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Chin. Phys. B, 2018, Vol. 27(6): 066803    DOI: 10.1088/1674-1056/27/6/066803
Special Issue: TOPICAL REVIEW — Electron microscopy methods for emergent materials and life sciences
TOPICAL REVIEW—Electron microscopy methods for the emergent materials and life sciences Prev   Next  

Cryo-ET bridges the gap between cell biology and structural biophysics

Xiao-Fang Cheng(程小芳)1,2, Rui Wang(王睿)1,2, Qing-Tao Shen(沈庆涛)1,2,3
1 iHuman Institute, ShanghaiTech University, Shanghai 201210, China;
2 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China;
3 School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
Abstract  

Cryo-electron tomography (cryo-ET) is a cutting-edge technology providing three-dimensional in situ ultra-structural information of macromolecular machineries, organelles, and eukaryotic cells in their native environment at an unprecedented level of detail. Cryo-ET enables the direct observation of dynamic macromolecular architectures of bio-samples in their naturally occurring physiological state, without any harmful artifacts introduced by heavy metal staining, dehydration, and chemical fixation, which occur in traditional transmission electron microscopy. Over decades, cryo-ET has been providing insights into numerous aspects of cellular biology by revealing the pristinely preserved ultra-structures of different cellular components comprising the crowded and complex environment of the cell, thus, bridging the gap between cellular biology and structural biophysics. In this paper, we review the fundamentals of this technique, its recent advances in optics, detection devices, and computational algorithms. The enhancement of our understanding of structural cellular biology by combining these improvements, when integrated with other methods, such as cryo-focused ion beam milling, correlative light and electron microscopy, is discussed via a few examples from research groups worldwide. We also believe that cryo-ET applications in cell biology continue to provide fundamental insights into the field, revolutionizing structural biology itself.

Keywords:  sub-tomogram averaging      segmentation      direct detection      phase plate  
Received:  02 January 2018      Revised:  23 April 2018      Accepted manuscript online: 
PACS:  68.37.Og (High-resolution transmission electron microscopy (HRTEM))  
  68.37.Lp (Transmission electron microscopy (TEM))  
  87.64.Ee (Electron microscopy)  
Fund: 

Project supported by the National Key Research and Development Program of China (Grant No.2017YFA0504800) and the Pujiang Talent Program (Grant No.17PJ1406700).

Corresponding Authors:  Rui Wang, Qing-Tao Shen     E-mail:  wangrui1@shanghaitech.edu.cn;shenqt@shanghaitech.edu.cn

Cite this article: 

Xiao-Fang Cheng(程小芳), Rui Wang(王睿), Qing-Tao Shen(沈庆涛) Cryo-ET bridges the gap between cell biology and structural biophysics 2018 Chin. Phys. B 27 066803

