AGO1 controls arabidopsis inflorescence architecture possibly by regulating TFL1 expression

BACKGROUND AND AIMS

The TERMINAL FLOWER 1 (TFL1) gene is pivotal in the control of inflorescence architecture in arabidopsis. Thus, tfl1 mutants flower early and have a very short inflorescence phase, while TFL1-overexpressing plants have extended vegetative and inflorescence phases, producing many coflorescences. TFL1 is expressed in the shoot meristems, never in the flowers. In the inflorescence apex, TFL1 keeps the floral genes LEAFY (LFY) and APETALA1 (AP1) restricted to the flower, while LFY and AP1 restrict TFL1 to the inflorescence meristem. In spite of the central role of TFL1 in inflorescence architecture, regulation of its expression is poorly understood. This study aims to expand the understanding of inflorescence development by identifying and studying novel TFL1 regulators.

METHODS

Mutagenesis of an Arabidopsis thaliana line carrying a TFL1::GUS (β-glucuronidase) reporter construct was used to isolate a mutant with altered TFL1 expression. The mutated gene was identified by positional cloning. Expression of TFL1 and TFL1::GUS was analysed by real-time PCR and histochemical GUS detection. Double-mutant analysis was used to assess the contribution of TFL1 to the inflorescence mutant phenotype.

KEY RESULTS

A mutant with both an increased number of coflorescences and high and ectopic TFL1 expression was isolated. Cloning of the mutated gene showed that both phenotypes were caused by a mutation in the ARGONAUTE1 (AGO1) gene, which encodes a key component of the RNA silencing machinery. Analysis of another ago1 allele indicated that the proliferation of coflorescences and ectopic TFL1 expression phenotypes are not allele specific. The increased number of coflorescences is suppressed in ago1 tfl1 double mutants.

CONCLUSIONS

The results identify AGO1 as a repressor of TFL1 expression. Moreover, they reveal a novel role for AGO1 in inflorescence development, controlling the production of coflorescences. AGO1 seems to play this role through regulating TFL1 expression.

The JAZ family of repressors is the missing link in jasmonate signalling

Jasmonates are essential phytohormones for plant development and survival. However, the molecular details of their signalling pathway remain largely unknown. The identification more than a decade ago of COI1 as an F-box protein suggested the existence of a repressor of jasmonate responses that is targeted by the SCF(COI1) complex for proteasome degradation in response to jasmonate. Here we report the identification of JASMONATE-INSENSITIVE 3 (JAI3) and a family of related proteins named JAZ (jasmonate ZIM-domain), in Arabidopsis thaliana. Our results demonstrate that JAI3 and other JAZs are direct targets of the SCF(COI1) E3 ubiquitin ligase and jasmonate treatment induces their proteasome degradation. Moreover, JAI3 negatively regulates the key transcriptional activator of jasmonate responses, MYC2. The JAZ family therefore represents the molecular link between the two previously known steps in the jasmonate pathway. Furthermore, we demonstrate the existence of a regulatory feed-back loop involving MYC2 and JAZ proteins, which provides a mechanistic explanation for the pulsed response to jasmonate and the subsequent desensitization of the cell.

Genome-wide linkage analysis of Arabidopsis genes required for leaf development

In most crop species, primary productivity depends mainly on the leaf. However, the genes that contribute to the making of plant leaves remain largely unknown. With a view to identifying the genes involved in leaf development in Arabidopsis thaliana, we previously isolated EMS-induced mutants with abnormally shaped leaves and demonstrated that they fall into 94 complementation groups. We present here the map positions of 76 of these genes, which have been obtained using a high-throughput genetic mapping method, based on the simultaneous coamplification by PCR of 21 polymorphic microsatellites and the semiautomated fluorescent detection of the products. The map positions and F2 mapping populations obtained in this work will be instrumental in the positional cloning of these genes, which are essential for leaf development.

