RNAs present in environmental samples
Encyclopedia
A wide variety of non-coding RNA
s 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 detected homolog
s of known bacteria
l RNAs in such metagenome samples. Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong.
The distinct environmental sequences were exploited to detect previously unknown RNAs in the marine bacterium Pelagibacter ubique
. P. ubique is extremely common in marine sequences. So sequences of DNA extracted from ocean
s, many of which are inevitably derived from species related to P. ubique, were exploited to facillitate the analysis of possible secondary structure
s of RNAs predicted in this species.
Subsequent studies identified novel RNAs exclusively using sequences extracted from environmental samples.
The first study determined the sequences of RNAs directly extracted from microbial biomass in the Pacific Ocean
. The researches found that a large fraction of the total extracted RNA molecules did not appear to code for protein
, but instead appear to conserve consistent RNA secondary structures. A number of these were shown to belong to known small RNA sequence families, including riboswitch
es. A larger fraction of these microbial small RNAs appeared to represent novel, non-coding small RNAs, not yet described in any databases.
A second study used sequences of DNA extracted from various environments, and inferred the presence of conserved RNA secondary structures among some of these sequences. Both studies identified RNAs that were not present in then-available genome sequences of any known organisms, and determined that some of the RNAs were remarkably abundant. In fact, two of the RNA classes (the IMES-1 RNA motif
and IMES-2 RNA motif
) exceeded ribosome
s in copy number, which is extremely unusual among RNAs in bacteria. IMES-1 RNAs were also determined to be highly abundant near the shore in the Atlantic Ocean
using different techniques.
RNAs that were identified in environmental sequence samples include the IMES-1
, IMES-3
, IMES-4
, Whalefall-1
, potC
, Termite-flg
and Gut-1 RNA motif
s. These RNA structures have not been detected in the genome of any known species. The IMES-2 RNA motif
, GOLLD RNA motif
and manA RNA motif
were discovered using environmental DNA or RNA sequence samples, and are present in a small number of known species. Additional non-coding RNAs are predicted in marine environments, although no specific conserved secondary structures have been published for these other candidates. Other conserved RNA structures were originally detected using environmental sequence data, e.g., the glnA RNA motif
, but were subsequently detected in numerous cultivated species of bacteria.
The discovery of RNAs that are not detected among currently known species mirrors findings of protein classes that are currently unique to environmental samples.
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
s have been identified in various 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...
of organisms known to science. However, RNAs have also been identified in "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...
" sequences derived from samples of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
or RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
extracted from the environment, which contain unknown species. Initial work in this area detected homolog
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
s of known bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
l RNAs in such metagenome samples. Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong.
The distinct environmental sequences were exploited to detect previously unknown RNAs in the marine bacterium Pelagibacter ubique
Pelagibacter ubique
Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name, although it has not yet been validly published according to the bacteriological code. It is an abundant member of the SAR11 clade in the phylum Alphaproteobacteria...
. P. ubique is extremely common in marine sequences. So sequences of DNA extracted from ocean
Ocean
An ocean is a major body of saline water, and a principal component of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas.More than half of this area is over 3,000...
s, many of which are inevitably derived from species related to P. ubique, were exploited to facillitate the analysis of possible secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
s of RNAs predicted in this species.
Subsequent studies identified novel RNAs exclusively using sequences extracted from environmental samples.
The first study determined the sequences of RNAs directly extracted from microbial biomass in 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...
. The researches found that a large fraction of the total extracted RNA molecules did not appear to code for protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
, but instead appear to conserve consistent RNA secondary structures. A number of these were shown to belong to known small RNA sequence families, including riboswitch
Riboswitch
In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the...
es. A larger fraction of these microbial small RNAs appeared to represent novel, non-coding small RNAs, not yet described in any databases.
A second study used sequences of DNA extracted from various environments, and inferred the presence of conserved RNA secondary structures among some of these sequences. Both studies identified RNAs that were not present in then-available genome sequences of any known organisms, and determined that some of the RNAs were remarkably abundant. In fact, two of the RNA classes (the IMES-1 RNA motif
IMES-1 RNA motif
The IMES-1 RNA motif is a conserved RNA structure that was identified in marine environmental sequences by two studies based on metagenomics and bioinformatics, the first analyzing metatranscriptome data and the second using metagenome data. These RNAs are present in environmental sequences, and...
and IMES-2 RNA motif
IMES-2 RNA motif
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...
