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Plant Cell Physiol. 43(2): 224–229 (2002) JSPP © 2002 C-Tubulin in Barley and Tobacco: Sequence Relationship and RNA Expression Patterns in Developing Leaves during Mitosis and Post-Mitotic Growth Jan Schröder, Kordula Kautz and Wolfgang Wernicke 1 Institut für Allgemeine Botanik, Johannes Gutenberg – Universität Mainz, P.O. Box 3980, D-55099 Mainz, Germany ; C-Tubulin is typically associated with microtubule organising centres, such as the centrosome, and appears to mediate microtubule nucleation. Centrosomes are usually not found in higher plants, but active genes homologous to C-tubulin have been identified in the plant kingdom, including the angiosperms Arabidopsis, maize and rice. We have isolated and characterised C-tubulin cDNA sequences of two further angiosperm species, barley and tobacco. Sequence comparison revealed a phylogenetic tree with distinct clusters corresponding to the systematic position of the species. Furthermore, domains, thought to be exposed in the folded protein and to be candidates for interaction with associated, nucleation-site related proteins, exhibited motifs highly specific of multicellular plants. Strong expression of the Ctubulin genes, as determined by Northern blotting, correlated with mitotic activity. Expression dropped distinctly when mitotic activity ceased. Thus, in post-mitotic tissues that showed intricate reshuffling of cortical microtubule arrays related to cell shaping only very low C-tubulin steady-state RNA levels were found, contrasting with the situation for =-tubulin. The findings indicate that C-tubulin expression in plants may be more tightly linked to mitosis, although there is some C-tubulin expression at the RNA level even after mitosis. It follows that the post-mitotic changes in microtubular arrays may be less dependent on concurrent C-tubulin RNA expression than mitotic cells. ing in interphase and terminally differentiating post-mitotic cells. Little is known as to how the successive establishment of the different arrays is accomplished (Vaughn and Harper 1998). There is increasing evidence that plant microtubules are prone to rapid turnover, with interphase microtubules turning over more than three times faster compared to those in animal cells (e.g. Hush et al. 1994, Moore et al. 1997). This indicates that assembly and disassembly cycles play a dominant role in rearrangement of microtubule arrays in plants, rather than shifting of whole stable microtubules. De novo assembly of microtubules in vivo appears to rely on specialised nucleation sites, typically in the form of a microtubule organising centre (MTOC). The dominant MTOC is the centrosome of mammalian cells. Here, nucleation is most likely mediated by g-tubulin, a member of the tubulin superfamily that is capable of forming complexes acting as templates (Oakley and Oakley 1989, Moritz et al. 2000, Oakley 2000). Such centrosome-like MTOCs are usually not observed in higher plants, especially not in angiosperms (Vaughn and Harper 1998), but genes homologous to g-tubulin have recently been found in the plant kingdom, including some angiosperm species, Arabidopsis (Liu et al. 1994), maize (Lopez et al. 1995) and rice (Kim et al. 1999). Several attempts have been made to detect the protein in cells by means of immunofluorescence microscopy. It emerges that higher plant g-tubulin co-localizes with most if not all of the microtubule patterns described above, more or less mirroring the arrays, albeit in a punctate fashion (e.g. Liu et al. 1993, Canaday et al. 2000, Panteris et al. 2000). The findings leave open the question as to whether g-tubulin acts in higher plants as a highly dispersed nucleation site or whether it has evolved different functions (Vaughn and Harper 1998, Panteris et al. 2000). In this context it is important to note that non-centrosomal microtubule nucleation has been observed in animals (Hyman and Karsenti 1998, Oakley 2000). We are interested in changes of microtubular arrays occurring during transition from cell division to cell differentiation. The dynamics of microtubules in cycling cells are well established and indirect evidence suggests that even post-mitotic changes in cortical microtubular arrays are not simply the result of shifting whole stable microtubules (e.g. Wymer and Lloyd 1996, Hellmann and Wernicke 1998, Schröder et al. 2001). This raises the intriguing question as to what extent gtubulin-associated nucleation occurs not only in cycling but also in differentiating plant cells. To approach this issue, we Key words: Cytoskeleton — Gene expression — Hordeum vulgare — Nicotiana tabacum — Phylogeny — g-tubulin. Abbreviations: MTOC, microtubule organizing centre; pfu, plaque forming unit. Introduction Successions of diverse arrays of microtubules drive crucial steps in cell division and differentiation in higher plants. The major microtubule patterns include preprophase bands related to determining the orientation of the future cell division plane, spindles for separating chromatids or chromosomes, phragmoplast microtubules involved in building the new cell plate and various cortical arrays associated with wall pattern1 Corresponding author: E-mail, [email protected]; Fax, +49-6131-3923075. 