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6 Literaturverzeichnis 110 6 Literaturverzeichnis 110 6 Literaturverzeichnis ABRAHAM , L.J., ROOD , J.I., 1985. Molecular Analysis of Transferable Tetracycline Resi- tance Plasmids from Clostridium perfringens . J. Bacteriol. 161: 636-640. ALBERT , A., DHANARAJ , V., GENSCHEL , U., KHAN , G., RAMJEE , M.K., PULIDO , R., SIBANDA , B.L., VON DELFT , F., WITTY , M., BLUNDELL , T.L., SMITH , A.G., ABELL , C., 1998. Crystal structure of aspartate decarboxylase at 2.2 resolution provides evidence for an ester in protein self-processing. Nat. Struct. Biol. 5: 289-293. ALLEN , S.P., BLASCHEK , H.P., 1988. Electroporation-induced transformation of intact cells of Clostridium perfringens . Appl. Environ. Microbiol. 54: 2322-2324. ANDREESEN , J.R., BAHL , H., GOTTSCHALK , G., 1989. Introduction to the physiology and biochemistry of the genus Clostridium . In: Biotechnology Handbook “Clostridia”. N.P. Minton, Clarke, D.P. (Hrsg.). New York: Plenum: 27-62. ANDREESEN , J.R., 1994. Glycine metabolism in anaerobes. Ant. v. Leeuwenhoek. 66: 223-237. ANDREESEN , J.R., 2004. Glycine reductase mechanism. Curr. Opin. Chem.Biol. 8: in press. ARKOWITZ , R.A., ABELES , R.H., 1989. Identification of acetyl phosphate as the product of clostridial glycine reductase: evidence for an acyl enzyme intermediate. Biochemistry 28: 4639-4644. ARKOWITZ , R.A., ABELES , R.H., 1990. Isolation and characterization of a covalent se- lenocysteine intermediate in the glycine reductase system. J. Am. Chem. Soc. 112: 870- 872. ARKOWITZ , R.A., ABELES , R.H., 1991. Mechanism of action of clostridial glycine reduc- tase: Isolation and characterization of a covalent acetyl enzyme intermediate. Biochem- istry 30: 4090-4097. ARKOWITZ , R.A., DHE -PAGANON , S., ABELES , R.H., 1994. The fate of the carboxyl oxy- gens during D-proline reduction by clostridial proline reductase. Arch. Biochem. Bio- phys. 311: 457-459. 6 Literaturverzeichnis 111 AUSUBEL , F.M., BRENT , R., KINGSTON , R.E., MOORE , D.D., SEIDMAN , J.G., SMITH , J.A., STRUHL , K. (Hrsg.), 1994. Current protocols in molecular biology. John Wiley and Sons, New York. BANNAM , T.L., ROOD , J.I., 1993. Clostridium perfringens -Escherichia coli shuttle vec- tors that carry single antibiotic resistance determinants. Plasmid 229: 233-235. BAUMANN , J.G.J., WIEGANT , J., VAN DUIJN , P., 1981. Cytochemical hybridization with fluorochrome labeled RNA. I. Development of a method using nucleic acids bound to agarose beads as a model. J. Histochem. Cytochem. 29: 227-237. BECKHOFER , D., 1993. 5’-mRNA stabilizers. In: Control of messenger RNA stability. J. Belasco, Brawerman, G. (Hrsg). San Diego, California, Academic Press: 31-52. BEDNARSKI , B., 1999. Molekulare Analyse der Pyruvyl-bindenden Proenzyme GrdE und PrdA der Glycin- und D-Prolin-Reduktase aus Clostridium sticklandii . Dipolmarbeit, Martin-Luther-Universität Halle. BEDNARSKI , B., ANDREESEN , J.R., PICH , A., 2001. In vitro processing of the proproteins GrdE of protein B of glycine reductase and PrdA of D-proline reduktase from Clostrid- ium sticklandii . Formation of a pyruvoyl group from a cysteine residue. Eur. J. Biochem. 