Genetic analysis of incurvata mutants reveals three independent genetic operations at work in Arabidopsis leaf morphogenesis

In an attempt to identify genes involved in the control of leaf morphogenesis, we have studied 13 Arabidopsis thaliana mutants with curled, involute leaves, a phenotype herein referred to as Incurvata (Icu), which were isolated by G. Röbbelen and belong to the Arabidopsis Information Service Form Mutants collection. The Icu phenotype was inherited as a single recessive trait in 10 mutants, with semidominance in 2 mutants and with complete dominance in the remaining 1. Complementation analyses indicated that the studied mutations correspond to five genes, representative alleles of which were mapped relative to polymorphic microsatellites. Although most double-mutant combinations displayed additivity of the Icu phenotypes, those of icu1 icu2 and icu3 icu4 double mutants were interpreted as synergistic, which suggests that the five genes studied represent three independent genetic operations that are at work for the leaf to acquire its final form at full expansion. We have shown that icu1 mutations are alleles of the Polycomb group gene CURLY LEAF (CLF) and that the leaf phenotype of the icu2 mutant is suppressed in an agamous background, as is known for clf mutants. In addition, we have tested by means of multiplex RT-PCR the transcription of several floral genes in Icu leaves. Ectopic expression of AGAMOUS and APETALA3 was observed in clf and icu2, but not in icu3, icu4, and icu5 mutants. Taken together, these results suggest that CLF and ICU2 play related roles, the latter being a candidate to belong to the Polycomb group of regulatory genes. We propose that, as flowers evolved, a new major class of genes, including CLF and ICU2, may have been recruited to prevent the expression of floral homeotic genes in the leaves.

A multiplex reverse transcriptase-polymerase chain reaction method for fluorescence-based semiautomated detection of gene expression in Arabidopsis thaliana

A non-radioactive, rapid and sensitive method is presented for the simultaneous detection of several mRNA molecules. The technique is based on conventional first-strand cDNA synthesis by reverse transcriptase, followed by multiplex polymerase chain reaction (PCR) co-amplification of several gene products in a reaction mix containing several primer sets, each including a fluorescently labeled oligonucleotide. The PCR products obtained are finally electrophoresed in a single lane of a polyacrylamide gel, in an automated DNA sequencer controlled by fragment-analysis software. The method has proven useful to efficiently detect nine mRNA transcripts, some of which are low copy number, from small specimens such as single flowers and leaves of Arabidopsis thaliana (L.) Heynh. This approach might be easily extended to other biological systems, for developmental and physiological analyses, population studies and diagnosis.

Genetic analysis of salt-tolerant mutants in Arabidopsis thaliana

Stress caused by the increased salinity of irrigated fields impairs plant growth and is one of the major constraints that limits crop productivity in many important agricultural areas. As a contribution to solving such agronomic problems, we have carried out a large-scale screening for Arabidopsis thaliana mutants induced on different genetic backgrounds by EMS treatment, fast neutron bombardment, or T-DNA insertions. From the 675,500 seeds we screened, 17 mutant lines were isolated, all but one of which yielded 25-70% germination levels on 250 mm NaCl medium, a condition in which their ancestor ecotypes are unable to germinate. Monogenic recessive inheritance of NaCl-tolerant germination was displayed with incomplete penetrance by all the selected mutants, which fell into five complementation groups. These were named SALOBRENO (SAN) and mapped relative to polymorphic microsatellites, the map positions of three of them suggesting that they are novel genes. Strains carrying mutations in the SAN1-SAN4 genes display similar responses to both ionic effects and osmotic pressure, their germination being NaCl and mannitol tolerant but KCl and Na(2)SO(4) sensitive. In addition, NaCl-, KCl-, and mannitol-tolerant as well as abscisic-acid-insensitive germination was displayed by sañ5, whose genetic and molecular characterization indicates that it carries an extremely hypomorphic or null allele of the ABI4 gene, its deduced protein product lacking the APETALA2 DNA binding domain.

OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana

In contrast to bacterial, fungal and vertebrate ornithine transcarbamylases (OTCs; EC 2.1.3.3), very little is known about the enzyme in plants. We report here the isolation of a T-DNA-tagged mutant displaying sensitivity to ornithine, whose characterization has allowed for the identification of several complementary and genomic DNA clones encoding the OTC and auxilin-like 1 (AUL1) proteins of the crucifer Arabidopsis thaliana. Transcript mapping revealed that at least 22 bp within the OTC-AUL1 intercoding region are transcribed from both strands, which makes this one of the rarely described cases of convergent and overlapping transcription units in the nuclear genome of a multicellular eukaryote. Transcription of the OTC gene was shown to be ubiquitous in aerial organs of adult plants, whereas that of AUL1 was obscured by the existence of a putative second copy of the gene. The OTC-AUL1 locus maps at the bottom of chromosome 1.

A mutational analysis of leaf morphogenesis in Arabidopsis thaliana

As a contribution to a better understanding of the developmental processes that are specific to plants, we have begun a genetic analysis of leaf ontogeny in the model system Arabidopsis thaliana by performing a large-scale screening for mutants with abnormal leaves. After screening 46,159 M2 individuals, arising from 5770 M1 parental seeds exposed to EMS, we isolated 1926 M2 putative leaf mutants, 853 of which yielded viable M3 inbred progeny. Mutant phenotypes were transmitted with complete penetrance and small variations in expressivity in 255 lines. Most of them were inherited as recessive monogenic traits, belonging to 94 complementation groups, which suggests that we did not reach saturation of the genome. We discuss the nature of the processes presumably perturbed in the phenotypic classes defined among our mutants.

Genetic analysis of leaf form mutants from the Arabidopsis Information Service collection

Although a vast inventory of morphological mutants of Arabidopsis thaliana is available, only some have been used for genetic studies of leaf development. Such is the case with the Arabidopsis Information Service (AIS) Form Mutants collection, assembled by A. R. Kranz and currently stored at the Nottingham Arabidopsis Stock Centre, which includes a large number of mutant lines, most of which have been little studied. With the aim of contributing to the genetic dissection of leaf ontogeny, we have subjected 57 mutant lines isolated by others to genetic analysis; 47 of which were from the AIS collection. These are characterized by vegetative leaves of abnormal shape or size, and were chosen as candidates for mutations in genes required for leaf morphogenesis. The mutant phenotypes studied were shown to be inherited as single recessive Mendelian traits and were classified into 10 phenotypic classes. These mutant strains were found to fall into 37 complementation groups, 7 of which corresponded to known genes. Results of the phenotypic analysis and data on the genetic interactions of these mutants are presented, and their possible developmental defects discussed.

Molecular characterization and phylogenetic analysis of SpBMP5-7, a new member of the TGF-beta superfamily expressed in sea urchin embryos

TGF-beta ligands are probably pan-bilaterian in phylogenetic distribution. The family appears to have diversified greatly with the evolution of the vertebrates, but only a few invertebrate deuterostome TGF-beta molecules have so far been isolated. A search for members of this family expressed in sea urchin embryos, using canonical PCR primers, revealed a single-copy gene encoding a new TGF-beta protein. The sequence which it encodes is closely related to those of vertebrate bone morphogenetic proteins (BMPs) 5-7. No additional TGF-beta family members were uncovered other than univin, which had previously been reported.

High-throughput genetic mapping in Arabidopsis thaliana

To facilitate rapid determination of the chromosomal location of novel mutations, we have improved current approaches to gene mapping using microsatellite length polymorphisms. The high-throughput linkage analysis method described here allows a novel gene to be tested for linkage against the whole genome of a multicellular eukaryote, Arabidopsis thaliana, in a single polyacrylamide gel. The procedure is based on the simultaneous co-amplification of 21 microsatellites in a single tube, using a multiplex PCR mix containing 21 primer pairs, each including one oligonucleotide labeled with one of three fluorescent dyes that have different emission wavelengths. The amplification products, which range in number from 21 to 42, depending on the genotype of the individual being tested, are electrophoresed in a single lane on a polyacrylamide gel. The use of an automated fragment analyzer makes it possible to perform linkage analysis on a one gel-one gene basis using DNA samples from 19 F2 individuals obtained from an outcross involving a mutant and a wild-type that is genetically polymorphic with respect to the ecotype in which the mutant was generated. Discrimination of the amplification products is facilitated not only by labeling with different fluorochromes, but also by prior testing of different sequences for the ability to prime the amplification of each microsatellite, in order to ensure that multiplex PCR yields compatible amplification products of non-overlapping size. The method is particularly useful in large-scale mutagenesis projects, as well as for routine mapping of single mutants, since it reveals the map position of a gene less than 24 h after the F2 individuals to be analyzed have become available. The concepts employed here can easily be extended to other biological systems.

