Size-variable zone in V3 region of 16S rRNA

Abstract

The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95). The sizes of different regions ranged from 96.7 to 283.1 nucleotides and had similar distribution patterns, except for the V3 region, which exhibited a bimodal distribution composed of 2 main peaks of 161 and 186 nt. The alignment of Consensuses95 of fractions 161 and 186 showed a high degree of similarity and conservation, except for the central positions (gap zone), where the sequence was highly variable and several deletions were observed. Structurally, the gap zone forms the central part of helix 17 (H17), and its extension was directly reflected in the size of this helix. H17 is part of a multihelix conjunction known as the 5-way junction (5 WJ), which is indispensable for 30 S ribosome assembly. However, because a drastic variation in the sequence size of V3 region occurs at a central position in loop H17 without affecting the base of the loop, it has no apparent effect on 5 WJ. Finally, considering that these differences were detected in non-redundant sequences, it can be concluded that this is not an uncommon or isolated event and that the V3 region is possibly more likely to mutate than are other regions.

Hot in Cold: Microbial Life in the Hottest Springs in Permafrost

“…Sample 3701, where archaea represented up to 40% of all the V3-V4 amplicon reads, made a remarkable exception. However, only 7.7% of V4 amplicon reads in this sample were assigned to Archaea ( Figure 4 ), which might be explained by a systematic underestimation of Acetothermia by V3–V4 amplicon reads due to the increased length of the V3 variable region in this phylum and significant amplification biases [ 29 ]. Therefore, the V4 amplicon data for that particular sample look more reliable than those obtained for the V3-V4 region.…”

BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities

“…Quality steps were then taken via the removal of aberrant eukaryotic, mitochondrial, chloroplastic, and ambiguous nucleotide-containing sequences. Moreover, sequences that were suspiciously short or long within their V4 region (relative to other sequences from the same genus) were removed on the basis that the V4 region should be highly consistent in length between closely related taxonomic group members ( 87 ). To do so, the V4-targeting primers in Table 1 were used to trim sequences to the V4 region using the pcr.seqs function of mothur (v.1.39.5) ( 88 ).…”

Reduced ribosome activity influences the non-uniform evolution of 16S rRNA hypervariable regions

“…The central region of V3 is highly variable and some bacteria have V3 versions lacking approximately 25 residues from the central portion, including members within a genus, e.g., Clostridioides ( Fig. 4A ) (34). This observation suggests that the central portion of V3 (encoding the outer stem-loop of H17) is not important for ribosome activity.…”

“…16S hypervariable regions from different bacteria tend to have similar sizes that symmetrically cluster around a mean value (34). One curious exception to this pattern is found in the V3 region encoding helix 17 (H17), the lower stem of which is involved in the assembly of the small subunit (35)(36)(37).…”