Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control.

MOTIVATION: Transcription factor interactions are the cornerstone of combinatorial control, which is a crucial aspect of the gene regulatory system. Understanding and predicting transcription factor interactions based on their sequence alone is difficult since they are often part of families of factors sharing high sequence identity. Given the scarcity of experimental data on interactions compared to available sequence data, however, it would be most useful to have accurate methods for the prediction of such interactions. RESULTS: We present a method consisting of a Random Forest-based feature-selection procedure that selects relevant motifs out of a set found using a correlated motif search algorithm. Prediction accuracy for several transcription factor families (bZIP, MADS, homeobox and forkhead) reaches 60-90%. In addition, we identified those parts of the sequence that are important for the interaction specificity, and show that these are in agreement with available data. We also used the predictors to perform genome-wide scans for interaction partners and recovered both known and putative new interaction partners.

Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants.

BACKGROUND: Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses in plants, yet its regulation is poorly understood. An increase in temperature promotes changes in plant morphology as well as the transition from the vegetative to the reproductive phase in Arabidopsis thaliana via changes in splicing of key regulatory genes. Here we investigate whether a particular histone modification affects ambient temperature-induced alternative splicing and flowering time. RESULTS: We use a genome-wide approach and perform RNA-sequencing (RNA-seq) analyses and histone H3 lysine 36 tri-methylation (H3K36me3) chromatin immunoprecipitation sequencing (ChIP-seq) in plants exposed to different ambient temperatures. Analysis and comparison of these datasets reveal that temperature-induced differentially spliced genes are enriched in H3K36me3. Moreover, we find that reduction of H3K36me3 deposition causes alteration in temperature-induced alternative splicing. We also show that plants with mutations in H3K36me3 writers, eraser, or readers have altered high ambient temperature-induced flowering. CONCLUSIONS: Our results show a key role for the histone mark H3K36me3 in splicing regulation and plant plasticity to fluctuating ambient temperature. Our findings open new perspectives for the breeding of crops that can better cope with environmental changes due to climate change.

The influence of antibiotics on the immune system. III. Investigations on the cellular functions of chicken leukocytes in vitro.

Tetracyclines are bacteriostatic antibiotics widely used in veterinary medicine. It is reported here that the tetracycline analogue oxytetracycline (OxyTC) interferes with the mitogenic response of chicken leukocytes. A dose-dependent suppression of lectin stimulation of peripheral blood and spleen leukocytes was observed. The kinetics of the DNA-synthetic activity were seriously affected. The antimicrobial agent does not seem to have any effect on interleukin 2 (IL-2) production, whereas the uptake of 3H-thymidine by IL-2-dependent T cell blasts was severely reduced. It is concluded that the T cell blast is the target for OxyTC.

Fate and biological activity of exogenous DNA sequences during serial transfections in NIH/3T3 cells.

The efficiency and accuracy of serial transfections in NIH/3T3 fibroblasts were investigated with two plasmids carrying a dominant gene. One plasmid carried the activated ras oncogene of human origin inducing morphological alteration and the oncogenic phenotype of NIH/3T3 cells. The second plasmid carried the bacterial neoR gene conferring resistance to the neomycine analogue G 418. We observed no correlation between the presence of biologically active DNAs in primary transfectants and the capacities of these DNAs to transmit the exogenous information in a second cycle of transfection. Cellular DNA of only two of 13 ras and only 1 of 3 neoR transformants could transform NIH/3T3 in a second cycle of transfections. About half of secondary transfectants, derived from those primary transfectants which did transmit the exogenous DNA, contained apparently complete exogenous sequences and transmitted it efficiently and even with the original site of integration in the host DNA in a third cycle of transfection. Exogenous DNA sequences were amplified in the majority of secondary transfectants but did not enhance biological activity in a third cycle of transfer. The exogenous DNA was found to undergo rearrangements in oncogenic transformants propagated in cell culture.

Expression of the 16K cistron of tobacco rattle virus in protoplasts.

