Revealing the functions of the transketolase enzyme isoforms in rhodopseudomonas palustris using a systems biology approach

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Hu, Chia Wei ^a   Chang, Ya Ling ^a   Chen, Shiang Jiuun ^a   Kuo Huang, Ling Long ^a   Liao, James C ^b   Huang, Hsuan Cheng ^c   Juan, Hsueh Fen ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL YANG MING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; TRANSKETOLASE; TRANSKETOLASE I; TRANSKETOLASE II; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; ISOENZYME; PHOSPHOENOLPYRUVATE CARBOXYKINASE (ATP);

AMINO ACID TRANSPORT; ARTICLE; AUTOTROPH; BACTERIAL GROWTH; BIOMASS PRODUCTION; CARBOHYDRATE TRANSPORT; CARBON DIOXIDE FIXATION; CARBON METABOLISM; CELLULAR DISTRIBUTION; CONTROLLED STUDY; CYTOPLASM; ENZYME ACTIVITY; ENZYME LOCALIZATION; GLYCOLYSIS; IMMUNOGOLD STAINING; MICROARRAY ANALYSIS; NONHUMAN; NUCLEIC ACID SYNTHESIS; PROTEIN EXPRESSION; PROTEIN FOLDING; REAL TIME POLYMERASE CHAIN REACTION; RHODOPSEUDOMONAS PALUSTRIS; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION; AUTOTROPHY; CELL FRACTIONATION; ENZYMOLOGY; GROWTH, DEVELOPMENT AND AGING; LIGHT; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT; RADIATION EXPOSURE; RHODOPSEUDOMONAS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

AUTOTROPHIC PROCESSES; BACTERIAL PROTEINS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ISOENZYMES; LIGHT; PHOSPHOENOLPYRUVATE CARBOXYKINASE (ATP); PROTEIN BINDING; PROTEIN INTERACTION MAPS; PROTEIN TRANSPORT; RHODOPSEUDOMONAS; SUBCELLULAR FRACTIONS; SYSTEMS BIOLOGY; TRANSKETOLASE;

EID: 82955187876     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028329     Document Type: Article

References (74)

1. Westerhoff HV, Palsson BO, (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22: 1249-1252.
2. Le Naour F, Hohenkirk L, Grolleau A, Misek DE, Lescure P, et al. (2001) Profiling changes in gene expression during differentiation and maturation of monocyte-derived dendritic cells using both oligonucleotide microarrays and proteomics. J Biol Chem 276: 17920-17931.
3. Hanash SM, Bobek MP, Rickman DS, Williams T, Rouillard JM, et al. (2002) Integrating cancer genomics and proteomics in the post-genome era. Proteomics 2: 69-75.
4. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, et al. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934.
5. Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, et al. (2001) An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res 29: E41-41.
6. Huang TC, Chang HY, Hsu CH, Kuo WH, Chang KJ, et al. (2008) Targeting therapy for breast carcinoma by ATP synthase inhibitor aurovertin B. J Proteome Res 7: 1433-1444.
7. Barbosa MJ, Rocha JM, Tramper J, Wijffels RH, (2001) Acetate as a carbon source for hydrogen production by photosynthetic bacteria. J Biotechnol 85: 25-33.
8. Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, et al. (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 22: 55-61.
9. Sasikala C, Ramana CV, (1998) Biodegradation and metabolism of unusual carbon compounds by anoxygenic phototrophic bacteria. Adv Microb Physiol 39: 339-377.
10. Wall JD, (2004) Rain or shine-a phototroph that delivers. Nat Biotechnol 22: 40-41.
11. Zhang B, VerBerkmoes NC, Langston MA, Uberbacher E, Hettich RL, et al. (2006) Detecting differential and correlated protein expression in label-free shotgun proteomics. J Proteome Res 5: 2909-2918.
12. McKinlay JB, Harwood CS, (2010) Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria. Proc Natl Acad Sci U S A 107: 11669-11675.
13. Paoli GC, Vichivanives P, Tabita FR, (1998) Physiological control and regulation of the Rhodobacter capsulatus cbb operons. J Bacteriol 180: 4258-4269.
14. Romagnoli S, Tabita FR, (2006) A novel three-protein two-component system provides a regulatory twist on an established circuit to modulate expression of the cbbI region of Rhodopseudomonas palustris CGA010. J Bacteriol 188: 2780-2791.
