Complete genome sequence of a Marinococcus sp. PL1-022 isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Marinococcus sp. PL1-022 was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a chromosome (3,140,198 bp; 48.2% GC) and two plasmids (58,083 bp and 19,399 bp; 41.4 and 50.7% GC-content, respectively). Isolation of Marinococcus sp. PL1-022 adds to the increasing repertoire of culturable extremophiles.

Complete genome sequence of Idiomarina sp. PL1-037 isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Idiomarina sp. PL1-037 was isolated from Pearse Lakes, Rottnest Island, Western Australia. The sequenced completed genome for PL1-037 is composed of a single chromosome (2,804,934 bp) with a GC content of 47.1%. Isolation of Idiomarina sp. PL1-037 provides insights about culturable extremophiles from the Pearse lakes microbiome.

Perturbation of endoplasmic reticulum proteostasis triggers tissue injury in the thyroid gland.

Defects in endoplasmic reticulum (ER) proteostasis have been linked to diseases in multiple organ systems. Here we examined the impact of perturbation of ER proteostasis in mice bearing thyrocyte-specific knockout of either HRD1 (to disable ER-associated protein degradation [ERAD]) or ATG7 (to disable autophagy) in the absence or presence of heterozygous expression of misfolded mutant thyroglobulin (the most highly expressed thyroid gene product, synthesized in the ER). Misfolding-inducing thyroglobulin mutations are common in humans but are said to yield only autosomal-recessive disease - perhaps because misfolded thyroglobulin protein might undergo disposal by ERAD or ER macroautophagy. We find that as single defects, neither ERAD, nor autophagy, nor heterozygous thyroglobulin misfolding altered circulating thyroxine levels, and neither defective ERAD nor defective autophagy caused any gross morphological change in an otherwise WT thyroid gland. However, heterozygous expression of misfolded thyroglobulin itself triggered significant ER stress and individual thyrocyte death while maintaining integrity of the surrounding thyroid epithelium. In this context, deficiency of ERAD (but not autophagy) resulted in patchy whole-follicle death with follicular collapse and degeneration, accompanied by infiltration of bone marrow-derived macrophages. Perturbation of thyrocyte ER proteostasis is thus a risk factor for both cell death and follicular demise.

Defective Thyroglobulin: Cell Biology of Disease.

The primary functional units of the thyroid gland are follicles of various sizes comprised of a monolayer of epithelial cells (thyrocytes) surrounding an apical extracellular cavity known as the follicle lumen. In the normal thyroid gland, the follicle lumen is filled with secreted protein (referred to as colloid), comprised nearly exclusively of thyroglobulin with a half-life ranging from days to weeks. At the cellular boundary of the follicle lumen, secreted thyroglobulin becomes iodinated, resulting from the coordinated activities of enzymes localized to the thyrocyte apical plasma membrane. Thyroglobulin appearance in evolution is essentially synchronous with the appearance of the follicular architecture of the vertebrate thyroid gland. Thyroglobulin is the most highly expressed thyroid gene and represents the most abundantly expressed thyroid protein. Wildtype thyroglobulin protein is a large and complex glycoprotein that folds in the endoplasmic reticulum, leading to homodimerization and export via the classical secretory pathway to the follicle lumen. However, of the hundreds of human thyroglobulin genetic variants, most exhibit increased susceptibility to misfolding with defective export from the endoplasmic reticulum, triggering hypothyroidism as well as thyroidal endoplasmic reticulum stress. The human disease of hypothyroidism with defective thyroglobulin (either homozygous, or compound heterozygous) can be experimentally modeled in thyrocyte cell culture, or in whole animals, such as mice that are readily amenable to genetic manipulation. From a combination of approaches, it can be demonstrated that in the setting of thyroglobulin misfolding, thyrocytes under chronic continuous ER stress exhibit increased susceptibility to cell death, with interesting cell biological and pathophysiological consequences.

Maintaining the thyroid gland in mutant thyroglobulin-induced hypothyroidism requires thyroid cell proliferation that must continue in adulthood.

