Structural and functional analyses of a saturated acyl ACP thioesterase, type B from immature seed tissue of Jatropha curcas

Plant Biology

Volumn 13, Issue 3, 2011, Pages 453-461

  Srikanta Dani, K G ^a,b   Hatti, K S ^a   Ravikumar, P ^a   Kush, A ^a  

^a JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH   (India)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Biofuel; Docking; Fatty acyl ACP thioesterase B; Molecular dynamics; Molecular modelling

Indexed keywords

COMPLEMENTARY DNA; OLEOYL (ACYL CARRIER PROTEIN) HYDROLASE; OLEOYL-(ACYL-CARRIER-PROTEIN) HYDROLASE; PALMITIC ACID; PLANT DNA; STEARIC ACID; STEARIC ACID DERIVATIVE; THIOL ESTER HYDROLASE;

BACTERIUM; BIOFUEL; CHLOROPLAST; COLIFORM BACTERIUM; DICOTYLEDON; ENZYME ACTIVITY; FATTY ACID; GENE EXPRESSION; GENETIC ANALYSIS; LIPID; MEMBRANE; MOLECULAR ANALYSIS; MUTATION; NUMERICAL MODEL; PEPTIDE; PROTEIN; SATURATION; SEED;

AMINO ACID SEQUENCE; ARTICLE; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; CHLOROPLAST; ENZYME SPECIFICITY; ENZYMOLOGY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; JATROPHA; METABOLISM; MOLECULAR GENETICS; PLANT SEED;

AMINO ACID SEQUENCE; CHLOROPLASTS; DNA, COMPLEMENTARY; DNA, PLANT; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, PLANT; JATROPHA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PALMITIC ACID; SEEDS; STEARIC ACIDS; SUBSTRATE SPECIFICITY; THIOLESTER HYDROLASES;

BACTERIA (MICROORGANISMS); JATROPHA; JATROPHA CURCAS;

EID: 79954465584     PISSN: 14358603     EISSN: 14388677     Source Type: Journal    
DOI: 10.1111/j.1438-8677.2010.00410.x     Document Type: Article

References (46)