15. Gibson JL, Tabita FR, (1996) The molecular regulation of the reductive pentose phosphate pathway in Proteobacteria and Cyanobacteria. Arch Microbiol 166: 141-150.
16. Badger MR, Bek EJ, (2008) Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J Exp Bot 59: 1525-1541.
17. Laguna R, Joshi GS, Dangel AW, Luther AK, Tabita FR, (2010) Integrative control of carbon, nitrogen, hydrogen, and sulfur metabolism: the central role of the Calvin-Benson-Bassham cycle. Adv Exp Med Biol 675: 265-271.
18. Laguna R, Tabita FR, Alber BE, (2011) Acetate-dependent photoheterotrophic growth and the differential requirement for the Calvin-Benson-Bassham reductive pentose phosphate cycle in Rhodobacter sphaeroides and Rhodopseudomonas palustris. Arch Microbiol 193: 151-154.
19. Joshi GS, Romagnoli S, Verberkmoes NC, Hettich RL, Pelletier D, et al. (2009) Differential accumulation of form I RubisCO in Rhodopseudomonas palustris CGA010 under photoheterotrophic growth conditions with reduced carbon sources. J Bacteriol 191: 4243-4250.
20. Ma W, Wei L, Wang Q, Shi D, Chen H, (2008) Increased activity of the tandem fructose-1,6-bisphosphate aldolase, triosephosphate isomerase and fructose-1,6-bisphosphatase enzymes in Anabaena sp. strain PCC 7120 stimulates photosynthetic yield. Journal of Applied Phycology 20: 437-443.
21. Miyagawa Y, Tamoi M, Shigeoka S, (2001) Overexpression of a cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase in tobacco enhances photosynthesis and growth. Nat Biotechnol 19: 965-969.
22. Ma W, Shi D, Wang Q, Wei L, Chen H, (2005) Exogenous expression of the wheat chloroplastic fructose-1,6-bisphosphatase gene enhances photosynthesis in the transgenic cyanobacterium, Anabaena sp. PCC7120. Journal of Applied Phycology 17: 273-280.
23. Jung YM, Lee JN, Shin HD, Lee YH, (2004) Role of tktA gene in pentose phosphate pathway on odd-ball biosynthesis of poly-beta-hydroxybutyrate in transformant Escherichia coli harboring phbCAB operon. J Biosci Bioeng 98: 224-227.
24. Schenk G, Duggleby RG, Nixon PF, (1998) Properties and functions of the thiamin diphosphate dependent enzyme transketolase. Int J Biochem Cell Biol 30: 1297-1318.
25. Bublitz C, Steavenson S, (1988) The pentose phosphate pathway in the endoplasmic reticulum. J Biol Chem 263: 12849-12853.
26. Teige M, Melzer M, Suss KH, (1998) Purification, properties and in situ localization of the amphibolic enzymes D-ribulose 5-phosphate 3-epimerase and transketolase from spinach chloroplasts. Eur J Biochem 252: 237-244.
27. Veitch NJ, Maugeri DA, Cazzulo JJ, Lindqvist Y, Barrett MP, (2004) Transketolase from Leishmania mexicana has a dual subcellular localization. Biochem J 382: 759-767.
28. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, et al. (1995) Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166: 175-176.
29. Bowien B, Kusian B, (2002) Genetics and control of CO(2) assimilation in the chemoautotroph Ralstonia eutropha. Arch Microbiol 178: 85-93.
30. Chinnasamy S, Ramakrishnan B, Bhatnagar A, Das KC, (2009) Biomass production potential of a wastewater alga Chlorella vulgaris ARC 1 under elevated levels of CO(2) and temperature. Int J Mol Sci 10: 518-532.
31. Carlozzi P, Buccioni A, Minieri S, Pushparaj B, Piccardi R, et al. (2010) Production of bio-fuels (hydrogen and lipids) through a photofermentation process. Bioresour Technol 101: 3115-3120.
32. Li M, Noll S, Beatty JT, (2010) Bacteriophytochrome-dependent regulation of light-harvesting complexes in Rhodopseudomonas palustris anaerobic cultures. Curr Microbiol 61: 429-434.
