Front Cover

Dyneins

Dyneins: STRUCTURE, BIOLOGY AND DISEASE: The Biology of Dynein Motors

Copyright

Contents

List of Contributors

Biography

Stephen King Biosketch

Preface

A Cautionary Note About Dynein Nomenclature

References

I - History and Evolution

1 - Discovery of dynein and its properties: a personal account

1.1 Introduction

1.1.1 Early years

1.1.2 Life in Cambridge

1.1.3 Moving to the United States

1.2 Research at Harvard

1.2.1 Electron microscopy of cilia and flagella

1.2.2 Discovery of dynein

1.2.3 Codiscovery of tubulin

1.2.4 A time for decisions

1.3 Research at the University of Hawaii

1.3.1 Moving to a new lab in Honolulu

1.3.2 Demembranated axonemes allow direct study of motility

1.3.2.1 Uniform preparations of demembranated flagellar axonemes

1.3.2.1.1 Motility of reactivated sperm flagella closely resembles that of live sperm

1.3.2.1.2 The robustness of flagellar beating indicates the presence of a well-regulated oscillatory system, with independent co...

1.3.2.1.3 Organic anions stabilize the reactivated motility of sperm flagella and the latency of dynein ATPase

1.3.2.2 ATP-dependent sliding of doublet tubules in trypsin-treated flagella

1.3.2.3 ATP-dependent sliding between adjacent doublet tubules is generated by the enzymatic dephosphorylation of ATP in the dyn...

1.3.2.4 Dynein arms make fixed crossbridges in the absence of MgATP

1.3.2.5 High-voltage electron microscopy of axonemal structure in rigor wave flagella

1.3.2.6 ATP-dependent motility and sliding of filaments in mammalian sperm flagella

1.3.2.7 Extension and confirmation of the sliding microtubule model

1.3.3 Protein chemistry reveals the complexity of dyneins

1.3.3.1 Revolution in cell biology: the development of denaturing gel electrophoresis

1.3.3.2 Multiple isoforms of dynein

1.3.3.3 The subunit composition of outer-arm dynein differs between sea urchins and Chlamydomonas

1.3.3.4 Discovery of dynein’s microtubule-binding domain

1.3.3.5 Vanadate inhibits the cross-bridge cycling of dynein ATPase

1.3.3.6 Vanadate-sensitized photocleavage

1.3.3.7 Properties of the isolated β heavy chain from sea urchin sperm flagella

1.3.3.8 Tryptic digestion and a linear map of the β heavy chain

1.3.4 Transition from protein chemistry to molecular biology

1.3.4.1 Getting setup

1.3.4.2 Sequencing the cDNA encoding the β heavy chain of outer-arm dynein

1.3.4.3 Experimental assay of nucleotide-binding to β and γ heavy chain subunits of outer-arm dynein

1.3.5 Exploring the dynein family of multiple isoforms

1.3.6 Function of cytoplasmic dynein in yeast

1.3.7 Regulation of microtubule sliding in cilia and flagella

1.3.7.1 Modulation of flagellar beating by Ca2+: asymmetric waveforms, quiescence, and chemotaxis

1.3.7.1.1 Background

1.3.7.1.2 Increasing concentrations of intracellular Ca2+ result in a progressive inhibition of reverse bend growth and can lead...

1.3.7.2 The central apparatus and radial spokes govern the plane of beat and the orientation of Ca2+-mediated asymmetry in sperm...

1.3.7.2.1 Sperm flagella lacking the two central tubules propagate only three-dimensional helicoidal bending waves

1.3.7.2.2 Forced rotation of the central complex causes rotation of the flagellar beat plane and the orientation of Ca2+-mediate...

1.3.7.3 Studies on bend initiation, growth, and propagation

1.3.7.3.1 Bend initiation requires a block to prevent sliding between adjacent doublet tubules at the flagellar base

1.3.7.3.2 Mechanical stress applied to the flagellar base can advance or retard the timing of new bend initiation without disrup...

