Equations of bark thickness and volume profiles at different heights with easy-measurement variables

A method to predict lipoprotein signal peptides in Gram-negative Eubacteria, LipoP, has been developed. The hidden Markov model (HMM) was able to distinguish between lipoproteins (SPaseII-cleaved proteins), SPaseI-cleaved proteins, cytoplasmic proteins, and transmembrane proteins. This predictor was able to predict 96.8% of the lipoproteins correctly with only 0.3% false positives in a set of SPaseI-cleaved, cytoplasmic, and transmembrane proteins. The results obtained were significantly better than those of previously developed methods. Even though Gram-positive lipoprotein signal peptides differ from Gram-negatives, the HMM was able to identify 92.9% of the lipoproteins included in a Gram-positive test set. A genome search was carried out for 12 Gram-negative genomes and one Gram-positive genome. The results for Escherichia coli K12 were compared with new experimental data, and the predictions by the HMM agree well with the experimentally verified lipoproteins. A neural network-based predictor was developed for comparison, and it gave very similar results. LipoP is available as a Web server at www.cbs.dtu.dk/services/LipoP/.

The protein complement of cellular membranes is notoriously resistant to standard proteomic analysis and structural studies. As a result, membrane proteomes remain ill-defined. Here, we report a global topology analysis of the Escherichia coli inner membrane proteome. Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins. By constraining a topology prediction algorithm with this data, we derived high-quality topology models for the 601 proteins, providing a firm foundation for future functional studies of this and other membrane proteomes. We also estimated the overexpression potential for 397 green fluorescent protein fusions; the results suggest that a large fraction of all inner membrane proteins can be produced in sufficient quantities for biochemical and structural work.

It is commonly accepted that a single primary endosymbiosis gave rise to the photosynthetic organelles of plants, the plastids. Recently, we presented evidence that photosynthetic inclusions, termed "chromatophores," present in the filose thecamoeba Paulinella chromatophora originated from an independent, more recent primary endosymbiotic event. To clarify metabolic capabilities of the chromatophore and its state of integration into the host, we present here the complete genome sequence of the chromatophore. Our data reveal a fundamental reduction of the chromatophore genome. The single, circular chromosome of 1.02 Mb encodes 867 protein-coding genes and is, therewith, the smallest cyanobacterial genome reported to date. Compared to Synechococcus WH5701, a free-living relative of the chromatophore, only 26% of the genes were retained. Eleven putative pseudogenes were identified, indicating that reductive genome evolution is ongoing. Although the chromatophore genome contains a complete set of photosynthesis genes, it lacks not only genes thought to be dispensable for an intracellular lifestyle but also genes of essential pathways for amino acid and cofactor synthesis. Our data characterize the chromatophore as a photosynthetic entity that is absolutely dependent on its host for growth and survival. Thus, the chromatophores of P. chromatophora are the only known cyanobacterial descendants besides plastids with a significantly reduced genome that confer photosynthesis to their eukaryotic host. Their comparison with plastids and bacterial endosymbionts of invertebrates sheds light on early steps of the integration of a photosynthetic prokaryote into a eukaryotic cell.