羧酶体的组成、结构、功能和检测及其在脱氮细菌中的意义
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摘要
羧酶体(Carboxysome)是一种具有CO2浓缩功能的"类细胞器",它存在于自养型脱氮细菌中,可增强细菌的自养生长能力。硝化细菌、厌氧氨氧化细菌和部分反硝化细菌都是重要的自养型脱氮细菌,探明其羧酶体的组成、结构和功能,将有助于揭示自养型脱氮菌的生长规律,进而强化生物脱氮过程。基于文献阅读和相关研究,本文对自养型细菌中羧酶体在组成、结构、功能和检测等方面的研究进展进行综述,以期为自养生物脱氮过程的深入理解和优化改进提供参考。
Carboxysome is an organelle-like structure that can concentrate CO2 from the environment. It exists in some autotrophic microorganisms and can promote cell growth. Among nitrogen-removal microorganisms, nitrifying bacteria, anaerobic ammonia oxidation(Anammox) bacteria and some denitrifying bacteria are autotrophic microorganisms. Understanding the composition, structure and function of carboxysome is helpful to reveal the growth of autotrophic microorganisms and to optimize the process of biological nitrogen-removal. Based on the literatures and our researches, the composition, structure, function and detection of carboxysome in autotrophic bacteria are summarized in this paper.
Carboxysome is an organelle-like structure that can concentrate CO2 from the environment. It exists in some autotrophic microorganisms and can promote cell growth. Among nitrogen-removal microorganisms, nitrifying bacteria, anaerobic ammonia oxidation(Anammox) bacteria and some denitrifying bacteria are autotrophic microorganisms. Understanding the composition, structure and function of carboxysome is helpful to reveal the growth of autotrophic microorganisms and to optimize the process of biological nitrogen-removal. Based on the literatures and our researches, the composition, structure, function and detection of carboxysome in autotrophic bacteria are summarized in this paper.
引文
[1]Schmidt I,Sliekers O,Schmid M,et al.New concepts of microbial treatment processes for the nitrogen removal in wastewater[J].FEMS Microbiology Reviews,2003,27(4):481-492
[2]Desmidt E,Monballiu A,de Clippeleir H,et al.Autotrophic nitrogen removal after ureolytic phosphate precipitation to remove both endogenous and exogenous nitrogen[J].Water Science&Technology,2013,67(7):1425-1433
[3]Wang C,Liu ST,Xu XC,et al.Potential coupling effects of ammonia-oxidizing and anaerobic ammonium-oxidizing bacteria on completely autotrophic nitrogen removal over nitrite biofilm formation induced by the second messenger cyclic diguanylate[J].Applied Microbiology and Biotechnology,2017,101(9):3821-3828
[4]Kerfeld CA,Erbilgin O.Bacterial microcompartments and the modular construction of microbial metabolism[J].Trends in Microbiology,2015,23(1):22-34
[5]Tanaka S,Kerfeld CA,Sawaya MR,et al.Atomic-level models of the bacterial carboxysome shell[J].Science,2008,319(5866):1083-1086
[6]Rae BD,Long BM,Badger MR,et al.Functions,compositions,and evolution of the two types of carboxysomes:polyhedral microcompartments that facilitate CO2 fixation in cyanobacteria and some proteobacteria[J].Microbiology and Molecular Biology Reviews,2013,77(3):357-379
[7]Holthuijzen YA,Vonck J,Kuenen JG,et al.The carboxysome of Thiobacillus neapolitanus[J].Antonie van Leeuwenhoek,1984,50(1):90
[8]Blanchard J,Abdul-Rahman F.Carboxysomes,Structure and Function[M].Berlin:Springer,2014:1-3
[9]Beudeker RF,Kuenen JG.Carboxysomes:‘calvinosomes’?[J].FEBS Letters,1981,131(2):269-274
[10]Holthuijzen YA,van Breemen JFL,Kuenen JG,et al.Protein composition of the carboxysomes of Thiobacillus neapolitanus[J].Archives of Microbiology,1986,144(4):398-404
[11]Vakeria D,Codd GA,Marsden WJN,et al.No evidence for DNA in cyanobacterial carboxysomes[J].FEMS Microbiology Letters,1984,25(2/3):149-152
[12]Heinhorst S,Williams EB,Cai F,et al.Characterization of the carboxysomal carbonic anhydrase Cso SCA from Halothiobacillus neapolitanus[J].Journal of Bacteriology,2006,188(23):8087-8094
[13]Heinhorst S,Cannon GC,Shively JM.Carboxysomes and Carboxysome-Like Inclusions[M].Berlin:Springer,2006:141-165
