Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes

Fleischer, Tracey C.; Weaver, Connie M.; McAfee, K. Jill; Jennings, Jennifer L.; Link, Andrew J.

doi:10.1101/gad.1422006

Cited by 262 publications

(277 citation statements)

References 62 publications

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“…However, we can not exclude the participation of eIF2D in the regulation of some general translational events (initiation, elongation or termination), under specific conditions or in specific cells [60]. Nevertheless, we found no similar proteins in the archaea and bacteria tested.…”

Section: Eif2d-like Proteinscontrasting

confidence: 47%

“…These C-terminal domains also occur in DENR. eIF2D, MCT1/DENR and Tma20/Tma22 (yeast orthologs) have been implicated in translation on the basis of bioinformatic, proteomic and overexpression/silencing analyses [57,60]. Many PUA domains bind dsRNA through either the major or the minor groove, but others, including MCT1, eIF2D and Nip7 [38], lack most or all of the conserved basic residues involved in these interactions, and their potential contacts with rRNA must thus involve different residues and may have an altered specificity.…”

Section: Eif2d-like Proteinsmentioning

confidence: 99%

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Protein universe containing a PUA RNA‐binding domain

2013

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Here, we review current knowledge about pseudouridine synthase and archaeosine transglycosylase (PUA)‐domain‐containing proteins to illustrate progress in this field. A methodological analysis of the literature about the topic was carried out, together with a ‘qualitative comparative analysis’ to give a more comprehensive review. Bioinformatics methods for whole‐protein or protein‐domain identification are commonly based on pairwise protein sequence comparisons; we added comparison of structures to detect the whole universe of proteins containing the PUA domain. We present an update of proteins having this domain, focusing on the specific proteins present in Homo sapiens (dyskerin, MCT1, Nip7, eIF2D and Nsun6), and explore the existence of these in other species. We also analyze the phylogenetic distribution of the PUA domain in different species and proteins. Finally, we performed a structural comparison of the PUA domain through data mining of structural databases, determining a conserved structural motif, despite the differences in the sequence, even among eukaryotes, archaea and bacteria. All data discussed in this review, both bibliographic and analytical, corroborate the functional importance of the PUA domain in RNA‐binding proteins.

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Section: Eif2d-like Proteinscontrasting

confidence: 47%

Section: Eif2d-like Proteinsmentioning

confidence: 99%

Protein universe containing a PUA RNA‐binding domain

2013

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“…The interaction of TCTP with eEF1Bβ was later confirmed by Langdon et al (2004), and a more recent structural analysis of this interaction demonstrated that it represents the most conserved interaction of TCTP, indicating that this might be a primary function of the protein (Wu et al 2015). A functional screen of proteins associated with ribosomal complexes in yeast identified TCTP as a translation-machinery-associated (TMA) protein, TMA19 (Fleischer et al 2006). Analysis of yeast mutant strains, deleted in TMA19, revealed that such strains have a reduced rate of protein synthesis and alterations in polysome profiles, lending further support to the notion that TCTP is involved in protein synthesis.…”

Section: The Involvement Of Tctp In Protein Synthesismentioning

confidence: 96%

“…Typically, in these papers, a two-letter suffix before 'TCTP' indicates the species, from which the protein sequence was derived (see Gutierrez-Galeano et al (2014) for an example). The yeast orthologue of TCTP was named 'microtubule and mitochondria interacting protein' (Mmi1p) (Rinnerthaler et al 2006), but in another paper, it was also identified as the 'translation-machinery-associated protein 19' (TMA19) (Fleischer et al 2006), and yet the gene symbol in yeast is YKL056c. In contrast, the gene symbol in higher eukaryotes is TPT1, for 'tumour protein, translationally controlled-1' (Thiele et al 2000).…”

Section: The 'Translationally Controlled Tumour Protein Tctp': Names mentioning

confidence: 99%

The Translational Controlled Tumour Protein TCTP: Biological Functions and Regulation

