Chemical reactivity drives spatiotemporal organisation of bacterial metabolism

FEMS Microbiology Reviews

Volumn 39, Issue 1, 2015, Pages 96-119

  de Lorenzo, Víctor ^a   Sekowska, Agnieszka ^b   Danchin, Antoine ^b  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

Author keywords

Carboxysomes; Metabolic frustration; Serine toxicity; Synthetic biology; TOL plasmid

Indexed keywords

METHIONINE SULFOXIDE REDUCTASE; REACTIVE OXYGEN METABOLITE;

AMINO ACID SYNTHESIS; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; BIODEGRADATION; CELL COMPARTMENTALIZATION; CELL ISOLATION; CHEMICAL REACTION; COVALENT BOND; DEHYDROGENATION; ENERGY CONSUMPTION; GENETIC ENGINEERING; HYDROXYLATION; MACROMOLECULE; METABOLIC ENGINEERING; METABOLISM; NITROGEN FIXATION; NONHUMAN; NONRIBOSOMAL PEPTIDE SYNTHESIS; NUCLEOTIDE METABOLISM; ONE POT SYNTHESIS; OXIDATION REDUCTION POTENTIAL; PROTEIN SYNTHESIS; REVIEW; SECONDARY METABOLISM; SPATIOTEMPORAL ANALYSIS; SULFOXIDATION; SYMBIONT; SYMBIOSIS; TRANSAMINATION; BACTERIUM; CHEMISTRY; PHYSIOLOGY;

BACTERIA; METABOLIC NETWORKS AND PATHWAYS;

EID: 84934300609     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1111/1574-6976.12089     Document Type: Review

References (280)

1. Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 2013;29:273-9.
2. Adachi O, Ano Y, Shinagawa E, Yakushi T, Matsushita K Conversion of quinate to 3-dehydroshikimate by Caalginate-immobilized membrane of Gluconobacter oxydans IFO 3244 and subsequent asymmetric reduction of 3-dehydroshikimate to shikimate by immobilized cytoplasmic NADP-shikimate dehydrogenase. Biosci Biotechnol Biochem 2010;74:2438-44.
3. Adams PG, Cadby AJ, Robinson B, Tsukatani Y, Tank M, Wen J, Blankenship RE, Bryant DA, Hunter CN Comparison of the physical characteristics of chlorosomes from three different phyla of green phototrophic bacteria. Biochim Biophys Acta 2013;1827:1235-44.
4. Agrawal GK, Bourguignon J, Rolland N et al. Plant organelle proteomics: collaborating for optimal cell function. Mass Spectrom Rev 2011;30:772-853.
5. Alvarez L, Espaillat A, Hermoso JA, de Pedro MA, Cava F Peptidoglycan remodeling by the coordinated action ofmultispecific enzymes. Microb Drug Resist 2014;20:190-8.
6. Anbazhagan V, Munz C, Tome L, Schneider D Fluidizing the membrane by a local anesthetic: phenylethanol affects membrane protein oligomerization. JMol Biol 2010;404:773-7.
7. Andersson SG, Kurland CG Origins of mitochondria and hydrogenosomes. Curr Opin Microbiol 1999;2:535-41.
8. Andersson SG, Karlberg O, Canback B, Kurland CG On the origin of mitochondria: a genomics perspective. Philos Trans R Soc Lond B Biol Sci 2003;358:165-77 discussion 177-169.
9. Andrianantoandro E, Basu S, Karig DK, Weiss R Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2006;2 2006 0028.
10. Antelmann H, Helmann JD Thiol-based redox switches and gene regulation. Antioxid Redox Signal 2011;14:1049-63.
11. Apostol I, Levine J, Lippincott J, Leach J, Hess E, Glascock CB, Weickert MJ, Blackmore R Incorporation of norvaline at leucine positions in recombinant human hemoglobin expressed in Escherichia coli. J Biol Chem 1997;272:28980-8.
12. Balasubramaniam S, Lio P Multi-hop conjugation based bacteria nanonetworks. IEEE Trans Nanobiosci 2013;12:47-59.
13. Banik SD, Nandi N Chirality and protein biosynthesis. Top Curr Chem 2012;333:255-305.
14. Bao Q, Tian Y, Li W et al. A complete sequence of the T. tengcongensis genome. Genome Res 2002;12:689-700.
15. Bayer EA, Belaich JP, Shoham Y, Lamed R The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 2004;58:521-54.
16. Baykal A, Chakraborty S, Dodoo A, Jordan F Synthesis with good enantiomeric excess of both enantiomers of alpha-ketols and acetolactates by two thiamin diphosphate-dependent decarboxylases. Bioorg Chem 2006;34:380-93.
17. Bazylinski DA, Frankel RB Magnetosome formation in prokaryotes. Nat Rev Microbiol 2004;2:217-30.
18. Belda E, Sekowska A, Le Fevre F, Morgat A, Mornico D, Ouzounis C, Vallenet D, Medigue C, Danchin A An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology 2013;159:757-70.
19. Bender A, Hajieva P, Moosmann B Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria. P Natl Acad Sci USA 2008;105:16496-501.
20. Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 2009;5:593-9.
21. Benveniste R, Davies J Aminoglycoside antibiotic-inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. P Natl Acad Sci USA 1973;70:2276-80.
22. Berger BJ, English S, Chan G, Knodel MH Methionine regeneration and aminotransferases in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. J Bacteriol 2003;185:2418-31.
23. Bernas R, Gradsztajn E, Reeves H, Schatzman E On the nucleosynthesis of lithium, beryllium, and boron. Ann Phys 1967;44:426-78.
24. Binder PM, Danchin A Life's demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life? EMBO Rep 2011;12: 495-9.
25. Blatt L, Dorer FE, Sallach HJ Occurrence of hydroxypyruvate-lglutamate transaminase in Escherichia coli and its separation from hydroxypyruvate-phosphate-l-glutamate transaminase. J Bacteriol 1966;92:668-75.
26. Bobik TA Polyhedral organelles compartmenting bacterial metabolic processes. Appl Microbiol Biotechnol 2006;70: 517-25.
27. Bogdanov M, Aboulwafa M, Saier MH, Jr Subcellular localization and logistics of integral membrane protein biogenesis in Escherichia coli. J Mol Microbiol Biotechnol 2013;23:24-34.
28. Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF Modularity of a carbon-fixing protein organelle. P Natl Acad Sci USA 2012;109:478-83.