[14]Schmid MF,Paredes AM,Khant HA,et al.Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography[J].Journal of Molecular Biology,2006,364(3):526-535
[15]Yeates TO,Kerfeld CA,Heinhorst S,et al.Protein-based organelles in bacteria:carboxysomes and related microcompartments[J].Nature Reviews Microbiology,2008,6(9):681-691
[16]Roberts EW,Cai F,Kerfeld CA,et al.Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein Cso S1D[J].Journal of Bacteriology,2012,194(4):787-795
[17]Cannon GC,Baker SH,Soyer F,et al.Organization of carboxysome genes in the thiobacilli[J].Current Microbiology,2003,46(2):115-119
[18]Baker SH,Lorbach SC,Rodriguez-Buey M,et al.The correlation of the gene cso S2 of the carboxysome operon with two polypeptides of the carboxysome in Thiobacillus neapolitanus[J].Archives of Microbiology,1999,172(4):233-239
[19]Espie GS,Kimber MS.Carboxysomes:cyanobacterial Rubis CO comes in small packages[J].Photosynthesis Research,2011,109(1/3):7-20
[20]Westphal K,Bock E,Cannon G,et al.Deoxyribonucleic acid in Nitrobacter carboxysomes[J].Journal of Bacteriology,1979,140(1):285-288
[21]Holthuijzen YA,Maathuis FJM,Kuenen JG,et al.Carboxysomes of Thiobacillus neapolitanus do not contain extrachromosomal DNA[J].FEMS Microbiology Letters,1986,35(2/3):193-198
[22]Kinney JN,Axen SD,Kerfeld CA.Comparative analysis of carboxysome shell proteins[J].Photosynthesis Research,2011,109(1/3):21-32
[23]Barton LL,Bazylinski DA,Xu HF.Nanomicrobiology[M].New York:Springer,2014:75-101
[24]Iancu CV,Ding HJ,Morris DM,et al.The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography[J].Journal of Molecular Biology,2007,372(3):764-773
[25]Tsai Y,Sawaya MR,Cannon GC,et al.Structural analysis of Cso S1A and the protein shell of the Halothiobacillus neapolitanus carboxysome[J].PLo S Biology,2007,5(6):e144
[26]Mahinthichaichan P,Morris D,Wang Y,et al.Bacterial carboxysome shell proteins are selectively permeable to carbon fixation substrates[J].Biophysical Journal,2017,112(3):239a
[27]Sutter M,Faulkner M,Aussignargues C,et al.Visualization of bacterial microcompartment facet assembly using high-speed atomic force microscopy[J].Nano Letters,2016,16(3):1590-1595
[28]Klein MG,Zwart P,Bagby SC,et al.Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport[J].Journal of Molecular Biology,2009,392(2):319-333
[29]Bonacci W,Teng PK,Afonso B,et al.Modularity of a carbon-fixing protein organelle[J].Proceedings of the National Academy of Sciences of the United States of America,2012,109(2):478-483
[30]Chaijarasphong T,Nichols RJ,Kortright KE,et al.Programmed ribosomal frameshifting mediates expression of theα-carboxysome[J].Journal of Molecular Biology,2016,428(1):153-164
[31]Cai F,Dou ZC,Bernstein SL,et al.Advances in understanding carboxysome assembly in Prochlorococcus and Synechococcus implicate Cso S2 as a critical component[J].Life,2015,5(2):1141-1171
[32]Cameron JC,Wilson SC,Bernstein SL,et al.Biogenesis of a bacterial organelle:the carboxysome assembly pathway[J].Cell,2013,155(5):1131-1140
[33]Kerfeld CA,Melnicki MR.Assembly,function and evolution of cyanobacterial carboxysomes[J].Current Opinion in Plant Biology,2016,31:66-75
[34]Cai F,Menon BB,Cannon GC,et al.The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier[J].PLo S One,2009,4(10):e7521
[35]Zhang X,Liu XD,Liang YL,et al.Metabolic diversity and adaptive mechanisms of iron-and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments[J].Environmental Microbiology Reports,2016,8(5):738-751
[36]Frost SC,Mc Kenna R.Carbonic Anhydrase:Mechanism,Regulation,Links to Disease,and Industrial Applications[M].Netherlands:Springer,2014
[37]Sawaya MR,Cannon GC,Heinhorst S,et al.The structure of?β-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two[J].Journal of Biological Chemistry,2006,281(11):7546-7555
[38]Cannon GC,Heinhorst S,Kerfeld CA.Carboxysomal carbonic anhydrases:structure and role in microbial CO2 fixation[J].Biochimica et Biophysica Acta(BBA)-Proteins and Proteomics,2010,1804(2):382-392
