Bacterial microcompartments: Widespread prokaryotic organelles for isolation and optimization of metabolic pathways

Molecular Microbiology

Volumn 98, Issue 2, 2015, Pages 193-207

  Bobik, Thomas A ^a   Lehman, Brent P ^a   Yeates, Todd O ^b,c  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ETHANOLAMINE; PROPYLENE GLYCOL; BACTERIAL PROTEIN;

ALLOSTERISM; AMINO ACID SEQUENCE; BACTERIAL METABOLISM; BACTERIAL MICROCOMPARTMENT; BIOTECHNOLOGY; CARBOXYSOME; CELL DIVISION; CELL ORGANELLE; ENCAPSULATION; METABOLITE; MORPHOGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; REVIEW; TRANSPORT KINETICS; BACTERIUM; CELL COMPARTMENTALIZATION; CYTOLOGY; ENZYMOLOGY; METABOLISM; ULTRASTRUCTURE;

BACTERIA; BACTERIAL PROTEINS; CELL COMPARTMENTATION; METABOLIC NETWORKS AND PATHWAYS;

EID: 84943449348     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/mmi.13117     Document Type: Review

References (129)

1. Abdul-Rahman, F., Petit, E., and Blanchard, J.L. (2013) The distribution of polyhedral bacterial microcompartments suggests frequent horizontal transfer and operon reassembly. J Phylogen Evolution Biol 1. doi: 10.4172/2329-9002.1000118
2. Axen, S.D., Erbilgin, O., and Kerfeld, C.A. (2014) A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 10: e1003898.
3. 2 concentrating mechanisms in cyanobacteria. Funct Plant Biol 29: 161-173.
4. Baker, S.H., Williams, D.S., Aldrich, H.C., Gambrell, A.C., and Shively, J.M. (2000) Identification and localization of the carboxysome peptide Csos3 and its corresponding gene in Thiobacillus neapolitanus. Arch Microbiol 173: 278-283.
5. Bobik, T.A. (2006) Polyhedral organelles compartmenting bacterial metabolic processes. Appl Microbiol Biotechnol 70: 517-525.
6. Bobik, T.A., Xu, Y., Jeter, R.M., Otto, K.E., and Roth, J.R. (1997) Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes for the propanediol dehydratase. J Bacteriol 179: 6633-6639.
7. 12-dependent 1, 2-propanediol degradation. J Bacteriol 181: 5967-5975.
8. Brinsmade, S.R., Paldon, T., and Escalante-Semerena, J.C. (2005) Minimal functions and physiological conditions required for growth of Salmonella enterica on ethanolamine in the absence of the metabolosome. J Bacteriol 187: 8039-8046.
9. Buan, N.R., and Escalante-Semerena, J.C. (2006) Purification and initial biochemical characterization of ATP:Cob(I)alamin adenosyltransferase (EutT) enzyme of Salmonella enterica. J Biol Chem 281: 16971-16977.
10. Buan, N.R., Suh, S.J., and Escalante-Semerena, J.C. (2004) The eutT gene of Salmonella enterica encodes an oxygen-labile, metal-containing ATP: corrinoid adenosyltransferase enzyme. J Bacteriol 186: 5708-5714.
11. Buchrieser, C., Rusniok, C., Kunst, F., Cossart, P., and 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.
12. Cai, F., Sutter, M., Cameron, J.C., Stanley, D.N., Kinney, J.N., and Kerfeld, C.A. (2013) The structure of CcmP, a tandem bacterial microcompartment domain protein from the β-carboxysome, forms a subcompartment within a microcompartment. J Biol Chem 288: 16055-16063.
13. Cameron, J.C., Wilson, S.C., Bernstein, S.L., and Kerfeld, C.A. (2013) Biogenesis of a bacterial organelle: the carboxysome assembly pathway. Cell 155: 1131-1140.
14. Cannon, G.C., and Shively, J.M. (1983) Characterization of a homogenous preparation of carboxysomes from Thiobacillus neapolitanus. Arch Microbiol 134: 52-59.
15. 2 fixation. Biochim Biophys Acta 1804: 382-392.
16. Caspar, D.L., and Klug, A. (1962) Physical principles in the construction of regular viruses. Cold Spring Harb Symp Quant Biol 27: 1-24.
17. Castellana, M., Wilson, M.Z., Xu, Y., Joshi, P., Cristea, I.M., Rabinowitz, J.D., etal. (2014) Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol 32: 1011-1018.