29. Brandt U Inside view of a giant proton pump. Angew Chem 2013;52:7358-60.
30. Brenner K, You L, Arnold FH Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol 2008;26:483-9.
31. Buchner P Endosymbiose der Tiere mit pflanzlichen Mikroorganismen 1953 Verlag Birkhäuser Basel-Stuttgart Budisa N, Steipe B, Demange P, Eckerskorn C, Kellermann J, Huber R High-level biosynthetic substitution of methionine in proteins by its analogs 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli. Eur J Biochem 1995;230:788-96.
32. Budovsky A, Fraifeld VE, Aronov S Linking cell polarity, aging and rejuvenation. Biogerontology 2010;12:167-75.
33. Burman JD, Stevenson CE, Sawers RG, Lawson DM The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family. BMC Struct Biol 2007;7:30.
34. Busch S, Bode HB, Brakhage AA, Braus GH Impact of the cross-pathway control on the regulation of lysine and penicillin biosynthesis in Aspergillus nidulans. Curr Genet 2003;42: 209-19.
35. Caballero JL, Martinez E, Malpartida F, Hopwood DA Organisation and functions of the actVA region of the actinorhodin biosynthetic gene cluster of Streptomyces coelicolor. Mol Gen Genet 1991;230:401-12.
36. Chan KK, O'Hagan D The rare fluorinated natural products and biotechnological prospects for fluorine enzymology. Methods Enzymol 2012;516:219-35.
37. Chan CM, Danchin A, Marlìere P, Sekowska A Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis. Environ Microbiol 2014;16:101-17.
38. Chandra G, Chater KF, Bornemann S Unexpected and widespread connections between bacterial glycogen and trehalose metabolism. Microbiology 2011;157:1565-72.
39. Changeux JP The feedback control mechanisms of biosynthetic l-threonine deaminase by l-isoleucine. Cold Spring Harb Symp Quant Biol 1961;26:313-8.
40. Cheung J, Beasley FC, Liu S, Lajoie GA, Heinrichs DE Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol Microbiol 2009;74:594-608.
41. Christensen KE, MacKenzie RE Mitochondrial one-carbon metabolism is adapted to the specific needs of yeast, plants and mammals. BioEssays 2006;28:595-605.
42. Comellas-Aragones M, Engelkamp H, Claessen VI, Sommerdijk NA, Rowan AE, Christianen PC, Maan JC, Verduin BJ, Cornelissen JJ, Nolte RJ A virus-based single-enzyme nanoreactor. Nat Nanotechnol 2007;2:635-9.
43. Condurso HL, Bruner SD Structure and noncanonical chemistry of nonribosomal peptide biosynthetic machinery. Nat Prod Rep 2012;29:1099-110.
44. Conrado RJ, Varner JD, DeLisa MP Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy. Curr Opin Biotechnol 2008;19:492-9.
45. Cooper AJ, Kuhara T alpha-Ketoglutaramate: an overlooked metabolite of glutamine and a biomarker for hepatic encephalopathy and inborn errors of the urea cycle. Metab Brain Dis 2013 10.1007/s11011-013-9444-9.
46. Coppola D, Giordano D, Tinajero-Trejo M, di Prisco G, Ascenzi P, Poole RK, Verde C Antarctic bacterial haemoglobin and its role in the protection against nitrogen reactive species. Biochim Biophys Acta 2013;1834:1923-31.
47. Corre J, Lucchini JJ, Mercier GM, Cremieux A Antibacterial activity of phenethyl alcohol and resulting membrane alterations. Res Microbiol 1990;141:483-97.
48. Cosloy SD, McFall E l-Serine-sensitive mutants of Escherichia coli K-12. J Bacteriol 1970;103:840-1.
49. Craney A, Ozimok C, Pimentel-Elardo SM, Capretta A, Nodwell JR Chemical perturbation of secondary metabolism demonstrates important links to primary metabolism. Chem Biol 2012;19:1020-7.
50. Dairi T, Kuzuyama T, Nishiyama M, Fujii I Convergent strategies in biosynthesis. Nat Prod Rep 2011;28:1054-86.
51. Danchin A Homeotopic transformation and the origin of translation. Prog Biophys Mol Biol 1989;54:81-6.
52. Danchin A Information of the chassis and information of the program in synthetic cells. Syst Synth Biol 2009;3:125-34.
53. Danchin A Bacteria as computers making computers. FEMS Microbiol Rev 2009;33:3-26.
54. Danchin A Cells need safety valves. BioEssays 2009;31:769-73.
55. Danchin A Scaling up synthetic biology: do not forget the chassis. FEBS Lett 2012;586:2129-37.
56. Danchin A, Sekowska A The logic of metabolism and its fuzzy consequences. Environ Microbiol 2014;16:19-28.
57. Davies JE, Benveniste RE Enzymes that inactivate antibiotics in transit to their targets. Ann NY Acad Sci 1974;235:130-6.
58. Davies J, Davies D Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 2010;74:417-33.
59. de Bary HA Die Erscheinung der Symbiose: Vortrag gehalten auf der Versammlung Deutscher Naturforscher und Aerzte zu Cassel 1879 Trübner, Strassburg Verlag von Karl J. 30.
60. de Lorenzo V Systems biology approaches to bioremediation. Curr Opin Biotechnol 2008;19:579-89.
61. de Lorenzo V From the selfish gene to selfish metabolism: revisiting the central dogma. BioEssays 2014;36: 226-35.
62. De Oliveira DC, Fernandes Junior A, Kaneno R, Silva MG, Araujo Junior JP, Silva NC, Rall VL Ability of Salmonella spp. to produce biofilm is dependent on temperature and surface material. Foodborne Pathog Dis 2014;11:478-83.
63. Demain AL, Fang A The natural functions of secondary metabolites. Adv Biochem Eng Biotechnol 2000;69:1-39.
64. Deppe VM, Bongaerts J, O'Connell T, Maurer KH, Meinhardt F Enzymatic deglycation of Amadori products in bacteria: mechanisms, occurrence and physiological functions. Appl Microbiol Biotechnol 2011;90:399-406.
65. Dietz KJ Peroxiredoxins in plants and cyanobacteria. Antioxid Redox Signal 2011;15:1129-59.
66. Docampo R, Moreno SN Acidocalcisomes. Cell Calcium 2011;50:113-9.
67. Docampo R, de Souza W, Miranda K, Rohloff P, Moreno SN Acidocalcisomes-conserved from bacteria to man. Nat Rev Microbiol 2005;3:251-61.