1.3.7.3.3 Information about an abrupt change in imposed beat frequency is communicated to the distal regions of the flagellum at...

1.3.7.3.4 Hydrodynamic boundary conditions at the basal end of the flagellum have an important role in determining the bend angl...

1.3.8 Loose ends in Honolulu

1.4 Semiretirement in Berkeley

1.4.1 Dynein as a member of the AAA+ class of chaperone-like ATPases

1.4.1.1 Background

1.4.1.2 Homology-based model for the motor domain of β heavy chain of sea urchin dynein

1.4.1.3 Genomic analysis of midasin, dynein’s nearest neighbor in the AAA+ family

1.4.2 Evolution within the dynein gene family

1.4.2.1 Early studies

1.4.2.2 Dynein heavy chains in the sea urchin genome

1.4.2.3 Natural history of the dynein heavy chain gene family

1.4.3 Regulation of binding affinity in dynein’s microtubule-binding domain

1.4.4 Helix sliding in the dynein stalk couples ATPase and microtubule-binding

1.4.5 Crystal structure of dynein’s ATP-sensitive microtubule-binding domain

1.5 The pluses of working on a minus-end directed motor

Acknowledgments

Epilogue

References

2 - Origins of cytoplasmic dynein

2.1 Early evidence for a potential cytoplasmic form of dynein

2.2 Microtubule-associated proteins

2.2.1 Nucleotide effects

2.2.2 Evidence for MAP1C as a cytoplasmic form of dynein

2.3 Cytoplasmic dynein as the retrograde transport factor

2.4 Implications for axonemal dyneins

2.5 Conclusions

Acknowledgments

References

3 - The evolutionary biology of dyneins

3.1 Introduction

3.1.1 Dynein classification

3.1.2 Dynein heavy chain families

3.1.2.1 Cytoplasmic dynein families

3.1.2.2 Outer-arm dyneins

3.1.2.3 Inner-arm dyneins

3.1.2.4 Additional dynein heavy chain families?

3.1.3 Intermediate chains

3.1.4 Light-intermediate and light chains

3.2 Dynein evolution in eukaryotes

3.2.1 Dyneins: a history of loss

3.2.1.1 Loss of cytoplasmic dynein 1

3.2.1.2 Loss of cytoplasmic dynein 2

3.2.1.3 Loss of ciliary dyneins

3.2.1.4 Organisms possessing no dynein

3.2.2 Unexpected presences

3.2.3 Duplication and diversification

3.3 Evolution in the protoeukaryote

3.3.1 A cytoplasmic dynein root: sensation before motility

3.3.2 Alternative rooting: motility drives ciliary evolution

3.3.3 Formation of the major dynein families

3.4 The origins of dynein

3.4.1 Evolution of structure

3.4.2 Evolution of function

3.5 Summary

References

II - Dyneins in Ciliary Biology

4 - Cytoplasmic preassembly and trafficking of axonemal dyneins

4.1 Introduction

4.2 Cytoplasmic chaperones

4.2.1 ODA7/DNAAF1

4.2.2 PIH domain proteins and the R2TP complex

4.2.3 Additional potential co-chaperones

4.3 Late cytoplasmic assembly/maturation

4.3.1 ODA8

4.4 Transport of axonemal dyneins via intraflagellar transport

4.5 Docking complex

4.6 Conclusions

References

5 - Composition and assembly of axonemal dyneins*

5.1 Introduction

5.2 Classes of dynein components

5.3 Monomeric inner dynein arms

5.4 Dimeric inner dynein arm I1/f

5.5 Outer dynein arms

5.6 Interdynein linkers

5.7 Properties and organization of axonemal dynein motor units

5.8 Core WD-repeat intermediate chains associated with oligomeric motors

5.9 Additional intermediate chains

5.10 Core light chains associated with oligomeric motors

5.10.1 DYNLL/LC8 group

5.10.2 DYNLT/LC9/Tctex1/Tctex2 group

5.10.3 DYNLRB/LC7/roadblock group

5.11 Regulatory components

5.11.1 Phosphorylation

5.11.2 Motor domain tethering

5.11.3 Ca2+ binding

5.11.4 Redox sensors

5.12 Docking motors onto the axoneme

5.13 Other dynein-associated components

5.14 Conclusions

Acknowledgments

References

6 - Organization of dyneins in the axoneme

6.1 “9+2” structure

6.2 Loci of axonemal dyneins

6.3 Connection of dyneins and other components in cilia

6.4 Conformational changes of single dynein molecules during the power stroke

6.5 Behavior of dimeric dyneins

6.6 How bending occurs?

6.7 Asymmetric arrangement

6.8 Future developments

Supplementary data

Acknowledgments

References

7 - Genetic approaches to axonemal dynein function in Chlamydomonas and other organisms

