Retrotransposons encode for proteins involved in retrotransposi- tion, and produce RNA both for protein production and for reverse transcription [although short interspersed nuclear elements (SINEs) are an exception]. As for class II elements, a defective retrotrans- poson can be trans-activated. Transposition has been shown for Bs1, Zeon-1, G, Stonor and TOC1, which all lack important coding regions or have coding domains interrupted by unsuitable stop codons. The presence of functional gag–pol domains is thus not a prerequisite for transposition, provided signals important for retro- transposition, such as priming sites or encapsidation signals, are still present. However, a retrotransposon will not transpose in the absence of the genomic RNA used as the template for reverse tran- scription. In terms of mutagenic impact on the host genome, the best criterion for activity is thus the ability to produce a transcript, and this criterion has been used, in addition to mobility, to establish the list of plant retrotransposons that are active or potentially active.
Improvement of plant fibers for use in the textile industry will require an understanding of how glucan chains are packed into a para-crystalline cellulose microfibril, how the microfibrils are oriented around the fiber cells and how, in some instances, non-cellulosic polysaccharides space the microfibrils apart and contribute to unique textures of the fiber. Cellulose synthesis is associated with six-membered particle rosettes located at the plasmamembrane. The full pathway of cellulose biosynthesis, from translocated sugar to the synthesis of a para-crystalline array of several dozen (1→4)-β- D -glucan chains into a single microfibril, is still unknown . For over 30 years, investigators have been stymied in their attempts to stabilize cellulose synthesis in vitro.
The large number of families of repetitive DNA, their high amplification and different characteristic locations fill most of the chromosome with repetitive DNA (Fig. 2). Together, the data from in situ hybrid- izations and molecular analyses suggest the integrated model for plant chromo- some organization presented in Box 2. Localization of major repetitive DNA fam- ilies by in situ hybridization in sugar beet indicates that genes occur in clusters between blocks of one or more different repeat arrays. We expect that the large-scale
Sterols are essential for all eukaryotes. In contrast to animal and fungal cells, which contain only one major sterol, plant cells synthesize a complex array of sterol mixtures in which sitosterol, stigmasterol and 24-methylcholesterol often predominate. Sitosterol and 24- methylcholesterol are able to regulate membrane fluidity and permeability in a similar manner to cholesterol in mammalian cell membranes. Plant sterols can also modulate the activity of membrane-bound enzymes. In contrast, stigmasterol might be specifically required for cell proliferation.
31. Tanzer MM, Thompson WF, Law MD, Wernsman EA, Uknes S: Characterization of post-transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco. Plant Cell 1997, 9:1411-1423. The authors show that the observed ‘immunity’ and ‘recovery’ resulting from transgene-mediated viral resistance are probably manifestations of the same phenomenon. Tobacco containing four or six copies of a nontranslatable tobacco etch viral (TEV) coat protein (CP) gene triggered co-suppression in immune plants prior to TEV infection, although 20–28 days of growth following germination was required to manifest both co-suppression and immunity as the silenced transgene underwent meiotic resetting. Prior to the onset of the silenced state, these plants were susceptible to TEV infection. The presence of only one or two copies of the TEV CP transgene was insuf- ficient to trigger co-suppression prior to TEV infection and such transgenics were susceptible until the multiplying TEV triggered co-suppression. This co-suppression, in turn, led to suppression of TEV replication in new leaf growth resulting in the ‘recovery’ observation. Transgene RNA degradation intermediates were present on polysomes as poly(A) – RNAs with intact 5′
At present, there is no efficient technique available for determin- ing the concentration of different amino acids in the subcellular com- partments of plant cells under non-invasive conditions. However, in vivo NMR might be able to clarify this situation. NMR correlation- peak imaging can resolve the spatial distribution of various amino acids and sugars in the hypocotyl of castor bean seedlings almost down to the level of individual cells. Glutamine and/or glutamate was detected in the cortex parenchyma and in the vascular bundles. Lysine and arginine were mainly present in the vascular bundles, whereas valine was observed in the cortex parenchyma, but not