68. Dorrestein PC, Kelleher NL Dissecting non-ribosomal and polyketide biosynthetic machineries using electrospray ionization Fourier-Transform mass spectrometry. Nat Prod Rep 2006;23:893-918.
69. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 2009;27:753-9.
70. Duggleby RG Suicide inhibition of acetohydroxyacid synthase by hydroxypyruvate. J Enzyme Inhib Med Chem 2005; 20:1-4.
71. Dyson FJ Origins of Life 1985 Cambridge, UK Cambridge University Press.
72. Eicher SC, Dehio C Bartonella entry mechanisms into mammalian host cells. Cell Microbiol 2012;14:1166-73.
73. Endo R, Ohtsubo Y, Tsuda M, Nagata Y Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26. J Bacteriol 2007;189: 3712-20.
74. Enos-Berlage JL, Langendorf MJ, Downs DM Complex metabolic phenotypes caused by a mutation in yjgF, encoding a member of the highly conserved YER057c/YjgF family of proteins. J Bacteriol 1998;180:6519-28.
75. Erjavec N, Nystrom T Sir2p-dependent protein segregation gives rise to a superior reactive oxygen species management in the progeny of Saccharomyces cerevisiae. P Natl Acad Sci USA 2007;104:10877-81.
76. Escapa IF, Garcia JL, Buhler B, Blank LM, Prieto MA The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida. Environ Microbiol 2012;14:1049-63.
77. Ezraty B, Grimaud R, El HassouniM, Moinier D, Barras FMethionine sulfoxide reductases protect Ffh from oxidative damages in Escherichia coli. EMBO J 2004;23:1868-77.
78. Fang G, Rocha E, Danchin A How essential are nonessential genes? Mol Biol Evol 2005;22:2147-56.
79. Ferguson GP Protective mechanisms against toxic electrophiles in Escherischia coli. Trends Microbiol 1999;7:242-7.
80. Fiedler E, Thorell S, Sandalova T, Golbik R, Konig S, Schneider G Snapshot of a key intermediate in enzymatic thiamin catalysis: crystal structure of the alpha-carbanion of (alpha, betadihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae. P Natl Acad Sci USA 2002;99:591-5.
81. Flynn JM, Christopherson MR, Downs DM Decreased coenzyme A levels in ridA mutant strains of Salmonella enterica result from inactivated serine hydroxymethyltransferase. Mol Microbiol 2013;89:751-9.
82. Forrester MT, Foster MW Protection from nitrosative stress: a central role for microbial flavohemoglobin. Free Radic Biol Med 2012;52:1620-33.
83. Frank S, Lawrence AD, Prentice MB, Warren MJ Bacterial microcompartments moving into a synthetic biological world. J Biotechnol 2013;163:273-9.
84. Friedman M, Henika PR, Mandrell RE Antibacterial activities of phenolic benzaldehydes and benzoic acids against Campylobacter jejuni, Escherichia coli, Listeria monocytogenes, and Salmonella enterica. J Food Prot 2003;66:1811-21.
85. Furuya T, Kuttruff CA, Ritter T Carbon-fluorine bond formation. Curr Opin Drug Discov Devel 2008;11:803-19.
86. Gazzani G, Fregnan GB, Vandoni G In vitro protection by erdosteine against oxidative inactivation of alpha-1-antitrypsin by cigarette smoke. Respiration 1989;55:113-8.
87. Gehring H, Rando RR, Christen P Active-site labeling of aspartate aminotransferases by the beta, gamma-unsaturated amino acid vinylglycine. Biochemistry 1977;16:4832-6.
88. Gerdes K, Howard M, Szardenings F Pushing and pulling in prokaryotic DNA segregation. Cell 2010;141:927-42.
89. Gil R, Silva FJ, Zientz E et al. The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. P Natl Acad Sci USA 2003;100:9388-93.
90. Giles GI, Jacob C Reactive sulfur species: an emerging concept in oxidative stress. Biol Chem 2002;383:375-88.
91. Gilles AM, Marliere P, Rose T, Sarfati R, Longin R, Meier A, Fermandjian S, Monnot M, Cohen GN, Barzu O Conservative replacement of methionine by norleucine in Escherichia coli adenylate kinase. J Biol Chem 1988;263:8204-9.
92. Giltner CL, Nguyen Y, Burrows LL Type IV pilin proteins: versatile molecular modules. Microbiol Mol Biol Rev 2012;76:740-72.
93. Gonidakis S, Longo VD Assessing chronological aging in bacteria. Methods Mol Biol 2013;965:421-37.
94. Gosalbes MJ, Lamelas A, Moya A, Latorre A The striking case of tryptophan provision in the cedar aphid Cinara cedri. J Bacteriol 2008;190:6026-9.
95. Grabowski R, Hofmeister AE, Buckel W Bacterial l-serine dehydratases: a new family of enzymes containing iron-sulfur clusters. Trends Biochem Sci 1993;18:297-300.
96. Gray MJ, Wholey WY, Jakob U Bacterial responses to reactive chlorine species. Annu Rev Microbiol 2013;67:141-60.
97. Greiner R, Konietzny U, Jany KD Purification and characterization of two phytases fromEscherichia coli. Arch Biochem Biophys 1993;303:107-13.
98. Gupta RS What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol Microbiol 1998;29:695-707.
99. Gupta RS Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes. Antonie Van Leeuwenhoek 2011;100:171-82.
100. Gutknecht J, Bisson MA, Tosteson FC Diffusion of carbon dioxide through lipid bilayer membranes: effects of carbonic anhydrase, bicarbonate, and unstirred layers. J Gen Physiol 1977;69:779-94.
101. Hagishita T, Yoshida T, Izumi Y, Mitsunaga T Efficient l-serine production from methanol and glycine by resting cells of Methylobacterium sp. strain MN43. Biosci Biotechnol Biochem 1996;60:1604-7.
102. Hardwick SW, Gubbey T, Hug I, Jenal U, Luisi BF Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly. Open Biol 2012;2:120028.
103. Hedrick JL, Sallach HJ The metabolism of hydroxypyruvate. I. The nonenzymatic decarboxylation and autoxddation of hydroxypyruvate. J Biol Chem 1961;236:1867-71.
104. Hedrick JL, Sallach HJ The metabolism of hydroxypyruvate. II. The enzymatic oxidation and decarboxylation of hydroxypyruvate. J Biol Chem 1961;236:1872-5.