Venation pattern formation in Arabidopsis thaliana vegetative leaves

Branching net-like structures are a trait common to most multicellular organisms. However, our knowledge is still poor when it comes to the genetic operations at work in pattern formation of complex network structures such as the vasculature of plants and animals. In order to initiate a causal analysis of venation pattern formation in dicotyledonous plant leaves, we have first studied its developmental profile in vegetative leaves of a wild-type strain of the model organism Arabidopsis thaliana. As landmarks of the complexity of the venation pattern, we have defined three main developmental parameters, which have been quantitatively followed in time: the ratios of (a) the length and (b) the number of branchpoints of the vein network with the surface of the lamina, which decrease in parallel as the leaf grows, only small differences existing between successive leaves, and (c) the number of hydathodes per leaf, which increases both during leaf expansion and from juvenile to adult rosette leaves. We next searched for natural variations in the first vegetative leaves of 266 ecotypes, finding only 2 which showed a venation pattern unequivocally different from that of the rest, Ba-1 and Ei-5, the latter displaying an extremely simple pattern that we have called Hemivenata. This phenotype, which is inherited as a monogenic recessive trait, is visible both in leaves and in cotyledons and seems to arise from a perturbation in an early acting patterning mechanism. Finally, we have screened for mutants with abnormal venation pattern but normally shaped leaves, concluding that such a phenotype is rare, since only one recessive mutation was obtained, extrahydathodes, characterized by the presence of an increased number of hydathodes per leaf.

Rapid discrimination of sequences flanking and within T-DNA insertions in the Arabidopsis genome

An improvement to previous methods for recovering Arabidopsis thaliana genomic DNA flanking T-DNA insertions is presented that allows for the avoidance of some of the cloning difficulties caused by the concatameric nature of T-DNA inserts. The principle of the procedure is to categorize by size restriction fragments of mutant DNA, produced in separate digestions with NdeI and Bst1107I. Given that the sites for these two enzymes are contiguous within the pGV3850:1003 T-DNA construct, the restriction fragments obtained fall into two categories: those showing identical size in both digestions, which correspond to sequences internal to T-DNA concatamers; and those of different sizes, that contain the junctions between plant DNA and the T-DNA insert. Such a criterion makes it possible to easily distinguish the digestion products corresponding to internal T-DNA parts, which do not deserve further attention, and those which presumably include a segment of the locus of interest. Discrimination between restriction fragments of genomic mutant DNA can be made on rescued plasmids, inverse PCR amplification products or bands in a genomic blot.

A genetic analysis of bx bxd cis double mutants in the Drosophila Ultrabithorax gene

The Ultrabithorax (Ubx) gene of Drosophila melanogaster includes two functionally distinguishable regions. One is the Ubx transcription unit, which gives rise by alternative splicing to a family of morphogenetic Ubx proteins (UBX). The other is its upstream bithoraxoid (bxd) region. On the basis of genetic and molecular studies, it is generally assumed that the Ubx transcription unit contains internal positively acting cis-regulatory elements controlling UBX expression in the T3a compartment of the body of Drosophila, while the bxd region contains positive cis-regulatory elements controlling UBX expression in the T3p and A1a compartments. We have performed a genetic analysis of bx bxd cis double mutant chromosomes containing one mutation (bx alleles) affecting the Ubx unit, and a second (bxd alleles) affecting the bxd region of the Ubx gene. Our study of different bx bxd/bx combinations shows that bxd alleles partially rescue the adult mutant phenotypes of bx alleles, which suggests that the bxd region contains a negative cis-regulatory element involved in the control of the activity of the Ubx gene in the T3a compartment.