[1] Ruska E 1987 Biosci. Rep. 7 607
[2] Kisielowski C, Freitag B, Bischoff M and et al. 2008 Microsc. Microanal. 14 469
[3] Zhang X and Zhou Z H 2011 J. Struct. Biol. 175 253
[4] Schmid M F, Jakana J, Matsudaira P and Chiu W 1992 J. Struct. Biol. 108 62
[5] Bammes B E, Jakana J, Schmid M F and Chiu W 2010 J. Struct. Biol. 169 331
[6] Cosslett V E 1978 J. Microsc. 113 113
[7] Dubochet J, Adrian M, Chang J J, Homo J C, Lepault J, McDowall A W and Schultz P 1988 Q. Rev. Biophys. 21 129
[8] Yu X, Jin L and Zhou Z H 2008 Nature 453 415
[9] Fischer N, Neumann P, Konevega A L, Bock L V, Ficner R, Rodnina M V and Stark H 2015 Nature 520 567
[10] Fernandez-Leiro R and Scheres S H 2016 Nature 537 339
[11] Li X M 2016 Chin. Phys. B 25
[12] Cheng Y, Grigorieff N, Penczek P A and Walz T 2015 Cell 161 438
[13] Lucic V, Rigort A and Baumeister W 2013 J. Cell Biol. 202 407
[14] Oikonomou C M and Jensen G J 2017 Ann. Rev. Biochem. 86 873
[15] Faruqi A R and McMullan G 2011 Q. Rev. Biophys. 44 357
[16] Li X, Mooney P, Zheng S, Booth C R, Braunfeld M B, Gubbens S, Agard D A and Cheng Y 2013 Nat. Methods 10 584
[17] Milazzo A C, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman M H, Xuong N H, Carragher B and Potter C S 2011 J. Struct. Biol. 176 404
[18] Xu Y, Wu J, Yin C C and Mao Y 2016 PLoS One 11 e0167765
[19] He S and Scheres S H W 2017 J. Struct. Biol. 198 163
[20] Scheres S H 2012 J. Struct. Biol. 180 519
[21] Scheres S H 2016 Methods Enzymol. 579 125
[22] Sigworth F J, Doerschuk P C, Carazo J M and Scheres S H 2010 Methods Enzymol. 482 263
[23] Wang Q, Matsui T, Domitrovic T, Zheng Y, Doerschuk P C and Johnson J E 2013 J. Struct. Biol. 181 195
[24] von der Ecken J, Heissler S M, Pathan-Chhatbar S, Manstein D J and Raunser S 2016 Nature 534 724
[25] Kellogg E H, Howes S, Ti S C, Ramirez-Aportela E, Kapoor T M, Chacon P and Nogales E 2016 Proc. Nat. Acad. Sci. USA 113 9430
[26] Oshima A, Tani K and Fujiyoshi Y 2016 Nat. Commun. 7 13681
[27] Sun L, Zhang X, Gao S, Rao P A, Padilla-Sanchez V, Chen Z, Sun S, Xiang Y, Subramaniam S, Rao V B and Rossmann M G 2015 Nat. Commun. 6 7548
[28] Bai X C, Fernandez I S, McMullan G and Scheres S H 2013 Elife 2 e00461
[29] De Colibus L and Stuart D I 2017 J. Struct. Biol. DOI:10.1016/j.jsb.2017.10.010
[30] Weiss G L, Medeiros J M and Pilhofer M 2017 Methods Mol. Biol. 1615 353
[31] Baker L A, Grange M and Grunewald K 2017 Curr. Opin. Struct. Biol. 46 149
[32] Wagner J, Schaffer M and Fernandez-Busnadiego R 2017 Febs Lett. 591 2520
[33] Beck M and Baumeister W 2016 Trends in Cell Biology 26 825
[34] Fridman K, Mader A, Zwerger M, Elia N and Medalia O 2012 Nat. Rev. Mol. Cell Biol. 13 736
[35] Schur F K, Hagen W J, de Marco A and Briggs J A 2013 J. Struct. Biol. 184 394
[36] Turonova B, Schur F K M, Wan W and Briggs J A G 2017 J. Struct. Biol. 199 187
[37] Subramaniam S and Henderson R 1999 J. Struct. Biol. 128 19
[38] Kunji E R, von Gronau S, Oesterhelt D and Henderson R 2000 Proc. Nat. Acad. Sci. USA 97 4637
[39] Fitzpatrick A W P, Falcon B, He S, Murzin A G, Murshudov G, Garringer H J, Crowther R A, Ghetti B, Goedert M and Scheres S H W 2017 Nature 547 185