105. Helou C, Marier D, Jacolot P, Abdennebi-Najar L, Niquet-Leridon C, Tessier FJ, Gadonna-Widehem P Microorganisms and Maillard reaction products: a review of the literature and recent findings. Amino Acids 2014;46:267-77.
106. Hernandez B, Pfluger F, Adenier A, Kruglik SG, Ghomi M Vibrational analysis of amino acids and short peptides in hydrated media. VIII. Amino acids with aromatic side chains: l-phenylalanine, l-tyrosine, and l-tryptophan. J Phys Chem B 2010;114:15319-30.
107. Hertweck C, Luzhetskyy A, Rebets Y, Bechthold A Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork. Nat Prod Rep 2007;24:162-90.
108. Hibi M, Kawashima T, Kodera T, Smirnov SV, Sokolov PM, Sugiyama M, Shimizu S, Yokozeki K, Ogawa J Characterization of Bacillus thuringiensis l-isoleucine dioxygenase for production of useful amino acids. Appl Environ Microbiol 2011;77:6926-30.
109. Higgins D, Dworkin J Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev 2012;36:131-48.
110. Huang X, Holden HM, Raushel FM Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu Rev Biochem 2001;70:149-80.
111. Huang X, Yan A, Zhang X, Xu Y Identification and characterization of a putative ABC transporter PltHIJKN required for pyoluteorin production in Pseudomonas sp. M18. Gene 2006;376:68-78.
112. Hughes JA In vivo hydrolysis of S-adenosyl-l-methionine in Escherichia coli increases export of 5-methylthioribose. Can J Microbiol 2006;52:599-602.
113. Hunter CA, Singh J, Thornton JMPi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins. J Mol Biol 1991;218:837-46.
114. Huseby DL, Roth JR Evidence that a metabolic microcompartment contains and recycles private cofactor pools. J Bacteriol 2013;195:2864-79.
115. Hutson S Structure and function of branched chain aminotransferases. Prog Nucleic Acid Res Mol Biol 2001;70:175-206.
116. Idan O, Hess H Origins of activity enhancement in enzyme cascades on scaffolds. ACS Nano 2013;7:8658-65.
117. Itel F, Al-Samir S, Oberg F et al. CO2 permeability of cell membranes is regulated by membrane cholesterol and protein gas channels. FASEB J 2012;26:5182-91.
118. Iturrate L, Sanchez-Moreno I, Doyaguez EG, Garcia-Junceda E Substrate channelling in an engineered bifunctional aldolase/kinase enzyme confers catalytic advantage for C-C bond formation. Chem Commun 2009 1721-3.
119. Jack DL, Yang NM, Saier MH, Jr The drug/metabolite transporter superfamily. Eur J Biochem 2001;268:3620-39.
120. Jacob C A scent of therapy: pharmacological implications of natural products containing redox-active sulfur atoms. Nat Prod Rep 2006;23:851-63.
121. Jakas A, Katic A, Bionda N, Horvat S Glycation of a lysinecontaining tetrapeptide by d-glucose and d-fructose-influence of different reaction conditions on the formation of Amadori/Heyns products. Carbohydr Res 2008;343: 2475-80.
122. Jakubowski H, Fersht AR Alternative pathways for editing noncognate amino acids by aminoacyl-tRNA synthetases. Nucleic Acids Res 1981;9:3105-17.
123. Jann A, Stalon V, Wauven CV, Leisinger T, Haas D NSuccinylated intermediates in an arginine catabolic pathway of Pseudomonas aeruginosa. P Natl Acad Sci USA 1986;83: 4937-41.
124. Jarboe LR, Royce LA, Liu P Understanding biocatalyst inhibition by carboxylic acids. Front Microbiol 2013;4:272.
125. Jenke-Kodama H, Dittmann E Evolution of metabolic diversity: insights from microbial polyketide synthases. Phytochemistry 2009;70:1858-66.
126. Jenkins T, Bovi A, Edwards R Plants: biofactories for a sustainable future? Philos Trans A Math Phys Eng Sci 2011;369:1826-39.
127. Jiang YY, Kong DX, Qin T, Li X, Caetano-Anolles G, Zhang HY The impact of oxygen on metabolic evolution: a chemoinformatic investigation. PLoS Comput Biol 2012;8:e1002426.
128. Jimenez JI, Perez-Pantoja D, Chavarria M, Diaz E, de Lorenzo V A second chromosomal copy of the catA gene endows Pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environ Microbiol 2013;16:1767-78.
129. Jimenez-Sanchez C, Wick LY, Ortega-Calvo JJ Chemical effectors cause differentmotile behavior and deposition of bacteria in porous media. Environ Sci Technol 2012;46:6790-7.
130. Jorda J, Lopez D, Wheatley NM, Yeates TO Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria. Protein Sci 2013;22:179-95.
131. Kanjee U, Houry WA Mechanisms of acid resistance in Escherichia coli. Annu Rev Microbiol 2013;67:65-81.
132. Karsten WE, Cook PF Detection of a gem-diamine and a stable quinonoid intermediate in the reaction catalyzed by serine-glyoxylate aminotransferase from Hyphomicrobium methylovorum. Biochim Biophys Acta 2009;1790:575-80.
133. Kartal B, de Almeida NM, Maalcke WJ, Op den Camp HJ, Jetten MS, Keltjens JT How to make a living from anaerobic ammonium oxidation. FEMS Microbiol Rev 2013;37:428-61.
134. Kell DB Finding novel pharmaceuticals in the systems biology era usingmultiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. FEBS J 2013;280:5957-80.
135. Khersonsky O, Tawfik DS Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 2010;79:471-505.
136. Khosravi-Darani K, Mokhtari ZB, Amai T, Tanaka K Microbial production of poly(hydroxybutyrate) from C(1) carbon sources. Appl Microbiol Biotechnol 2013;97:1407-24.
137. Killian JA, Fabrie CH, Baart W, Morein S, de Kruijff B Effects of temperature variation and phenethyl alcohol addition on acyl chain order and lipid organization in Escherichia coli derived membrane systems. A 2H-and 31P-NMR study. Biochim Biophys Acta 1992;1105:253-62.
138. Kirnos MD, Khudyakov IY, Alexandrushkina NI, Vanyushin BF 2-aminoadenine is an adenine substituting for a base in S-2L cyanophage DNA. Nature 1977;270:369-70.