An antiserum was raised against a synthetic peptide corresponding to the 18 C-terminal amino acids of a putative 16K protein encoded by the 3'-terminal open reading frame of tobacco rattle virus (TRV) RNA-1. This antiserum was used to demonstrate expression of the 16K cistron in vivo. TRV-infected tobacco protoplasts accumulated similar amounts of 16K protein and viral coat protein but in tobacco plants only the coat protein was detectable. Time course experiments revealed that in protoplasts the accumulation of 16K protein lagged somewhat behind that of coat protein. The 16K protein was incorporated in a high-molecular-weight cellular component that was resistant to treatment with nonionic detergents.

Biological activity of transcripts synthesized in vitro from full-length and mutated DNA copies of tobacco rattle virus RNA 2.

Full-length cDNA clones of RNA 2 of tobacco rattle virus (TRV) strain PLB have been cloned into the transcription vector pPM1. Products of in vitro transcription by Escherichia coli RNA polymerase, either capped or uncapped, were as infectious as native RNA 2 when coinoculated with RNA 1 of TRV strain TCM. At least 70% of the internal sequence of the cDNA could be deleted without reduction of the replication efficiency of the transcripts. Sequences of 340 nucleotides at the 5' end and 405 nucleotides at the 3' end of PLB RNA 2 were found to be sufficient for replication. The encapsidation of deletion mutants of PLB RNA 2 was investigated after addition of native PLB RNA 1 and RNA 2. Accumulation of these mutants was distinguished from that of wild-type RNA 2 by insertion of nonviral sequences in the deleted parts. Three mutant forms of RNA 2 with extensive deletions in the coat protein (CP) gene were replicated but failed to encapsidate, while mutants with nonviral sequences inserted downstream from the CP gene showed a large reduction in replication efficiency.

Susceptibility to virus infection of transgenic tobacco plants expressing structural and nonstructural genes of tobacco rattle virus.

Tobacco plants were transformed with the coat protein (CP) genes and several nonstructural genes of tobacco rattle virus (TRV) strains PLB and TCM. Accumulation of RNA transcripts from the integrated viral genes was detectable in all types of transformants. Plants expressing CP were resistant to infection with virions of the homologous strain but susceptible to infection with RNA of the homologous strain or nucleoprotein of the heterologous strain. No resistance was detectable in plants transformed with the nonstructural 13K and 16K genes of strain PLB, or with the 29K gene that is unique to RNA-2 of strain TCM. When protoplasts from plants expressing TCM-CP were inoculated with TCM virions, there was a normal production of genomic RNAs and CP but the synthesis of mRNA and protein corresponding to the 16K gene was selectively defective. Because this defect was not observed when protoplasts from plants expressing PLB-CP were inoculated with PLB virions, it probably plays no role in the coat protein-mediated protection observed in transgenic plants.

Genome structure of tobacco rattle virus strain PLB: further evidence on the occurrence of RNA recombination among tobraviruses.

RNA-2 (2196 nucleotides) of tobacco rattle virus (TRV) strain PLB was found to consist of a 5'-terminal sequence of 1376 nucleotides identical to the 5'-sequence of RNA-2 of TRV strain PSG and a 3'-terminal sequence of 820 nucleotides that is identical to the 3'-sequence of RNA-1 of strain PLB. Thus, in strains PLB and PSG the same coat protein gene is fused to different RNA-1 derived 3'-termini. By combining RNA-1 of TRV strain TCM with RNA-2 of strain PLB, a viable pseudo-recombinant was formed with genome segments that have nonidentical 3'-sequences. After 25 passages in tobacco each RNA retained its strain-specific 3'-sequences. This indicates that the perfect 3'-homology that occurs between the two genome segments of all natural TRV isolates analyzed so far is not a prerequisite for a stable genotype.

Sex determination in the monoecious species cucumber is confined to specific floral whorls.

