Ribosomes are macromolecular machines, found within all cells, that perform biological protein synthesis. Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA molecules and many ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.
In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon.
In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules.
Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins, though this ratio differs between prokaryotes and eukaryotes.
Bacterial translation is the process by which messenger RNA is translated into proteins in bacteria.
A ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. E. coli, other bacteria and Archaea have a 30S small subunit and a 50S large subunit, whereas humans and yeasts have a 40S small subunit and a 60S large subunit. Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans.
fis is an E. coli gene encoding the Fis protein. The regulation of this gene is more complex than most other genes in the E. coli genome, as Fis is an important protein which regulates expression of other genes. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.
In the field of molecular biology the 6S RNA is a non-coding RNA that was one of the first to be identified and sequenced. What it does in the bacterial cell was unknown until recently. In the early 2000s scientists found out the function of 6S RNA to be as a regulator of sigma 70-dependent gene transcription. All bacterial RNA polymerases have a subunit called a sigma factor. The sigma factors are important because they control how DNA promoter binding and RNA transcription start sites. Sigma 70 was the first one to be discovered in Escherichia coli.
L19 Ribosomal protein leaders are part of the ribosome biogenesis. They are used as an autoregulatory mechanism to control the concentration of ribosomal proteins L19, and are located in the 5′ untranslated regions of mRNAs encoding ribosomal protein L19 (rplS). L19 ribosomal protein leaders have been bioinformatically predicted in B. subtilis and other low-GC Gram-positive bacteria in the phylum Bacillota. More examples that share a similar structure were predicted in Flavobacteria, also using bioinformatic approaches.
L20 ribosomal protein leader is a ribosomal protein leader involved in the ribosome biogenesis. It is used as an autoregulatory mechanism to control the concentration of ribosomal proteins L20. The structure is typically located in the 5′ untranslated regions of mRNAs encoding initiation factor 3 followed by ribosomal proteins L35 and L20 (infC-rpmI-rplT), but the regulated mRNAs always contain an L20 gene. A Rho-independent transcription terminator structure that is probably involved in regulation is included at the 3′ end in many examples of L20 ribosomal protein leaders. Three structurally distinct forms of L20 leaders have been experimentally established. One such leader motif occurs in Bacillota and the other two are found in Gammaproteobacteria. Of the latter two, one is found in a wide variety of Gammaproteobacteria, while the other is only reported in Escherichia coli. All three types of leader exhibit apparent similarities to the region of Ribosomal RNA to which the L20 protein normally binds. However, in terms of RNA secondary structure, the context of the similar region is distinct in each leader type.
A ribosomal protein L21 leader is a ribosomal protein leader autoregulatory structure that regulates mRNAs containing a gene that encodes ribosomal protein L21. An RNA motif was predicted to function as an L21 leader in a bioinformatics study, and is found in B. subtilis and other low-GC Gram-positive bacteria within the phylum Bacillota. It is located in the 5′ untranslated regions of mRNAs encoding ribosomal protein L21, a protein of unknown function, and ribosomal protein L27 (rplU-ysxB-rpmA).
S15 Ribosomal protein leaders perform an important regulatory function in ribosome biogenesis. They were used as an autoregulatory mechanism to control the concentration of ribosomal proteins S15. The structure is located in the 5′ untranslated regions of mRNAs encoding ribosomal proteins S15 (rpsO). Multiple distinct structural types of S15 ribosomal protein leaders are known in different organisms.
The glutamine riboswitch 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. It is also found in DNA extracted from uncultivated bacteria living in the ocean that are presumably species of cyanobacteria.
Bacterial small RNAs are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.
In molecular biology, bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins. Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. They are commonly referred to as histone-like and have many similar traits with the eukaryotic histone proteins. Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. Examples include the HU protein in Escherichia coli, a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of bacteria and archaea, and are also encoded in the chloroplast genome of some algae. The integration host factor (IHF), a dimer of closely related chains which is suggested to function in genetic recombination as well as in translational and transcriptional control is found in Enterobacteria and viral proteins including the African swine fever virus protein A104R.
L25 ribosomal protein leader is a ribosomal protein leader involved in the ribosome biogenesis. It is used as an autoregulatory mechanism to control the concentration of the ribosomal protein L25. Known Examples were predicted in Gammaproteobacteria with bioinformatic approaches. or in Enterobacteria. The structure is located in the 5′ untranslated regions of mRNAs encoding ribosomal protein L25 (rplY).
S10 ribosomal protein leader is a ribosomal protein leader involved in the ribosome biogenesis. It is used as an autoregulatory mechanism to control the concentration of the ribosomal protein S10. Known Examples were predicted in Clostridia or other lineages of Bacillota with bioinformatic approaches. The structure is located in the 5′ untranslated regions of mRNAs encoding ribosomal proteins S10 (rpsJ), L3 (rplc) and L4 (rplD). There is an uncertainty about the ligand, because of a lack of experimental investigation.
The S4 ribosomal protein leader is a ribosomal protein leader involved in ribosome biogenesis. It is used as an autoregulatory mechanism to control the concentration of the ribosomal protein S4. Two examples of such leaders that use different conserved structures, in Bacillota and Gammaproteobacteria, have been experimentally confirmed. Four additional S4 ribosomal protein leaders, each with distinct structures, were predicted in various bacteria phyla. In Bacteroidia or Bacillota, the structure is located in the 5′ untranslated regions of mRNAs encoding ribosomal proteins S4 (rpsD), RNA polymerase alpha subunit (rpoA) and L17 (rplQ). In Clostridia and Gammaproteobacteria, the ribosomal proteins S13 (rpsM) and S11 (rpsK) were also part of the mRNA encoding region.
An L31 ribosomal protein leader is a ribosomal protein leader involved in ribosome biogenesis. It is used as an autoregulatory mechanism to control the concentration of the ribosomal protein L31. Five structurally distinct types of L31 ribosomal protein leader were predicted with a bioinformatic approach. The structure is located in the 5′ untranslated regions of mRNAs encoding ribosomal protein L31 (rpmE), and in one case L32 (rpmF). These are found in different species of Actinomycetota, Bacillota or Gammaproteobacteria. The gammaproteobacterial type was also detected and validated in an independent experimental study using the organism Escherichia coli.
S6:S18 ribosomal protein leader is a ribosomal protein leader involved in the ribosome biogenesis. It is used as an autoregulatory mechanism to control the concentration of the ribosomal proteins S6:S18 complex. An experimentally confirmed example of such a leader occurs in a wide variety of bacteria, though not all phyla. A S6:S18 ribosomal leader was predicted in Chlorobia, and its predicted structure differs from that of the validated S6:S18 ribosomal leader. This structure is located in the 5′ untranslated regions of mRNAs encoding ribosomal proteins rpsF (S6), the Single-strand DNA-binding protein A (ssbA), S18 (rpsR) and L7/L12 (rpll).