[39]Frey R,Mantri S,Rocca M,et al.Bottom-up construction of a primordial carboxysome mimic[J].Journal of the American Chemical Society,2016,138(32):10072-10075
[40]Spreitzer RJ,Salvucci ME.Rubisco:structure,regulatory interactions,and possibilities for a better enzyme[J].Annual Review of Plant Biology,2002,53:449-475
[41]Br?ndén CI,Lindqvist Y,Schneider G.Protein engineering of rubisco[J].Acta Crystallographica Section B:Structural Science,Crystal Engeering and Materials,1991,47(6):824-835
[42]Chapman MS,Suh SW,Curmi PM,et al.Tertiary structure of plant Ru Bis CO:domains and their contacts[J].Science,1988,241(4861):71-74
[43]Menning KJ,Menon BB,Fox G,et al.Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 isΔp-and ATP-sensitive and enhances Rubis CO-mediated carbon fixation[J].Archives of Microbiology,2016,198(2):149-159
[44]Giessen TW,Silver PA.Engineering carbon fixation with artificial protein organelles[J].Current Opinion in Biotechnology,2017,46:42-50
[45]Walker BJ,Van Loocke A,Bernacchi CJ,et al.The costs of photorespiration to food production now and in the future[J].Annual Review of Plant Biology,2016,67:107-129
[46]Badger MR,Bek EJ.Multiple Rubisco forms in proteobacteria:their functional significance in relation to CO2 acquisition by the CBB cycle[J].Journal of Experimental Botany,2008,59(7):1525-1541
[47]Sutter M,Roberts EW,Gonzalez RC,et al.Structural characterization of a newly identified component ofα-carboxysomes:the AAA+domain protein Cso Cbb Q[J].Scientific Reports,2015,5:16243
[48]Wheatley NM,Eden KD,Ngo J,et al.A PII-like protein regulated by bicarbonate:structural and biochemical studies of the carboxysome-associated CPII protein[J].Journal of Molecular Biology,2016,428(20):4013-4030
[49]Wheatley NM,Sundberg CD,Gidaniyan SD,et al.Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase(Ru Bis CO)assembly factor in the?α-carboxysome[J].Journal of Biological Chemistry,2014,289(11):7973-7981
[50]Badger MR,Kaplan A,Berry JA.Internal inorganic carbon pool of Chlamydomonas reinhardtii:evidence for a carbon dioxide-concentrating mechanism[J].Plant Physiology,1980,66(3):407-413
[51]Price GD,Sültemeyer D,Klughammer B,et al.The functioning of the CO2 concentrating mechanism in several cyanobacterial strains:a review of general physiological characteristics,genes,proteins,and recent advances[J].Canadian Journal of Botany,1998,76(6):973-1002
[52]Badger MR,Price GD.CO2 concentrating mechanisms in cyanobacteria:molecular components,their diversity and evolution[J].Journal of Experimental Botany,2003,54(383):609-622
[53]Prescott LM,Harley JP,Klein DA.Microbiology[M].Shen P,Peng ZR,Trans.5th ed.Beijing:Higher Education Press,2003:209-210(in Chinese)Prescott LM,Harley JP,Klein DA.微生物学[M].沈萍,彭珍荣,译.5版.北京:高等教育出版社,2003:209-210
[54]Ting CS,Hsieh C,Sundararaman S,et al.Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus,a globally important marine cyanobacterium[J].Journal of Bacteriology,2007,189(12):4485-4493
[55]Liberton M,Austin JR,Berg RH,et al.Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography[J].Plant Physiology,2011,155(4):1656-1666
[56]Iancu CV,Morris DM,Dou ZC,et al.Organization,structure,and assembly ofα-carboxysomes determined by electron cryotomography of intact cells[J].Journal of Molecular Biology,2010,396(1):105-117
[57]Fiencke C,Bock E.Immunocytochemical localization of membrane-bound ammonia monooxygenase in cells of ammonia oxidizing bacteria[J].Archives of Microbiology,2006,185(2):99-106
[58]Sorokin DY,Lysenko AM,Mityushina LL,et al.Thioalkalimicrobium aerophilum gen.nov.,sp.nov.and Thioalkalimicrobium sibericum sp.nov.,and Thioalkalivibrio versutus gen.nov.,sp.nov.,Thioalkalivibrio nitratis sp.nov.,novel and Thioalkalivibrio denitrificancs sp.nov.,novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes[J].International Journal of Systematic and Evolutionary Microbiology,2001,51(2):565-580
