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16s Ribosomal Rna - Crossref

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Last Updated: 12 June 2022

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Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli

"The bacterial ribosome, which is composed of three rRNA molecules and 57 proteins, plays a key role in translating mRNA-encoded information into proteins. " However, we have recently discovered that an active hybrid ribosome with non-u2013 E. coli bacteria can be recreated in vivo, using Escherichia coli u03947 as a host. We used a metagenomic approach to screen for 16S rRNA genes that match E. coli u03947's growth to investigate the mutational robustness of 16S rRNA and the functional basis for its function. Despite the large sequence variety of the functional 16S rRNA molecules, each mutant's doubling times increased only marginally with decreasing sequence identity. Our results show that 16S rRNA functionality is largely dependent on the secondary structure, not on the sequence itself.

Source link: https://doi.org/10.1073/pnas.1213609109


Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA

Complexes of ribosomal RNAs and a variety of proteins are present in both the small and large subunits of the ribosome's molecular machine that synthesizes proteins. " The central domain of the 16S rRNA folds independently, either by Mg 2+ ions or by interaction with ribosomal proteins. The rRNA folds cooperatively throughout the world, according to Mg 2+'s dependence on the radius of gyration. Various neogenic components order at different Mg 2+ concentrations, hinting at the heterogeneous assembly even within a single domain of the rRNA. Mg 2+ ions binding is highly specific, with ion condensation leading to nucleation of tertiary structures. "We also estimate the Mg 2+ -dependent protection factors, which are tangible in hydroxyl radical footprinting studies, which further confirm Mg 2+ -induced folding's specificity. ".

Source link: https://doi.org/10.1101/2020.04.08.032474


Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling

"16S ribosomal RNA gene sequencing is widely used for microbiota profiling with NGS technologies. " Sequencing the full-length 16S RNA gene is impractical since most common NGS platforms produce short reads, so sequencing the full-length 16S rRNA gene is impractical. All nine 16S rRNA hypervariable regions are taxonomically valuable, but choosing the right 16S rRNA hypervariable region will depend on the habitat under study's bacterial composition. However, there is no current study that has evaluated the results of various 16S rRNA hypervariable regions for male urinary microbiota profiling. We obtained urine samples from male volunteers and analyzed their urinary microbiota by sequencing a panel of six amplicons covering the nine 16S rRNA hypervariable regions. According to V1V2 hypervariable regions, more suitable for male urinary microbiota testing is more appropriate for male urinary microbiota analysis.

Source link: https://doi.org/10.3389/fcimb.2022.862338


Site-directed hydroxyl radical probing of 30S ribosomal subunits by using Fe(II) tethered to an interruption in the 16S rRNA chain

One corresponding to the 5:u2032 and central domains of 16S rRNA and the other corresponding to its 3rd domain assemble quickly in trans with 30S ribosomal proteins to produce a cohesive ribonucleoprotein particle cosediments with natural 30S subunits. The particles have a reduced ability to bind tRNA near conditions that have been implicated in tRNA binding. "From Fe tethered to the 532 end of the 3192 transcript, the trans construct was used to investigate the three-dimensional RNA community around position 922 of 16S rRNA by producing hydroxyl radicals from Fe tethered to the 5u2032 transcript. ".

Source link: https://doi.org/10.1073/pnas.96.2.366


Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy

"Ribosomal protein S8 of Escherichia coli, a key player in 30S ribosomal subunit assembly assembly" is due to the association of 16S rRNA. By using NMR spectroscopy, we have investigated the rRNA binding site for S8 both in the free state and in the presence of protein. Nevertheless, S8 binding promotes the establishment of the U598-u00b7A640 base pair and helps to maintain the G597-u00b7A643 base pair and A614 base pairs. ".

Source link: https://doi.org/10.1073/pnas.94.6.2139


Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4.