7.1 Introduction

7.2 Genetic studies of Chlamydomonas axonemal dyneins

7.2.1 General characteristics of Chlamydomonas mutants

7.2.2 Mutants deficient in outer-arm dynein

7.2.3 Mutants lacking inner-arm dyneins

7.3 Genetic studies in various organisms

7.3.1 Tetrahymena

7.3.2 Trypanosoma

7.3.3 Planaria

7.3.4 Fruit fly

7.3.5 Zebrafish and medaka

7.3.6 Mouse

7.3.7 Human

7.4 Conclusion and perspective

References

8 - Regulatory mechanics of outer-arm dynein motors

8.1 Introduction

8.2 Mechanosensory control

8.3 Calcium control

8.4 Thioredoxins and the effects of redox poise

8.5 Phosphorylation and cyclic nucleotides

8.6 Lis1-dependent alterations in mechanochemistry

8.7 Interheavy chain interactions and effects of the intermediate chain/light chain complex

8.8 Integrating outer arm regulatory mechanisms

Acknowledgment

References

9 - Control of axonemal inner dynein arms

9.1 Overview

9.2 Organization and assembly of the inner dynein arms

9.2.1 Chlamydomonas mutants and advances in electron microscopy

9.2.2 Each inner dynein arm is targeted to a precise position in the 96-nm repeat

9.3 Functional role of I1 dynein and dynein c

9.4 Regulation of I1 dynein

9.4.1 The central pair–radial spoke–I1 dynein regulatory mechanism

9.4.2 The MIA complex

9.4.3 An axonemal phosphoregulatory mechanism: the kinases and phosphatases

9.5 New questions

References

10 - Ciliary and flagellar motility and the nexin-dynein regulatory complex

10.1 Introduction

10.2 The central pair, radial spokes, and dynein regulatory complex

10.3 The dynein heavy chain suppressors

10.4 The dynein regulatory complex and the inner dynein arms

10.5 The dynein regulatory complex and nexin link

10.6 Identification and localization of dynein regulatory complex subunits within the nexin link

10.6.1 DRC4/trypanin/Gas8/Gas11

10.6.2 DRC1/CCDC164

10.6.3 DRC2/FAP250/CCDC65/CMF70

10.6.4 DRC3/FAP134/LRRC48

10.6.5 DRC5/FAP155/TCTE1 and DRC6/FAP169/FBXL13

10.6.6 DRC7/FAP50/CCDC135/CG34110

10.6.7 DRC8-DRC11

10.7 Identification of polypeptides that may interact with the nexin–dynein regulatory complex

10.7.1 The 96nm repeat ruler proteins: FAP59/CCDC39 and FAP172/CCDC40

10.7.2 The calmodulin-spoke complex

10.8 Function of the DRC–nexin link in motility and future directions

Acknowledgments

References

11 - Regulation of dynein-driven ciliary and flagellar movement

11.1 Introduction

11.2 Basic features of the components of cilia and flagella

11.2.1 Dynein arms

11.2.2 Microtubules

11.2.3 Beat plane and the central pair microtubules

11.3 Regulation of microtubule sliding in the axoneme

11.3.1 Microtubule sliding in trypsin-treated axonemes

11.3.2 Microtubule sliding in elastase-treated axonemes

11.3.3 Patterns of splitting in elastase-treated axonemes

11.4 Sliding microtubule theory and bend formation

11.5 The mechanism of oscillation

11.5.1 Theoretical models of oscillation and the oscillator

11.5.2 Mechanical activation and flagellar oscillation