[59]van de Meene AML,Hohmann-Marriott MF,Vermaas WFJ,et al.The three-dimensional structure of the cyanobacterium Synechocystis sp.PCC 6803[J].Archives of Microbiology,2006,184(5):259-270
[60]Dobrinski KP.Thiomicrospira crunogena:a chemoautotroph with a carbon concentrating mechanism[D].Florida:Doctoral Dissertation of University of South Florida,2009:2-3
[61]Orús MI,Rodríguez-Buey ML,Marco E,et al.Changes in carboxysome structure and grouping and in photosynthetic affinity for inorganic carbon in Anabaena strain PCC 7119(Cyanophyta)in response to modification of CO2 and Na+supply[J].Plant&Cell Physiology,2001,42(1):46-53
[62]Wu TF,Liu YD,Song LR.Selection and ultrastructural observation of a high-CO2-requiring mutant of cyanobacterium Synechococcus sp.PCC7942[J].Acta Botanica Sinica,2000,42(2):116-121
[63]Rasmussen RE,Erstad SM,Ramos-Martinez EM,et al.An easy and efficient permeabilization protocol for in vivo enzyme activity assays in cyanobacteria[J].Microbial Cell Factories,2016,15:186
[64]Cannon GC,English RS,Shively JM.In situ assay of ribulose-1,5-bisphosphate carboxylase/oxygenase in Thiobacillus neapolitanus[J].Journal of Bacteriology,1991,173(4):1565-1568
[65]Faulkner M,Rodriguez-Ramos J,Dykes GF,et al.Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes[J].Nanoscale,2017,9(30):10662-10673
[66]Di Marco G,Tricoli D.Ru BP carboxylase determination by enzymic estimation of D-3-PGA formed[J].Photosynthesis Research,1983,4(2):145-149
[67]Kang D,Zheng P,Hu QY.Structure,morphology and function of Anammox granular sludge[J].CIESC Journal,2016,67(10):4040-4046(in Chinese)康达,郑平,胡倩怡.厌氧氨氧化结构体、形态与功能[J].化工学报,2016,67(10):4040-4046
[68]Zheng P,Zhang L.Characterization and classification of anaerobic ammonium oxidation(anammox)bacteria[J].Journal of Zhejiang University(Agriculture&Life Science),2009,35(5):473-481(in Chinese)郑平,张蕾.厌氧氨氧化菌的特性与分类[J].浙江大学学报:农业与生命科学版,2009,35(5):473-481
[69]Schouten S,Strous M,Kuypers MMM,et al.Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria[J].Applied and Environmental Microbiology,2004,70(6):3785-3788
[70]Ding S,Zheng P,Lu HF,et al.New understanding on metabolism of anaerobic ammonium oxidationbacteria based on metagenomics technology[J].Chinese Journal of Appplied Environmental Biology,2012,18(4):697-704(in Chinese)丁爽,郑平,陆慧锋,等.基于宏基因组技术获得的对厌氧氨氧化菌代谢的新理解[J].应用与环境生物学报,2012,18(4):697-704
[71]Ragsdale SW.Enzymology of the acetyl-Co A pathway of CO2fixation[J].Critical Reviews in Biochemistry and Molecular Biology,1991,26(3/4):261-300
[72]van de Vossenberg J,Woebken D,Maalcke WJ,et al.The metagenome of the marine anammox bacterium‘Candidatus Scalindua profunda’illustrates the versatility of this globally important nitrogen cycle bacterium[J].Environmental Microbiology,2013,15(5):1275-1289
[73]Shah V,Chang BX,Morris RM.Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium[J].The ISME Journal,2017,11(1):263-271
[74]Baumgart M,Huber I,Abdollahzadeh I,et al.Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum[J].Journal of Biotechnology,2017,258:126-135
[75]Parikh MR,Greene DN,Woods KK,et al.Directed evolution of Ru Bis CO hypermorphs through genetic selection in engineered E.coli[J].Protein Engineering,Design and Selection,2006,19(3):113-119
[76]Gonzalez-Esquer CR,Shubitowski TB,Kerfeld CA.Streamlined construction of the cyanobacterial CO2-fixing organelle via protein domain fusions for use in plant synthetic biology[J].The Plant Cell,2015,27(9):2637-2644
[77]Kerfeld CA.Plug-and-play for improving primary productivity[J].American Journal of Botany,2015,102(12):1949-1950
[78]Long BM,Rae BD,Rolland V,et al.Cyanobacterial CO2-concentrating mechanism components:Function and prospects for plant metabolic engineering[J].Current Opinion in Plant Biology,2016,31:1-8
[79]Gilbert N.Gates Foundation backs high-risk science for big wins[J].Nature Plants,2015,1(3):15022
