The Plant Cytoskeleton: a Key Tool for Agro-Biotechnology

459 Pages·2009·8.92 MB·English

by  Virginie Seltzer

The Plant Cytoskeleton: a Key Tool
for Agro-Biotechnology
NATO Science for Peace and Security Series
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Series C:Environmental Security
The Plant Cytoskeleton: a Key Tool
for Agro-Biotechnology
edited by
Yaroslav B. Blume
Institute of Food Biotechnology and Genomics
National Academy of Sciences
of Ukraine, Kiev
Ukraine
W. Vance Baird
Clemson University
Clemson, SC
U.S.A.
Alla I. Yemets
Institute of Cell Biology and Genetic Engineering
National Academy of Sciences
of Ukraine, Kiev
Ukraine
and
Diego Breviario
CNR, Milano
Italy
Published in cooperation with NATO Public Diplomacy Division
Proceedings of the NATO Advanced Research Workshop on

The Plant Cytoskeleton: Genomic and Bioinformatic Tools
for Biotechnology and Agriculture
Yalta, Crimea, Ukraine
19–2 3 September 2006
Library of Congress Control Number: 2008932215
ISBN 978-1-4020-8842-1 (PB)
ISBN 978-1-4020-8841-4 (HB)
ISBN 978-1-4020-8843 -8 (e-book)
Published by Springer,
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TABLE OF CONTENTS
Preface..........................................................................................................ix

Acknowledgements......................................................................................xi

PART 1 CYTOSKELETON FUNDAMENTALS

Plant Gamma-TuSC-like Components: Their Role in Microtubule
Nucleation....................................................................................................3
V. Seltzer, T. Pawlowski, J.-L. Evrard, J. Canaday,
E. Herzog, and A.-C. Schmit
1. Introduction...........................................................................................4
2. Microtubule nucleation complexes........................................................5
2.1. The gamma-TuSC, a minimal nucleating unit...............................6
2.2. The gamma-TuRC, a structured seed controlling microtubule
nucleation.......................................................................................8
3. Microtubule nucleation is a conserved process.....................................8
3.1. Plant extracts restore the nucleating function of inactivated
centrosomes...................................................................................9
3.2. The Plant nuclear surface acts as microtubule nucleator.............10
3.3. Membrane-associated complexes show a microtubule nucleation
activity.........................................................................................11
4. Tracking microtubule nucleation sites.................................................11
4.1. Centrosomes and SPBs................................................................11
4.2. Microtubule nucleation in animal cells possessing inactive
centrosomes.................................................................................12
4.3. Are kinetochores necessary for spindle assembly?......................12
4.4. Organelle and membranous nucleating sites...............................13
4.5. Plant microtubule nucleation sites...............................................13
4.5.1. Interphase cells.................................................................14
4.5.2. Spindle microtubule assembly and cell plate development14
5. Multiple functions of γ-TuSC components.........................................16
5.1. Gamma-tubulin mutants..............................................................16
5.2. SPC97/GCP2 and SPC98/GCP3 mutants....................................17
6. Concluding remarks............................................................................17

v
vi TABLE OF CONTENTS
Gamma-tubulins and their Functions in Plant Cells.............................23
P. Binarova, V. Cenklova, Z. Pochylova, E. Draberova,
and P. Draber
1. Introduction.........................................................................................24
2. Microtubule organizing centers...........................................................24
3. Non-centrosomal microtubule nucleation...........................................25
4. γ-Tubulin in eukaryotic cells is present in multiple forms and its
structure suggests multiple interactions...............................................26
5. Subcellular distribution of γ-tubulin in acentrosomal higher
plant cells.............................................................................................28
6. γ-Tubulin complexes and their effect on microtubule nucleation.......30
7. Plant γ-tubulin complexes are associated with membranes.................31
8. Association of plant γ-tubulin with αβ-tubulin dimers and
microtubules........................................................................................32
9. Conclusions.........................................................................................36

Coiled-coil- and Intermediate Filament-proteins in the Plant
Nucleoskeleton....................................................................................................45
S. Moreno Díaz de la Espina and C. de la Torre
1. The nucleoskeleton..............................................................................46
2. Ultrastructural organization of the plant NSK.....................................47
3. Protein composition of the plant NSK.................................................48
4. Coiled-coil and IF proteins..................................................................49
5. Binding of IF and coiled-coil proteins to nucleic acids.......................50
6. IF-related proteins in the NSK............................................................50
7. NuMA (Nuclear Mitotic Apparatus) protein.......................................51
7.1. Self-assembly of NuMA..............................................................51
7.2. NuMA partners............................................................................52
7.3. NuMA in mitosis.........................................................................53
7.4. Nuclear functions of NuMA........................................................54
7.5. Plant NuMA homologues............................................................55
8. Lamins.................................................................................................56
8.1. Secondary structure of lamins......................................................57
8.2. Lamin-associated proteins...........................................................57
8.3. Polymerization of lamins.............................................................58
8.4. Internal lamins.............................................................................59
8.5. Roles of lamins............................................................................60
8.6. Do plants have nuclear lamins?...................................................61
9. Other IF components of the plant nuclear matrix: MFP1,
NMCP1 and NMP1.............................................................................62
10. FPP (Filament-like Plant Proteins)......................................................63
11. Concluding remarks and perspectives.................................................64
TABLE OF CONTENTS vii

PART 2 CYTOSKELETON AND DEVELOPMENT

Microtubules and the Control of Cell Elongation in Arabidopsis
Roots ..........................................................................................................73
J.-P. Verbelen, J. Le, K. Vissenberg, T. de Cnodder, F. Vandenbussche,
K. Sugimoto, and D. Van Der Straeten
1. Introduction.........................................................................................74
2. Results and discussion.........................................................................75
2.1. Defining fast elongation...............................................................75
2.2. The control of fast elongation......................................................76
2.3. Microtubules and microfibrils.....................................................77
2.4. Microtubule reorientation is not involved in the control of cell
elongation....................................................................................83
2.5. The cell wall and control of cell elongation................................85
3. Conclusions.........................................................................................87

Regulation of Root Hair Tip Growth: Can Mitogen-activated
Protein Kinases be Taken into Account?................................................91
M. Ovečka, I. K. Lichtscheidl, F. Baluška, J. Šamaj,
D. Volkmann, and H. Hirt
1. Introduction.........................................................................................92
2. Morphogenesis of plant roots..............................................................93
3. Root hair formation and tip growth.....................................................95
3.1. Root hair initiation.......................................................................95
3.2. Cell wall.......................................................................................96
3.3. Transition from the bulge to hair elongation...............................96
3.4. Cell elongation by tip growth......................................................97
3.4.1. Cytoskeleton.....................................................................97
3.4.2. Calcium.............................................................................99
3.4.3. Other ions and pH...........................................................100
3.4.4. Plant hormones...............................................................101
4. Signal transduction and MAPKs.......................................................102
4.1. Plant MAPKs.............................................................................105
4.2. MAPKs in plant pathogen, hormone and stress response..........105
4.3. MAPKs in developmental processes.........................................106
5. SIMK in Medicago root hairs............................................................107
6. Conclusions.......................................................................................116

Cytoskeletal Changes During Spermatogenesis in Chara
Antheridia................................................................................................129
Q. Jin and K. H. Hasenstein
1. Introduction.......................................................................................130
viii TABLE OF CONTENTS
2. Materials and methods.......................................................................131
2.1. Culture conditions......................................................................131
2.2. Chemical treatments..................................................................131
2.3. Immuno-cytolocalization...........................................................131
2.3.1. MT staining.....................................................................131
2.3.2. F-actin staining...............................................................132
2.3.3. Nuclear staining and confocal microscopy.....................132
3. Results...............................................................................................132
3.1. Mitosis of the antheridial filaments............................................132
3.1.1. Microtubules...................................................................132
3.1.2. Actin...............................................................................134
3.2. Differentiation............................................................................135
3.2.1. Microtubules...................................................................135
3.2.2. F-actin.............................................................................136
3.3. Oryzalin treatment......................................................................137
4. Discussion.........................................................................................139

PART 3 CYTOSKELETON AND SIGNALLING

Plant Tubulin Phosphorylation and its Role in Cell Cycle
Progression..............................................................................................145
Y. B. Blume, C. W. Lloyd, and A. I. Yemets
1. Introduction.......................................................................................146
2. Plant tubulin- and microtubule related protein kinases.....................147
2.1. Cyclic nucleotide- and calcium-dependent tubulin
phosphorylation..........................................................................147
2.2. Role of cyclin-dependent kinases in plant microtubule
organization................................................................................150
2.3. Putative role of tyrosine kinases in plant microtubule
phosphorylation..........................................................................153
3. Interaction of serine/threonine protein phasphatases with plant
microtubules......................................................................................154
4. Conclusions.......................................................................................155

Plant Myosins: Do they Have Roles in Gravi- and
Mechanosensing?....................................................................................161
D. Volkmann and F. Baluška
1. Introduction.......................................................................................161
2. The cytoskeleton in root gravisensing...............................................163
3. Differential expression of critical cytoskeletal molecules
in the root cap....................................................................................164
4. Domain organization of unconventional plant myosins....................167
5. Conclusions and outlook...................................................................168
TABLE OF CONTENTS ix
The Role of the Cytoskeleton in Plant Cell Gravisensitivity...............173
E. L. Kordyum, G. V. Shevchenko, I. M. Kalinina,
O. T. Demkiv, and Y. D. Khorkavtsiv
1. Introduction.......................................................................................173
2. Cytoskeleton in graviperception........................................................175
2.1. Gravitropic reaction in moss protonema....................................179
2.2. Possible links between light and gravisensing...........................180
2.2.1. Microtubules reorganization during red light mediated
phototropism...................................................................180
2.2.2. Gravity-dependent morphogenesis of protonemata cell.182
3. Cytoskeleton in gravisensing.............................................................184
4. Interrelations between cytoskeleton elements during gravisensing..189
5. Conclusions.......................................................................................191

PART 4 GENOMICS OF THE CYTOSKELETON

The Importance of Being an Intron, by Wild….Type
Tubulin Genes.........................................................................................199
D. Breviario, L. Morello, A. Manca, and S. Gianì
1. Introduction.......................................................................................199
1.1. Spliceosomal introns: evolutionary genomics aspects...............200
1.2. Spliceosomal introns: regulatory aspects...................................201
2. Introns in cytoskeletal genes regulate gene expression.....................203
2.1. Intron-mediated enhancement of gene expression: IME............203
2.2. Intron dependent spatial expression: IDSE................................204
2.3. Predictable functional versatility of the introns of
cytoskeletal genes.......................................................................205
2.4. Additional predictable regulatory features?...............................206
3. Introns in tubulin genes: a rationale for the cTBP method................207
3.1. Intron length polymorphism: ILP...............................................207
3.2. Combinatorial tubulin-based polymorphism: cTBP..................208
4. cTBP method: some applications......................................................209
4.1. Genotyping plant species...........................................................209
4.2. Plant origin recognition..............................................................211
4.3. Genotyping plant varieties.........................................................212
4.4. Parental assessment....................................................................213
4.5. In vitro genomic instability........................................................214
5. Conclusions.......................................................................................215

The Transcriptome of the Tubulin Gene Family in Plants..................219
V. V. Radchuk
1. Introduction.......................................................................................219
2. Genes and gene families for tubulins................................................220
x TABLE OF CONTENTS
3. Expression of tubulin genes..............................................................225
3.1. Tubulin genes are expressed highly redundantly in vegetative
tissues.........................................................................................225
3.2. Pollen-specific tubulin genes.....................................................229
3.3. Role of the microtubules during seed development...................231
3.4. Modification of tubulin gene expression in response to
different factors..........................................................................233
4. Regulation of the expression of tubulin genes..................................234
Array Technology for Studying Maize Tubulin...................................243
D. P. Griffin and S. M. Wick
1. Introduction.......................................................................................244
2. Array platforms.................................................................................245
2.1. Single-channel and two-color microarray analyses...................246
2.1.1. Two-color spotted microarray (also known as two-dye
design, ratio-based, or two-channel microarrays)...........246
2.1.2. Single-channel microarray (also known as one-color
and single-dye oligonucleotide microarrays)..................247
2.1.3. Affymetrix maize GeneChip®........................................248
3. Analysis software packages and their properties...............................249
4. Considerations when designing a microarray experiment.................250
5. Materials and methods...................................................................... 253
5.1. Plant growth and tissue collection..............................................253
5.2. RNA isolation and microarray hybridizations...........................253
5.3. Present-absent gene analysis......................................................254
5.4. Statistical analysis using MAS5.0 and RMA.............................254
5.5. Determination of significance....................................................254
6. Results...............................................................................................255
6.1. Presence of transcripts................................................................255
6.2. Expression patterns of each β-tub gene between B73 tissues....255
6.3. Comparison of expression of each β-tub gene across
B73 tissues.................................................................................256
7. Discussion.........................................................................................258
7.1. Determining significance of expression levels...........................258
7.2. Choosing replication strategy when designing a microarray
study...........................................................................................258
7.3. Determination of presence of transcript correlated to intensity
of GeneChip® signal..................................................................259
7.4. Comparison of gene chip analyses and previous studies
on tub transcripts........................................................................259
7.5. Differential expression of the tub genes.....................................260
7.5.1. β-tubulin 1......................................................................260
7.5.2. β-tubulin 2......................................................................260