A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that benefit the survival of the organism and confer selective advantage such as antibiotic resistance. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation. Synthetic plasmids are available for procurement over the internet.
Lactococcus lactis is a gram-positive bacterium used extensively in the production of buttermilk and cheese, but has also become famous as the first genetically modified organism to be used alive for the treatment of human disease. L. lactis cells are cocci that group in pairs and short chains, and, depending on growth conditions, appear ovoid with a typical length of 0.5 - 1.5 µm. L. lactis does not produce spores (nonsporulating) and are not motile (nonmotile). They have a homofermentative metabolism, meaning they produce lactic acid from sugars. They've also been reported to produce exclusive L-(+)-lactic acid. However, reported D-(−)-lactic acid can be produced when cultured at low pH. The capability to produce lactic acid is one of the reasons why L. lactis is one of the most important microorganisms in the dairy industry. Based on its history in food fermentation, L. lactis has generally recognized as safe (GRAS) status, with few case reports of it being an opportunistic pathogen.
R1162-like plasmid antisense RNA is a 75-base RNA molecule which negatively regulates the RepI region of the plasmid. The protein product of this gene region, along with another protein, controls the copy number of the 8.75kB R1162 plasmid.
The ykkC/yxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The function of this family is unclear for many years although it has been suggested that it may function to switch on efflux pumps and detoxification systems in response to harmful environmental molecules. The Thermoanaerobacter tengcongensis sequence AE013027 overlaps with that of purine riboswitch suggesting that the two riboswitches may work in conjunction to regulate the upstream gene which codes for TTE0584 (Q8RC62), a member of the permease family.
The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in Escherichia coli. It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein.
The Bacillus-plasmid RNA motif is a predicted conserved RNA structure usually located in plasmids. It is known in species under the genera Bacillus and Lactobacillus. In Bacillus subtilis, it is found upstream of the hypothetical gene ydcS, whose function is unknown.
The Chlorobi-1 RNA motif is a conserved RNA secondary structure identified by bioinformatics. It is predicted to be used only by Chlorobiota, a phylum of bacteria. The motif consists of two stem-loops that are followed by an apparent rho-independent transcription terminator. The motif is presumed to function as an independently transcribed non-coding RNA.
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.
The L17 downstream element RNA motif is a conserved RNA structure identified in bacteria by bioinformatics. All known L17 downstream elements were detected immediately downstream of genes encoding the L17 subunit of the ribosome, and therefore might be in the 3' untranslated regions of these genes. The element is found in a variety of lactic acid bacteria and in the genus Listeria.
The Lacto-rpoB RNA motif is a conserved RNA structure identified by bioinformatics. It has been detected only in lactic acid bacteria, and is always located in the presumed 5' untranslated regions of rpoB genes. These genes encode a subunit of RNA polymerase, and it is hypothesized that Lacto-rpoB RNA participate in the regulation of these genes.
The Lacto-usp RNA motif is a conserved RNA structure identified in bacteria by bioinformatics. Lacto-usp RNAs are found exclusively in lactic acid bacteria, and exclusively in the possible 5′ untranslated regions of operons that contain a hypothetical gene and a usp gene. The usp gene encodes the universal stress protein. It was proposed that the Lacto-usp might correspond to the 6S RNA of the relevant species, because four of five of these species lack a predicted 6S RNA, and 6S RNAs commonly occur in 5′ UTRs of usp genes. However, given that the Lacto-usp RNA motif is much shorter than the standard 6S RNA structure, the function of Lacto-usp RNAs remains unclear.
The leu/phe-leader RNA motif is a conserved RNA structure identified by bioinformatics. These RNAs function as peptide leaders. They contain a short open reading frame (ORF) that contains many codons for leucine or phenylalanine. Normally, expression of the downstream genes is suppressed. However, when cellular concentrations of the relevant amino acid is low, ribosome stalling leads to an alternate structure that enables downstream gene expression.
The sbcD RNA motif is a conserved RNA structure identified using bioinformatics. sbc RNAs are found some species of bacteria classified under the family Burkholderiaceae, and usually reside in plasmids. They are always located in what might be the 5' untranslated regions of operons that include sbcD genes. sbcD genes are involved in DNA repair.
The Ssbp, Topoisomerase, Antirestriction, XerDC Integrase RNA motif is a conserved RNA-like structure identified using bioinformatics. STAXI RNAs are located near to genes encoding proteins that interact with DNA or are associated with such proteins. This observation raised the possibility that instances of the STAXI motif function as single-stranded DNA molecules, perhaps during DNA replication or DNA repair. On the other hand, STAXI motifs often contain terminal loops conforming to the stable UNCG tetraloop, but the DNA version of this tetraloop (TNCG) is not especially stable. The STAXI motif consists of a simple pseudoknot structure that is repeated two or more times.
The sucA-II RNA motif is a conserved RNA structure identified by bioinformatics. It is consistently found in the presumed 5' untranslated regions of sucA genes, which encode Oxoglutarate dehydrogenase enzymes that participate in the citric acid cycle. Given this arrangement, sucA-II RNAs might regulate the downstream sucA gene. This genetic arrangement is similar to the previously reported sucA RNA motif. However, sucA-II RNAs are found only in bacteria classified within the genus Pseudomonas, whereas the previously reported motif is found only in betaproteobacteria.
The sucC RNA motif is a conserved RNA structure discovered using bioinformatics. sucC RNAs are found in the genus Pseudomonas, and are consistently found in possible 5' untranslated regions of sucC genes. These genes encode Succinyl coenzyme A synthetase, and are hypothesised to be regulated by the sucC RNAs. sucC genes participate in the citric acid cycle, and another gene involved in the citric acid cycle, sucA, is also predicted to be regulated by a conserved RNA structure.
The Termite-leu RNA motif is a conserved RNA structure discovered by bioinformatics. It is found only in DNA sequences extracted from uncultivated bacteria living in termite hindguts, and has not yet been detected in any known cultivated organism. In many cases, Termite-leu RNAs are found in the likely 5′ untranslated regions of multive genes related to the synthesis of the amino acid leucine. However, in several cases it is not found in this type of location. Therefore, it was considered ambiguous as to whether Termite-leu RNAs constitute cis-regulatory elements.
The traJ-II RNA motif is a conserved RNA structure discovered in bacteria by using bioinformatics. traJ-II RNAs appear to be in the 5' untranslated regions of protein-coding genes called traJ, which functions in the process of bacterial conjugation. A previously identified motif known as TraJ 5' UTR is also found upstream of traJ genes functions as the target of FinP antisense RNAs, so it is possible that traJ-II RNAs play a similar role as targets of an antisense RNA. However, some sequence features within the traJ-II RNA motif suggest that the biological RNA might be transcribed from the reverse-complement strand. Thus is it unclear whether traJ-II function as cis-regulatory elements. traJ-II RNAs are found in a variety of Pseudomonadota.
A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Non-coding RNAs have been discovered using both experimental and bioinformatic approaches. Bioinformatic approaches can be divided into three main categories. The first involves homology search, although these techniques are by definition unable to find new classes of ncRNAs. The second category includes algorithms designed to discover specific types of ncRNAs that have similar properties. Finally, some discovery methods are based on very general properties of RNA, and are thus able to discover entirely new kinds of ncRNAs.
