Small RNA-directed epigenetic natural variation in Arabidopsis thaliana

Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA) is involved in both the initiation and maintenance of gene silencing by directing DNA methylation and/or histone methylation. Here, we report that, in the model plant Arabidopsis thaliana, a cluster of approximately 24 nt siRNAs found at high levels in the ecotype Landsberg erecta (Ler) could direct DNA methylation and heterochromatinization at a hAT element adjacent to the promoter of FLOWERING LOCUS C (FLC), a major repressor of flowering, whereas the same hAT element in ecotype Columbia (Col) with almost identical DNA sequence, generates a set of low abundance siRNAs that do not direct these activities. We have called this hAT element MPF for Methylated region near Promoter of FLC, although de novo methylation triggered by an inverted repeat transgene at this region in Col does not alter its FLC expression. DNA methylation of the Ler allele MPF is dependent on genes in known silencing pathways, and such methylation is transmissible to Col by genetic crosses, although with varying degrees of penetrance. A genome-wide comparison of Ler and Col small RNAs identified at least 68 loci matched by a significant level of approximately 24 nt siRNAs present specifically in Ler but not Col, where nearly half of the loci are related to repeat or TE sequences. Methylation analysis revealed that 88% of the examined loci (37 out of 42) were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes.     

The E-class PPR protein MEF3 of Arabidopsis thaliana can also function in mitochondrial RNA editing with an additional DYW domain

In plants, RNA editing is observed in mitochondria and plastids, changing selected C nucleotides into Us in both organelles. We here identify the PPR (pentatricopeptide repeat) protein MEF3 (mitochondrial editing factor 3) of the E domain PPR subclass by genetic mapping of a variation between ecotypes Columbia (Col) and Landsberg erecta (Ler) in Arabidopsis thaliana to be required for a specific RNA editing event in mitochondria. The Ler variant of MEF3 differs from Col in two amino acids in repeats 9 and 10, which reduce RNA editing levels at site atp4-89 to about 50% in Ler. In a T-DNA insertion line, editing at this site is completely lost. In Vitis vinifera the gene most similar to MEF3 continues into a DYW extension beyond the common E domain. Complementation assays with various combinations of PPR and E domains from the vine and A. thaliana proteins show that the vine E region can substitute for the A. thaliana E region with or without the DYW domain. These findings suggest that the additional DYW domain does not disturb the MEF3 protein function in mitochondrial RNA editing in A. thaliana.     

Development and growth of several strains of Arabidopsis seedlings in microgravity

Growth and development of dark-grown Arabidopsis thaliana seedlings were studied in microgravity during space shuttle mission STS-84. The major purpose of this project was to determine if there were developmental differences among the four ecotypes studied--Wassilewskija (Ws), Columbia (Col), Landsberg erecta (Ler), and C24--and to evaluate whether particular ecotypes are better suited for spaceflight experimentation compared with others. A secondary goal was to study the growth of three starch-deficient strains of Arabidopsis by extending the observations made in a previously published report. For all strains, seed germination was not affected by microgravity, but seedlings were smaller in the spaceflight samples compared with the ground controls. The starch-deficient strains continued to exhibit vigorous growth until the termination of the experiment at 121 h after imbibition of seeds. However, ethylene effects, i.e., reduced growth and exaggerated hypocotyl hooks, were observed in all strains studied. Nevertheless, the Ler and C24 ecotypes seem to be more suitable for spaceflight research, compared with the other two ecotypes, based on measurements of their relative and absolute growth. This type of information should aid in the design of plant experiments for the International Space Station.     

Effect of Vernalization,Photoperiod, and Light Quality on the Flowering Phenotype of Arabidopsis Plants Containing the FRIGIDA Gene

We have compared the flowering response to vernalization, photoperiod, and far-red (FR) light of the Columbia (Col) and Landsberg erecta (Ler) ecotypes of Arabidopsis into which the flowering-time locus FRIGIDA (FRI) has been introgressed with that of the wild types Col, Ler, and San Feliu-2 (Sf-2). In the early-flowering parental ecotypes, Col and Ler, a large decrease in flowering time in response to vernalization was observed only under short-day conditions. However, Sf-2 and the Ler and Col genotypes containing FRI showed a strong response to vernalization when grown in either long days or short days. Although vernalization reduced the responsiveness to photoperiod, plants vernalized for more than 80 d still showed a slight photoperiod response. The effect of FRI on flowering was eliminated by 30 to 40 d of vernalization; subsequently, the response to vernalization in both long days and short days was the same in Col and Ler with or without FRI. FR-light enrichment accelerated flowering in all ecotypes and introgressed lines. However, the FR-light effect was most conspicuous in the FRI-containing plants. Saturation of the vernalization effect eliminated the effect of FR light on flowering, although vernalization did not eliminate the increase of petiole length in FR light.     