268: 1-8. BENNETT , E.M., EKSTROM , J.L., PEGG , A.E., EALICK , S.E., 2002. Monomeric S- adenosylmethionine decarboxylase from plants provides an alternative to putrescine stimulation. Biochemistry 41: 14509-14517. BERTRAM , J., DÜRRE , P., 1989. Conjugal transfer and expression of streptococcal trans- posons in Clostridium acetobutylicum . Arch. Microbiol. 152: 551-557. BERTRAM , J., GASSEN , H.G., 1991. Gentechnische Methoden. Jena, Stuttgart, New York, Gustav Fischer Verlag. BEVERIDGE , T.J., GRAHAM , L.L., 1991. Surface layers of bacteria. Microbiol. Rev. 55: 684-705. BIRNBOIM , C., DOLY , J., 1979. Rapid alkaline extraction procedure for screening recom- binant plasmid DNA. Nucl. Acids Res. 7: 1513-1523. BLAKE , M.S., JOHNSTON , K.H., RUSSEL -JONES , G.J., GOTTSCHLICH , E.C., 1984. A rapid, sensitive method for detection of alkaline phosphatase-conjugated anti-antibody on western blots. Anal. Biochem. 136: 175-179. BOORSTEIN , W.R., CRAIG , E.A., 1989. Primer extension analysis of RNA. Meth. Enzy- mol. 180: 247-369. 6 Literaturverzeichnis 112 BOOT , H.J., POUWELS , P.H., 1996. Expression, secretion and antigenic variation of bac- terial S-layer proteins. Mol. Microbiol. 21: 1117-1123. BÖHRINGER , M., 1997. Vektor-Konstruktion, Untersuchung von Antibiotika-Resistenzen und Elektrotransformation von Clostridium acetobutylicum DSM 792. Diplomarbeit, Universität Ulm. BRADFORD , M.M., 1976. A rapid and sensitive method for the quantitation of micro- gram quantities of protein utilizing the prinziple of protein-dye binding. Biochem. J. 214: 687-694. BRANNINGAN , J.A., DODSEN , G., DUGGLEBY , H. J., MOODY , P.C.E., SMITH , J.L., TOMCHIK , D.R., MURZIN , A.G., 1995. A protein catalytic framework with N-terminal nucleophile is capable of self-activation. Nature 378: 416-419. BRINKMANN , U., MATTES , R.E., BUCKEL , P., 1989. High-level expression of recombi- nant genes in Escherichia coli is dependent on the availability of the dnaY gene product. Gene 85: 109-114. BUCK , M., GALLEGOS , M.-T., STUDHOLME , D.J., GUO , Y., GRALLA , J.D., 2000. The bac- terial enhancer-dependent σ54 ( σN) transcription factor. J. Bacteriol. 182: 4129-4136. BUCKEL , W., 1990. Amino acid fermentations: Coenzyme B12-dependent and - independent pathways. In: The molecular basis of bacterial metabolism. G. Hauska, Thauer, R. (Hrsg.), Springer Verlag. 41: 22-30. CHAE , HZ., KIM , I. H., KIM K., RHEE , S.G., 1993. Cloning, sequencing and mutation of thiol-specific antioxidant gene of Saccharomyces cerevisiae . J. Biol. Chem. 268: 16815- 16821. CHONG , S., SHAO , Y., PAULUS , H., BENNER , J., PERLER , F.B., XU, M.-Q., 1996. Protein splicing involving the Saccharomyces cerevisiae VMA intein. J. Biol. Chem. 271: 22159-22168. CHONG , S., WILLIAMS , K.S., WOTKOWITZ , C., XU, M.-Q., 1998. Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein. J. Biol. Chem. 273: 10567-10577. CLYNE , T., KINCH , L.N., PHILLIPS , M.A., 2002. Putrescine activation of Trypanosoma cruzi S-adenosylmethionine decarboxylase. Biochemistry 41: 13207-13216. COLLINS , M.D., LAWSON , P.A., WILLEMS , A., CORDOBA , J.J., FERNANDEZ -GARAYZABAL , J., GARCIA , P., CAI , P., HIPPE , H., FARROW , J.A.E., 1994. The phylogeny of the genus Clostridium : proposal of five new genera and eleven new species combinations. Int. J. System. Bacteriol. 