Ribosome-binding site

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A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers to bacterial sequences, although internal ribosome entry sites (IRES) have been described in mRNAs of eukaryotic cells or viruses that infect eukaryotes. Ribosome recruitment in eukaryotes is generally mediated by the 5' cap present on eukaryotic mRNAs.

Contents

Prokaryotes

The RBS in prokaryotes is a region upstream of the start codon. This region of the mRNA has the consensus 5'-AGGAGG-3', also called the Shine-Dalgarno (SD) sequence. [1] The complementary sequence (CCUCCU), called the anti-Shine-Dalgarno (ASD) is contained in the 3’ end of the 16S region of the smaller (30S) ribosomal subunit. Upon encountering the Shine-Dalgarno sequence, the ASD of the ribosome base pairs with it, after which translation is initiated. [2] [3]

Variations of the 5'-AGGAGG-3' sequence have been found in Archaea as highly conserved 5′-GGTG-3′ regions, 5 basepairs upstream of the start site. Additionally, some bacterial initiation regions, such as rpsA in E.coli completely lack identifiable SD sequences. [4]

Effect on translation initiation rate

Prokaryotic ribosomes begin translation of the mRNA transcript while DNA is still being transcribed. Thus translation and transcription are parallel processes. Bacterial mRNA are usually polycistronic and contain multiple ribosome binding sites. Translation initiation is the most highly regulated step of protein synthesis in prokaryotes. [5]

The rate of translation depends on two factors:

The RBS sequence affects both of these factors.

Factors affecting rate of ribosome recruitment

The ribosomal protein S1 binds to adenine sequences upstream of the RBS. Increasing the concentration of adenine upstream of the RBS will increase the rate of ribosome recruitment. [5]

Factors affecting the efficiency of translation initiation

The level of complementarity of the mRNA SD sequence to the ribosomal ASD greatly affects the efficiency of translation initiation. Richer complementarity results in higher initiation efficiency. [6] It is worth noting that this only holds up to a certain point - having too rich of a complementarity is known to paradoxically decrease the rate of translation as the ribosome then happens to be bound too tightly to proceed downstream. [6]

The optimal distance between the RBS and the start codon is variable - it depends on the portion of the SD sequence encoded in the actual RBS and its distance to the start site of a consensus SD sequence. Optimal spacing increases the rate of translation initiation once a ribosome has been bound. [6] The composition of nucleotides in the spacer region itself was also found to affect the rate of translation initiation in one study. [7]

Heat shock proteins

Secondary structures formed by the RBS can affect the translational efficiency of mRNA, generally inhibiting translation. These secondary structures are formed by H-bonding of the mRNA base pairs and are sensitive to temperature. At a higher-than-usual temperature (~42 °C), the RBS secondary structure of heat shock proteins becomes undone thus allowing ribosomes to bind and initiate translation. This mechanism allows a cell to quickly respond to an increase in temperature. [5]

Eukaryotes

5' cap

Ribosome recruitment in eukaryotes happens when eukaryote initiation factors elF4F and poly(A)-binding protein (PABP) recognize the 5' capped mRNA and recruit the 43S ribosome complex at that location. [8]

Translation initiation happens following recruitment of the ribosome, at the start codon (underlined) found within the Kozak consensus sequence ACCAUGG. Since the Kozak sequence itself is not involved in the recruitment of the ribosome, it is not considered a ribosome binding site. [2] [8]

Internal ribosome entry site (IRES)

Eukaryotic ribosomes are known to bind to transcripts in a mechanism unlike the one involving the 5' cap, at a sequence called the internal ribosome entry site. This process is not dependent on the full set of translation initiation factors (although this depends on the specific IRES) and is commonly found in the translation of viral mRNA. [9]

Gene annotation

The identification of RBSs is used to determine the site of translation initiation in an unannotated sequence. This is referred to as N-terminal prediction. This is especially useful when multiple start codons are situated around the potential start site of the protein coding sequence. [10] [11]

Identification of RBSs is particularly difficult, because they tend to be highly degenerated. [12] One approach to identifying RBS in E.coli is using neural networks. [13] Another approach is using the Gibbs sampling method. [10]

History

The Shine-Dalgarno sequence, of the prokaryotic RBS, was discovered by John Shine and Lynne Dalgarno in 1975. [1] [14] The Kozak consensus sequence was first identified by Marilyn Kozak in 1984 [15] while she was in the Department of Biological Sciences at the University of Pittsburgh. [16]

See also

Related Research Articles

<span class="mw-page-title-main">Ribosome</span> Intracellular organelle consisting of RNA and protein functioning to synthesize proteins

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 (mRNA) 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 (rRNA) molecules and many ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.