In unisexual flowers, sex is determined by the selective repression of growth or the abortion of either male or female reproductive organs. The mechanism by which this process is controlled in plants is still poorly understood. Because it is known that the identity of reproductive organs in plants is controlled by homeotic genes belonging to the MADS box gene family, we analyzed floral homeotic mutants from cucumber, a species that bears both male and female flowers on the same individual. To study the characteristics of sex determination in more detail, we produced mutants similar to class A and C homeotic mutants from well-characterized hermaphrodite species such as Arabidopsis by ectopically expressing and suppressing the cucumber gene CUCUMBER MADS1 (CUM1). The cucumber mutant green petals (gp) corresponds to the previously characterized B mutants from several species and appeared to be caused by a deletion of 15 amino acid residues in the coding region of the class B MADS box gene CUM26. These homeotic mutants reveal two important concepts that govern sex determination in cucumber. First, the arrest of either male or female organ development is dependent on their positions in the flower and is not associated with their sexual identity. Second, the data presented here strongly suggest that the class C homeotic function is required for the position-dependent arrest of reproductive organs.

Suppression of cell expansion by ectopic expression of the Arabidopsis SUPERMAN gene in transgenic petunia and tobacco.

Molecular and genetic analyses have shown that the Arabidopsis thaliana gene SUPERMAN (SUP) has at least two functions in Arabidopsis flower development. SUP is necessary to control the correct distribution of cells with either a stamen or carpel fate, and is essential for proper outgrowth of the ovule outer integument. Both these functions indicate a role for SUP in cell proliferation. To study the function of the Arabidopsis SUP gene in more detail, we over-expressed the SUP gene in petunia and tobacco in a tissue-specific manner. The petunia FLORAL BINDING PROTEIN 1 (FBP1) gene promoter was used to restrict the expression of SUP to petals and stamens. The development of petals and stamens was severely affected in both petunia and tobacco plants over-expressing SUP. Petals remained small and did not unfold, resulting in closed flowers. Stamen filaments were thin and very short. Detailed analysis of these floral organs from the petunia transformants showed that cell expansion was dramatically reduced without affecting cell division. These results reveal a novel activity for SUP as a regulator of cell expansion.

Petal and stamen formation in petunia is regulated by the homeotic gene fbp1.

For Arabidopsis and Antirrhinum, the so-called ABC model has been developed, which postulates that the determination of floral organ primordia is controlled by the action of three classes of homeotic genes. A number of these ABC genes encode putative transcription factors with the MADS box DNA binding motif. This paper reports on the functional analysis of the petunia MADS box gene fbp1. The temporal and spatial expression of fbp1 has been investigated in detail in transgenic plants containing the beta-glucuronidase (GUS) reporter gene fused to an fbp1 promoter fragment. fbp1-driven GUS activity was specifically detected in emerging petal and stamen primordia, suggesting a function of fbp1 in the control of second and third floral whorl identity. To test this hypothesis, transgenic petunia plants were generated in which fbp1 expression was inhibited by a co-suppression approach. The flowers of such plants exhibited homeotic conversions of petals towards sepals and stamens towards carpels. Occasionally, the third whorl carpels are fused forming a pentalocular gynoecium. This dominant fbp1 mutation acted as a single Mendelian trait in genetic crosses. These results strongly indicate that fbp1 is a petunia class B homeotic gene which is required for the correct initiation and determination of petals and stamens.

Functional interaction between the homeotic genes fbp1 and pMADS1 during petunia floral organogenesis.