44: 812-826. 6 Literaturverzeichnis 113 DAI , S., SCHWENDTMAYER , C., SCHÜRMANN , P., RAMASWAMY , S., EKLUND , H., 2000. Redox signaling in chloroplasts: cleavage of disulfides by an iron-sulfur cluster. Science 287: 655-658. DIETRICHS , D., MEYER , M., RIETH , M., ANDREESEN , J.R., 1991. Purification of the se- lenoprotein P A by interaction with the thioredoxin system, all being components of the glycine reductase complex in Eubacterium acidaminophilum and Clostridium litorale . J. Bacteriol. 173: 5983-5991. DIXON , H.B.F., FIELDS , R., 1972. Spezific modification of NH 2-terminal residues by transamination. Methods Enzymol. 25: 409-419. DOVE , S.L., DARST , S.A., HOCHSCHILD , A., 2003. Region 4 of σ as a target for transcrip- tion regulation. Mol. Microbiol. 48: 863-874. DOWER , W.J., MILLER , J.F., RAGSDALE , C.W., 1988. High efficiency transformation of E. coli by high voltage electroporation. Nucl. Acids Res. 16: 387-395. DUGAICZYK , A., BOYER , H.W., GOODMAN , H.M., 1975. Ligation of EcoRI endonuclease generated DNA fragments into linear structures. J. Mol. Biol. 96: 171-184. DÜRRE , P., 1993. The Clostridia and biotechnology. In: Transposons in clostridia. D. R. Woods (Hrsg.). Butterworth-Heinemann, Stoneham. MA, 227-246. EKSTROM , J.L., MATHEWS , I.I., ATANLEY , B.A., PEGG , A., EALICK , S.E., 1999. The crys- tal structure of human S-adenosylmethionine decarboxylase at 2.25 resolution reveals a novel fold. Structure 7: 583-595. EKSTROM , J.L., TOLBERT , W.D., XIONG , H., PEGG , A.E., EALICK , S.E., 2001. Structure of a human S-adenosylmethionene decarboxylase self-processing ester intermediate an mechanism of putrescine stimulation of processing as revealed by the H243A mutant. Biochemistry 40: 9495-9504. EVANS , J.T.C., BENNER , J., XU, M.-Q., 1998. Semisynthesis of cytotoxic proteins using a modified protein splicing element. Protein Science 7: 2256-2264. FENDRICH , C., HIPPE , H., GOTTSCHALK , G., 1990. Clostridium halophilium sp. nov. and C. litorale sp. nov., an obligate halophilic and a marine species degrading betaine in the Stickland reaction. Arch. Microbiol. 154: 127-132. FIELD , L., SWEETMAN , B.J., 1969. Biologically oriented organic sulfur chemistry. I. Re- actions of thiols with highly reactive carbonyl compounds. J. Org. Chem. 34: 1799- 1803. 6 Literaturverzeichnis 114 FRANKE , A.E., CLEWELL , D.B., 1981. Evidence for a chromosome-borne resistance transposon (Tn 916 ) in Streptococcus faecalis that is capable of conjugal transfer in the absence of a conjugative plasmid. J. Bacteriol. 145: 494-502. GALLHAGER , T., ROZWARSKI , D.A., ERNST S.R., HACKERT , M.L., 1993. Refined struc- ture of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a . J. Mol. Biol. 230: 516-528. GENTHER , B.R.S., DAVIS , C.L., BRYANT , C.L., 1981. Features of rumen and sewage sludge strains of Eubacterium limosum , a methanol and H 2/CO 2 utilizing species. Appl. Environ. Microbiol. 41: 12-19. GILCHRIST , A., SMIT , J., 1991. Transformation of freshwater and marine caulobacters by electroporation. J. Bacteriol. 173: 921-925. GRANDERATH , K., 1993.
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