224 g-Tubulin in barley and tobacco 225 Fig. 1 Comparison of predicted complete amino acid sequences of the g-tubulin cDNAs derived from barley (Hordeum vulgare: H. v.) and tobacco (Nicotiana tabacum: N. t.), including the first known g-tubulin sequence (Aspergillus nidulans: A. n.). Sequences were aligned and displayed using the software programmes ClustalX and GeneDoc, respectively. The barley sequence was taken as the reference. Dots indicate sequence homologies; dashes indicate gaps included for optimal alignment, # indicate end of protein sequence corresponding to translational stop codon. Arrows mark the locations of the primers initially used for amplifying conserved open reading frames and thus probes. tested a dicotyledonous and a monocotyledonous species, tobacco and barley, respectively, for the presence of expressed g-tubulin genes. cDNA sequences were isolated and compared to known g-tubulins to determine potential plant-specific features. In addition, Northern blot experiments were performed to reveal general expression patterns during early development of leaves, as model systems covering the phases of cell division and differentiation. Results Isolation and characterisation of the C-tubulin cDNA sequences The potentially g-tubulin-specific PCR primer-sets applied in barley yielded two fragments, 621 and 656 bp in length, respectively. Both fragments were 100% identical in their overlapping sequence and database alignment showed highest homologies to the already known sequence of rice (Oryza sativa) g-tubulin. Both sequences were used as conserved gtubulin-specific probes in further experiments with barley. Probing of cDNA libraries yielded several positive clones. In a library derived from the meristematic base of the leaf, i.e. the basal 5 mm, 21 clones were found in a screening of 5.5´105 plaque-forming units (pfu). The yield was one order of magnitude lower when a library derived from an only slightly more advanced developmental stage, 5–10 mm, was tested. The clones appeared to be identical with one exception. There were two variants with regard to the length of the 3¢-untranslated region (UTR), 456 bp and 285 bp, respectively. Southern blot analysis of genomic DNA digested with restriction enzymes (EcoRI, HindIII, XbaI, data not shown) indicated the presence of only one g-tubulin gene. The deduced amino acid sequence of the complete open reading frame is shown in Fig. 1, for nucleotide sequence see accession no. AJ272313, GenBank data base. Fig. 2 Phylogenetic tree for predicted amino acid sequences of barley and tobacco and all the other plant g-tubulins known so far and the human g-tubulin, with Aspergillus nidulans as outgroup sequence. The tree was derived using the neighbour-joining method (PHYLIP 3.5c software package: J. Felsenstein, University of Washington, Seattle, U.S.A.). Numbers at nodes represent the confidence level of 100 bootstrap samples. The horizontal bar indicates ‘percentage accepted mutations’ (PAM) distance. Non-barley or -tobacco sequences were taken from the Swissprot database. In tobacco, application of the more degenerate primers resulted in the amplification of a 845 bp fragment that exhibited highest homology to the already known g-tubulin sequences of Arabidopsis. A cDNA library derived from a 226 g-Tubulin in barley and tobacco Fig. 3 Northern blots of barley, aligned with a diagram of the leaf and a bar graph showing the mitotic indices (mean derived from four leaves) of the corresponding leaf regions. No mitotic activity was observed beyond the region to 9 mm from the leaf base. Twelve mg RNA were blotted per sample. Please note that the intensities of the signals represent relative values. No conclusions can be drawn as to absolute ratios between a- and g-tubulin levels. Fig. 4 Northern blots of various tobacco tissues (numbered consecutively). The sketch indicates the shoot tip, including the successive leaves, from which the various RNA samples were derived. The bar graph shows the mitotic indices of the corresponding tissues (mean derived from six shoots). Twelve mg RNA were blotted per sample. highly meristematic cell suspension culture (mitotic index >6) yielded 17 positive clones after screening of only 4.2´104 pfu with the potentially tobacco g-tubulin-specific, RT-PCR derived probe. The predicted amino acid sequence of a full length clone, aligned with the barley sequence and with the first gtubulin sequence identified (Aspergillus nidulans), is shown in Fig. 1; for complete nucleotide sequence see accession no. AJ278739. A phylogenetic