139. Kisumi M, Sugiura M, Chibata I Biosynthesis of norvaline, norleucine, and homoisoleucine in Serratia marcescens. J Biochem 1976;80:333-9.
140. Kisumi M, Sugiura M, Takagi T, Chibata I Norvaline accumulation by regulatory mutants of Serratia marcescens. J Antibiot 1977;30:111-7.
141. Kitao A, Yonekura K, Maki-Yonekura S, Samatey FA, Imada K, Namba K, Go N Switch interactions control energy frustration and multiple flagellar filament structures. P Natl Acad Sci USA 2006;103:4894-9.
142. Kjaergaard K, Schembri MA, Ramos C, Molin S, Klemm P Antigen 43 facilitates formation of multispecies biofilms. Environ Microbiol 2000;2:695-702.
143. Komeili A Molecular mechanisms of compartmentalization and biomineralization in magnetotactic bacteria. FEMS Microbiol Rev 2012;36:232-55.
144. Kreuzer-Martin HW, Lott MJ, Ehleringer JR, Hegg EL Metabolic processes account for the majority of the intracellular water in log-phase Escherichia coli cells as revealed by hydrogen isotopes. Biochemistry 2006;45:13622-30.
145. Kuhn ML, Zemaitaitis B, Hu LI et al. Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS ONE 2014;9:e94816.
146. Kurland CG, Canback B, Berg OG The origins of modern proteomes. Biochimie 2007;89:1454-63.
147. Lai S, Zhang Y, Liu S, Liang Y, Shang X, Chai X, Wen T Metabolic engineering and flux analysis of Corynebacterium glutamicum for l-serine production. Sci China Life Sci 2012;55:283-90.
148. Lal PB, Schneider BL, Vu K, Reitzer L The redundant aminotransferases in lysine and arginine synthesis and the extent of aminotransferase redundancy in Escherichia coli. Mol Microbiol 2014 [Epub ahead of print] 10.1111/mmi.12801.
149. Lambrecht JA, Downs DM Anthranilate phosphoribosyl transferase (TrpD) generates phosphoribosylamine for thiamine synthesis from enamines and phosphoribosyl pyrophosphate. ACS Chem Biol 2013;8:242-8.
150. Lambrecht JA, Flynn JM, Downs DM Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J Biol Chem 2012;287:3454-61.
151. Lambrecht JA, Schmitz GE, Downs DM RidA proteins prevent metabolic damage inflicted by PLP-dependent dehydratases in all domains of life. mBio 2013;4:e00033-13.
152. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA, 3rd, Smith HO, Venter JC Genome transplantation in bacteria: changing one species to another. Science 2007;317:632-8.
153. Lazova MD, Butler MT, Shimizu TS, Harshey RM Salmonella chemoreceptors McpB and McpC mediate a repellent response to l-cystine: a potential mechanism to avoid oxidative conditions. Mol Microbiol 2012;84:697-711.
154. Le Saux T, Plasson R, Jullien L Energy propagation throughout chemical networks. Chem Commun 2014;50:6189-95.
155. Ledwidge R, Blanchard JS The dual biosynthetic capability of N-acetylornithine aminotransferase in arginine and lysine biosynthesis. Biochemistry 1999;38:3019-24.
156. Levy S, Danchin A Phylogeny of metabolic pathways: Oacetylserine sulphydrylase A is homologous to the tryptophan synthase beta subunit. Mol Microbiol 1988;2: 777-83.
157. Lloyd-Price J, Hakkinen A, Kandhavelu M, Marques IJ, Chowdhury S, Lihavainen E, Yli-Harja O, Ribeiro AS Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time. J Bacteriol 2012;194:1747-52.
158. Lotlikar SR, Hnatusko SB, Dickenson NE, Choudhari SP, Picking WL, Patrauchan MA Three functional beta-carbonic anhydrases in P. aeruginosa PAO1. Role in survival in ambient air. Microbiology 2013;159:1748-59.
159. Luo S, Levine RL Methionine in proteins defends against oxidative stress. FASEB J 2009;23:464-72.
160. Mally M, Shin H, Paroz C, Landmann R, Cornelis GR Capnocytophaga canimorsus: a human pathogen feeding at the surface of epithelial cells and phagocytes. PLoS Pathog 2008;4:e1000164.
161. Martinez KA, 2nd, Kitko RD, Mershon JP, Adcox HE, Malek KA, Berkmen MB, Slonczewski JL Cytoplasmic pH response to acid stress in individual cells of Escherichia coli and Bacillus subtilis observed by fluorescence ratio imaging microscopy. Appl Environ Microbiol 2012;78:3706-14.
162. Mattei PJ, Neves D, Dessen A Bridging cell wall biosynthesis and bacterialmorphogenesis. Curr Opin Struct Biol 2010;20:749-55.
163. Maxwell JC Theory of Heat 1871 London Longmans, Reed and Co McBurney CH, Bollen WB, Williams RJ Pantothenic acid and the nodule bacteria-legume symbiosis. P Natl Acad Sci USA 1935;21:301-4.
164. McCleary WR, Stock JB Acetyl phosphate and the activation of two-component response regulators. J Biol Chem 1994;269:31567-72.
165. Mendes P, Kell DB On the role of enzyme kinetic parameters in determining the effectiveness with which channelling can decrease the size of a metabolite pool. Acta Biotheor 1993;41:63-73.
166. Mishra S, Imlay J Why do bacteria use so many enzymes to scavenge hydrogen peroxide? Arch Biochem Biophys 2012;525:145-60.
167. Mooney BP, Miernyk JA, Randall DD The complex fate of alphaketoacids. Annu Rev Plant Biol 2002;53:357-75.
168. Mora J Glutamine metabolism and cycling in Neurospora crassa. Microbiol Rev 1990;54:293-304.
169. Muramatsu R, Negishi T, Mimoto T, Miura A, Misawa S, Hayashi H Existence of beta-methylnorleucine in recombinant hirudin produced by Escherichia coli. J Biotechnol 2002;93:131-42.
170. Muro-Pastor MI, Reyes JC, Florencio FJ Ammonium assimilation in cyanobacteria. Photosynth Res 2005;83:135-50.
171. Newman EB, Walker C l-serine degradation in Escherichia coli K-12: a combination of l-serine, glycine, and leucine used as a source of carbon. J Bacteriol 1982;151:777-82.