[40] Zhang R, Alushin G M, Brown A and Nogales E 2015 Cell 162 849
[41] Grigorieff N and Harrison S C 2011 Curr. Opin. Struct. Biol. 21 265
[42] Alberts B 1998 Cell 92 291
[43] Robinson C V, Sali A and Baumeister W 2007 Nature 450 973
[44] Asano S, Engel B D and Baumeister W 2016 J. Mol. Biol. 428 332
[45] Koster A J, Grimm R, Typke D, Hegerl R, Stoschek A, Walz J and Baumeister W 1997 J. Struct. Biol. 120 276
[46] Wagner J, Schaffer M and Fernandez-Busnadiego R 2017 FEBS Lett. 591 2520
[47] Wrobel G, Holler M, Ingebrandt S, Dieluweit S, Sommerhage F, Bochem H P and Offenhausser A 2008 J. R. Soc. Interface 5 213
[48] Makabe S, Naguro T and Stallone T 2006 Microsc. Res. Tech. 69 436
[49] Hautekeete M L, Geerts A, Seynaeve C, Lazou J M, Kloppel G and Wisse E 1993 Eur. J. Morphol. 31 72
[50] Barth O M and Majerowicz S 1988 Mem. Inst. Oswaldo. Cruz. 83 63
[51] Simon J R and Salmon E D 1990 J. Cell Sci. 96 (Pt 4) 571
[52] Giannotti J and Milne R G 1977 Virology 80 347
[53] Leberman R 1965 J. Mol. Biol. 13 606
[54] Fassel T A, Sohnle P G and Kushnaryov V M 1997 Biotech. Histochem. 72 268
[55] Guimaraes Fde S, de Oliveira S M, de Oliveira C C, Donatti L and Buchi Dde F 2009 Ultrastruct. Pathol. 33 169
[56] Holbrook K A, Perkins W D and Glick B 1974 J. Reticuloendothel. Soc. 16 300
[57] Chemnitz J and Bichel P 1973 Exp. Cell Res. 82 319
[58] Haugen A and Laerum O D 1979 J. Nat. Cancer Inst. 63 455
[59] Dedonder S E, Cheng C, Willard L H, Boyle D L and Ganta R R 2012 PLoS One 7 e36749
[60] Setum C M, Serie J R and Hegre O D 1993 Anat. Rec. 235 285
[61] Beck M and Baumeister W 2016 Trends Cell Biol. 26 825
[62] Vanhecke D, Asano S, Kochovski Z, Fernandez-Busnadiego R, Schrod N, Baumeister W and Lucic V 2011 J. Microsc. 242 221
[63] Gruska M, Medalia O, Baumeister W and Leis A 2008 J. Struct. Biol. 161 384
[64] Iancu C V, Tivol W F, Schooler J B, Dias D P, Henderson G P, Murphy G E, Wright E R, Li Z, Yu Z, Briegel A, Gan L, He Y and Jensen G J 2007 Nat. Protoc. 1 2813
[65] Masich S, Ostberg T, Norlen L, Shupliakov O and Daneholt B 2006 J. Struct. Biol. 156 461
[66] Talmon Y, Prasad B V, Clerx J P, Wang G J, Chiu W and Hewlett M J 1987 J. Virol. 61 2319
[67] Iancu C V, Tivol W F, Schooler J B, Dias D P, Henderson G P, Murphy G E, Wright E R, Li Z, Yu Z H, Briegel A, Gan L, He Y N and Jensen G J 2007 Nat. Protocols 1 2813
[68] Aebi U and Pollard T D 1987 J. Electron. Microsc. Tech. 7 29
[69] Mitchell D R and Schaffer B 2005 Ultramicroscopy 103 319
[70] Irobalieva R N, Martins B and Medalia O 2016 J. Cell Sci. 129 469
[71] Mastronarde D N 2005 J. Struct. Biol. 152 36
[72] Hagen W J, Wan W and Briggs J A 2017 J. Struct. Biol. 197 191
[73] Mastronarde D N and Held S R 2017 J. Struct. Biol. 197 102
[74] Castano-Diez D 2017 Acta Crystallogr D-Struct. Biol. 73 478
[75] Han R, Wan X, Wang Z, Hao Y, Zhang J, Chen Y, Gao X, Liu Z, Ren F, Sun F and Zhang F 2017 J. Struct. Biol. 199 196
[76] Zurner A, Doblinger M, Cauda V, Wei R and Bein T 2012 Ultramicroscopy 115 41
[77] Deng Y, Chen Y, Zhang Y, Wang S, Zhang F and Sun F 2016 J. Struct. Biol. 195 100
[78] Liu J, Chen C Y, Shiomi D, Niki H and Margolin W 2011 Virology 417 304
