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The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.

Jay ZJ, Inskeep WP - Biol. Direct (2015)

Bottom Line: Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically.The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

View Article: PubMed Central - PubMed

Affiliation: Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA. zackary.jay@montana.edu.

ABSTRACT

Background: Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences.

Results: Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.

Conclusions: The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

No MeSH data available.


Related in: MedlinePlus

The location (E. coli numbering) of intron sequences (identified in the current study) within the transcribed secondary structure of the 16S rRNA gene. Variable regions (V1 - V9) are shown for reference
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Fig3: The location (E. coli numbering) of intron sequences (identified in the current study) within the transcribed secondary structure of the 16S rRNA gene. Variable regions (V1 - V9) are shown for reference

Mentions: Analysis of the intron insertion loci in the modeled secondary structure of an archaeal 16S rRNA molecule [39] revealed that nearly all of the intron loci (loci 374, 722, 781, 803, 901, 908, 919, 978, 1093, 1213, 1391) were either located in a bulge motif or in a helix structure very near a bulge motif (548, 1205; Fig. 3). These locations may provide the necessary flexibility in secondary structure for the insertion of intron sequences, which are often > 700 nt. There are many other bulge motifs in the secondary structure of the 16S rRNA molecule that do not contain intron sequences. This might be attributed to secondary or tertiary structure restrictions (e.g., steric hindrance), sequence specificity of insertion, or an inability to detect introns at these locations in the environment. Alternatively, these loci may not provide sufficient access to the tRNA splicing endoribonuclease. All V-regions (V1 - V9; [40]) of the 16S rRNA gene were free of introns, indicating that many introns are confined to the most highly-conserved loci in the 16S rRNA gene. Intron loci 374 and 803 flank variable regions V4 and V8, respectively, and could interrupt primers designed around these regions (see below).Fig. 3


The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.

Jay ZJ, Inskeep WP - Biol. Direct (2015)

The location (E. coli numbering) of intron sequences (identified in the current study) within the transcribed secondary structure of the 16S rRNA gene. Variable regions (V1 - V9) are shown for reference
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4496867&req=5

Fig3: The location (E. coli numbering) of intron sequences (identified in the current study) within the transcribed secondary structure of the 16S rRNA gene. Variable regions (V1 - V9) are shown for reference
Mentions: Analysis of the intron insertion loci in the modeled secondary structure of an archaeal 16S rRNA molecule [39] revealed that nearly all of the intron loci (loci 374, 722, 781, 803, 901, 908, 919, 978, 1093, 1213, 1391) were either located in a bulge motif or in a helix structure very near a bulge motif (548, 1205; Fig. 3). These locations may provide the necessary flexibility in secondary structure for the insertion of intron sequences, which are often > 700 nt. There are many other bulge motifs in the secondary structure of the 16S rRNA molecule that do not contain intron sequences. This might be attributed to secondary or tertiary structure restrictions (e.g., steric hindrance), sequence specificity of insertion, or an inability to detect introns at these locations in the environment. Alternatively, these loci may not provide sufficient access to the tRNA splicing endoribonuclease. All V-regions (V1 - V9; [40]) of the 16S rRNA gene were free of introns, indicating that many introns are confined to the most highly-conserved loci in the 16S rRNA gene. Intron loci 374 and 803 flank variable regions V4 and V8, respectively, and could interrupt primers designed around these regions (see below).Fig. 3

Bottom Line: Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically.The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

View Article: PubMed Central - PubMed

Affiliation: Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA. zackary.jay@montana.edu.

ABSTRACT

Background: Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences.

Results: Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.

Conclusions: The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

No MeSH data available.


Related in: MedlinePlus