Bommer

2017

Results and Problems in Cell Differentiation

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The Translational Controlled Tumour Protein TCTP (gene symbol TPT1, also called P21, P23, Q23, fortilin or histamine-releasing factor, HRF) is a highly conserved protein present in essentially all eukaryotic organisms and involved in many fundamental cell biological and disease processes. It was first discovered about 35 years ago, and it took an extended period of time for its multiple functions to be revealed, and even today we do not yet fully understand all the details. Having witnessed most of this history, in this chapter, I give a brief overview and review the current knowledge on the structure, biological functions, disease involvements and cellular regulation of this protein. TCTP is able to interact with a large number of other proteins and is therefore involved in many core cell biological processes, predominantly in the response to cellular stresses, such as oxidative stress, heat shock, genotoxic stress, imbalance of ion metabolism as well as other conditions. Mechanistically, TCTP acts as an anti-apoptotic protein, and it is involved in DNA-damage repair and in cellular autophagy. Thus, broadly speaking, TCTP can be considered a cytoprotective protein. In addition, TCTP facilitates cell division through stabilising the mitotic spindle and cell growth through modulating growth signalling pathways and through its interaction with the proteosynthetic machinery of the cell. Due to its activities, both as an anti-apoptotic protein and in promoting cell growth and division, TCTP is also essential in the early development of both animals and plants. Apart from its involvement in various biological processes at the cellular level, TCTP can also act as an extracellular protein and as such has been involved in modulating whole-body defence processes, namely in the mammalian immune system. Extracellular TCTP, typically in its dimerised form, is able to induce the release of cytokines and other signalling molecules from various types of immune cells. There are also several examples, where TCTP was shown to be involved in antiviral/antibacterial defence in lower animals. In plants, the protein appears to have a protective effect against phytotoxic stresses, such as flooding, draught, too high or low temperature, salt stress or exposure to heavy metals. The finding for the latter stress condition is corroborated by earlier reports that TCTP levels are considerably up-regulated upon exposure of earthworms to high levels of heavy metals. Given the involvement of TCTP in many biological processes aimed at maintaining cellular or whole-body homeostasis, it is not surprising that dysregulation of TCTP levels may promote a range of disease processes, foremost cancer. Indeed a large body of evidence now supports a role of TCTP in at least the most predominant types of human cancers. Typically, this can be ascribed to both the anti-apoptotic activity of the protein and to its function in promoting cell growth and division. However, TCTP also appears to be involved in the later stages of cancer progression, such ...

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“…Thus, it does not appear that pbp1-mediated suppression of ccr4⌬ HU lethality occurs at the level of the CRT1 poly(A) tail. Since Pbp1 is a ribosome-associated factor (Fleischer et al, 2006) and has been previously implicated in 3Ј end-dependent translation (Tadauchi et al, 2004), we posit that the suppression of ccr4⌬ HU sensitivity upon removal of Pbp1 is mediated through decreased translation of the CRT1 transcript in the ccr4⌬ pbp1⌬ strain.…”

Section: Journal Of Cell Science 119 (24)mentioning

confidence: 99%

Ccr4 contributes to tolerance of replication stress through control ofCRT1mRNA poly(A) tail length

Woolstencroft

Cook

Preiß

et al. 2006

Journal of Cell Science

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In Saccharomyces cerevisiae, DNA replication stress activates the replication checkpoint, which slows S-phase progression, stabilizes slowed or stalled replication forks, and relieves inhibition of the ribonucleotide reductase (RNR) complex. To identify novel genes that promote cellular viability after replication stress, the S. cerevisiae non-essential haploid gene deletion set (4812 strains) was screened for sensitivity to the RNR inhibitor hydroxyurea (HU). Strains bearing deletions in either CCR4 or CAF1/POP2, which encode components of the cytoplasmic mRNA deadenylase complex, were particularly sensitive to HU. We found that Ccr4 cooperated with the Dun1 branch of the replication checkpoint, such that ccr4Δ dun1Δ strains exhibited irreversible hypersensitivity to HU and persistent activation of Rad53. Moreover, because ccr4Δ and chk1Δ exhibited epistasis in several genetic contexts, we infer that Ccr4 and Chk1 act in the same pathway to overcome replication stress. A counterscreen for suppressors of ccr4Δ HU sensitivity uncovered mutations in CRT1, which encodes the transcriptional repressor of the DNA-damage-induced gene regulon. Whereas Dun1 is known to inhibit Crt1 repressor activity, we found that Ccr4 regulates CRT1 mRNA poly(A) tail length and may subtly influence Crt1 protein abundance. Simultaneous overexpression of RNR2, RNR3 and RNR4 partially rescued the HU hypersensitivity of a ccr4Δ dun1Δ strain, consistent with the notion that the RNR genes are key targets of Crt1. These results implicate the coordinated regulation of Crt1 via Ccr4 and Dun1 as a crucial nodal point in the response to DNA replication stress.

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Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes

Cited by 262 publications

References 62 publications

Protein universe containing a PUA RNA‐binding domain

Protein universe containing a PUA RNA‐binding domain

The Translational Controlled Tumour Protein TCTP: Biological Functions and Regulation

Ccr4 contributes to tolerance of replication stress through control ofCRT1mRNA poly(A) tail length

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