Interplay of HD-Zip II and III transcription factors in auxin-regulated plant development.

The homeodomain-leucine zipper (HD-Zip) class of transcription factors is unique to plants. HD-Zip proteins bind to DNA exclusively as dimers recognizing dyad symmetric sequences and act as positive or negative regulators of gene expression. On the basis of sequence homology in the HD-Zip DNA-binding domain, HD-Zip proteins have been grouped into four families (HD-Zip I-IV). Each HD-Zip family can be further divided into subfamilies containing paralogous genes that have arisen through genome duplication. Remarkably, all the members of the HD-Zip IIγ and -δ clades are regulated by light quality changes that induce in the majority of the angiosperms the shade-avoidance response, a process regulated at multiple levels by auxin. Intriguingly, it has recently emerged that, apart from their function in shade avoidance, the HD-Zip IIγ and -δ transcription factors control several auxin-regulated developmental processes, including apical embryo patterning, lateral organ polarity, and gynoecium development, in a white-light environment. This review presents recent advances in our understanding of HD-Zip II protein function in plant development, with particular emphasis on the impact of loss-of-function HD-Zip II mutations on auxin distribution and response. The review also describes evidence demonstrating that HD-Zip IIγ and -δ genes are directly and positively regulated by HD-Zip III transcription factors, primary determinants of apical shoot development, known to control the expression of several auxin biosynthesis, transport, and response genes. Finally, the interplay between HD-Zip II and III transcription factors in embryo apical patterning and organ polarity is discussed.

Mechanism of chromatin assembly in Xenopus oocytes.

We have analyzed the chromatin assembly reaction catalyzed by the Xenopus oocyte extract (S-150). A 50 S complex is formed upon mixing the 17 S pUC DNA and the S-150. Mature histones are not detected in this complex, which contains relaxed DNA and protein, and generates subnucleosomal 7 S particles upon digestion with micrococcal nuclease. The relaxed nucleoprotein is gradually supercoiled into nucleosomal chromatin in the S-150, via a pathway that requires ATP and is blocked by novobiocin, and this process is accompanied by the appearance of mature histones H3 and H4. Isolated complexes also supercoil in vitro, which implies the complex is a kit that contains histone precursors, as well as topoisomerases and other enzymes required for assembly. We discuss the biological implications of these findings.

DNA-binding specificity of the homeodomain-leucine zipper domain.

Homeodomain-leucine zipper (HD-Zip) proteins are putative transcription factors identified only in plants. The study of the DNA-binding properties of the ATHB-1 and -2 HD-Zip (HD-Zip-1 and -2) domains showed that they interact with DNA as homodimers and recognize two distinct 9 bp pseudopalindromic sequences, CAAT(A/T)ATTG (BS-1) and CAAT(G/C)ATTG (BS-2), respectively, as determined by selecting high-affinity binding sites from random-sequence DNA. Here, we report a mutational analysis of the HD-Zip-2 domain. We determined that conserved amino acid residues of helix 3, Val47 and Asn51, and Arg55 are essential for the DNA-binding activity of the HD-Zip-2 domain. We demonstrated that the preferential recognition of a G/C base-pair at the central position by the HD-Zip-2 domain is abolished either by the replacement of Arg55 with lysine or by the substitution of Glu46 and Thr56 with the corresponding residues of the HD-Zip-1 domain (alanine and tryptophan, respectively). In contrast, substitution of Arg55 with lysine in the HD-Zip-1 domain significantly reduced DNA-binding activity without changing the specificity of recognition. Finally, we determined that differences in residues outside helix 3 further contribute to the DNA-binding specificity of the HD-Zip domain. Taken together, the data strongly suggest that the preferential recognition of BS-2 and -1 by the HD-Zip-2 and -1 domains, respectively, may be attributable to a distinct orientation of the side-chain of Arg55 in these two domains.

Chromatin-specific hypersensitive sites are assembled on a Xenopus histone gene injected into Xenopus oocytes.