[80]Chessher A,Breitling R,Takano E.Bacterial microcompartments:biomaterials for synthetic biology-based compartmentalization strategies[J].ACS Biomaterials Science&Engineering,2015,1(6):345-351
[81]Jordan PC,Patterson DP,Saboda KN,et al.Self-assembling biomolecular catalysts for hydrogen production[J].Nature Chemistry,2015,8(2):179-185
[82]Cai F,Sutter M,Bernstein SL,et al.Engineering bacterial microcompartment shells:chimeric shell proteins and chimeric carboxysome shells[J].ACS Synthetic Biology,2015,4(4):444-453
[83]Klanchui A,Cheevadhanarak S,Prommeenate P,et al.Exploring components of the CO2-concentrating mechanism in alkaliphilic cyanobacteria through genome-based analysis[J].Computational and Structural Biotechnology Journal,2017,15:340-350
[84]Ting CS,Dusenbury KH,Pryzant RA,et al.The Prochlorococcus carbon dioxide-concentrating mechanism:evidence of carboxysome-associated heterogeneity[J].Photosynthesis Research,2015,123(1):45-60
[2]Desmidt E,Monballiu A,de Clippeleir H,et al.Autotrophic nitrogen removal after ureolytic phosphate precipitation to remove both endogenous and exogenous nitrogen[J].Water Science&Technology,2013,67(7):1425-1433
[3]Wang C,Liu ST,Xu XC,et al.Potential coupling effects of ammonia-oxidizing and anaerobic ammonium-oxidizing bacteria on completely autotrophic nitrogen removal over nitrite biofilm formation induced by the second messenger cyclic diguanylate[J].Applied Microbiology and Biotechnology,2017,101(9):3821-3828
[4]Kerfeld CA,Erbilgin O.Bacterial microcompartments and the modular construction of microbial metabolism[J].Trends in Microbiology,2015,23(1):22-34
[5]Tanaka S,Kerfeld CA,Sawaya MR,et al.Atomic-level models of the bacterial carboxysome shell[J].Science,2008,319(5866):1083-1086
[6]Rae BD,Long BM,Badger MR,et al.Functions,compositions,and evolution of the two types of carboxysomes:polyhedral microcompartments that facilitate CO2 fixation in cyanobacteria and some proteobacteria[J].Microbiology and Molecular Biology Reviews,2013,77(3):357-379
[7]Holthuijzen YA,Vonck J,Kuenen JG,et al.The carboxysome of Thiobacillus neapolitanus[J].Antonie van Leeuwenhoek,1984,50(1):90
[8]Blanchard J,Abdul-Rahman F.Carboxysomes,Structure and Function[M].Berlin:Springer,2014:1-3
[9]Beudeker RF,Kuenen JG.Carboxysomes:‘calvinosomes’?[J].FEBS Letters,1981,131(2):269-274
[10]Holthuijzen YA,van Breemen JFL,Kuenen JG,et al.Protein composition of the carboxysomes of Thiobacillus neapolitanus[J].Archives of Microbiology,1986,144(4):398-404
[11]Vakeria D,Codd GA,Marsden WJN,et al.No evidence for DNA in cyanobacterial carboxysomes[J].FEMS Microbiology Letters,1984,25(2/3):149-152
[12]Heinhorst S,Williams EB,Cai F,et al.Characterization of the carboxysomal carbonic anhydrase Cso SCA from Halothiobacillus neapolitanus[J].Journal of Bacteriology,2006,188(23):8087-8094
[13]Heinhorst S,Cannon GC,Shively JM.Carboxysomes and Carboxysome-Like Inclusions[M].Berlin:Springer,2006:141-165
[14]Schmid MF,Paredes AM,Khant HA,et al.Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography[J].Journal of Molecular Biology,2006,364(3):526-535
[15]Yeates TO,Kerfeld CA,Heinhorst S,et al.Protein-based organelles in bacteria:carboxysomes and related microcompartments[J].Nature Reviews Microbiology,2008,6(9):681-691
[16]Roberts EW,Cai F,Kerfeld CA,et al.Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein Cso S1D[J].Journal of Bacteriology,2012,194(4):787-795
[17]Cannon GC,Baker SH,Soyer F,et al.Organization of carboxysome genes in the thiobacilli[J].Current Microbiology,2003,46(2):115-119
[18]Baker SH,Lorbach SC,Rodriguez-Buey M,et al.The correlation of the gene cso S2 of the carboxysome operon with two polypeptides of the carboxysome in Thiobacillus neapolitanus[J].Archives of Microbiology,1999,172(4):233-239
[19]Espie GS,Kimber MS.Carboxysomes:cyanobacterial Rubis CO comes in small packages[J].Photosynthesis Research,2011,109(1/3):7-20
