Role for Arf3p in development of polarity,but not endocytosis,in Saccharomyces cerevisiae

ADP-ribosylation factors (ARFs) are ubiquitous regulators of virtually every step of vesicular membrane traffic. Yeast Arf3p, which is most similar to mammalian ARF6, is not essential for cell viability and not required for endoplasmic reticulum-to-Golgi protein transport. Although mammalian ARF6 has been implicated in the regulation of early endocytic transport, we found that Arf3p was not required for fluid-phase, membrane internalization, or mating-type receptor-mediated endocytosis. Arf3p was partially localized to the cell periphery, but was not detected on endocytic structures. The nucleotide-binding, N-terminal region, and N-terminal myristate of Arf3p are important for its proper localization. C-Terminally green fluorescent protein-tagged Arf3, expressed from the endogenous promoter, exhibited a polarized localization to the cell periphery and buds, in a cell cycle-dependent manner. Arf3-GFP achieved its proper localization during polarity growth through an actin-independent pathway. Both haploid and homologous diploid arf3 mutants exhibit a random budding defect, and the overexpression of the GTP-bound form Arf3p(Q71L) or GDP-binding defective Arf3p(T31N) mutant interfered with budding-site selection. We conclude that the GTPase cycle of Arf3p is likely to be important for the function of Arf3p in polarizing growth of the emerging bud and/or an unidentified vesicular trafficking pathway.     

Assessing Progress towards Public Health,Human Rights,and International Development Goals Using Frontier Analysis

Indicators to measure progress towards achieving public health, human rights, and international development targets, such as 100% access to improved drinking water or zero maternal mortality ratio, generally focus on status (i.e., level of attainment or coverage) or trends in status (i.e., rates of change). However, these indicators do not account for different levels of development that countries experience, thus making it difficult to compare progress between countries. We describe a recently developed new use of frontier analysis and apply this method to calculate country performance indices in three areas: maternal mortality ratio, poverty headcount ratio, and primary school completion rate. Frontier analysis is used to identify the maximum achievable rates of change, defined by the historically best-performing countries, as a function of coverage level. Performance indices are calculated by comparing a country’s rate of change against the maximum achievable rate at the same coverage level. A country’s performance can be positive or negative, corresponding to progression or regression, respectively. The calculated performance indices allow countries to be compared against each other regardless of whether they have only begun to make progress or whether they have almost achieved the target. This paper is the first to use frontier analysis to determine the maximum achievable rates as a function of coverage level and to calculate performance indices for public health, human rights, and international development indicators. The method can be applied to multiple fields and settings, for example health targets such as cessation in smoking or specific vaccine immunizations, and offers both a new approach to analyze existing data and a new data source for consideration when assessing progress achieved.     

The genome of B. subtilis phage SPP1:

Summary DNA molecules of B. subtilis phage SPP1 exhibit terminal redundancy and are partially circularly permuted. This was established by the hybridization of selected EcoRI restriction fragments to single strands of SPP1 DNA and by an analysis of the distribution of denaturation loops in partially denatured SPP1 DNA molecules. Deletions in SPP1 DNA are not compensated by an increase in terminally repetitious DNA. This finding, which is unique to SPP1, is discussed in terms of a modification of the Streisinger/Botstein model of phage maturation.     

A Targeted Bypass Screen Identifies Ynl187p,Prp42p,Snu71p,and Cbp80p for Stable U1 snRNP/Pre-mRNA Interaction