[79] Wan W and Briggs J A 2016 Methods Enzymol. 579 329
[80] Galaz-Montoya J G and Ludtke S J 2017 Biophys. Rep. 3 17
[81] Schur F K, Obr M, Hagen W J, Wan W, Jakobi A J, Kirkpatrick J M, Sachse C, Krausslich H G and Briggs J A 2016 Science 353 506
[82] Hecksel C W, Darrow M C, Dai W, Galaz-Montoya J G, Chin J A, Mitchell P G, Chen S, Jakana J, Schmid M F and Chiu W 2016 Microsc. Microanal. 22 487
[83] Rigort A, Gunther D, Hegerl R, Baum D, Weber B, Prohaska S, Medalia O, Baumeister W and Hege H C 2012 J. Struct. Biol. 177 135
[84] Chen M, Dai W, Sun S Y, Jonasch D, He C Y, Schmid M F, Chiu W and Ludtke S J 2017 Nat. Methods 14 983
[85] Koyfman A Y, Schmid M F, Gheiratmand L, Fu C J, Khant H A, Huang D, He C Y and Chiu W 2011 Proc. Nat. Acad. Sci. USA 108 11105
[86] Wang R, Stone R L, Kaelber J T, Rochat R H, Nick A M, Vijayan K V, Afshar-Kharghan V, Schmid M F, Dong J F, Sood A K and Chiu W 2015 Proc. Nat. Acad. Sci. USA 112 14266
[87] Traenkle B and Rothbauer U 2017 Front. Immunol. 8 1030
[88] Wolff G, Hagen C, Grunewald K and Kaufmann R 2016 Biol. Cell 108 245
[89] Schaffer M, Engel B D, Laugks T, Mahamid J, Plitzko J M and Baumeister W 2015 Bio. Protoc. 5
[90] Rigort A, Villa E, Bauerlein F J, Engel B D and Plitzko J M 2012 Methods Cell Biol. 111 259
[91] Villa E, Schaffer M, Plitzko J M and Baumeister W 2013 Curr. Opin. Struct. Biol. 23 771
[92] Raddi G, Morado D R, Yan J, Haake D A, Yang X F and Liu J 2012 J. Bacteriol. 194 1299
[93] Liu J, Lin T, Botkin D J, McCrum E, Winkler H and Norris S J 2009 J. Bacteriol. 191 5026
[94] Jasnin M, Ecke M, Baumeister W and Gerisch G 2016 Structure 24 1031
[95] Eibauer M, Pellanda M, Turgay Y, Dubrovsky A, Wild A and Medalia O 2015 Nat. Commun. 6 7532
[96] Razi A, Britton R A and Ortega J 2017 Nucleic Acids Res. 45 1027
[97] Franken L E, Oostergetel G T, Pijning T, Puri P, Arkhipova V, Boekema E J, Poolman B and Guskov A 2017 Nat. Commun. 8 722
[98] Hashem Y, des Georges A, Fu J, Buss S N, Jossinet F, Jobe A, Zhang Q, Liao H Y, Grassucci R A, Bajaj C, Westhof E, Madison-Antenucci S and Frank J 2013 Nature 494 385
[99] Jomaa A, Stewart G, Martin-Benito J, Zielke R, Campbell T L, Maddock J R, Brown E D and Ortega J 2011 RNA 17 697
[100] Englmeier R, Pfeffer S and Forster F 2017 Structure 25 1574
[101] Szwedziak P, Wang Q, Bharat T A, Tsim M and Lowe J 2014 Elife 3 e04601
[102] Schlimpert S, Klein E A, Briegel A, Hughes V, Kahnt J, Bolte K, Maier U G, Brun Y V, Jensen G J, Gitai Z and Thanbichler M 2012 Cell 151 1270
[103] Engel B D, Schaffer M, Kuhn Cuellar L, Villa E, Plitzko J M and Baumeister W 2015 Elife 4
[104] Ingerson-Mahar M, Briegel A, Werner J N, Jensen G J and Gitai Z 2010 Nat. Cell Biol. 12 739
[105] Booth C R, Jakana J and Chiu W 2006 J. Struct. Biol. 156 556
[106] Wu S, Armache J P and Cheng Y 2016 Microscopy (Oxf) 65 35
[107] Grigorieff N 2013 Elife 2 e00573
[108] Bammes B E, Rochat R H, Jakana J, Chen D H and Chiu W 2012 J. Struct. Biol. 177 589
[109] Li X, Zheng S Q, Egami K, Agard D A and Cheng Y 2013 J. Struct. Biol. 184 251
[110] Nogales E 2016 Nat. Methods 13 24