18. Chen, A.H., Robinson-Mosher, A., Savage, D.F., Silver, P.A., and Polka, J.K. (2013) The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS ONE 8: e76127.
19. Chen, P., Andersson, D.I., and Roth, J.R. (1994) The control region of the pdu/cob regulon in Salmonella typhimurium. J Bacteriol 176: 5474-5482.
20. Cheng, S., and Bobik, T.A. (2010) Characterization of the PduS cobalamin reductase of Salmonella enterica and its role in the Pdu microcompartment. J Bacteriol 192: 5071-5080.
21. Cheng, S., Liu, Y., Crowley, C.S., Yeates, T.O., and Bobik, T.A. (2008) Bacterial microcompartments: their properties and paradoxes. Bioessays 30: 1084-1095.
22. 12-dependent 1, 2-propanediol degradation by Salmonella. J Bacteriol 193: 1385-1392.
23. + internally within the Pdu microcompartment of Salmonella enterica. PLoS ONE 7: e47144.
24. Choudhary, S., Quin, M.B., Sanders, M.A., Johnson, E.T., and Schmidt-Dannert, C. (2012) Engineered protein nano-compartments for targeted enzyme localization. PLoS ONE 7: e33342.
25. Chowdhury, C., Sinha, S., Chun, S., Yeates, T.O., and Bobik, T.A. (2014) Diverse bacterial microcompartment organelles. Microbiol Mol Biol Rev 78: 438-468.
26. Chowdhury, C., Chun, S., Pang, A., Sawaya, M.R., Sinha, S., Yeates, T.O., and Bobik, T.A. (2015) Selective molecular transport through the protein shell of a bacterial microcompartment organelle. Proc Natl Acad Sci USA 112: 2990-2995.
27. Conner, C.P., Heithoff, D.M., Julio, S.M., Sinsheimer, R.L., and Mahan, M.J. (1998) Differential patterns of acquired virulence genes distinguish Salmonella strains. Proc Natl Acad Sci USA 95: 4641-4645.
28. Cot, S.S., So, A.K., and Espie, G.S. (2008) A multiprotein bicarbonate dehydration complex essential to carboxysome function in cyanobacteria. J Bacteriol 190: 936-945.
29. Crowley, C.S., Cascio, D., Sawaya, M.R., Kopstein, J.S., Bobik, T.A., and Yeates, T.O. (2010) Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J Biol Chem 285: 37838-37846.
30. 2. J Biol Chem 283: 10377-10384.
31. Dryden, K.A., Crowley, C.S., Tanaka, S., Yeates, T.O., and Yeager, M. (2009) Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals. Protein Sci 18: 2629-2635.
32. English, R.S., Lorbach, S.C., Qin, X., and Shively, J.M. (1994) Isolation and characterization of a carboxysome shell gene from Thiobacillus neapolitanus. Mol Microbiol 12: 647-654.
33. English, R.S., Jin, S., and Shively, J.M. (1995) Use of electroporation to generate a Thiobacillus neapolitanus carboxysome mutant. Appl Environ Microbiol 61: 3256-3260.
34. Erbilgin, O., McDonald, K.L., and Kerfeld, C.A. (2014) Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Appl Environ Microbiol 80: 2193-2205.
35. Fan, C., and Bobik, T.A. (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.
36. Fan, C., Cheng, S., Liu, Y., Escobar, C.M., Crowley, C.S., Jefferson, R.E., etal. (2010) Short N-terminal sequences package proteins into bacterial microcompartments. Proc Natl Acad Sci USA 107: 7509-7514.
37. Fan, C., Cheng, S., Sinha, S., and Bobik, T.A. (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.
38. Forouhar, F., Kuzin, A., Seetharaman, J., Lee, I., Zhou, W., Abashidze, M., etal. (2007) Functional insights from structural genomics. J Struct Funct Genomics 8: 37-44.
39. Fukuzawa, H., Suzuki, E., Komukai, Y., and Miyachi, S. (1992) A gene homologous to chloroplast carbonic-anhydrase (IcfA) is essential to photosynthetic carbon-dioxide fixation by Synechococcus Pcc7942. Proc Natl Acad Sci USA 89: 4437-4441.
40. Garsin, D.A. (2010) Ethanolamine utilization in bacterial pathogens: roles and regulation. Nat Rev Microbiol 8: 290-295.
