Birds have played a central role in many biological disciplines, particularly ecology, evolution, and behavior. The chicken, as a model vertebrate, also represents an important experimental system for developmental biologists, immunologists, cell biologists, and geneticists. However, genomic resources for the chicken have lagged behind those for other model organisms, with only 1845 nonredundant full-length chicken cDNA sequences currently deposited in the EMBL databank. We describe a large-scale expressed-sequence-tag (EST) project aimed at gene discovery in chickens (http://www.chick.umist.ac.uk). In total, 339,314 ESTs have been sequenced from 64 cDNA libraries generated from 21 different embryonic and adult tissues. These were clustered and assembled into 85,486 contiguous sequences (contigs). We find that a minimum of 38% of the contigs have orthologs in other organisms and define an upper limit of 13,000 new chicken genes. The remaining contigs may include novel avian specific or rapidly evolving genes. Comparison of the contigs with known chicken genes and orthologs indicates that 30% include cDNAs that contain the start codon and 20% of the contigs represent full-length cDNA sequences. Using this dataset, we estimate that chickens have approximately 35,000 genes in total, suggesting that this number may be a characteristic feature of vertebrates.

Pyst1 is an inducible antagonist of FGF signaling in embryos and acts in a negative feedback loop to regulate the activity of MAPK. Our results demonstrate both the importance of MAPK signaling in neural induction and limb bud outgrowth and the critical role played by dual specificity MAP kinase phosphatases in regulating developmental outcomes in vertebrates.

The PA subunit of the influenza virus polymerase complex is a phosphoprotein that induces proteolytic degradation of coexpressed proteins. Point mutants with reduced proteolysis induction reconstitute viral ribonucleoproteins defective in replication but not in transcriptional activity. To look for cellular factors that could associate with PA protein, we have carried out a yeast two-hybrid screen. Using a human kidney cDNA library, we identified two different interacting clones. One of them was identified as the human homologue of a previously described cDNA clone from Gallus gallus called CLE. The human gene encodes a protein of 36 kDa (hCLE) and is expressed ubiquitously in all human organs tested. The interaction of PA and hCLE was also observed with purified proteins in vitro by using pull-down and pep-spot experiments. Mapping of the interaction showed that hCLE interacts with PA subunit at two regions (positions 493 to 512 and 557 to 574) in the PA protein sequence. Immunofluorescence studies showed that the hCLE protein localizes in both the nucleus and the cytosol, although with a predominantly cytosolic distribution. hCLE was found associated with active, highly purified virus ribonucleoproteins reconstituted in vivo from cloned cDNAs, suggesting that PA-hCLE interaction is functionally relevant. Searches in the databases showed that hCLE has 38% sequence homology to the central region of the yeast factor Cdc68, which modulates transcription by interaction with transactivators. Similar homologies were found with the other members of the Cdc68 homologue family of transcriptional activators, including the human FACT protein.The genome of influenza A virus consists of a set of eight single-stranded RNA segments of negative polarity. These RNAs form ribonucleoproteins (RNPs) with four viral proteins: the nucleoprotein (NP) and the three subunits of the polymerase (PB1, PB2, and PA). These elements are required for both transcription and replication of the viral genome (10,16,18,29).The roles of the polymerase subunits have been partly outlined. The PB1 subunit contains sequence motifs typical of the viral RNA-dependent RNA polymerases (43), which have been shown to be essential for RNA synthesis (3), suggesting that this subunit is the polymerase itself. PB2 protein binds to CAP1 structures (4, 51) and is involved in the endonucleolytic cleavage of cellular mRNAs to generate the precursors used as primers for the viral transcription (6,22). PA is a phosphoprotein in vivo and is a substrate of casein kinase II in vitro (47). This subunit induces a proteolytic process when expressed individually, affecting both coexpressed proteins and PA protein itself (46). The amino-terminal third of the molecule is sufficient to activate this proteolysis (48). Recently, we have reconstituted RNPs in vivo from cloned genes using PA point mutants deficient in proteolytic activity. These mutant RNPs are as active as the wild type in their transcription activity but have a lower capacity to support replication of model vRNA ...

Tetrapods have two pairs of limbs, each typically with five digits, each of which has a defined number of phalanges derived from an archetypal formula. Much progress has been made in understanding vertebrate limb initiation and the patterning processes that determine digit number in developing limb buds, but little is known about how phalange number is controlled. We and others previously showed that an additional phalange can be induced in a chick toe if sonic hedgehog protein is applied in between developing digit primordia. Here we show that formation of an additional phalange is associated with prolonged Fgf8 expression in the overlying apical ridge and that an Fgf Receptor inhibitor blocks its formation. The additional phalange is produced by elongation and segmentation of the penultimate phalange, suggesting that the digit tip forms when Fgf signaling ceases by a special mechanism, possibly involving Wnt signaling. Consistent with this, Fgfs inhibit tip formation whereas attenuation of Fgf signaling induces tip formation prematurely. We propose that duration of Fgf signaling from the ridge, responsible for elongation of digit primordia, coupled with a characteristic periodicity of joint formation, generates the appropriate number of phalanges in each digit. We also propose that the process that generates the digit tips is independent of that which generates more proximal phalanges. This has implications for understanding human limb congenital malformations and evolution of digit diversity.

