Articles in 2010

Myotonic dystrophy type 1 (DM1), a multisystem disorder affecting skeletal and smooth muscle and other essential systems, belongs to a group of RNA gain-of-function disorders caused by the expansion of a CUG trinucleotide repeat (CUG^exp) in the 3' untranslated region of the DM protein kinase (DMPK) gene. Furling and coworkers have developed an optimized human U7-snRNA containing a poly-CAG antisense sequence to target the CUG^exp RNAs. These constructs cause specific degradation of pathogenic but not wild-type DMPK RNA products. By abolishing the RNA gain-of-function toxicity responsible for pathogenesis, these hU7-snRNAs could affect gene silencing in other RNA-dominant disorders expressing expanded repeats.

The anaphase-promoting complex/cyclosome (APC/C) is key to cell cycle regulation and is an E3 ubiquitin ligase. The overall shape of the substrate-free complex has previously been determined in various species. Budding yeast and human APC/Cs are now analyzed by EM structural and biochemical approaches to assess the substrate-binding site and elucidate the relative positioning of Doc1, a factor known to promote processive substrate ubiquitylation.

The K+ channels can display three distinct gating modes. The molecular basis for two of these modes (low open probability and flickery) are now examined by a combination of single-channel recording, crystallography and modeling of mutants in Glu71, revealing that changes in ion and water occupancy in and around the selectivity filter determine modal gating.

Prdm14 is expressed in embryonic stem (ES) cells and germ cells. It is now shown that this transcription factor safeguards the stem cell state by preventing development of mouse ES cells into extraembryonic endoderm cells by repressing loci related to differentiation along this developmental pathway. This suggests that Pdrm14 is part of the network of factors that maintains the ES cell state in mice.

Mitochondria go through cycles of fusion and fission. The yeast dynamin-related protein, Dnm1, localizes to sites of membrane fission and fusion. Hinshaw and coworkers solve the structure of Dnm1-lipid tubes by cryo-EM and compare it to dynamin. Upon GTP addition, the Dnm1-lipid tubes constrict by ~50 nm, reducing the underlying lipid membrane. This suggests that Dnm1 has the ability to impart a large contractile force during mitochondrial division.

The chaperone Hsp90 interacts with different cochaperones during its reaction cycle. Now a ternary complex of Hsp90 with ATPase inhibitor Sti1 and prolyl isomerase Cpr6 is identified as an intermediate by fluorescence resonance energy transfer (FRET) and analytical ultracentrifugation, with support from genetic data.

The human ether-a-go-go–related gene (hERG) channel regulates the heartbeat rhythm. The transition from the open to the inactivated state of human K⁺ channel ERG is analyzed by phi-value analysis, revealing a complex rearrangement of all domains (extracellular, transmembrane and cytoplasmic). The work thus reveals the sequence of conformational changes underlying selectivity filter gating, and may be relevant for other K⁺ channels.

Nascent peptides with signal sequences must be recognized in order to be correctly targeted within the cell. The cryo-EM structure of the E. coli signal recognition particle in complex with its receptor and the translating ribosome is now presented, indicating conformational changes that lead to receptor recruitment.

CCT/TRiC is a eukaryotic multi-subunit chaperonin that promotes the correct folding of many cytosolic proteins, including tubulin, within its cavity. Now the crystal structure of CCT in its open state is solved to 5.5-Å resolution and, together with EM and biochemical analysis, allows the observation of a bound tubulin molecule interacting with CCT loops in the apical and equatorial domains.

Dmc1 is a Rad51 paralog with a central role in meiotic recombination. Both Rad51 and Dmc1 form filaments on single-stranded DNA that can promote strand exchange with similar efficiencies. Now, D loops formed with DMC1 are shown to be more resistant to dissociation by BLM or RAD54 than those formed with RAD51.

In fission yeast, the RNAi pathway has been linked to formation of heterochromatin at centromeres. Fusing Dicer to DNA adenine methyltransferase now revealed that Dcr1 also associates with euchromatic regions of the S. pombe genome to mediate co-transcriptional gene silencing.

DNA methyltransferase-1 (DNMT1) is involved in CpG methylation, and its stability is known to be regulated by lysine methylation. Now it has been shown that methylation of DNMT1 and AKT1 phosphorylation of DNMT1 are mutually exclusive and that antagonism between these modifications affects DNMT1 turnover.

Crystallization of RNA molecules can pose a challenge, and the U1A RNA binding protein has been used to facilitate the process. Now a different portable RNA sequence and a synthetic Fab are presented as tools for RNA structural determination. In addition to functioning as a crystallization chaperone, the Fab also serves as the search model to provide phase information.

Chromosomal translocations can occur as a consequence of the repair of DNA double-strand breaks via the alternative nonhomologous end-joining pathway. Now the DNA end processing factor CtIP is shown to play a role during the formation of chromosomal translocations.

Mammalian protein CtIP processes DNA double-stranded breaks during homologous recombination and possibly for repair via alternative nonhomologous end-joining (alt-NHEJ). Now CtIP is shown to promote alt-NHEJ during class switch recombination in murine B cells.

Antibodies are a primary tool to assess histone post-translational modifications. However, different antibodies and batches might vary in their ability to recognize those modifications, depending on the kind of assay used. Now a systematic analysis of different antibodies and an open database containing the validation results are presented.

The precise execution of biological processes depends on various different macromolecules, such as proteins, working together in a coordinated manner. The idea is that the mRNA level of essential genes encoding proteins in the same complex or pathway would be more correlated than transcripts of functionally unrelated genes. It turns out that this holds true for induced genes but not for transcripts of constitutive genes encoding essential subunits of multi-protein complexes. These transcripts are not correlated any more than functionally unrelated genes. The coordination of these functional complexes must occur post-transcriptionally, and likely post-translationally.

Understanding genomic organization in three dimensions may be one key to understanding gene regulation. Through the combination of an advanced version of chromosome conformation capture technology and an integrated modeling platform, the structure of the α-globin locus in cells where it is silent is compared to that in cells with high α-globin expression.

β2-microglobulin can form different forms of amyloid fibrils within joints of dialysis patients. Now the crystal structures of a β2m domain swapped dimer and of the steric zipper formed by a short peptide indicate how these fibrils might form.