Positive and negative cis-regulatory elements in the bithoraxoid region of the Drosophila Ultrabithorax gene

The Ultrabithorax (Ubx) gene is required during embryogenesis and larval development to specify the third thoracic and first abdominal segments of Drosophila melanogaster. Mutations in the bithoraxoid (bxd) region, a 40 kb DNA stretch upstream of the Ubx promoter, affect cis-regulatory elements responsible for the ectodermal expression of the Ubx gene in the posterior compartment of the third thoracic segment and anterior compartment of the first abdominal segment. Our genetic data and the available molecular information are used to map the adult epidermal cis-regulatory elements within the bxd region. Genetic combinations involving mutations affecting the bxd region show that (1) redundant or cooperatively acting sequences are required for Ubx gene expression in the anterior compartment of the first abdominal segment, and (2) the expression of Ubx in the posterior compartment of the third thoracic segment is modulated by positive and negative cis-regulatory elements.

PCR amplification of long DNA fragments

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Genetic analysis of transvection effects involving cis-regulatory elements of the Drosophila Ultrabithorax gene

The Ultrabithorax (Ubx) gene of Drosophila melanogaster contains two functionally distinguishable regions: the protein-coding Ubx transcription unit and, upstream of it, the transcribed but nonprotein-coding bxd region. Numerous recessive, partial loss-of-function mutations which appear to be regulatory mutations map within the bxd region and within the introns of the Ubx transcription unit. In addition, mutations within the Ubx unit exons are known and most of these behave as null alleles. Ubx1 is one such allele. We have confirmed that, although the Ubx1 allele does not produce detectable Ubx proteins (UBX), it does retain other genetic functions detectable by their effects on the expression of a paired, homologous Ubx allele, i.e., by transvection. We have extended previous analyses made by E. B. Lewis by mapping the critical elements of the Ubx gene which participate in transvection effects. Our results show that the Ubx1 allele retains wild-type functions whose effectiveness can be reduced (1) by additional cis mutations in the bxd region or in introns of the Ubx transcription unit, as well as (2) by rearrangements disturbing pairing between homologous Ubx genes. Our results suggest that those remnant functions in Ubx1 are able to modulate the activity of the allele located in the homologous chromosome. We discuss the normal cis regulatory role of these functions involved in trans interactions between homologous Ubx genes, as well as the implications of our results for the current models on transvection.

Developmental genetic analysis of Contrabithorax mutations in Drosophila melanogaster

A developmental analysis of the Contrabithorax (Cbx) alleles offers the opportunity to examine the role of the Ultrabithorax (Ubx) gene in controlling haltere, as alternative to wing, morphogenesis in Drosophila. Several Cbx alleles are known with different spatial specificity in their wing toward haltere homeotic transformation. The molecular data on these mutations, however, does not readily explain differences among mutant phenotypes. In this work, we have analyzed the "apogenetic" mosaic spots of transformation in their adult phenotype, in mitotic recombination clones and in the spatial distribution of Ubx proteins in imaginal discs. The results suggest that the phenotypes emerge from early clonality in some Cbx alleles, and from cell-cell interactions leading to recruitment of cells to Ubx gene expression in others. We have found, in addition, mutual interactions between haltere and wing territories in pattern and dorsoventral symmetries, suggesting short distance influences, "accommodation," during cell proliferation of the anlage. These findings are considered in an attempt to explain allele specificity in molecular and developmental terms.

Transvection in the Drosophila Ultrabithorax gene: a Cbx1 mutant allele induces ectopic expression of a normal allele in trans