<span class="mw-page-title-main">Translation (biology)</span> Cellular process of protein synthesis

In biology, translation is the process in living cells in which proteins are produced using RNA molecules as templates. The generated protein is a sequence of amino acids. This sequence is determined by the sequence of nucleotides in the RNA. The nucleotides are considered three at a time. Each such triple results in addition of one specific amino acid to the protein being generated. The matching from nucleotide triple to amino acid is called the genetic code. The translation is performed by a large complex of functional RNA and proteins called ribosomes. The entire process is called gene expression.

The 5′ untranslated region is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. While called untranslated, the 5′ UTR or a portion of it is sometimes translated into a protein product. This product can then regulate the translation of the main coding sequence of the mRNA. In many organisms, however, the 5′ UTR is completely untranslated, instead forming a complex secondary structure to regulate translation.

The Shine–Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon. Once recruited, tRNA may add amino acids in sequence as dictated by the codons, moving downstream from the translational start site.

<span class="mw-page-title-main">Ribosomal RNA</span> RNA component of the ribosome, essential for protein synthesis in all living organisms

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 by mass.

An internal ribosome entry site, abbreviated IRES, is an RNA element that allows for translation initiation in a cap-independent manner, as part of the greater process of protein synthesis. In eukaryotic translation, initiation typically occurs at the 5' end of mRNA molecules, since 5' cap recognition is required for the assembly of the initiation complex. The location for IRES elements is often in the 5'UTR, but can also occur elsewhere in mRNAs.

Bacterial translation is the process by which messenger RNA is translated into proteins in bacteria.

Eukaryotic translation is the biological process by which messenger RNA is translated into proteins in eukaryotes. It consists of four phases: initiation, elongation, termination, and recapping.

The Kozak consensus sequence is a nucleic acid motif that functions as the protein translation initiation site in most eukaryotic mRNA transcripts. Regarded as the optimum sequence for initiating translation in eukaryotes, the sequence is an integral aspect of protein regulation and overall cellular health as well as having implications in human disease. It ensures that a protein is correctly translated from the genetic message, mediating ribosome assembly and translation initiation. A wrong start site can result in non-functional proteins. As it has become more studied, expansions of the nucleotide sequence, bases of importance, and notable exceptions have arisen. The sequence was named after the scientist who discovered it, Marilyn Kozak. Kozak discovered the sequence through a detailed analysis of DNA genomic sequences.

Initiation factors are proteins that bind to the small subunit of the ribosome during the initiation of translation, a part of protein biosynthesis.

Eukaryotic initiation factors (eIFs) are proteins or protein complexes involved in the initiation phase of eukaryotic translation. These proteins help stabilize the formation of ribosomal preinitiation complexes around the start codon and are an important input for post-transcription gene regulation. Several initiation factors form a complex with the small 40S ribosomal subunit and Met-tRNAiMet called the 43S preinitiation complex. Additional factors of the eIF4F complex recruit the 43S PIC to the five-prime cap structure of the mRNA, from which the 43S particle scans 5'-->3' along the mRNA to reach an AUG start codon. Recognition of the start codon by the Met-tRNAiMet promotes gated phosphate and eIF1 release to form the 48S preinitiation complex, followed by large 60S ribosomal subunit recruitment to form the 80S ribosome. There exist many more eukaryotic initiation factors than prokaryotic initiation factors, reflecting the greater biological complexity of eukaryotic translation. There are at least twelve eukaryotic initiation factors, composed of many more polypeptides, and these are described below.

<span class="mw-page-title-main">Prokaryotic small ribosomal subunit</span> Smaller subunit of the 70S ribosome found in prokaryote cells

The prokaryotic small ribosomal subunit, or 30S subunit, is the smaller subunit of the 70S ribosome found in prokaryotes. It is a complex of the 16S ribosomal RNA (rRNA) and 19 proteins. This complex is implicated in the binding of transfer RNA to messenger RNA (mRNA). The small subunit is responsible for the binding and the reading of the mRNA during translation. The small subunit, both the rRNA and its proteins, complexes with the large 50S subunit to form the 70S prokaryotic ribosome in prokaryotic cells. This 70S ribosome is then used to translate mRNA into proteins.

