羧酶体

羧酶体（英語：carboxysome）是一種細菌微區室，為細菌微區室中被研究最多者^[2]。羧酶体為多面體的蛋白結構，外為結構蛋白（BMC-H、BMC-P與BMC-T），內為RuBisCO（固碳酵素）與碳酸酐酶兩種酵素^[3]。此胞器最早於1956年在藍菌Phormidium uncinatum中發現^[4]，後來也在數種其他藍菌與化學自營細菌（亦進行固碳）中發現，包括鹽硫杆狀菌、酸硫杆狀菌與硝化菌等^[3][5][6] 。1973年研究人員首次自Halothiobacillus neapolitanus（法语：Halothiobacillus neapolitanus）純化羧酶体^[7]。

化學自營細菌Halothiobacillus neapolitanus的羧酶体（電子顯微鏡圖像），比例尺為100奈米^[1]

羧酶体可能是細菌因應大氣中氧氣濃度上升演化出的機制，因氧氣會與二氧化碳競爭RuBisCO的結合位^[8]，羧酶体提供了二氧化碳濃度較高的微環境，碳酸酐酶生成二氧化碳後可馬上將其供應給RuBisCO進行固碳，避免發生光呼吸的損耗^[9][10]。

結構

 

羧酶体的結構模型，RuBP與碳酸酐酶被結構蛋白包裹與其中

低溫電子顯微鏡顯示羧酶体的形狀為正二十面體或接近正二十面體^[11][12][13]，其外殼為數千個蛋白複合體組成，包裹內部的RuBisCO與碳酸酐酶^[11][13]。外殼蛋白大多為組成六聚體的BMC-H，也有少數為組成三聚體的BMC-T與組成五聚體的BMC-P（兩者皆為形似六聚體的假六聚體）^[14][15]。BMC-H六聚體中間的孔洞可供固碳作用的受質（碳酸根離子）與產物（3-磷酸甘油酸）經擴散作用進出，此區域帶正電的氨基酸可協助擴散進行^[14]；BMC-P占據正二十面體的頂點^[16]；BMC-T三聚體中間的孔洞較大且可受調控開關，可使固碳作用較大的受質（RuBP）與產物（3-磷酸甘油酸）進出^[17][18]。

種類

 

（A）Halothiobacillus neapolitanus的α型羧酶体；（B）细长聚球蓝细菌（英语：Synechococcus elongatus）的β型羧酶体。比例尺為200奈米

羧酶体可分為α與β兩型，前者存在α型藍菌、硝化菌、硫氧化菌與紫細菌中，後者則存在部分藍菌中^[19]，兩者外觀相似，但組成的蛋白種類有異^{[20][21][22][23]}，其組成細節、組裝機制可能也有差異，經分析外殼蛋白的序列顯示兩型的羧酶体應是獨立演化產生的^[23][24]。

α型羧酶体

α型羧酶体又稱cso型羧酶体，其中的RuBisCO為IA型，為最早被純化、研究的細菌微區室^[25][26]。此類羧酶体的直徑約為100至160奈米^[27]，BMC-H的種類為CsoS1A、B、C等，BMC-P的種類為CsoS4A、B等，BMC-T的種類則為CsoS1D。

β型羧酶体

β型羧酶体的體積一般大於α型羧酶体，其直徑約為200至400奈米^[28]，其中的RuBisCO為IB型^[2]。此類羧酶体中的蛋白由Ccm基因編碼，其BMC-H為CcmK、BMC-P為CcmL，BMC-T則為CcmO，其組裝為由內至外，即內部的酵素先組裝後，再被外部的結構蛋白包裹^[29]。

應用

羧酶体為合成生物學研究所關注^[30][31][32]，已有研究透過基因轉殖成功在大腸桿菌中表現α型羧酶体^[33]，也有生物工程研究透過微調羧酶体外殼蛋白而影響其性質^[34]。透過基因轉殖將羧酶体轉入作物的葉綠體中可能可顯著提升其固碳作用的效率而增加產量^[35][36]，目前已有相關研究進行中^[37][38]。