A cloned histone H4 gene of Xenopus laevis is efficiently transcribed after injection into germinal vesicles of X. laevis oocytes. Deletion analyses indicate that less than 140 base-pairs of 5' flanking sequences and 50 base-pairs of 3' flanking sequences are required for efficient transcription of this gene in Xenopus oocytes. Chromatin footprint analysis by a direct end-label technique reveals discrete DNase I-hypersensitive and micrococcal nuclease-hypersensitive sites at the 5' and 3' boundaries of the gene, which bracket the transcribed region of this minichromosome. The specific chromatin structure assembled around this homologous gene, together with the finding that histone genes of Drosophila melanogaster are not assembled into specific nucleoprotein structures within Xenopus oocytes, strongly suggest that sequence-specific and species-specific factors may be responsible for generating the chromatin-specific hypersensitive sites at the boundaries of active genes.

A cDNA encoding Arabidopsis thaliana cytoplasmic ribosomal protein L18.

A cDNA encoding ribosomal (r) protein L18 of Arabidopsis thaliana (At) was isolated and characterized. The nucleotide sequence contains a 563-bp open reading frame that encodes a 20.9-kDa basic protein. Amino-acid comparison indicated that the predicted L18 r-protein of At has a high degree of homology with L18 of distantly related organisms such as yeast, Xenopus laevis and rat. Genomic DNA analysis suggested that L18 is encoded by a single locus in At. An mRNA of approx. 0.9 kb is detected in all the tissues and developmental stages analyzed.

Synchronous division induced in Escherichia coli K12 by phage Mu: analysis of DNA topology and gene expression during the cell cycle.

Bacteriophage Mu mutants in gene gem (Mu gemts2) induce cycles of synchronous divisions after infection of a bacterial population in steady-state conditions. In this paper, two classes of gyrB mutants, synchronizable and non-synchronizable, are described. The existence of the non-synchronizable class suggests that the gyrase B subunit is involved with Gem in the process of synchronization. Cyclical variations in DNA topology of a resident multicopy plasmid occur during synchronous growth and correlate with a modulation of the chromosomal lacZ gene expression. Transcription data for the cell division genes, ftsZ and envA, obtained studying first steps in synchronous growth after infection, show that synthesis of the two mRNA is not constant. The specific mRNA of envA seems to be stimulated soon after infection, whereas the two transcripts initiating upstream from ftsZ apparently decrease to a basal level. In both cases, however, synthesis of the mRNA virtually doubles at the time of cell division.

Mu gem3 as a tool to investigate the influence of chromosome supercoiling on gene expression in Escherichia coli K12.

We have developed a rapid method to investigate the influence of chromosome supercoiling on gene expression in Escherichia coli K12. This method exploits the ability of the gem3 mutant of the bacteriophage Mu, even in the prophagic state in immune cells, to induce relaxation of the host chromosome. The experiments can thus be performed under physiological conditions, and without the use of the drugs. In theory, this method can be applied to any bacterial gene. Here, we report the results obtained with four DNA replication and three cell division genes.

Plant adaptation to dynamically changing environment: the shade avoidance response.

The success of competitive interactions between plants determines the chance of survival of individuals and eventually of whole plant species. Shade-tolerant plants have adapted their photosynthesis to function optimally under low-light conditions. These plants are therefore capable of long-term survival under a canopy shade. In contrast, shade-avoiding plants adapt their growth to perceive maximum sunlight and therefore rapidly dominate gaps in a canopy. Daylight contains roughly equal proportions of red and far-red light, but within vegetation that ratio is lowered as a result of red absorption by photosynthetic pigments. This light quality change is perceived through the phytochrome system as an unambiguous signal of the proximity of neighbors resulting in a suite of developmental responses (termed the shade avoidance response) that, when successful, result in the overgrowth of those neighbors. Shoot elongation induced by low red/far-red light may confer high relative fitness in natural dense communities. However, since elongation is often achieved at the expense of leaf and root growth, shade avoidance may lead to reduction in crop plant productivity. Over the past decade, major progresses have been achieved in the understanding of the molecular basis of shade avoidance. However, uncovering the mechanisms underpinning plant response and adaptation to changes in the ratio of red to far-red light is key to design new strategies to precise modulate shade avoidance in time and space without impairing the overall crop ability to compete for light.

Dynamic measure of gene co-regulation.