No abstract

The PA subunit of the influenza virus polymerase complex is a phosphorylated protein that induces a proteolytic process that decreases its own accumulation levels and those of coexpressed proteins. The aminoterminal third of the protein is responsible for the induction of proteolysis. We mutated five potential casein kinase II phosphorylation sites located in the amino-terminal third of the protein. The influenza virus RNA polymerase is a heterotrimer formed by the PB1, PB2, and PA subunits. It associates with nucleoprotein (NP)-complexed viral RNA (vRNA) to form virion ribonucleoproteins (vRNPs). In influenza virus-infected cells, the vRNPs direct two types of RNA synthesis: mRNA synthesis (transcription) and vRNA amplification (replication). For mRNA synthesis, 5Ј-capped oligonucleotides derived from cellular mRNAs by cap-snatching are used as primers (21). These primers are elongated until polyadenylation occurs at a signal of five to seven U residues close to the 5Ј end of the template (24,(32)(33)(34). Replication, in contrast, occurs without primer. The vRNA template is copied to form full-length positive-stranded RNA (cRNA), which serves as a template for vRNA synthesis (18,21). Free NP is required as an antitermination factor to ignore the polyadenylation signal during the synthesis of cRNA (39). However, a detailed picture of the mechanism of the transcription-replication switch is still lacking.The PB1 subunit contains several sequence motifs characteristic of the vRNA-dependent RNA polymerases (31). These motifs have been shown to be essential for vRNA synthesis (6), suggesting that PB1 is the polymerase itself. PB2 protein binds CAP1 structures (7, 41) and might contain the endonucleolytic activity responsible of the cleavage of host mRNA precursors (8, 23). The phenotype of viral temperature-sensitive (ts) mutants indicates that the PA subunit is involved in vRNA replication (reviewed in reference 25), but its precise role in this process is unknown. The PA subunit induces a generalized proteolytic process when expressed individually from cloned cDNA (36), and the amino-terminal third of the molecule (positions 1 to 247) is sufficient to activate this proteolysis (38).We recently showed that the PA protein is phosphorylated in vivo and that it is a substrate of casein kinase II in vitro (37). PA protein contains 11 potential phosphorylation sites for casein kinase II in its molecule, 8 of them located in a cluster inside the first 247 N-terminal amino acids. Therefore we produced point mutations of several putative casein kinase II phosphorylation sites located at the amino-terminal third of the protein and studied the consequences of these genetic changes in the activity of the mutated PA proteins. Some of these PA mutants presented decreased ability to induce proteolysis. Interestingly, the capacity of these mutants to support replication of model vRNA in a polymerase reconstituted in vivo from cloned cDNAs strongly correlated with their proteolysis induction, but all mutants were as active as wil...

The RNA polymerase activity and PB1 binding of influenza virus PA mutants were studied using an in vivo-reconstituted polymerase assay and a two hybrid system. Deletions covering the whole PA protein abolished polymerase activity, but the deletion of the 154 N-terminal amino acids allowed PB1 binding, indicating that the PA protein N terminus is not absolutely required for this interaction. Further internal or C-terminal deletions abolished PB1 interaction, suggesting that most of the protein is involved in this association. As a novel finding we showed that a single amino acid insertion mutant, PAI672, was responsible for a temperature-sensitive phenotype. Hutant PAS509, which had a serine insertion at position 509, bound to PBI like wild-type PA but did not show any polymerase activity. Over-expression of PAS509 interfered with the polymerase activity of wild-type PA, identifying PAS509 as a dominant negative mutant.The influenza virus RNA polymerase is composed of three polymerase proteins, PB1, PB2 and PA, and catalyses two distinct types of RNA synthesis: (i) synthesis of mRNA (transcription) and (ii) amplification of the vRNA (replication). For mRNA synthesis, 5'-capped, host cell-derived RNA fragments are used as primers and polyadenylation occurs at a signal located 17-22 nucleotides before the 5' end of the template. Replication occurs without primer and the vRNA template is copied to a full-length positive-stranded RNA (cRNA), which serves as template for vRNA synthesis. It has been shown that free nucleoprotein (NP) might be a control element for anti-termination, but little is known about the

Candida albicans is a frequent aetiologic agent of sepsis associated with high mortality in immunocompromised patients. Developing new antifungal therapies is a medical need due to the low efficiency and resistance to current antifungal drugs. Here, we show that p38γ and p38δ regulate the innate immune response to C. albicans. We describe a new TAK1‐TPL2‐MKK1‐ERK1/2 pathway in macrophages, which is activated by Dectin‐1 engagement and positively regulated by p38γ/p38δ. In mice, p38γ/p38δ deficiency protects against C. albicans infection by increasing ROS and iNOS production and thus the antifungal capacity of neutrophils and macrophages, and by decreasing the hyper‐inflammation that leads to severe host damage. Leucocyte recruitment to infected kidneys and production of inflammatory mediators are decreased in p38γ/δ‐null mice, reducing septic shock. p38γ/p38δ in myeloid cells are critical for this effect. Moreover, pharmacological inhibition of p38γ/p38δ in mice reduces fungal burden, revealing that these p38MAPKs may be therapeutic targets for treating C. albicans infection in humans.