參考文獻

•  分子与细胞生物学主题

1. Tsai Y, Sawaya MR, Cannon GC, et al. Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome. PLOS Biol. June 2007, 5 (6): e144. PMC 1872035  . PMID 17518518. doi:10.1371/journal.pbio.0050144. 
2. Kerfeld, Cheryl A.; Erbilgin, Onur. Bacterial microcompartments and the modular construction of microbial metabolism. Trends in Microbiology. 2015, 23 (1): 22–34. ISSN 0966-842X. PMID 25455419. doi:10.1016/j.tim.2014.10.003  . 
3. Yeates, Todd O.; Kerfeld, Cheryl A.; Heinhorst, Sabine; Cannon, Gordon C.; Shively, Jessup M. Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nature Reviews Microbiology. 2008, 6 (9): 681–691. ISSN 1740-1526. PMID 18679172. S2CID 22666203. doi:10.1038/nrmicro1913. 
4. G. Drews; W. Niklowitz. Cytology of Cyanophycea. II. Centroplasm and granular inclusions of Phormidium uncinatum. Archiv für Mikrobiologie. 1956, 24 (2): 147–162. PMID 13327992. S2CID 46171409. doi:10.1007/BF00408629. 
5. E. Gantt; S. F. Conti. Ultrastructure of blue-green algae. Journal of Bacteriology. March 1969, 97 (3): 1486–1493. PMC 249872  . PMID 5776533. doi:10.1128/JB.97.3.1486-1493.1969. 
6. Shively, J M. Inclusion Bodies of Prokaryotes. Annual Review of Microbiology. 1974, 28 (1): 167–188. ISSN 0066-4227. PMID 4372937. doi:10.1146/annurev.mi.28.100174.001123. 
7. Shively, J. M.; Ball, F.; Brown, D. H.; Saunders, R. E. Functional Organelles in Prokaryotes: Polyhedral Inclusions (Carboxysomes) of Thiobacillus neapolitanus. Science. 1973, 182 (4112): 584–586. Bibcode:1973Sci...182..584S. ISSN 0036-8075. PMID 4355679. S2CID 10097616. doi:10.1126/science.182.4112.584. 
8. Badger, M. R. CO
   2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution. Journal of Experimental Botany. 2003, 54 (383): 609–622. ISSN 1460-2431. PMID 12554704. doi:10.1093/jxb/erg076  . 
9. Cai, Fei; Menon, Balaraj B.; Cannon, Gordon C.; Curry, Kenneth J.; Shively, Jessup M.; Heinhorst, Sabine. The Pentameric Vertex Proteins Are Necessary for the Icosahedral Carboxysome Shell to Function as a CO
   2 Leakage Barrier. PLOS ONE. 2009, 4 (10): e7521. Bibcode:2009PLoSO...4.7521C. ISSN 1932-6203. PMC 2760150  . PMID 19844578. doi:10.1371/journal.pone.0007521  . 
10. Dou, Z.; Heinhorst, S.; Williams, E. B.; Murin, C. D.; Shively, J. M.; Cannon, G. C. CO
    2 Fixation Kinetics of Halothiobacillus neapolitanus Mutant Carboxysomes Lacking Carbonic Anhydrase Suggest the Shell Acts as a Diffusional Barrier for CO
    2. Journal of Biological Chemistry. 2008, 283 (16): 10377–10384. ISSN 0021-9258. PMID 18258595. doi:10.1074/jbc.M709285200  . 
11. Iancu, Cristina V.; Ding, H. Jane; Morris, Dylan M.; Dias, D. Prabha; Gonzales, Arlene D.; Martino, Anthony; Jensen, Grant J. The Structure of Isolated Synechococcus Strain WH8102 Carboxysomes as Revealed by Electron Cryotomography. Journal of Molecular Biology. 2007, 372 (3): 764–773. ISSN 0022-2836. PMC 2453779  . PMID 17669419. doi:10.1016/j.jmb.2007.06.059. 
12. Iancu, Cristina V.; Morris, Dylan M.; Dou, Zhicheng; Heinhorst, Sabine; Cannon, Gordon C.; Jensen, Grant J. Organization, Structure, and Assembly of α-Carboxysomes Determined by Electron Cryotomography of Intact Cells. Journal of Molecular Biology. 2010, 396 (1): 105–117. ISSN 0022-2836. PMC 2853366  . PMID 19925807. doi:10.1016/j.jmb.2009.11.019. 
13. Schmid, Michael F.; Paredes, Angel M.; Khant, Htet A.; Soyer, Ferda; Aldrich, Henry C.; Chiu, Wah; Shively, Jessup M. Structure of Halothiobacillus neapolitanus Carboxysomes by Cryo-electron Tomography. Journal of Molecular Biology. 2006, 364 (3): 526–535. ISSN 0022-2836. PMC 1839851  . PMID 17028023. doi:10.1016/j.jmb.2006.09.024. hdl:11147/2128. 