172. Niederweis M Mycobacterial porins-new channel proteins in unique outer membranes. Mol Microbiol 2003;49: 1167-77.
173. Nishida H, Nishiyama M Evolution of lysine biosynthesis in the phylum Deinococcus-Thermus. Int J Evol Biol 2012;2012:745931.
174. Njau RK, Herndon CA, Hawes JW Novel beta-hydroxyacid dehydrogenases in Escherichia coli and Haemophilus influenzae. J Biol Chem 2000;275:38780-6.
175. Norris V, den Blaauwen T, Doi RH et al. Toward a hyperstructure taxonomy. Annu Rev Microbiol 2007;61:309-29.
176. Ogawa J, Soong CL, Honda M, Shimizu S Novel metabolic transformation pathway for cyclic imides in Blastobacter sp. strain A17p-4. Appl Environ Microbiol 1996;62:3814-7.
177. Ohtsu I, Wiriyathanawudhiwong N, Morigasaki S, Nakatani T, Kadokura H, Takagi H The l-cysteine/l-cystine shuttle system provides reducing equivalents to the periplasm in Escherichia coli. J Biol Chem 2010;285:17479-87.
178. Oostergetel GT, van Amerongen H, Boekema EJ The chlorosome: a prototype for efficient light harvesting in photosynthesis. Photosynth Res 2010;104:245-55.
179. Osipiuk J, Zhou M, Moy S, Collart F, Joachimiak A X-ray crystal structure of GarR-tartronate semialdehyde reductase from Salmonella typhimurium. J Struct Funct Genomics 2009;10:249-53.
180. Paczia N, Nilgen A, Lehmann T, Gatgens J, Wiechert W, Noack S Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms. Microb Cell Fact 2012;11:122.
181. Parsons L, Bonander N, Eisenstein E, Gilson M, Kairys V, Orban J Solution structure and functional ligand screening of HI0719, a highly conserved protein from bacteria to humans in the YjgF/YER057c/UK114 family. Biochemistry 2003;42: 80-9.
182. Pascal G, Medigue C, Danchin A Universal biases in protein composition of model prokaryotes. Proteins 2005;60:27-35.
183. Pazos F, Valencia A Protein co-evolution, co-adaptation and interactions. EMBO J 2008;27:2648-55.
184. Perez-Pantoja D, Nikel PI, Chavarria M, de Lorenzo V Endogenous stress caused by faulty oxidation reactions fosters evolution of 2, 4-dinitrotoluene-degrading bacteria. PLoS Genet 2013;9:e1003764.
185. Perez-Pantoja D, Kim J, Silva-Rocha R, de Lorenzo V The differential response of the Pben promoter of Pseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts in mxylene biodegradation. Environ Microbiol 2014 10.1111/1462-2920.12443.
186. Petit E, LaTouf WG, Coppi MV et al. Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans. PLoS ONE 2013;8:e54337.
187. Peyraud R, Schneider K, Kiefer P, Massou S, Vorholt JA, Portais JC Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Syst Biol 2011;5:189.
188. Pfeifer F Distribution, formation and regulation of gas vesicles. Nat Rev Microbiol 2012;10:705-15.
189. Pitts AC, Tuck LR, Faulds-Pain A, Lewis RJ, Marles-Wright J Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment. PLoS ONE 2012;7:e48360.
190. Ponce-de-Leon MM, Pizer LI Serine biosynthesis and its regulation in Bacillus subtilis. J Bacteriol 1972;110:895-904.
191. Porcar M, Danchin A, de Lorenzo V Confidence, tolerance and allowance in biological engineering: The nuts and bolts of living things. BioEssays 2014 In Press.
192. Portier PJ Les Symbiotes 1918 Paris Masson et compagnie Puk O, Bischoff D, Kittel C, Pelzer S, Weist S, Stegmann E, Sussmuth RD, Wohlleben W Biosynthesis of chloro-betahydroxytyrosine, a nonproteinogenic amino acid of the peptidic backbone of glycopeptide antibiotics. J Bacteriol 2004;186:6093-100.
193. Ramos JL, Marqués S, Timmis KN Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 1997;51:341-73.
194. Rapaport DC Studies of reversible capsid shell growth. J Phys Condens Matter 2010;22:104115.
195. Rasko I, Alfoldi L Biosynthetic l-threonine deaminase as the origin of l-serine sensitivity of Escherichia coli. Eur J Biochem 1971;21:424-7.
196. Reid RE Peptide and Protein Drug Analysis 2000 New York Marcel Dekker.
197. Renzi F, Manfredi P, Mally M, Moes S, Jeno P, Cornelis GR The N-glycan glycoprotein deglycosylation complex (Gpd) from Capnocytophaga canimorsus deglycosylates human IgG. PLoS Pathog 2011;7:e1002118.
198. Richards GR, Patel MV, Lloyd CR, Vanderpool CK Depletion of glycolytic intermediates plays a key role in glucose-phosphate stress in Escherichia coli. J Bacteriol 2013;195:4816-25.
199. Roberts EW, Cai F, Kerfeld CA, Cannon GC, Heinhorst S Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D. J Bacteriol 2012;194:787-95.
200. Robinson N, Robinson A Molecular Clocks Deamidation of Asparaginyl and Glutaminyl Residues in Peptides and Proteins 2004 Cave Junction, OR Althouse Press.
201. Rokney A, Shagan M, Kessel M, Smith Y, Rosenshine I, Oppenheim AB E. coli transports aggregated proteins to the poles by a specific and energy-dependent process. J Mol Biol 2009;392:589-601.
202. Romano S, Dittmar T, Bondarev V, Weber RJ, Viant MR, Schulz-Vogt HN Exo-Metabolome of Pseudovibrio sp. FOBEG1 Analyzed by Ultra-High Resolution Mass Spectrometry and the Effect of Phosphate Limitation. PLoS ONE 2014;9: e96038.
203. Ros R, Muñoz-Bertomeu J, Krueger S Serine in plants: biosynthesis, metabolism and functions. Trends in Plants Science 2014;19:564-9.
204. Rosen BP, Tamas MJ Arsenic transport in prokaryotes and eukaryotic microbes. Adv Exp Med Biol 2010;679:47-55.
205. Sampson EM, Bobik TA Microcompartments for B12-dependent 1, 2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. J Bacteriol 2008;190:2966-71.
206. Santarella-Mellwig R, Pruggnaller S, Roos N, Mattaj IW, Devos DP Three-dimensional reconstruction of bacteria with a complex endomembrane system. PLoS Biol 2013;11:e1001565.