Gene expression is to a large extent controlled at the level of mRNA accumulation. Genes whose products function together are likely under a common regulatory system (e.g., signal transduction pathways, sets of regulatory proteins) such that they are expressed in a coordinated manner. This property has been frequently used in the analysis of genome-wide expression data, as the experimental observation that a group of genes is co-expressed frequently implies that the genes share a common regulatory mechanism. The authors have investigated the situation in which dissimilarity in gene-expression time profiles may still result from the presence of the same regulatory signal, as in the case of common transcription factors. To this aim, a dynamic model that takes into account the effect of specific mRNA degradation on the shape of gene-expression time series has been developed, and the concept of 'dynamically co-regulated' genes has accordingly been introduced as the goodness-of-fit to such a model (called dynamic R2). The statistical analysis of dynamic R2 over a number of different experimental data sets and organisms shows that the presence of dynamically co-regulated genes is by far more significant than that expected from the randomised data. Furthermore, as an example of the usefulness of the proposed method, genome-wide yeast measurements such as cell-cycle time series and transcription factors targets data, were used to prove that dynamic co-regulation is statistically related to the presence of common transcription factor(s). This latter property is very useful when trying to infer computational indications of co-regulation for not-yet annotated genes that do not display a co-expression pattern.

Assembly of correctly spaced chromatin in a nuclear extract from Xenopus laevis oocytes.

Assembly of nucleosomes on relaxed, covalently closed DNA has been studied in a nuclear extract of Xenopus laevis oocytes. Nucleosomes containing the four histones H3, H4, H2A and H2B but lacking histone H1 are readily assembled on the DNA. The pattern of micrococcal nuclease digestion shows that the nucleosomes assembled in the absence of ATP and Mg (II) are closely packed, with a periodicity of 150 base pairs (bp). In contrast, in the presence of ATP and Mg (II) the spacing of the nucleosomes is 180 bp, similar to that observed for nucleosomes assembled on DNA microinjected into oocyte nuclei. The ATP and Mg (II) requirements for the assembly of correctly spaced nucleosomes are unrelated to the activity of the ATP and Mg (II) dependent DNA topoisomerase II in the extract; addition of specific inhibitors of eukaryotic DNA topoisomerase II has no effect on the spacing of the reconstituted nucleosomes. The ATP requirement in the assembly of correctly spaced nucleosomes can be substituted by adenosine 5'-O-3'-thiotriphosphate (gamma-S-ATP) but not by adenyl-5'-yl imidodiphosphate (AMP-P-(NH)-P).

The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities.

The Arabidopsis Athb-1 and -2 proteins are characterized by the presence of a homeodomain (HD) with a closely linked leucine zipper motif (Zip). We have suggested that the HD-Zip motif could, via dimerization of the leucine zippers, recognize dyad-symmetric DNA sequences. Here we report an analysis of the DNA binding properties of the Athb-1 homeodomain-leucine zipper (HD-Zip-1) domain in vitro. DNA binding analysis performed using random-sequence DNA templates showed that the HD-Zip-1 domain, but not the Athb-1 HD alone, binds to DNA. The HD-Zip-1 domain recognizes a 9 bp dyad-symmetric sequence [CAAT(A/T)ATTG], as determined by selecting high-affinity binding sites from random-sequence DNA. Gel retardation assays demonstrated that the HD-Zip-1 domain binds to DNA as a dimer. Moreover, the analysis of the DNA binding activity of Athb-1 derivatives indicated that a correct spatial relationship between the HD and the Zip is essential for DNA binding. Finally, we determined that the Athb-2 HD-Zip domain recognizes a distinct 9 bp dyad-symmetric sequence [CAAT(G/C)ATTG]. A model of DNA binding by the HD-Zip proteins is proposed.

Twilight-zone and canopy shade induction of the Athb-2 homeobox gene in green plants.

We present evidence that a novel phytochrome (other than phytochromes A and B, PHYA and PHYB) operative in green plants regulates the "twilight-inducible" expression of a plant homeobox gene (Athb-2). Light regulation of the Athb-2 gene is unique in that it is not induced by red (R)-rich daylight or by the light-dark transition but is instead induced by changes in the ratio of R to far-red (FR) light. These changes, which normally occur at dawn and dusk (end-of-day FR), also occur during the daytime under the canopy (shade avoidance). By using pure light sources and phyA/phyB null mutants, we demonstrated that the induction of Athb-2 by changes in the R/FR ratio is mediated for the most part by a novel phytochrome operative in green plants. Furthermore, PHYB plays a negative role in repressing the accumulation of Athb-2 mRNA in the dark and a minor role in the FR response. The strict correlation of Athb-2 expression with FR-induced growth phenomena suggests a role for the Athb-2 gene in mediating cell elongation. This interpretation is supported by the finding that the Athb-2 gene is expressed at high levels in rapidly elongating etiolated seedlings. Furthermore, as either R or FR light inhibits cell elongation in etiolated tissues, they also down-regulate the expression of Athb-2 mRNA. Thus, these data support the notion that changes in light quality perceived by a novel phytochrome regulate plant development through the action of the Athb-2 homeobox gene.

