Translational regulation

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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.

Contents

In prokaryotes

Initiation

Initiation of translation is regulated by the accessibility of ribosomes to the Shine-Dalgarno sequence. This stretch of four to nine purine residues are located upstream the initiation codon and hybridize to a pyrimidine-rich sequence near the 3' end of the 16S RNA within the 30S bacterial ribosomal subunit. [1] Polymorphism in this particular sequence has both positive and negative effects on the efficiency of base-pairing and subsequent protein expression. [2] Initiation is also regulated by proteins known as initiation factors which provide kinetic assistance to the binding between the initiation codon and tRNAfMet, which supplies the 3'-UAC-5' anticodon. IF1 binds the 30S subunit first, instigating a conformational change [3] that allows for the additional binding of IF2 and IF3. [4] IF2 ensures that tRNAfMet remains in the correct position while IF3 proofreads initiation codon base-pairing to prevent non-canonical initiation at codons such as AUU and AUC. [5] Generally, these initiation factors are expressed in equal proportion to ribosomes, however experiments using cold-shock conditions have shown to create stoichiometric imbalances between these translational machinery. In this case, two to three fold changes in expression of initiation factors coincide with increased favorability towards translation of specific cold-shock mRNAs. [6]

Elongation

Due to the fact that translation elongation is an irreversible process, there are few known mechanisms of its regulation. However, it has been shown that translational efficiency is reduced via diminished tRNA pools, which are required for the elongation of polypeptides. In fact, the richness of these tRNA pools are susceptible to change through cellular oxygen supply. [7]

Termination

The termination of translation requires coordination between release factor proteins, the mRNA sequence, and ribosomes. Once a termination codon is read, release factors RF-1, RF-2, and RF-3 contribute to the hydrolysis of the growing polypeptide, which terminates the chain. Bases downstream the stop codon affect the activity of these release factors. In fact, some bases proximal to the stop codon suppress the efficiency of translation termination by reducing the enzymatic activity of the release factors. For instance, the termination efficiency of a UAAU stop codon is near 80% while the efficiency of UGAC as a termination signal is only 7%. [8]

In eukaryotes

Initiation

When comparing initiation in eukaryotes to prokaryotes, perhaps one of the first noticeable differences is the use of a larger 80S ribosome. Regulation of this process begins with the supply of methionine by a tRNA anticodon that basepairs AUG. This base pairing comes about by the scanning mechanism that ensues once the small 40S ribosomal subunit binds the 5' untranslated region (UTR) of mRNA. The usage of this scanning mechanism, in opposition to the Shine-Dalgarno sequence that was referenced in prokaryotes, is the ability to regulate translation through upstream RNA secondary structures. This inhibition of initiation through complex RNA structures may be circumvented in some cases by way of internal ribosomal entry sites (IRESs) that localize pre-initiation complexes (PIC) to the start site. [9] In addition to this, the guidance of the PIC to the 5' UTR is coordinated by subunits of the PIC, known as eukaryotic initiation factors (eIFs). When some of these proteins are down-regulated through stresses, translation initiation is reduced by inhibiting cap dependent initiation, the activation of translation by binding eIF4E to the 5' 7-methylguanylate cap. eIF2 is responsible for coordinating the interaction between the Met-tRNAiMet and the P-site of the ribosome. Regulation by phosphorylation of eIF2 is largely associated with the termination of translation initiation. [10] Serine kinases, GCN2, PERK, PKR, and HRI are examples of detection mechanisms for differing cellular stresses that respond by slowing translation through eIF2 phosphorylation.

Elongation

The hallmark difference of elongation in eukaryotes in comparison to prokaryotes is its separation from transcription. While prokaryotes are able to undergo both cellular processes simultaneously, the spatial separation that is provided by the nuclear membrane prevents this coupling in eukaryotes. Eukaryotic elongation factor 2 (eEF2) is a regulateable GTP-dependent translocase that moves nascent polypeptide chains from the A-site to the P-site in the ribosome. Phosphorylation of threonine 56 is inhibitory to the binding of eEF2 to the ribosome. [11] Cellular stressors, such as anoxia have proven to induce translational inhibition through this biochemical interaction. [12]

Termination

Mechanistically, eukaryotic translation termination matches its prokaryotic counterpart. In this case, termination of the polypeptide chain is achieved through the hydrolytic action of a heterodimer consisting of release factors, eRF1 and eRF3. Translation termination is said to be leaky in some cases as noncoding-tRNAs may compete with release factors to bind stop codons. This is possible due to the matching of 2 out 3 bases within the stop codon by tRNAs that may occasionally outcompete release factor base pairing. [13] An example of regulation at the level of termination is functional translational readthrough of the lactate dehydrogenase gene LDHB. This readthrough provides a peroxisomal targeting signal that localizes the distinct LDHBx to the peroxisome. [14]

In plants

Translation in plants is tightly regulated as in animals, however, it is not as well understood as transcriptional regulation. There are several levels of regulation including translation initiation, mRNA turnover and ribosome loading. Recent studies have shown that translation is also under the control of the circadian clock. Like transcription, the translation state of numerous mRNAs changes over the diel cycle (day night period). [15]

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. Ribosomal RNA is found in the ribosomal nucleus where this synthesis happens. 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.

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">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.

