A general method to identify plant structural genes among genomic DNA clones using transposable element induced mutations

Optimum chalcone synthase for flavonoid biosynthesis in microorganisms

Chalcones and the subsequently generated flavonoids, as well as flavonoid derivatives, have been proven to have a variety of physiological activities and are widely used in: the pharmaceutical, food, feed, and cosmetic industries. As the content of chalcones and downstream products in native plants is low, the production of these compounds by microorganisms has gained the attention of many researchers and has a history of more than 20 years. The mining and engineering of chalcone synthase (CHS) could be one of the most important ways to achieve more efficient production of chalcones and downstream products in microorganisms. CHS has a broad spectrum of substrates, and its enzyme activity and expression level can significantly affect the efficiency of the biosynthesis of flavonoids. This review summarizes the recent advances in the: structure, mechanism, evolution, substrate spectrum, transformation, and expression regulation in the flavonoid biosynthesis of this vital enzyme. Future development directions were also suggested. The findings may further promote the research and development of flavonoids and health products, making them vital in the fields of human diet and health.

Maize kernel development

Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.

Genome engineering in ornamental plants: Current status and future prospects

Ornamental plants, like roses, carnations, and chrysanthemums, are economically important and are sold all over the world. In addition, numerous cut and garden flowers add colors to homes and gardens. Various strategies of plant breeding have been employed to improve traits of many ornamental plants. These approaches span from conventional techniques, such as crossbreeding and mutation breeding, to genetically modified plants. Recently, genome editing has become available as an efficient means for modifying traits in plant species. Genome editing technology is useful for genetic analysis and is poised to become a common breeding method for ornamental plants. In this review, we summarize the benefits and limitations of conventional breeding techniques and genome editing methods and discuss their future potential to accelerate the rate breeding programs in ornamental plants.

Survey of natural and transgenic gene markers used to monitor transposon activity

Marker genes have played a critical role in the discovery of plant transposable elements, our understanding of transposon biology, and the utility of transposable elements as tools in functional genomics. Marker traits in model plants have been useful to detect transposable elements and to study the dynamics of transposition. Transposon-induced changes in the sequence of marker genes and consequently their expression have contributed to our understanding of molecular mechanisms of transposition and associated genome rearrangements. Further, marker genes that have been cloned and are compatible in heterologous systems have found versatile utility in the design of DNA constructs that have enabled us to understand the finer details of transposition mechanisms, and also allowed the use of transposon-based tools for functional genomics. This chapter traces the role of marker traits and marker genes (endogenous and transgenic) in various plant systems, and their contributions to the advancement of transposon biology over the past several decades.

Why do so many petals have conical epidermal cells?

BACKGROUND

The conical epidermal cells found on the petals of most Angiosperm species are so widespread that they have been used as markers of petal identity, but their function has only been analysed in recent years. This review brings together diverse data on the role of these cells in pollination biology.

SCOPE

The published effects of conical cells on petal colour, petal reflexing, scent production, petal wettability and pollinator grip on the flower surface are considered. Of these factors, pollinator grip has been shown to be of most significance in the well-studied Antirrhinum majus/bumble-bee system. Published data on the relationship between epidermal cell morphology and floral temperature were limited, so an analysis of the effects of cell shape on floral temperature in Antirrhinum is presented here. Statistically significant warming by conical cells was not detected, although insignificant trends towards faster warming at dawn were found, and it was also found that flat-celled flowers could be warmer on warm days. The warming observed is less significant than that achieved by varying pigment content. However, the possibility that the effect of conical cells on temperature might be biologically significant in certain specific instances such as marginal habitats or weather conditions cannot be ruled out.

CONCLUSIONS

Conical epidermal cells can influence a diverse set of petal properties. The fitness benefits they provide to plants are likely to vary with pollinator and habitat, and models are now required to understand how these different factors interact.

Conical epidermal cells allow bees to grip flowers and increase foraging efficiency

The plant surface is by default flat, and development away from this default is thought to have some function of evolutionary advantage. Although the functions of many plant epidermal cells have been described, the function of conical epidermal cells, a defining feature of petals in the majority of insect-pollinated flowers, has not. The location and frequency of conical cells have led to speculation that they play a role in attracting animal pollinators. Snapdragon (Antirrhinum) mutants lacking conical cells have been shown to be discriminated against by foraging bumblebees. Here we investigated the extent to which a difference in petal surface structure influences pollinator behavior through touch-based discrimination. To isolate touch-based responses, we used both biomimetic replicas of petal surfaces and isogenic Antirrhinum lines differing only in petal epidermal cell shape. We show that foraging bumblebees are able to discriminate between different surfaces via tactile cues alone. We find that bumblebees use color cues to discriminate against flowers that lack conical cells--but only when flower surfaces are presented at steep angles, making them difficult to manipulate. This facilitation of physical handling is a likely explanation for the prevalence of conical epidermal petal cells in most flowering plants.

