IMES-2 RNA motif
Encyclopedia
The IMES-2 RNA motif is a conserved RNA
structure that was identified by a study based on metagenomics
and bioinformatics
, and the underlying RNA sequences were identified independently by a similar earlier study. These RNAs are present in environmental sequences
, and when discovered were not known to be present in any cultivated species
. However, an IMES-2 RNA has been detected in alphaproteobacterium
HIMB114, which is classified in the SAR11 clade
of marine bacteria. This finding fits with earlier predictions that species that use IMES-2 RNAs are most closely related to alphaproteobacteria
. IMES-2 RNAs are exceptionally abundant, as twice as many IMES-2 RNAs were found as ribosome
s in RNAs sampled from the Pacific Ocean
. Only two bacterial RNAs are known (6S RNA and transfer RNA
) to be more highly transcribed than ribosomes.
The IMES-2 RNA secondary structure contains four stem-loop
structures and one pseudoknot
.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure that was identified by a study based on metagenomics
Metagenomics
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures...
and bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
, and the underlying RNA sequences were identified independently by a similar earlier study. These RNAs are present in environmental sequences
RNAs present in environmental samples
A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area...
, and when discovered were not known to be present in any cultivated species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
. However, an IMES-2 RNA has been detected in alphaproteobacterium
Alphaproteobacteria
Alphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative.-Characteristics:The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds , symbionts of plants and animals, and a group of pathogens, the...
HIMB114, which is classified in the SAR11 clade
SAR11 clade
The SAR11 clade, or Pelagibacteraceae, defines a lineage of bacteria that is extremely common in the ocean. Bacteria in the SAR11 clade make up roughly one in three cells at the ocean's surface...
of marine bacteria. This finding fits with earlier predictions that species that use IMES-2 RNAs are most closely related to alphaproteobacteria
Alphaproteobacteria
Alphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative.-Characteristics:The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds , symbionts of plants and animals, and a group of pathogens, the...
. IMES-2 RNAs are exceptionally abundant, as twice as many IMES-2 RNAs were found as ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
s in RNAs sampled from the Pacific Ocean
Pacific Ocean
The Pacific Ocean is the largest of the Earth's oceanic divisions. It extends from the Arctic in the north to the Southern Ocean in the south, bounded by Asia and Australia in the west, and the Americas in the east.At 165.2 million square kilometres in area, this largest division of the World...
. Only two bacterial RNAs are known (6S RNA and transfer RNA
Transfer RNA
Transfer RNA is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the three-letter genetic code in messenger RNA with the twenty-letter code of amino acids in proteins. The role of tRNA as an adaptor is best understood by...
) to be more highly transcribed than ribosomes.
The IMES-2 RNA secondary structure contains four stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
structures and one pseudoknot
Pseudoknot
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982...
.