[20]Westphal K,Bock E,Cannon G,et al.Deoxyribonucleic acid in Nitrobacter carboxysomes[J].Journal of Bacteriology,1979,140(1):285-288
[21]Holthuijzen YA,Maathuis FJM,Kuenen JG,et al.Carboxysomes of Thiobacillus neapolitanus do not contain extrachromosomal DNA[J].FEMS Microbiology Letters,1986,35(2/3):193-198
[22]Kinney JN,Axen SD,Kerfeld CA.Comparative analysis of carboxysome shell proteins[J].Photosynthesis Research,2011,109(1/3):21-32
[23]Barton LL,Bazylinski DA,Xu HF.Nanomicrobiology[M].New York:Springer,2014:75-101
[24]Iancu CV,Ding HJ,Morris DM,et al.The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography[J].Journal of Molecular Biology,2007,372(3):764-773
[25]Tsai Y,Sawaya MR,Cannon GC,et al.Structural analysis of Cso S1A and the protein shell of the Halothiobacillus neapolitanus carboxysome[J].PLo S Biology,2007,5(6):e144
[26]Mahinthichaichan P,Morris D,Wang Y,et al.Bacterial carboxysome shell proteins are selectively permeable to carbon fixation substrates[J].Biophysical Journal,2017,112(3):239a
[27]Sutter M,Faulkner M,Aussignargues C,et al.Visualization of bacterial microcompartment facet assembly using high-speed atomic force microscopy[J].Nano Letters,2016,16(3):1590-1595
[28]Klein MG,Zwart P,Bagby SC,et al.Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport[J].Journal of Molecular Biology,2009,392(2):319-333
[29]Bonacci W,Teng PK,Afonso B,et al.Modularity of a carbon-fixing protein organelle[J].Proceedings of the National Academy of Sciences of the United States of America,2012,109(2):478-483
[30]Chaijarasphong T,Nichols RJ,Kortright KE,et al.Programmed ribosomal frameshifting mediates expression of theα-carboxysome[J].Journal of Molecular Biology,2016,428(1):153-164
[31]Cai F,Dou ZC,Bernstein SL,et al.Advances in understanding carboxysome assembly in Prochlorococcus and Synechococcus implicate Cso S2 as a critical component[J].Life,2015,5(2):1141-1171
[32]Cameron JC,Wilson SC,Bernstein SL,et al.Biogenesis of a bacterial organelle:the carboxysome assembly pathway[J].Cell,2013,155(5):1131-1140
[33]Kerfeld CA,Melnicki MR.Assembly,function and evolution of cyanobacterial carboxysomes[J].Current Opinion in Plant Biology,2016,31:66-75
[34]Cai F,Menon BB,Cannon GC,et al.The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier[J].PLo S One,2009,4(10):e7521
[35]Zhang X,Liu XD,Liang YL,et al.Metabolic diversity and adaptive mechanisms of iron-and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments[J].Environmental Microbiology Reports,2016,8(5):738-751
[36]Frost SC,Mc Kenna R.Carbonic Anhydrase:Mechanism,Regulation,Links to Disease,and Industrial Applications[M].Netherlands:Springer,2014
[37]Sawaya MR,Cannon GC,Heinhorst S,et al.The structure of?β-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two[J].Journal of Biological Chemistry,2006,281(11):7546-7555
[38]Cannon GC,Heinhorst S,Kerfeld CA.Carboxysomal carbonic anhydrases:structure and role in microbial CO2 fixation[J].Biochimica et Biophysica Acta(BBA)-Proteins and Proteomics,2010,1804(2):382-392
[39]Frey R,Mantri S,Rocca M,et al.Bottom-up construction of a primordial carboxysome mimic[J].Journal of the American Chemical Society,2016,138(32):10072-10075
[40]Spreitzer RJ,Salvucci ME.Rubisco:structure,regulatory interactions,and possibilities for a better enzyme[J].Annual Review of Plant Biology,2002,53:449-475
[41]Br?ndén CI,Lindqvist Y,Schneider G.Protein engineering of rubisco[J].Acta Crystallographica Section B:Structural Science,Crystal Engeering and Materials,1991,47(6):824-835
[42]Chapman MS,Suh SW,Curmi PM,et al.Tertiary structure of plant Ru Bis CO:domains and their contacts[J].Science,1988,241(4861):71-74
[43]Menning KJ,Menon BB,Fox G,et al.Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 isΔp-and ATP-sensitive and enhances Rubis CO-mediated carbon fixation[J].Archives of Microbiology,2016,198(2):149-159
[44]Giessen TW,Silver PA.Engineering carbon fixation with artificial protein organelles[J].Current Opinion in Biotechnology,2017,46:42-50
