Volume 17 Issue 5, May 2010

In this issue, three papers report the distribution of the RNA polymerase III (Pol III) machinery, including transcription factor IIIB, transcription factor IIIC and Pol III itself, across the human genome. These studies reveal cell type–specific expression of Pol III genes, functional interplay between the Pol II and Pol III transcriptional machineries and the potential involvement of Pol III genes in chromosome organization.

Crystal structures of a calcium-dependent protein kinase from Toxoplasma gondii uncover a unique mechanism of activation and potential avenues for selective inhibition.

A new crystal structure of an anti–HIV-1 envelope antibody bound to an envelope–receptor complex shows the antibody binding both the HIV-1 envelope and the CD4 receptor, raising the question of what the role of antibody autoreactivity in host responses to HIV-1 may be.

Some viruses carry suppressors to inhibit host response to infection through the RNAi pathways. Previously the insect virus DCV was found to target host response by inhibiting Drosophila Dicer function. The related virus CrPV is now shown to target and inhibit the function of Drosophila Argonaute 2 specifically.

An important aspect of translational fidelity is that the reading frame of a translating mRNA be maintained on the ribosome. Structures representing the initiating and elongating ribosome now show that a tunnel narrows to facilitate a network of interactions that may hold the message in frame in the latter complex.

Amyloid-β42 (Aβ42) peptide aggregates to form oligomers, protofibrils and fibrils en route to the deposition of amyloid plaques associated with Alzheimer's disease. Structural and functional analyses show that the conversion of Aβ42 oligomers to fibrils is accompanied by reduced neurotoxicity and involves the formation of parallel, in-register β-sheets that are staggered at an intermolecular contact.

Complexins facilitate and inhibit neurotransmitter release through distinct domains, and their function is thought to be coupled to the Ca2+ sensor synaptotagmin-1. Biophysical and physiological analyses suggest that the N terminus of complexin stabilizes the C terminus of the SNARE complex and that this interaction increases synaptic vesicle fusogenicity at a step that precedes Ca2+ triggering.

Streptococcus pneumoniae develop a state of genetic competence, in which the bacteria can acquire exogenous DNA; the competent bacteria also secrete enzymes that trigger the lysis of neighboring non-competent cells. Now the structure of pneumococcal autolysin LytC provides insight into its role in cell wall metabolism and fratricide.

Gram-positive bacteria have a thick cell wall composed of peptidoglycan and teichoic acid, a complex anionic polymer that is important for cellular integrity and virulence. The crystal structures of TagF polymerase from Staphylococcus epidermidis in its apo form and in complex with a model susbtrate are now presented, providing insight into teichoic acid biosynthesis.

Motor proteins such as myosin use the energy from ATP to drive a conformational change that generates mechanical force, or power stroke. Using a single-molecule, optical-trap setup, the reverse movement could be observed for myosin-V heads bound to actin when external load is applied, which has implications for myosin's mechanochemical cycle.

A family of calcium-dependent protein kinases (CDPK), containing a calcium-binding domain, is present in apicomplexan parasites, ciliates and plants, but not in animals. Now crystal structures of CDPKs from Toxoplasma gondii and Cryptosporidium parvum in their apo or calcium-bound states reveal the structural reorganization induced by calcium that results in activation.

A family of calcium-dependent protein kinases (CDPK) is present in apicomplexan parasites but not in animals, indicating their potential as targets for anti-parasitic drugs. Structural and functional studies on Toxoplasma gondii CDPK1 now reveal that this kinase is sensitive to a class of drugs called bumped kinase inhibitors, which can inhibit the parasite's growth and host cell invasion.

The first envelope structure from HIV-1 clade C, the most prevalent subtype in Africa, is now presented. The gp120 core is crystallized in complex with its receptor CD4 and a CD4-induced human mAb fragment. The structure reveals that the antibody makes contacts with both gp120 and CD4, which is confirmed by in vitro binding studies.

Many actin-binding proteins contain calponin homology (CH) domains, but the manner in which these domains interact with F-actin has been controversial. Electron microscopy analyses show that the tandem CH domains of α-actinin bind to F-actin in an open conformation and that opening of these domains might be a key regulatory mechanism for proteins with tandem CH domains.

The PWWP domain has been identified in a number of nuclear proteins that interact with histones including BRPF1. Structural and functional analysis of this domain from BRPF1 now argue that it specifically recognizes methylated histone H3 Lys36, identifying this widely conserved domain as a reader of this mark.

RNA polymerase (Pol) III transcribes small noncoding RNAs important in translation. Using genomics approaches, Pol III genes are now found to be in close proximity to Pol II genes and Pol III is localized to regions of active chromatin and high CpG content. One idea is that active chromatin could provide Pol III with access to the genome.

Genome-wide analysis of the chromatin modification patterns at Pol III genes showed a correlation between histone modifications and tissue specific transcription of Pol III genes. Surprisingly, it was also discovered that Pol II and its associated basal factors are recruited to expressed Pol III transcribed genes. One idea is that Pol II could help keep chromatin around Pol III genes in an open state.

Genome wide analysis of human RNA Polymerase III (Pol) reveals both known and new targets of Pol III, with many of the latter binding regions found near SINEs. Active Pol III genes are near active Pol II promoters, whereas inactive Pol III genes are not. ETC loci, which are bound by TFIIIC but not TFIIIB and Pol III, are near active Pol II promoters and CTCF binding sites.