Prokaryotic small ribosomal subunit

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Atomic structure of the 30S Subunit from Thermus thermophilus. Proteins are shown in blue and the single RNA strand in orange. 010 small subunit-1FKA.gif
Atomic structure of the 30S Subunit from Thermus thermophilus . Proteins are shown in blue and the single RNA strand in orange.

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. [1] This complex is implicated in the binding of transfer RNA to messenger RNA (mRNA). [2] 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.

Contents

Function

The 30S subunit is an integral part of mRNA translation. It binds three prokaryotic initiation factors: IF-1, IF-2, and IF-3. [3]

A portion of the 30S subunit (the 16S rRNA) guides the initiating start codon (5′)-AUG-(3′) of mRNA into position by recognizing the Shine-Dalgarno sequence, a complementary binding site about 8 base pairs upstream from the start codon. [4] This ensures the ribosome starts translation at the correct location. The tightness of the bonding between the Shine-Dalgarno sequence on the mRNA and the 16S rRNA determines how efficiently translation proceeds. [4] Once the 16S rRNA recognizes the mRNA start codon, a special transfer RNA, f-Met-tRNA, binds and protein translation begins. [5] The binding site of the f-Met-tRNA on the 30S ribosomal subunit is called the "D-site" [6] This step is required in order for protein synthesis to occur. Then the large ribosomal subunit will bind and protein synthesis will continue. [7] The binding of the large subunit causes a conformational change in the 70S, which opens another site for protein translation. [6]

In order to form the translation complex with the 50S subunit, the 30S subunit must bind IF-1, IF-2, IF-3, mRNA, and f-met-tRNA. Next, the 50S subunit binds and a guanosine triphosphate is cleaved to guanosine diphosphate and inorganic phosphate, thus dissociating the initiation factors and resulting in protein translation. [8] [5] This process is called "initiation" and is the slowest process of translation. [5]

Structure

The small ribosomal subunit is made up of 16S rRNA and 19 full proteins. [9] There is also one polypeptide chain that consists of 26 amino acids. [10] Conventionally, the rRNA is labeled with "H#" to indicate the helix number in high resolution images. Proteins are labelled "S#" to indicate the different peptides involved in rRNA stabilization. S11 and H45 are located near the Shine-Dalgarno binding site, which is also near the IF-3 binding site. Proteins S3, S4, S5, and S12, along with H18, are located near the channel where mRNA is present in the 30S subunit. [1]

Inhibition

The 30S subunit is the target of antibiotics such as tetracycline and gentamicin. [11] These antibiotics specifically target the prokaryotic ribosomes, hence their usefulness in treating bacterial infections in eukaryotes. Tetracycline interacts with H27 in the small subunit as well as binding to the A-site in the large subunit. [11] Puromycin is an inhibitor of ribosomal translation. [6] Pactamycin interrupts the binding in the Shine-Dalgarno binding region in the small subunit, thus disrupting activity. Hygromycin B also interacts with H44 and inhibits the translocation movement that is necessary during protein synthesis. [11]

See also

Related Research Articles

<span class="mw-page-title-main">Ribosome</span> Synthesizes proteins in cells

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.

<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, though this ratio differs between prokaryotes and eukaryotes.

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.

A bacterial initiation factor (IF) is a protein that stabilizes the initiation complex for polypeptide translation.

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.

<span class="mw-page-title-main">Prokaryotic large ribosomal subunit</span>

50S is the larger subunit of the 70S ribosome of prokaryotes, i.e. bacteria and archaea. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the 5S ribosomal RNA and 23S ribosomal RNA.

<span class="mw-page-title-main">EF-G</span> Prokaryotic elongation factor

EF-G is a prokaryotic elongation factor involved in mRNA translation. As a GTPase, EF-G catalyzes the movement (translocation) of transfer RNA (tRNA) and messenger RNA (mRNA) through the ribosome.

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.

