Elsevier S & T

The Enzymes: Molecular Machines Involved in Protein Transport across Cellular Membranes

Dalbey, Ross; Koehler, Carla; Tamanoi, Fuyuhiko

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Table of contents

Contentsv
Prefacexiii
Part I: Crossing Bacterial Membranes1
Chapter 1: Cotranslational Protein Targeting in Escherichia coli
I. Introduction3
II. The Ribosome4
A. The Ribosomal Tunnel4
B. Sensing Nascent Secretory and Membrane Proteins in the Tunnel?6
C. L23 at the Exit Site8
III. Chaperones and Targeting Factors at the Ribosomal Tunnel Exit8
A. SRP-Ribosome Interaction8
B. TF-Ribosome Interaction9
C. Interplay Between TF and SRP on the Ribosome11
D. The Nascent Polypeptide-Associated Complex13
E. The Hsp70-RAC Triad14
IV. SRP-Mediated Targeting14
A. General Features of SRP16
B. Signal Peptide Binding to the M-Domain17
C. The SRP Receptor FtsY17
D. Inter- and Intramolecular Communication Between the SRP Components18
V. Selection of Protein for SRP-Mediated Targeting19
A. SRP-Mediated Targeting in E. coli Occurs Cotranslationally21
B. How Important Is SRP for Bacteria?22
VI. Concluding Remarks23
Acknowledgments24
References24
Chapter 2: Sec Protein-Conducting Channel and SecA35
II. Introduction35
III. Outline37
IV. Variation and Evolution of the Sec Machinery37
A. The Canonical Bacterial Sec Machinery37
B. Evolutionary History of the E. coli Sec Machinery38
C. Sec Paralogues40
V. SecA Structure, Function, and Dynamics41
A. The Involvement of SecA in Cotranslational Protein Translocation41
B. The Overall Mechanism of Posttranslational Protein Translocation42
C. Structure of the SecA Protomer43
D. Structure of the Functional SecA Dimer48
E. Conformational Changes Within SecA49
F. SecA-SecB Interaction50
G. SecA-Membrane Interaction51
VI. SecYEG Structure, Function, and Dynamics51
A. Structure of the SecYEG Protomer51
B. Arrangement of SecYEG Protomers Within an Oligomeric Assembly56
C. Induction of Conformational Changes in SecYEG58
D. The Role of the Plug59
VII. Concluding Remarks59
References59
Chapter 3: Targeting of Proteins by the Twin-Arginine Translocation System in Bacteria and Chloropla69
I. Introduction69
II. Basic Features of Tat Systems, Their Discovery, and Their Distribution70
III. tat Genes and Mutant Phenotypes71
A. tat Genes in Gram-Negative Bacteria71
B. tat Mutant Phenotypes and Substrate Specificities in Gram-Negative Bacteria72
C. tat Genes in Plants76
D. tat Genes in Gram-Positive Organisms and Archaea77
IV. The Tat Subunits: Structures and Conserved Regions78
V. Structures of Tat Complexes80
VI. Tat Signal Peptides82
VII. The Tat Mechanism84
A. The Translocation Mechanism Used by the E.coli and Thylakoid Tat Systems84
B. A Different Translocation Mechanism in B. subtilis?85
References87
Chapter 4: YidC: A Protein with Multiple Functions in Bacterial Membrane Biogenesis93
I. Introduction93
II. The YidC Pathway96
III. Sec-YidC Pathway97
IV. YidC Substrates99
V. YidC Family of Proteins100
VI. Concluding Remarks and Outlook105
References
Chapter 5: Disulfide Bond Formation Enzymes111
I. Disulfides Stabilize Secreted Proteins111
II. The Need for a Catalyst112
III. DsbA: The Primary Oxidant112
IV. Structure of DsbA116
V. How Is DsbA Reoxidized?117
VI. Reoxidation of DsbB119
VII. Disulfide Bond Isomerization121
VIII. DsbD a Disulfide Transporter?123
References
Chapter 6: The Identification of the YaeT Complex and Its Role in the Assembly of Bacterial Outer Me129
II. Gram-Negative Bacterial Envelope130
III. Protein Transport Across the Bacterial Envelope130
IV. Identification of OM Biogenesis Factors: The Search for Needles in a Haystack135
V. Chemical Conditionality: The YfgL Connection to OM Assembly136
VI. Identification and Characterization of the YaeT Complex138
