Volume 16 Issue 5, May 2009

Previous structural snapshots of snurportin have provided insights into its cargo recognition and nuclear import. The structure of snurportin bound to its export factor CRM1 now reveals the molecular basis of its recycling back into the cytoplasm, illuminating general principles of nuclear export sequence recognition.

Type III secretions systems (T3SSs) are major bacterial virulence factors responsible for secretion and injection of protein effectors into host cells. New structures illuminate their ring structure and identify novel ring-mediating structural scaffolds.

The type III secretion system (T3SS) of pathogenic bacteria is composed of a series of rings in the inner and outer bacterial membranes. Crystallographic studies of EscJ and PrgH, proteins that comprise the two inner membrane rings of the T3SS, suggest that a conserved structural motif serves as a platform for ring assembly. Additional docking and modeling studies reveal details of the T3SS architecture and assembly.

Gram-negative bacteria use type III secretion systems (T3SSs) to pass virulence factors into host cells, making them potential therapeutic targets to combat bacterial infection. A new EM study of the needle complex from the Shigella T3SS reveals 12-fold symmetry throughout and suggests interactions important for self-assembly and complex stability.

Gemin5 is a WD repeat protein that binds small nuclear RNAs (snRNAs) through a specific sequence in the context of the SMN complex, a function required for spliceosomal snRNP biogenesis. Reduced levels of SMN cause spinal muscular atrophy. A series of biochemical experiments now indicate that the WD repeat region of Gemin5 recognizes the snRNAs in a sequence-specific fashion, suggesting that WD repeats are capable of RNA binding.

Most terminally differentiated cells have a diminished capacity to respond to and repair DNA damage. Now a microRNA is shown to have a role in this phenotype in blood cells: miR-24 is upregulated in blood cells differentiated in vitro and decreases the levels of H2AX, a histone variant with a key role in the response to DNA double-stranded breaks.

V(D)J recombination is mediated by the products of the recombination activation genes, RAG1 and RAG2. DNA binding and cleavage are targeted by recombination sequences that flank each gene segment and are composed of well-conserved heptamer and nonamer sequences separated either by 12 or 23 base pairs. Schatz and co-workers report the crystal structure of the RAG1 nonamer binding domain (NBD) bound to its cognate sequence. The NBD adopts an intertwined dimer that mediates the synapsis of two DNA molecules. Biochemical and FRET experiments support the structural findings and have implications for the regulation of DNA binding and cleavage by RAG1/2.

Dysfunction of SUMO or Rad60 causes overlapping phenotypes that include genomic instability. Now, a nonsubstrate interaction between SUMO-like domain 2 (SLD2) of Rad60 and the SUMO-conjugating enzyme Ubc9 is shown to suppress aberrant replication-associated homologous recombination. Thus, SUMO mimicry provides critical regulation in the SUMO pathway.

The enzyme activation-induced deaminase (AID) promotes antibody diversification after B-cell activation, by causing mutagenic lesions on DNA. Hence, AID's actions must be tightly controlled. AID is found mainly in the cytosolic compartment and contains a known nuclear export sequence. Now a structural nuclear localization sequence and a cytosolic-retention determinant are identified in AID and found to have a role in localization and function.

Protein synthesis is catalyzed in the peptidyl transferase center of the ribosome. The structure of the 70S ribosome containing tRNAs now gives insight into the active site of a complete ribosome and reveals a direct interaction between the tRNA substrate and ribosomal proteins.

In eukaryotic cells, DNA is wrapped around histones to form nucleosomes, which are further organized into the 30-nm chromatin fiber. A single-molecule study with homogeneous chromatin fibers now shows that the chromatin fiber behaves as a simple spring, stretching up to three times in response to pulling, a behavior indicative of a one-start helix structure. Linker histones stabilize the fiber but do not make it stiffer.

Production of complex machines such as the ribosome requires coordinated regulation of the components. A widely conserved plant regulator of alternative splicing on the TFIIIA transcription factor mRNA has been found. The RNA structurally mimics the 5S rRNA and, accordingly, binds ribosomal protein L5, which thus affects splicing and production of TFIIIA. As TFIIIA is needed for transcription of the 5S rRNA, this work defines a regulatory circuit for coordinating 5S rRNA production by its binding protein.

The Msh2–Msh3 complex recognizes DNA mismatch lesions, with stronger affinity for small insertion and deletion loops. Now the nucleotide binding properties of Msh2–Msh3 are studied, revealing the changes upon binding to DNA molecules with a loop lesion, indicating how this mismatch sensor can signal the repair machinery.

The nuclear transport receptor CRM1 mediates protein export from the nucleus through recognition of leucine-rich nuclear export signals on substrates. Structural analysis, based in part on the recent structure of a CRM1-SNUPN complex, reveal determinants for substrate binding and suggest a mechanism for binding partner-assisted dissociation of SNUPN in the cytoplasm.

WAVE proteins in the WASP family are controlled by incorporation into the WAVE regulatory complex (WRC), which transmits information from the Rac GTPase to the actin cytoskeleton. By reconstituting human and fly WRCs, the native complex is shown to be inactive. Rac activates the WRC, but does not cause subunit dissociation. These results reconcile previous work and reveal common regulatory principles for the WASP family.

A genome-wide analysis of methylated DNA from human embryonic stem cells and adult tissues provides a comprehensive view of unmethylated regions and leads to the identification of sequence motifs that can predict whether a region escapes de novo methylation. This algorithm is used to identify novel, non-CpG unmethylated regions, including intragenic and tissue-specific ones.