vapC4 led to increased biofilm formation, suggesting its role in regulating biofilm formation. Thus, during heat stress, the liberated VapC4 toxin in cells could potentially signal a preference for persister cell formation over biofilm growth. Thus, our findings shed light on the diverse roles of the VapC4 toxin in inhibiting translation, inducing persister cell formation, and regulating biofilm formation in S. acidocaldarius, enhancing our understanding of TA systems in archaea. IMPORTANCEThis research enhances our knowledge of Toxin-antitoxin (TA) systems in archaea, specifically in the thermoacidophilic archaeon Sulfolobus acidocaldarius. TA systems are widespread in both bacterial and archaeal genomes, indicating their evolutionary importance. However, their exact functions in archaeal cellular physiology are still not well understood. This study sheds light on the complex roles of TA systems and their critical involvement in archaeal stress adaptation, including persistence and biofilm formation. By focusing on S. acidocaldarius, which lives in habitats with fluctuating temperatures that can reach up to 90, the study reveals the unique challenges and survival mechanisms of this organism. The detailed biochemical analysis of the VapBC4 TA system, and its crucial role during heat stress, provides insights into how extremophiles can survive in harsh conditions. The findings of this study show the various functions of the VapC4 toxin, including inhibiting translation, inducing persister-like cell formation, and regulating biofilm formation. This knowledge improves our understanding of TA systems in thermoacidophiles and has broader implications for understanding how microorganisms adapt to extreme environments.

microbiology↗

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Cienegas Basin, Mexico

The sheer diversity of unculturable viruses has prompted the need to describe new viruses through culture-independent techniques. The associated host is one important phenotypic feature that can be inferred from metagenomic viral contigs -- thanks to the development of various bioinformatic tools. Here we compare the performance of recently developed tools for virus-host prediction on a dataset of 1,046 virus-host pairs and then apply the best-performing tools on a metagenomic dataset derived from a highly diverse transiently hypersaline site known as Archaean Domes within the Cuatro Cienegas Basin, Coahuila, Mexico. We also introduce a virus-host prediction tool called CrisprCustomDB, which uses specific criteria to solve controversial host assignments with custom spacers databases. Host-dependent alignment-based methods showed an average precision of 83% and a sensitivity from 13.7% to 17.7%, whereas host-dependent alignment-free methods achieved an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best performance overall (F1_score = 95.7%). However, when applied to the highly diverse metagenomic dataset, the host-dependent alignment-based (e.g., CrisprCustomDB) and alignment-free (e.g., PHP) methods showed the greatest agreement with each other, even though they are fundamentally different methods. This is because instead of depending on known hosts or viruses-with-known-host databases, they can directly relate metagenomic viral contigs and metagenome-assembled genomes from the same dataset. Such methods also showed the greatest consistency between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism, revealing that Archaean Domes viruses likely infect halophilic Archaea as well as a variety of Bacteria which may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing or marine-related. Consequently, using a combination of methods and qualitative validations relating to the source environment and the predicted host biology will increase the number of correct predictions, mainly when dealing with novel viruses.

bioinformatics↗