Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.

White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These fungi use extracellular oxidative enzymes that are also able to transform related aromatic compounds found in explosive contaminants, pesticides and toxic waste. We have sequenced the 30-million base-pair genome of Phanerochaete chrysosporium strain RP78 using a whole genome shotgun approach. The P. chrysosporium genome reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay. Analysis of the genome data will enhance our understanding of lignocellulose degradation, a pivotal process in the global carbon cycle, and provide a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching. This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens.

Falsifications and corroborations: Karl Popper's influence on systematics.

Over the last three decades, the philosophy of Karl Raimund Popper has had a strong influence on the field of systematic biology. Unequivocally, no other philosopher's work has had such an influence during this formative period in systematics. Much, but not all, of the early discourse on Popper and systematics dealt with the philosophical basis of systematics as a science. More recently Popper's work has been discussed in the systematics literature in relation to specific methodologies such as parsimony and maximum likelihood. In this paper, we provide the reader with a concise summary of Popper's ideas relevant to systematics, review the systematic literature invoking or declining Popper's importance to the field, and make a recommendation for the future course of philosophical thinking in systematics. We try to make clear various authors' interpretations of Popper's work and how those interpretations have impacted systematic thought. Although the reader may come away from this review with a clearer idea of Popper's relevance or lack thereof, our primary hope is that the reader will be compelled to question him- or herself about the philosophical basis of the systematic work that he or she does, and to delve into the literature herein cited. We begin by presenting a synopsis of Popper's philosophical views to allow those views to be placed in the context of systematics.

The mitochondrial genome of Phoronis architecta--comparisons demonstrate that phoronids are lophotrochozoan protostomes.

The proper reconstruction of the relationships among the animal phyla is central to interpreting patterns of animal evolution from the genomic level to the morphological level. This is true not only of the more speciose phyla but also of smaller groups. We report here the nearly complete DNA sequence of the mitochondrial genome of the phoronid Phoronis architecta, which has a gene arrangement remarkably similar to that of a protostome animal, the chiton Katharina tunicata. Evolutionary analysis of both gene arrangements and inferred amino acid sequences of these taxa, along with those of three brachiopods and other diverse animals, strongly supports the hypothesis that lophophorates are part of the large group that includes mollusks and annelids-i.e., the Lophotrochozoa-and solidly refutes the alternative of their being deuterostomes.

Aep3p stabilizes the mitochondrial bicistronic mRNA encoding subunits 6 and 8 of the H+-translocating ATP synthase of Saccharomyces cerevisiae.

Subunits 6 and 8 of the mitochondrial ATPase in Saccharomyces cerevisiae are encoded by the mitochondrial genome and translated from bicistronic mRNAs containing both reading frames. The stability of the two major species of ATP8/6 mRNA, which differ in the length of the 5'-untranslated region, depends on the expression of several nuclear-encoded factors. In the present study, the product of the gene designated AEP3 (open reading frame YPL005W) is shown to be required for stabilization and/or processing of both ATP8/6 mRNA species. In an aep3-disruptant strain, the shorter ATP8/6 mRNA was undetectable, and the level of the longer mRNA was reduced to approximately 35% that of wild type. Localization of a hemagglutinin-tagged version of Aep3p showed that the protein is an extrinsic constituent of the mitochondrial inner membrane facing the matrix.

The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes.

We report the complete mtDNA sequence from a member of the phylum Chaetognatha (arrow worms). The Paraspadella gotoi mtDNA is highly unusual, missing 23 of the genes commonly found in animal mtDNAs, including atp6, which has otherwise been found universally to be present. Its 14 genes are unusually arranged into two groups, one on each strand. One group is punctuated by numerous noncoding intergenic nucleotides although the other group is tightly packed, having no noncoding nucleotides, leading to speculation that there are two transcription units with differing modes of expression. The phylogenetic position of the Chaetognatha within the Metazoa has long been uncertain, with conflicting or equivocal results from various morphological analyses and rRNA sequence comparisons. Comparisons here of amino acid sequences from mitochondrially encoded proteins give a single most parsimonious tree that supports a position of Chaetognatha as sister to the protostomes studied here. From this analysis, one can more clearly interpret the patterns of evolution of various developmental features, especially regarding the embryological fate of the blastopore.

ATP22, a nuclear gene required for expression of the F0 sector of mitochondrial ATPase in Saccharomyces cerevisiae.

Expression of the mitochondrial proton-translocating ATPase of Saccharomyces cerevisiae has been shown to depend on chaperones that target the F1 and F0 sectors of this inner membrane complex. Here we report a new gene, designated ATP22 (reading frame YDR350C on chromosome IV), that provides an essential function in the assembly of F0. ATP22 was cloned by transformation of C208/L2, a strain previously assigned to complementation group G99 of a collection of respiration-defective nuclear pet mutants. C208/L2 and the other atp22 mutants have oligomycin-insensitive F1-ATPase, suggesting that the lesion is confined to F0. This is supported by the sedimentation properties of the mutant ATPase and results of immunochemical analysis of F0 subunit polypeptides. Northern analysis of ATPase transcripts and in vivo pulse labeling of the mitochondrial translation products in the mutant indicate normal expression of subunits 6, 8, and 9, the three mitochondrial gene products of F0. Atp22p therefore functions at a post-translational stage in assembly of F0. Localization studies indicate Atp22p to be a component of the mitochondrial inner membrane. Protease protection experiments further indicate that Atp22p faces the matrix side of the membrane where most of the ATPase proteins are located and assembled.