Genome based identification and analysis of the pre-replicative complex of Arabidopsis thaliana.

Eukaryotic DNA replication requires an ordered and regulated machinery to control G1/S transition. The formation of the pre-replicative complex (pre-RC) is a key step involved in licensing DNA for replication. Here, we identify all putative components of the full pre-RC in the genome of the model plant Arabidopsis thaliana. Different from the other eukaryotes, Arabidopsis houses in its genome two putative homologs of ORC1, CDC6 and CDT1. Two mRNA variants of AtORC4 subunit, with different temporal expression patterns, were also identified. Two-hybrid binary interaction assays suggest a primary architectural organization of the Arabidopsis ORC, in which AtORC3 plays a central role in maintaining the complex associations. Expression profiles differ among pre-RC components suggesting the existence of various forms of the complex, possibly playing different roles during development. In addition, the expression of the putative pre-RC genes in non-proliferating plant tissues suggests that they might have roles in processes other than DNA replication licensing.

Molecular characterization of Arabidopsis PHO80-like proteins, a novel class of CDKA;1-interacting cyclins.

Cyclins are regulatory proteins that interact with cyclin-dependent kinases (CDKs) to control progression through the cell cycle. In Arabidopsis thaliana, 34 cyclin genes have been described, grouped into five different types (A, B, D, H, and T). A novel class of seven cyclins was isolated and characterized in Arabidopsis, designated P-type cyclins (CYCPs). They all share a conserved central region of 100 amino acids ("cyclin box") displaying homology to the corresponding region of the PHO80 cyclin from Saccharomyces cerevisiae and the related G1 cyclins from Trypanosoma cruzi and T. brucei. The CYCP4;2 gene was able to partially re-establish the phosphate-dependent expression of the PHO5 gene in a pho80 mutant strain of yeast. The CYCPs interact preferentially with CDKA;1 in vivo and in vitro as shown by yeast two-hybrid analysis and co-immunoprecipitation experiments. P-type cyclins were mostly expressed in proliferating cells, albeit also in differentiating and mature tissues. The possible role of CYCPs in linking cell division, cell differentiation, and the nutritional status of the cell is discussed.

The cytoskeleton in nematode feeding sites.

Sedentary edoparasitic nematodes induce specialised feeding cells in plant roots. Giant cells induced by root knot nematodes and syncytia generated by cyst nematodes in plant roots are large multinucleated cells containing a dense cytoplasm. To examine the plant cytoskeleton during feeding cell development, transcriptional activity of actin and tubulin genes and organization of the actin filaments and of the microtubules were analyzed in situ. Immunolocalizations of actins and tubulins and in vivo observation of green fluorescent protein decorated actin filaments and microtubules in nematode infected root cells revealed that major rearrangements of the cytoskeleton occur during the formation of nematode induced feeding cells.

DNA replication in plants: characterization of a cdc6 homologue from Arabidopsis thaliana.

Cdc6 is a key regulator of DNA replication in eukaryotes. In this work, the expression pattern of an Arabidopsis cdc6 homologue is characterized by RT-PCR and in situ hybridization. The data suggest that cdc6At expression is cell cycle regulated. During development, high cdc6At mRNA levels are found in regular cycling cells. In addition, cdc6At expression is also observed in cells that are probably undergoing endoreduplication, suggesting a possible role of Cdc6At in this process in plants.

In situ hybridization to mRNA of Arabidopsis tissue sections.

In situ hybridization detection of mRNA is an essential tool for understanding regulation of gene expression in cells and tissues of different organisms. Over the years, numerous in situ protocols have been developed ranging from whole-mount techniques that allow fast transcript localization in intact organs to high-resolution methods based on the electron microscopic detection of mRNAs at the subcellular level. Here, we present a detailed protocol for the detection of mRNAs in plant tissues using radiolabeled single-stranded RNA probes. Hybridizations are carried out on tissue sections of paraffin- and plastic-embedded plant tissues. Although this in situ protocol is appropriate for plant tissues in general, it has been optimized for Arabidopsis thaliana. Variations on the procedure, required to obtain optimal results with different Arabidopsis tissues, are described.

Developmental expression of the Arabidopsis thaliana CycA2;1 gene.

The associations of cyclins with highly conserved cyclin-dependent kinases are key events in the regulation of cell cycle progression. The spatio-temporal expression of an Arabidopsis thaliana (L.) Heynh. mitotic cyclin, Arath;CycA2;1, was studied by histochemical beta-glucuronidase (GUS) analysis and in-situ hybridizations. The CycA2,1] promoter was active in the egg apparatus before fertilization. During embryogenesis, CycA2;1:gus expression was found in the embryo and the developing endosperm. Throughout plant development, CycA2;1 transcripts were found in both dividing and non-dividing cells, indicating that the expression of this cyclin is not a limiting factor for cell division. In the pericycle and stelar parenchyma, CycA2;1 transcripts were located at the xylem poles, a position that can be correlated with competence for lateral root formation. In addition, CycA2;1:gus expression was upregulated in roots by auxins and in the shoot apex by cytokinins. Transcription of CycA2;1 was shown by reverse transcription-polymerase chain reaction to be strongly induced by sucrose in A. thaliana cell suspensions.