<span class="mw-page-title-main">Protein synthesis inhibitor</span> Inhibitors of translation

A protein synthesis inhibitor is a compound that stops or slows the growth or proliferation of cells by disrupting the processes that lead directly to the generation of new proteins.

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.

<span class="mw-page-title-main">Kasugamycin</span> Chemical compound

Kasugamycin (Ksg) is an aminoglycoside antibiotic that was originally isolated in 1965, from Streptomyces kasugaensis, a Streptomyces strain found near the Kasuga shrine in Nara, Japan. Kasugamycin was discovered by Hamao Umezawa, who also discovered kanamycin and bleomycin, as a drug that prevent growth of a fungus causing rice blast disease. It was later found to inhibit bacterial growth also. It exists as a white, crystalline substance with the chemical formula C14H28ClN3O10 (kasugamycin hydrochloride). It is also known as kasumin.

The P-site is the second binding site for tRNA in the ribosome. The other two sites are the A-site (aminoacyl), which is the first binding site in the ribosome, and the E-site (exit), the third. During protein translation, the P-site holds the tRNA which is linked to the growing polypeptide chain. When a stop codon is reached, the peptidyl-tRNA bond of the tRNA located in the P-site is cleaved releasing the newly synthesized protein. During the translocation step of the elongation phase, the mRNA is advanced by one codon, coupled to movement of the tRNAs from the ribosomal A to P and P to E sites, catalyzed by elongation factor EF-G.

<span class="mw-page-title-main">Translation initiation factor IF-3</span>

In molecular biology, translation initiation factor IF-3 is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consists of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit. The chloroplast homolog enhances the poly(A,U,G)-dependent binding of the initiator tRNA to its ribosomal 30s subunits. IF1–IF3 may also perform ribosome recycling.

References

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  6. 1 2 3 Igarashi, Kazuei; Tanaka, Shigeaki; Kaji, Akira (1971-02-11). "On the aminoacyl-tRNA binding site of the 30-S ribosomal subunit and its relation to the chain initiation site of the ribosome". Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis. 228 (3): 728–731. doi:10.1016/0005-2787(71)90737-4. PMID   4929429.
  7. ↑ Slobin, Lawrence I (December 1972). "Structural and Functional Properties of Ribosomes Crosslinked with Dimethylsuberimidate". Proceedings of the National Academy of Sciences of the United States of America. 69 (12): 3769–3773. Bibcode:1972PNAS...69.3769S. doi: 10.1073/pnas.69.12.3769 . PMC   389868 . PMID   4566460.
  8. ↑ Milon P, Carotti M, Konevega AL, Wintermeyer W, Rodnina MV, Gualerzi CO (2010). "The ribosome-bound initiation factor 2 recruits initiator tRNA to the 30S initiation complex". EMBO Reports. 11 (4): 312–316. doi:10.1038/embor.2010.12. PMC   2854590 . PMID   20224578.
  9. ↑ Tsiboli, Paraskevi; Herfurth, Elke; Choli, Theodora (1994-11-01). "Purification and Characterization of the 30S Ribosomal Proteins from the Bacterium Thermus thermophilus". European Journal of Biochemistry. 226 (1): 169–177. doi:10.1111/j.1432-1033.1994.0t169.x. ISSN   1432-1033. PMID   7957245.
  10. ↑ Choli T, Franceschi F, Yonath A, Wittmann-Liebold B (1993). "Isolation and characterization of a new ribosomal protein from the thermophilic eubacteria, Thermus thermophilus, T. aquaticus and T. flavus" (PDF). Biological Chemistry Hoppe-Seyler. 374 (6): 377–383. doi:10.1515/bchm3.1993.374.1-6.377. PMID   8357533.
  11. 1 2 3 Brodersen, Ditlev E.; Clemons, William M.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, V. (2000-12-22). "The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit". Cell. 103 (7): 1143–1154. doi: 10.1016/S0092-8674(00)00216-6 . PMID   11163189.
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