The Etched1 gene of Zea mays (L.) encodes a zinc ribbon protein that belongs to the transcriptionally active chromosome (TAC) of plastids and is similar to the transcription factor TFIIS

Etched1 (et1) is a pleiotropic, recessive mutation of maize that causes fissured and cracked mature kernels and virescent seedlings. Microscopic examinations of the et1 phenotype revealed an aberrant plastid development in mutant kernels and mutant leaves. Here, we report on the cloning of the et1 gene by transposon tagging, the localization of the gene product in chloroplasts, and its putative function in the plastid transcriptional apparatus. Several alleles of Mutator (Mu)-induced et1 mutants, the et1-reference (et1-R) mutant, and Et1 wild-type were cloned and analyzed at the molecular level. Northern analyses with wild-type plants revealed that Et1 transcripts are present in kernels, leaves, and other types of tissue, and no Et1 expression could be detected in the et1 mutants analyzed. The ET1 protein is imported by chloroplasts and has been immunologically detected in transcriptionally active chromosome (TAC) fractions derived from chloroplasts. Accordingly, the relative transcriptional activity of TAC fractions was significantly reduced in chloroplasts of et1-R plants. ET1 is the first zinc ribbon (ZR) protein shown to be targeted to plastids. With regard to its localization and its striking structural similarity to the eukaryotic transcription elongation factor TFIIS, it is feasible that ET1 functions in plastid transcription elongation by reactivation of arrested RNA polymerases.

An everlasting pioneer: the story of Antirrhinum research

Despite the tremendous success of Arabidopsis thaliana, no single model can represent the vast range of form that is seen in the approximately 250,000 existing species of flowering plants (angiosperms). Here, we consider the history and future of an alternative angiosperm model--the snapdragon Antirrhinum majus. We ask what made Antirrhinum attractive to the earliest students of variation and inheritance, and how its use led to landmark advances in plant genetics and to our present understanding of plant development. Finally, we show how the wide diversity of Antirrhinum species, combined with classical and molecular genetics--the two traditional strengths of Antirrhinum--provide an opportunity for developmental, evolutionary and ecological approaches. These factors make A. majus an ideal comparative angiosperm.

A family of polyketide synthase genes expressed in ripening Rubus fruits

Quality traits of raspberry fruits such as aroma and color derive in part from the polyketide derivatives, benzalacetone and dihydrochalcone, respectively. The formation of these metabolites during fruit ripening is the result of the activity of polyketide synthases (PKS), benzalcetone synthase and chalcone synthase (CHS), during fruit development. To gain an understanding of the regulation of these multiple PKSs during fruit ripening, we have characterized the repertoire of Rubus PKS genes and studied their expression patterns during fruit ripening. Using a PCR-based homology search, a family of ten PKS genes (Ripks1-10) sharing 82-98% nucleotide sequence identity was identified in the Rubus idaeus genome. Low stringency screening of a ripening fruit-specific cDNA library, identified three groups of PKS cDNAs. Group 1 and 2 cDNAs were also represented in the PCR amplified products, while group 3 represented a new class of Rubus PKS gene. The Rubus PKS gene-family thus consists of at least eleven members. The three cDNAs exhibit distinct tissue-specific and developmentally regulated patterns of expression. RiPKS5 has high constitutive levels of expression in all organs, including developing flowers and fruits, while RiPKS6 and RiPKS11 expression is consistent with developmental and tissue-specific regulation in various organs. The recombinant proteins encoded by the three RiPKS cDNAs showed a typical CHS-type PKS activity. While phylogenetic analysis placed the three Rubus PKSs in one cluster, suggesting a recent duplication event, their distinct expression patterns suggest that their regulation, and thus function(s), has evolved independently of the structural genes themselves.

Molecular analysis of C1 alleles in Zea mays defines regions involved in the expression of this regulatory gene

The structure and function of several C1 alleles have been investigated molecularly and the importance of C1 promoter sequences for gene expression was studied using transient transformation assays. The C1 mutants analyzed were the overexpressing allele C1-S, the light-inducible allele c1-p, the null recessive allele c1-n, and the Ds element-induced allele c1-m1. Nucleotide sequence analysis of the alleles revealed a number of differences, predominantly located at the 3' end of the gene. The promoter sequences of the C1 alleles investigated so far (including wild-type and the dominant inhibitor C1-I allele) are almost identical except for two short footprint-like sequences (Box I and Box II) close to the putative CAAT box. Northern blot experiments and transient expression in particle gun experiments indicate that these sequences may be correlated with the different expression patterns of the alleles in the aleurone of maturing and germinating kernels.

