Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.

Rapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.

The R2R3-MYB gene family in Arabidopsis thaliana.

MYB factors represent a family of proteins that include the conserved MYB DNA-binding domain. In contrast to animals, plants contain a MYB-protein subfamily that is characterised by the R2R3-type MYB domain. 'Classical' MYB factors, which are related to c-Myb, seem to be involved in the control of the cell cycle in animals, plants and other higher eukaryotes. Systematic screens for knockout mutations in MYB genes, followed by phenotypic analyses and the dissection of mutants with interesting phenotypes, have started to unravel the functions of the 125 R2R3-MYB genes in Arabidopsis thaliana. R2R3-type MYB genes control many aspects of plant secondary metabolism, as well as the identity and fate of plant cells.

Phenylpropanoid biosynthesis and its regulation.

In the past year progress has been made in the manipulation of phenylpropanoid metabolism but several studies highlight gaps in our understanding of the biochemistry of these pathways. New components involved in transcriptional regulation of phenylpropanoid genes have been identified, including transcription factors and novel proteins that function upstream of DNA-binding proteins.

Reactivation of the methylation-inactivated late E2A promoter of adenovirus type 2 by E1A (13 S) functions.

The inactivating effect of sequence-specific promoter methylations was extensively studied by using the late E2A promoter of adenovirus type 2 (Ad2) DNA. The modification of the three 5' CCGG 3' sequences at nucleotides +24, +6 and -215, relative to the cap site in this promoter, sufficed to silence the gene in transient expression either in Xenopus laevis oocytes or in mammalian cells, and after the fixation of the E2A promoter-chloramphenicol-acetyltransferase (CAT) gene construct in the genome of hamster cells. It will now be demonstrated that the inactivation of the late promoter of Ad2 DNA can be reversed by transactivating functions that are encoded in the 13S messenger RNA of the E1A region of Ad2 DNA. The reactivation of a methylation-inactivated eukaryotic promoter by transactivating functions has general significance in that the value of a regulatory signal can be fully realized only by its controlled reversibility. It was demonstrated in transient expression experiments that the 5' CCGG 3'-methylated late E2A promoter was at least partly reactivated in cell lines constitutively expressing the E1 region of Ad2 or of adenovirus type 5 (Ad5) DNA. The reactivation led to transcriptional initiation at the authentic cap sites of the late E2A promoter and was not associated with promoter demethylation, at least not in both DNA complements. Reactivation of the methylation-inactivated E2A promoter could also be demonstrated in two BHK21 cell lines (mc14 and mc20), which carried the late E2A promoter-CAT gene assembly in an integrated form. In these cell lines the late E2A promoter was methylated and the CAT gene was not expressed. By transfection of cell lines mc14 and mc20, the reactivating functions were shown to reside in the pAd2E1A-13 S cDNA clone of Ad2 DNA. The pAd2E1A-12 S cDNA clone or the pAd2E1B clone showed no reactivating function. These findings implicated the E1A 289 amino acid residue protein of Ad2, a well-known transactivator, as the reactivating function of the endogenous, previously dormant, late E2A promoter-CAT gene assembly. The methylated promoter was not demethylated, at least not in both complements, and it was shown that reactivation of the methylated promoter entailed transcriptional initiation at the authentic late E2A cap site. Since E1A and E1B jointly had a more pronounced effect, it was conceivable that genes in both regions acted together in the abrogation of the inhibitory effect of promoter methylations in the late E2A promoter.

The low molecular weight form of microtubule-associated protein 2 is transported into both axons and dendrites.

In the developing brain microtubule-associated protein MAP2 occurs as both a high molecular weight form, MAP2b, which is present only in dendrites, and a low molecular weight form, MAP2c, which is also present in axons. Because the MAP2c amino acid sequence is entirely contained within that of MAP2b it is not possible to raise a MAP2c-specific antibody, so that it has been impossible to determine whether MAP2c is present in dendrites along with MAP2b. To answer this question we have generated a MAP2c cDNA clone tagged with a 10 amino acid epitope from human c-myc. This additional sequence does not alter either the binding of MAP2c to microtubules or its effects on microtubules in non-neuronal cells. When expressed in cultured primary neurons by transfection, the myc tag allowed the distribution of MAP2c to be determined independently of endogenous MAP2 protein by immunostaining with an anti-myc antibody. This showed that MAP2c is present in all processes, indicating that it can enter all kinds of processes and is stable in their cytoplasm. The results further suggest that the selective association of high molecular weight MAP2 with dendrites depends on a mechanism that prevents either its entrance or survival in the axonal compartment.

