Volume 6 Issue 1, January 2010

Complete and accurate annotation of gene function is an essential starting point for genome interpretation and a host of systems and synthetic biology endeavors. Detecting errors in existing annotation now has an important new tool.

Control of gene expression at the mRNA level is used extensively by cells. Now a biomimetic strategy yields a synthetic genetic switch in which an RNA-binding protein bound at the translation start site blocks progression of the ribosome.

Aggregation of huntingtin protein with an expanded polyglutamine region is enhanced by its 17-residue N-terminal domain, which binds to itself and to the polyglutamine region. This enhancement is inhibited when the N-terminal domain binds to the chaperonin TRiC.

Allantoin catabolism provides nitrogen, carbon and energy for several species, but the biochemical route to these resources in some species was unclear. A multidimensional bioinformatic search across organisms has now led to the identification of two enzymes that complete the degradation pathway.

Successive rounds of selection of an RNA library in a mouse cancer model resulted in the identification of an aptamer that specifically bound a cancer-associated protein, providing an in vivo approach for identifying RNA motifs that can reveal and potentially inhibit tumor-specific targets.

The trafficking defect associated with the cystic fibrosis disease-linked allele of the CFTR chloride channel is alleviated by inhibitors of histone deacetylases, suggesting that altering the transcription of genes associated with protein misfolding can ameliorate disease.

Errors in functional annotations can cause significant problems in later research. A new method to identify misannotations by analyzing the genomic context correlations corrects these errors, such as in the reassignment of genes now demonstrated to have roles in leucine and fatty acid degradation.

Quorum sensing refers to a signaling mechanism allowing the behavior of bacterial populations to be coordinated based on cell density. Physical isolation of individual bacterial cells revealed that a single bacterium can respond to quorum sensing signals resulting in genetic reprogramming and enhanced.

Binding of HIV-1 Nef to host cell membranes is a biphasic process that involves electrostatic curvature-sensitive Nef-lipid interactions followed by a slower formation of an amphipathic helix. Nef action on the membrane may promote curvature and subsequent endocytosis of the host-cell proteins.

Spatial- and time-resolution FRET methods on single pre-translocation ribosome complexes reveal that aminoglycoside antibiotics inhibit translocation by altering structural and dynamic parameters to stabilize the binding of aminoacyl tRNAs to the classical A-site of the ribosome.

Comparing the Michaelis constants and rates of inhibition of wild-type and mutant hydrogenases reveals the quantitative impact of amino acid changes on the diffusion rates of H₂, CO and O₂ and suggests design strategies for creating oxygen-tolerant hydrogenases.

The ribosomal protein L7Ae and its RNA partner were used to construct a synthetic translational regulator that can be used to activate or repress protein expression, even performing both functions at once. Repression in human cells is highly effective, rivaling the potency of RNAi.