cDNA sequence and expression of an intron-containing histone H2A gene from Norway spruce, Picea abies

High Concentration of Melatonin Regulates Leaf Development by Suppressing Cell Proliferation and Endoreduplication in Arabidopsis

N-acetyl-5-methoxytryptamine (Melatonin), as a crucial messenger in plants, functions in adjusting biological rhythms, stress tolerance, plant growth and development. Several studies have shown the retardation effect of exogenous melatonin treatment on plant growth and development. However, the in vivo role of melatonin in regulating plant leaf growth and the underlying mechanism are still unclear. In this study, we found that high concentration of melatonin suppressed leaf growth in Arabidopsis by reducing both cell size and cell number. Further kinetic analysis of the fifth leaves showed that melatonin remarkably inhibited cell division rate. Additionally, flow cytometic analysis indicated that melatonin negatively regulated endoreduplication during leaf development. Consistently, the expression analysis revealed that melatonin regulated the transcriptional levels of key genes of cell cycle and ribosome. Taken together, this study suggests that high concentration of melatonin negatively regulated the leaf growth and development in Arabidopsis, through modulation of endoreduplication and the transcripts of cell cycle and ribosomal key genes.

GhH2A12, a replication-dependent histone H2A gene from Gossypium hirsutum, is negatively involved in the development of cotton fiber cells

GhH2A12 was preferentially expressed at the initiation and early elongation stage of cotton fiber development, and overexpression of GhH2A12 caused retardation of fiber initiation and produced shorter fibers. Histone H2A is a component of eukaryotic chromatin whose function has not been studied in cotton. We have isolated an H2A gene encoding 156 amino acids, named GhH2A12. Like other plant histone H2As, GhH2A12 contains a typical SPKK motif in the carboxy-terminal and a plant-unique peptide-binding A/T-rich DNA region, and it was localized to the nucleus. GhH2A12 was preferentially expressed at the initiation and early elongation stage of cotton fiber, from 0 to 5 days post anthesis and the transcript level declined rapidly when the fiber entered the fast elongation stage, suggesting that GhH2A12 was involved in fiber differentiation. Therefore, GhH2A12 overexpression and RNAi transgenic cotton lines were developed via Agrobacterium tumefaciens-mediated transformation. Overexpression of GhH2A12 caused retardation of fiber initiation and produced shorter fibers and lower lint percentages. Moreover, the overexpressors showed negative effects on seedling growth, and the leaf emergence was delayed compared to wild type. However, no significant change in the GhH2A12 suppression line was observed. Coupled with retardation of fiber initiation, upregulation of GhH2A12 downregulated the expression of genes involved in cell-cycle performance. These results suggest that GhH2A12 might regulate fiber differentiation via regulating the cell cycle-related genes.

Maize histone H2B-mCherry: a new fluorescent chromatin marker for somatic and meiotic chromosome research

Cytological studies of fluorescent proteins are rapidly yielding insights into chromatin structure and dynamics. Here we describe the production and cytological characterization of new transgenic maize lines expressing a fluorescent histone fusion protein, H2B-mCherry. The transgene is expressed under the control of the maize ubiquitin1 promoter, including its first exon and intron. Polymerase chain reaction-based genotyping and root-tip microscopy showed that most of the lines carrying the transgene also expressed it, producing bright uniform staining of nuclei. Further, plants showing expression in root tips at the seedling stage also showed expression during meiosis, late in the life cycle. Detailed high-resolution three-dimensional imaging of cells and nuclei from various somatic and meiotic cell types showed that H2B-mCherry produced remarkably clear images of chromatin and chromosome fiber morphology, as seen in somatic, male meiotic prophase, and early microgametophyte cells. H2B-mCherry also yielded distinct nucleolus staining and was shown to be compatible with fluorescence in situ hybridization. We found several instances where H2B-mCherry was superior to DAPI as a generalized chromatin stain. Our study establishes these histone H2B-mCherry lines as new biological reagents for visualizing chromatin structure, chromosome morphology, and nuclear dynamics in fixed and living cells in a model plant genetic system.