"Localized hydroxyl radical probing has been used to investigate the rRNA neighborhood within a small area of the Escherichia coli 30S ribosomal subunit's architecture. " By in vitro reconstitution using 16S rRNA and a mixture of the remaining 30S subunit proteins, the S4 was either complicateded with 16S rRNA or incorporated into active 30S ribosomal subunits. [Fe-Cys31]S4 was then converted into active 30S ribosomal subunits. [Fe-Cys31]S4 was then reconstituted with 16S rRNA or incorporated into active 30S4 was then o reconstitution with 16S subunit proteins [Fe-Cys subunit proteins [Fe subunit proteins. These findings provide valuable insight into the three-dimensional organization of 16S rRNA, as well as showing that these two regions of its 5' domain are in close geographical proximity to Cys-31 of protein S4. ".

Source link: https://doi.org/10.1073/pnas.92.4.1113


An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum.

"The 16S rRNA genes of Pyrobaculum aerophilum and Pyrobaculum islandicum were amplified by polymerase chain reaction, and the resulting products were sequenced in a linear fashion. " Pyrobaculum aerophilum's rRNA gene contains a 713-bp intron that is not present in the corresponding gene of Pyrobaculum islandicum, but they differ in that the 16S rRNA gene of Pyrobaculum aerophilum contains a 713-bp intron not present in the corresponding gene. The intron's open reading frame whose protein translation shows no such homology with any known protein sequence.

Source link: https://doi.org/10.1073/pnas.90.6.2547


Evidence for functional interaction between elongation factor Tu and 16S ribosomal RNA.

"We find that mutant ribosomes are impaired in EF-Tu-dependent binding of aminoacyl-tRNA in vitro, but nonenzymatic binding of tRNA to the A and P sites is unaffected, indicating that the defect involves an EF-Tu-related function rather than tRNA-ribosome interactions per se; in contrast, tRNA-ribosome interactions are not affected. " The mutant ribosomes are present in polysomes at low rates and contain reduced amounts of A-site-bound tRNA, but not at normal levels of P-site tRNA, which are in agreement with the in vitro findings; thus, the primary in vitro mutation rate in G530 can be explained by the lack of mutant ribosomes and ternary complex interaction.

Source link: https://doi.org/10.1073/pnas.90.4.1364


Assembly of the Escherichia coli 30S ribosomal subunit reveals protein-dependent folding of the 16S rRNA domains.

"The 16S rRNA underwent significant conformational changes during the assembly of the 30S subunit that were governed by the ribosomal proteins' cooperative interactions. " The continuous association of the first 12 proteins with the 16S rRNA resulted in the production of core particles containing up to three mass centers at separate stages of the assembly process. These global mass centers may correspond to the 16S rRNA's three key domains. Two of the three domains merge, giving the basic structural characteristics of the native 30S subunit. The E. coli 30S ribosomal subunit's folding of the 16S RNA was domain-specific folding of the 16S rRNA by the growth of distinct intermediate core particles hitherto unobserved. ".

Source link: https://doi.org/10.1073/pnas.88.18.8174


In vitro methylation of Escherichia coli 16S ribosomal RNA and 30S ribosomes.

"The transformation of synthetic 30S particles lacking all of the normally methylated nucleotides with S-adenosyl-[3H]methionine and either a S100 or ribosomal high salt wash extract resulted in ribosome-dependent incorporation of [3H]methyl groups into trichloroacetic acid-insoluble material," the author reports. The 30S ribosome fractions were 6-8 times more active on synthetic unmethylated 16S RNA than on synthetic 30S ribosomes, while N2-methylation activity preferred 30S ribosomes to 16S RNA by a factor of more than 10%. In vivo, two m5C residues, positions 967 and 1407, are found in vivo, with two m5C enzymes present in the 55-85% ammonium sulfate fraction of the high salt wash yielding a maximum of 1. 0 mol of 16S RNA. Methylation of m5C-967 did not need prior methylation of G-966, nor did not require prior methylation of A-1518 and A-1519, and was not dependent on previous methylation of G-1516. ".

Source link: https://doi.org/10.1073/pnas.86.13.4902

* 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