33. Jaubert M, Zappa S, Fardoux J, Adriano JM, Hannibal L, et al. (2004) Light and redox control of photosynthesis gene expression in Bradyrhizobium: dual roles of two PpsR. J Biol Chem 279: 44407-44416.
34. Tam R, Saier MH Jr, (1993) Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev 57: 320-346.
35. Walshaw DL, Poole PS, (1996) The general L-amino acid permease of Rhizobium leguminosarum is an ABC uptake system that also influences efflux of solutes. Mol Microbiol 21: 1239-1252.
36. Walshaw DL, Reid CJ, Poole PS, (1997) The general amino acid permease of Rhizobium leguminosarum strain 3841 is negatively regulated by the Ntr system. FEMS Microbiol Lett 152: 57-64.
37. Kamada N, Yasuhara A, Takano Y, Nakano T, Ikeda M, (2001) Effect of transketolase modifications on carbon flow to the purine-nucleotide pathway in Corynebacterium ammoniagenes. Appl Microbiol Biotechnol 56: 710-717.
38. Hara KY, Mori H, (2006) An efficient method for quantitative determination of cellular ATP synthetic activity. J Biomol Screen 11: 310-317.
39. Hara KY, Shimodate N, Ito M, Baba T, Mori H, (2009) Systematic genome-wide scanning for genes involved in ATP generation in Escherichia coli. Metab Eng 11: 1-7.
40. Inui M, Dumay V, Zahn K, Yamagata H, Yukawa H, (1997) Structural and functional analysis of the phosphoenolpyruvate carboxylase gene from the purple nonsulfur bacterium Rhodopseudomonas palustris No. 7. J Bacteriol 179: 4942-4945.
41. Sprenger GA, (1995) Genetics of pentose-phosphate pathway enzymes of Escherichia coli K-12. Arch Microbiol 164: 324-330.
42. Leegood RC, Walker RP, (2003) Regulation and roles of phosphoenolpyruvate carboxykinase in plants. Arch Biochem Biophys 414: 204-210.
43. Kim P, Laivenieks M, Vieille C, Zeikus JG, (2004) Effect of overexpression of Actinobacillus succinogenes phosphoenolpyruvate carboxykinase on succinate production in Escherichia coli. Appl Environ Microbiol 70: 1238-1241.
44. Henkes S, Sonnewald U, Badur R, Flachmann R, Stitt M, (2001) A small decrease of plastid transketolase activity in antisense tobacco transformants has dramatic effects on photosynthesis and phenylpropanoid metabolism. Plant Cell 13: 535-551.
45. Schocke L, Weimer PJ, (1997) Purification and characterization of phosphoenolpyruvate carboxykinase from the anaerobic ruminal bacterium Ruminococcus flavefaciens. Arch Microbiol 167: 289-294.
46. Yakandawala N, Romeo T, Friesen AD, Madhyastha S, (2008) Metabolic engineering of Escherichia coli to enhance phenylalanine production. Appl Microbiol Biotechnol 78: 283-291.
47. Hosie AH, Allaway D, Jones MA, Walshaw DL, Johnston AW, et al. (2001) Solute-binding protein-dependent ABC transporters are responsible for solute efflux in addition to solute uptake. Mol Microbiol 40: 1449-1459.
48. Seth A, Connell ND, (2000) Amino acid transport and metabolism in mycobacteria: cloning, interruption, and characterization of an L-Arginine/gamma-aminobutyric acid permease in Mycobacterium bovis BCG. J Bacteriol 182: 919-927.
49. Shruthi H, Babu MM, Sankaran K, (2010) TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes. J Mol Evol 70: 359-370.
50. Lu Y, Wu YR, Han B, (2005) Anaerobic induction of isocitrate lyase and malate synthase in submerged rice seedlings indicates the important metabolic role of the glyoxylate cycle. Acta Biochim Biophys Sin (Shanghai) 37: 406-414.
51. Garcia B, Olivera ER, Minambres B, Fernandez-Valverde M, Canedo LM, et al. (1999) Novel biodegradable aromatic plastics from a bacterial source. Genetic and biochemical studies on a route of the phenylacetyl-coa catabolon. J Biol Chem 274: 29228-29241.
52. Crosby HA, Heiniger EK, Harwood CS, Escalante-Semerena JC, (2010) Reversible N epsilon-lysine acetylation regulates the activity of acyl-CoA synthetases involved in anaerobic benzoate catabolism in Rhodopseudomonas palustris. Mol Microbiol 76: 874-888.