41. 12-dependent degradation of 1, 2-propanediol in Salmonella enterica serovar typhimurium LT2. J Bacteriol 184: 1253-1261.
42. Heithoff, D.M., Conner, C.P., Hentschel, U., Govantes, F., Hanna, P.C., and Mahan, M.J. (1999) Coordinate intracellular expression of Salmonella genes induced during infection. J Bacteriol 181: 799-807.
43. Horswill, A.R., and Escalante-Semerena, J.C. (1997) Propionate catabolism in Salmonella typhimurium LT2: two divergently transcribed units comprise the prp locus at 8.5 centisomes, prpR encodes a member of the sigma-54 family of activators, and the prpBCDE genes constitute an operon. J Bacteriol 179: 928-940.
44. Horswill, A.R., and Escalante-Semerena, J.C. (1999) Salmonella typhimurium LT2 catabolizes propionate via the 2-methylcitric acid cycle. J Bacteriol 181: 5615-5623.
45. Huseby, D.L., and Roth, J.R. (2013) Evidence that a metabolic microcompartment contains and recycles private cofactor pools. J Bacteriol 195: 2864-2879.
46. Iancu, C.V., Ding, H.J., Morris, D.M., Dias, D.P., Gonzales, A.D., Martino, A., and Jensen, G.J. (2007) The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography. J Mol Biol 372: 764-773.
47. Iancu, C.V., Morris, D.M., Dou, Z., Heinhorst, S., Cannon, G.C., and Jensen, G.J. (2010) Organization, structure, and assembly of α-carboxysomes determined by electron cryotomography of intact cells. J Mol Biol 396: 105-117.
48. Jeter, R.M. (1990) Cobalamin-dependent 1, 2-propanediol utilization by Salmonella typhimurium. J Gen Microbiol 136: 887-896.
49. Johnson, C.L., Pechonick, E., Park, S.D., Havemann, G.D., Leal, N.A., and Bobik, T.A. (2001) Functional genomic, biochemical, and genetic characterization of the Salmonella pduO gene, an ATP:cob(I)alamin adenosyltransferase gene. J Bacteriol 183: 1577-1584.
50. Johnson, C.L., Buszko, M.L., and Bobik, T.A. (2004) Purification and initial characterization of the Salmonella enterica PduO ATP:Cob(I)alamin adenosyltransferase. J Bacteriol 186: 7881-7887.
51. Jorda, J., Lopez, D., Wheatley, N.M., and Yeates, T.O. (2013) Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria. Protein Sci 22: 179-195.
52. Jorda, J., Bobik, T.A., and Yeates, T.O. (2015) Exploring bacterial organelle interactomes: a model of the protein-protein interaction network in the Pdu microcompartment. PloS Comp Biol 11: e1004067.
53. Joseph, B., Przybilla, K., Stuhler, C., Schauer, K., Slaghuis, J., Fuchs, T.M., and Goebel, W. (2006) Identification of Listeria monocytogenes genes contributing to intracellular replication by expression profiling and mutant screening. J Bacteriol 188: 556-568.
54. Kaneko, Y., Danev, R., Nagayama, K., and Nakamoto, H. (2006) Intact carboxysomes in a cyanobacterial cell visualized by hilbert differential contrast transmission electron microscopy. J Bacteriol 188: 805-808.
55. Kerfeld, C.A., Sawaya, M.R., Tanaka, S., Nguyen, C.V., Phillips, M., Beeby, M., and Yeates, T.O. (2005) Protein structures forming the shell of primitive bacterial organelles. Science 309: 936-938.
56. Kerfeld, C.A., Heinhorst, S., and Cannon, G.C. (2010) Bacterial microcompartments. Annu Rev Microbiol 64: 391-408.
57. Kinney, J.N., Axen, S.D., and Kerfeld, C.A. (2011) Comparative analysis of carboxysome shell proteins. Photosynth Res 109: 21-32.
58. Kinney, J.N., Salmeen, A., Cai, F., and Kerfeld, C.A. (2012) Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly. J Biol Chem 287: 17729-17736.
59. Klein, M.G., Zwart, P., Bagby, S.C., Cai, F., Chisholm, S.W., Heinhorst, S., etal. (2009) Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol 392: 319-333.
60. Kofoid, E., Rappleye, C., Stojiljkovic, I., and Roth, J. (1999) The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181: 5317-5329.
