* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Table 3S
Fatty acid synthesis wikipedia , lookup
Sulfur cycle wikipedia , lookup
Biochemical cascade wikipedia , lookup
Genomic imprinting wikipedia , lookup
Promoter (genetics) wikipedia , lookup
Peptide synthesis wikipedia , lookup
Point mutation wikipedia , lookup
Genetic code wikipedia , lookup
Ridge (biology) wikipedia , lookup
Endogenous retrovirus wikipedia , lookup
Ribosomally synthesized and post-translationally modified peptides wikipedia , lookup
Proteolysis wikipedia , lookup
Magnesium transporter wikipedia , lookup
Metalloprotein wikipedia , lookup
Biochemistry wikipedia , lookup
Gene regulatory network wikipedia , lookup
Silencer (genetics) wikipedia , lookup
Gene expression profiling wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Table 3S: Transcriptome data summary for genes of the Arg, Cys and His biosynthesis pathways. gene description Ag(I) Arginine Biosynthesis argC N-acetylglutamate gamma-semialdehyde dehydrogenase argJ ornithine acetyltransferase argB N-acetylglutamate 5-phosphotransferase argD N-acetylornithine aminotransferase carA carbamoyl-phosphate transferase-arginine carB carbamoyl-phosphate transferase-arginine argG argininosuccinate synthase argH argininosuccinate lyase yqiX high affinity Arg transport yqiY high affinity Arg transport yqiZ high affinity Arg transport As(V) Fold induction1 Cd(II) Ni(II) Zn(II) reference Cu(II) 35.3 1.0 1.0 1.0 1.0 1.0 (Belitsky, 2002) 133.1 39.0 20.9 11.0 15.8 26.8 14.9 26.2 12.2 11.0 0.9 1.0 1.0 1.0 1.0 0.5 0.8 0.6 0.8 0.6 0.4 0.5 0.6 1.0 1.0 1.0 0.8 0.9 0.8 0.8 1.0 1.0 1.0 1.0 1.0 1.3 1.0 1.3 1.1 1.1 1.1 1.1 1.0 1.0 0.9 1.1 0.9 1.0 1.0 1.2 1.0 1.1 1.0 0.9 1.0 0.9 1.0 1.0 1.8 1.1 Cysteine Biosynthesis cysH phosphoadenosine phosphosulfate 15.2 12.6 0.4 1.2 1.9 cysP sulfate permease 27.0 16.8 0.4 1.2 2.9 sat cysC ylnD ylnE yrhA yrhB probable sulfate adenylyltransferase probable adenylylsulfate kinase uroporphyrin-III C-methyltransferase unknown; cysH operon similar to cysteine synthase similar to cystathionine gamma-synthase 24.0 29.42 19.1 4.6 25.3 21.8 16.7 2.0 10.3 2.9 4.9 5.1 0.4 0.4 0.4 0.6 1.8 1.1 1.3 1.2 1.3 1.1 1.1 1.2 2.3 2.8 2.6 1.6 5.7 3.2 1.2 (Mansilla and de Mendoza, 1997) 1.5 (Mansilla and de Mendoza, 2000) 1.4 (Grundy and Henkin, 2002) 1.2 (Grundy and Henkin, 2002) 1.3 (Grundy and Henkin, 2002) 1.0 (Grundy and Henkin, 2002) 3.0 (Grundy and Henkin, 2002) 3.0 (Grundy and Henkin, 2002) (Belitsky, 2002) (Belitsky, 2002) (Belitsky, 2002) (Belitsky, 2002) (Belitsky, 2002) (Belitsky, 2002) (Belitsky, 2002) (Sekowska et al., 2001) (Sekowska et al., 2001) (Sekowska et al., 2001) cysK yxeK yxeL yxeM yxeN yxeO yxeP yhcL yrrT ytlI cysteine synthetase A similar to monooxygenase similar to acetyltransferase amino acid ABC transporter amino acid ABC transporter amino acid ABC transporter similar to aminoacylase similar to sodium-glutamate symporter similar to SAM dep. methyltransferase LysR family regulatory protein Histidine Biosynthesis hisZ histidyl-tRNA synthetase hisG ATP phosphoribosyltransferase hisD histidinol dehydrogenase hisB imidazoleglycerol-phosphate dehydratase hisH amidotransferase hisA isomerase hisF HisF cyclase-like protein hisI pyrophosphohydrolase yuiF histidine transporter 7.7 18.5 34.1 18.7 6.9 14.9 15.4 20.9 5.4 29.2 10.2 3.9 5.9 4.7 1.6 2.7 1.3 3.4 1.4 2.4 0.6 1.3 1.1 0.8 0.7 1.2 0.9 0.9 1.2 3.2 1.2 1.0 1.5 1.6 1.1 1.1 1.0 1.1 1.2 1.0 1.6 4.8 8.8 2.2 2.4 2.2 4.0 6.2 2.04 4.9 2.8 3.1 3.0 2.3 1.7 1.8 1.4 3.0 3.2 3.0 (Grundy and Henkin, 2002) (Auger et al., 2002) (Auger et al., 2002) (Auger et al., 2002) (Auger et al., 2002) (Auger et al., 2002) (Auger et al., 2002) (Burguiere et al., 2004) (Grundy and Henkin, 2003) (Coppee et al., 2001) 58.4 15.0 57.4 47.0 39.4 31.1 26.4 8.6 21.4 1.0 1.6 1.0 1.0 1.0 1.0 1.0 1.0 0.5 0.7 0.7 0.9 0.9 0.4 0.4 0.4 0.6 0.9 2.7 1.8 4.1 5.3 4.2 5.7 6.7 2.8 2.4 1.5 1.3 2.1 0.9 1.0 1.3 1.0 1.0 1.8 2.8 1.7 3.6 4.5 2.1 3.9 3.1 2.0 4.2 (Sonenshein, 1993) (Sonenshein, 1993) (Sonenshein, 1993) (Sonenshein, 1993) (Sonenshein, 1993) (Sonenshein, 1993) (Sonenshein, 1993) (Sonenshein, 1993) (Vitreschak et al., 2004) Fold induction by 3 min. metal stress at OD600=0.3 in LB medium at the following concentrations: 10 M Ag(II); 10 M As(V); 10 M Cd(II); 10 M Cu(II); 500 M Ni(II) or 300 M Zn(II). 