[45]Walker BJ,Van Loocke A,Bernacchi CJ,et al.The costs of photorespiration to food production now and in the future[J].Annual Review of Plant Biology,2016,67:107-129
[46]Badger MR,Bek EJ.Multiple Rubisco forms in proteobacteria:their functional significance in relation to CO2 acquisition by the CBB cycle[J].Journal of Experimental Botany,2008,59(7):1525-1541
[47]Sutter M,Roberts EW,Gonzalez RC,et al.Structural characterization of a newly identified component ofα-carboxysomes:the AAA+domain protein Cso Cbb Q[J].Scientific Reports,2015,5:16243
[48]Wheatley NM,Eden KD,Ngo J,et al.A PII-like protein regulated by bicarbonate:structural and biochemical studies of the carboxysome-associated CPII protein[J].Journal of Molecular Biology,2016,428(20):4013-4030
[49]Wheatley NM,Sundberg CD,Gidaniyan SD,et al.Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase(Ru Bis CO)assembly factor in the?α-carboxysome[J].Journal of Biological Chemistry,2014,289(11):7973-7981
[50]Badger MR,Kaplan A,Berry JA.Internal inorganic carbon pool of Chlamydomonas reinhardtii:evidence for a carbon dioxide-concentrating mechanism[J].Plant Physiology,1980,66(3):407-413
[51]Price GD,Sültemeyer D,Klughammer B,et al.The functioning of the CO2 concentrating mechanism in several cyanobacterial strains:a review of general physiological characteristics,genes,proteins,and recent advances[J].Canadian Journal of Botany,1998,76(6):973-1002
[52]Badger MR,Price GD.CO2 concentrating mechanisms in cyanobacteria:molecular components,their diversity and evolution[J].Journal of Experimental Botany,2003,54(383):609-622
[53]Prescott LM,Harley JP,Klein DA.Microbiology[M].Shen P,Peng ZR,Trans.5th ed.Beijing:Higher Education Press,2003:209-210(in Chinese)Prescott LM,Harley JP,Klein DA.微生物学[M].沈萍,彭珍荣,译.5版.北京:高等教育出版社,2003:209-210
[54]Ting CS,Hsieh C,Sundararaman S,et al.Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus,a globally important marine cyanobacterium[J].Journal of Bacteriology,2007,189(12):4485-4493
[55]Liberton M,Austin JR,Berg RH,et al.Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography[J].Plant Physiology,2011,155(4):1656-1666
[56]Iancu CV,Morris DM,Dou ZC,et al.Organization,structure,and assembly ofα-carboxysomes determined by electron cryotomography of intact cells[J].Journal of Molecular Biology,2010,396(1):105-117
[57]Fiencke C,Bock E.Immunocytochemical localization of membrane-bound ammonia monooxygenase in cells of ammonia oxidizing bacteria[J].Archives of Microbiology,2006,185(2):99-106
[58]Sorokin DY,Lysenko AM,Mityushina LL,et al.Thioalkalimicrobium aerophilum gen.nov.,sp.nov.and Thioalkalimicrobium sibericum sp.nov.,and Thioalkalivibrio versutus gen.nov.,sp.nov.,Thioalkalivibrio nitratis sp.nov.,novel and Thioalkalivibrio denitrificancs sp.nov.,novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes[J].International Journal of Systematic and Evolutionary Microbiology,2001,51(2):565-580
[59]van de Meene AML,Hohmann-Marriott MF,Vermaas WFJ,et al.The three-dimensional structure of the cyanobacterium Synechocystis sp.PCC 6803[J].Archives of Microbiology,2006,184(5):259-270
[60]Dobrinski KP.Thiomicrospira crunogena:a chemoautotroph with a carbon concentrating mechanism[D].Florida:Doctoral Dissertation of University of South Florida,2009:2-3
[61]Orús MI,Rodríguez-Buey ML,Marco E,et al.Changes in carboxysome structure and grouping and in photosynthetic affinity for inorganic carbon in Anabaena strain PCC 7119(Cyanophyta)in response to modification of CO2 and Na+supply[J].Plant&Cell Physiology,2001,42(1):46-53
[62]Wu TF,Liu YD,Song LR.Selection and ultrastructural observation of a high-CO2-requiring mutant of cyanobacterium Synechococcus sp.PCC7942[J].Acta Botanica Sinica,2000,42(2):116-121
[63]Rasmussen RE,Erstad SM,Ramos-Martinez EM,et al.An easy and efficient permeabilization protocol for in vivo enzyme activity assays in cyanobacteria[J].Microbial Cell Factories,2016,15:186
