HIV-1 Vif versus APOBEC3G: newly appreciated warriors in the ancient battle between virus and host

Characterization of urease active calcite-producing strain YX-3 combined with the whole genome

Urease found in a wide range of microorganisms plays a vital role in ureolytic induced calcite precipitation (UICP). However, the genomic information on urease-producing strains is limited, and there is a need for further in-depth studies on aspects such as the regulation of urease activity by nickel ligand residues. The present study delved into the elucidation of urease activity in a newly isolated strain YX-3 coupled with nickel-ligand residues by employing the genetic architecture of biomineralization-controlled growth, molecular docking, molecular dynamics simulation (MDS), and site-directed mutagenesis. Genome-wide sequencing showed the presence of urease gene clusters, comprising structural genes ureA, ureB, and ureC, alongside auxiliary genes ureD, ureE, ureF, and ureG. RT-qPCR analysis showed that the addition of NiCl2 resulted in a significant up-regulation of ureC expression. His267, His294, and Gly325 in the domain of UreC were further proved to coordinate with nickel ions and urea simultaneously through homology modeling and molecular docking, and molecular dynamics simulations (MDS) showed the urease-urea docking complexes exhibited degressive binding stability by four metrics including root mean square deviations (RMSD) when those residues were mutated into alanine respectively. Western blotting exhibited that mutations of H267A, H294A, and G325A led to a reduction in the relative expression of urease, wherein urease activity was about 62%, 45%, and 20% times that of the wild type (WT), respectively. The overexpression results further confirmed the importance of these residues for urease activity and CaCO3 precipitation. These results would help to deepen the understanding of urease-producing strains at a molecular level and expand the theoretical basis for modulating urease activity.

Biomineralization in Cave Bacteria—Popcorn and Soda Straw Crystal Formations, Morphologies, and Potential Metabolic Pathways

Caves are extreme, often oligotrophic, environments that house diverse groups of microorganisms. Many of these microbes can perform microbiologically induced carbonate precipitation (MICP) to form crystalline secondary cave deposits known as speleothems. The urease family is a group of enzymes involved in MICP that catalyze the breakdown of urea, which is a source of energy, into ammonia and carbonate. Carbonate anions are effluxed to the extracellular surface of the bacterium where it then binds to environmental calcium to form calcium carbonate which then continues to grow in crystal form. Here, we studied bacterial communities from speleothems collected from the Iron Curtain Cave (ICC) in Chilliwack, B.C., Canada, to characterize these organisms and determine whether urease-positive (U+) bacteria were present in the cave and their potential impact on speleothem formation. The ICC is a carbonate cave located on the northside of Chipmunk Ridge, presenting a unique environment with high iron content sediment and limestone structures throughout. With six pools of water throughout the cave, the environment is highly humid, with temperatures ranging between 4 and 12°C depending on the time of year. Ninety-nine bacterial strains were isolated from popcorn (PCS) and soda straw (SSS) speleothems. These isolates were screened for urease enzymatic activity, with 11 candidates found to be urease-positive. After incubation, species-specific crystal morphologies were observed. Popcorn speleothem provided more bacterial diversity overall when compared to soda straw speleothem when examined under a culture-based method. Nearly twice as many U+ isolates were isolated from popcorn speleothems compared to soda straw speleothems. The U+ candidates were identified to the genus level by 16S rRNA analysis, and two isolates underwent whole-genome sequencing. Two novel species were identified as Sphingobacterium sp. PCS056 and Pseudarthrobacter sp. SSS035. Both isolates demonstrated the most crystal production as well as the most morphologically dissimilar crystal shapes in broth culture and were found to produce crystals as previously observed in both agar and broth media. The results from this study are consistent with the involvement of urease-positive bacteria isolated from the ICC in the formation of cave speleothems. 16S rRNA sequencing revealed a diverse set of microbes inhabiting the speleothems that have urease activity. Whole-genome sequencing of the two chosen isolates confirmed the presence of urease pathways, while revealing differences in urease pathway structure and number. This research contributes to understanding microbial-associated cave formation and degradation, with applications to cave conservation, microbiota composition, and their role in shaping the cave environment.

The HIV-1 transcriptional activator Tat has potent nucleic acid chaperoning activities in vitro

The human immunodeficiency virus type 1 (HIV-1) is a primate lentivirus that causes the acquired immunodeficiency syndrome (AIDS). In addition to the virion structural proteins and enzyme precursors, that are Gag, Env and Pol, HIV-1 encodes several regulatory proteins, notably a small nuclear transcriptional activator named Tat. The Tat protein is absolutely required for virus replication since it controls proviral DNA transcription to generate the full-length viral mRNA. Tat can also regulate mRNA capping and splicing and was recently found to interfere with the cellular mi- and siRNA machinery. Because of its extensive interplay with nucleic acids, and its basic and disordered nature we speculated that Tat had nucleic acid-chaperoning properties. This prompted us to examine in vitro the nucleic acid-chaperoning activities of Tat and Tat peptides made by chemical synthesis. Here we report that Tat has potent nucleic acid-chaperoning activities according to the standard DNA annealing, DNA and RNA strand exchange, RNA ribozyme cleavage and trans-splicing assays. The active Tat(44–61) peptide identified here corresponds to the smallest known sequence with DNA/RNA chaperoning properties.