Cloning and characterization of a novel Mg(2+)/H(+) exchanger.

Cellular functions require adequate homeostasis of several divalent metal cations, including Mg(2+) and Zn(2+). Mg(2+), the most abundant free divalent cytoplasmic cation, is essential for many enzymatic reactions, while Zn(2+) is a structural constituent of various enzymes. Multicellular organisms have to balance not only the intake of Mg(2+) and Zn(2+), but also the distribution of these ions to various organs. To date, genes encoding Mg(2+) transport proteins have not been cloned from any multicellular organism. We report here the cloning and characterization of an Arabidopsis thaliana transporter, designated AtMHX, which is localized in the vacuolar membrane and functions as an electrogenic exchanger of protons with Mg(2+) and Zn(2+) ions. Functional homologs of AtMHX have not been cloned from any organism. Ectopic overexpression of AtMHX in transgenic tobacco plants render them sensitive to growth on media containing elevated levels of Mg(2+) or Zn(2+), but does not affect the total amounts of these minerals in shoots of the transgenic plants. AtMHX mRNA is mainly found at the vascular cylinder, and a large proportion of the mRNA is localized in close association with the xylem tracheary elements. This localization suggests that AtMHX may control the partitioning of Mg(2+) and Zn(2+) between the various plant organs.

A new D-type cyclin of Arabidopsis thaliana expressed during lateral root primordia formation.

D-type cyclins are believed to regulate the onset of cell division upon mitogenic signaling. Here, the isolation is reported of a new D-type cyclin gene (CYCD4;1) of Arabidopsis thaliana (L.) Heynh. during a two-hybrid screen using the cyclin-dependent kinase CDC2aAt as bait. Transcription of CYCD4;1 can be induced by sucrose. The co-regulated expression of CYCD4;1 and CDC2aAt in starved suspension cultures upon mitogenic stimulation indicates that the formation of a complex between these two partners is important for the resumption of cell division activity. By in-situ hybridizations CYCD4;1 was shown to be expressed during vascular tissue development, embryogenesis, and formation of lateral root primordia. Expression during the latter process suggests that the induced expression of D-type cyclins by mitogenic stimuli might be one of the rate-limiting events for the initiation of lateral roots.

Molecular markers and cell cycle inhibitors show the importance of cell cycle progression in nematode-induced galls and syncytia.

Root knot and cyst nematodes induce large multinucleated cells, designated giant cells and syncytia, respectively, in plant roots. We have used molecular markers to study cell cycle progression in these specialized feeding cells. In situ hybridization with two cyclin-dependent kinases and two cyclins showed that these genes were induced very early in galls and syncytia and that the feeding cells progressed through the G2 phase. By using cell cycle blockers, DNA synthesis and progression through the G2 phase, or mitosis, were shown to be essential for gall and syncytium establishment. When mitosis was blocked, further gall development was arrested. This result demonstrates that cycles of endoreduplication or other methods of DNA amplification are insufficient to drive giant cell expansion. On the other hand, syncytium development was much less affected by a mitotic block; however, syncytium expansion was inhibited.

Arabidopsis STERILE APETALA, a multifunctional gene regulating inflorescence, flower, and ovule development.

A recessive mutation in the Arabidopsis STERILE APETALA (SAP) causes severe aberrations in inflorescence and flower and ovule development. In sap flowers, sepals are carpelloid, petals are short and narrow or absent, and anthers are degenerated. Megasporogenesis, the process of meiotic divisions preceding the female gametophyte formation, is arrested in sap ovules during or just after the first meiotic division. More severe aberrations were observed in double mutants between sap and mutant alleles of the floral homeotic gene APETALA2 (AP2) suggesting that both genes are involved in the initiation of female gametophyte development. Together with the organ identity gene AGAMOUS (AG) SAP is required for the maintenance of floral identity acting in a manner similar to APETALA1. In contrast to the outer two floral organs in sap mutant flowers, normal sepals and petals develop in ag/sap double mutants, indicating that SAP negatively regulates AG expression in the perianth whorls. This supposed cadastral function of SAP is supported by in situ hybridization experiments showing ectopic expression of AG in the sap mutant. We have cloned the SAP gene by transposon tagging and revealed that it encodes a novel protein with sequence motifs, that are also present in plant and animal transcription regulators. Consistent with the mutant phenotype, SAP is expressed in inflorescence and floral meristems, floral organ primordia, and ovules. Taken together, we propose that SAP belongs to a new class of transcription regulators essential for a number of processes in Arabidopsis flower development.