VII. Interactions Among YaeT Complex Members141
VIII. POTRA Domains142
IX. Properties of the YaeT-Like beta-Barrel Domains144
X. Conclusions and Future Study145
References
Chapter 7: The Function of the ABC Transporter LolCDE in Protein Transport to the Outer Membrane of151
II. Introduction152
A. Structure and Function of Outer Membrane Proteins in Gram-Negative Bacteria152
B. Biogenesis of Lipoproteins154
C. Lipoprotein-Sorting Signals156
III. Sorting of Lipoproteins by the Lol System157
A. Localization of Lipoproteins157
B. LolA, a Periplasmic Chaperon for Lipoproteins157
C. LolB, an Outer Membrane Receptor for Lipoproteins158
D. Structures of LolA and LolB159
E. LolCDE, an ABC Transporter Mediating the Membrane Detachment of Lipoproteins160
F. Perspectives169
Acknowledgments170
References170
Part II: Crossing Endoplasmic Reticulum Membranes175
Chapter 8: The Signal Recognition Particle and Its Receptor in ER Protein Targeting177
II. Introduction178
III. Cotranslational Translocation: A Historical Perspective180
A. The Signal Hypothesis181
B. mRNA Partitioning183
IV. Targeting of Proteins to the ER Is Regulated by Unusual GTPases186
A. Characterization of the SRbeta Subunit of the SR187
B. Docking the Ribosome on the Translocon190
V. Structure-Function Analysis191
A. Signal Recognition Particle191
B. SRP RNA192
C. SRP9 and SRP14194
D. SRP68 and SRP72195
E. SRP19196
F. SRP54196
G. SRP21, an SRP Subunit Unique to Yeast199
H. Engaging the Translocation Complex199
VI. Conclusions200
Acknowledgments200
References
Chapter 9: The Translocation Apparatus of the Endoplasmic Reticulum207
II. Translocons Receive Substrates via Two Distinct Pathways208
III. Substrate Recognition by the ER Translocon Is a Decisive Step in Protein Translocation209
IV. The Remarkable Diversity of Sequences Recognized by the Translocon213
V. The Machinery of Signal Sequence Recognition214
VI. A Combined Framework for Signal and TMD Recognition216
VII. Gating of the Protein-Conducting Channel of the Translocon219
VIII. The Energetics of Protein Translocation223
IX. The Biogenesis of Membrane Proteins225
X. Lateral Exit of TMDs from the Translocon228
XI. Regulation of Protein Translocation231
References
Chapter 10: The Role of BiP/Kar2p in the Translocation of Proteins Across the ER Membrane
II. Hsp70
A. The Structure of Hsp70
B. The Hsp70 Reaction Cycle248
C. BiP/Kar2p249
III. Protein Translocation into the ER250
A. The Sec Complex251
B. Posttranslational Translocation254
C. Cotranslational Translocation256
IV. Folding of Nascent Proteins in the ER and ER-Associated Degradation (ERAD)259
V. Unanswered Questions261
Acknowledgments262
References262
Chapter 11: Calnexin, Calreticulin, and Their Associated Oxidoreductase ERp57
II. Introduction
III. Structural Characteristics of Calnexin and Calreticulin
A. Carbohydrate-Binding Site
B. P-Domain280
C. Retention Signals281
D. Regulatory Domains281
IV. The Roles of Calnexin and Calreticulin in Glycoprotein Maturation and Quality Control
A. Topological Constraints Control Lectin Chaperone Functions283
B. Lectin Chaperones Involvement in Quality Control285
C. Peptide-Binding Function286
V. The Calnexin-Binding Cycle in Yeast288
VI. ERp57, a Member of the PDI Family of Oxidoreductases289
A. Structural Insights into ERp57 from the PDI Crystal Structure289
B. ERp57 Docking onto Its Partner Lectin Chaperones292
VII. Redox Activity of ERp57292
VIII. The Role of ERp57 in Glycoprotein Folding294
IX. Regulation of Calcium Signaling296
X. Summary297
References298
Part III: Crossing Mitochondrial Membranes307
Chapter 12: TOM and SAM Machineries in Mitochondrial Protein Import and Outer Membrane Biogenesis309
II. Introduction310
A. Structural Features of Mitochondrial Proteins311
III. The TOM Complex313
A. The Core TOM Complex: A Primitive Protein Translocase?313