11.5.3 Mechanical induction of the switching of dynein activity

11.5.4 Multiple modes of dynein and their significance for flagellar oscillation

11.6 Outlook

Acknowledgments

References

12 - Dynein-mediated photobehavioral responses in Chlamydomonas

12.1 Introduction: photobehavioral responses and the eyespot in Chlamydomonas

12.2 Flagellar behavior during phototaxis

12.2.1 Difference between the two flagella necessary for phototactic turning

12.2.2 Phototaxis and outer-arm dynein

12.2.3 Phototaxis and inner-arm dyneins

12.3 Flagellar behavior during photoshock response

12.3.1 Ca2+-dependent waveform conversion

12.3.2 Dyneins and waveform conversion

12.4 Photokinesis

12.4.1 Redox: a possible factor for photokinesis

12.4.2 Redox effects on dyneins

12.5 Conclusion

Acknowledgments

References

13 - Dynein and intraflagellar transport

13.1 Introduction

13.2 Intraflagellar transport

13.3 Discovery of the cytoplasmic dynein 2 heavy chain and early proposals for its function

13.4 Identification of cytoplasmic dynein 2 as the retrograde intraflagellar transport motor

13.5 Structure and subunit content of cytoplasmic dynein 2

13.5.1 DHC1b/DYNC2H1

13.5.2 Light-intermediate chain D1bLIC/DYNC2LI1

13.5.3 D1bIC2/WDR34: a cytoplasmic dynein 2 intermediate chain

13.5.4 D1bIC1/WDR60, a second cytoplasmic dynein 2 intermediate chain

13.5.5 LC8/DYNLL family

13.5.6 Tctex2b/Tctex1d2

13.5.7 Additional light chains likely are associated with dynein 2

13.5.8 Overall architecture of cytoplasmic dynein 2

13.6 Variations on the theme: multiple dynein 2 HCs and a possible alternative dynein for retrograde IFT

13.7 Biological functions of cytoplasmic dynein 2 and retrograde intraflagellar transport

13.7.1 Recycling of intraflagellar transport components

13.7.2 Return of axonemal and membrane proteins to the cell body

13.7.3 Signal transduction

13.7.4 Ciliary maintenance

13.7.5 Gliding motility

13.7.6 Not all protein removal from cilia is mediated by dynein 2

13.8 Cytoplasmic function of dynein 2

13.9 Regulation of dynein 2 expression, localization, and function

13.10 Conclusion

Acknowledgments

References

III - Cytoplasmic Dynein Biology

14 - Cytoplasmic dynein function defined by subunit composition

14.1 Introduction

14.2 Heavy chain (DYNC1H)

14.3 Light-intermediate chain (DYNC1LI)

14.4 Intermediate chain (DYNC1I)

14.5 DYNLL (LC8 light chain)

14.6 DYNLT (Tctex light chain)

14.7 DYNLRB (roadblock light chain)

14.8 Conclusion

Acknowledgment

References

15 - Regulation of cytoplasmic dynein motility

15.1 Introduction

15.2 Cytoplasmic dynein’s allosteric regulatory systems

15.3 Dynactin

15.4 Dynein is autoinhibited

15.5 Dynactin relieves dynein’s autoinhibition and activates processive directional motility

15.6 The role of the dynactin–microtubule interaction

15.7 Cargo-mediated licensing of dynein motor activity

15.8 Conclusion

References

16 - Insights into cytoplasmic dynein function and regulation from fungal genetics

16.1 Introduction

16.2 Discoveries of dynein function in spindle orientation/nuclear migration

16.3 Identification of dynein regulators using fungal genetics

16.4 Dissecting the mechanism and function of the microtubule plus-end accumulation of cytoplasmic dynein

16.4.1 Mechanisms of the microtubule plus-end accumulation of cytoplasmic dynein

16.4.2 Functional significance of the microtubule plus-end accumulation of cytoplasmic dynein

16.5 Understanding the functions of various components of the dynein and dynactin complexes

16.5.1 Functions of the individual components of the dynein complex

16.5.2 Functions of the individual components of the dynactin complex

16.6 Identification of proteins required for dynein–cargo interaction

16.6.1 The FTS-Hook-FHIP complex linking early endosomes to dynein–dynactin

16.6.2 VezA, a regulator important for the dynein–early endosome interaction in vivo

16.6.3 The hitchhiking mechanism of dynein-mediated cargo transport using PxdA and Upa1 for linking cargos to motile early endos...

16.7 Conclusions

Acknowledgments

References

17 - Role of dynactin in dynein-mediated motility

17.1 Dynactin: three structural domains with distinct functions

17.2 Teasing out interactions among dynactins, microtubules, and dyneins

17.2.1 Dynactin–microtubule binding

17.2.2 Dynactin–dynein binding

17.3 Mechanism of dynein activation

17.3.1 Free dynein is highly flexible

17.3.2 Head stacking: front-to-front versus front-to-back

17.4 Dynactin pointed-end complex subunits govern dynein–cargo binding

References

18 - Role of cytoplasmic dynein and dynactin in mitotic checkpoint silencing

18.1 Kinetochore

18.2 Kinetochore–microtubule attachment and error correction

18.3 The mitotic checkpoint

18.4 Mitotic checkpoint silencing

18.5 Dynein/dynactin and Spindly

18.6 Dynein/dynactin-mediated shedding of kinetochore mitotic checkpoint proteins

18.7 Outstanding questions

Acknowledgments

References

19 - Cytoplasmic dynein during mitosis

19.1 Introduction

19.2 Model systems of mitotic dynein

19.3 Dynein at the nuclear envelope

19.4 Spindle pole dynein

19.5 Cortical dynein

19.6 Kinetochore dynein

19.7 Phosphorylation

19.8 Future questions

19.9 Conclusions

References

20 - Dynein and dynactin at microtubule plus ends

20.1 Introduction

20.2 Growing microtubule plus end accumulation of dynein and dynactin

20.2.1 EB-dependent plus end tracking

20.2.2 Kinesin-1-dependent microtubule plus end accumulation

20.2.3 Kinesin-7-dependent plus end accumulation

20.2.4 Variations on a theme

20.3 Future perspectives

Acknowledgments

References

21 - Drosophila cytoplasmic dynein: mutations, tools, and developmental functions

21.1 Introduction

21.2 Drosophila dynein genes and mutations

21.3 Drosophila as a model system: tools and advantages

21.3.1 Manipulation of transgenesis and expression

21.3.2 Protein purification and in vitro assays

21.3.3 Cell lines as models

21.4 Dynein function in gametogenesis

21.4.1 Oocyte development

21.4.2 Sperm development

21.5 Dynein function in embryogenesis

21.5.1 Mitosis in syncytial embryos

21.5.2 mRNA localization in embryos

21.5.3 Epithelial polarity, cell fate, and tissue morphogenesis

21.6 Dynein function in neurons

21.6.1 Neuroblast polarity

21.6.2 Intracellular organization and structure of neurons

21.6.3 Axonal transport

21.7 Conclusion

Acknowledgments

References

Index

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

R

S

T

U

V

W

X

Y

Z

Back Cover