Metatranscriptomic analysis of microbes in an oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation

Shinnosuke Murakami, Kosuke Fujishima, Masaru Tomita, Akio Kanai

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Studies of small noncoding RNAs (sRNAs) have been conducted predominantly using culturable organisms, and the acquisition of further information about sRNAs from global environments containing uncultured organisms now is very important. In this study, hot spring water (57°C, pH 8.1) was collected directly from the underground environment at depths of 250 to 1,000min Yunohama, Japan, and small RNA sequences obtained from the environment were analyzed. A phylogenetic analysis of both archaeal and bacterial 16S rRNA gene sequences was conducted, and the results suggested the presence of unique species in the environment, corresponding to the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) group and three new Betaproteobacteria. A metatranscriptomic analysis identified 64,194 (20,057 nonredundant) cDNA sequences. Of these cDNAs, 90% were either tRNAs, tRNA fragments, rRNAs, or rRNA fragments, whereas 2,181 reads (10%) were classified as previously uncharacterized putative candidate sRNAs. Among these, 15 were particularly abundant, 14 of which showed no sequence similarity to any known noncoding RNA, and at least six of which form very stable RNA secondary structures. The analysis of a large number of tRNA fragments suggested that unique relationships exist between the anticodons of the tRNAs and the sites of tRNA degradation. Previous bacterial tRNA degradation studies have been limited to specific organisms, such as Escherichia coli and Streptomyces coelicolor, and the current results suggest that specific tRNA decay occurs more frequently than previously expected.

Original languageEnglish
Pages (from-to)1015-1022
Number of pages8
JournalApplied and Environmental Microbiology
Volume78
Issue number4
DOIs
Publication statusPublished - 2012 Feb

Fingerprint

Hot Springs
hot springs
thermal spring
Transfer RNA
RNA
microorganisms
degradation
Small Untranslated RNA
ribosomal RNA
organisms
Streptomyces coelicolor
nucleotide sequences
beta-Proteobacteria
subterranean environment
Complementary DNA
Betaproteobacteria
secondary structure
Anticodon
deterioration
spring water

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology

Cite this

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title = "Metatranscriptomic analysis of microbes in an oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation",
abstract = "Studies of small noncoding RNAs (sRNAs) have been conducted predominantly using culturable organisms, and the acquisition of further information about sRNAs from global environments containing uncultured organisms now is very important. In this study, hot spring water (57°C, pH 8.1) was collected directly from the underground environment at depths of 250 to 1,000min Yunohama, Japan, and small RNA sequences obtained from the environment were analyzed. A phylogenetic analysis of both archaeal and bacterial 16S rRNA gene sequences was conducted, and the results suggested the presence of unique species in the environment, corresponding to the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) group and three new Betaproteobacteria. A metatranscriptomic analysis identified 64,194 (20,057 nonredundant) cDNA sequences. Of these cDNAs, 90{\%} were either tRNAs, tRNA fragments, rRNAs, or rRNA fragments, whereas 2,181 reads (10{\%}) were classified as previously uncharacterized putative candidate sRNAs. Among these, 15 were particularly abundant, 14 of which showed no sequence similarity to any known noncoding RNA, and at least six of which form very stable RNA secondary structures. The analysis of a large number of tRNA fragments suggested that unique relationships exist between the anticodons of the tRNAs and the sites of tRNA degradation. Previous bacterial tRNA degradation studies have been limited to specific organisms, such as Escherichia coli and Streptomyces coelicolor, and the current results suggest that specific tRNA decay occurs more frequently than previously expected.",
author = "Shinnosuke Murakami and Kosuke Fujishima and Masaru Tomita and Akio Kanai",
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AU - Kanai, Akio

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