A novel class of plant proteins containing a homeodomain with a closely linked leucine zipper motif.

The homeobox, a 183 bp DNA sequence element, was originally identified as a region of sequence similarity between many Drosophila homeotic genes. The homeobox codes for a DNA-binding motif known as the homeodomain. Homeobox genes have been found in many animal species, including sea urchins, nematodes, frogs, mice and humans. To isolate homeobox-containing sequences from the plant Arabidopsis thaliana, a cDNA library was screened with a highly degenerate oligonucleotide corresponding to a conserved eight amino acid sequence from the helix-3 region of the homeodomain. Using this strategy two cDNA clones sharing homeobox-related sequences were identified. Interestingly, both of the cDNAs also contain a second element that potentially codes for a leucine zipper motif which is located immediately 3' to the homeobox. The close proximity of these two domains suggests that the homeodomain-leucine zipper motif could, via dimerization of the leucine zippers, recognize dyad-symmetrical DNA sequences.

A class of gyrB mutants, substantially unaffected in DNA topology, suppresses the Escherichia coli K12 ftsZ84 mutation.

Previous work in our laboratory suggested that DNA topology could be implicated in the regulation of the division gene ftsZ. To settle this question, we have selected and characterized mutants in the gyrB gene able to phenotypically suppress the defects of the ftsZ84 mutation. No strict correlation was found between the degree of plasmid DNA relaxation and the level of suppression of the thermosensitivity of the ftsZ84 strain. Interestingly, the class of mutants that shows maximal suppression is substantially unaffected in DNA topology. In addition, the amount of ftsZ-specific mRNA in this class of mutants is comparable to that present in the ftsZ84 strain. These results hint that the ability of these gyrB mutants to correct the effects of the ftsZ84 mutation is largely unrelated to the function of the GyrB (as a part of DNA gyrase) in the control of DNA superhelicity and suggest hitherto unsuspected interaction between the ftsZ and gyrB gene products.

Chromatin assembly in Xenopus oocytes: in vitro studies.

We describe and characterize a complex reaction that catalyzes DNA supercoiling and chromatin assembly in vitro. A Xenopus oocyte extract supplemented with ATP and Mg++ converts DNA circles into minichromosomes that display a native, 200 bp periodicity. When supercoiled DNA is added to this extract it undergoes a time-dependent series of topological changes, which precisely mimic those found when the DNA is microinjected into oocytes. As judged by the conformation of the subsequently deproteinized DNA, the supercoiled DNA is first relaxed, in a reaction that takes 4 min, and then it is resupercoiled in a slower process that takes 4 hr. The relaxation is partially inhibited by EDTA, to an extent that suggests that that it is catalyzed by a type I DNA topoisomerase. The resupercoiling , on the other hand, requires ATP and Mg++, is completely inhibited by EDTA, and is inhibited by novobiocin in a manner that suggests it is catalyzed by a type II DNA topoisomerase. These findings, and the ones reported in the preceding paper ( Ryoji and Worcel , 1984), lead us to propose that chromatin assembly is an active, ATP-driven process.

The Arabidopsis Athb-8, -9 and -14 genes are members of a small gene family coding for highly related HD-ZIP proteins.

We report the isolation and characterization of two Arabidopsis homeobox genes highly related to the Athb-8 gene. The full-length cDNAs encode proteins of 841 and 852 amino acids which we have designated Athb-9 and -14, respectively. Athb-8, -9 and -14 are members of a small family of HD-Zip proteins (HD-ZIP III) characterized by a HD-Zip motif confined to the N-terminus of the polypeptide. The spatial organization of the HD-Zip domain of Athb-8, -9 and -14 is different from that of the Athb-1 (a member of the HD-ZIP I family) and Athb-2 (a member of the HD-ZIP II family) HD-Zip domains. DNA binding analysis performed with random-sequence DNA templates showed that the Athb-9 HD-Zip (HD-Zip-9) domain, but not the Athb-9 HD alone, binds to DNA. The HD-Zip-9 domain recognizes a 11 bp pseudopalindromic sequence (GTAAT(G/C)ATTAC), as determined by selecting high-affinity binding sites from random-sequence DNA. Moreover, gel retardation assays demonstrated that the HD-Zip-9 domain binds to DNA as a dimer. These data support the notion that the HD-ZIP III domain interacts with DNA recognition elements in a fashion similar to the HD-ZIP I and II domains.