<span class="mw-page-title-main">Untranslated region</span> Non-coding regions on either end of mRNA

In molecular genetics, an untranslated region refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the 5' side, it is called the 5' UTR, or if it is found on the 3' side, it is called the 3' UTR. mRNA is RNA that carries information from DNA to the ribosome, the site of protein synthesis (translation) within a cell. The mRNA is initially transcribed from the corresponding DNA sequence and then translated into protein. However, several regions of the mRNA are usually not translated into protein, including the 5' and 3' UTRs.

In molecular cloning, a vector is any particle used as a vehicle to artificially carry a foreign nucleic sequence – usually DNA – into another cell, where it can be replicated and/or expressed. A vector containing foreign DNA is termed recombinant DNA. The four major types of vectors are plasmids, viral vectors, cosmids, and artificial chromosomes. Of these, the most commonly used vectors are plasmids. Common to all engineered vectors are an origin of replication, a multicloning site, and a selectable marker.

The eukaryotic small ribosomal subunit (40S) is the smaller subunit of the eukaryotic 80S ribosomes, with the other major component being the large ribosomal subunit (60S). The "40S" and "60S" names originate from the convention that ribosomal particles are denoted according to their sedimentation coefficients in Svedberg units. It is structurally and functionally related to the 30S subunit of 70S prokaryotic ribosomes. However, the 40S subunit is much larger than the prokaryotic 30S subunit and contains many additional protein segments, as well as rRNA expansion segments.

Leaky scanning is a mechanism used during the initiation phase of eukaryotic translation that enables regulation of gene expression. During initiation, the small 40S ribosomal subunit "scans" or moves in a 5' --> 3' direction along the 5'UTR to locate a start codon to commence elongation. Sometimes, the scanning ribosome bypasses the initial AUG start codon and begins translation at further downstream AUG start codons. Translation in eukaryotic cells according to most scanning mechanisms occurs at the AUG start codon proximal to the 5' end of mRNA; however, the scanning ribosome may encounter an “unfavorable nucleotide context” around the start codon and continue scanning.

<span class="mw-page-title-main">Eukaryotic ribosome</span> Large and complex molecular machine

Ribosomes are a large and complex molecular machine that catalyzes the synthesis of proteins, referred to as translation. The ribosome selects aminoacylated transfer RNAs (tRNAs) based on the sequence of a protein-encoding messenger RNA (mRNA) and covalently links the amino acids into a polypeptide chain. Ribosomes from all organisms share a highly conserved catalytic center. However, the ribosomes of eukaryotes are much larger than prokaryotic ribosomes and subject to more complex regulation and biogenesis pathways. Eukaryotic ribosomes are also known as 80S ribosomes, referring to their sedimentation coefficients in Svedberg units, because they sediment faster than the prokaryotic (70S) ribosomes. Eukaryotic ribosomes have two unequal subunits, designated small subunit (40S) and large subunit (60S) according to their sedimentation coefficients. Both subunits contain dozens of ribosomal proteins arranged on a scaffold composed of ribosomal RNA (rRNA). The small subunit monitors the complementarity between tRNA anticodon and mRNA, while the large subunit catalyzes peptide bond formation.

Translational regulation refers to the control of the levels of protein synthesized from its mRNA. This regulation is vastly important to the cellular response to stressors, growth cues, and differentiation. In comparison to transcriptional regulation, it results in much more immediate cellular adjustment through direct regulation of protein concentration. The corresponding mechanisms are primarily targeted on the control of ribosome recruitment on the initiation codon, but can also involve modulation of peptide elongation, termination of protein synthesis, or ribosome biogenesis. While these general concepts are widely conserved, some of the finer details in this sort of regulation have been proven to differ between prokaryotic and eukaryotic organisms.

Archaeal initiation factors are proteins that are used during the translation step of protein synthesis in archaea. The principal functions these proteins perform include ribosome RNA/mRNA recognition, delivery of the initiator Met-tRNAiMet, methionine bound tRNAi, to the 40s ribosome, and proofreading of the initiation complex.

<span class="mw-page-title-main">Translation regulation by 5′ transcript leader cis-elements</span>

Translation regulation by 5′ transcript leader cis-elements is a process in cellular translation.