sequence analysis including all known deduced amino acid sequences for g-tubulin is shown in Fig. 2. These sequences not only include tobacco (Nicotiana tabacum) and barley (Hordeum vulgare) and the other angiosperms, i.e. Arabidopsis thaliana, maize (Zea mays) and rice (Oryza sativa) (Liu et al. 1994, Lopez et al. 1995, Kim et al. 1999), but also the green alga Chlamydomonas reinhardtii (Silflow et al. 1999), the moss Physcomitrella patens (GenBank accession no AF142098) and the fern Anemia phyllitidis (Fuchs et al. 1993). Northern blot analysis A scheme representing the barley leaf analysis is depicted in Fig. 3. Mitotic indices were determined in 1 mm long intervals to get better temporal/spatial resolution, starting with the leaf base. Meristematic activity was restricted to the basal 9 mm of the leaf, with highest rates in the first 5 mm. No mitotic figures were found beyond this region. Samples taken in regular intervals of 5–10 mm (compare Fig. 3) were subjected to Northern blot analysis, starting at the base and extending up to 70 mm, thus covering the meristem and the whole area of cell expansion and shaping. Samples were probed with conserved barley g-tubulin sequences. a-Tubulin RNA expression was taken as an appropriate and convenient reference (Schröder et al. 2001). There appeared to be a distinct correlation between developmental stage and tubulin expression. The a-tubulin expression pattern was similar to that described recently (Schröder et al. 2001), with highest levels found in the g-Tubulin in barley and tobacco 227 Fig. 5 g-Tubulin sequence comparison across different phyla and/or taxa. Only the domain referred to as g-Peptide B by Burns (1995) is shown, including the conserved flanking regions. The conserved, apparently multicellular plant-specific motif is boxed. Note that only ‘conventional’ gtubulins (Oakley 2000) are compared, i.e. Saccharomyces and Caenorhabditis sequences are not included. Sequences were initially aligned with the software ClustalX and then manually amended to maximize homologies and displayed using the GeneDoc program. Non-barley or -tobacco sequences were taken from the Swissprot data base. cell expansion and shaping region. However, highest g-tubulin RNA steady-state levels were found in the meristematic basal 5 mm of the leaf, followed by a steady decline in more advanced regions. Densitometric analysis of the blots revealed that steady-state RNA g-tubulin levels in early post-mitotic tissue (10–15 mm distance from the leaf base) dropped to ca 30% of that found in the most basal, meristematic section (0–5 mm). Nevertheless, there was still a ca 10% level in the clearly nonmeristematic, cell-shaping region of 20–25 mm distance from the meristematic base. Incidentally, no differences in the expression patterns were found between the two g-tubulins showing different lengths in the 3¢-UTR. Tobacco leaves do not exhibit the stringent developmental gradient found in grass leaves. To overcome this limitation, whole leaves of various developmental stages had to be taken, starting with the shoot tip. A diagram of the corresponding tobacco shoot with its succession of leaves is shown in Fig. 4. The youngest sample taken consisted of the shoot apical meristem including the highly meristematic ensheathing leaf primordia with a maximum length of ca 2 mm (1). The next older stage was a rapidly expanding leaf of ca 30 mm length (2), followed by still growing leaves of ca 60 and 100 mm (3 and 4, respectively). The next leaf (5) in the succession was ca 180 mm long and almost fully expanded. The oldest leaves included were ca 200 mm in length (6) and just fully expanded. There was a steady decline in the mitotic indices with increasing leaf age. No apparent mitotic activity was found in the almost fully expanded leaf 5 and beyond (Fig. 4). The g-tubulin expression pattern detected was basically similar to that observed in barley with highest steady-state g-tubulin RNA levels found in the samples with the highest meristematic rates. The g-tubulin RNA levels decreased more rapidly than those of a-tubulin. Consequently, a-tubulin expression was still found in the fully expanded, no longer meristematic leaves, but only barely detectable traces of g-tubulin RNA. Discussion The present study adds two angiosperm species to the still brief list of plants with known g-tubulin sequences. In fact, tobacco represents only the second dicotyledonous and barley the third monocotyledonous species. A phylogenetic analysis of predicted protein sequences revealed distinct clusters (Fig. 2). The multicellular green land plants were clearly separated from the unicellular green alga Chlamydomonas. The archegoniates Anemia and Physcomitrella formed a cluster, as did the angiosperms. Within the angiosperms a cluster corresponded to dicots and another to monocots or, more precisely, to grasses. A comprehensive sequence alignment including