To understand how DEXD/H-box proteins recognize and interact with their cellular substrates, we have been studying Prp28p, a DEXD/H-box splicing factor required for switching the U1 snRNP with the U6 snRNP at the precursor mRNA (pre-mRNA) 5′ splice site. We previously demonstrated that the requirement for Prp28p can be eliminated by mutations that alter either the U1 snRNA or the U1C protein, suggesting that both are targets of Prp28p. Inspired by this finding, we designed a bypass genetic screen to specifically search for additional, novel targets of Prp28p. The screen identified Prp42p, Snu71p, and Cbp80p, all known components of commitment complexes, as well as Ynl187p, a protein of uncertain function. To examine the role of Ynl187p in splicing, we carried out extensive genetic and biochemical analysis, including chromatin immunoprecipitation. Our data suggest that Ynl187p acts in concert with U1C and Cbp80p to help stabilize the U1 snRNP-5′ splice site interaction. These findings are discussed in the context of DEXD/H-box proteins and their role in vivo as well as the potential need for more integral U1-snRNP proteins in governing the fungal 5′ splice site RNA-RNA interaction compared to the number of U1 snRNP proteins needed by metazoans.Nuclear precursor mRNA (pre-mRNA) splicing takes place in the spliceosome, a large dynamic complex consisting of over 100 proteins and five small nuclear RNAs (snRNAs) (32, 70). During spliceosome assembly, the U1 small nuclear ribonucleoprotein particle (snRNP) first contacts the pre-mRNA 5′ splice site (5′ss), followed by binding of the U2 snRNP to the branch site and the joining of the U5-U4/U6 tri-snRNP (32, 64, 70). The step in which U1 snRNP binds to the 5′ss is arguably one of the most critical, because it probably commits pre-mRNA to the splicing pathway (38, 48, 49, 60, 74). In the budding yeast Saccharomyces cerevisiae in vitro system, two U1-snRNP-containing commitment complexes (CCs), CC1 and CC2, can be detected by native gel electrophoresis prior to the U2 snRNP''s joining to form the prespliceosome (38, 60). CC1, whose formation is dependent on a functional 5′ss, appears to be a kinetic precursor to CC2, whose formation requires both a functional 5′ss and branch site and the participation of the branch-site-binding protein (BBP) and Mud2p, which are likely equivalent to SF1 and U2AF65, respectively, in the mammalian system (1-3, 75).Accumulating evidence suggests that formation of the canonical 5- to 7-bp RNA duplex between U1 snRNA and the 5′ss region is not sufficient to cause a stable CC to form in the yeast system (59, 62, 78); protein-RNA contacts are also important. For example, Zhang and Rosbash (77) identified eight proteins, all present in CCs, that make physical contact with the pre-mRNA at or near the 5′ss. Four of these proteins, U1C, U1-70K, Snu56p, and Nam8p, are integral parts of the U1 snRNP (20), and another three, SmB, SmD1, and SmD3, belong to the seven-member ring that binds the conserved Sm site present on U1, U2, U4, and U5 snRNAs (33, 71). The remaining protein, Cbp80p, is a subunit of the nuclear cap-binding complex (CBC), which also contains a second subunit, Cbp20p (28, 39). Interestingly, despite being a non-snRNP factor, Cbp80p is known to collaborate with U1 snRNP to help form or stabilize CC1 (8, 40). Furthermore, the contact between the C-terminal tails of SmB, SmD1, and SmD3 and the pre-mRNA may contribute to stabilizing the U1 snRNP/pre-mRNA interaction (76). Finally, Du and Rosbash (11) more recently showed that U1C is capable of selecting splice-site-like sequences in which the first four nucleotides, GUAU, are identical to the first four nucleotides of the yeast splice-site consensus sequence.Once fully assembled, the spliceosome must progress through a number of major structural and conformational changes to form the catalytic center; these include a series of highly orchestrated RNA-RNA rearrangements (53, 64, 70). Some of these are mutually exclusive; i.e., the formation of one RNA duplex requires the disruption of another. For example, the base-pairing interaction between the U1 snRNA and the 5′ss is replaced by a U6 snRNA/5′ss pairing. This exchange appears to be coupled to U4/U6 RNA unwinding (53, 64, 70). It is now known that splicing factors belonging to the ATPase II superfamily (18), which are also termed the DEXD/H-box proteins (5, 43), promote spliceosomal RNA rearrangements (64). However, the precise roles of most DEXD/H-box proteins remain unclear.It has been nearly 2 decades since DEXD/H-box proteins were first proposed to be RNA helicases (44). Over the years, a wealth of data revealed that DEXD/H-box proteins are essential in most, if not all, RNA-related pathways, e.g., splicing, mRNA export, and ribosomal biogenesis (5, 43, 64). Their modes of action in vivo remain a mystery, however. For example, Lorsch and Herschlag (45, 46) proposed that DEXD/H-box proteins may perform functions which are distinct from RNA unwinding and include mediating large-scale RNA structural rearrangements, disrupting protein-RNA or protein-protein interactions, and functioning as fidelity sensors in RNA-RNA interactions and rearrangements. Indeed, recent data confirm that DEXD/H-box proteins can catalyze protein displacement in a manner independent of RNA duplex unwinding (30). Therefore, the essential functions of DExH/D proteins can be exerted on a wide range of RNP substrates. This “RNPase” (or ATPase for RNP remodeling) hypothesis appears especially attractive in light of the fact that RNA duplexes in vivo are rarely more than ∼10 contiguous base pairs in length and that they often require protein binding for stabilization (21, 63). To fully understand how DEXD/H-box proteins function in the cell, it is critical to identify their physiological substrates.Inspired by our previous finding that the requirement for Prp28p, an essential DEXD/H-box splicing factor, can be bypassed by mutations that alter the YHC1 gene, which encodes U1C protein (7), we sought to exploit the bypass concept to deepen our understanding of the role of Prp28p in splicing. The underlying hypothesis is that bypass mutations define gene products that Prp28p may counteract. Here we describe the outcome of this approach and provide a detailed analysis of Ynl187p, a novel protein that probably contributes to stabilizing the U1 snRNP-5′ss interaction.     