Congenital hypothyroidism with biallelic thyroglobulin (Tg protein, encoded by the TG gene) mutation is an endoplasmic reticulum (ER) storage disease. Many patients (and animal models) grow an enlarged thyroid (goiter), yet some do not. In adulthood, hypothyroid TGcog/cog mice (bearing a Tg-L2263P mutation) exhibit a large goiter, whereas adult WIC rats bearing the TGrdw/rdw mutation (Tg-G2298R) exhibit a hypoplastic thyroid. Homozygous TG mutation has been linked to thyroid cell death, and cytotoxicity of the Tg-G2298R protein was previously thought to explain the lack of goiter in WIC-TGrdw/rdw rats. However, recent studies revealed that TGcog/cog mice also exhibit widespread ER stress-mediated thyrocyte death, yet under continuous feedback stimulation, thyroid cells proliferate in excess of their demise. Here, to examine the relative proteotoxicity of the Tg-G2298R protein, we have used CRISPR-CRISPR-associated protein 9 technology to generate homozygous TGrdw/rdw knock-in mice in a strain background identical to that of TGcog/cog mice. TGrdw/rdw mice exhibit similar phenotypes of defective Tg protein folding, thyroid histological abnormalities, hypothyroidism, and growth retardation. TGrdw/rdw mice do not show evidence of greater ER stress response or stress-mediated cell death than TGcog/cog mice, and both mouse models exhibit sustained thyrocyte proliferation, with comparable goiter growth. In contrast, in WIC-TGrdw/rdw rats, as a function of aging, the thyrocyte proliferation rate declines precipitously. We conclude that the mutant Tg-G2298R protein is not intrinsically more proteotoxic than Tg-L2263P; rather, aging-dependent difference in maintenance of cell proliferation is the limiting factor, which accounts for the absence of goiter in adult WIC-TGrdw/rdw rats.

Second-line treatment for metastatic pancreatic cancer.

Pancreatic cancer is the fourth-leading cause of cancer-related death. It is commonly diagnosed at an advanced stage, when no curative options exist. Over the last decade, combination chemotherapy has shown a survival benefit compared with single-agent gemcitabine and has become established as first-line therapy in metastatic pancreatic cancer. The choice of frontline regimen, which is based on clinical factors, plays an important role in subsequent management. Limited second-line standard therapeutic options are available. Studies have not definitively established that chemotherapy with a fluoropyramidine (5-fluorouracil or capecitabine), gemcitabine, oxaliplatin, irinotecan, or a combination of oxaliplatin and irinotecan improves patient survival after the failure of first-line chemotherapy. Nanoliposomal irinotecan has been approved for use in patients who have progressive disease while on gemcitabine-based treatment. Although combination chemotherapy is associated with a modest survival benefit, this comes at the expense of increased toxicity and costs. Furthermore, the optimal sequencing of these agents in subsequent lines of treatment is unknown. Randomized controlled trials provide little evidence of greater benefit from second-line therapy compared with best supportive care alone. Therefore, treatment decisions should be patient-centered and based on functional status, medical comorbidities, and anticipated adverse effects. The clinical context and prior treatment-related toxicities have a significant influence on the choice of optimal salvage treatment. We review the published data focused on second-line treatment for advanced pancreatic cancer.

Poly(1,4-phenylene vinylene) Derivatives with Ether Substituents to Improve Polymer Solubility for Use in Organic Light-Emitting Diode Devices.

New ether-substituted poly(1,4-phenylene vinylene) (PPV) derivatives were synthesized via Horner-Emmons coupling. The structures of the monomers and the resultant oligomers were confirmed by 1H and 13C NMR spectroscopies. The molecular weights of the oligomers were characterized by gel permeation chromatography, giving the number-average and weight-average molecular weights and the corresponding polydispersity indices. Measurements of UV-vis absorption and fluorescence were used to characterize the optical properties of the oligomers. Estimation of the highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels and other electrochemical characteristics of the oligomers were investigated by cyclic voltammetry. Dialkyl and dialkoxy PPV oligomers were also prepared and characterized following the same instrumental methods used for the ether-substituted oligomers, providing a known reference system to judge the performance of the new conjugated oligomers. Devices were fabricated to analyze the electroluminescent characteristics of the oligomers in organic light-emitting diodes.

Cofactor-dependent specificity of a DEAD-box protein.

