The greatest catch: big game fishing for mRNA-bound proteins

Sibley, Christopher R.; Attig, Jan; Ule, Jernej

doi:10.1186/gb-2012-13-7-163

Cited by 4 publications

(3 citation statements)

References 10 publications

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“…However, in addition to purely sequence-based determinants, a number of context-dependent attributes (often hard to separate) govern the translational speed in vivo . This includes the presentation of secondary structures, the accessibility of ribosomes and masking of the transcript by RNA binding proteins [56] , [57] . Isolating these determinants is context dependent and naturally also cell specific (e.g., some cells may contain RNA binding proteins that interfere with the ribosome flow).…”

Section: Discussionmentioning

confidence: 99%

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

Mahlab

Linial

2014

PLoS Comput Biol

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Protein translation is the most expensive operation in dividing cells from bacteria to humans. Therefore, managing the speed and allocation of resources is subject to tight control. From bacteria to humans, clusters of relatively rare tRNA codons at the N′-terminal of mRNAs have been implicated in attenuating the process of ribosome allocation, and consequently the translation rate in a broad range of organisms. The current interpretation of “slow” tRNA codons does not distinguish between protein translations mediated by free- or endoplasmic reticulum (ER)-bound ribosomes. We demonstrate that proteins translated by free- or ER-bound ribosomes exhibit different overall properties in terms of their translation efficiency and speed in yeast, fly, plant, worm, bovine and human. We note that only secreted or membranous proteins with a Signal peptide (SP) are specified by segments of “slow” tRNA at the N′-terminal, followed by abundant codons that are considered “fast.” Such profiles apply to 3100 proteins of the human proteome that are composed of secreted and signal peptide (SP)-assisted membranous proteins. Remarkably, the bulks of the proteins (12,000), or membranous proteins lacking SP (3400), do not have such a pattern. Alternation of “fast” and “slow” codons was found also in proteins that translocate to mitochondria through transit peptides (TP). The differential clusters of tRNA adapted codons is not restricted to the N′-terminal of transcripts. Specifically, Glycosylphosphatidylinositol (GPI)-anchored proteins are unified by clusters of low adapted tRNAs codons at the C′-termini. Furthermore, selection of amino acids types and specific codons was shown as the driving force which establishes the translation demands for the secretory proteome. We postulate that “hard-coded” signals within the secretory proteome assist the steps of protein maturation and folding. Specifically, “speed control” signals for delaying the translation of a nascent protein fulfill the co- and post-translational stages such as membrane translocation, proteins processing and folding.

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Section: Discussionmentioning

confidence: 99%

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

Mahlab

Linial

2014

PLoS Comput Biol

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“…A second approach for studying the RBPome looks at the global RBP footprint on the transcriptome; that is, the totality of RNA sequences bound by RBPs, rather than the binding profile of a single RBP. This strategy was pioneered in mammalian cells by the groups of Markus Landthaler, Christoph Dieterich, Matthias Hentze and Jeroen Krijgsveld ( [ 16 , 17 ]; reviewed in [ 18 ]), and was explored last year in Genome Biology in a yeast setting [ 19 ]. In this issue, Landthaler and Dieterich extend their previous study by assaying a second mammalian cell line and developing a bioinformatics approach, POPPI, for analyzing these datasets and the differences between them [ 20 ].…”

Section: Why the Rbpome Remained Unloved: Methods!mentioning

confidence: 99%

The RBPome: where the brains meet the brawn

Attar

2014

Genome Biol

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“…At least 800 distinct RBDs are known[ 2 ]; among the most frequent in humans are the single-stranded-RNA-binding RRM, KH, zf-CCCH and zf-CCHC domains, and the double-stranded-RNA-binding DSRM domain. Recent proteomic analysis consolidated the number of mRBPs to 700 proteins and revealed at least 20 previously unknown RBDs [ 1 , 3 ].…”

Section: The Challenges Of Characterizing Post-transcriptional Gene Rmentioning

confidence: 99%

Learning the language of post-transcriptional gene regulation

2013

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The greatest catch: big game fishing for mRNA-bound proteins

Abstract: Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics.

Cited by 4 publications

References 10 publications

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective

The RBPome: where the brains meet the brawn

Learning the language of post-transcriptional gene regulation

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