Genetic and molecular analysis of a three-component transposable-element system in maize

Two different factors control the mutability of an unstable allele (c2-m881058Y) of the C2 gene of maize. Both an autonomous En/Spm element and an unrelated independent factor, named Mediator, are coordinately required for the excision of the insert in c2-m881058Y. According to genetic analysis, Mediator does not have the suppressor (S) function or mutator (M) function of En/Spm. Mediator has no effect on the timing or frequency of excision of En1, En-low, or various I/dSpm elements. Hence, Mediator only mediates a specific interaction between En and the insert at c2-m881058Y. Molecular analysis of c2-m881058Y has revealed a 3.3 kb, complex, En-related receptor element inserted into the second exon of the C2 gene. The ends of this element are homologous to the ends of En/Spm, but an internal 1.7 kb region shows no En/Spm homology. A great degree (11-14%) of nucleotide changes, relative to En1, occur within and between the 12 bp TNPA binding motifs. Alterations of these critical cis-determinants may account for the need for a "helper" factor for excision. This element is named Irma, for Inhibitor that requires Mediator also, and represents a unique, low copy number class of receptor element.

Expression of chalcone synthase, dihydroflavonol reductase, and flavanone-3-hydroxylase in mutants of barley deficient in anthocyanin and proanthocyanidin biosynthesis

A barley (cv Triumph) cDNA library was screened with a cDNA probe encoding flavanone-3-hydroxylase of Antirrhinum majus. A full-length clone coding for a protein of 377 amino acids (42 kDa), with an overall homology of 71% and a central domain homology of 85% to the Antirrhinum protein, was isolated. This novel barley cDNA and two previously isolated cDNAs encoding chalcone synthase and dihydroquercetin reductase, respectively, were used to study the transcription of the corresponding genes in testa pericarp tissue from ant 13 mutants of barley. No or very low levels of transcripts are found in mutants ant 13-152, ant 13-351, and ant 13-353. It is concluded that the gene Ant 13 encodes a transcription factor operating in the flavonoid biosynthesis of barley. Transcription of the gene for the flavanone-3-hydroxylase (subunit) was also studied in an ant 17 mutant of barley. Mutant ant 17-352 transcribes the gene at normal or elevated levels. The mutant is blocked in the synthesis of dihydroquercetin and accumulates derivatives of eriodictyol, the precursor of dihydroquercetin. The combined observations suggest that Ant 17 is the structural gene for a barley flavanone-3-hydroxylase subunit, and that the mutant allele is a mutation in the structural domain of the gene.

Pigmentation mutants produced by transposon mutagenesis in Antirrhinum majus

New pigmentation mutants were generated by transposon mutagenesis in Antirrhinum majus, in three previously described loci, nivea, delila and incolorata, and two new loci, daphne and olive. The wild-type olive gene is required for the production of dark-green leaves, and the daphne gene for the synthesis of flavones. Five out of the six mutants were both germinally and somatically unstable, indicating that they resulted from transposon insertions. Molecular analysis of the mutant at nivea (niv-600) showed that it was caused by insertion of a new transposon, Tam4. The sequence of Tam4 suggests that it is unable to transpose autonomously and that it is related to Tam1 and Tam2. All three of these transposons have identical inverted repeats, produce 3 bp target duplications, leave similar excision footprints and share at one end a 600-700 bp region containing many palindromic copies of a motif sequence, possibly required in cis for transposition. The somatic excision of Tam4 in niv-600 is at a very low rate compared to germinal excision but it can be activated by crossing to lines carrying derivative alleles of a Tam1 insertion at niv. Molecular analysis of four different pigmentation mutants has shown that insertions of Tam1, Tam2, Tam3 and Tam4 have been obtained, illustrating the potential of general transposon mutagenesis for trapping and isolating new transposons as well as for tagging genes.

Control of anthocyanin biosynthesis in flowers of Antirrhinum majus

The intensity and pattern of anthocyanin biosynthesis in Antirrhinum flowers is controlled by several genes. We have isolated six cDNA clones encoding enzymes in the pathway committed to flavonoid biosynthesis and used these to assay how the regulatory genes that modify colour pattern affect the expression of biosynthetic genes. The biosynthetic genes of the later part of the pathway appear to be co-ordinately regulated by two genes, Delila (Del), and Eluta (El), while the early steps (which also lead to flavone synthesis) are controlled differently. This division of control is not the same as control of anthocyanin biosynthesis by the regulatory genes R (S) and C1 in maize aleurone, and may result from the adaptive significance of different flavonoids in flowers and seeds, reflecting their attractiveness to insects and mammals respectively. El and del are probably involved in transcriptional control and both genes appear to be able to repress expression of some biosynthetic genes and activate expression of others.

