Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

Background  

Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins.     

Lipid synthesis in the adult dog heartworm, Dirofilaria immitis.

1. Incorporation studies with three labelled substrates--[14C]2-glycerol, [14C]1-acetate and [14C]1-oleic acid--demonstrated that adult dog heartworms can synthesize all classes of complex lipids present, including free cholesterol. 2. Diacylglycerols and phosphoglycerides were most rapidly labelled regardless of the precursor employed. 3. 14C from glycerol was found in the aqueous phase of saponified lipids, whereas that from oleic acid was in the fatty acid portion. 4. Tag from acetate was predominantly in the fatty acid portion of saponified lipids and also occurred in the unesterified fatty acids. 5. Acetate and unesterified fatty acids, as represented by oleic acid, were more readily used for lipid synthesis than was glycerol.     

Glycolytic end products of the adult dog heartworm, Dirofilaria immitis.

1. Adult dog heartworms remained alive and motile for 24 hr without oxygen present and with only glucose available as a substrate. 2. Lactate accounted for 55% of the carbon from the 1-14C-glucose utilized in 1 hr and 14CO2 for 1.9%. 3. Only traces of 14C were found in glycogen and no net accumulation of acetate was demonstrated. 4. Dirofilaria immitis resembles Litomosoides carinii in the percent of utilized glucose appearing as lactate but is more akin to Brugia pahangi and Dipetalonema viteae in survival under anaerobic conditions and in negligible acetate production.