207. Saraiva MA, Borges CM, Florencio MH Reactions of a modified lysine with aldehydic and diketonic dicarbonyl compounds: an electrospray mass spectrometry structure/activity study. J Mass Spectrom 2006;41:216-28.
208. Sauer U, Eikmanns BJ The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev 2005;29:765-94.
209. Schiffer P Condensed-matter physics: magnetic frustration squeezed out. Nature 2002;420:35-8.
210. Schmidt M Xenobiology: a new form of life as the ultimate biosafety tool. BioEssays 2010;32:322-31.
211. Schmitz G, Downs DM Reduced transaminase B (IlvE) activity caused by the lack of yjgF is dependent on the status of threonine deaminase (IlvA) in Salmonella enterica serovar Typhimurium. J Bacteriol 2004;186:803-10.
212. Schnackerz KD, Ehrlich JH, Giesemann W, Reed TA Mechanism of action of d-serine dehydratase. Identification of a transient intermediate. Biochemistry 1979;18:3557-63.
213. Schnell R, Oehlmann W, Singh M, Schneider G Structural insights into catalysis and inhibition of O-acetylserine sulfhydrylase from Mycobacterium tuberculosis. Crystal structures of the enzyme alpha-aminoacrylate intermediate and an enzyme-inhibitor complex. J Biol Chem 2007;282:23473-81.
214. Seebeck FP, Szostak JWRibosomal synthesis of dehydroalaninecontaining peptides. J Am Chem Soc 2006;128:7150-1.
215. Seibold G, Dempf S, Schreiner J, Eikmanns BJ Glycogen formation in Corynebacterium glutamicum and role of ADP-glucose pyrophosphorylase. Microbiology 2007;153:1275-85.
216. Sekowska A, Kung HF, Danchin A Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction. J Mol Microbiol Biotechnol 2000;2:145-77.
217. Serreli V, Lee CF, Kay ER, Leigh DA A molecular information ratchet. Nature 2007;445:523-7.
218. Sharif S, Powell DR, Schagen D, Steiner T, ToneyMD, Fogle E, Limbach HH X-ray crystallographic structures of enamine and amine Schiff bases of pyridoxal and its 1:1 hydrogen-bonded complexes with benzoic acid derivatives: evidence for coupled inter-and intramolecular proton transfer. Acta Crystallogr B 2006;62:480-7.
219. Sharon I, Alperovitch A, Rohwer F et al. Photosystem I gene cassettes are present in marine virus genomes. Nature 2009;461:258-62.
220. Shen P, Chao H, Jiang C, Long Z, Wang C, Wu B Enhancing production of l-serine by increasing the glyA gene expression in Methylobacterium sp. MB200. Appl Biochem Biotechnol 2010;160:740-50.
221. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 2000;407:81-6.
222. Shisler KA, Broderick JB Emerging themes in radical SAM chemistry. Curr Opin Struct Biol 2012;22:701-10.
223. Shomura Y, Higuchi Y Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases. J Biol Chem 2012;287: 28409-19.
224. Silva F, Queiroz JA, Domingues FC Evaluating metabolic stress and plasmid stability in plasmid DNA production by Escherichia coli. Biotechnol Adv 2012;30:691-708.
225. Silva-Rocha R, de Jong H, Tamames J, de Lorenzo V The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC Syst Biol 2011;5: 191.
226. Silver S, Wendt L Mechanism of action of phenethyl alcohol: breakdown of the cellular permeability barrier. J Bacteriol 1967;93:560-6.
227. Singh SP, Montgomery BL Determining cell shape: adaptive regulation of cyanobacterial cellular differentiation and morphology. Trends Microbiol 2011;19:278-85.
228. Sletten EM, Bertozzi CR Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009;48:6974-98.
229. Snell K Textbook error. The duality of pathways for serine biosynthesis is a fallacy. Trends Biochem Sci 1986;11:214-43.
230. Soini J, Falschlehner C, Liedert C, Bernhardt J, Vuoristo J, Neubauer P Norvaline is accumulated after a down-shift of oxygen in Escherichia coli W3110. Microb Cell Fact 2008;7:30.
231. Sommer MO, Church GM, Dantas G A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Mol Syst Biol 2010;6:360.
232. Srere PA Complexes of sequential metabolic enzymes. Annu Rev Biochem 1987;56:89-124.
233. Stephanopoulos G Synthetic biology and metabolic engineering. ACS Synth Biol 2012;1:514-25.
234. Stolz M, Peters-Wendisch P, Etterich H, Gerharz T, Faurie R, Sahm H, Fersterra H, Eggeling L Reduced folate supply as a key to enhanced l-serine production by Corynebacterium glutamicum. Appl Environ Microbiol 2007;73:750-5.
235. Surber MW, Maloy S The PutA protein of Salmonella typhimurium catalyzes the two steps of proline degradation via a leaky channel. Arch Biochem Biophys 1998;354:281-7.
236. Tamames J, Gil R, Latorre A, Pereto J, Silva FJ, Moya A The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol Biol 2007;7:181.
237. Tanaka S, Sawaya MR, Yeates TO Structure and mechanisms of a protein-based organelle in Escherichia coli. Science 2010;327:81-4.
238. Tchantchou F Homocysteine metabolism and various consequences of folate deficiency. J Alzheimers Dis 2006;9: 421-7.
239. Thomas G, Diefenbach R, Duggleby RG Inactivation of pyruvate decarboxylase by 3-hydroxypyruvate. Biochem J 1990;266:305-8.
240. Timm S, Florian A, Jahnke K, Nunes-Nesi A, Fernie AR, Bauwe H The hydroxypyruvate-reducing system in Arabidopsis: multiple enzymes for the same end. Plant Physiol 2011;155: 694-705.
241. Timmis KN, Steffan RJ, Unterman R Designing microorganisms for the treatment of toxic wastes. Annu Rev Microbiol 1994;48:525-57.
242. Tresguerres MEF, Ingledew WM, Canovas JL Potential competition for 5-dehydroshikimate between the aromatic biosynthetic route and the catabolic hydroaromatic pathway. Arch Mikrobiol 1972;82:111-9.
243. Tuval I, Cisneros L, Dombrowski C, Wolgemuth CW, Kessler JO, Goldstein RE Bacterial swimming and oxygen transport near contact lines. P Natl Acad Sci USA 2005;102: 2277-82.
244. Urbonavicius J, Jager G, Bjork GR Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity. Nucleic Acids Res 2007;35:3297-305.