Phylogenomics of unusual histone H2A Variants in Bdelloid rotifers

Rotifers of Class Bdelloidea are remarkable in having evolved for millions of years, apparently without males and meiosis. In addition, they are unusually resistant to desiccation and ionizing radiation and are able to repair hundreds of radiation-induced DNA double-strand breaks per genome with little effect on viability or reproduction. Because specific histone H2A variants are involved in DSB repair and certain meiotic processes in other eukaryotes, we investigated the histone H2A genes and proteins of two bdelloid species. Genomic libraries were built and probed to identify histone H2A genes in Adineta vaga and Philodina roseola, species representing two different bdelloid families. The expressed H2A proteins were visualized on SDS-PAGE gels and identified by tandem mass spectrometry. We find that neither the core histone H2A, present in nearly all other eukaryotes, nor the H2AX variant, a ubiquitous component of the eukaryotic DSB repair machinery, are present in bdelloid rotifers. Instead, they are replaced by unusual histone H2A variants of higher mass. In contrast, a species of rotifer belonging to the facultatively sexual, desiccation- and radiation-intolerant sister class of bdelloid rotifers, the monogononts, contains a canonical core histone H2A and appears to lack the bdelloid H2A variant genes. Applying phylogenetic tools, we demonstrate that the bdelloid-specific H2A variants arose as distinct lineages from canonical H2A separate from those leading to the H2AX and H2AZ variants. The replacement of core H2A and H2AX in bdelloid rotifers by previously uncharacterized H2A variants with extended carboxy-terminal tails is further evidence for evolutionary diversity within this class of histone H2A genes and may represent adaptation to unusual features specific to bdelloid rotifers.

Male gametic cell-specific histone gH2A gene of Lilium longiflorum: genomic structure and promoter activity in the generative cell

A genomic clone containing the gH2A gene, a histone variant specifically expressed in male gametic cells within the pollen of Lilium longiflorum, was isolated. Sequence analysis revealed that the coding region of the gene is interrupted by one intron, as is the case with the somatic type of plant histone H2A genes, suggesting derivation from the same ancestral gene containing one intron. In addition, a 2.8-kbp fragment of the 5' upstream region of gH2A contained TATA and CAAT boxes, but neither a plant histone-specific regulatory DNA element nor vegetative cell-specific cis-elements were found. A histochemical study of stable transformants demonstrated that the 5' upstream region of the gene can drive gene expression specifically in the generative cell of pollen; no activity was detectable in the vegetative cell or in other reproductive and vegetative tissues of transgenic Nicotiana tabacum. These results strongly suggest that the generative cell can direct specific gene expression, that this expression may be regulated by a putative male gametic factor, and that the gH2A promoter may therefore serve as a useful male gametic cell fate marker in angiosperms.

Nonconcerted evolution of histone 3 genes in a liverwort, Conocephalum conicum

To estimate the extent of genetic variation at the DNA level, the histone 3 (H3) genes were sequenced from single individual each from the three cryptic species recognized based on allozyme analyses, YFS, J and T types of Conocephalum conicum and two closely related species, C. japonicum and Marchantia polymorpha. Although the H3 genes are known to be highly conserved, the nucleotide diversities were 0.128, 0.109, 0.108, 0.049 and 0.034. These values are 30 to 100 times higher than that in Drosophila melanogaster (0.001). Besides, there were considerable differences in the position, length and number of introns among the loci of H3 genes. The observed high level of nucleotide diversities was explained by the fixation of many random mutations, and non-concerted evolution that resulted from low rates of unequal crossing-over and gene conversion probably due to the dispersed structure of H3 genes on genome in this species. The non-concerted evolutionary pattern was established by the analysis of phylogenetic tree and divergence rates. This study confirmed previous results suggesting that natural populations of liverwort maintains high extent of variation at DNA level.