It is possible that post-transcriptional RNA editing plays a role in fertility restoration in some systems. For example, editing might change the length of predicted CMS-associated ORFs by creating new start (AUG) and/or stop (i.e. UAA, UAG, or UGA) codons, be- cause the most prevalent example of editing in plant mitochondrial sequences is C-to-U (Ref. 31). It is also possible that tissue-specific editing might allow a CMS-associated sequence to become deleteri- ous only at microsporogenesis or microgametogenesis. For exam- ple, editing of the mitochondrial atp6 gene of CMS sorghum is strongly reduced relative to normal fertile sorghum in anthers, but not in seedlings 50 . RNA editing of this gene increases following fer-
The development of molecular genetics and associated technology has facilitated a quan- tum leap in our understanding of the under- lying genetics of the traits sought through plant breeding. The usefulness of DNA mark- ers for germplasm characterization, and of marker-assisted selection – the manipulation through DNA markers of genomic regions that are involved in the expression of traits of interest – for single-gene transfer, has been well demonstrated. However, when several gen- omic regions must be manipulated, marker- assisted selection has turned out to be less useful. The efficient and effective application of marker-assisted selection for polygenic trait improvement certainly needs new technology but, more importantly, it requires the devel- opment of innovative strategies that bypass the conceptual bottlenecks imposed by current approaches.
allotetraploid originating from two diploid progenitors, N. sylvestris (S subgenome) and either N. tomentosiformis or N. otophora (T subgenome). Tetraploid tobacco has a bimodal sequence composition, indicating that, despite several local S–T exchanges [8,43], extensive intermixing of subgenomes has not yet occurred. The GC contents of parental subgenomes in tobacco range from 37–41% (T) to 42–50% (S) . The distribution of tobacco TEs is not completely random and presumably reflects integration into compatible regions. Retroelement TntI is enriched in a compartment characterized by a GC content of 36.6% . The average GC content of four remnants of a different retroelement family [25,26 •• ] is 41%, consistent with enrichment of this family in the T subgenome. Incompatibilities could arise from cross-infiltrations of species-specific elements: a copy of a T subgenome enriched element present on an S chromosome was found in the flanking plant DNA of an unstable transgene [26 •• ]. Prokaryotic DNA might be recognized as foreign because of its generally high GC content and/or because it cannot be packaged properly with eukaryotic proteins. Sharp discontinuities in GC composition are present at the junction of nopaline synthase promoter and BV fragments at a NOSpro trans-silencing locus; all of these sequences are heavily methylated (J Jakowitsch, J Narangayavana, AJM Matzke, unpublished data).
class have no other known functions apart from disease resistance. Similarities between the NBS domain of these proteins and animal proteins regulating apoptosis (detailed below), however, suggest that researchers be mindful of the possibility that some NBS-LRR proteins may function in plant developmental processes involving programmed cell death. One example of a ‘multiskilled’ family of proteins is the LRR-TM-PK class. Although Xa21 is the only resistance protein in this class, several plant protein ‘relatives’ involved in developmental control and hormone perception have now been identified, suggesting that Xa21 may have been ‘recruited’ for pathogen detection. Hs1 pro-1 : an unusual resistance gene
Plant resistance genes are highly polymorphic and have diverse recognition specificities. These genes often occur as members of clustered gene families that have evolved through duplication and diversification. Regions of nucleotides conserved between family members and flanking sequences facilitate equal or unequal recombination events. Transposition contributes to allelic diversity. Resistance gene clusters appear to evolve more rapidly than other regions of the genome, and domains responsible for recognitional specificity, such as the leucine-rich repeat domain, are subject to adaptive selection.