The petunia MADS box floral binding protein (fbp) gene 1 represents a class B homeotic gene determining the identity of second and third floral whorl organs. Suppression of fbp1, which is highly homologous to the Antirrhinum gene globosa and Arabidopsis gene pistillata, results in the conversion of petals to sepals and stamens to carpels. In contrast to fbp1, the petunia homeotic gene pMADS1, encoding a protein homologous to the Antirrhinum protein DEFICIENS, has been shown to be involved in the formation of petals only. We demonstrated that the induction of fbp1 is established independent of pMADS1, whereas at later developmental stages, fbp1 is up-regulated by pMADS1 in petals. On the other hand, the induction and maintenance of pMADS1 expression are not affected by fbp1. To obtain information about the functional interaction between fbp1 and pMADS1, an fbp1 cosuppression mutant with mild phenotypic alterations was crossed with a green petals mutant in which pMADS1 expression was abolished. Progeny plants, heterozygous for the pMADS1 gene, had flowers with a more pronounced reversion from petals into sepals than was observed for the parent fbp1 mutant. The morphology of the third whorl organs was not changed. These observations, together with expression levels of pMADS1 and fbp1 in mutant flowers, provide evidence for functional control of fbp1 by PMADS1 in vivo.

Differential expression of two MADS box genes in wild-type and mutant petunia flowers.

We isolated and characterized two flower-specific genes from petunia. The protein products of these genes, designated floral binding protein 1 (FBP1) and 2 (FBP2), are putative transcription factors with the MADS box DNA binding domain. RNA gel blot analysis showed that the fbp1 gene is exclusively expressed in petals and stamen of petunia flowers. In contrast, the FBP1 protein was only detectable in petals and not in stamens, suggesting post-transcriptional regulation of the fbp1 gene in these tissues. The fbp2 gene is expressed in petals, stamen, carpels, and at a very low level in sepals but not in vegetative tissues. We analyzed the spatial expression of these fbp genes in floral organs of two homeotic flower mutants. In the blind mutant, whose flower limbs are transformed into antheroid structures on top of normal tubes, identical expression levels of both genes were observed in the antheroid structures as in normal anthers. In the homeotic mutant green petals, the petals are replaced by sepaloid organs in which the expression of fbp1 is strongly reduced but not completely abolished. Our results suggest a regulation of the fbp1 gene expression by the green petals (gp) gene. Expression of the fbp2 gene was not affected in the green petals mutant. In contrast to the proposed models describing floral morphogenesis, our data indicated that homeotic genes can be functional in one whorl only.

Co-suppression of the petunia homeotic gene fbp2 affects the identity of the generative meristem.

The function of the petunia MADS box gene fbp2 in the control of floral development has been investigated. Inhibition of fbp2 expression in transgenic plants by a co-suppression approach resulted in the development of highly aberrant flowers with modified whorl two, three and four organs. This mutant flower phenotype inherited as a single Mendelian trait. The flowers possess a green corolla which is reduced in size. Furthermore, the stamens are replaced by green petaloid structures and the inner gynoecial whorl is dramatically reduced. No ovules or placenta are formed and instead two new inflorescences developed in the axils of the carpels. These homeotic transformations are accompanied by a complete down-regulation of the petunia MADS box gene fbp6 which is highly homologous to the Arabidopsis and Antirrhinum genes agamous (ag) and plena (ple). In contrast to this, two other petunia MADS box genes, exclusively expressed in whorls two and three, are still transcribed. Our results indicate that the fbp2 gene belongs to a new class of morphogenesis genes involved in the determination of the central part of the generative meristem.

Downregulation of ovule-specific MADS box genes from petunia results in maternally controlled defects in seed development.

A maternally determined seed defect has been obtained by downregulation of the petunia MADS box genes Floral Binding Protein 7 (FBP7) and FBP11. These genes have been previously shown to play central roles in the determination of ovule identity. Aberrant development of the seed coat and consequent degeneration of the endosperm have been observed in transgenic plants in which these two genes are downregulated by cosuppression. Analysis of the expression pattern of FBP7 and FBP11 and genetic analysis confirmed the maternal inheritance of the phenotype. The FBP7 promoter was cloned and fused to reporter genes. One of these reporter genes was the BARNASE gene for targeted cell ablation. Our results indicate that FBP7 promoter activity is restricted to the seed coat of developing seeds and that it is completely silent in the gametophytically derived tissues. The mutants used in this study provided a unique opportunity to investigate one of the poorly understood aspects of seed development: the interaction of embryo, endosperm, and maternal tissues.