53. Horwich AL, Fenton WA, Chapman E, Farr GW, (2007) Two families of chaperonin: physiology and mechanism. Annu Rev Cell Dev Biol 23: 115-145.
54. Lin Z, Madan D, Rye HS, (2008) GroEL stimulates protein folding through forced unfolding. Nat Struct Mol Biol 15: 303-311.
55. Ellis RJ, (2005) Chaperomics: in vivo GroEL function defined. Curr Biol 15: R661-663.
56. Tang YC, Chang HC, Chakraborty K, Hartl FU, Hayer-Hartl M, (2008) Essential role of the chaperonin folding compartment in vivo. EMBO J 27: 1458-1468.
57. Goloubinoff P, Christeller JT, Gatenby AA, Lorimer GH, (1989) Reconstitution of active dimeric ribulose bisphosphate carboxylase from an unfoleded state depends on two chaperonin proteins and Mg-ATP. Nature 342: 884-889.
58. Goloubinoff P, Gatenby AA, Lorimer GH, (1989) GroE heat-shock proteins promote assembly of foreign prokaryotic ribulose bisphosphate carboxylase oligomers in Escherichia coli. Nature 337: 44-47.
59. Wang X, Tabita FR, (1992) Interaction of inactivated and active ribulose 1,5-bisphosphate carboxylase/oxygenase of Rhodobacter sphaeroides with nucleotides and the chaperonin 60 (GroEL) protein. J Bacteriol 174: 3607-3611.
60. Liu C, Young AL, Starling-Windhof A, Bracher A, Saschenbrecker S, et al. (2010) Coupled chaperone action in folding and assembly of hexadecameric Rubisco. Nature 463: 197-202.
61. Tabita FR, (2007) Rubisco: the enzyme that keeps on giving. Cell 129: 1039-1040.
62. Mukhopadhyay B, Johnson EF, Ascano M Jr, (1999) Conditions for vigorous growth on sulfide and reactor-scale cultivation protocols for the thermophilic green sulfur bacterium Chlorobium tepidum. Appl Environ Microbiol 65: 301-306.
63. Dispensa M, Thomas CT, Kim MK, Perrotta JA, Gibson J, et al. (1992) Anaerobic growth of Rhodopseudomonas palustris on 4-hydroxybenzoate is dependent on AadR, a member of the cyclic AMP receptor protein family of transcriptional regulators. J Bacteriol 174: 5803-5813.
64. Simon R, Priefer U, Puhler A, (1983) A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Nat Biotech 1: 784-791.
65. Lynch HC, Bushell ME, (1995) The physiology of erythromycin biosynthesis in cyclic fed batch culture. Microbiology 141 (Pt 12): 3105-3111.
66. Faucher SP, Porwollik S, Dozois CM, McClelland M, Daigle F, (2006) Transcriptome of Salmonella enterica serovar Typhi within macrophages revealed through the selective capture of transcribed sequences. Proc Natl Acad Sci U S A 103: 1906-1911.
67. Nicolas MT, Bassot JM, Nicolas G, (1989) Immunogold labeling of luciferase in the luminous bacterium Vibrio harveyi after fast-freeze fixation and different freeze-substitution and embedding procedures. J Histochem Cytochem 37: 663-674.
68. Gralnick JA, Vali H, Lies DP, Newman DK, (2006) Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1. Proc Natl Acad Sci U S A 103: 4669-4674.
69. Juan HF, Wang IH, Huang TC, Li JJ, Chen ST, et al. (2006) Proteomics analysis of a novel compound: cyclic RGD in breast carcinoma cell line MCF-7. Proteomics 6: 2991-3000.
70. Snel B, Lehmann G, Bork P, Huynen MA, (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res 28: 3442-3444.
71. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
72. Enright AJ, Van Dongen S, Ouzounis CA, (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584.
73. Dongen SMv, (2000) Graph clustering by flow simulation. PhD Thesis, University of Utrecht, The Netherlands.
74. Kwon YD, Kwon OH, Lee HS, Kim P, (2007) The effect of NADP-dependent malic enzyme expression and anaerobic C4 metabolism in Escherichia coli compared with other anaplerotic enzymes. J Appl Microbiol 103: 2340-2345.