Downstream-peptide motif
Encyclopedia
The Downstream-peptide motif refers to a conserved RNA
structure identified by bioinformatics
in the cyanobacterial genera
Synechococcus
and Prochlorococcus
and one phage that infects such bacteria
. It was also detected in marine
samples of DNA
from uncultivated bacteria
, which are presumably other species of cyanobacteria.
Downstream-peptide RNAs are found upstream of short open reading frame
s (ORFs) that are predicted to encode short peptide
s (usually between 17 and 100 amino acid
s). One of the ORFs is apparently down-regulated when cells are grown with an insufficient supply of nitrogen
sources. Downstream-peptide RNAs overlap a predicted non-coding RNA
called yfr6 that is over 200 nucleotide
s in length, but it was proposed that only the upstream region (corresponding to the Downstream-peptide motif) functions as an RNA structure. A distinct predicted non-coding RNA called yfr14 overlaps both yfr6 and Downstream-peptide RNAs. However, no experimental data has been published to resolve the question of which and how many of these RNAs are functional.
The Downstream-peptide motif has a structural resemblance to a different candidate RNA structure called the glnA RNA motif
. The most striking similarity is the nucleotide conservation within the P1 stem of both motifs, and this and other similarities was discussed previously.
It was hypothesized that Downstream-peptide RNAs correspond to riboswitch
es, based on multiple lines of evidence. First, glnA RNAs are often located in the presumed 5' untranslated regions of multiple classes of genes involved in nitrogen metabolism. This, and other evidence, suggests that glnA RNAs are riboswitches, and their structural similarity to Downstream-peptide RNAs in turn suggests that Downstream-peptide RNAs are also riboswitches. Second, Downstream-peptides are consistently positioned in a place that is consistent with a cis-regulatory
role in regulating the downstream ORFs, although the biological role of the ORFs is unknown. Third, the pseudoknot structure has a moderate complexity that is typical of riboswitches. Finally, the observation of regulation of a downstream ORF by nitrogen available also suggests a cis-regulatory role of the element. The subsequent determination that both Downstream-peptide RNAs and glnA RNAs selectively bind glutamine
supports these hypotheses.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure identified by 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...
in the cyanobacterial genera
Genus
In biology, a genus is a low-level taxonomic rank used in the biological classification of living and fossil organisms, which is an example of definition by genus and differentia...
Synechococcus
Synechococcus
Synechococcus is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 µm to 1.5 µm...
and Prochlorococcus
Prochlorococcus
Prochlorococcus is a genus of very small marine cyanobacteria with an unusual pigmentation . These bacteria belong to the photosynthetic picoplankton and are probably the most abundant photosynthetic organism on Earth....
and one phage that infects such 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...
. It was also detected in marine
Marine (ocean)
Marine is an umbrella term. As an adjective it is usually applicable to things relating to the sea or ocean, such as marine biology, marine ecology and marine geology...
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...
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...
, which are presumably other species of cyanobacteria.
Downstream-peptide RNAs are found upstream of short open reading frame
Open reading frame
In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...
s (ORFs) that are predicted to encode short peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...
s (usually between 17 and 100 amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s). One of the ORFs is apparently down-regulated when cells are grown with an insufficient supply of nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
sources. Downstream-peptide RNAs overlap a predicted non-coding RNA
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...
called yfr6 that is over 200 nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s in length, but it was proposed that only the upstream region (corresponding to the Downstream-peptide motif) functions as an RNA structure. A distinct predicted non-coding RNA called yfr14 overlaps both yfr6 and Downstream-peptide RNAs. However, no experimental data has been published to resolve the question of which and how many of these RNAs are functional.
The Downstream-peptide motif has a structural resemblance to a different candidate RNA structure called 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...
. The most striking similarity is the nucleotide conservation within the P1 stem of both motifs, and this and other similarities was discussed previously.
It was hypothesized that Downstream-peptide RNAs correspond to 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, based on multiple lines of evidence. First, glnA RNAs are often located in the presumed 5' untranslated regions of multiple classes of genes involved in nitrogen metabolism. This, and other evidence, suggests that glnA RNAs are riboswitches, and their structural similarity to Downstream-peptide RNAs in turn suggests that Downstream-peptide RNAs are also riboswitches. Second, Downstream-peptides are consistently positioned in a place that is consistent with a cis-regulatory
Cis-regulatory element
A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA . This term is constructed from the Latin word cis, which means "on the same side as". These cis-regulatory elements are often binding sites for one or...
role in regulating the downstream ORFs, although the biological role of the ORFs is unknown. Third, the pseudoknot structure has a moderate complexity that is typical of riboswitches. Finally, the observation of regulation of a downstream ORF by nitrogen available also suggests a cis-regulatory role of the element. The subsequent determination that both Downstream-peptide RNAs and glnA RNAs selectively bind glutamine
Glutamine
Glutamine is one of the 20 amino acids encoded by the standard genetic code. It is not recognized as an essential amino acid but may become conditionally essential in certain situations, including intensive athletic training or certain gastrointestinal disorders...
supports these hypotheses.