[64]Cannon GC,English RS,Shively JM.In situ assay of ribulose-1,5-bisphosphate carboxylase/oxygenase in Thiobacillus neapolitanus[J].Journal of Bacteriology,1991,173(4):1565-1568
[65]Faulkner M,Rodriguez-Ramos J,Dykes GF,et al.Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes[J].Nanoscale,2017,9(30):10662-10673
[66]Di Marco G,Tricoli D.Ru BP carboxylase determination by enzymic estimation of D-3-PGA formed[J].Photosynthesis Research,1983,4(2):145-149
[67]Kang D,Zheng P,Hu QY.Structure,morphology and function of Anammox granular sludge[J].CIESC Journal,2016,67(10):4040-4046(in Chinese)康达,郑平,胡倩怡.厌氧氨氧化结构体、形态与功能[J].化工学报,2016,67(10):4040-4046
[68]Zheng P,Zhang L.Characterization and classification of anaerobic ammonium oxidation(anammox)bacteria[J].Journal of Zhejiang University(Agriculture&Life Science),2009,35(5):473-481(in Chinese)郑平,张蕾.厌氧氨氧化菌的特性与分类[J].浙江大学学报:农业与生命科学版,2009,35(5):473-481
[69]Schouten S,Strous M,Kuypers MMM,et al.Stable carbon isotopic fractionations associated with inorganic carbon fixation by anaerobic ammonium-oxidizing bacteria[J].Applied and Environmental Microbiology,2004,70(6):3785-3788
[70]Ding S,Zheng P,Lu HF,et al.New understanding on metabolism of anaerobic ammonium oxidationbacteria based on metagenomics technology[J].Chinese Journal of Appplied Environmental Biology,2012,18(4):697-704(in Chinese)丁爽,郑平,陆慧锋,等.基于宏基因组技术获得的对厌氧氨氧化菌代谢的新理解[J].应用与环境生物学报,2012,18(4):697-704
[71]Ragsdale SW.Enzymology of the acetyl-Co A pathway of CO2fixation[J].Critical Reviews in Biochemistry and Molecular Biology,1991,26(3/4):261-300
[72]van de Vossenberg J,Woebken D,Maalcke WJ,et al.The metagenome of the marine anammox bacterium‘Candidatus Scalindua profunda’illustrates the versatility of this globally important nitrogen cycle bacterium[J].Environmental Microbiology,2013,15(5):1275-1289
[73]Shah V,Chang BX,Morris RM.Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium[J].The ISME Journal,2017,11(1):263-271
[74]Baumgart M,Huber I,Abdollahzadeh I,et al.Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum[J].Journal of Biotechnology,2017,258:126-135
[75]Parikh MR,Greene DN,Woods KK,et al.Directed evolution of Ru Bis CO hypermorphs through genetic selection in engineered E.coli[J].Protein Engineering,Design and Selection,2006,19(3):113-119
[76]Gonzalez-Esquer CR,Shubitowski TB,Kerfeld CA.Streamlined construction of the cyanobacterial CO2-fixing organelle via protein domain fusions for use in plant synthetic biology[J].The Plant Cell,2015,27(9):2637-2644
[77]Kerfeld CA.Plug-and-play for improving primary productivity[J].American Journal of Botany,2015,102(12):1949-1950
[78]Long BM,Rae BD,Rolland V,et al.Cyanobacterial CO2-concentrating mechanism components:Function and prospects for plant metabolic engineering[J].Current Opinion in Plant Biology,2016,31:1-8
[79]Gilbert N.Gates Foundation backs high-risk science for big wins[J].Nature Plants,2015,1(3):15022
[80]Chessher A,Breitling R,Takano E.Bacterial microcompartments:biomaterials for synthetic biology-based compartmentalization strategies[J].ACS Biomaterials Science&Engineering,2015,1(6):345-351
[81]Jordan PC,Patterson DP,Saboda KN,et al.Self-assembling biomolecular catalysts for hydrogen production[J].Nature Chemistry,2015,8(2):179-185
[82]Cai F,Sutter M,Bernstein SL,et al.Engineering bacterial microcompartment shells:chimeric shell proteins and chimeric carboxysome shells[J].ACS Synthetic Biology,2015,4(4):444-453
[83]Klanchui A,Cheevadhanarak S,Prommeenate P,et al.Exploring components of the CO2-concentrating mechanism in alkaliphilic cyanobacteria through genome-based analysis[J].Computational and Structural Biotechnology Journal,2017,15:340-350
[84]Ting CS,Dusenbury KH,Pryzant RA,et al.The Prochlorococcus carbon dioxide-concentrating mechanism:evidence of carboxysome-associated heterogeneity[J].Photosynthesis Research,2015,123(1):45-60