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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

Predicted secondary structures of 16S rRNA gene introns. a Predicted secondary structure of the Pyrobaculum yellowstonensis strain WP30 16S rRNA gene intron at locus 1391, illustrating the highly-structured nature of transcribed intron sequences. Numbers denote nucleotide position along the intron sequence. b-e Predicted secondary structures based on consensus sequences (weblogo) of four different 16S rRNA gene introns. Lower and upper case nucleotides denote 16S rRNA gene sequence and intron sequence, respectively. Arrows indicate hypothesized excision locations (EL) within the bulge-helix-bulge motif
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Fig4: Predicted secondary structures of 16S rRNA gene introns. a Predicted secondary structure of the Pyrobaculum yellowstonensis strain WP30 16S rRNA gene intron at locus 1391, illustrating the highly-structured nature of transcribed intron sequences. Numbers denote nucleotide position along the intron sequence. b-e Predicted secondary structures based on consensus sequences (weblogo) of four different 16S rRNA gene introns. Lower and upper case nucleotides denote 16S rRNA gene sequence and intron sequence, respectively. Arrows indicate hypothesized excision locations (EL) within the bulge-helix-bulge motif

Mentions: Transcribed intron sequences also had predictable, thermodynamically favorable secondary structures (e.g., Fig. 4a), similar to observations of 23S rRNA gene introns [25]. Intron sequences sharing high nucleotide identity within the same insertion locus maintained similar secondary structure (data not shown). However, the predicted secondary structures were not generally conserved within insertion loci. The predicted folding of each transcribed intron is thermodynamically favorable (at 37 °C; Fig. 4), but considering the predominance of introns in high-temperature habitats, the themostability of secondary structures may play a yet uncharacterized role in intron distribution and propagation. The average G + C content of the intron sequences was 57 ± 11 %, indicating that some thermostability could be attributed to strong G + C bonding; however, this value is still lower than the average % G + C content of the host 16S rRNA genes (67 ± 2 %).Fig. 4


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

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

Predicted secondary structures of 16S rRNA gene introns. a Predicted secondary structure of the Pyrobaculum yellowstonensis strain WP30 16S rRNA gene intron at locus 1391, illustrating the highly-structured nature of transcribed intron sequences. Numbers denote nucleotide position along the intron sequence. b-e Predicted secondary structures based on consensus sequences (weblogo) of four different 16S rRNA gene introns. Lower and upper case nucleotides denote 16S rRNA gene sequence and intron sequence, respectively. Arrows indicate hypothesized excision locations (EL) within the bulge-helix-bulge motif
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Predicted secondary structures of 16S rRNA gene introns. a Predicted secondary structure of the Pyrobaculum yellowstonensis strain WP30 16S rRNA gene intron at locus 1391, illustrating the highly-structured nature of transcribed intron sequences. Numbers denote nucleotide position along the intron sequence. b-e Predicted secondary structures based on consensus sequences (weblogo) of four different 16S rRNA gene introns. Lower and upper case nucleotides denote 16S rRNA gene sequence and intron sequence, respectively. Arrows indicate hypothesized excision locations (EL) within the bulge-helix-bulge motif
Mentions: Transcribed intron sequences also had predictable, thermodynamically favorable secondary structures (e.g., Fig. 4a), similar to observations of 23S rRNA gene introns [25]. Intron sequences sharing high nucleotide identity within the same insertion locus maintained similar secondary structure (data not shown). However, the predicted secondary structures were not generally conserved within insertion loci. The predicted folding of each transcribed intron is thermodynamically favorable (at 37 °C; Fig. 4), but considering the predominance of introns in high-temperature habitats, the themostability of secondary structures may play a yet uncharacterized role in intron distribution and propagation. The average G + C content of the intron sequences was 57 ± 11 %, indicating that some thermostability could be attributed to strong G + C bonding; however, this value is still lower than the average % G + C content of the host 16S rRNA genes (67 ± 2 %).Fig. 4

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