1. Agne B., Kessler F. (2009) Protein transport in organelles: the Toc complex way of preprotein import. FEBS Journal, 276, 1156-1165.
2. Anandakrishnan R., Onufriev A. (2008) Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules. Journal of Computational Biology, 15, 165-184.
3. Bruce B.D. (2000) Chloroplast transit peptides: structure, function and evolution. Trends in Cell Biology, 10, 440-447.
4. Chu H., Zheng Q., Zhao Y., Zhang H. (2009) Homology modeling and molecular dynamics study on N-acetylneuraminate lyase. Journal of Molecular Modeling, 15, 323-328.
5. Comeau S.R., Gatchell D.W., Vajda S., Camacho C.J. (2004) ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research, 32, W96-W99.
6. Dehesh K., Jones A., Knutzon D.S., Voelkar T.A. (1996) Production of high levels of 8:0 and 10:0 fatty acids in transgenic canola by over-expression of ChFATB2, a thioesterase cDNA from Cuphea hookeriana. The Plant Journal, 9, 167-192.
7. Dörmann P., Voelker T.A., Ohlrogge J.B. (1995) Cloning and expression in Escherichia coli of a novel thioesterase from Arabidopsis thaliana specific for long-chain acyl-acyl carrier proteins. Archives of Biochemistry and Biophysics, 316, 612-618.
8. Dörmann P., Voelkar T.A., Ohlrogge J.B. (2000) Accumulation of palmitate in Arabidopsis mediated by the acyl-acyl carrier protein thioesterase FATB1. Plant Physiology, 123, 637-643.
9. Dunbrack R.L. Jr (2002) Rotamer libraries in the 21st century. Current Opinion in Structural Biology, 12, 431-440.
10. Durrett T.P., Benning C., Ohlrogge J. (2008) Plant triacylglycerols as feed stocks for the production of biofuels. The Plant Journal, 54, 593-607.
11. Emanuelsson O., Nielsen H., von Heijne G. (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Science, 8, 978-984.
12. Emanuelsson O., Brunak S., von Heijne G., Nielsen H. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protocols, 2, 953-971.
13. Facciotti M.T., Yuan L. (1998) Molecular dissection of the plant acyl-acyl carrier protein thioesterases. Lipid-Fett, 100, 167-172.
14. Ghosh S.K., Bhattacharjee A., Jha J.K., Mondal A.K., Maiti M.K., Basu A., Ghosh D., Ghosh S., Sen S.K. (2007) Characterization and cloning of a stearoyl/oleoyl specific fatty acyl-acyl carrier protein thioesterase from the seeds of Madhuca longifolia (latifolia). Plant Physiology and Biochemistry, 45, 887-897.
15. Gordon J.C., Myers J.B., Folta T., Shoja V., Heath L.S., Onufriev A. (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research, 33, W368-W371.
16. Hawkins D.J., Kridl J. (1998) Characterization of acyl-ACP thioesterases of mangosteen (Garcinia mangostana) seed and high levels of stearate production in transgenic canola. The Plant Journal, 13, 743-752.
17. von Heijne G. (1992) Membrane protein structure prediction, hydrophobicity analysis and the positive-inside rule. Journal of Molecular Biology, 225, 487-494.
18. Hess B., Kutzner C., van der Spoel D., Lindahl E. (2008) GROMACS4: algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Journal of Chemical Theory and Computation, 4, 435-447.
19. Jones A., Davies H.M., Voelkar T.A. (1995) Palmitoyl-acyl carrier protein (ACP) Thioesterase and the evolutionary-origin of plant acyl-ACP thioesterases. The Plant Cell, 7, 359-371.
20. Koo A.J.K., Ohlrogge J.B., Pollard M. (2004) On the export of fatty acids from the chloroplast. Journal of Biological Chemistry, 279, 16101-16110.
21. Lang P.T., Brozell S.R., Mukherjee S., Pettersen E.F., Meng E.C., Thomas V., Rizzo R., Case D.A., James T.L., Kuntz I.D. (2009) DOCK 6: combining techniques to model RNA-small molecule complexes. RNA, 15, 1219-1230.
22. Lee D.W., Lee S., Lee J., Lee K.H., Kim S., Cheong W., Hwang I. (2006) Functional characterization of sequence motifs in the transit peptide of Arabidopsis small subunit of Rubisco. Plant Physiology, 140, 466-483.
23. Lee D.W., Kim J.K., Lee S., Choi S., Kim S., Hwang I. (2008) Arabidopsis nuclear-encoded plastid transit peptides contain multiple sequence subgroups with distinctive chloroplast-targeting sequence motifs. The Plant Cell, 20, 1603-1622.
24. Li M., Schnell D.J. (2006) Reconstitution of protein targeting to the inner envelop membrane of chloroplasts. Journal of Cell Biology, 175, 249-259.