Arrangement and expression of integrated adenovirus type 12 DNA in the transformed hamster cell line HA12/7: amplification of Ad12 and c-myc DNAs and evidence for hybrid viral-cellular transcripts.

In the genome of the adenovirus type 12 (Ad12)-transformed hamster cell line HA12/7 about three copies of the viral DNA are fixed by integration. The results of blot-hybridization, molecular cloning, and nucleotide sequencing experiments suggest a model for the arrangement of Ad12 DNA molecules in which the left hand terminus of one of the Ad12 DNA copies is linked to unique hamster DNA. The right hand end of this DNA molecule is fused to an inverted copy of a left terminal approximately 4.3 kb fragment of Ad12 DNA. This ensemble is followed by the second Ad12 DNA copy whose right terminus is again joined to an inverted, supernumerary left terminal approximately 4.3 kb Ad12 DNA fragment. There is a third Ad12 DNA copy whose right terminus is linked to cellular DNA. In this sequence arrangement, the left terminus of Ad12 DNA is overrepresented, as had been shown earlier (S. Stabel, W. Doerfler and R.R. Friis (1980) J. Virol. 36, 22-40). In the presented model, cellular DNA sequences are interspersed in between the three copies of Ad12 DNA. In the left terminus of the integrated Ad12 DNA, transcription of RNA is initiated which extends out into cellular DNA. The interviral DNA junctions are also transcribed. The c-myc gene in cell line HA12/7 is amplified about 10-fold and considerably more c-myc RNA has been identified in the Ad12-transformed cells than in BHK21 or in LSH hamster cells. It has been shown previously that the E1 region of Ad12 DNA is transcribed into mRNA in HA12/7 cells (Ortin et al. (1976) J. Virol. 20, 355-372). It remains to be investigated whether c-myc amplification and expression are related to the transformed phenotype of HA12/7 cells.

Two differentially expressed MATE factor genes from apple complement the Arabidopsis transparent testa12 mutant.

Proanthocyanidins (PAs) are a class of flavonoids with numerous functions in plant ecology and development, including protection against microbial infection, animal foraging and damage by UV light. PAs are also beneficial in the human diet and livestock farming, preventing diseases of the cardiovascular system and lowering the risk of cancer, asthma and diabetes. Apples (Malus x domestica Borkh.) are naturally rich in flavonoids, but the flavonoid content and composition varies significantly between cultivars. In this work, we applied knowledge from the model plant Arabidopsis thaliana, for which the main features of flavonoid biosynthesis have been elucidated, to investigate PA accumulation in apple. We identified functional homologues of the Multidrug And Toxic compound Extrusion (MATE) gene TRANSPARENT TESTA12 from A. thaliana using a comparative genomics approach. MdMATE1 and MdMATE2 were differentially expressed, and the function of the encoded proteins was verified by complementation of the respective A. thaliana mutant. In addition, MdMATE genes have a different gene structure in comparison to homologues from other species. Based on our findings, we propose that MdMATE1 and MdMATE2 are vacuolar flavonoid/H(+) -antiporters, active in PA accumulating cells of apple fruit. The identification of these flavonoid transporter genes expands our understanding of secondary metabolite biosynthesis and transport in apple, and is a prerequisite to improve the nutritional value of apples and apple-derived beverages.

Iron assimilation and transcription factor controlled synthesis of riboflavin in plants.

Iron homeostasis is vital for many cellular processes and requires a precise regulation. Several iron efficient plants respond to iron starvation with the excretion of riboflavin and other flavins. Basic helix-loop-helix transcription factors (TF) are involved in the regulation of many developmental processes, including iron assimilation. Here we describe the isolation and characterisation of two Arabidopsis bHLH TF genes, which are strongly induced under iron starvation. Their heterologous ectopic expression causes constitutive, iron starvation independent excretion of riboflavin. The results show that both bHLH TFs represent an essential component of the regulatory pathway connecting iron deficiency perception and riboflavin excretion and might act as integrators of various stress reactions.

Microtubule-associated protein 2 and the organization of cellular microtubules.