B. The Holo-TOM Complex: The Addition of Recently Evolved TOM Receptor Proteins321
IV. The SAM Complex326
A. Machinery for the Assembly of Complex Proteins into the Mitochondrial Outer Membrane326
B. Additional Modules of the SAM in the Outer Membrane330
V. Concluding Remarks332
Acknowledgments333
References333
Chapter 13: The Role of the Mia40-Erv1 Disulfide Relay System in Import and Folding of Proteins of t345
II. Introduction346
III. Protein Import Routes into the IMS347
IV. Mia40, an Import Receptor in the IMS349
A. Structural Organization of Mia40 Proteins349
B. The Function of Mia40 in the IMS350
V. Erv1, a Disulfide Oxidase in the IMS351
A. Structural Organization of Erv1 Proteins351
B. Other Proteins with Erv1-Like Domains353
C. Functions of Erv1 in the IMS355
VI. A Model of Mia40-Erv1-Mediated Import357
VII. Substrate Proteins of the Mia40-Erv1 Pathway360
A. Proteins of the Twin Cx3C Family360
B. Proteins of the Twin Cx9C Family360
VIII. Perspectives361
Acknowledgments362
References362
Chapter 14: The Function of TIM22 in the Insertion of Inner Membrane Proteins in Mitochondria367
II. Introduction368
III. Properties of Precursors that Utilize the TIM22 Import Pathway370
IV. The Small Tim Proteins373
V. The TIM22 Inner Membrane Complex375
VI. Disease Connections377
References379
Chapter 15: The Role of the TIM23 Complex and Its Associated Motor Complex in Mitochondrial Protein387
II. Introduction388
III. Mitochondrial Presequence Proteins390
A. The Structure of the Presequence391
B. Functions of the Presequence391
C. Processing and Sorting of the Mature Protein392
IV. The Presequence Translocase: TIM23 Complex392
A. Components of the TIM23 Complex393
B. The Tim23 Channel and Its Regulation394
V. Energy Requirement for Matrix Translocation: The Motor Complex395
A. The Membrane Potential and ATP-Hydroplysis Drive Protein Import395
B. MtHsp70: The Central Component of the Motor Complex395
C. Components of the Motor Complex396
VI. Models of Motor Function398
A. Protein Unfolding for Import398
B. Two Models of Hsp70 Function for Matrix Import398
C. Functional Implication of PAM Organization for Hsp70 Regulation399
VII. Transport of Proteins Across Two Membranes400
A. Structural Connection Between Translocases on the Outer and Inner Membrane400
B. The .TOM-TIM.23 Supercomplex401
VIII. Protein Transport Through Two Different Forms of the Presequence Translocase402
Acknowledgments403
References403
Part IV: Crossing Chloroplast Membranes413
Chapter 16: The Toc Machinery of the Protein Import Apparatus of Chloroplasts415
I. Introduction415
II. General Overview of Toc Complexes417
III. Toc Receptors418
IV. The Toc Translocon Channel and Membrane Translocation423
V. Cytoplasmic Events425
VI. Toc Complex Evolution and Diversity426
VII. Toc Complex Assembly430
VIII. Future Directions432
References433
Chapter 17: The Role of the Tic Machinery in Chloroplast Protein Import439
II. Introduction440
III. Tic110: The Translocation Channel441
IV. Tic40: The Cochaperone446
V. Tic20: A Putative Channel Protein449
VI. Tic22: A Connection to Toc in the Intermembrane Space451
VII. Tic32: A Short Chain Dehydrogenase452
VIII. Tic62: The FNR-Binding Protein453
IX. Tic55: The Rieske-Family Member454
X. Traveling Back in Time455
References
Chapter 18: The Sec and Tat Protein Translocation Pathways in Chloroplasts463
II. Overview of Protein Trafficking to the Plant Thylakoid Membrane and Lumen464
III. Targeting to the Sec and Tat Pathways466
IV. The Sec Transport System in Chloroplasts468
A. Introduction468
B. Thylakoid Components469
C. Capabilities and Operation of the Thylakoid Sec System469
D. cpSecY2 and cpSecA2471
E. Prospects472
V. The Tat System in Chloroplasts472
A. Introduction472
B. Capabilities and Requirements of the Thylakoid Tat System473