Large scale isolation of nuclei from oocytes of Xenopus laevis.

We describe an improvement on the procedure of Scalenghe et al. (F. Scalenghe, M. Buscaglia, C. Steinheil, and M. Crippa (1978) Chromosoma 66, 299-308) for the large scale isolation of nuclei from Xenopus laevis oocytes. The nuclear extract obtained was tested for its ability to transcribe a cloned Xenopus 5 S RNA gene and for the presence of nuclear factors interacting with a X. laevis ribosomal protein gene promoter. Efficiency of accurate transcription and of factor binding is comparable with that of an extract prepared from manually isolated nuclei.

Characterization of histone genes isolated from Xenopus laevis and Xenopus tropicalis genomic libraries.

Using a cDNA clone for the histone H3 we have isolated, from two genomic libraries of Xenopus laevis and Xenopus tropicalis, clones containing four different histone gene clusters. The structural organization of X. laevis histone genes has been determined by restriction mapping, Southern blot hybridization and translation of the mRNAs which hybridize to the various restriction fragments. The arrangement of the histone genes in X. tropicalis has been determined by Southern analysis using X. laevis genomic fragments, containing individual genes, as probes. Histone genes are clustered in the genome of X. laevis and X. tropicalis and, compared to invertebrates, show a higher organization heterogeneity as demonstrated by structural analysis of the four genomic clones. In fact, the order of the genes within individual clusters is not conserved.

Nucleotide sequence of the L1 ribosomal protein gene of Xenopus laevis: remarkable sequence homology among introns.

Ribosomal protein L1 is encoded by two genes in Xenopus laevis. The comparison of two cDNA sequences shows that the two L1 gene copies (L1a and L1b) have diverged in many silent sites and very few substitution sites; moreover a small duplication occurred at the very end of the coding region of the L1b gene which thus codes for a product five amino acids longer than that coded by L1a. Quantitatively the divergence between the two L1 genes confirms that a whole genome duplication took place in Xenopus laevis approximately 30 million years ago. A genomic fragment containing one of the two L1 gene copies (L1a), with its nine introns and flanking regions, has been completely sequenced. The 5' end of this gene has been mapped within a 20-pyridimine stretch as already found for other vertebrate ribosomal protein genes. Four of the nine introns have a 60-nucleotide sequence with 80% homology; within this region some boxes, one of which is 16 nucleotides long, are 100% homologous among the four introns. This feature of L1a gene introns is interesting since we have previously shown that the activity of this gene is regulated at a post-transcriptional level and it involves the block of the normal splicing of some intron sequences.

Negative autoregulation of the Arabidopsis homeobox gene ATHB-2.

The Arabidopsis homeobox gene ATHB-2 is tightly regulated by light signals, and is thought to direct morphological changes during shade avoidance responses. To understand how ATHB-2 mediates light signals in plant morphogenesis, we investigated its transcriptional network. We constructed a gene encoding a chimeric transcription factor (HD-Zip-2-V-G) that is expected to activate target genes of ATHB-2 in a glucocorticoid-dependent manner. In transgenic Arabidopsis plants expressing HD-Zip-2-V-G, glucocorticoid treatment activates the ATHB-2 gene itself, independent of de novo protein synthesis. An in vitro DNase I-footprinting experiment showed that recombinant ATHB-2 protein specifically bound to an ATHB-2 promoter region. These complementary results indicate that ATHB-2 recognizes its own promoter. Consistent with the fact that ATHB-2 itself has been shown to act as a repressor, expression of the endogenous ATHB-2 gene was repressed in transgenic plants overexpressing an ATHB-2 transgene. Moreover, target-gene analysis using the HD-Zip-2-V-G suggested that ATHB-2 recognizes other HD-Zip II subfamily genes. We conclude that ATHB-2 has a negative autoregulatory loop and may be involved in a complicated transcriptional network involving paralogous genes, as is the case with animal homeobox genes.