Microtubule-associated proteins (MAPs) are prominent components of the neuronal cytoskeleton that can promote microtubule formation and whose expression is under strong developmental regulation. They are thought to be involved in organizing the structure of microtubule fascicles in axons and dendrites, although whether they form active cross-links between microtubules or serve as strut-like spacer elements has yet to be resolved. In the experiments reported here we explored their influence on microtubules by expressing them in non-neuronal cells using DNA transfection techniques. We confirm earlier reports that microtubule-associated proteins of the MAP2/tau class can induce bundling of microtubules. In addition we find that MAP2 causes the rearrangement of microtubules in the cytoplasm in a manner that is dependent on the length of the microtubule bundles. Short bundles are straight and run across the cytoplasm whereas long bundles form a marginal band-like array at the periphery. We suggest that the latter arrangement is produced when microtubule bundles that are too long to fit inside the diameter of the cell bend under the restraining influence of the cortical cytoskeleton. In confirmation of this, we show that when the cortical actin network is depolymerized by cytochalasin B the MAP2-containing microtubule bundles push out cylindrical extensions from the cell surface. These results suggest that the induction of stiff microtubules bundles by MAP2, coupled with a breach in the cortical actin network, can confer two of the properties characteristic of neuronal processes; their cylindrical form and the presence of fasciculated microtubules.

Reorganisation of the microtubular cytoskeleton by embryonic microtubule-associated protein 2 (MAP2c).

Microtubule-associated protein 2c (MAP2c) is one of a set of embryonic MAP forms that are expressed during neuronal differentiation in the developing nervous system. We have investigated its mode of action by expressing recombinant protein in non-neuronal cell lines using cell cDNA transfection techniques. At every level of expression, all the MAP2c was bound to cellular microtubules. At low MAP2c levels, the microtubules retained their normal arrangement, radiating from the centrosomal microtubule-organising centre (MTOC) but at higher levels an increasing proportion of microtubules occurred independently of the MTOC. In most cells, radially oriented microtubules still attached to the MTOC co-existed with detached microtubules, suggesting that the primary effect of MAP2 is to increase the probability that tubulin polymerisation will occur independently of the MTOC. The MTOC-independent microtubules formed bundles whose distribution depended on their length in relation to the diameter of the transfected cell. Short bundles were attached to the cell cortex at one end and followed a straight course through the cytoplasm, whereas longer bundles followed a curved path around the periphery of the cell. By comparing these patterns to those produced by two chemical agents that stabilise microtubules, taxol and dimethyl sulphoxide, we conclude that effects of MAP2c arise from two sources. It stabilises microtubules without providing assembly initiation sites and as a result produces relatively few, long microtubule bundles. These bend only when they encounter the restraining influence of the cortical cytoskeleton of the cell, indicating that MAP2c also imparts stiffness to them. By conferring these properties of stability and stiffness to neuronal microtubules MAP2c contributes to supporting the structure of developing neurites.

c-MYB oncogene-like genes encoding three MYB repeats occur in all major plant lineages.

Since the identification of the first plant MYB-like protein, the Zea mays factor C1, the number of MYB-related genes described has greatly increased. All of the more than 150 plant MYB-like proteins known so far contain either two or only one sequence-related helix-turn-helix motif in their DNA-binding domain. Animal c-MYB genes contain three such helix-turn-helix motif-encoding repeats (R1R2R3 class genes). It has therefore been concluded that R2R3-MYB genes are the plant equivalents of c-MYB and that there are significant differences in the basic structure of MYB genes of plants and animals. Here, we describe expressed R1R2R3-MYB genes from Physcomitrella patients++ and Arabidopsis thaliana, designated PpMYB3R-1 and AtMYB3R-1. The amino acid sequences of their DNA-binding domains show high similarity to those of animal MYB factors, and less similarity to R2R3-MYB proteins from plants. In addition, R1R2R3-MYB genes were identified in different plant evolutionary lineages including mosses, ferns and monocots. Our data show that a DNA-binding domain consisting of three MYB repeats existed before the divergence of the animal and plant lineages. R1R2R3-MYB genes may have a conserved function in eukaryotes, and R2R3-MYB genes may predominantly regulate plant-specific processes which evolved during plant speciation.

Transactivation properties of parsley proline-rich bZIP transcription factors.