Eukaryotic Initiation Factor 2 (eIF2) is an eukaryotic initiation factor. It is required for most forms of eukaryotic translation initiation. eIF2 mediates the binding of tRNAiMet to the ribosome in a GTP-dependent manner. eIF2 is a heterotrimer consisting of an alpha, a beta, and a gamma subunit.

The eukaryotic initiation factor-4A (eIF4A) family consists of 3 closely related proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA.

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.

<span class="mw-page-title-main">Ribosomal pause</span> Queueing or stacking of ribosomes during translation of the nucleotide sequence of mRNA transcripts

Ribosomal pause refers to the queueing or stacking of ribosomes during translation of the nucleotide sequence of mRNA transcripts. These transcripts are decoded and converted into an amino acid sequence during protein synthesis by ribosomes. Due to the pause sites of some mRNA's, there is a disturbance caused in translation. Ribosomal pausing occurs in both eukaryotes and prokaryotes. A more severe pause is known as a ribosomal stall.

<span class="mw-page-title-main">Eukaryotic initiation factor 3</span> Multiprotein complex that functions during the initiation phase of eukaryotic translation

Eukaryotic initiation factor 3 (eIF3) is a multiprotein complex that functions during the initiation phase of eukaryotic translation. It is essential for most forms of cap-dependent and cap-independent translation initiation. In humans, eIF3 consists of 13 nonidentical subunits (eIF3a-m) with a combined molecular weight of ~800 kDa, making it the largest translation initiation factor. The eIF3 complex is broadly conserved across eukaryotes, but the conservation of individual subunits varies across organisms. For instance, while most mammalian eIF3 complexes are composed of 13 subunits, budding yeast's eIF3 has only six subunits.

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. ↑ Nelson, David L.; Cox, Michael M. (2008). Lehnniger: Principles of Biochemistry(Fifth ed.). W.H. Freeman and Company. p. 243. ISBN   978-0716771081.
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  3. ↑ Carter, A. P.; Clemons, W. M.; Brodersen, D. E.; Morgan-Warren, R. J.; Hartsch, T.; Wimberly, B. T.; Ramakrishnan, V. Crystal Structure of an Initiation Factor Bound to the 30≪Em≫S≪/Em≫ Ribosomal Subunit. Science 2001,  291,  498– 501, doi : 10.1126/science.1057766
  4. ↑ Milón P, Maracci C, Filonava L, Gualerzi CO, Rodnina MV. Real-time assembly landscape of bacterial 30S translation initiation complex. Nat Struct Mol Biol. 2012;19:609–615.
  5. ↑ Hartz D, McPheeters DS, Gold L. Selection of the initiator tRNA by Escherichia coli initiation factors. Genes Dev. 1989;3:1899–1912. doi : 10.1101/gad.3.12a.1899
  6. ↑ Giuliodori A. M., Brandi A., Gualerzi C. O., Pon C. L., 2004.  Preferential translation of cold-shock mRNAs during cold adaptation. RNA 10(2): 265–276. doi : 10.1261/rna.5164904
  7. ↑ Taylor, R. C., Webb Robertson, B.-J. M., Markille, L. M., Serres, M. H., Linggi, B. E., Aldrich, J. T., … Wiley, S. (2013). Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria. Integrative Biology : Quantitative Biosciences from Nano to Macro, 5(11), 1393–1406. doi : 10.1039/c3ib40120k
  8. ↑ Poole, E. S., Brown, C. M., & Tate, W. P. (1995). The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. The EMBO Journal, 14(1), 151–158.
  9. ↑ López-Lastra, M; Rivas, A; Barría, MI (2005). "Protein synthesis in eukaryotes: the growing biological relevance of cap-independent translation initiation". Biological research. 38 (2–3): 121–46. doi : 10.4067/s0716-97602005000200003 PMID 16238092.
  10. ↑ Kimball S.R. Eukaryotic initiation factor eIF2. Int. J. Biochem. Cell Biol. 1999;31:25–29.
  11. ↑ Ovchinnikov LP, Motuz LP, Natapov PG, Averbuch LJ, Wettenhall RE, Szyszka R, Kramer G, Hardesty B. 1990. Three phosphorylation sites in elongation factor 2. FEBS Lett. 275: 209– 212
  12. ↑ Horman S, Browne G, Krause U, Patel J, Vertommen D, Bertrand L, Lavoinne A, Hue L, Proud C, Rider M. 2002. Activation of AMP-activated protein kinase leads to the phosphorylation of elongation factor 2 and an inhibition of protein synthesis. Curr. Biol. 12: 1419– 1423
  13. ↑ Dabrowski M, Bukowy-Bieryllo Z, Zietkiewicz E. Translational readthrough potential of natural termination codons in eucaryotes - the impact of RNA sequence. RNA Biol. 2015;12:950–8.
  14. ↑ Schueren F, Lingner T, George R, Hofhuis J, Gartner J, Thoms S (2014). "Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals". eLife. 3: e03640. doi : 10.7554/eLife.03640
  15. ↑ Missra, Anamika; Ernest, Ben; Lohoff, Tim; Jia, Qidong; Satterlee, James; Ke, Kenneth; Arnim, Albrecht G. von. "The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading". The Plant Cell. 27 (9): 2582–2599. doi : 10.1105/tpc.15.00546 PMC 4815098 . PMID 26392078.
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