Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.
The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.
Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.
an orderly manner on the pre-mRNA, thereby forming the Jü rgen Lauber 1 , William S.Lane 2 and catalytic splicing machinery known as the spliceosome. Reinhard Lü hrmann 3Despite the fact that exogenous phosphates are not Keller, 1985) and has been shown to be involved in Cambridge, MA 02138, USA several steps from spliceosome assembly to product release 1 Present address: Qiagen GmbH, Max-Volmer-Strasse 4, 40724 Hilden, (reviewed in Guthrie, 1991;Moore et al., 1993). GermanyTwo classes of splicing factors are distinguished cur-3 Corresponding author rently. The first class comprises four evolutionarily cone-mail: luehrmann@imt.uni-marburg.de served small nuclear ribonucleoprotein (snRNP) particles, U1, U2, U4/U6 and U5, that contain either one (U1, U2, The driving forces behind the many RNA conform-U5) or two (U4/U6) snRNA components (for review, see ational changes occurring in the spliceosome are not Green, 1991;Guthrie, 1991;Rymond and Rosbash, 1992; well understood. Here we characterize an evolu- Moore et al., 1993); the second class consists of an as yet tionarily conserved human U5 small nuclear ribounknown number of proteins that are not tightly bound to nucleoprotein (snRNP) protein (U5-116kD) that is snRNPs and are therefore termed non-snRNP splicing strikingly homologous to the ribosomal elongation factors (see Lamm and Lamond, 1993;Beggs, 1995 ; factor EF-2 (ribosomal translocase). A 114 kDa proteinKrämer, 1995). (Snu114p) homologous to U5-116kD was identified inThe composition of the U snRNPs has been studied Saccharomyces cerevisiae and was shown to be essential most extensively in HeLa cells . At low for yeast cell viability. Genetic depletion of Snu114p salt concentrations (up to 100 mM), where HeLa nuclear results in accumulation of unspliced pre-mRNA, extracts support pre-mRNA splicing in vitro, a 12S U1 indicating that Snu114p is essential for splicing in vivo.snRNP, 17S U2 snRNP and a 25S [U4/U6·U5] tri-snRNP Antibodies specific for U5-116kD inhibit pre-mRNA complex are found. At high salt concentrations (350-splicing in a HeLa nuclear extract in vitro. In HeLa 450 mM), the tri-snRNP complex dissociates into a 20S cells, U5-116kD is located in the nucleus and co-U5 and a 12S U4/U6 particle. In the U4/U6 snRNP, the localizes with snRNP-containing subnuclear structures U4 and U6 snRNAs interact through extensive sequence referred to as speckles. The G domain of U5-116kD/ complementarity (Bringmann et al., 1984; Hashimoto and Snu114p contains the consensus sequence elements Steitz, 1984;Rinke et al., 1985;Brow and Guthrie, 1988). G1-G5 important for binding and hydrolyzing GTP.The proteins of the snRNPs fall into two groups, the Consistent with this, U5-116kD can be cross-linked common proteins (B/BЈ, D1, D2, D3, E, F and G), specifically to GTP by UV irradiation of U5 snRNPs.which are present in each snRNP, and the particle-specific Moreover, a single amino acid substitution in the G1proteins. While U1 and U2 snRNPs contain three (70K, sequence motif of Snu114p, expected to abolish GTP-A and C...
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