Light-responsive chalcone synthase (CHS) gene activation requires LRUCHS, a light regulatory promoter unit including the MYB recognition element MRECHS and the ACGT-containing element ACECHS. ACECHS is bound by the parsley basic region/leucine zipper (bZIP) factors CPRF1 and 4. Factors containing the bZIP domain exist in animals, plants and yeast, and recognize DNA sequence-specifically after formation of homo- or heterodimers. To determine the potential role of CPRFs in the regulation of CHS promoter activity, we investigated the functions of distinct CPRF domains in a homologous co-transfection system. The proline-rich domains of CPRF1 and CPRF4 activate transcription, indicating that CPRF1 and CPRF4 have transactivating properties. Over-expression of the CPRF1 bZIP domain caused a reduction of LRUCHS-mediated light inducibility, and point mutations throughout ACECHS affected both responsiveness to UV-containing white light and transactivation by CPRF1:VP16. The data suggest that a CPRF1-containing bZIP heterodimer interacts with ACECHS in vivo. We discuss regulatory steps in light-induced CHS transcription that may be influenced by CPRF1 and/or related bZIP factors.

Two distinct cis-acting elements are involved in light-dependent activation of the pea elip promoter.

Light activation of the pea (Pisum sativum) elip gene promoter was analysed in transgenic plants and in transiently transfected plant protoplasts. A series of promoter deletions fused to the gusA reporter was tested, and the results obtained by the two experimental approaches were in good agreement. We identified two nucleotide sequence elements involved in light-regulated expression of the elip gene. One element is similar to the GT1 binding site of the rbcS-3A gene, and the other resembles a G-box-like ACGT element. The region containing both elements was able to confer light responsiveness on a heterologous basic promoter. Electrophoretic mobility shift assays demonstrated that each element is specifically recognized by DNA-binding proteins present in nuclear extracts from pea seedlings. The G-box-like ACGT element is necessary but not sufficient for light inducibility, indicating that the two elements act together in confering light responsiveness.

Actin depolymerisation induces process formation on MAP2-transfected non-neuronal cells.

We have previously shown that microtubules in nonneuronal cells form long, stable bundles after transfection with the embryonic neuronal microtubule-associated protein MAP2c. In this study, we found that treating MAP2c-transfected cells with the actin depolymerising drug cytochalasin B led to the outgrowth of microtubule-containing processes from the cell surface. This effect was specific to MAP2c and did not occur in untransfected cells whose microtubules had been stabilised by treatment with taxol. The outgrowth and retraction of these processes during repeated cycles of cytochalasin addition and removal was followed by video time-lapse microscopy and was suggestive of a physical interaction between compressive forces exerted by the MAP2c-stabilised microtubule bundles and tensile forces originating in the cortical actin network. We suggest that MAP2c confers three properties on cellular microtubules that are essential for process outgrowth: stability, bundling and stiffness. The latter probably arises from the linking together of neighbouring tubulin subunits by three closely spaced tubulin-binding motifs in the MAP2 molecule that limits their motion relative to one another and thus reduces the flexibility of the polymer. Similar multimeric tubulin-binding domains in other proteins of the MAP2 class, including tau in axons and MAP4 in glial cells, may play the same role in the development and support of asymmetric cell morphology. Axial bundles of microtubules are found in growing neurites but not in growth cones, suggesting that the regulated expression of these MAP-induced properties makes an important contribution to the establishment of a stable process behind the advancing growth cone.

The transcriptional regulator CPRF1: expression analysis and gene structure.

Many eukaryotic DNA-binding proteins share a conserved amino acid sequence known as the basic region leucine zipper (bZIP) domain. bZIP proteins recognise DNA, upon dimerization, in a sequence-specific manner. The Common Plant Regulatory Factor 1 (CPRF1) is a bZIP transcription factor from parsley (Petroselinum crispum), which recognises defined elements containing ACGT cores. CPRF1 genomic DNA was cloned and the gene was sequenced. Analysis of the sequence data revealed the existence of 12 exons and 11 introns within a stretch of about 9 kb. A second RNA species hybridising to CPRF1 probes was identified as an alternatively spliced, additional CPRF1 transcript containing intron 8. This polyadenylated RNA species showed accumulation characteristics very similar to those of the CPRF1 mRNA. CPRF1 specifically binds an ACGT-containing element which is located within the composite regulatory unit that is necessary and sufficient for light activation of the parsley chalcone synthase (CHS) minimal promoter. Expression studies at the mRNA level demonstrated that CPRF1 mRNA is present in all organs of light-grown plants in which CHS mRNA expression is detectable, and light-dependent CHS mRNA accumulation was shown to be blocked by cycloheximide. Therefore, translation of a protein factor, possibly CPRF1, may be a prerequisite for CHS promoter activation.

Familial defective apolipoprotein B-100 in 12 subjects and their kindred.