Expression of the Arabidopsis histone H2A-1 gene correlates with susceptibility to Agrobacterium transformation

Transformation of plant cells by Agrobacterium tumefaciens involves both bacterial virulence proteins and host proteins. We have previously shown that the Arabidopsis thaliana gene H2A-1 (RAT5), which encodes histone H2A-1, is involved in T-DNA integration into the plant genome. Mutation of RAT5 results in a severely decreased frequency of transformation, whereas overexpression of RAT5 enhances the transformation frequency (Mysore et al., 2000b). We show here that the expression pattern of RAT5 correlates with plant root cells most susceptible to transformation. As opposed to a cyclin-GUS fusion gene whose expression is limited to meristematic tissues, the H2A-1 gene is expressed in many non-dividing cells. Under normal circumstances, the H2A-1 gene is expressed in the elongation zone of the root, the region that is most susceptible to Agrobacterium transformation. In addition, when roots are incubated on medium containing phytohormones, a concomitant shift in H2A-1 expression and transformation susceptibility to the root base is observed. Inoculation of root segments with a transfer-competent, but not a transformation-deficient Agrobacterium strain induces H2A-1 expression. Furthermore, pre-treatment of Arabidopsis root segments with phytohormones both induces H2A-1 expression and increases the frequency of Agrobacterium transformation. Our results suggest that the expression of the H2A-1 gene is both a marker for, and a predictor of, plant cells most susceptible to Agrobacterium transformation.

Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis

Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.

Identification of three kinds of mutually related composite elements conferring S phase-specific transcriptional activation

Conservation of the Oct motif (CGCGGATC) is a remarkable feature of plant histone gene promoters. Many of the Oct motifs are paired with a distinct motif, Hex, TCA or CCAAT-box, constituting the type I element (CCACGTCANCGATCCGCG), type II element (TCACGCGGATC) and type III element (GATCCGCG-N14-ACCAATCA). To clarify the roles of these Oct-containing composite elements (OCEs) in cell cycle-dependent and tissue-specific expression, we performed gain-of-function experiments with transgenic tobacco cell lines and plants harboring a derivative of the 35S core promoter/beta-glucuronidase fusion gene in which three or four copies of an OCE had been placed upstream. Although their activities were slightly different, results showed that each of the three types of OCEs could confer the ability to direct S phase-specific expression on a heterologous promoter. In transgenic plants, the type I and III elements exhibited a similar activity, directing expression in meristematic tissues, whereas the activity of the type II element appeared to be restricted to young cotyledons and maturating guard cells. Mutational analyses demonstrated that the co-operation of Oct with another module (Hex, TCA or CCAAT-box) was absolutely required for both temporal and spatial regulation. Thus, OCEs play a pivotal role in regulation of the expression of plant histone genes.

Cloning and characterization of the major histone H2A genes completes the cloning and sequencing of known histone genes of Tetrahymena thermophila

A truncated cDNA clone encoding Tetrahymena thermophila histone H2A2 was isolated using synthetic degenerate oligonucleotide probes derived from H2A protein sequences of Tetrahymena pyriformis. The cDNA clone was used as a homologous probe to isolate a truncated genomic clone encoding H2A1. The remaining regions of the genes for H2A1 (HTA1) and H2A2 (HTA2) were then isolated using inverse PCR on circularized genomic DNA fragments. These partial clones were assembled into intact HTA1 and HTA2 clones. Nucleotide sequences of the two genes were highly homologous within the coding region but not in the noncoding regions. Comparison of the deduced amino acid sequences with protein sequences of T. pyriformis H2As showed only two and three differences respectively, in a total of 137 amino acids for H2A1, and 132 amino acids for H2A2, indicating the two genes arose before the divergence of these two species. The HTA2 gene contains a TAA triplet within the coding region, encoding a glutamine residue. In contrast with the T. thermophila HHO and HTA3 genes, no introns were identified within the two genes. The 5'- and 3'-ends of the histone H2A mRNAs; were determined by RNase protection and by PCR mapping using RACE and RLM-RACE methods. Both genes encode polyadenylated mRNAs and are highly expressed in vegetatively growing cells but only weakly expressed in starved cultures. With the inclusion of these two genes, T. thermophila is the first organism whose entire complement of known core and linker histones, including replication-dependent and basal variants, has been cloned and sequenced.

