The identification of co-regulated genes and their transcription-factor binding sites (TFBS) are key steps toward understanding transcription regulation. In addition to effective laboratory assays, various computational approaches for the detection of TFBS in promoter regions of coexpressed genes have been developed. The availability of complete genome sequences combined with the likelihood that transcription factors and their cognate sites are often conserved during evolution has led to the development of phylogenetic footprinting. The modus operandi of this technique is to search for conserved motifs upstream of orthologous genes from closely related species. The method can identify hundreds of TFBS without prior knowledge of co-regulation or coexpression. Because many of these predicted sites are likely to be bound by the same transcription factor, motifs with similar patterns can be put into clusters so as to infer the sets of co-regulated genes, that is, the regulons. This strategy utilizes only genome sequence information and is complementary to and confirmative of gene expression data generated by microarray experiments. However, the limited data available to characterize individual binding patterns, the variation in motif alignment, motif width, and base conservation, and the lack of knowledge of the number and sizes of regulons make this inference problem difficult. We have developed a Gibbs sampling-based Bayesian motif clustering (BMC) algorithm to address these challenges. Tests on simulated data sets show that BMC produces many fewer errors than hierarchical and K-means clustering methods. The application of BMC to hundreds of predicted gamma-proteobacterial motifs correctly identified many experimentally reported regulons, inferred the existence of previously unreported members of these regulons, and suggested novel regulons.
A novel multicellular form of Methanosarcina mazei S-6 is described. It was termed lamina, and it formed during the exponential growth phase when packets or single cells were grown in 40 mM trimethylamine and a total concentration of 8.3 to 15.6 mM Ca2`and/or Mg2+, in cultures that were not shaken. A distinct molecular event represented by the increment in expression and a spatial redistribution of an antigen during lamina formation is documented.Methanosarcinae are the only members of the archaebacterial domain, Archaea (33, 34), for which uni-and multicellular forms have been observed (20,26,29,31), suggesting an underlying complexity in gene regulation not hitherto observed in other archaebacteria. There are other features of methanosarcinae that remind one of higher organisms, such as the cell wall polymer methanochondroitin, which closely resembles eukaryotic chondroitin (14, 15). Also, Methanosarcina gene organization, although typically prokaryotic, shows conserved molecules involved in replication, transcription, and translation with a higher degree of homology to those of eukaryotes than to those of eubacteria (4,33,37).Among methanosarcinae, Methanosarcina mazei S-6 (20, 21) is one of the better-studied species in pure culture concerning different morphologies-i.e., single cells and small and large packets (1,12,26,27,35). These morphologies have also been observed in complex ecosystems like anaerobic bioreactors (18). Different morphologies allow analysis from various perspectives. Packets of M. mazei S-6 can easily be monitored in different types of anaerobic bioreactors (18,19), whereas single cells facilitate molecular biologic studies (12). In addition, the multicellular structures in M. mazei S-6 afford the opportunity to examine cell-cell interaction in archaebacteria.The use of monoclonal antibodies has proven to be a powerful tool for examining developmentally regulated antigens in both prokaryotic and eukaryotic systems (5, 10). Investigations of the cell surface's architecture and antigenic mosaic of methanosarcinae have revealed antigens whose expression is associated with morphology (22, 23), and thus these antigens can be useful as markers in the study of temporal gene expression during morphologic changes. A multicellular form of M. mazei S-6, which we have termed lamina, and the temporal variations of a cell surface antigen (AgIc) paralleling the morphological rearrangements involved in lamina formation are described here. The word lamina best illustrates the structure's distinctive morphologic feature, i.e., its flat shape observed macro-and microscopically, its thickness being minimal in comparison with its length and width. Monoclonal antibody IC (MAbIC) generated and characterized as described previously (9, 17) was used for immunologic assays. The presence of antigen (AgIc) in sections of M. mazei S-6 was detected with MAbIC by immunohistochemistry and indirect immunofluorescence (6,7,13 (Fig. la). These packets were inoculated into medium containing 40
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