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16s Rrna - Astrophysics Data System

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Last Updated: 10 May 2022

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Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity

Small ribosomal subunit assembly is required for small ribosomal subunit assembly assembly, and it is indispensable for SSU function. Previously, we found a point mutation in S5, which alters both SSU formation and translational fidelity in vivo, which is unprecedented for other characterized S5 mutations. Analyses of p16S rRNA-containing ribosomes from other strains have shown a correlation between the number of 5'end maturation of 16S rRNA and translational miscoding, which has been supported by the investigation of a correlation between the two strains' end maturation of 16S rRNA and translational miscoding. Genetic profiling of mutant ribosomes with additional leader sequences at the 5' end of 16S rRNA compared to WT ribosomes revealed structural differences in the region of helix 1. The presence of additional nucleotides at the 5' end of 16S rRNA's translation ribosomes could also change fidelity by altering the architecture of 16S rRNA translation ribosomes, implying that fidelity is governed by accuracy and completeness of the SSU biogenesis cascade.

Source link: https://ui.adsabs.harvard.edu/abs/2010PNAS..107.4567R/abstract


Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

Here we show that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis, are regularly present in multiple self-splicing introns of variable length. The 16S rRNA genes can now be expanded to up to 3. 5 kb. Introns have never been identified in bacterial 16S rRNA genes before, although they are the most commonly sequenced genes today, introns have never been found in bacterial 16S rRNA genes. Even though an elongation of rRNA genes due to intervening sequences has previously been reported, the elongation of rRNA genes due to intervening sequences has so far been considered when designing 16S rRNA-based clone libraries. The finding of elongated 16S rRNA genes has significant implications for traditional molecular biology research, as well as the emergence of systematic biases in several techniques.

Source link: https://ui.adsabs.harvard.edu/abs/2012PNAS..109.4203S/abstract


Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing

However, the microbial community involved in water treatment is highly seasonal, and biological reactions can be sensitive to cold temperatures, as for most treatment plants in temperate/continental climates. In this research, we used 16S RNA transcript sequencing to identify "active" populations and gain a deeper understanding of microbial activity patterns within activated sludge. As seasons change, seasonal abundances of individual populations in activated sludge change, but a small group of key microorganisms remains throughout the year, with some remaining or absent without any evidence of their presence or growth. Nonproliferating OTUs were mainly human health related, while seasonal abundance changes had previously been identified as being associated with floc formation and bulking. Based on determining and sequencing 16S rRNA transcripts, the study provides an analysis of the seasonal dynamics of microbial activity variations in activated sludge. IMPORTANCE Sequencing batch reactors are a common style for wastewater treatment plants, especially in smaller municipalities, due to their low footprint and ease of operation. The microbial community involved in water treatment is highly seasonal, as for most treatment plants in temperate/continental climates, but the biological reactions can be sensitive to cold temperatures, as shown by this article. However, the activated sludge microbial community is quite diverse, and finding which organisms are active and which are simply present is often difficult, as it is often difficult to determine which organisms are present and which are simply present. We learned new insights into seasonal microbial populations' dynamics and activity patterns affecting wastewater treatment by addressing these topics.

Source link: https://ui.adsabs.harvard.edu/abs/2020ApEnM..86E.597J/abstract


Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold

A methodological shift in how research teams investigate microbial diversity has been introduced by advances in the analysis of amplicon sequence datasets, moving from sequence identification-based clustering to denoising techniques. While denoising techniques have several inherent characteristics that make them more effective than clustering-based strategies, questions remain as to the effect that these pipelines have on the ecological patterns being investigated, particularly in comparison to other methodological choices made when processing data and computing diversity indices. We compared the empirical results of two widely used techniques, DADA2 vs. Mothur on 16S rRNA gene amplicon datasets, and compared such results to the rarefaction of the community table and the OTU identity threshold on the ecological signals identified, comparing the ecological signals found. In six rivers in the southeastern United States, we used a database containing freshwater invertebrate gut and environmental groups sampled.

Source link: https://ui.adsabs.harvard.edu/abs/2022PLoSO..1764443C/abstract


The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA

We reported previously that the protein recognizes nine nucleotides near the end of 16S rRNA's 3' end, and that this recognition enhances GTP-hydrolyzing activity of Era. However, whether Era works with G1530 and/or h45, and whether such interactions contribute to Era's GTPase production were unknown. Two RNA structures with nucleotides 1506-1542, one in complicated with Era and GDPNP, a non-hydrolysable GTP-analogue, and the other in a complex with Era and GDPNP, a non-hydrolysable GTP-analogue, and the other in difficult with Era, GNP, and the KsgA methyltransferase are shown here. The structures reveal that Era recognizes ten nucleotides, including G1530, and that the h45 is also binds h45. Moreover, GTPase assay experiments show that G1530 does not boost Era's GTPase production in the Era. Although G1530 does not contribute to Era's intrinsic GTPase activity, its involvement with Era is crucial for binding and is required for the protein to function, contributing to the discovery of a new cold-sensitive phenotype of Age.

Source link: https://ui.adsabs.harvard.edu/abs/2011PNAS..10810156T/abstract


MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Here, we sequenced more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants around the world and use the sequences to build the 'MiDAS 4' database. MiDAS 4 is an amplicon sequence variant that has been mapped, full-length 16S rRNA gene reference database with a complete taxonomy for all sequences from domain to species level for all sequences. MiDAS 4, compared to commonly used universal reference databases, gives greater coverage of WWTP bacteria and a higher rate of genus and species level classification, according to an independent survey. We perform an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common primers targeting regions of the 16S rRNA gene, demonstrating how environmental conditions and biogeography influence the activated sludge microbiota.

Source link: https://ui.adsabs.harvard.edu/abs/2022NatCo..13.1908D/abstract


16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis

Both children and adults with ulcerative colitis have been identified in association with human gut microbiota in association with ulcerative colitis, whether 16S rRNA gene or shotgun sequencing results were used. Based on cross validation, several species of the Christensenellaceae family were found to be depleted and some species in the Enterobacteriaceae family were found to be enriched in pediatric UC, and both 16S rRNA and shotgun sequencing results can help determine pediatric UC status, with areas under receiver operating characteristic curves below 0. 90 based on cross validation. We found that 16S rRNA data produced similar findings as shotgun results in terms of alpha diversity, beta diversity, and prediction accuracy. Pediatric UC patients have a dysbiotic and less diverse gut microbial population with distinct differences from healthy children, according to our review. In comparison to shotgun data, which can be more expensive and laborious, we also showed that 16S rRNA data delivered accurate disease prediction results in comparison to shotgun data.

Source link: https://ui.adsabs.harvard.edu/abs/2022NatSR..12.6421Z/abstract

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions