New Frontiers in Bryology: Physiology, Molecular Biology and Functional Genomics

207 Pages·2004·5.398 MB·English

by  Volker Knoop, Yin-Long Qiu, Koichi Yoshinaga (auth.), Andrew J. Wood, Melvin J. Oliver, David J. Cove (eds.)

New Frontiers in Bryology
New Frontiers in Bryology
Physiology, Molecular Biology
and Functional Genomics
Edited by
Andrew J. Wood
Southern Illinois University-Carbondale,
Carbondale, Us.A.
Melvin J. Oliver
USDA-ARS, Lubbock, us.A.
and
David J. Cove
University of Leeds,
Leeds, UK. and
Washington University,
St. Louis, US.A.
SPRINGER-SCIENCE+BUSINESS MEDIA, B.V.
A c.I.P. Catalogue record for this book is available rrom the Library of Congress.
ISBN 978-90-481-6569-8 ISBN 978-0-306-48568-8 (eBook)
DOI 10.1007/978-0-306-48568-8
Printed 0/7 acid-free paper
All Rights Reserved
© 2004 Springer Science+Business Media Dordrecht
Originally published by Kluwer Academic Publishers in 2004
Softcover reprint of the hardcover 1s t edition 2004
No part of this work may be reproduced, stored in a retrieval system, or transmitted
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or otherwise, without written permission from the Publisher. with the exception
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TABLE OF CONTENTS
Preface VB
Colour section IX
Chapter 1: Molecular Phylogeny ofBryophytes and Peculiarities of
Their Chloroplast and Mitochondrial DNAs
V. Knoop Y.-L. Qiu, and K. Yoshinaga
Chapter 2: Genomes and Databases 17
Y. Kamisugi and A. Cuming
Chapter 3: Principles of Targeted Mutagenesis in the Moss
Physcomitrella patens 37
D. Schaefer and J.-P. Zryd
Chapter 4: Applied Genomics in Physcomitrella 51
H. Holtorf, W. Frank and R. Reski
Chapter 5: Molecular Biology and Genomics of the Desiccation-tolerant
Moss Tortula ruralis 71
A. J. Wood and M. J. Oliver
Chapter 6: Evolution of the Organellar Transcription Machinery in
Bryophytes and Vascular Plants 91
Y. Kabeya, K. Sekine, and N. Sato
Chapter 7: Gene tagging, Gene-and Enhancer-trapping, and Full-length
cDNA Overexpression in Physcomitrella patens 111
T. Fujita, T. Nishiyama, Y. Hiwatashi, M. Hasebe
Chapter 8: Lipid Metabolism in Mosses 133
K. Mikami and E. Hartmann
Chapter 9: Phytochrome in Mosses 157
T. Lamparter & G. Brucker
Chapter 10: Blue/UV-A Light Signaling in Moss 177
E. B. Tucker
Chapter 11: The Use of Mosses for the Study of Cell Polarity 189
D. J. Cove and R.S. Quatrano
v
PREFACE
The mosses (Bryophatea, Musci) are a diverse and widely distributed group of
land plants. Mosses are attractive experimental plants because they exhibit the traditional
attributes of good model systems (Le. ease of growth & maintenance, fast generation
time, and amenable genetics) with the added advantage of a haploid gametophyte that
allowed developmental mutants to be recovered with relative ease. In addition, mosses
with the ability to tolerate extreme environmental conditions offer realistic models for
the analysis of environmental stress-tolerance; particularly when compared to
tracheophytes such as Arabidopsis thaliana in which these important plant phenotypes
are either not clearly expressed or entirely lacking. And, in one of the most exciting
developments in Plant Biology, efficient homologous recombination occurs in the moss
Physcomitrella patens. The ability to perform efficient homologous recombination (Le.
gene knock-outs) in P. patens is at present unique amongst all plants and represents an
extremely powerful technique for the functional analysis of many plant genes.
Over the past 5 years, a world-wide community of moss researchers has evolved. A
highly successful "Moss" conference has been held annually (l998-Mumbai, India;
1999-Carbondale, IL, USA; 2000-Villars, Switzerland; 200l-0kazaki, Japan;
2002-Ambleside, UK; 2003-St. Louis, MO, USA) with "Moss 2004" planned to be
held in Frieburg Germany. These conferences have been instrumental in the creation &
development of strong collaborative ties, and the free exchange of both ideas and
materials. Mosses are powerful experimental tools for the elucidation of complex
biological processes in plants-from evolution & development to the homologus
recombination & the creation of novel molecular tools. This book provides a synopsis of
the outstanding basic research being conducted using mosses as a model multi-cellular
eukaryote.
Finally, we gratefully acknowledge Professor Govindjee (Emeritus, Department of
Plant Biology, University of Illinois at Urbana-Champaign) for encouraging the
production of a volume devoted to recent advances in bryology.
Andrew J. Wood
Melvin J. Oliver
David J. Cove
October 15th, 2003
VB
COLOUR SECTION
x
1)
(e) '00 n~-lrilP
" gene-trap
(c)
Figure 2. GUS expression patterns of gene-trap and enhancer-trap lines,
and a tagged mutant with an altered hormone response. Staining of a
rhizoid apical cell of gene-trap line YH87. (b) A bud of a young
gametophore of gene-trap line YH229, showing staining of an apical cell
and its surrounding cells. (c) A gemetophore of gene-trap line YH209,
showing staining of the basal region of the gametophore, where rhizoid
filaments emarged. (d) A shoot apex of gene-trap line YH440, showing
staining of an antheridium. Bars in (a) and (b) = 50 jlm, in (c) = 500 jlm,
and in (d) = 100 jlm. (e) Patterns of expression of the uidA gene in gene
trap and enhancer -trap lines generated with the homelogus integration
method. Y-axis values indicate the percentage of lines with expression in
the indicated portions relative to the number of GUS-positive gametophytes,
which was set at 100%. Apex indicates the number of lines displaying GUS
staining in an apical cell and its surrounding cells. (f) A month-old wild
type gametophyte grown on medium supplemented with 1 mM BA,
showing malformed bud formation. (g) A month-old gametophyte of
tagged line 8617-7, which is resistant to cytokinin, grown on the same
medium as the wild type. (see Fig. 2. on p. 117)
Xl
2)
Figure 1. Batch culture of Ceratodon purpurenus in white light (70 Wlm-2;
16h Iightl8 h dark; 2IJ'C)_ The colour changes form deep green to brownish
during the culture of 21 days_ Cells of this type are full of oil drops like in
figure 2. (see Fig 1. on p. 136)
3)
Figure 2. Senescent protonema filaments of Ceratodon purpureus from 21
day-old batch culture. The cells are full ofo il drops. (see Fig. 2 on p. 137)
MOLECULAR PHYLOGENY OF BRYOPHYTES
AND PECULIARITIES OF THEIR CHLOROPLAST
AND MITOCHONDRIAL DNAS
VOLKER KNOOP, YIN-LONG QIU, KOICHI YOSIDNAGA
Institut fUr ZelluHire und Molekulare Botanik, Abt. Molekulare
Evolution,Universitat Bonn, Kirschallee 1, D-53115 Bonn, Gennany
(VK); Department of Ecology and Evolution, 830 North University
Ave., University of Michigan, Ann Arbor, MI 48109-1048(YQ);
Shizuoka University, Faculty of Science, Oya 836, 422-8529
Shizuoka, Japan(KY)
Abstract. Molecular sequence data have contributed enormously to our knowledge about the phylogeny
of land plants. Bryophytes are of fundamental importance to the full picture of land plant evolution as it is
becoming increasingly evident that they represent the extant relatives of the earliest land plants. The three
classically distinguished bryophyte classes mosses, liverworts and hornworts each are confirmed as well
founded monophyletic groups by the majority of molecular data. However, it has also become clear that
the term bryophytes describes a division. which is a paraphyletic group - most likely with only one of its
classes linked to the vascular plants and another one sister to all other land plants. Hitherto enigmatic
genera like Takakia or Haplomitrium can now be phylogenetically assigned and more detailed placements
of these and other genera will be straightforward with yet more informative data accumulating. The use of
concatenated alignments will likewise resolve other questions on the monophyly of orders or families
defined by classical systematics and will paint a clear picture on their branching pattern. Extending the
conventionally used nuclear gene sequences (mostly ribosomal RNA genes) or chloroplast gene markers,
the plant mitochondrial genes appear to be of particular suitability to address questions of deep level plant
phylogeny. Two idiosyncratic phenomena of gene expression in plant organellar DNAs make their
evolution particularly interesting: RNA editing and Trans-Splicing. RNA editing, the frequently observed
site-specific exchange of pyrimidines to reconstitute conserved codon identities is class-specifically
shaped in the bryophytes: Moderate exchange of cytidine to uridine is observed in mosses - very similar
to angiosperms, where the phenomenon was discovered. Hornworts, however, display a strikingly higher
frequency of pyrimidine exchange and, most notably, many replacements in the opposite direction, i.e.
from uridine to cytidine. A peculiar case are the liverworts where we observe RNA editing of variable
frequency among taxa in the jungermanniid species but so far a mysterious absence of RNA editing in the
marchantiid mitochondrial sequences. Two other genomic features make the mitochondrial DNA of
plants particularly well suited for deep level phylogenetic analyses: A very low primary sequence drift
coinciding with a low degree of homoplasy and the presence of characteristic, positional stable organellar
introns, mostly of the group II type. Investigating the intron-rich genes nadS, nad2, nad4 and nad7 one
finds that intron presence fully coincides with class membership, with the mosses displaying
spermatophyte-type mitochondrial introns. These and other observations so far converge on the liverworts
as sister group to all other land plants.
1. INTRODUCTION
1.1. The bryophytes.
Bryophytes are key to understanding the evolution of land plant life, because data
from different sources, including cladistic analyses of molecular sequences,
converge on the view that bryophyte-like organisms were the first plants on land,
emerging more than 450 million years ago (Kenrick & Crane, 1997; Bremer,
A.J. Wood et al. (ed.!.
New Frontiers in Bryology: Physiology, Molecular Biology and Functional Genomics, 1-16.
© 2004 Kluwer Academic Publishers. Printed in the Netherlands.
2
Humphries, Mishler, & Churchill, 1987). Alternative claims that view bryophytes as
a degeneration of early vascular plants have only rarely received support from
molecular observations (Yoshinaga, Kubota, Ishii, & Wada, 1992) and never from
any cladistic analyses of molecular data of adequate taxon sampling. The early
diversification of the division bryophytes into its classes mosses, hornworts and
liverworts may have been a very early event of land plant (embryophyte) evolution
and this, together with long-branching algal outgroups, are most likely the
fundamental reasons why a fully resolved phylogeny of earliest land plants is still
lacking. However, the emerging molecular consensus stands in contrast to the
disappointing lack of bryophyte macrofossil documents (Edwards, Duckett, &
Richardson, 1995; Edwards, 2000; Edwards, Wellman, & Axe, 1998). Only the
microfossil record gives evidence for early land plants with a bryophyte-level of
organization in the mid-Ordovician (Wellman & Gray, 2000; Graham, 1996), more
specifically of land plant spores with a liverwort-like morphology (Taylor, 1995).
It is mostly agreed upon that the origin of land plant life has to be searched
among extinct relatives of the Charophyte algae (Graham, 1996; Graham, Cook, &
Busse, 2000; McCourt, 1995), more specifically among members of the order
Charales (Malek, Uittig, Hiesel, Brennicke, & Knoop, 1996; Karol, McCourt,
Cimino, & Delwiche, 2001). New molecular data, among which the complete
organellar sequences of the chloroplast and mitochondrial DNAs (Turmel, Otis, &
Lemieux, 2002), the "plastomes" and the "chondriomes", appear most promising,
will help to ultimately resolve this issue in the near future.
Given that mosses have frequently served as model organisms in biology in
which many fundamental insights have been gathered, see (Reski, 1998a) for
examples, and given that Physcomitrella has emerged as a new model plant of
molecular biology (Reski, 1998b) it is of utmost importance to understand how
bryophytes relate to other forms of land plant life in evolutionary terms.
1.2. Cladistics and molecular characters.
More than twenty years ago Miller had already stated that "we have come a long
way since Micheli (1729) established the discreetness of several taxa of bryophytes
and Linnaeus incorporated mosses and liverworts into the Species Plantarum
(1753)" (Miller, 1979). From today's retrospective this statement may have come a
little early at a time when molecular sequence data had not yet made their way into
phylogeny and systematics. His and other articles in the same book (Schuster, 1979)
give examples for discussion on "primitive" and "advanced" characters when
consequent cladistic argumentation were not yet rigorously enough applied. New
insights during the following two decades have mainly come from consequent
implementation of cladistic analyses following the trend-setting contributions of
Mishler and colleagues (Mishler & Churchill, 1984; Mishler, 1986).
Today it is highly unlikely that morphological, biochemical or
physiological investigations alone could provide significant numbers of new
characters allowing to answer remaining phylogenetic questions unambiguously and
with statistical reliability. Thus, only molecular sequence data can be expected to