245. Uzan M, Danchin A A rapid test for the relA mutation in E. coli. Biochem Biophys Res Commun 1976;69:751-8.
246. Uzan M, Danchin A Correlation between the serine sensitivity and the derepressibility of the ilv genes in Escherichia coli relAmutants. Mol Gen Genet 1978;165:21-30.
247. van Ham RC, Moya A, Latorre A Putative evolutionary origin of plasmids carrying the genes involved in leucine biosynthesis in Buchnera aphidicola (endosymbiont of aphids). J Bacteriol 1997;179:4768-77.
248. van Ham R, Martinez-Torres D, Moya A, Latorre A Plasmidencoded anthranilate synthase (TrpEG) in Buchnera aphidicola from aphids of the family pemphigidae. Appl Environ Microbiol 1999;65:117-25.
249. van Lanen SG, Shen B Advances in polyketide synthase structure and function. Curr Opin Drug Discov Devel 2008;11: 186-95.
250. van Leeuwen BN, van der Wulp AM, Duijnstee I, van Maris AJ, Straathof AJ Fermentative production of isobutene. Appl Microbiol Biotechnol 2012;93:1377-87.
251. van Schaftingen E, Rzem R, Marbaix A, Collard F, Veiga-da-Cunha M, Linster CL Metabolite proofreading, a neglected aspect of intermediary metabolism. J Inherit Metab Dis 2013;36:427-34.
252. Vangnai AS, Toyama H, De-Eknamkul W, Yoshihara N, Adachi O, Matsushita K Quinate oxidation in Gluconobacter oxydans IFO3244: purification and characterization of quinoprotein quinate dehydrogenase. FEMS Microbiol Lett 2004;241: 157-62.
253. Venditti V, Ghirlando R, Clore GM Structural basis for enzyme I inhibition by alpha-ketoglutarate. ACS Chem Biol 2013;8:1232-40.
254. Vetsigian K, Jajoo R, Kishony R Structure and evolution of Streptomyces interaction networks in soil and in silico. PLoS Biol 2011;9:e1001184.
255. Vrljic M, Sahm H, Eggeling L A new type of transporter with a newtype of cellular function: l-lysine export from Corynebacterium glutamicum. Mol Microbiol 1996;22:815-26.
256. Wachtershauser G On the chemistry and evolution of the pioneer organism. Chem Biodivers 2007;4:584-602.
257. Wang M, Yafremava LS, Caetano-Anolles D, Mittenthal JE, Caetano-Anolles G Reductive evolution of architectural repertoires in proteomes and the birth of the tripartiteworld. Genome Res 2007;17:1572-85.
258. Wang Y, Shaikh SA, Tajkhorshid E Exploring transmembrane diffusion pathways with molecular dynamics. Physiology 2010;25:142-54.
259. Wang M, Jiang YY, Kim KM, Qu G, Ji HF, Mittenthal JE, Zhang HY, Caetano-Anolles G A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol Biol Evol 2011;28:567-82.
260. Wang X, Montero Llopis P, Rudner DZ Bacillus subtilis chromosome organization oscillates between two distinct patterns. P Natl Acad Sci USA 2014;111:12877-82.
261. Watson JD Type 2 diabetes as a redox disease. Lancet 2014;383:841-3.
262. Weiss M Crowding, diffusion, and biochemical reactions. Int Rev Cell Mol Biol 2014;307:383-417.
263. Welch GR, Easterby JS Metabolic channeling versus free diffusion: transition-time analysis. Trends Biochem Sci 1994;19:193-7.
264. Westheimer FH Why nature chose phosphates. Science 1987;235:1173-8.
265. Windrem DA, Plachy WZ The diffusion-solubility of oxygen in lipid bilayers. Biochim Biophys Acta 1980;600: 655-65.
266. Woehl EU, Tai CH, Dunn MF, Cook PF Formation of the alpha-aminoacrylate immediate limits the overall reaction catalyzed by O-acetylserine sulfhydrylase. Biochemistry 1996;35:4776-83.
267. Wolfe AJ Physiologically relevant small phosphodonors link metabolism to signal transduction. Curr Opin Microbiol 2010;13:204-9.
268. Worthington AS, Burkart MD The old is new again: asparagine oxidation in calcium-dependent antibiotic biosynthesis. ACS Chem Biol 2007;2:152-4.
269. Wydau S, van der Rest G, Aubard C, Plateau P, Blanquet S Widespread distribution of cell defense against daminoacyl-tRNAs. J Biol Chem 2009;284:14096-104.
270. Xu Y, Tiago Guerra L, Li Z, LudwigM, Charles Dismukes G, Bryant DA Altered carbohydrate metabolism in glycogen synthase mutants of Synechococcus sp. strain PCC 7002: cell factories for soluble sugars. Metab Eng 2013;16:56-67.
271. Yadavalli SS, Ibba M Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 2012;86:1-43.
272. Yeates TO, Tsai Y, Tanaka S, Sawaya MR, Kerfeld CA Selfassembly in the carboxysome: a viral capsid-like protein shell in bacterial cells. Biochem Soc Trans 2007;35: 508-11.
273. Yim MB, Yim HS, Lee C, Kang SO, Chock PB Protein glycation: creation of catalytic sites for free radical generation. Ann NY Acad Sci 2001;928:48-53.
274. Yin X, Zabriskie TM The enduracidin biosynthetic gene cluster from Streptomyces fungicidicus. Microbiology 2006;152:2969-83.
275. You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang YP, Lenz P, Yan D, Hwa T Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature 2013;500:301-6.
276. Zettler J, Mootz HD Biochemical evidence for conformational changes in the cross-talk between adenylation and peptidylcarrier protein domains of nonribosomal peptide synthetases. FEBS J 2010;277:1159-71.
277. Zhan J Biosynthesis of bacterial aromatic polyketides. Curr Top Med Chem 2009;9:1598-610.
278. Zhang XH, Weissbach H Origin and evolution of the proteinrepairing enzymes methionine sulphoxide reductases. Biol Rev Camb Philos Soc 2008;83:249-57.
279. Zhao L, Hoi SC, Wong L, Hamp T, Li J Structural and functional analysis of multi-interface domains. PLoS ONE 2012;7:e50821.
280. Zheng L, White RH, Cash VL, Dean DR Mechanism for the desulfurization of l-cysteine catalyzed by the nifS gene product. Biochemistry 1994;33:4714-20.