Expression of CKS1At in Arabidopsis thaliana indicates a role for the protein in both the mitotic and the endoreduplication cycle.

Although endoreduplication is common in plants, little is known about the mechanisms regulating this process. Here, we report the patterns of endoreduplication at the cellular level in the shoot apex of Arabidopsis thaliana L. Heynh. plants grown under short-day conditions. We show that polyploidy is developmentally established in the pith, maturing leaves, and stipules. To investigate the role of the cell cycle genes CDC2aAt, CDC2bAt, CYCB1;1, and CKS1At in the process of endoreduplication, in-situ hybridizations were performed on the vegetative shoot apices. Expression of CDC2aAt, CDC2bAt, and CYCB1;1 was restricted to mitotically dividing cells. In contrast, CKS1At expression was present in both mitotic and endoreduplicating tissues. Our data indicate that CDC2aAt, CDC2bAt, and CYCB1;1 only operate during mitotic divisions, whereas CKS1At may play a role in both the mitotic and endoreduplication cycle.

Induction of cdc2a and cyc1At expression in Arabidopsis thaliana during early phases of nematode-induced feeding cell formation.

Root-knot and cyst nematodes are plant parasites that induce large multinucleated feeding cells in the roots of their hosts. Cytological observations have shown that root-knot nematodes induce giant cells by cycles of mitosis without cytokinesis whereas cyst nematodes provoke cell wall degradation leading to the formation of a large syncytium. This study was intended to characterize and compare the ability of both types of nematodes to induce progression through the cell cycle. For this purpose, the expression, upon nematode infection, of two cell cycle markers was followed: a marker for division competence, the cyclin-dependent kinase cdc2a and a marker for the G2 phase, the mitotic cyclin cyc1At. For both types of nematodes, transcriptional activation of these markers was correlated with early phases of feeding cell development. Using molecular markers, it was thus possible to confirm and extend the observations of repeated mitosis in root-knot nematode-induced giant cells. Surprisingly, promoter activation of both cdc2a and cyc1At markers was also found upon cyst nematode infection, in feeding cells in which mitosis has not been clearly reported. Incorporation of tritiated thymidine in these syncytia confirms that they progress through the S phase of the cell cycle. One possibility is that cyst nematodes induce cycles of DNA endoreduplication shunting the M phase. Despite obvious differences in ontogeny, common molecular mechanisms, involving cycles of DNA endoreduplication and cdc2a and cyc1At expression, might thus be involved in the formation of a giant cell or a syncytium.

The Arabidopsis cyclin-dependent kinase gene cdc2bAt is preferentially expressed during S and G2 phases of the cell cycle.

Cell cycle progression is regulated by cyclin-dependent kinases (CDKs). Arabidopsis thaliana contains two cdk genes, cdc2aAt and cdc2bAt. This paper compares the developmental and cell cycle phase-dependent transcription of both cdk genes. In situ hybridizations revealed that cdc2bAt steady-state mRNAs, much like cdc2aAt, are found both in meristematic cells and cells with a high proliferative competence. Cdc2aAt is expressed in every meristematic cell whereas cdc2bAt is found to be expressed in a patchy pattern. An even smaller number of meristematic cells express the mitotic cyc1At. These data indicate that cdc2bAt and cyc1At mRNAs accumulate in a particular cell cycle phase in agreement with evidence provided by hybridization experiments of flow cytometrysorted nuclei and the use of cell cycle blockers on roots. The data indicate that cdc2bAt is preferentially expressed in S and G2 phases whereas cdc2aAt expression is constitutive throughout the cell cycle, as shown previously. The existence of two distinct CDK classes in plants is proposed: (i) constitutively expressed CDKs containing a PSTAIRE motif (e.g. cdc2aAt) and (ii) CDKs with divergent motifs which are expressed during a limited interval of the cell cycle (e.g. cdc2bAt).

Evidence for the nitrate-dependent spatial regulation of the nitrate reductase gene in chicory roots.

Young chicory plants (Cichorium intybus L. var. Witloof) show a tenfold higher nitrate reductase NR activity in roots compared to leaves. Northern analysis revealed, besides the nitrate inducibility of the nitrate reductase gene (nia), a higher level of expression in the roots. By modifying the external nitrate concentration the NR activity in the leaves remained negligible whereas a maximal activity was observed in the roots when grown in the presence of 5 mM nitrate. Surprisingly, variation of the external nitrate concentration induced changes in the spatial regulation of nia within the root. In-situ hybridization mainly localized nia mRNA in the cortical cells of roots grown at low nitrate concentrations (0.2 nM). At high nitrate concentrations (5 mM), nia mRNA was more abundant in the vascular tissues. The root apex revealed a strong signal under both conditions. The isolation and characterization of the NR structural gene from chicory is also presented. Southern blot analysis revealed the presence of a single nia gene per haploid genome of chicory.