MADS box genes expressed in developing inflorescences of rice and sorghum.

With the aim of elucidating the complex genetic system controlling flower morphogenesis in cereals, we have characterized two rice and two sorghum MADS box genes isolated from cDNA libraries made from developing inflorescences. The rice clones OsMADS24 and OsMADS45, which share high homology with the Arabidopsis AGL2 and AGL4 MADS box genes, are expressed in the floral meristem, in all the primordia, and in mature floral organs. High expression levels have also been found in developing kernels. The sorghum clone SbMADS1 is also homologous to AGL2 and AGL4: expression analysis and mapping data suggest that it is the ortholog of OsMADS24. The pattern of expression of SbMADS2, the other sorghum MADS box gene, suggests that it may play a role as a meristem identity gene, as does AP1 in Arabidopsis, to which it shows considerable homology. The four genes have been mapped on a rice RFLP genetic map: the results are discussed in terms of synteny among cereals.

Analysis of the petunia MADS-box transcription factor family.

Transcription factors are key regulators of plant development. One of the major groups of transcription factors is the MADS-box family, of which at least 80 members are encoded in the Arabidopsis genome. In this study, 23 members of the petunia MADS-box transcription factor family were investigated by Northern hybridisation, phylogenetic and yeast two-hybrid analyses. Many of the genes characterised appeared to have one or more close relatives that shared similar expression patterns. Comparison of the binding interactions of these proteins revealed that some show similar interaction patterns, and hence are likely to be functionally redundant. From an evolutionary point of view, their coding genes are probably derived from a recent duplication event. Furthermore, protein-protein interaction patterns, in combination with expression patterns and phylogenetic classification, appear to offer good criteria for the identification of functional homologues. Based on comparison of such data between petunia and Arabidopsis, functions can be predicted for several MADS-box transcription factors in both species.

RNA 2 of tobacco rattle virus strain TCM encodes an unexpected gene.

The sequence of the 3'-terminal 1210 nucleotides of RNA 1 and the complete sequence of 3389 nucleotides of RNA 2 of tobacco rattle virus (TRV) strain TCM has been deduced. The sequence of the 3'-terminal 1099 nucleotides of RNAs 1 and 2 was found to be identical. Thus the genome of this TRV strain is partially diploid, encoding a 16K protein in both RNA 1 and RNA 2. The sequence that is unique to RNA 2 contains two open reading frames: the coat protein cistron and a cistron for a 29.1K protein, which shows no homology with the RNA 1 encoded 28.8K protein. cDNA probes corresponding to these two open reading frames cross-hybridized to pea early-browning virus RNA 2, but not to RNA 2 of five other tobraviruses tested.

Partial silencing of the NEC1 gene results in early opening of anthers in Petunia hybrida.

The NEC1 gene, previously isolated from Petunia hybrida, is expressed at high levels in nectaries, and in a very localized fashion in stamens, particularly in the anther stomium cells and the upper part of the filament. To elucidate the function of the NEC1 gene, co-suppression was employed for down-regulation of NEC1 expression, and transposon insertion mutagenesis was used to knock out the NEC1 function. Among the transgenic plants and plants carrying dTph1 inserted in the NEC1 gene, an "early open anther" phenotype was observed. In this mutant phenotype, the anthers already open in young flower buds (1.8 cm) that still contain immature pollen, resulting in poor pollen quality and impaired pollen release. The results obtained indicate that NEC1 might be involved in the development of stomium cells, which are ruptured during the normal process of anther dehiscence to release mature pollen. Southern analysis revealed the presence of a highly homologous NEC1-like gene, named NEC2, in the P. hybrida genome. The presence of NEC2 was confirmed by segregation analysis and sequencing of genomic clones. The implications of these results and possible reasons why no visually obvious phenotype in nectaries could be produced by co-suppression or transposon insertion mutagenesis are discussed.