The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5′TOP sequence

Lahr, Roni M.; Mack, Seshat M.; Héroux, A.; Blagden, Sarah P.; Bousquet‐Antonelli, Cécile; Deragon, Jean-Marc; Berman, Andrea J.

doi:10.1093/nar/gkv748

Cited by 61 publications

(98 citation statements)

References 52 publications

(107 reference statements)

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“…17! associates with 5' TOP mRNAs to mediate the mTOR signal (Lahr et al, 2015), and another recent report uncovered that 5' UTR LARP1 binding sites rarely overlapped with 5' TOP sequences, but instead it binds predominantly at the 3'-most end of 5' UTRs of 5' TOP mRNAs (Hong et al, 2017). Together with our findings, these observations suggest an interesting possibility that the binding of RBP(s), such as LARP1, to the CUIC sequence controls the translation initiation at the initiation codon located immediately downstream of the CUIC sequence.…”

Section: Discussionmentioning

confidence: 99%

On-site ribosome remodeling by locally synthesized ribosomal proteins in axons

Shigeoka

Koppers

Wong

et al. 2018

Preprint

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2!SUMMARY Ribosomes are known to be assembled in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Using subcellular proteomics and live-imaging, we show that locally synthesized RPs incorporate into axonal ribosomes in a nucleolus-independent fashion. We revealed that axonal RP translation is regulated through a novel sequence motif, CUIC, that forms a RNA-loop structure in the region immediately upstream of the initiation codon. Inhibition of axonal CUICregulated RP translation leads to defects in local translation activity and axon branching, demonstrating the physiological relevance of the axonal ribosome remodeling. These results indicate that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus. INTRODUCTIONRNA localization and local translation play key roles in the assembly and maintenance of neuronal connections (Campbell and Holt, 2001;Holt and Schuman, 2013;Wu et al., 2005).Recent genome-wide studies on the axonal transcriptome revealed that thousands of mRNAs are localized to the axon. A consistent but unexpected finding of these studies is the robust enrichment of mRNAs that encode ribosomal proteins (RPs), protein components of ribosomes. Axons are long neuronal processes that carry out many vital specific cellular functions far from their cell bodies, including translation, and must therefore maintain their protein synthetic machinery in good order. However, because most eukaryotic ribosome assembly is well known to occur in the nucleolus (Fromont-Racine et al., 2003;Lastick and McConkey, 1976), the physiological function of RP-coding mRNAs in a neuronal subcellular compartment far distant from the nucleus was enigmatic. RP-coding mRNAs have been abundantly detected in axons of a variety of neuron types, such as retinal ganglion cells (RGCs) (Zivraj et al., 2010), sympathetic neurons (Andreassi et al., 2010) and motor ! 5!In this study, we explore intra-ribosomal roles of axonally synthesized RPs using a range of technical approaches including live imaging, in vivo gene knockdown, bioinformatics, nascent protein labeling and mass spectrometry-based proteomics. We found that axonal translation of RPs coordinately peaks at the axon branching stage in RGCs in vivo, and their translation is regulated by a branch-promoting factor, Netrin-1, through a novel loop structure-forming sequence motif, CUIC, that is shared by ~70% of RP-coding mRNAs. Using nascent protein labeling and proteomic mass spectrometry analysis on ribosomes isolated from pure axons, together with live-imaging approaches, we show that axonally synthesized RPs are physically incorporated into axonal ribosomes in a nucleolus-independent fashion. Furthermore, we demonstrate the physiological importance of the axonal ribosome remodeling by showing that inhibition of axonal RP translation leads to a significant decrease in the level of axonal mRNA translation and s...

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Section: Discussionmentioning

confidence: 99%

On-site ribosome remodeling by locally synthesized ribosomal proteins in axons

Shigeoka

Koppers

Wong

et al. 2018

Preprint

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“…The specific role of LARP1 in translational regulation depends on the context: both phosphorylation and dimerization have been suggested to modulate LARP1 activity (Stavraka and Blagden, 2015). We suggest that acetylation (and deacetylation) might be an additional player: the acetylated lysine substrate, LS K 1017 FRR [k cat /K M =349], is located adjacent to the suggested RNA binding site in the recently solved structure of these HEAT repeats (Lahr et al, 2015), and its modification might thus affect binding to RNA, or to PABP.…”

Section: Discussionmentioning

confidence: 99%

Structure-Based Identification of HDAC8 Non-histone Substrates

et al. 2016

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Summary HDAC8 is a member of the family of Histone Deacetylases (HDAC) that catalyze the deacetylation of acetyl lysine residues within histone and non-histone proteins. The recent identification of novel non-histone HDAC8 substrates such as SMC3, ERRα and ARID1A indicates a complex functionality of this enzyme in cellular homeostasis. To discover additional HDAC8 substrates we developed a comprehensive, structure-based approach based on Rosetta FlexPepBind, a protocol that evaluates peptide-binding ability to a receptor from structural models of this interaction. Here we adapt this protocol to identify HDAC8 substrates using peptide sequences extracted from proteins with known acetylated sites. The many new in vitro HDAC8 peptide substrates identified in this study suggest that numerous cellular proteins are HDAC8 substrates, thus expanding our view of the acetylome and its regulation by HDAC8.

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“…HEAT domains are also involved in binding and transporting protein ligands within the inner channel of the superhelix . More recently, this channel has been identified as a nucleic acid binding surface in a set of proteins with diverse functions, including RNA nuclear export, regulation of mRNA stability, and chromosome segregation …”

Section: Introductionmentioning

confidence: 99%

Structural Biology of the HEAT‐Like Repeat Family of DNA Glycosylases

et al. 2018

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DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl‐DNA glycosylases AlkC and AlkD adopt a unique structure based on α‐helical HEAT repeats. Both enzymes identify and excise their substrates without a base‐flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double‐helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non‐enzymatic HEAT‐like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.

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The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5′TOP sequence

Cited by 61 publications

References 52 publications

On-site ribosome remodeling by locally synthesized ribosomal proteins in axons

On-site ribosome remodeling by locally synthesized ribosomal proteins in axons

Structure-Based Identification of HDAC8 Non-histone Substrates

Structural Biology of the HEAT‐Like Repeat Family of DNA Glycosylases

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