DEAD-box proteins, a large class of RNA-dependent ATPases, regulate all aspects of gene expression and RNA metabolism. They can facilitate dissociation of RNA duplexes and remodeling of RNA-protein complexes, serve as ATP-dependent RNA-binding proteins, or even anneal duplexes. These proteins have highly conserved sequence elements that are contained within two RecA-like domains; consequently, their structures are nearly identical. Furthermore, crystal structures of DEAD-box proteins with bound RNA reveal interactions exclusively between the protein and the RNA backbone. Together, these findings suggest that DEAD-box proteins interact with their substrates in a nonspecific manner, which is confirmed in biochemical experiments. Nevertheless, this contrasts with the need to target these enzymes to specific substrates in vivo. Using the DEAD-box protein Rok1 and its cofactor Rrp5, which both function during maturation of the small ribosomal subunit, we show here that Rrp5 provides specificity to the otherwise nonspecific biochemical activities of the Rok1 DEAD-domain. This finding could reconcile the need for specific substrate binding of some DEAD-box proteins with their nonspecific binding surface and expands the potential roles of cofactors to specificity factors. Identification of helicase cofactors and their RNA substrates could therefore help define the undescribed roles of the 19 DEAD-box proteins that function in ribosome assembly.

A translation-like cycle is a quality control checkpoint for maturing 40S ribosome subunits.

Assembly factors (AFs) prevent premature translation initiation on small (40S) ribosomal subunit assembly intermediates by blocking ligand binding. However, it is unclear how AFs are displaced from maturing 40S ribosomes, if or how maturing subunits are assessed for fidelity, and what prevents premature translation initiation once AFs dissociate. Here we show that maturation involves a translation-like cycle whereby the translation factor eIF5B, a GTPase, promotes joining of large (60S) subunits with pre-40S subunits to give 80S-like complexes, which are subsequently disassembled by the termination factor Rli1, an ATPase. The AFs Tsr1 and Rio2 block the mRNA channel and initiator tRNA binding site, and therefore 80S-like ribosomes lack mRNA or initiator tRNA. After Tsr1 and Rio2 dissociate from 80S-like complexes Rli1-directed displacement of 60S subunits allows for translation initiation. This cycle thus provides a functional test of 60S subunit binding and the GTPase site before ribosomes enter the translating pool.

Analysis of cofactor effects on RNA helicases.

RNA helicases are involved in all aspects of RNA metabolism. Since the helicase core is conserved between all helicases, specificity for particular cellular roles must arise from interactions with specific cofactors, which can regulate RNA binding and enzymatic activity. While recent structural studies have provided invaluable insight into some mechanisms of cofactor effects on RNA helicases, biochemical experiments must ultimately be conducted in order to validate these predictions. Here, we provide a guide for identifying helicase-specific cofactors and then studying their effects on helicase function. By measuring RNA binding and release, ATPase activity, nucleotide affinity, and unwinding and annealing activities, cofactor effects on an RNA helicase can be fully characterized.

The roles of S1 RNA-binding domains in Rrp5's interactions with pre-rRNA.

RNA-binding proteins mediate the function of all RNAs. Since few distinct RNA-binding domains (RBDs) exist, with most RBDs contacting only a few nucleotides, RNA-binding proteins often combine multiple RNA-binding motifs to achieve a higher affinity and selectivity for their targets. Rrp5, a ribosome assembly factor essential for both 40S and 60S ribosome maturation, is an extreme example as it contains 12 tandem S1 RNA-binding domains. In this study, we use a combination of RNA binding and DMS probing experiments to probe interactions of Rrp5 with pre-rRNA mimics. Our data localize Rrp5's binding site to three distinct regions within internal transcribed spacer 1 (ITS1), the sequence between 18S and 5.8S rRNAs. One of these regions is directly adjacent to a recently uncovered helical structure, which prevents premature cleavage at the 3'-end of 18S rRNA. This finding, together with previous results, suggests a role for Rrp5 in regulating the above-mentioned helical element. Furthermore, we have produced two truncated forms of the protein, Rrp5N and Rrp5C, which together encompass the entire protein and fully restore growth. Quantitative analysis of the RNA affinity of these Rrp5 fragments indicates that the first nine S1 motifs contribute much of Rrp5's RNA affinity, while the last three domains alone provide its specificity for the pre-rRNA. This surprising division of labor is unique, as it suggests that S1 domains can bind RNA both specifically as well as nonspecifically with high affinity; this has important implications for the molecular details of the Rrp5•pre-rRNA complex.