In wild-type Drosophila melanogaster larvae, the Ultrabithorax (Ubx) gene is expressed in the haltere imaginal discs but not in the majority of cells of the wing imaginal discs. Ectopic expression of the Ubx gene in wing discs can be elicited by the presence of Contrabithorax (Cbx) gain-of-function alleles of the Ubx gene or by loss-of-function mutations in Polycomb (Pc) or in other trans-regulatory genes which behave as repressors of Ubx gene activity. Several Ubx loss-of-function alleles cause the absence of detectable Ubx proteins (UBX) or the presence of truncated UBX lacking the homeodomain. We have compared adult wing phenotypes with larval wing disc UBX patterns in genotypes involving double mutant chromosomes carrying in cis one of those Ubx mutations and the Cbx1 mutation. We show that such double mutant genes are (1) active in the same cells in which the single mutant Cbx1 is expressed, although they are unable to yield functional proteins, and (2) able to induce ectopic expression of a normal homologous Ubx allele in a part of the cells in which the single mutant Cbx1 is active. That induction is conditional upon pairing of the homologous chromosomes (the phenomenon known as transvection), and it is not mediated by UBX. Depletion of Pc gene products by Pc3 mutation strongly enhances the induction phenomenon, as shown by (1) the increase of the number of wing disc cells in which induction of the homologous allele is detectable, and (2) the induction of not only a paired normal allele but also an unpaired one.

Genetic analysis of "transvection" effects involving contrabithorax mutations in Drosophila melanogaster

Contrabithorax (Cbx) alleles are dominant mutations in the Ultrabithorax (Ubx) gene of Drosophila that cause its ectopic expression in the mesothorax. We have studied the role of the homologous chromosome in the mesothoracic phenotype in several Cbx heterozygotes. None of the Cbx alleles studied shows variations in phenotype with extra doses of the Ubx gene. Only Cbx2 and CbxIRM (a revertant of Cbx1) show synapsis-dependent gene expression ("transvection"). The mesothoracic phenotypes of CbxIRM and Cbx2 heterozygotes are strongly modified when the homologous chromosome carries breakpoints proximal to or at the Ubx locus or null alleles of this gene. These lesions in the homologous chromosome enhance the Cbx2 mutant phenotype and reduce that of CbxIRM one. The genetic analysis of these transvection effects suggests that the transcription of the CbxIRM and Cbx2 alleles depends on RNAs of short radius of action from the homologous Ubx gene.

Two different approaches to computer-aided teaching of microbial genetics

Two computer packages have been developed to teach bacterial genetics on an introductory genetics course for undergraduate students in biology. The first package, 'CONJUGACION', is designed to teach bacterial conjugation and its genetic outcomes. It includes four main parts. Firstly, a tutorial part presents a theoretical framework using screens of text and animated graphics. Secondly, an interactive concept application section requires students to carry out experiments for the determination of the correct sex and genotype of 10 bacterial strains. The third part uses the previously obtained data for simulating interrupted mating experiments and mapping the bacterial genome. Finally, an evaluation section allows the students to test their understanding through a series of multiple choice questions. The second package, 'LURIDEL', is intended for teaching the preadaptative character of mutation in bacterial populations on the basis of the fluctuation test of Luria and Delbrück. It simulates, graphically, the appearance of mutations in microbial cultures and gives results of simulated fluctuation experiments. Programs were written under the PCOS operating system in MBASIC extended to graphics for running on Olivetti M20 microcomputers.

A method for the selection of mutants of Phycomyces blakesleeanus defective in germination

A simple method for the physical separation of dormant and germinated cells of Phycomyces blakesleeanus has been designed. Separation was attained by isopycnic centrifugation in a preformed discontinuous density gradient of Urografin. In this gradient, dormant spores and active cells at two different stages of germination were separated in three homogeneous and clearly distinct bands. The method has been used to follow the kinetics of the variation of cellular density during germination of wild type spores and to select for mutants temperature-sensitive for heat-shock induced germination. Sixty-nine mutants have been isolated by various procedures which include a separation step in the described Urografin gradient.

Characterization of Phycomyces blakesleeanus mutants temperature-sensitive for heat-shock induced germination

Sixty-nine mutants of the fungus Phycomyces blakesleeanus, temperature-sensitive for heat-shock induced germination, have been characterized. All of them show a low viability at 26 degrees C and normal viability at 16 degrees C. Eleven mutants recover the wild type phenotype if yeast extract is added to the minimal medium; the mutant phenotype of eight of these mutants is also suppressed by the addition of putrescine or other polyamines. The majority of the mutants are affected very early in germination. Spontaneous, heat-shock and acetate induced germination are not equally impaired by some of the mutations, so specific and independent steps seem to be involved in part of the activation mechanism of germination.