A molecular study of root-knot nematode-induced feeding sites.

In a compatible interaction, root-knot nematodes (Meloidogyne) induce a sophisticated feeding site shortly after they have penetrated the plant root. The feeding site contains metabolically highly active giant cells. To gain insight into the molecular aspects that are typical for giant cells, a cDNA library from tomato roots infected with Meloidogyne incognita was differentially screened to find induced genes. Among the genes identified, two extensin genes (Lemmi8 and Lemmi11) and a Lea-like gene (Lemmi9) were studied further.

Identification and analysis of a cuticular collagen-encoding gene from the plant-parasitic nematode Meloidogyne incognita.

The vast majority of proteins in the nematode cuticle are collagens. Cuticular collagen-encoding genes (col) have been described for the animal parasites Ascaris suum and Haemonchus contortus and for the free-living Caenorhabditis elegans. The proteins encoded by all these genes seem to have the same basic structure, indicating that there is a conserved subfamily of cuticular col in these nematodes. In this paper, we describe the identification and characterization of a cDNA (Lemmi 5) which corresponds to a cuticular col of the plant-parasitic nematode Meloidogyne incognita. The derived protein structure is very similar to the basic structure of the C. elegans cuticular collagens. Using PCR technology, we have shown the presence of Lemmi 5-related sequences in the genome of Ditylenchus destructor. Our data strongly support the existence of a cuticular col subfamily which is highly conserved in the phylum Nemata.

Three discrete classes of Arabidopsis cyclins are expressed during different intervals of the cell cycle.

We have isolated cDNAs encoding four additional mitotic-like cyclins from Arabidopsis: cyc2aAt, cyc2bAt, cyc3aAt, and cyc3bAt. Examination of amino acid sequences deduced from plant cyclin cDNAs isolated so far showed that they can be grouped into three distinct classes. The members of each plant cyclin family are more related to each other than to any animal or yeast cyclin. Reverse transcription-PCR analysis demonstrated that cyc2aAt was expressed in all plant organs, whereas cyc2bAt mRNAs were found only in roots; cyc3aAt was not expressed in leaves and was barely expressed in flowers. On the other hand, cyc3bAt transcripts were observed in all organs. Whole-mount in situ hybridizations on roots showed that the cyclin mRNAs were confined to parts of the roots with mitotic activity. Furthermore, results of whole-mount in situ hybridizations on roots treated with either oryzalin or hydroxyurea suggest that the different cyclin classes have distinct functions in the cell cycle.

cdc2a expression in Arabidopsis is linked with competence for cell division.

A key regulator of the cell cycle is a highly conserved protein kinase whose catalytic subunit, p34(cdc2), is encoded by the cdc2 gene. We studied the control of the expression of the Arabidopsis cdc2a gene in cell suspensions and during plant development. In cell cultures, arrest of the cell cycle did not significantly affect cdc2a mRNA levels, but nutrient conditions were important for cdc2a expression. During plant development, the pattern of cdc2a expression was strongly correlated with the cell proliferation potential. The effects of external signals on cdc2a expression were analyzed. Wounding induced expression in leaves. Lack of light altered temporal regulation of cdc2a in the apical but not root meristem of seedlings. Differential cdc2a responses were obtained after different hormone treatments. Signals present only in intact plants were necessary to mediate these responses. Although other control levels have yet to be analyzed, these results suggest that the regulation of cdc2a expression may contribute greatly to spatial and temporal regulation of cell division in plants. Our results also show that cdc2a expression is not always coupled with cell proliferation but always precedes it. We propose that cdc2a expression may reflect a state of competence to divide, and that the release of other controls is necessary for cell division to occur.

Induction Patterns of an Extensin Gene in Tobacco upon Nematode Infection.

When sedentary endoparasitic nematodes infect plants, they induce complex feeding sites within the root tissues of their host. To characterize cell wall changes induced within these structures at a molecular level, we studied the expression of an extensin gene (coding for a major structural cell wall protein) in nematode-infected tobacco roots. Extensin gene expression was observed to be induced very early upon infection. This induction was weak, transient, and probably due to wounding during penetration and migration of the tobacco cyst nematode Globodera tabacum ssp solanacea-rum. In contrast, high extensin gene expression was observed during the whole second larval stage (an ~2-week-long phase of establishment of the feeding site) of the root knot nematode Meloidogyne javanica. During later stages of this interaction, expression gradually decreased. Extensin gene expression was found in at least three different tissues of the gall. We propose that distinct mechanisms lead to induced expression in these different cell types. The significance of these results for the understanding of plant-nematode interactions as well as the function of structural cell wall proteins, such as extensin, is discussed.