Characterization of the low mol. wt zinc-binding ligand from rat small intestine by comparison to the organic zinc-binding ligands

1. 65Zn complexes of picolinate (PA), citrate (CA), L-histidine (L-his), arachidonic acid (AA) or low mol. wt zinc-binding ligand from rat intestine (LMW-ZBL) gave 65Zn eluting peak fraction numbers of 53, 53, 56, 59 and 59 respectively, in a Sephadex G-75 column chromatography. 2. The 65Zn eluting peak fraction numbers with CA, L-his, PA, prostaglandin (PG)E2, AA, no ligand, arachidonate (AT) or LMW-ZBL were 49, 50, 54, 55, 58, 64, 75 and 76 respectively in a Sephadex G-25 column chromatography. 3. In a Sephadex G-15 column chromatography, the 65Zn eluting peak fraction numbers with CA, PGE2, AA, L-his, LMW-ZBL or PA were 49, 50, 51, 52, 52 and 55 respectively. 4. The LMW-ZBL in rat small intestine appears to be an AA-like substance.     

Adjuvant immunotherapy with intrapleuralStreptococcus pyogenes (OK-432) in lung cancer patients after resection

A prospective randomized study to evaluate the effect of adjuvant intrapleural OK-432 immunotherapy after resection of lung tumor was conducted in 93 patients with primary lung cancer. Among them, 46 patients had had intrapleural OK-432 injection, 47 had not. In the meantime, serial measurements of serum immunosuppressive acidic protein, of serum interleukin-2 receptor and of the sub-population of the peripheral blood cells and lymphocytes were performed in all these patients. Patient characteristics in these two groups (sex, age, histological type, pathological stage, type of operation, and performance status) were compatible. The results showed that adjuvant intrapleural OK-432 injection after resection had no beneficial effect on a patient's survival time. Patients who received intrapleural OK-432, had an increase in blood leukocytes, granulocytes and monocytes and serum immunosuppressive acidic protein level. But the cell numbers of total T cells, suppressor/cytoxic cells, helper/inducer cells and natural killer cells of peripheral blood were decreased in the OK-432 positive group. Over half of the patients had transient 1- or 2-day febrile reactions after intrapleural OK-432 injection. It was concluded that neither clinical observation nor immunological monitoring of peripheral blood could demonstrate a beneficial effect from intrapleural OK-432 immunotherapy after complete resection of the tumor.