14. Kerfeld, C. A. Protein Structures Forming the Shell of Primitive Bacterial Organelles. Science. 2005, 309 (5736): 936–938. Bibcode:2005Sci...309..936K. CiteSeerX 10.1.1.1026.896  . ISSN 0036-8075. PMID 16081736. S2CID 24561197. doi:10.1126/science.1113397. 
15. Melnicki, Matthew R.; Sutter, Markus; Kerfeld, Cheryl A. Evolutionary relationships among shell proteins of carboxysomes and metabolosomes. Current Opinion in Microbiology. October 2021, 63: 1–9. PMC 8525121  . PMID 34098411. doi:10.1016/j.mib.2021.05.011. 
16. Tanaka, S.; Kerfeld, C. A.; Sawaya, M. R.; Cai, F.; Heinhorst, S.; Cannon, G. C.; Yeates, T. O. Atomic-Level Models of the Bacterial Carboxysome Shell. Science. 2008, 319 (5866): 1083–1086. Bibcode:2008Sci...319.1083T. ISSN 0036-8075. PMID 18292340. S2CID 5734731. doi:10.1126/science.1151458. 
17. Cai, F.; Sutter, M.; Cameron, J. C.; Stanley, D. N.; Kinney, J. N.; Kerfeld, C. A. The Structure of CcmP, a Tandem Bacterial Microcompartment Domain Protein from the β-Carboxysome, Forms a Subcompartment Within a Microcompartment. Journal of Biological Chemistry. 2013, 288 (22): 16055–16063. ISSN 0021-9258. PMC 3668761  . PMID 23572529. doi:10.1074/jbc.M113.456897  . 
18. Klein, Michael G.; Zwart, Peter; Bagby, Sarah C.; Cai, Fei; Chisholm, Sallie W.; Heinhorst, Sabine; Cannon, Gordon C.; Kerfeld, Cheryl A. Identification and Structural Analysis of a Novel Carboxysome Shell Protein with Implications for Metabolite Transport (PDF). Journal of Molecular Biology. 2009, 392 (2): 319–333. ISSN 0022-2836. PMID 19328811. S2CID 42771660. doi:10.1016/j.jmb.2009.03.056. hdl:1721.1/61355  . 
19. Sommer, Manuel; Cai, Fei; Melnicki, Matthew; Kerfeld, Cheryl A. β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. Journal of Experimental Botany. 22 June 2017, 68 (14): 3841–3855. PMC 5853843  . PMID 28419380. doi:10.1093/jxb/erx115. 
20. Zarzycki, J.; Axen, S. D.; Kinney, J. N.; Kerfeld, C. A. Cyanobacterial-based approaches to improving photosynthesis in plants. Journal of Experimental Botany. 2012, 64 (3): 787–798. ISSN 0022-0957. PMID 23095996. doi:10.1093/jxb/ers294  . 
21. Rae, B. D.; Long, B. M.; Badger, M. R.; Price, G. D. Functions, Compositions, and Evolution of the Two Types of Carboxysomes: Polyhedral Microcompartments That Facilitate CO
    2 Fixation in Cyanobacteria and Some Proteobacteria. Microbiology and Molecular Biology Reviews. 2013, 77 (3): 357–379. ISSN 1092-2172. PMC 3811607  . PMID 24006469. doi:10.1128/MMBR.00061-12. 
22. Turmo, Aiko; Gonzalez-Esquer, C. Raul; Kerfeld, Cheryl A. Carboxysomes: metabolic modules for CO
    2 fixation. FEMS Microbiology Letters. 2017-08-14, 364 (18). ISSN 1574-6968. PMID 28934381. doi:10.1093/femsle/fnx176. 
23. Kerfeld, Cheryl A; Melnicki, Matthew R. Assembly, function and evolution of cyanobacterial carboxysomes. Current Opinion in Plant Biology. June 2016, 31: 66–75. ISSN 1369-5266. PMID 27060669. doi:10.1016/j.pbi.2016.03.009. 
24. Melnicki, Matthew R.; Sutter, Markus; Kerfeld, Cheryl A. Evolutionary relationships among shell proteins of carboxysomes and metabolosomes. Current Opinion in Microbiology. October 2021, 63: 1–9. PMC 8525121  . PMID 34098411. doi:10.1016/j.mib.2021.05.011. 
25. Shively JM, Bock E, Westphal K, Cannon GC. Icosahedral inclusions (carboxysomes) of Nitrobacter agilis. Journal of Bacteriology. November 1977, 132 (2): 673–675. PMC 221910  . PMID 199579. doi:10.1128/JB.132.2.673-675.1977. 
