Translation initiation factor eIF1A possesses RNA annealing activity in its oligonucleotide-binding fold

Kwon, Sung-Hun; Lee, In-Hwan; Kim, Na-Yeon; Choi, Do-Hee; Oh, Young-Mi; Bae, Sung‐Ho

doi:10.1016/j.bbrc.2007.07.084

Cited by 9 publications

(5 citation statements)

References 16 publications

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“…In contrast, the OB-fold domains of both KREPA1 and KREPA2 did not have any cross-links with their interaction partners within the subcomplexes. This finding suggests that the anchor domains of KREPA1 and KREPA2 are the main interaction domains that unite deletion or insertion subcomplex subunits, and that the OB-fold domains in KREPA1 and KREPA2 are available for interactions with proteins other than subcomplex components or with RNA substrates (61,62). Indeed, the availability of the KREPA1 and KREPA2 OB-folds for substrate binding is potentially vital for KREL1 and KREL2 activity.…”

Section: Discussionmentioning

confidence: 98%

The Architecture of Trypanosoma brucei editosomes

McDermott

Luo

Carnes

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei. Editing is catalyzed by three distinct ∼20S editosomes that have a common set of 12 proteins, but are typified by mutually exclusive RNase III endonucleases with distinct cleavage specificities and unique partner proteins. Previous studies identified a network of protein-protein interactions among a subset of common editosome proteins, but interactions among the endonucleases and their partner proteins, and their interactions with common subunits were not identified. Here, chemical cross-linking and mass spectrometry, comparative structural modeling, and genetic and biochemical analyses were used to define the molecular architecture and subunit organization of purified editosomes. We identified intra-and interprotein cross-links for all editosome subunits that are fully consistent with editosome protein structures and previously identified interactions, which we validated by genetic and biochemical studies. The results were used to create a highly detailed map of editosome protein domain proximities, leading to identification of molecular interactions between subunits, insights into the functions of noncatalytic editosome proteins, and a global understanding of editosome architecture.cross-linking | proteomics | Trypanosoma brucei | RNA editing | editosome T he kinetoplastid Trypanosoma brucei is the causative agent of human African trypanosomiasis, which is transmitted by the tsetse fly and is a health threat to millions of people in subSaharan Africa. Kinetoplastids are named for their distinctive mitochondrial DNA network, known as the kinetoplast DNA, which is composed of interlocked DNA maxicircles and minicircles (1, 2). Several identical maxicircles encode two ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs) for 18 mitochondrial proteins, 12 of which undergo posttranscriptional RNA editing (3-9). RNA editing was first described in kinetoplastids (6,8,9), where it is essential (10) and involves insertion and deletion of uridines (Us) to generate translatable mitochondrial transcripts. The sequence information for editing is specified by ∼60-nucleotide guide RNAs (gRNAs) that are encoded in thousands of heterogeneous minicircles (11)(12)(13)(14)(15)(16)(17). Editing occurs by rounds of coordinated catalytic steps that require a number of different enzymes: cleavage of the mRNA substrate by endonucleases, addition of Us by 3′ terminal uridylytransferase (TUTase) or removal of Us by U-specific 3′ exonuclease (exoUase) at insertion or deletion editing sites, respectively, and rejoining of mRNA fragments by RNA ligases. The enzymes that catalyze RNA editing in T. brucei are in ∼20S editosome complexes that also contain proteins with no known catalytic functions (16,(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28).There are three similar versions of ∼20S editosomes that have a common set of 12 proteins (SI Appendix, Fig. S1 and Table S1). However, they are compositionally and functionally distinct in that each...

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Section: Discussionmentioning

confidence: 98%

The Architecture of Trypanosoma brucei editosomes

McDermott

Luo

Carnes

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…For TbMP18, TbMP42 and TbMP81 the crystal structures of the OB-fold domains are known [50,51]. OB-fold proteins in other RNA-based biochemical systems have been shown to provide RNA chaperone-type activities [52,53]. Especially, the yeast exosome core protein Rrp44 has been demonstrated to catalyze the unwinding of RNA molecules through a novel mechanism utilizing three OB-fold domains [54,55].…”

Section: Ob-fold Domains In Editosome Proteinsmentioning

confidence: 99%

Structure and intrinsic disorder of the proteins of theTrypanosoma brucei editosome

et al. 2015

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a b s t r a c tMitochondrial pre-mRNAs in trypanosomatids undergo RNA editing to be converted into translatable mRNAs. The reaction is characterized by the insertion and deletion of uridine residues and is catalyzed by a macromolecular protein complex called the editosome. Despite intensive research, structural information for the majority of editosome proteins is still missing and no high resolution structure for the editosome exists. Here we present a comprehensive structural bioinformatics analysis of all proteins of the Trypanosoma brucei editosome. We specifically focus on the interplay between intrinsic order and disorder. According to computational predictions, editosome proteins involved in the basal reaction steps of the processing cycle are mostly ordered. By contrast, thirty percent of the amino acid content of the editosome is intrinsically disordered, which includes most prominently proteins with OB-fold domains. Based on the data we suggest a functional model, in which the structurally disordered domains of the complex are correlated with the RNA binding and RNA unfolding activity of the T. brucei editosome.

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“…In addition, binding of eIF1A – together with eIF1 – maintains the ribosome in an open, scanning‐competent conformation,47 and mutations in its S1 domain lead to defects in scanning 48. The S1 domain of eIF1A has RNA‐annealing activity, although the relevance of this activity for the multiple functions of eIF1A is unclear 49…”

Section: Csd‐ and S1 Domain‐containing Proteinsmentioning

confidence: 99%

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

et al. 2010

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Cold shock domain (CSD)-containing proteins have been found in all three domains of life and function in a variety of processes that are related, for the most part, to post-transcriptional gene regulation. The CSD is an ancient beta-barrel fold that serves to bind nucleic acids. The CSD is structurally and functionally similar to the S1 domain, a fold with otherwise unrelated primary sequence. The flexibility of the CSD/S1 domain for RNA recognition confers an enormous functional versatility to the proteins that contain them. This review summarizes the current knowledge on eukaryotic CSD/S1 domain-containing proteins with a special emphasis on UNR (upstream of N-ras), a member of this family with multiple copies of the CSD.

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Translation initiation factor eIF1A possesses RNA annealing activity in its oligonucleotide-binding fold

Cited by 9 publications

References 16 publications

The Architecture of Trypanosoma brucei editosomes

The Architecture of Trypanosoma brucei editosomes

Structure and intrinsic disorder of the proteins of theTrypanosoma brucei editosome

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

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