61. Lawrence, A.D., Frank, S., Newnham, S., Lee, M.J., Brown, I.R., Xue, W.-F., etal. (2014) Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. ACS Synthetic Biology 3: 454-465.
62. 12-dependent 1, 2-propanediol degradation by Salmonella enterica serovar Typhimurium LT2. Arch Microbiol 180: 353-361.
63. Lin, M.T., Occhialini, A., Andralojc, P.J., Devonshire, J., Hines, K.M., Parry, M.A., and Hanson, M.R. (2014) β-Carboxysomal proteins assemble into highly organized structures in Nicotiana chloroplasts. Plant J 79: 1-12.
64. 12-dependent 1, 2-propanediol degradation by Salmonella enterica serovar Typhimurium LT2. J Bacteriol 189: 1589-1596.
65. Liu, Y., Jorda, J., Yeates, T.O., and Bobik, T.A. (2015) The PduL phosphotransacylase is used to recycle coenzyme A within the Pdu microcompartment. J Bacteriol 197: 2392-2399.
66. Long, B., Badger, M., Whitney, S., and Price, D. (2007a) A structural role for CcmM in β-carboxysome shell formation. Photosynth Res 91: 223.
67. Long, B.M., Badger, M.R., Whitney, S.M., and Price, G.D. (2007b) Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA. J Biol Chem 282: 29323-29335.
68. Long, B.M., Tucker, L., Badger, M.R., and Price, G.D. (2010) Functional cyanobacterial β-carboxysomes have an absolute requirement for both long and short forms of the CcmM protein. Plant Physiol 153: 285-293.
69. Long, B.M., Rae, B.D., Badger, M.R., and Price, G.D. (2011) Over-expression of the β-carboxysomal CcmM protein in Synechococcus PCC7942 reveals a tight co-regulation of carboxysomal carbonic anhydrase (CcaA) and M58 content. Photosynth Res 109: 33-45.
70. 12-dependent diol dehydratase by a molecular chaperone-like reactivating factor. Biochemistry 38: 13170-13178.
71. Mori, K., Tobimatsu, T., and Toraya, T. (1997) A protein factor is essential for in situ reactivation of glycerol-inactivated adenosylcobalamin-dependent diol dehydratase. Biosci Biotechnol Biochem 61: 1729-1733.
72. Mori, K., Bando, R., Hieda, N., and Toraya, T. (2004) Identification of a reactivating factor for adenosylcobalamin-dependent ethanolamine ammonia lyase. J Bacteriol 186: 6845-6854.
73. 2 conditions. Photosynth Res 117: 121-131.
74. Murat, D., Byrne, M., and Komeili, A. (2010) Cell biology of prokaryotic organelles. Cold Spring Harb Perspect Biol 2: a000422.
75. van Niftrik, L., and Jetten, M.S. (2012) Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties. Microbiol Mol Biol Rev 76: 585-596.
76. Obradors, N., Badia, J., Baldoma, L., and Aguilar, J. (1988) Anaerobic metabolism of the L-rhamnose fermentation product 1, 2-propanediol in Salmonella typhimurium. J Bacteriol 170: 2159-2162.
77. Palacios, S., Starai, V.J., and Escalante-Semerena, J.C. (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.
78. Pang, A., Warren, M.J., and Pickersgill, R.W. (2011) Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site. Acta Crystallogr D Biol Crystallogr 67: 91-96.
79. Pang, A., Liang, M., Prentice, M.B., and Pickersgill, R.W. (2012) Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB. Acta Crystallogr D Biol Crystallogr 68: 1642-1652.
80. Parsons, J.B., Frank, S., Bhella, D., Liang, M., Prentice, M.B., Mulvihill, D.P., and Warren, M.J. (2010a) Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement. Mol Cell 38: 305-315.
81. Parsons, J.B., Lawrence, A.D., McLean, K.J., Munro, A.W., Rigby, S.E., and Warren, M.J. (2010b) Characterisation of PduS, the pdu metabolosome corrin reductase, and evidence of substructural organisation within the bacterial microcompartment. PLoS ONE 5: e14009.
82. Penrod, J.T., and Roth, J.R. (2006) Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol 188: 2865-2874.
83. 2 concentrating mechanism. Plant Physiol 91: 505-513.
84. 2 within the Carboxysome. Plant Physiol 91: 514-525.
