The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity

Abstract

Summary During eukaryotic evolution, ribosomes have considerably increased in size forming a surface exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identified hundreds of ribosome associated proteins (RAPs) from categories including metabolism, cell cycle, as well as RNA and protein modifying enzymes that functionally diversify mammalian ribosomes. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific posttranslational modification, on ribosomes and define its direct substrates. Moreover, we show that the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA binding protein in the translation of ER-destined mRNAs. Therefore, RAPs interconnect one of life’s most ancient molecular machines with diverse cellular processes, providing an additional layer of regulatory potential to protein expression.

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

“…The great number of protein and RNA components involved in ribosome initiation, scanning, elongation and recycling of mRNAs highlights that translation — especially translation initiation, which is one of the most crucial steps in translation 7,8 — is a highly regulated process (BOX 1). Indeed, the ribosome itself, which for a long time was regarded as a constitutive, housekeeping molecular machine, has only recently been appreciated to be functionally heterogeneous with respect to its associated proteins 9,10 . Translation regulation can also involve structures in the mRNA itself, which are rearranged and unfolded by the ribosome and by RNA remodellers such as RNA helicases.…”

Ribosome Mediated Quinary Interactions Modulate In-Cell Protein Activities

“…The decrease in Me-THF decreases TS utilization of the substrate and results in an increase in dUMP. Because TS binds to total RNA (Figure S4) as well as to mRNA 41 and ribosomes, 5 we examined the possibility that ribosome-mediated quinary interactions also affect TS activity to reduce cellular levels of mutagenic dUMP.…”

How Ribosomes Translate Cancer

“…Moreover, extensive analysis of ribosomes in mouse embryonic stem cells revealed heterogeneity in ribosomal protein composition that is associated with translation of distinct subsets of mRNAs by different ribosomal subpopulations (113), suggesting that ribosomes can function in the absence of specific ribosomal proteins (115). Yet another layer of heterogeneity is added by ribosome-associated proteins which are differentially expressed in subcellular locations, enabling another mechanism for transcript-specific translation and regulatory potential (112). …”