The promise of genomics rests on the theory that infor- mation obtained from gene sequences in one organism will have physiological and evolutionary implications for all organisms that maintain a similar coding region. Thus, with each finished genome, evaluation of subsequent chromosomal sequences and their functional relevance have been advanced. This is indeed the case for plant research with information on photosynthesis derived from the model prokaryote Synechocystis  and insight into cellular physiology derived from the model eukaryote Sac- charomyces cerevisiae [44 •• ,45 • ]. Likewise, the Arabidopsis genome will pave the way for comparative analyses of genome sequence from all other plant species.
maize gene for a 27 kDa zein, a rice gene for ADP-glucose pyrophosphorylase and a rice gene for the seed storage protein glutelin 1 in maize endosperm ; and the promoter of a maize DnaJ-related gene in maize . Promoters connected to selectable marker genes were compared after transformation of Indica rice. The pro- moter of a maize gene for ubiquitin and the promoter of a maize E mu gene were more effective than the 35S promoter of cauliflower mosaic virus and the promoter of a rice gene for actin . Activity of promoters may be different from plant to plant and choice of promoters which can be expressed properly in cereals is important. Integration and expression of transgenes In general, Agrobacterium-mediated transformation results in integration of small numbers of copies of transgenes in plant genomes in both dicotyledons and monocotyledons. By contrast, direct transformation tends to create more complicated patterns of integration [22,38 •• ]. Fewer than three copies of transgenes were introduced into rice and maize by Agrobacterium in a majority of transformants examined [30 •• ,44]. Stable inheritance of transgenes up to the fourth generation of rice plants after transformation by A. tumefaciens has been demonstrated . Thus, in this respect, Agrobacterium-mediated transformation is the method of choice.
The yeast gene SLC 1-1 was isolated as a variant of the yeast gene SLC 1, which itself was isolated from a mutant unable to make sphingolipids . SLC 1-1 was able to complement the mutant and it was suggested that its function was to transfer long-chain acyl groups to the sn-2 position of phosphatidylinositols. The mutant gene, slc 1, had a single base change which caused it to lack this function. Recently it was shown that the SLC 1-1-gene was also able to transfer acyl groups to the sn-2 position of plant triacylglycerols when it was expressed in Arabidopsis and oilseed rape seeds [10 •• ]. Furthermore, transgenic seeds over-expressing SLC 1-1 had an increased total oil content. Thus, in this instance, it appears that increased activity of a terminal reaction resulted in increased flux through the entire pathway. It will be interesting to determine if this is an isolated case or if similar results will be obtained for other oilseed plants or for other metabolic pathways. Another example of increasing flux into product by increasing the activity of a near-terminal enzyme comes from the isoprenoid pathway. This is a highly branched pathway which originates with 3-hydroxy-3-methyl glu- taryl coenzyme A (HMG-CoA) . From the essentially linear conversion of HMG-CoA to ubiquinone there are many branches to important metabolites such as cytokinins, squalene, sterols, carotenoids and tocopherols. The activity of the enzyme HMG-CoA reductase was for many years believed to be a rate-limiting step in sterol biosynthesis and possibly that of other isoprenoids. Increasing the activity of this enzyme was then an obvious target for increasing flux through the entire pathway and thus the concentration of useful isoprenoid end-products. A few years ago, however, it was shown that increasing the catalytic activity of HMG-CoA reductase in transgenic tobacco, corn and tomatoes resulted in an accumulation of only cycloartenol rather than sterols or other isoprenoids [P2]. More recently a number of groups [P3 •• ,P4 •• ,P5 • ] have demonstrated that overexpression of phytoene desaturase, an enzyme close to the terminal reactions of carotenoid biosynthesis, resulted in a large increase in the concentration of the orange pigment lutein in various transgenic plants — thus supporting the hypothesis that increased levels of terminal enzymes in a pathway may indeed have more effect on pathway products than directly manipulating those enzymes that were traditionally thought of as rate-limiting. The results of metabolic flux experiments in transgenic plants must be interpreted with care if they are to be used to devise a strategy for the increased production of products of commercial value.