85. Price, G.D., Coleman, J.R., and Badger, M.R. (1992) Association of carbonic anhydrase activity with carboxysomes isolated from the cyanobacterium Synechococcus PCC7942. Plant Physiol 100: 784-793.
86. Price, G.D., Howitt, S.M., Harrison, K., and Badger, M.R. (1993) Analysis of a genomic DNA region from the cyanobacterium Synechococcus sp. strain PCC7942 involved in carboxysome assembly and function. J Bacteriol 175: 2871-2879.
87. 12-dependent anaerobic growth of Salmonella enterica serovar Typhimurium on ethanolamine or 1, 2-propanediol. J Bacteriol 183: 2463-2475.
88. Rae, B.D., Long, B.M., Badger, M.R., and Price, G.D. (2012) Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL. PLoS ONE 7: e43871.
89. 2 fixation in cyanobacteria and some proteobacteria. Microbiol Mol Biol Rev 77: 357-379.
90. Reinhold, L., Zviman, M., and Kaplan, A. (1987) Inorganic carbon fluxes and photosynthesis in cyanobacteria: a quantitative model. In Progress in photosynthesis research. Proceedings of the VIIth International Congress on Photosynthesis, Providence, Rhode Island, USA 10-15 August 1986. Biggins, J. (ed.). Dordrecht: Martinus Nijhoff, pp. 289-296.
91. Reinhold, L., Kosloff, R., and Kaplan, A. (1991) A model for inorganic carbon fluxes and photosynthesis in cyanobacterial carboxysomes. Can J Bot 69: 984-988.
92. Rondon, M.R., Kazmierczak, R., and Escalante-Semerena, J.C. (1995a) Glutathione is required for maximal transcription of the cobalamin biosynthetic and 1, 2-propanediol utilization (cob/pdu) regulon and for the catabolism of ethanolamine, 1, 2-propanediol, and propionate in Salmonella typhimurium LT2. J Bacteriol 177: 5434-5439.
93. Rondon, R.R., Horswill, A.R., and Escalante-Semerena, J.C. (1995b) DNA polymerase I function is required for the utilization of ethanolamine, 1, 2-propanediol, and propionate by Salmonella typhimurium LT2. J Bacteriol 177: 7119-7124.
94. Roof, D.M., and Roth, J.R. (1988) Ethanolamine utilization in Salmonella typhimurium. J Bacteriol 170: 3855-3863.
95. 12-dependent ethanolamine utilization in Salmonella typhimurium. J Bacteriol 171: 3316-3323.
96. Sagermann, M., Ohtaki, A., and Nikolakakis, K. (2009) Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment. Proc Natl Acad Sci USA 106: 8883-8887.
97. Saier, M.H., Jr, and Bogdanov, M.V. (2013) Membranous organelles in bacteria. J Mol Microbiol Biotechnol 23: 5-12.
98. Samborska, B., and Kimber, M.S. (2012) A dodecameric CcmK2 structure suggests β-carboxysomal shell facets have a double-layered organization. Structure 20: 1353-1362.
99. 12-dependent 1, 2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. J Bacteriol 190: 2966-2971.
100. Sampson, E.M., Johnson, C.L., and Bobik, T.A. (2005) Biochemical evidence that the pduS gene encodes a bifunctional cobalamin reductase. Microbiology 151: 1169-1177.
101. Savage, D.F., Afonso, B., Chen, A.H., and Silver, P.A. (2010) Spatially ordered dynamics of the bacterial carbon fixation machinery. Science 327: 1258-1261.
102. 12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica. J Bacteriol 186: 7635-7644.
103. Shively, J.M., Ball, F., Brown, D.H., and Saunders, R.E. (1973) Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus. Science 182: 584-586.
104. Shively, J.M., van Keulen, G., and Meijer, W.G. (1998) Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu Rev Microbiol 52: 191-230.
105. Sinha, S., Cheng, S., Sung, Y.W., McNamara, D.E., Sawaya, M.R., Yeates, T.O., and Bobik, T.A. (2014) Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment. J Mol Biol 426: 2328-2345.
106. So, A.K., Espie, G.S., Williams, E.B., Shively, J.M., Heinhorst, S., and Cannon, G.C. (2004) A novel evolutionary lineage of carbonic anhydrase (ε class) is a component of the carboxysome shell. J Bacteriol 186: 623-630.