Structural and functional characterization of two wheat histone H2B promoters

Two wheat histone H2B genes (TH123 and TH153) were isolated. Nucleotide sequence analysis revealed that some characteristic sequence motifs were conserved in both the 5'- and 3'-flanking regions. A canonical TATA box and several CCAAT sequences were present in the presumed promoter regions. Motifs similar or identical to the hexamer (ACGTCA) and octamer (CGCGGATC) motifs that are positive cis-acting elements of the wheat H3 (TH012) promoter were also observed in both the H2B promoters. A gel mobility shift assay indicated that the hexamer and hexamer-like motifs bound the wheat bZIP proteins HBP-1a and/or HBP-1b in vitro. A novel sequence motif, (A/T)(G/A)AAAT(A/G), was found downstream of a translational stop codon as observed in several plant histone H2B cDNAs. Promoter activity was analyzed with H2B promoter-GUS fusion genes in the transient system using tobacco protoplasts. Studies of the promoter function in transgenic tobacco plants showed that the H2B promoters were preferentially active in meristematic tissues. Taken together, our data indicate that the H2B genes are regulated, in part, by the same mechanism as found in H3 and H4 gene transcription.

Differential expression of the two types of histone H2A genes in wheat

Five histone H2A cDNA clones have been isolated from a wheat cDNA library. They were divided into two groups, termed type 1 and type 2, based on their deduced amino acid sequences and their gene expression patterns. Three type 1 clones had ORFs encoding proteins similar to angiosperm histone H2As known so far, whereas two type 2 clones encoded an identical protein, which was more similar to Norway spruce (gymnosperm) H2A than to the angiosperm H2As. The C-terminus of the type 2 H2A was shorter than that of the type 1 H2As and lacked the characteristic SPKK motif that is conserved in angiosperm H2As. Northern analysis revealed that the mRNA levels of the type 1 H2A genes were high in proliferating cells during germination and in various tissues of young seedlings, while the mRNA levels of the type 2 genes were high in non-proliferating cells in which the type 1 gene was poorly expressed. This result suggests that the expression of these two groups of H2A genes is differently regulated during development in wheat.

A cdc2 homologue and closely related processed retropseudogenes from Norway spruce

The p34cdc2 protein kinase is a key component in the regulation of the eukaryotic cell cycle and has been conserved during evolution. We have isolated cDNA clones corresponding to a cdc2 gene (cdc2Pa) from the conifer Norway spruce, Picea abies (L.) Karst. The deduced amino acid sequence is 85-90% identical to p34cdc2 homologues from other plants, contains eleven subdomains characteristic for the protein kinase family, and three sequence motifs specific for the cdc2 protein kinases. A partial genomic clone of cdc2Pa reveals two introns at positions identical to intron positions in Arabidopsis thaliana cdc2a. A Southern blot analysis shows that cdc2Pa is a single-copy gene belonging to a family of about 10 related genes. Partial genomic sequences of six of the genes in this family (86-92% identical to cdc2Pa) show distinct features of processed retropseudogenes. These lack introns and contain deletions, insertions and/or non-silent point mutations. This result is consistent with the hypothesis that processed retropseudogenes in plants may be common among genes expressed in the apical meristem, that is, in cells which have the potential to take part in the formation of reproductive organs. Although cdc2Pa transcripts were abundant in the epicotyl and thus likely in the apical meristem, we observed no strict coupling of expression to cell division in embryos and seedlings.