GOLLD RNA motif
Encyclopedia
Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD) 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. GOLLD RNAs are extraordinarily large compared to other RNAs with a conserved, complex secondary structure
, and average roughly 800 nucleotides. Such large, complex RNAs are often ribozyme
s, although the biochemical function of GOLLD RNAs remains unknown. The discovery of large RNAs like GOLLD RNAs among bacteria that are mostly uncultivated under laboratory conditions suggests that many other unusually large RNAs might be found in bacteria that have not yet been studied.
The GOLLD RNA in Lactobacillus brevis
ATCC 367 was studied experimentally. This GOLLD RNA is apparently encoded by a prophage
, and its transcription is increased during the phage lytic cycle
. Therefore, this GOLLD RNA presumably serves a function that is useful to the phage during this process. GOLLD RNAs are often located near transfer RNA
s (tRNAs), and in some cases a tRNA is predicted to be inside the GOLLD RNA structure itself. However, the biological reason underlying this association is not understood.
The Rfam
model of GOLLD RNA uses only the 3' half of GOLLD, as this region of the full RNA is highly consistent in its structure.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure present in 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...
. GOLLD RNAs were originally detected based on metagenome
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 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...
isolated from Lake Gatun in Panama. However, they are known to be present in at least eight strains of cultivated bacteria. GOLLD RNAs are extraordinarily large compared to other RNAs with a conserved, complex 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...
, and average roughly 800 nucleotides. Such large, complex RNAs are often ribozyme
Ribozyme
A ribozyme is an RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA enzyme or catalytic RNA. Many natural ribozymes catalyze either the hydrolysis of one of their own...
s, although the biochemical function of GOLLD RNAs remains unknown. The discovery of large RNAs like GOLLD RNAs among bacteria that are mostly uncultivated under laboratory conditions suggests that many other unusually large RNAs might be found in bacteria that have not yet been studied.
The GOLLD RNA in Lactobacillus brevis
Lactobacillus brevis
Lactobacillus brevis is a species of lactic acid bacteria. It can be found in many different environments and in fermented foods such as sauerkraut and pickles. It is also one of the most common causes of beer spoilage. Ingestion has been shown to improve human immune function, and it has been...
ATCC 367 was studied experimentally. This GOLLD RNA is apparently encoded by a prophage
Prophage
A prophage is a phage genome inserted and integrated into the circular bacterial DNA chromosome. A prophage, also known as a temperate phage, is any virus in the lysogenic cycle; it is integrated into the host chromosome or exists as an extrachromosomal plasmid. Technically, a virus may be called...
, and its transcription is increased during the phage lytic cycle
Lytic cycle
The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle is typically considered the main method of viral replication, since it results in the destruction of the infected cell...
. Therefore, this GOLLD RNA presumably serves a function that is useful to the phage during this process. GOLLD RNAs are often located near 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...
s (tRNAs), and in some cases a tRNA is predicted to be inside the GOLLD RNA structure itself. However, the biological reason underlying this association is not understood.
The Rfam
Rfam
Rfam is a database containing information about non-coding RNA families and other structured RNA elements. It is an annotated, open access database hosted by the Wellcome Trust Sanger Institute in collaboration with Janelia Farm...
model of GOLLD RNA uses only the 3' half of GOLLD, as this region of the full RNA is highly consistent in its structure.