Articles in 2013

Direct time-resolved single-molecule observations of promoter search by Escherichia coli RNA polymerase indicate no evidence of facilitated diffusion, according to a new report.

Given the recent successes in determining membrane-protein structures, we explore the tractability of determining representatives for the entire human membrane proteome. This proteome contains 2,925 unique integral α-helical transmembrane-domain sequences that cluster into 1,201 families sharing more than 25% sequence identity. Structures of 100 optimally selected targets would increase the fraction of modelable human α-helical transmembrane domains from 26% to 58%, providing structure and function information not otherwise available.

The regulatory importance of the C-terminal coiled-coil domain of PLCβ has long been known yet remains poorly understood. The crystal structure and cryo-EM reconstruction of full-length PLCβ3 bound to its activator Gα_q reveals that the C terminus makes contact with both the catalytic core and Gα_q to contribute to the complex regulation of the enzyme.

Competitive binding of 53BP1 and BRCA1 determines DNA repair pathway choice at double-strand breaks. New work shows that acetylation of H4K16 by TIP60 tips the balance in favor of BRCA1 by limiting 53BP1 binding, thereby promoting repair through homologous recombination over nonhomologous end joining.

Trim24 and Trim33 are co-repressor complexes that suppress hepatocarcinogenesis. A new study now uncovers a function for Trim24 and Trim33 as repressors of VL30-type endogenous retroviruses in the liver. When derepressed, VL30 long terminal repeats (LTRs) function as promoter and enhancer elements deregulating expression of neighboring genes and generating noncoding enhancer RNAs that are required for LTR enhancer activity in hepatocytes.

Oligomeric Trax–Translin complexes, known as C3PO, are involved in RNA interference and tRNA processing in eukaryotic species including humans. Structural and functional analysis of a Trax-like protein from Archaeoglobus fulgidus that forms an octameric assembly resembling human C3PO provides insight into the mechanism of RNA recognition and cleavage.

Repetitive elements in differentiated cells are usually silenced. Genome-wide analyses in early mouse development show that repetitive-element expression decreases during development accompanied by the loss of active chromatin marks. LINE-1 and IAP retrotransposons become reactivated after fertilization, and LINE-1 transcription is regulated by short LINE-1 RNAs, which suggests that repetitive elements may be regulated through RNA during the earliest developmental stages.

Prokaryotic condensins usually comprise an SMC homodimer, kleisin ScpA and ScpB. Structural and functional analyses of Bacillus subtilis condesin reveal an asymmetric bridge in which the termini of ScpA bind to distinct regions in each of the two SMC monomers. The findings suggest that the basic architecture for the tripartite condensin ring evolved before the emergence of eukaryotes.

GltPh is a homotrimeric Na+-coupled aspartate transporter that belongs to the glutamate transporter family. The conformational changes that occur during GltPh transport are now directly observed using EPR spectroscopy, revealing that the transporting domains sample multiple states, regardless of the presence of substrate or ions.

The ISWI chromatin remodelers interact with extranucleosomal DNA to mediate nucleosome positioning. A new study now shows that the conserved SLIDE domain in the Isw2 subunit, which binds linker DNA, facilitates unidirectional linker DNA movement into nucleosomes. These findings suggest that the SLIDE domain functions in conjunction with the ATPase domain to mobilize nucleosomes.

The sodium and aspartate symporter Glt_Ph mediates transport by alternating between outward-facing and inward-facing states. These conformational changes are now probed using double electron-electron resonance (DEER) spectroscopy. The data show that Glt_Ph samples both states with similar probabilities, and that each protomer in the Glt_Ph homotrimer behaves independently of the others.

Crystal structures of HIV-1 reverse transcriptase (RT) bound to an RNA/DNA hybrid (without any cross-linking) and in the presence of non-nucleotide RT inhibitors (NNRTIs) nevirapine and efavirenz are now reported. The structures show the RNA/DNA hybrid in a previously unseen conformation with ready access to the RNase-H active site of RT.

In budding yeast, EcoI acetylates cohesin to establish sister chromatid cohesion in S phase. EcoI is subsequently modified by the ubiquitin E3 ligase SCF-Cdc4 and rapidly degraded. New work shows how sequential phosphorylation by three independent kinases generates a binding site for SCF-Cdc4 to promote EcoI degradation, thereby coupling EcoI activity, and thus sister chromatid cohesion, to the cell cycle.

The MSL complex acts on chromatin to and is required for X-chromosome dosage compensation. Chromatin-interacting protein MS (ChIP-MS) is now used to identify proteins and histone modifications interacting with the MSL complex, leading to the identification of CG4747. Functional analysis indicates that this protein is involved in targeting MSL to H3K36me3-containing chromatin.

The protein α-catenin has an essential role in stabilizing cell-cell junctions, and it is involved in multiple interactions with other cytoskeleton proteins. The crystal structure of nearly full-length human α-catenin now reveals a handshake-like dimer with the two monomers in distinct conformations. This dimer asymmetry is important for F-actin binding and for interactions with activated vinculin.

Histone deacetylase 3 (HDAC3) has low enzymatic activity in vitro unless associated with the nuclear receptor corepressors NCOR1 and SMRT through the deacetylase activation domain (DAD). Mice lacking functional DADs in both NCOR1 and SMRT are born and reach adulthood but lack HDAC3 activity, whereas mice lacking HDAC3 are embryonic lethal, which suggests an essential deacetylase-independent function of HDAC3.

Three recent studies converged on a specific protein-protein interface between TPP1 and telomerase as being crucial for the regulation of both telomerase recruitment and processivity in mammalian cells. An equivalent interaction appears to exist in budding yeast, making this a nearly universal means of telomerase regulation.