26. Cannon, G. C.; Shively, J. M. Characterization of a homogenous preparation of carboxysomes from Thiobacillus neapolitanus. Archives of Microbiology. 1983, 134 (1): 52–59. ISSN 0302-8933. S2CID 22329896. doi:10.1007/BF00429407. 
27. Heinhorst, Sabine; Cannon, Gordon C.; Shively, Jessup M. Carboxysomes and Their Structural Organization in Prokaryotes. Nanomicrobiology. 2014: 75–101. ISBN 978-1-4939-1666-5. doi:10.1007/978-1-4939-1667-2_4. 
28. Cai, Fei; Dou, Zhicheng; Bernstein, Susan; Leverenz, Ryan; Williams, Eric; Heinhorst, Sabine; Shively, Jessup; Cannon, Gordon; Kerfeld, Cheryl. Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component. Life. 2015, 5 (2): 1141–1171. ISSN 2075-1729. PMC 4499774  . PMID 25826651. doi:10.3390/life5021141  . 
29. Cameron, Jeffrey?C.; Wilson, Steven?C.; Bernstein, Susan?L.; Kerfeld, Cheryl?A. Biogenesis of a Bacterial Organelle: The Carboxysome Assembly Pathway. Cell. 2013, 155 (5): 1131–1140. ISSN 0092-8674. PMID 24267892. doi:10.1016/j.cell.2013.10.044  . 
30. Kerfeld, Cheryl A. Plug-and-play for improving primary productivity. American Journal of Botany. December 2015, 102 (12): 1949–1950. ISSN 0002-9122. PMID 26656128. doi:10.3732/ajb.1500409  . 
31. Zarzycki, Jan; Axen, Seth D.; Kinney, James N.; Kerfeld, Cheryl A. Cyanobacterial-based approaches to improving photosynthesis in plants. Journal of Experimental Botany. 2012-10-23, 64 (3): 787–798. ISSN 1460-2431. PMID 23095996. doi:10.1093/jxb/ers294  . 
32. Gonzalez-Esquer, C. Raul; Newnham, Sarah E.; Kerfeld, Cheryl A. Bacterial microcompartments as metabolic modules for plant synthetic biology. The Plant Journal. 2016-06-20, 87 (1): 66–75. ISSN 0960-7412. PMID 26991644. doi:10.1111/tpj.13166. 
33. Bonacci, W.; Teng, P. K.; Afonso, B.; Niederholtmeyer, H.; Grob, P.; Silver, P. A.; Savage, D. F. Modularity of a carbon-fixing protein organelle. Proceedings of the National Academy of Sciences. 2011, 109 (2): 478–483. ISSN 0027-8424. PMC 3258634  . PMID 22184212. doi:10.1073/pnas.1108557109  . 
34. Cai, Fei; Sutter, Markus; Bernstein, Susan L.; Kinney, James N.; Kerfeld, Cheryl A. Engineering Bacterial Microcompartment Shells: Chimeric Shell Proteins and Chimeric Carboxysome Shells. ACS Synthetic Biology. 2015, 4 (4): 444–453. ISSN 2161-5063. PMID 25117559. doi:10.1021/sb500226j. 
35. McGrath, JM; Long, SP. Can the cyanobacterial carbon-concentrating mechanism increase photosynthesis in crop species? A theoretical analysis.. Plant Physiology. 2014, 164 (4): 2247–61. PMC 3982776  . PMID 24550242. doi:10.1104/pp.113.232611. 
36. Yin, X; Struik, PC. Can increased leaf photosynthesis be converted into higher crop mass production? A simulation study for rice using the crop model GECROS.. Journal of Experimental Botany. 2017, 68 (9): 2345–2360. PMC 5447886  . PMID 28379522. doi:10.1093/jxb/erx085. 
37. Long, BM; Hee, WY. Carboxysome encapsulation of the CO
    2-fixing enzyme Rubisco in tobacco chloroplasts.. Nature Communications. 2018, 9 (1): 3570. Bibcode:2018NatCo...9.3570L. PMC 6120970  . PMID 30177711. doi:10.1038/s41467-018-06044-0. 
38. Lin, Myat T.; Occhialini, Alessandro; Andralojc, P. John; Parry, Martin A. J.; Hanson, Maureen R. A faster Rubisco with potential to increase photosynthesis in crops. Nature. 2014, 513 (7519): 547–550. Bibcode:2014Natur.513..547L. ISSN 0028-0836. PMC 4176977  . PMID 25231869. doi:10.1038/nature13776.