gtubulin sequences of various organisms confirmed relatively conserved domains, but also highly variable regions, such as the C-terminus. Most interestingly, there were particular gtubulin-specific, closely linked domains, referred to as g-Peptide A and B by Burns (1995) that revealed conserved motifs, apparently specific to multicellular plants. In g-Peptide A it was the motif VERQ(A/V)N (data not shown, compare Burns 1995); g-Peptide B exhibited the motif SYAR(T/N)KEASQAK (Fig. 5). Both motifs are flanked by sequences that are highly conserved across most phyla and/or taxa. It appears that the corresponding domains are exposed in the folded protein 228 g-Tubulin in barley and tobacco (Burns 1995), permitting interactions with associated proteins, e.g. in the ring-forming complexes (Inclán and Nogales 2001). Perhaps the variant motifs are involved in allowing g-tubulin to perform its particular functions in multicellular land plants lacking centrosomes. In this context it should be noted that the flagellated unicellular green alga Chlamydomonas exhibited a different peptide. It will be very worthwhile to elucidate to what extent the differences in g-tubulin sequences observed reflect simple phylogenetic distances or actual functional specialisation (see also Oakley 2000). Reports describing attempts to localize g-tubulin in plants by immunofluorescence microscopy suggest a surprisingly dispersed distribution of g-tubulin, almost mirroring every microtubule pattern (e.g. Joshi and Palevitz 1996, Canaday et al. 2000, Panteris et al. 2000). Most data reported were derived from meristematic tissues or cell cultures, but apparent colocalization has also been found in cortical arrays of interphase cells (e.g. Canaday et al. 2000). Interestingly, a more localised distribution of g-tubulin has been implicated in the organisation of cortical microtubules of post-mitotic, differentiating guard cells, associated with wall deposition and cell shaping (McDonald et al. 1993). These data indicate at least presence, if not function of g-tubulin throughout all phases of microtubule occurrence. It remains to be seen whether the apparent decoration of plant microtubules with g-tubulin is actually indicative of highly dispersed nucleation sites or a result of further functions or features (Joshi and Palevitz 1996, Canaday et al. 2000, Panteris et al. 2000). An analysis of gene expression at the RNA level could give some additional clues concerning expression and perhaps evolution of function of g-tubulin in plants. Our Northern blot experiments indicate that g-tubulin gene expression in higher plants coincides with mitotic, rather than with post-mitotic activities of the microtubular cytoskeleton. This was particularly obvious in the barley leaf with its stringent developmental gradient typical of monocotyledonous grass species, even though steady-state levels of g-tubulin RNA did not drop as dramatically as apparent mitotic rates. The barley leaf experimental system permitted discrimination between timing of mitotic activity and of post-mitotic growth, much better than in the dicotyledonous tobacco. In grasses, such as barley, intricate rearrangements of microtubular arrays occur in developing leaves after completion of the last mitotic cycle and result in the formation of complex cell shapes in the terminally differentiating leaf tissue (Wernicke and Jung 1992). These highly synchronous post-mitotic rearrangements correlated with a transient increase in tubulin levels in early post-mitotic cells (compare Fig. 3) and with differential expression of members of the a-tubulin gene family in a characteristic fashion, indicating that they are not simply mediated by shifting whole, stable microtubules (Hellmann and Wernicke 1998, Schröder et al. 2001). The g-tubulin expression data presented here could suggest that the post-mitotic changes in microtubule arrays are less dependent on concurrent g-tubulin gene expression at the RNA level than mitotic stages. It will be worthwhile to eluci- date whether the residual, but distinct g-tubulin RNA levels observed in post-mitotic tissues are of significance in this context. We do not wish to over-interpret our current results. In order to be able to draw further conclusions data need to be quantified, but then additional cell-cycle- and differentiationspecific parameters, not a mitotic index alone, should be taken as a reference. Nevertheless, the data as shown here reveal the intriguing fact that g-tubulin RNA expression predominates in mitotic higher plant cells, despite the absence of centrosomes. Yet, gene activity was still apparent in post-mitotic tissues, if the presence of RNA is a valid indicator. Perhaps the establishment of the conserved novel motifs described played a crucial role within the context of loss of centrosomes and gain of novel, plant specific functions during phylogeny. Materials and Methods Plant