Purification and characterization of transcription factor IIIA from higher plants

Genome-wide study of C2H2 zinc finger gene family in Medicago truncatula

BACKGROUND

C2H2 zinc finger proteins (C2H2 ZFPs) play vital roles in shaping many aspects of plant growth and adaptation to the environment. Plant genomes harbor hundreds of C2H2 ZFPs, which compose one of the most important and largest transcription factor families in higher plants. Although the C2H2 ZFP gene family has been reported in several plant species, it has not been described in the model leguminous species Medicago truncatula.

RESULTS

In this study, we identified 218 C2H2 type ZFPs with 337 individual C2H2 motifs in M. truncatula. We showed that the high rate of local gene duplication has significantly contributed to the expansion of the C2H2 gene family in M. truncatula. The identified ZFPs exhibit high variation in motif arrangement and expression pattern, suggesting that the short C2H2 zinc finger motif has been adopted as a scaffold by numerous transcription factors with different functions to recognize cis-elements. By analyzing the public expression datasets and quantitative RT-PCR (qRT-PCR), we identified several C2H2 ZFPs that are specifically expressed in certain tissues, such as the nodule, seed, and flower.

CONCLUSION

Our genome-wide work revealed an expanded C2H2 ZFP gene family in an important legume M. truncatula, and provides new insights into the diversification and expansion of C2H2 ZFPs in higher plants.

In vitro analysis of the sequences required for transcription of the Arabidopsis thaliana 5S rRNA genes

In vivo, we have already shown that only two of the 5S rDNA array blocks of the Arabidopsis thaliana genome produce the mature 5S rRNAs. Deletions and point mutations were introduced in an Arabidopsis 5S rDNA-transcribed region and its 5'- and 3'-flanks in order to analyse their effects on transcription activity. In vitro transcription revealed different transcription control regions. One control region essential for transcription initiation was identified in the 5'-flanking sequence. The major sequence determinants were a TATA-like motif (-28 to -23), a GC dinucleotide (-12 to -11), a 3-bp AT-rich region (-4 to -2) and a C residue at -1. They are important for both accurate transcription initiation and transcription efficiency. Transcription level was regulated by polymerase III (Pol III) re-initiation rate as in tRNA genes in which TATA-like motif is involved. Active 5S rDNA transcription additionally required an intragenic promoter composed of an A-box, an Intermediate Element (IE) and a C-box. Double-stranded oligonucleotides corresponding to different fragments of the transcribed region, used as competitors, revealed the main importance of internal promoter elements. A stretch of four T is sufficient for transcription termination. Transcription of Arabidopsis 5S rDNA requires 30 bp of 5'-flanking region, a promoter internal to the transcribed region, and a stretch of T for transcription termination.

Identification and characterization of transcription factor IIIA and ribosomal protein L5 from Arabidopsis thaliana

Thus far, no transcription factor IIIA (TFIIIA) from higher plants has been cloned and characterized. We have cloned and characterized TFIIIA and ribosomal protein L5 from Arabidopsis thaliana. Primary sequence comparison revealed a high divergence of AtTFIIIA and a relatively high conservation of AtL5 when compared with other organisms. The AtTFIIIA cDNA encodes a protein with nine Cys(2)-His(2)-type zinc fingers, a 23 amino acid spacer between fingers 1 and 2, a 66 amino acid spacer between fingers 4 and 5, and a 50 amino acid non-finger C-terminal tail. Aside from the amino acids required for proper zinc finger folding, AtTFIIIA is highly divergent from other known TFIIIAs. AtTFIIIA can bind 5S rDNA, as well as 5S rRNA, and efficiently stimulates the transcription of an Arabidopsis 5S rRNA gene in vitro. AtL5 identity was confirmed by demonstrating that this protein binds to 5S rRNA but not to 5S rDNA. Protoplast transient expression assays with green fluorescent protein fusion proteins revealed that AtTFIIIA is absent from the cytoplasm and concentrated at several nuclear foci including the nucleolus. AtL5 protein accumulates in the nucleus, especially in the nucleolus, and is also present in the cytoplasm.

Replication of 5 S ribosomal genes precedes the appearance of early nuclear replication complexes

The present work shows that replication of the 5 S ribosomal genes differs in time and 3'deoxyadenosine sensitivity from replication of other nuclear genes, in Allium cepa L. root meristems. Fluorescence in situ hybridization with the pTa794 DNA probe which contains a complete 410 bp 5 S gene from Triticum aestivum allowed to detect four clusters of 5 S genes in these diploid cells (2n = 16), two of them in the short arm of the smallest metacentric chromosomal pair 7. Replication of the 5 S ribosomal genes occurred very early in interphase, as discerned by their resolution as doubled spots only two hours after interphase was initiated in synchronous binucleate cells. Codetection of nuclear replication (by immunodetection of 5-bromo-2'-deoxyuridine incorporation) showed that the replication of the 5 S ribosomal genes occurred before any incorporation of 5-bromo-2'deoxyuridine could be detected in the nuclei. The earliest Br-DNA detected in these cells followed a radial pattern from different foci apparently dispersed along some chromosomal arms. These structures seem to represent early replication complexes, as a result of the displacement of multiple DNA forks from the foci known as pre-replication complexes where the replication machinery of the earliest replicating genes assembles. No consistent positional correlation existed between the formation of the early replication complexes and the already replicated 5 S ribosomal clusters. Finally, nuclear replication but not that of the 5 S genes was prevented by 3'deoxyadenosine, and the earliest replicating 5 S ribosomal gene cluster differed in both sister nuclei resulting from the segregation of one single chromosome in anaphase.