Twelve unrelated subjects with heterozygous familial defective apolipoprotein B-100 were identified in a group of 252 patients with type IIa hypercholesterolaemia. Approximately 5% of hypercholesterolaemia can be explained by this mutation in the collective studied. Familial defective apolipoprotein B-100 is therefore the most common known mutation causing primary hypercholesterolaemia. Family studies revealed an additional 14 affected subjects. All family members with the mutation had elevated cholesterol concentrations. In a normolipidaemic control group of 146 subjects the mutation was not present. In the affected individuals a variable expression of total cholesterol concentrations and atherosclerosis was observed. Plasma cholesterol ranged from 6.60 to 14.89 mmol/l with a mean of 9.43 mmol/l. Premature atherosclerosis was present in 4 patients, while one affected woman is now 92 years old and has no symptoms of coronary heart disease or peripheral atherosclerosis. Analysis of the haplotypes and genotypes by 3 biallelic and 1 multi-allelic DNA marker suggests that the disorder is caused in all affected patients by the same rare allele. The fact that the same mutant allele was also identified in other European populations and in a North American population of Caucasian origin argues for a common European origin of this mutation.

Homodimeric and heterodimeric leucine zipper proteins and nuclear factors from parsley recognize diverse promoter elements with ACGT cores.

Four short nucleotide sequences (boxes I to IV) contribute to the light responsiveness of the parsley chalcone synthase promoter. The sequence-related boxes II and III resemble several plant, viral, and bacterial promoter elements that share ACGT core sequences and are associated with diversely regulated genes. We have analyzed the binding characteristics and protein-protein interactions of factors from nuclear extracts and of three putative leucine zipper (bZIP) transcription factors potentially involved in the regulation of this promoter. These common plant regulatory factors (CPRFs) bind specifically to boxes II and III as well as other ACGT-containing promoter elements (hex1, Em1a, and as-1), though with markedly different affinities. Intact bZIP domains are crucial for CPRF binding to DNA. Distinct ensembles of nuclear factors bind to boxes II and III, despite their sequence similarity. The parsley CPRFs bind to DNA as dimers, selectively form heterodimeric DNA binding complexes, and interact with nuclear proteins.

Rapid diagnosis of familial defective apolipoprotein B-100.

A method is described for the rapid, economic and non-radioactive examination of DNA samples from hypercholesterolaemic patients for familial defective apolipoprotein B-100, using a modified polymerase chain reaction (PCR) protocol and restriction enzyme isoform genotyping. Because of the high prevalence of familial defective apolipoprotein B-100, which is estimated to be one in 500 in most screened general populations, interest is focussed on a simple method for detection of this point mutation. In our protocol a diagnostic restriction site is created by PCR, using a specifically designed partly mismatched primer. In the case of familial defective apolipoprotein B-100 the amplified DNA segment contains an additional ScaI site, whereas DNA amplified from the normal allele is resistant to ScaI digestion. A rapid differentiation between the two alleles is achieved by agarose gel electrophoresis of the ScaI-digested PCR product.

PcMYB1, a novel plant protein containing a DNA-binding domain with one MYB repeat, interacts in vivo with a light-regulatory promoter unit.

Light regulatory unit 1 (LRU1) is necessary for and sufficient to mediate light-dependent activation of the chalcone synthase (CHS) minimal promoter in Petroselinum crispum. This composite promoter unit consists of at least two distinct cis-acting elements, designated ACECHS and MRECHS, both of which are required for light induction. The ACGT-containing element ACECHS interacts with common plant regulatory factors (CPRFs) which belong to the basic region/leucine zipper (bZIP) class of transcription factors. Here, we demonstrate that MRECHS, originally identified as an in vivo DNA footprint, is a MYB recognition element. This element possesses a functional core that is essential for light responsiveness and is specifically recognized by two distantly related MYB-like proteins: MYB305 and the novel factor MYB1 from P. crispum. PcMYB1 was identified by both its specific binding to MRECHS in vitro and recognition of MRECHS in vivo. The deduced amino acid sequence revealed that PcMYB1 contains only one MYB-like repeat. This portion of the protein constitutes the DNA-binding domain. Mutational analysis of PcMYB1 in combination with sequence comparison suggests the presence of a helix-turn-helix structure containing a recognition helix that is sufficient for sequence-specific binding. The structure of this distinct MYB-like DNA-binding domain appears to be conserved in proteins from all three eukaryotic phyla.