107. Sriramulu, D.D., Liang, M., Hernandez-Romero, D., Raux-Deery, E., Lunsdorf, H., Parsons, J.B., etal. (2008) Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol dehydratase in metabolosomes and metabolizes 1, 2-propanediol by disproportionation. J Bacteriol 190: 4559-4567.
108. Stojiljkovic, I., Baeumler, A.J., and 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.
109. Sutter, M., Wilson, S.C., Deutsch, S., and Kerfeld, C.A. (2013) Two new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species. Photosynth Res 118: 9-16.
110. Tabita, F.R. (1999) Microbial ribulose 1, 5-bisphosphate carboxylase/oxygenase: a different perspective. Photosynth Res 60: 1-28.
111. Talarico, T.L., Casas, I.A., Chung, T.C., and Dobrogosz, W.J. (1988) Production and isolation of reuterin, a growth inhibitor produced by Lactobacillus reuteri. Antimicrob Agents Chemother 32: 1854-1858.
112. Tanaka, S., Kerfeld, C.A., Sawaya, M.R., Cai, F., Heinhorst, S., Cannon, G.C., and Yeates, T.O. (2008) Atomic-level models of the bacterial carboxysome shell. Science 319: 1083-1086.
113. Tanaka, S., Sawaya, M.R., Phillips, M., and Yeates, T.O. (2009) Insights from multiple structures of the shell proteins from the β-carboxysome. Protein Sci 18: 108-120.
114. Tanaka, S., Sawaya, M.R., and Yeates, T.O. (2010) Structure and mechanisms of a protein-based organelle in Escherichia coli. Science 327: 81-84.
115. Thiennimitr, P., Winter, S.E., Winter, M.G., Xavier, M.N., Tolstikov, V., Huseby, D.L., etal. (2011) Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc Natl Acad Sci USA 108: 17480-17485.
116. Thompson, M.C., Crowley, C.S., Kopstein, J., Bobik, T.A., and Yeates, T.O. (2014) Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor. Acta Crystallogr F Struct Biol Commun 70: 1584-1590.
117. Thompson, M.C., Wheatley, N.M., Jorda, J., Sawaya, M.R., Gidaniyan, S.D., Ahmed, H., etal. (2014) Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein. J Mol Biol 426: 3287-3304.
118. Thompson, M.C., Cascio, D., Leibly, D.J., and Yeates, T.O. (2015) An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein. Protein Sci 24: 956-975.
119. 12-dependent diol dehydratase. J Biol Chem 274: 3372-3377.
120. Tsai, S.J., and Yeates, T.O. (2011) Bacterial microcompartments insights into the structure, mechanism, and engineering applications. Prog Mol Biol Transl Sci 103: 1-20.
121. Tsai, Y., Sawaya, M.R., Cannon, G.C., Cai, F., Williams, E.B., Heinhorst, S., etal. (2007) Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol 5: e144.
122. Wheatley, N.M., Gidaniyan, S.D., Liu, Y., Cascio, D., and Yeates, T.O. (2013) Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins. Protein Sci 22: 660-665.
123. Winter, S.E., and Baumler, A.J. (2011) A breathtaking feat: to compete with the gut microbiota, Salmonella drives its host to provide a respiratory electron acceptor. Gut Microbes 2: 58-60.
124. Winter, S.E., Thiennimitr, P., Winter, M.G., Butler, B.P., Huseby, D.L., Crawford, R.W., etal. (2010) Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467: 426-429.
125. Yeates, T.O., Kerfeld, C.A., Heinhorst, S., Cannon, G.C., and Shively, J.M. (2008) Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat Rev Microbiol 6: 681-691.
126. Yeates, T.O., Thompson, M.C., and Bobik, T.A. (2011) The protein shells of bacterial microcompartment organelles. Curr Opin Struct Biol 21: 223-231.
127. Yeates, T.O., Jorda, J., and Bobik, T.A. (2013) The shells of BMC-type microcompartment organelles in bacteria. J Mol Microbiol Biotechnol 23: 290-299.
128. Yu, J.W., Price, G.D., Song, L., and Badger, M.R. (1992) Isolation of a putative carboxysomal carbonic anhydrase gene from the cyanobacterium Synechococcus PCC7942. Plant Physiol 100: 794-800.
129. Zarzycki, J., Axen, S.D., Kinney, J.N., and Kerfeld, C.A. (2013) Cyanobacterial-based approaches to improving photosynthesis in plants. J Exp Bot 64: 787-798.