References

  1. 1 2 Shine, J.; Dalgarno, L. (1975-03-06). "Determinant of cistron specificity in bacterial ribosomes". Nature. 254 (5495): 34–38. Bibcode:1975Natur.254...34S. doi:10.1038/254034a0. PMID   803646. S2CID   4162567.
  2. 1 2 "Ribosomal Binding Site Sequence Requirements". www.thermofisher.com. Retrieved 2015-10-16.
  3. ↑ "Help:Ribosome Binding Site - parts.igem.org". parts.igem.org. Retrieved 2015-10-16.
  4. ↑ Omotajo, Damilola; Tate, Travis; Cho, Hyuk; Choudhary, Madhusudan (2015-08-14). "Distribution and diversity of ribosome binding sites in prokaryotic genomes". BMC Genomics. 16 (1): 604. doi:10.1186/s12864-015-1808-6. ISSN   1471-2164. PMC   4535381 . PMID   26268350.
  5. 1 2 3 Laursen, Brian Søgaard; Sørensen, Hans Peter; Mortensen, Kim Kusk; Sperling-Petersen, Hans Uffe (2005-03-01). "Initiation of Protein Synthesis in Bacteria". Microbiology and Molecular Biology Reviews. 69 (1): 101–123. doi:10.1128/MMBR.69.1.101-123.2005. ISSN   1092-2172. PMC   1082788 . PMID   15755955.
  6. 1 2 3 De Boer, Herman A.; Hui, Anna S. (1990-01-01). "[9] Sequences within ribosome binding site affecting messenger RNA translatability and method to direct ribosomes to single messenger RNA species". In Enzymology, BT - Methods in (ed.). Gene Expression Technology. Gene Expression Technology. Vol. 185. Academic Press. pp. 103–114. doi:10.1016/0076-6879(90)85011-C. ISBN   9780121820862. PMID   2199771.
  7. ↑ Stormo, Gary D.; Schneider, Thomas D.; Gold, Larry M. (1982-05-11). "Characterization of translational initiation sites in E. coli". Nucleic Acids Research. 10 (9): 2971–2996. doi:10.1093/nar/10.9.2971. ISSN   0305-1048. PMC   320669 . PMID   7048258.
  8. 1 2 Hellen, Christopher U. T.; Sarnow, Peter (2001-07-01). "Internal ribosome entry sites in eukaryotic mRNA molecules". Genes & Development. 15 (13): 1593–1612. doi: 10.1101/gad.891101 . ISSN   0890-9369. PMID   11445534.
  9. ↑ Pisarev, Andrey V.; Shirokikh, Nikolay E.; Hellen, Christopher U.T. (2005). "Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites". Comptes Rendus Biologies. 328 (7): 589–605. doi:10.1016/j.crvi.2005.02.004. PMID   15992743.
  10. 1 2 Hayes, William S.; Borodovsky, Mark (1998). "Deriving ribosomal binding site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction" (PDF). Pacific Symposium on Biocomputing. 3: 279–290.
  11. ↑ Noguchi, Hideki; Taniguchi, Takeaki; Itoh, Takehiko (2008-12-01). "MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes". DNA Research. 15 (6): 387–396. doi:10.1093/dnares/dsn027. ISSN   1340-2838. PMC   2608843 . PMID   18940874.
  12. ↑ Oliveira, Márcio Ferreira da Silva; Mendes, Daniele Quintella; Ferrari, Luciana Itida; Vasconcelos, Ana Tereza Ribeiro (2004). "Ribosome binding site recognition using neural networks". Genetics and Molecular Biology. 27 (4): 644–650. doi: 10.1590/S1415-47572004000400028 . ISSN   1415-4757.
  13. ↑ Stormo, Gary D. (2000-01-01). "DNA binding sites: representation and discovery". Bioinformatics. 16 (1): 16–23. doi:10.1093/bioinformatics/16.1.16. ISSN   1367-4803. PMID   10812473.
  14. ↑ "Prof John Shine — Garvan Institute of Medical Research". www.garvan.org.au. Retrieved 2015-11-10.
  15. ↑ Kozak, Marilyn (1984-01-25). "Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs". Nucleic Acids Research. 12 (2): 857–872. doi:10.1093/nar/12.2.857. ISSN   0305-1048. PMC   318541 . PMID   6694911.
  16. ↑ "Research: Top 10 Women Scientists Of The '80s: Making A Difference | The Scientist Magazine®". The Scientist. Retrieved 2015-11-10.
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