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Ribosome-binding site

January 01, 1970

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.

Prokaryotes edit

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 edit

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 rate at which a ribosome is recruited to the RBS
  • the rate at which a recruited ribosome is able to initiate translation (i.e. the translation initiation efficiency)

The RBS sequence affects both of these factors.

Factors affecting rate of ribosome recruitment edit

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 edit

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 edit

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 edit

5' cap edit

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) edit

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 edit

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 edit

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 edit

References edit

  1. ^ a b 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. ^ a b "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. ^ a b c 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. ^ a b c 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. 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. ^ a b 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. ^ a b 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.

January 01, 1970
ribosome, binding, site, ribosome, binding, site, ribosomal, binding, site, sequence, nucleotides, upstream, start, codon, mrna, transcript, that, responsible, recruitment, ribosome, during, initiation, translation, mostly, refers, bacterial, sequences, althou. 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 1 Prokaryotes 1 1 Effect on translation initiation rate 1 1 1 Factors affecting rate of ribosome recruitment 1 1 2 Factors affecting the efficiency of translation initiation 1 2 Heat shock proteins 2 Eukaryotes 2 1 5 cap 2 2 Internal ribosome entry site IRES 3 Gene annotation 4 History 5 See also 6 ReferencesProkaryotes editThe 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 edit 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 rate at which a ribosome is recruited to the RBS the rate at which a recruited ribosome is able to initiate translation i e the translation initiation efficiency The RBS sequence affects both of these factors Factors affecting rate of ribosome recruitment edit 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 edit 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 edit 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 edit5 cap edit 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 edit 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 editThe 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 editThe 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 editAlpha operon ribosome binding site Eukaryotic translation Bacterial translation Archaeal translation Gene predictionReferences edit a b 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 a b Ribosomal Binding Site Sequence Requirements www thermofisher com Retrieved 2015 10 16 Help Ribosome Binding Site parts igem org parts igem org Retrieved 2015 10 16 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 a b c Laursen Brian Sogaard Sorensen 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 a b c 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 Vol 185 Academic Press pp 103 114 doi 10 1016 0076 6879 90 85011 C ISBN 9780121820862 PMID 2199771 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 a b Hellen Christopher U T Sarnow Peter 2001 07 01 Internal ribosome entry sites in eukaryotic mRNA molecules Genes amp Development 15 13 1593 1612 doi 10 1101 gad 891101 ISSN 0890 9369 PMID 11445534 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 a b 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 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 Oliveira Marcio 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 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 Prof John Shine Garvan Institute of Medical Research www garvan org au Retrieved 2015 11 10 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 Research Top 10 Women Scientists Of The 80s Making A Difference The Scientist Magazine The Scientist Retrieved 2015 11 10 Retrieved from https en wikipedia org w index php title Ribosome binding site amp oldid 1186765485, wikipedia, wiki, book, books, library,

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