) exceeded 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 copy number, which is extremely unusual among RNAs in bacteria. IMES-1 RNAs were also determined to be highly abundant near the shore in the Atlantic Ocean
Atlantic Ocean
The Atlantic Ocean is the second-largest of the world's oceanic divisions. With a total area of about , it covers approximately 20% of the Earth's surface and about 26% of its water surface area...
using different techniques.
RNAs that were identified in environmental sequence samples include the IMES-1
IMES-1 RNA motif
The IMES-1 RNA motif is a conserved RNA structure that was identified in marine environmental sequences by two studies based on metagenomics and bioinformatics, the first analyzing metatranscriptome data and the second using metagenome data. These RNAs are present in environmental sequences, and...
, IMES-3
IMES-3 RNA motif
The IMES-3 RNA motif is a conserved RNA structure that was identified based on metagenomics and bioinformatics, and the underlying RNA sequences were identified independently by an earlier study. These RNAs are present in environmental sequences, and as of 2009 are not known to be present in any...
, IMES-4
IMES-4 RNA motif
The IMES-4 RNA motif is a conserved RNA structure that was identified in marine environmental sequences by metagenomics and bioinformatics. These RNAs are present in environmental sequences, and as of 2009 are not known to be present in any cultivated species. IMES-4 RNAs are fairly abundant in...
, Whalefall-1
Whalefall-1 RNA motif
The Whalefall-1 RNA motif refers to a conserved RNA structure that was discovered using bioinformatics. Structurally, the motif consists of two stem-loops , the second of which is often terminated by a CUUG tetraloop, which is an energetically favorable RNA sequence...
, potC
PotC RNA motif
The potC RNA motif is a conserved RNA structure discovered using bioinformatics. The RNA is detected only in genome sequences derived from DNA that was extracted from uncultivated marine bacteria...
, Termite-flg
Termite-flg RNA motif
The Termite-flg RNA motif is a conserved RNA structure identified by bioinformatics. Genomic sequences corresponding to Termite-flg RNAs have been identified only in uncultivated bacteria present in the termite hindgut...
and Gut-1 RNA motif
Gut-1 RNA motif
The Gut-1 RNA motif is a conserved RNA structure identified by bioinformatics. These RNAs are present in environmental sequences, and as of 2010 are not known to be present in any species that has been grown under laboratory conditions. Gut-1 RNA is exclusively found in DNA from uncultivated...
s. These RNA structures have not been detected in the genome of any known species. The IMES-2 RNA motif
IMES-2 RNA motif
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...
, GOLLD RNA motif
GOLLD RNA motif
Giant, Ornate, Lake- and Lactobacillales-Derived RNA is a conserved RNA structure present in bacteria. GOLLD RNAs were originally detected based on metagenome sequences of DNA isolated from Lake Gatun in Panama. However, they are known to be present in at least eight strains of cultivated bacteria...
and manA RNA motif
ManA RNA motif
The manA RNA motif refers to a conserved RNA structure that was identified by bioinformatics. Instances of the manA RNA motif were detected in bacteria in the genus Photobacterium and phages that infect certain kinds of cyanobacteria. However, most predicted manA RNA sequences are derived from...
were discovered using environmental DNA or RNA sequence samples, and are present in a small number of known species. Additional non-coding RNAs are predicted in marine environments, although no specific conserved secondary structures have been published for these other candidates. Other conserved RNA structures were originally detected using environmental sequence data, e.g., the glnA RNA motif
GlnA RNA motif
The glnA RNA motif is a conserved RNA structure that was predicted by bioinformatics. It is present in a variety of lineages of cyanobacteria, as well as some phages that infect cyanobacteria...
, but were subsequently detected in numerous cultivated species of bacteria.
The discovery of RNAs that are not detected among currently known species mirrors findings of protein classes that are currently unique to environmental samples.