David H. Clapham

Metacaspase-dependent programmed cell death is essential for plant embryogenesis

In plants, as in animals, programmed cell death (PCD) is a key process responsible for the elimination of unneeded structures and for overall shape remodeling during development [1]; however, the molecular mechanisms remain poorly understood. Despite the absence of canonical caspases in plants, dying plant cells show an increased proteolytic caspase-like activity [2]. Moreover, the cell death can be suppressed using synthetic [2] or natural [3] caspase inhibitors. This raises the question of whether plants have specific cysteine proteases with a role similar to metazoan caspases in the execution of PCD. Metacaspases are the best candidates to perform this role, because they contain a caspase-specific catalytic diad of histidine and cysteine as well as conserved caspase-like secondary structure [4,5]. Here we show the first experimental evidence for metacaspase function in the activation and/or execution of PCD in plants, and also demonstrate the fundamental requirement of plant metacaspase for embryogenesis. We explored the role of plant metacaspases in PCD using a model system of somatic embryogenesis of Norway spruce (Picea abies), where the pathway of embryo development (Figure 1A) resembles zygotic embryogeny, even though the embryo origin is different in each case (i.e., somatic cells in proembryogenic mass (PEM) versus zygote) [6]. In this developmental pathway autophagic PCD ablates PEMs at the time of their differentiation to embryos and then eliminates terminally differentiated embryo suspensor as the embryos enter late embryogeny [6,7] (Figure 1A). We have isolated a 1687 bp cDNA sequence from the embryogenic cell cultures (EMBL database accession number AJ534970). The encoded protein shows a significant degree of conservation with metacaspases and falls into the type II plant metacaspase subfamily (Figure S1A). The protein was named mcII-Pa. The predicted secondary structure of mcII-Pa contains conserved domains and motifs present in all members of the caspase/metacaspase/paracaspase superfamily [5] (Figure S1B). The putative mcII-Pa catalytic diad of cysteine and histidine is placed in the α α/β β fold characteristic for the caspase-hemoglobinase fold (CHF)-containing proteins [5]. The predicted mcII-Pa protein lacks both the death-effector domain and the caspase-activating recruitment domain found in classical initiator caspases, but has a p20-like domain including the active-site pentapeptide DXCHS (where X is A or S) shared by all metacaspases [5] (Figure S1B). This domain is fused to the 268 amino acid carboxy-terminal region consisting of a large insert of approximately 180 amino acids and a p10-like domain. In situ hybridization analysis has revealed restricted accumulation …

Microarray Analyses of Gene Expression during Adventitious Root Development in Pinus contorta

In order to investigate the gene expression pattern during adventitious root development, RNA of Pinus contorta hypocotyls, pulse-treated with the auxin indole-3-butyric acid and harvested at distinct developmental time points of root development, was hybridized to microarrays containing 2,178 cDNAs from Pinus taeda. Over the period of observation of root development, the transcript levels of 220 genes changed significantly. During the root initiation phase, genes involved in cell replication and cell wall weakening and a transcript encoding a PINHEAD/ZWILLE-like protein were up-regulated, while genes related to auxin transport, photosynthesis, and cell wall synthesis were down-regulated. In addition, there were changes in transcript abundance of genes related to water stress. During the root meristem formation phase the transcript abundances of genes involved in auxin transport, auxin responsive transcription, and cell wall synthesis, and of a gene encoding a B-box zinc finger-like protein, increased, while those encoding proteins involved in cell wall weakening decreased. Changes of transcript abundance of genes related to water stress during the root meristem formation and root formation phase indicate that the plant roots had become functional in water transport. Simultaneously, genes involved in auxin transport were up-regulated, while genes related to cell wall modification were down-regulated. Finally, during the root elongation phase down-regulation of transcripts encoding proteins involved in cell replication and stress occurred. Based on the observed changes in transcript abundances, we suggest hypotheses about the relative importance of various physiological processes during the auxin-induced development of roots in P. contorta.

Up, down and up again is a signature global gene expression pattern at the beginning of gymnosperm embryogenesis

Somatic embryogenesis of a gymnosperm, Picea abies, represents a sequence of specifically regulated developmental stages including proembryogenic mass (PEM), PEM-to-embryo transition, and early and late embryogeny. Here, we report cDNA array analysis of expression patterns of 373 genes in the beginning of P. abies embryo development. The analysis revealed a group of 107 genes (29% of arrayed cDNAs) which were upregulated upon PEM-to-embryo transition, then downregulated during early embryogeny and finally upregulated again at the beginning of late embryogeny. This major gene expression pattern was abrogated in a developmentally arrested cell line that is unable to pass through the PEM-to-embryo transition. Thirty-five genes (9.4% of arrayed cDNAs) were found to be differentially expressed during normal embryonic pattern formation. Among them, 22 genes (5.9% of arrayed cDNAs) were directly associated with embryo pattern formation and can be considered as marker genes for early stages of P. abies embryogenesis. The majority of the marker genes encode for proteins involved in translation and posttranslational modification. Among them, 18 genes displayed the major expression pattern.

Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. Taeda, P. Sylvestris or Picea abies.

Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.

Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays

BackgroundThe need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.ResultsHere we compare expression data from Pinus taeda cDNA microarrays using transcripts amplified either exponentially by PCR or linearly by T7 transcription. The amplified transcripts vary significantly in estimated length, GC content and expression depending on amplification technique. Amplification by T7 RNA polymerase gives transcripts with a greater range of lengths, greater estimated mean length, and greater variation of expression levels, but lower average GC content, than those from PCR amplification. For genes with significantly higher expression after T7 transcription than after PCR, the transcripts were 27% longer and had about 2 percentage units lower GC content. The correlation of expression intensities between technical repeats was high for both methods (R2 = 0.98) whereas the correlation of expression intensities using the different methods was considerably lower (R2 = 0.52). Correlation of expression intensities between amplified and unamplified transcripts were intermediate (R2 = 0.68–0.77).ConclusionAmplification with T7 transcription better reflects the variation of the unamplified transcriptome than PCR based methods owing to the better representation of long transcripts. If transcripts of particular interest are known to have high GC content and are of limited length, however, PCR-based methods may be preferable.

Expression of an abscisic acid responsive promoter in Picea abies (L.) Karst. following bombardment from an electric discharge particle accelerator

The 1.5 kilobase promoter sequence upstream of Dc8, a late embryo abundant gene of Daucus, fused to the reporter β-glucuronidase gene was introduced into several tissues of Picea abies via a custom-made electric-discharge particle accelerator. Transient expression was measured histochemically as spot number 2 d after bombardment. Embryogenic suspensions gave higher levels of expression depending upon cell line than embryogenic callus or zygotic embryos. Expression was enhanced when cultures were treated with abscisic acid for 3 d before bombardment. A mean and maximum of 17 and 34 spots/disk, respectively, were observed with the best cell line, which was comparable with the level of expression driven by an enhanced 35S promoter.

Phytochrome types in Picea and Pinus. Expression patterns of PHYA-related types

Knowledge of the genes in gymnosperms encoding the apoproteins of the plant photoreceptor phytochrome is currently scanty as for gymnosperm nuclear protein coding sequences in general. Here we report two complete cDNA-derived sequences which code for two different types of gymnosperm phytochrome. One sequence stems from Norway spruce (Picea abies) and the other from Scots pine (Pinus sylvestris). More detailed studies have shown that both types of phytochrome gene are present in Norway spruce. From phylogenetic analyses, these types appear to branch off from progenitors that are also the common ancestors of the angiosperm PHYA/PHYC and PHYB/PHYD/PHYE lineages. Partial phytochrome sequences of other gymnosperms cluster with either the one type or the other of the gymnosperm phytochrome genes characterized here. Southern blot analysis of Picea DNA using probes derived from the full-length Picea gene indicated a family of at least five members. Whether they code for new types may be doubted since only two phylogenetic clusters were found. Studies using RNA-PCR of Picea RNA extracted from either light- or dark-grown seedlings indicated that the steady-state levels of the transcripts of two PHYA/C-related genes were hardly affected by light.

T-DNA presence and opine production in tumors of Picea abies (L.) Karst induced by Agrobacterium tumefaciens A281

The hypervirulent Agrobacterium tumefaciens strain A281 formed frequent tumors (31%) on Picea abies (Norway spruce), an economically important tree species in Swedish forests. Three-month-old seedlings were inoculated and tumors were established that grew hormone-independently in culture. Tumors contained agropine and mannopine/mannopinic acid as determined by acid pH paper electrophoresis. In addition, DNA hybridization studies showed that the DNA from these tumor lines contained sequences homologous to Ti plasmid T-DNA, whereas wild-type spruce seedling DNA did not. These results suggest that Agrobacterium vectors can be used for gene transfer into this important forest species.

Induction of tumours by various strains of Agrobacterium tumefaciens on Abies nordmanniana and Picea abies

Abies nordmanniana and Picea abies seedlings were inoculated with a wild‐type (C 58) or an attenuated strain (rooter or shooter mutants) of Agrobacterium tumefaciens. Large tumours were formed on A. nordmanniana in response to the wild‐type and rooter strains, 60–65 % of the seedlings being susceptible. Smaller tumours were formed on Picea abies in response to the wild‐type strain, at least 12% of the seedlings being susceptible. Tumours from both species induced by the wild‐type strain grew in vitro on medium without added phytohormones.

Within-population variation in susceptibility to Agrobacterium tumefaciens A281 in Picea abies (L.) Karst.

SummaryThe purpose of this study was to investigate the genetic variation of susceptibility to Agrobacterium within a Picea abies population. Tumor formation was studied in 16 open-pollinated families belonging to a central Swedish population of Picea abies. Strain A281 of Agrobacterium tumefaciens was used to infect 3-monthold seedlings in a five-block greenhouse experiment. The analysis of variance showed strong significance for the between-family variation of tumor-formation percentages, varying from 28% to 73%. The most susceptible material will be suitable for experiments on the production of transgenic plants in vitro using disarmed Agrobacterium strains.