Flower stalk segments of Arabidopsis thaliana ecotype Columbia lack the capacity to grow in response to exogenously applied auxin

Exogenously applied IAA stimulated cell elongation of segments excised from flower stalks of Arabidopsis thaliana ecotype Landsberg erecta (Ler) by increasing the cell wall extensibility, but it did not affect that of ecotype Columbia (Col). Treatment with a low pH buffer solution (pH 4.0) or fusicoccin (FC), a reagent activating H(+)-ATPases, significantly increased the cell wall extensibility and promoted elongation growth of flower stalk segments of both ecotypes, indicating that the flower stalk segments of Col possess the capacity to grow under acidic pH conditions. IAA promoted the proton excretion in segments of Ler but not of Col. On the other hand, FC increased the proton excretion in segments of Col as much as that of Ler. These results suggest that IAA activates the plasma membrane H(+)-ATPases in the segments of Ler but not those of Col, while FC activates them in both ecotypes. Flower stalks of Col may lack the mechanisms of activation by IAA of the plasma membrane H(+)-ATPases.     

Nucleotide sequencing of an apparent proviral copy of env mRNA defines determinants of expression of the mouse mammary tumor virus env gene.

To extend our understanding of the organization and expression of the mouse mammary tumor virus genome, we determined the nucleotide sequence of large regions of a cloned mouse mammary tumor virus strain C3H provirus that appears to be a DNA copy of env mRNA. In conjunction with analysis of several additional clones of integrated and unintegrated mouse mammary tumor virus DNAs, we came to the following conclusions: (i) the mRNA for env is generated by splicing mechanisms that recognize conventional eucaryotic signals at donor and acceptor sites with a leader of at least 289 bases in length; (ii) the first of three possible initiation codons for translation of env follows the splice junction by a single nucleotide and produces a signal peptide of 98 amino acids; (iii) the amino terminal sequence of the major virion glycoprotein gp52env is confirmed by nucleotide sequencing and is encoded by a sequence beginning 584 nucleotides from the 5' end of env mRNA; (iv) the final 17 amino acids at the carboxyl terminus of the primary product of env are encoded within the long terminal repeat by the 51 bases at the 5' end of the U3 domain; and (v) bases 2 through 4 at the 5' end of the long terminal repeat constitute an initiation codon that commences an open reading frame capable of directing the synthesis of a 36-kilodalton protein.     

Studies of defective interfering RNAs of Sindbis virus with and without tRNAAsp sequences at their 5'' termini.

Three of six independently derived defective interfering (DI) particles of Sindbis virus generated by high-multiplicity passaging in cultured cells have tRNAAsp sequences at the 5' terminus of their RNAs (Monroe and Schlesinger, J. Virol. 49:865-872, 1984). In the present work, we found that the 5'-terminal sequences of the three tRNAAsp-negative DI RNAs were all derived from viral genomic RNA. One DI RNA sample had the same 5'-terminal sequence as the standard genome. The DI RNAs from another DI particle preparation were heterogeneous at the 5' terminus, with the sequence being either that of the standard 5' end or rearrangements of regions near the 5' end. The sequence of the 5' terminus of the third DI RNA sample consisted of the 5' terminus of the subgenomic 26S mRNA with a deletion from nucleotides 24 to 67 of the 26S RNA sequence. These data showed that the 5'-terminal nucleotides can undergo extensive variations and that the RNA is still replicated by virus-specific enzymes. DI RNAs of Sindbis virus evolve from larger to smaller species. In the two cases in which we followed the evolution of DI RNAs, the appearance of tRNAAsp-positive molecules occurred at the same time as did the emergence of the smaller species of DI RNAs. In pairwise competition experiments, one of the tRNAAsp-positive DI RNAs proved to be the most effective DI RNA, but under identical conditions, a second tRNAAsp-positive DI RNA was unable to compete with the tRNAAsp-negative DIs. Therefore, the tRNAAsp sequence at the 5' terminus of a Sindbis DI RNA is not the primary factor in determining which DI RNA becomes the predominant species in a population of DI RNA molecules.