Whalefall-1 RNA motif
Encyclopedia
The Whalefall-1 RNA motif (also called wf-1) refers to a conserved RNA
structure that was discovered using bioinformatics
. Structurally, the motif consists of two stem-loop
s (see diagram), the second of which is often terminated by a CUUG tetraloop
, which is an energetically favorable RNA sequence. Whalefall-1 RNAs are found only in DNA
extracted from uncultivated bacteria
found on whale fall
, i.e., a whale
carcass. As of 2010, Whalefall-1 RNAs have not been detected in any known, cultivated species of bacteria, and are thus one of several RNAs present in environmental samples
.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure that was discovered using 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...
. Structurally, the motif consists of two 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,...
s (see diagram), the second of which is often terminated by a CUUG tetraloop
Tetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG. The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3'...
, which is an energetically favorable RNA sequence. Whalefall-1 RNAs are found only in 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...
extracted from uncultivated 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...
found on whale fall
Whale fall
Whale fall is the term used for a whale carcass that has fallen to the ocean floor. Whale falls were first observed in the 1980s, with the advent of deep-sea robotic exploration....
, i.e., a whale
Whale
Whale is the common name for various marine mammals of the order Cetacea. The term whale sometimes refers to all cetaceans, but more often it excludes dolphins and porpoises, which belong to suborder Odontoceti . This suborder also includes the sperm whale, killer whale, pilot whale, and beluga...
carcass. As of 2010, Whalefall-1 RNAs have not been detected in any known, cultivated species of bacteria, and are thus one of several RNAs present in environmental samples
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...
.