C. Operation of the Tat System479
D. Models for the Tat Translocase and Future Directions484
Acknowledgments486
References
Chapter 19: Chloroplast SRP/FtsY and Alb3 in Protein Integration into the Thylakoid Membrane493
II. Introduction494
III. The General Pathway for Posttranslational Targeting of LHCPs by cpSRP495
IV. Soluble and Membrane Components of the Posttranslational SRP Pathway497
A. cpSRP Is Composed of a Conserved 54-kDa GTPase and a 43-kDa Subunit Unique to Chloroplasts497
B. A cpSRP Receptor Homologue Is Required for cpSRP-Based Protein Targeting to the Thylakoid Membran499
C. LHCP Integration Appears Independent of Thylakoid Sec and TAT Transport Pathways500
D. The Oxa1/Alb3/YidC Family Functions in LHCP Integration500
E. Posttranslational Binding to cpSRP is Linked to an Alb3 Requirement for Integration502
V. Steps in the Posttranslational SRP Targeting Pathway502
A. cpSRP Assembly502
B. Transit Complex Formation504
C. Membrane Events in the Posttranslational cpSRP Pathway507
VI. An Overlapping Post- and Cotranslational Function of cpSRP/cpFtsY/Alb3509
A. Biochemical Evidence for a Cotranslational cpSRP-Targeting Pathway509
B. Analysis of Mutants Lacking Components of the cpSRP Pathway510
VII. Conclusions and Outlook515
Note Added In Proof516
Acknowledgments516
References516
Part V: Crossing Peroxisomal Membranes523
Chapter 20: The Role of Shuttling Targeting Signal Receptors and Heat-Shock Proteins in Peroxisomal525
I. Catalytic Machines Involved in Peroxisomal Matrix Protein Import525
II. Components Involved in Peroxisomal Matrix Protein Import526
A. Receptor Shuttling During Peroxisomal Matrix Protein Import528
B. The Peroxisomal RADAR Pathway530
C. PTS Receptor-Mediated Steps in the Matrix Protein Import Cycle531
D. Energetics of Receptor Recycling and Cargo Import533
III. Role of Hsp70 Family of Proteins in Peroxisomal Matrix Protein Import534
Acknowledgments536
References536
Chapter 21: Function of the Ubiquitin-Conjugating Enzyme Pex4p and the AAA Peroxin Complex Pex1p/Pex541
I. Introduction541
II. Peroxisomal Matrix Protein Import542
A. Import of Folded and Oligomeric Proteins Across the Peroxisomal Membrane543
B. Sequential Model for PTS-Receptor Cycle543
III. Overview: Enzymes Involved in Ubiquitination546
A. Enzymatic Cascade for Protein Modification546
B. Downstream Components of Ubiquitin-Based Protein-Targeting Systems547
IV. The Ubiquitin-Conjugating Enzyme Pex4p in Peroxisome Biogenesis548
A. Ubiquitin-Conjugating Enzymes of the Ubc4p Family Involved in PTS Receptor Regulation548
B. Function of Pex4p/Ubc10p in Receptor Recycling551
C. Peroxisomal RING-Finger Proteins as Putative Ubiquitin-Ligase-Complex553
V. The AAA Family ATPases555
A. Function and Structure of AAA-Type ATPases555
B. AAA ATPases in Protein Transport556
VI. Pex1p and Pex6p: AAA Proteins Required for Peroxisomal Biogenesis557
A. ATP-Dependency of Matrix Protein Import557
B. Structural Characterization of the AAA Peroxins558
C. Similarities of the Peroxisomal Import Machinery with ERAD Components558
VII. Receptor Ubiquitination: A Link Between Pex4p, AAA Peroxins, and Protein Transport?561
References564
Author Index573
Index623

Book details

Vendor Elsevier S & T
SKU 9780123739162
ISBN-13 9780080552163
Author Dalbey, Ross; Koehler, Carla; Tamanoi, Fuyuhiko
Category Science
Subject Biochemistry

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This volume of The Enzymes features high-caliber thematic articles on the topic of molecular machines involved in protein transport across cellular membranes. The book consists of five parts which span the range of membranes including bacterial, endoplasmic reticulum, mitochondrial, chloroplast, and peroxismal.

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