material Barley plants (Hordeum vulgare L., cv Igri, seeds kindly provided by Ackermann Co., Irlbach, Germany) were grown in vermiculite in a growth cabinet under standardised conditions, as described (Hellmann et al. 1995). Second foliage leaves (100–120-mm long) were selected for analysis. This size was reached ca 9 d after sowing. Leaves were dissected transversely into sections of defined length (compare Fig. 3), starting at the base. The distance from the base strictly correlated with the developmental state of the tissue because of the developmental gradient along the leaf, characteristic of growing grass leaves. Tobacco plants (Nicotiana tabacum L. cv Petit Havana, SR I) were grown from seeds in a greenhouse. The upper part of shoots comprising the apical meristem and a succession of leaves ranging from young primordia to fully expanded leaves (compare diagram in Fig. 4) were excised from the plants about 10 weeks after sowing. The leaf lamina was processed after removal of the midrib, when possible. A rapidly proliferating friable cell suspension established from the same tobacco line several years ago was grown on a rotary shaker in Murashige and Skoog (1962) liquid medium supplemented with 5 mM 2,4-dichlorophenoxyacetic acid. Mitotic indices were determined after fixing of tissues in ethanol/ acetic acid and staining of chromatin in aceto-orcein or -carmin. A minimum of 1,000 cells was counted in each tissue sample. The data shown in the graphs represent means derived from 4–6 samples. No standard deviations have been shown, to avoid a degree of precision not intended. The only purpose of the counts was to show general tendencies and, particularly, to delimit the phase of meristematic activity from that of post-mitotic growth. RNA isolation and establishment of cDNA-libraries RNA was isolated using guanidine hydrochloride/LiCl as described recently (Schröder et al. 2001) or a commercial product (peqGold RNAPure, peqlab Biotechnologie GmbH, Erlangen, Germany). RNA concentrations were determined photometrically. For construction of cDNA-libraries, poly(A)+-RNA was recovered from total RNA by oligo(dT)-cellulose column chromatography (Stratagene, Heidelberg, Germany) according to Sambrook et al. (1989) and primed with an oligo(dT)-tailed linker-primer for cDNA preparation. cDNA libraries were established using the Uni-ZAP™ XR- or ZAP Express™ vector-systems (Stratagene, Heidelberg, Germany). Positive clones were identified by plaque lift hybridisation (Benton and Davies 1977) and sequenced by the dideoxy chain termination method (Sanger et al. 1977). g-Tubulin in barley and tobacco Probes for cDNA library screening Total RNA preparations were subjected to RT-PCR with sets of degenerate primers. In barley, RNA was isolated from the basal 10 mm of the young leaf, comprising the highly meristematic base and the early elongation zone. The primers were designed after taking into account known maize g-tubulin sequences. One downstream primer (GD3: GCC AAC CAG ATC ATT GTT C) was combined with two different upstream primers covering different regions (GU1: TCG AGG ACT TCG C(C/T)A CTC A; GU2: GA(C/T) GTC TTC TTT TAC CAG G). In tobacco, RNA was isolated from a highly meristematic cell suspension. The primers were designed with a higher degree of degeneracy, because the more specific primers used for barley yielded no signals. Upstream primer, GU2-DEG: GA(C/T) GTI TT(C/T) TT(C/T) TA(C/T) CA(A/G) GC; downstream primer according to Fuchs et al. (1993), sequence information kindly confirmed by Dr. B. Moepps. The positions of the barley and tobacco primers are indicated in Fig. 1. Annealing temperatures were determined according to Sambrook et al. (1989). PCR was performed using the Primus 25 thermal cycler (MWG Biotech, Ebersberg, Germany). The PCR-fragments obtained were electrophoresed and cloned into pBluescript vectors (Stratagene, Heidelberg, Germany). Probes for screening cDNA libraries were labeled with [a-32P]dATP by random priming (Feinberg and Vogelstein 1983) using the RadPrime DNA Labeling System (GibcoBRL, Eggenstein, Germany). Northern blotting Samples of total RNA were mixed with denaturing buffer and blotted onto nylon membranes (Hybond-N+, Amersham-Pharmacia, Freiburg, Germany). Probes used were labeled with [a-32P]dATP by PCR, similar to Mertz and Rashtchian (1994), in order to obtain selective labeling with high specific activity. Hybridisation was performed under high-stringency conditions at 65°C according to Hellmann et al. (1995). After hybridisation the membranes were washed twice in buffer containing 5% SDS and twice in 1% SDS buffer. The blots were exposed to imaging plates (BAS-MP 2025P, Fujifilm, Japan), that were scanned in a phospho-imager (BAS 1500, Raytest, Straubenhardt, Germany). The strongest signals were set to 100% on a linear gray scale for both, a- and g-tubulin. 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