Volume 19 Issue 6, June 2012

The recent X-ray structures of the complete ribosome and large and small subunits from eukaryotes allow these structures to be compared to the previously determined structures of bacterial ribosomes. This Review describes bacterial and eukaryotic ribosomes as a conserved core and two specific shells and focuses on selected bacteria- and eukaryote-specific structural features and their functional implications.

Translation initiation requires the formation of a pre-initiation complex that recruits the 5′ end of the mRNA and scans along it to locate the start codon. Genetic, biochemical and structural studies have shed light on the molecular mechanisms underlying the individual steps of this complex process. This Review describes our current understanding of eukaryotic translation initiation and outlines some important outstanding questions in the field.

Recent studies have revealed how poly(A) tail length and the selection of alternative polyadenylation sites contribute to translational control. This Review discusses how mechanisms of alternative polyadenylation, deadenylation and cytoplasmic polyadenylation are coordinated to modulate gene expression in inflammation, learning and memory acquisition, and early development.

Understanding how microRNAs (miRNAs) silence targeted mRNAs has been the focus of intensive research. This Review describes recent advances, with an emphasis on how the miRNA-mediated silencing complex (miRISC) controls gene expression by inhibiting translation and/or mRNA decay, and how trans-acting factors control miRNA action.

Cells have evolved so-called mRNA surveillance mechanisms to monitor mRNAs as they are translated and to degrade troublesome transcripts. Studies of mRNA surveillance have traditionally focused on mRNA fate. In this Perspective, the authors explore mRNA surveillance from the viewpoint of its origins on the ribosome, which should lead to new and unanticipated insights that inform future studies.

Although the poly(A) tail and poly(A) binding protein (PABP) have emerged as important effectors of miRNA function, how they contribute to miRNA-mediated gene silencing has been unclear. A combination of biochemical and functional studies now demonstrate that PABP promotes the association of miRISC with its target mRNAs.

Translation initiation proceeds in several steps, and one of the early events involves the binding of three initiation factors, mRNA and initiator tRNA to the 30S ribosomal subunit, which is known as the 30S pre-initiation complex (PIC) assembly. Systematic FRET studies now uncover the kinetically favored assembly pathway of the 30S PIC.

A biochemical study reveals the AAA+ protein unfoldase ClpX functions as a closed ring and identifies regions required for intersubunit coupling during the ATPase cycle. These findings provide important insights on the ClpX mechanism that may be extended to other AAA+ proteins.

Sequence recognition through base pairing is essential for DNA repair and gene regulation, but the basic rules underlying this process have been unclear. Data from single-molecule fluorescence studies, used to visualize annealing and melting reactions of two untethered strands containing a single mismatch, suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA.

Cisplatin forms intrastrand cross-links on DNA and is a widely used chemotherapy agent. Among human translesion DNA polymerases, Pol-η can bypass cisplatin adducts. The crystal structure of human Pol-η in complex with a DNA template with a cisplatin lesion is now presented. In addition to the larger active site, the structure reveals specific interactions with the adduct by residues that are not conserved in other translesion polymerases.

The voltage-sensing domain of Ci-VSP regulates the enzymatic activity of its PTEN-like phosphatase domain. New structural and functional data identify a gating loop that controls access to the enzyme's active site and is coupled to voltage sensor movements.

Pentameric ligand-gated ion channels (pLGICs) mediate fast synaptic signaling in response to neurotransmitter binding, but the conformational changes induced by neurotransmitter binding are unknown. The crystal structures of mutated GLIC, a bacterial pLGIC homolog, reveal a novel, locally closed channel conformation that provides insight into pLGIC allosteric transitions.

Primary microRNA cleavage by the Microprocessor complex comprising Drosha and DGCR8 needs to be specific yet efficient. Mathematical modeling complemented with experimental analysis now shows that autoregulatory feedback on DGCR8 expression is crucial for balancing the efficiency and specificity of Microprocessor activity.

Poly ADP-ribosylation regulates cellular processes such as genomic stability maintenance, transcription and cell death. The structure of a mammalian poly(ADP-ribose) glycohydrolase gives insight into the enzyme's endoglycosidase activity and provides a basis for the development of therapeutic inhibitors.

Translational control has become a major focus of attention and research activity in the field of gene expression, and it is intricately linked to other mechanisms of gene regulation. Translation can be modulated by a myriad of factors and control mechanisms that target either the initiation step or a post-initiation event. Protein synthesis is of course mediated by the ribosome, so structural, functional and mechanistic insights into the translation machinery will help our understanding of how translation can be controlled. The latest developments will be covered in four Reviews and one Perspective, written by leaders in the field.