The PduL phosphotransacylase is used to recycle coenzyme A within the Pdu microcompartment

Journal of Bacteriology

Volumn 197, Issue 14, 2015, Pages 2392-2399

  Liu, Yu ^a   Jorda, Julien ^b   Yeates, Todd O ^b   Bobik, Thomas A ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL ENZYME; COENZYME A; GREEN FLUORESCENT PROTEIN; PDUL PHOSPHOTRANSACYLASE; PROPYLENE GLYCOL; UNCLASSIFIED DRUG; ENHANCED GREEN FLUORESCENT PROTEIN; PHOSPHATE ACETYLTRANSFERASE;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GROWTH; BACTERIAL MICROCOMPARTMENT; BACTERIAL STRUCTURES; BIOTECHNOLOGY; CONTROLLED STUDY; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; SALMONELLA ENTERICA; SEQUENCE ANALYSIS; WESTERN BLOTTING; AMINO ACID SEQUENCE; CELL ORGANELLE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; MOLECULAR MODEL; PHYSIOLOGY; PROTEIN CONFORMATION;

BACTERIA (MICROORGANISMS); SALMONELLA ENTERICA;

AMINO ACID SEQUENCE; COENZYME A; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GREEN FLUORESCENT PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; ORGANELLES; PHOSPHATE ACETYLTRANSFERASE; PROPYLENE GLYCOL; PROTEIN CONFORMATION; SALMONELLA ENTERICA;

EID: 84932090530     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00056-15     Document Type: Article

References (49)

1. Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA. 2014. Diverse bacterial microcompartment organelles. Microbiol Mol Biol Rev 78:438-468. http://dx.doi.org/10.1128/MMBR.00009-14.
2. 2 fixation in cyanobacteria and some proteobacteria. Microbiol Mol Biol Rev 77:357-379. http://dx.doi.org/10.1128/MMBR.00061-12.
3. Abdul-Rahman F, Petit E, Blanchard JL. 2013. The distribution of polyhedral bacterial microcompartments suggests frequent horizontal transfer and operon reassembly. J Phylogen Evolution Biol 1:1000118. http://dx.doi.org/10.4172/2329-9002.1000118.
4. Axen SD, Erbilgin O, Kerfeld CA. 2014. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 10:e1003898. http://dx.doi.org/10.1371/journal.pcbi.1003898.
5. Jorda J, Lopez D, Wheatley NM, Yeates TO. 2013. Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria. Protein Sci 22:179-195. http://dx.doi.org/10.1002/pro.2196.
6. Shively JM, Ball F, Brown DH, Saunders RE. 1973. Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus. Science 182:584-586. http://dx.doi.org/10.1126/science.182.4112.584.
7. 12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2. J Bacteriol 184:1253-1261. http://dx.doi.org/10.1128/JB.184.5.1253-1261.2002.
8. Penrod JT, Roth JR. 2006. Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol 188:2865-2874. http://dx.doi.org/10.1128/JB.188.8.2865-2874.2006.
9. Buchrieser C, Rusniok C, Kunst F, Cossart P, Glaser P. 2003. Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: clues for evolution and pathogenicity. FEMS Immunol Med Microbiol 35:207-213. http://dx.doi.org/10.1016/S0928-8244(02)00448-0.
10. Conner CP, Heithoff DM, Julio SM, Sinsheimer RL, Mahan MJ. 1998. Differential patterns of acquired virulence genes distinguish Salmonella strains. Proc Natl Acad Sci USA 95:4641-4645. http://dx.doi.org/10.1073/pnas.95.8.4641.
11. Heithoff DM, Conner CP, Hentschel U, Govantes F, Hanna PC, Mahan MJ. 1999. Coordinate intracellular expression of Salmonella genes induced during infection. J Bacteriol 181:799-807.
12. Joseph B, Przybilla K, Stuhler C, Schauer K, Slaghuis J, Fuchs TM, Goebel W. 2006. Identification of Listeria monocytogenes genes contributing to intracellular replication by expression profiling and mutant screening. J Bacteriol 188:556-568. http://dx.doi.org/10.1128/JB.188.2.556-568.2006.
13. 12-dependent anaerobic growth of Salmonella enterica serovar Typhimurium on ethanolamine or 1,2-propanediol. J Bacteriol 183:2463-2475. http://dx.doi.org/10.1128/JB.183.8.2463-2475.2001.
14. Thiennimitr P, Winter SE, Winter MG, Xavier MN, Tolstikov V, Huseby DL, Sterzenbach T, Tsolis RM, Roth JR, Baumler AJ. 2011. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc Natl Acad Sci USA 108:17480-17485. http://dx.doi.org/10.1073/pnas.1107857108.
15. Winter SE, Thiennimitr P, Winter MG, Butler BP, Huseby DL, Crawford RW, Russell JM, Bevins CL, Adams LG, Tsolis RM, Roth JR, Baumler AJ. 2010. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467:426-429. http://dx.doi.org/10.1038/nature09415.
16. 12-dependent 1,2-propanediol degradation by Salmonella. J Bacteriol 193: 1385-1392. http://dx.doi.org/10.1128/JB.01473-10.
17. 12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2. J Bacteriol 185:5086-5095. http://dx.doi.org/10.1128/JB.185.17.5086-5095.2003.
18. 12-dependent 1,2-propanediol degradation by Salmonella enterica. J Bacteriol 194:1912-1918. http://dx.doi.org/10.1128/JB.06529-11.
19. Bobik TA, Xu Y, Jeter RM, Otto KE, Roth JR. 1997. Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes for the propanediol dehydratase. J Bacteriol 179:6633-6639.
20. Cheng S, Fan C, Sinha S, Bobik TA. 2012. The PduQ enzyme is an alcohol dehydrogenase used to recycle NAD+ internally within the Pdu microcompartment of Salmonella enterica. PLoS One 7:e47144. http://dx.doi.org/10.1371/journal.pone.0047144.
21. 12-dependent 1,2-propanediol degradation by Salmonella enterica serovar Typhimurium LT2. Arch Microbiol 180:353-361. http://dx.doi.org/10.1007/s00203-003-0601-0.
22. 12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. J Bacteriol 190:2966-2971. http://dx.doi.org/10.1128/JB.01925-07.
23. Palacios S, Starai VJ, Escalante-Semerena JC. 2003. Propionyl coenzyme A is a common intermediate in the 1,2-propanediol and propionate catabolic pathways needed for expression of the prpBCDE operon during growth of Salmonella enterica on 1,2-propanediol. J Bacteriol 185:2802-2810. http://dx.doi.org/10.1128/JB.185.9.2802-2810.2003.
24. Stojiljkovic I, Baeumler AJ, Heffron F. 1995. Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster. J Bacteriol 177:1357-1366.
25. Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, Yeates TO, Bobik TA. 2010. Short N-terminal sequences package proteins into bacterial microcompartments. Proc Natl Acad Sci USA 107:7509-7514. http://dx.doi.org/10.1073/pnas.0913199107.
26. Choudhary S, Quin MB, Sanders MA, Johnson ET, Schmidt-Dannert C. 2012. Engineered protein nano-compartments for targeted enzyme localization. PLoS One 7:e33342. http://dx.doi.org/10.1371/journal.pone.0033342.
27. Fan C, Bobik TA. 2011. The N-terminal region of the medium subunit (PduD) packages adenosylcobalamin-dependent diol dehydratase (PduCDE) into the Pdu microcompartment. J Bacteriol 193:5623-5628. http://dx.doi.org/10.1128/JB.05661-11.
28. Huseby DL, Roth JR. 2013. Evidence that a metabolic microcompartment contains and recycles private cofactor pools. J Bacteriol 195:2864-2879. http://dx.doi.org/10.1128/JB.02179-12.
29. Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO. 2005. Protein structures forming the shell of primitive bacterial organelles. Science 309:936-938. http://dx.doi.org/10.1126/science.1113397.
30. Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO. 2008. Atomic-level models of the bacterial carboxysome shell. Science 319:1083-1086. http://dx.doi.org/10.1126/science.1151458.
31. Yeates TO, Jorda J, Bobik TA. 2013. The shells of BMC-type microcompartment organelles in bacteria. J Mol Microbiol Biotechnol 23:290-299. http://dx.doi.org/10.1159/000351347.
32. Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO. 2007. Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol 5:e144. http://dx.doi.org/10.1371/journal.pbio.0050144.
33. Tsai Y, Sawaya MR, Yeates TO. 2009. Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C. Acta Crystallogr D Biol Crystallogr 65(Pt 9):980-988. http://dx.doi.org/10.1107/S0907444909025153.
34. Cai F, Sutter M, Cameron JC, Stanley DN, Kinney JN, Kerfeld CA. 2013. The structure of CcmP, a tandem bacterial microcompartment domain protein from the beta-carboxysome, forms a subcompartment within a microcompartment. J Biol Chem 288:16055-16063. http://dx.doi.org/10.1074/jbc.M113.456897.
35. Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA. 2009. Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol 392:319-333. http://dx.doi.org/10.1016/j.jmb.2009.03.056.
36. Sagermann M, Ohtaki A, Nikolakakis K. 2009. Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment. Proc Natl Acad Sci USA 106:8883-8887. http://dx.doi.org/10.1073/pnas.0902324106.
37. Tanaka S, Sawaya MR, Yeates TO. 2010. Structure and mechanisms of a protein-based organelle in Escherichia coli. Science 327:81-84. http://dx.doi.org/10.1126/science.1179513.
38. 12-dependent 1,2-propanediol degradation by Salmonella enterica serovar Typhimurium LT2. J Bacteriol 189:1589-1596. http://dx.doi.org/10.1128/JB.01151-06.
39. Bertani G. 1951. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62:293-300.
40. Vogel HJ, Bonner DM. 1956. Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem 218:97-106.
41. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410. http://dx.doi.org/10.1016/S0022-2836(05)80360-2.
42. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404.
43. Thevenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tuffery P. 2012. PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res 40:W288-W293. http://dx.doi.org/10.1093/nar/gks419.
44. Fan C, Cheng S, Sinha S, Bobik TA. 2012. Interactions between the termini of lumen enzymes and shell proteins mediate enzyme encapsulation into bacterial microcompartments. Proc Natl Acad Sci USA 109: 14995-15000. http://dx.doi.org/10.1073/pnas.1207516109.
45. Lawrence AD, Frank S, Newnham S, Lee MJ, Brown IR, Xue W-F, Rowe ML, Mulvihill DP, Prentice MB, Howard MJ, Warren MJ. 2014. Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. ACS Synth Biol 3:454-465. http://dx.doi.org/10.1021/sb4001118.
46. Tanaka S, Sawaya MR, Phillips M, Yeates TO. 2009. Insights from multiple structures of the shell proteins from the beta-carboxysome. Protein Sci 18:108-120. http://dx.doi.org/10.1002/pro.14.
47. Chowdhury C, Chun S, Pang A, Sawaya MR, Sinha S, Yeates TO, Bobik TA. 2015. Selective molecular transport through the protein shell of a bacterial microcompartment organelle. Proc Natl Acad Sci USA 112: 2990-2995. http://dx.doi.org/10.1073/pnas.1423672112.
48. Frank S, Lawrence AD, Prentice MB, Warren MJ. 2013. Bacterial microcompartments moving into a synthetic biological world. J Biotechnol 163:273-279. http://dx.doi.org/10.1016/j.jbiotec.2012.09.002.
49. Tsai SJ, Yeates TO. 2011. Bacterial microcompartments insights into the structure, mechanism, and engineering applications. Prog Mol Biol Transl Sci 103:1-20. http://dx.doi.org/10.1016/B978-0-12-415906-8.00008-X.