25. Li Y., Beisson F., Pollard M., Ohlrogge J. (2006) Oil content of Arabidopsis seeds: the influence of seed anatomy, light and plant-to-plant variation. Phytochemistry, 67, 904-915.
26. Lu Z., Vora H., Khosla C. (2008) Overproduction of free fatty acids in E. coli: implications for biodiesel production. Metabolic Engineering, 10, 333-339.
27. Lubeck J., Heins L., Soll J. (1997) A nuclear-coded chloroplastic inner envelope membrane protein uses a soluble sorting intermediate upon import into the organelle. Journal of Cell Biology, 137, 1279-1286.
28. Mayer K.M., Shanklin J. (2005) A structural model of the plant acyl-acyl carrier protein thioesterase FatB comprises two helix/4-stranded sheet domains, the N-terminal domain containing residues that affect specificity and the C-terminal domain containing catalytic residues. Journal of Biological Chemistry, 280, 3621-3627.
29. Mayer K.M., Shanklin J. (2007) Identification of amino acid residues involved in substrate specificity of plant acyl-ACP thioesterases using a bioinformatics-guided approach. BMC Plant Biology, 7, 1.
30. Ohlrogge J., Browse J. (1995) Lipid Biosynthesis. The Plant Cell, 7, 957-970.
31. Ohlrogge J.B., Kuhn D.N., Stumpf P.K. (1979) Subcellular localization of acyl carrier protein in leaf protoplasts of Spinacia oleracea. Proceedings of the National Academy of Sciences USA, 76, 1194-1198.
32. Pilon M., Wienk H., Sips W., Swaaf M., Talboom I., v'Hof R., Korte-Kool G.D., Demel R., Weisbeek P., Kruijff B.D. (1995) Functional domains of the ferredoxin transit sequence involved in chloroplast import. Journal of Biological Chemistry, 270, 3882-3893.
33. Reyes-Prieto A., Bhattacharya D. (2007) Phylogeny of nuclear-encoded plastid-targeted proteins supports an early divergence of glaucophytes within plantae. Molecular Biology and Evolution, 24, 2358-2361.
34. Roujeinikova A., Baldock C., Simon W.J., Gilroy J., Baker P.J., Stuitje A.R. (2002) X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site. Structure, 10, 825-835.
35. Roy A., Kucukural A., Zhang Y. (2010) I-TASSER: a unified platform for automated protein structure and functional prediction. Nature Protocols, 5, 725-738.
36. Salas J.J., Ohlrogge J.B. (2002) Characterization of substrate specificity of plant FatA and FatB acyl-ACP thioesterases. Archives of Biochemistry and Biophysics, 403, 25-34.
37. Sánchez-García A., Moreno-Pérez A.J., Muro-Pastor A.M., Salas J.J., Garcés R., Martínez-Force E. (2010) Acyl-ACP thioesterases from castor (Ricinus communis L.): an enzymatic system appropriate for high rates of oil synthesis and accumulation. Phytochemistry, 71, 860-869.
38. Serrano-Vega M.J., Venegas-Caleron M., Garcés R., Martinez-Force E. (2003) Cloning and expression of fatty acid biosynthesis key enzymes from sunflower Helianthus annuus in Escherichia coli. Journal of Chromatography B, 786, 221-228.
39. Shine W.E., Mancha M., Stumpf P.K. (1976) Fat metabolism in higher plants: the function of acyl thioesterases in the metabolism of Acyl-coenzymes A and acyl-Acyl Carrier Proteins. Archives of Biochemistry and Biophysics, 172, 110-116.
40. Somerville C., Browse J., Ohlrogge J. (2004) Lipids. In: Buchanan B.B., Gruissem W., Jones R.L. (Eds), Biochemistry and molecular biology of plants. American Society of Plant Physiologists, Rockville, MD, pp 456-526.
41. Spoel D.V.D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J.C. (2005) GROMACS: fast, flexible, and free. Journal of Computational Chemistry, 26, 1701-1718.
42. Voelker T.A., Davies H.M. (1994) Alteration of the specificity and regulation of fatty acid synthesis of Escherichia coli by expression of a plant medium-chain acyl-acyl carrier protein thioesterase. Journal of Bacteriology, 176, 7320-7327.
43. Wang J., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. (2004) Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157-1174.
44. Wu P.Z., Li J., Wei Q., Zeng L., Chen P., Li M., Jiang H., Wu G. (2009) Cloning and functional characterization of an acyl-acyl carrier protein thioesterase (JcFATB1) from Jatropha curcas. Tree Physiology, 29, 1299-1305.
45. Zhang Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40.
46. Zornetzer G.A., Fox B.G., Markley J.L. (2006) Solution structures of spinach Acyl Carrier Protein with decanoate and stearate. Biochemistry, 45, 5217-5227.