[111] Frank J 2006 Three-dimensional electron microscopy of macromolecular assemblies:visualization of biological molecules in their native state, 2nd edn., (Oxford, New York:Oxford University Press)
[112] Glaeser R M 2013 Rev. Sci. Instrum. 84
[113] Danev R and Nagayama K 2001 Ultramicroscopy 88 243
[114] Danev R, Buijsse B, Khoshouei M, Plitzko J M and Baumeister W 2014 Proc. Nat. Acad. Sci. USA 111 15635
[115] Asano S, Fukuda Y, Beck F, Aufderheide A, Forster F, Danev R and Baumeister W 2015 Science 347 439
[116] Mahamid J, Pfeffer S, Schaffer M, Villa E, Danev R, Cuellar L K, Forster F, Hyman A A, Plitzko J M and Baumeister W 2016 Science 351 969
[117] Fan X, Zhao L, Liu C, Zhang J C, Fan K, Yan X, Peng H L, Lei J and Wang H W 2017 Structure 25 1623
[118] Schaffer M, Mahamid J, Engel B D, Laugks T, Baumeister W and Plitzko J M 2017 J. Struct. Biol. 197 73
[119] Khoshouei M, Pfeffer S, Baumeister W, Forster F and Danev R 2017 J. Struct. Biol. 197 94
[120] Pierson J, Fernandez J J, Bos E, Amini S, Gnaegi H, Vos M, Bel B, Adolfsen F, Carrascosa J L and Peters P J 2010 J. Struct. Biol. 169 219
[121] Kishimoto-Okada A, Murakami S, Ito Y, Horii N, Furukawa H, Takagi J and Iwasaki K 2010 J. Electron. Microsc. (Tokyo) 59 419
[122] Mesman R J 2013 J. Struct. Biol. 183 527
[123] Hsieh C E, Leith A, Mannella C A, Frank J and Marko M 2006 J. Struct. Biol. 153 1
[124] Al-Amoudi A and Frangakis A S 2008 Biochem. Soc. Trans. 36 181
[125] Bouchet-Marquis C, Zuber B, Glynn A M, Eltsov M, Grabenbauer M, Goldie K N, Thomas D, Frangakis A S, Dubochet J and Chretien D 2007 Biol. Cell 99 45
[126] Delgado L, Carrion O, Martinez G, Lopez-Iglesias C and Mercade E 2013 PLoS One 8 e73297
[127] Dittmann C, Han H M, Grabenbauer M and Laue M 2015 J. Struct. Biol. 191 156
[128] Villa E, Schaffer M, Plitzko J M and Baumeister W 2013 Curr. Opin. Struct. Biol. 23 771
[129] Marko M, Hsieh C, Schalek R, Frank J and Mannella C 2007 Nat. Methods 4 215
[130] Villa E, Schaffer M, Plitzko J M and Baumeister W 2014 Biophys. J. 106 600a
[131] Hsieh C, Schmelzer T, Kishchenko G, Wagenknecht T and Marko M 2014 J. Struct. Biol. 185 32
[132] Hsieh C, Schmelzer T, Kishchenko G, Wagenknecht T and Marko M 2014 J. Struct. Biol. 185 32
[133] Zhang J, Ji G, Huang X, Xu W and Sun F 2016 J. Struct. Biol. 194 218
[134] Hagen C, Dent K C, Zeev-Ben-Mordehai T and et al. 2015 Cell 163 1692
[135] He J, Hsieh C, Wu Y P, Schmelzer T, Wang P, Lin Y, Marko M and Sui H X 2017 J. Struct. Biol. 199 114
[136] Sartori A, Gatz R, Beck F, Rigort A, Baumeister W and Plitzko J M 2007 J. Struct. Biol. 160 135
[137] Wang K, Strunk K, Zhao G, Gray J L and Zhang P 2012 J. Struct. Biol. 180 318
[138] Koning R I, Celler K, Willemse J, Bos E, van Wezel G P and Koster A J 2014 Methods Cell Biol. 124 217
[139] Hampton C M, Strauss J D, Ke Z, Dillard R S, Hammonds J E, Alonas E, Desai T M, Marin M, Storms R E, Leon F, Melikyan G B, Santangelo P J, Spearman P W and Wright E R 2016 Nat. Protoc. 12 150
[140] Galaz-Montoya J G, Hecksel C W, Baldwin P R, Wang E, Weaver S C, Schmid M F, Ludtke S J and Chiu W 2016 J. Struct. Biol. 194 383
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