1 Genes included for each pathway were: Arg (argCJBDcarAB, argGHytzD, yqiXYZ), Cys (cysHcysP(ylnA)sat(ylnB)cysC(ylnC)ylnDE, yrhAB, cysK, yxeKLMNOP, yhcL, yrrT, ytlI) and His (hisZGDBHAFI, yuiF). The argC operon encodes the enzyme for synthesis of citrulline which is converted to Arg by the products of the argGH genes (Belitsky, 2002). The yqiXYZ operon encodes a high affinity Arg transport system (Sekowska et al., 2001).The cysH operon together with cysK encodes enzymes for the synthesis of Cys from sulfate and O-acetylserine and the yrhAB genes encode the cystathionine -synthase and lyase for conversion of homocysteine to Cys (Grundy and Henkin, 2002). The yrrT gene is located upstream of the yrhAB genes, appears to be regulated by a Met-specific antitermination mechanism (T-box; (Grundy and Henkin, 2003) and is postulated to function in a reverse pathway of synthesis of Cys from Met (Rodionov et al., 2004). The yxeK operon, yhcL, and ytlI are known to be strongly up-regulated during growth on methionine as sole sulfur source (relative to sulfate-grown cells; (Auger et al., 2002) . YhcL is a symporter that functions in the uptake of cystine and has been renamed TcyP (Burguiere et al., 2004). The YtlI protein functions as a positive activator of the divergent ytmI operon (although this operon was not induced under the tested conditions) which is apparently involved in some aspect of sulfur assimilation (Coppee et al., 2001). The hisZ operon encodes the major enzymes for His biosynthesis and YuiF has recently been proposed to be a histidine transporter (Vitreschak et al., 2004). Note that not all genes in every predicted operon made the 5-fold cut-off for inclusion in this analysis. Further, many genes regulated by the SAM-dependent S-box termination mechanism (Grundy and Henkin, 2003) were not detected as strongly regulated in this analysis. References Auger, S., Danchin, A., and Martin-Verstraete, I. (2002) Global expression profile of Bacillus subtilis grown in the presence of sulfate or methionine. J Bacteriol 184: 5179-5186. Belitsky, B.R. (2002) Biosynthesis of Amino Acids of the Glutamate and Aspartate Families, Alanine, and Polyamines. In Bacillus subtilis and its closest relatives. Sonenshein, A.L., Hoch, J.A. and Losick, R. (eds). Washington, D. C.: ASM Press, pp. 203-231. Burguiere, P., Auger, S., Hullo, M.F., Danchin, A., and Martin-Verstraete, I. (2004) Three different systems participate in Lcystine uptake in Bacillus subtilis. J Bacteriol 186: 4875-4884. Coppee, J.Y., Auger, S., Turlin, E., Sekowska, A., Le Caer, J.P., Labas, V., Vagner, V., Danchin, A., and Martin-Verstraete, I. (2001) Sulfur-limitation-regulated proteins in Bacillus subtilis: a two-dimensional gel electrophoresis study. Microbiology 147: 1631-1640. Grundy, F.J., and Henkin, T.M. (2002) Synthesis of Serine, Glycine, Cysteine, and Methionine. In Bacillus subtilis and its closest relatives. Sonenshein, A.L., Hoch, J.A. and Losick, R. (eds). Washington, D. C.: ASM Press, pp. 245-254. Grundy, F.J., and Henkin, T.M. (2003) The T box and S box transcription termination control systems. Front Biosci 8: d20-31. Mansilla, M.C., and de Mendoza, D. (1997) L-cysteine biosynthesis in Bacillus subtilis: identification, sequencing, and functional characterization of the gene coding for phosphoadenylylsulfate sulfotransferase. J Bacteriol 179: 976-981. Mansilla, M.C., and de Mendoza, D. (2000) The Bacillus subtilis cysP gene encodes a novel sulphate permease related to the inorganic phosphate transporter (Pit) family. Microbiology 146 ( Pt 4): 815-821. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A., and Gelfand, M.S. (2004) Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res 32: 3340-3353. Sekowska, A., Robin, S., Daudin, J.J., Henaut, A., and Danchin, A. (2001) Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis. Genome Biol 2: RESEARCH0019. Sonenshein, A.L. (1993) Introduction to Metabolic Pathways. In Bacillus subtilis and other Gram-Positive Bacteria. Sonenshein, A.L., Hoch, J.A. and Losick, R. (eds). Washington, D.C.: ASM Press. Vitreschak, A.G., Lyubetskaya, E.V., Shirshin, M.A., Gelfand, M.S., and Lyubetsky, V.A. (2004) Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis. FEMS Microbiol Lett 234: 357-370.