Archaeal initiation factors

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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-tRNA iMet, methionine bound tRNAi, to the 40s ribosome, and proofreading of the initiation complex. [1]

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Conservation of archaeal initiation factors

Of the three domains of life, archaea, eukaryotes, and bacteria, the number of archaeal TIFs is somewhere between eukaryotes and bacteria; eukaryotes have the largest number of TIFs, and bacteria, having streamlined the process, have only three TIFs. [1] Not only are archaeal TIF numbers between that of bacteria and eukaryote numbers, but archaeal initiation factors are seen to have both traits of eukaryotic and prokaryotic initiation factors. [2] Two core TIFs, IF1/IF1A and IF2/IF5B are conserved across the three domains of life. [1] There is also a semi-universal TIF found in all archaea and eukaryote called SUI1, but only in certain bacterial species (YciH). In archaea and eukaryotes, these TIFs help correct the identification of the initiation codon, while its function is unknown in bacteria. [1] Just between eukaryote and archaea, a/eIF2 (trimer) and aIF6 in archaea are conserved in eukaryotes as eIF2 (trimer) and eIF6 TIFs. [1]

Archaea may also carry homologs of eukaryotic eIF2B (the GTP-exchange factor for eIF2). However, only the α subunit is definitively identified, so it probably does not act as a GTP-exchange factor in archaea. [3] [4] There is also a homolog of eIF4A, but it does not seem to participate in translation initiation. [5]

List of initiation factors

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 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.

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.

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. Initiation of eukaryotic translation nearly always occurs at and is dependent on the 5' cap of mRNA molecules, where the translation initiation complex forms and ribosomes engage the mRNA. IRES elements, however allow ribosomes to engage the mRNA and begin translation independently of the 5' cap.

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.

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.

<span class="mw-page-title-main">Hepatitis C virus internal ribosome entry site</span>

The Hepatitis C virus internal ribosome entry site, or HCV IRES, is an RNA structure within the 5'UTR of the HCV genome that mediates cap-independent translation initiation.

Ribosomal particles are denoted according to their sedimentation coefficients in Svedberg units. The 60S subunit is the large subunit of eukaryotic 80S ribosomes, with the other major component being the eukaryotic small ribosomal subunit (40S). It is structurally and functionally related to the 50S subunit of 70S prokaryotic ribosomes. However, the 60S subunit is much larger than the prokaryotic 50S subunit and contains many additional protein segments, as well as ribosomal RNA expansion segments.

<span class="mw-page-title-main">EIF1AX</span> Protein-coding gene in humans

Eukaryotic translation initiation factor 1A, X-chromosomal (eIF1A) is a protein that in humans is encoded by the EIF1AX gene. This gene encodes an essential eukaryotic translation initiation factor. The protein is a component of the 43S pre-initiation complex (PIC), which mediates the recruitment of the small 40S ribosomal subunit to the 5' cap of messenger RNAs.

<span class="mw-page-title-main">EIF5B</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 5B is a protein that in humans is encoded by the EIF5B gene.

<span class="mw-page-title-main">EIF1</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 1 (eIF1) is a protein that in humans is encoded by the EIF1 gene. It is related to yeast SUI1.

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.

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.

<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.

<span class="mw-page-title-main">SUI1</span>

In molecular biology, the single-domain protein SUI1 is a translation initiation factor often found in the fungus, Saccharomyces cerevisiae but it is also found in other eukaryotes and prokaryotes as well as archaea. It is otherwise known as Eukaryotic translation initiation factor 1 (eIF1) in eukaryotes or YciH in bacteria.

The 43S preinitiation complex is a ribonucleoprotein complex that exists during an early step of eukaryotic translation initiation. The 43S PIC contains the small ribosomal subunit (40S) bound by the initiation factors eIF1, eIF1A, eIF3, and the eIF2-Met-tRNAiMet-GTP ternary complex (eIF2-TC).

Archaeal translation is the process by which messenger RNA is translated into proteins in archaea. Not much is known on this subject, but on the protein level it seems to resemble eukaryotic translation.

References

  1. 1 2 3 4 5 6 7 Hernández, Greco; Jagus, Rosemary (2016-08-10). "Evolution of Translational Initiation: From Archaea to Eukarya". Evolution of the Protein Synthesis Machinery and Its Regulation. Hernández, Greco,, Jagus, Rosemary. Switzerland. pp. 61–79. doi:10.1007/978-3-319-39468-8_4. ISBN   9783319394688. OCLC   956539514.{{cite book}}: CS1 maint: location missing publisher (link)
  2. 1 2 Dmitriev, Sergey E.; Stolboushkina, Elena A.; Terenin, Ilya M.; Andreev, Dmitri E.; Garber, Maria B.; Shatsky, Ivan N. (2011). "Archaeal Translation Initiation Factor aIF2 Can Substitute for Eukaryotic eIF2 in Ribosomal Scanning during Mammalian 48S Complex Formation". Journal of Molecular Biology. 413 (1): 106–114. doi:10.1016/j.jmb.2011.08.026. PMID   21884705.
  3. ↑ Gogoi, P; Srivastava, A; Jayaprakash, P; Jeyakanthan, J; Kanaujia, SP (1 January 2016). "In silico analysis suggests that PH0702 and PH0208 encode for methylthioribose-1-phosphate isomerase and ribose-1,5-bisphosphate isomerase, respectively, rather than aIF2Bβ and aIF2Bδ". Gene. 575 (1): 118–26. doi:10.1016/j.gene.2015.08.048. PMID   26318479.
  4. ↑ Schmitt, Emmanuelle; Coureux, Pierre-Damien; Kazan, Ramy; Bourgeois, Gabrielle; Lazennec-Schurdevin, Christine; Mechulam, Yves (18 September 2020). "Recent Advances in Archaeal Translation Initiation". Frontiers in Microbiology. 11. doi: 10.3389/fmicb.2020.584152 . PMC   7531240 . PMID   33072057.
  5. ↑ Schramm, F; Borst, A; Linne, U; Soppa, J (2021). "Elucidation of the Translation Initiation Factor Interaction Network of Haloferax volcanii Reveals Coupling of Transcription and Translation in Haloarchaea". Frontiers in Microbiology. 12: 742806. doi: 10.3389/fmicb.2021.742806 . PMC   8576121 . PMID   34764944.
  6. 1 2 3 4 5 Benelli, D; Londei, P (January 2011). "Translation initiation in Archaea: conserved and domain-specific features". Biochemical Society Transactions. 39 (1): 89–93. doi:10.1042/BST0390089. PMID   21265752.
  7. ↑ Gogoi, Prerana; Kanaujia, Shankar Prasad (2018). "Archaeal and eukaryal translation initiation factor 1 differ in their RNA interacting loops". FEBS Letters. 592 (9): 1602–1610. doi: 10.1002/1873-3468.13044 . PMID   29608219. S2CID   4559350.
  8. ↑ Dever, TE; Gutierrez, E; Shin, BS (2014). "The hypusine-containing translation factor eIF5A". Critical Reviews in Biochemistry and Molecular Biology. 49 (5): 413–25. doi:10.3109/10409238.2014.939608. PMC   4183722 . PMID   25029904.
  9. ↑ Rossi, D; Kuroshu, R; Zanelli, CF; Valentini, SR (2013). "eIF5A and EF-P: two unique translation factors are now traveling the same road". Wiley Interdisciplinary Reviews. RNA. 5 (2): 209–22. doi:10.1002/wrna.1211. PMID   24402910. S2CID   25447826.
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