Knowledge of plant relationships has increased rapidly in the past decade, reflecting partly the development of molecular systematics. It has been known for some time that plant classifications do not reflect phylogeny accurately, even though both phylogeny and classification are hierarchical. The hierarchy of classification was imposed in the late 18th century, well before ideas of descent with modification (evolution) were prevalent . These pre-evolutionary groups were then re-interpreted in an evolutionary context, and were assumed to be products of evolution, rather than man-made artefacts. Thus, every named group represents an historic assumption of relationship that may or may not be accurate but these assumptions can now be tested. Data are accumulating that show, in some cases, historically recognized groups are indeed phylogenetically linked (monophyletic), and other ‘groups’ are quite miscellaneous and made up of unrelated elements (polyphyletic). In addition, taxa whose placement have been ambiguous can frequently now be placed.
Evidence for the disruption of the AM mutualism by Collem- bola is equivocal. Indeed, the opposite might be true; Collembola might allow enhanced mycorrhizal growth and thereby be of indirect benefit to plants. However, there is an urgent need for the design of microcosm experiments that are ecologically realistic, so as to better understand this fascinating interaction. In particular, densities of Collembola need to mimic those found in the field, with eco- logically realistic combinations of AM and non-AM fungi. The mechanism determining fungal palatability needs to be established and experiments conducted to determine whether preferential feeding is caused by chemical or mor- phological differences in AM and non-AM fungi. Finally, to determine if Collembola do reduce mycorrhizal functioning in the field, technologically difficult experiments need to be done, in which populations of animals and fungi are manipu- lated, although other soil organisms are unaffected. Given that AM fungi can affect the structure of plant communities, enhancing diversity and productivity 36 , an understanding
The protons and electrons released in this process are ulti- mately used in starch production; to the plant, O 2 is simply a waste product. This remarkable redox chemistry is initi- ated by photon absorption by the PSII reaction-center chlorophyll, P 680 , which produces the charge-separated state, P 680 + Q A – . Reduction of P 680 + by water is mediated
Lacking a clearly developed picture for proximal regula- tory systems, I turn now to the consideration of higher order regulatory systems that appear to control the timing and progression of leaf senescence. Reminiscent of the proverbial blind men and the elephant, one’s concept of how leaf senescence is controlled depends very much on which plant system one is examining. The relevant systems have been the subjects of recent reviews so I will just mention them briefly here. There are clearly examples where specific hormones have a controlling influence over organ senescence. Cytokinins can have a dramatic effect on delaying leaf senescence in some species . The effectiveness of applied cytokinin, however, varies considerably between plant species. Ethylene promotes senescence in many species but several recent studies indicate that ethylene is neither necessary nor sufficient to cause senescence in Arabidopsis or tomato [15,16 • ]. On the other hand ethylene is the key regulatory factor in the senescence of floral organs in some species . Environmental signals can also trigger senescence. Shad- ing of lower leaves by upper leaves induces senescence in some species (see [6 •• ]), while deciduous trees are affected by temperature and day length. Reproductive development can trigger senescence of vegetative tissue both proximally and even on a global scale in monocarpic species. Evidence from soybean is consistent with a chemical communication system between fruits and leaves that triggers the senescence syndrome [2 •• ]. Finally, leaf age may be the best predictor of when senescence will occur; this seems to be the case in Arabidopsis .
Fig. 2. Map position of the known plant matrix attachment regions (MARs) with respect to genes or other relevant features of the source region. (The adh1 locus from maize is shown separately in Fig. 3.) The DNA regions of different species are shown at the same scale. Genes are represented by arrows indicating the direc- tion of transcription and are marked with the gene name. Matrix attachment regions are represented by open boxes below the source DNA and name, if available. There are no characterized genes in the proximity of the two petunia MARs: TBS is a trans- formation booster sequence and T-DNA is a vector carrying a transgene. References for the different species, starting from the top of the diagram: soybean, 14; pea, 12; tobacco, 13; Phaseolus vulgaris, 18; tomato, 20; potato, 11; petunia, 17; petunia, 19; soy- bean, 16; Arabidopsis, 22; rice, 23; and tomato, 21.