Genetic and molecular characterization of an Adh-1 null mutant in tomato

Treatment of tomato seeds with ethyl methanesulphonate (EMS) followed by allyl alcohol selection of M2 seeds has led to the identification of one plant (B15-1) heterozygous for an alcohol dehydrogenase (Adh) null mutation. Genetic analysis and expression studies indicated that the mutation corresponded to the structural gene of the Adh-1 locus on chromosome 4. Homozygous Adh-1 null mutants lacked ADH-1 activity in both pollen and seeds. Using an antiserum directed against ADH from Arabidopsis thaliana, which cross-reacts with ADH-1 and ADH-2 proteins from tomato, no ADH-1 protein was detected in seeds of the null mutant. Northern blot analysis showed that Adh-1 mRNA was synthesized at wild-type levels in immature seeds of the null mutant, but dropped to 25% in mature seeds. Expression of the Adh-2 gene on chromosome 6 was unaffected. The potential use of the Adh-1 null mutant in selecting rare transposon insertion mutations in a cross with "mutable" Adh-1+ tomato lines is discussed.

Genetic interactions underlying flower color patterns in Antirrhinum majus

Diverse spatial patterns of flower color in Antirrhinum can be produced by a series of alleles of pallida, a gene encoding an enzyme required for pigment biosynthesis. The alleles arose by imprecise excision of a transposable element, Tam3, and we show that they carry a series of deletions involving progressive removal of sequences adjacent to the excision site. This has enabled us to define three cis-acting upstream regions, A, B, and C, which differentially affect the level of pallida expression in distinct areas of the flower. We show further that an unlinked locus, delila, regulates the spatial distribution of pallida transcript. Deletion of regions ABC at the pallida locus uncouples pallida from regulation by delila, whereas deletion of A or AB brings pallida under regulation by delila in a new area of the flower. These results suggest that diverse patterns of pallida expression reflect the different ways in which alleles interact with a prepattern of both common and spatially specific genetic signals in the flower.

Transposon-induced alterations in the promoter region affect transcription of the chalcone synthase gene of Antirrhinum majus

Four solid-colour revertants were isolated from the highly variegated niv-53::Tam1 mutant, in which the transposable element Tam1 is integrated in the promoter region of the chalcone synthase (chs) gene. DNA sequence analysis revealed that in all four lines the Tam1 element was deleted together with flanking nucleotides of the chs promoter. In one case the TATA box of the chs gene was removed resulting in extremely low expression of the gene, and initiation of transcription occurring at a new position. The other three deletions defined a sequence motif (TAC-CAT) which is apparently required for maximal gene expression. Thus transposable elements seem to be useful for probing gene structure, in this case the signal structure in the promoter region, by virtue of imprecise excision.

Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus

The pallida gene of A. majus encodes a product required for the synthesis of red flower pigment. We have shown that the unstable pallida(recurrens) mutation is due to the insertion of the Tam3 transposable element near the promoter of the gene. Imprecise excision of Tam3 alters pallida gene expression and generates new spatial patterns or different intensities of flower pigmentation. Distinct spatial patterns may also result from rearrangements induced by Tam3 that alter the relative position of the pallida gene. Changes in Tam3 structure or position result in new unstable phenotypes. These findings suggest that genes may be rendered genetically hypervariable as a consequence of transposable element insertion and excision.

Characterization and expression of chalcone synthase in different genotypes of Matthiola incana R.Br. during flower development

The expression of the key enzyme of flavonoid biosynthesis, chalcone synthase (CHS), has been followed in different genotypes of Matthiola incana R.Br. (Brassicaceae) which are genetically defined with respect to anthocyanin production. Enzyme activity was determined by a radioactive assay in crude flower extracts. The amount of enzyme protein in the developing flower was determined by use of SDS-PAGE, protein blotting, reaction with an antiserum against CHS of parsley (Petroselinum hortense), and PAP staining. The molecular weight of about 41 500 of the CHS subunits corresponds with that obtained from other higher plants. Steps of flower development were subdivided into stages-1,0, I-IV. During flower development of a Matthiola line with coloured petals (line 07) a defined pattern of CHS enzyme production can be observed: At the stage of bud opening (stage 0-I) a dramatic increase of the amount of CHS enzyme prodein in the petals occurs. This is quite different from results obtained with petals of the white flowering mutant line 18 bearing a genetic defect in the gene f coding for CHS. Here a reduced and nearly constant level of CHS enzyme protein can be observed during flower development. This line is most attractive for our studies of the regulation of enzyme synthesis because under stress conditions a slight colouring of the flower petals occurs, which is uniformly distributed and line-specific. This suggests that we are dealing with a CHS mutant producing a rather inactive enzyme protein at a low level. This protein may regain enzyme activity under certain environmental conditions. Preliminary investigations suggest a rather high level of CHS mRNA transcription at the bud opening stage of the flowers. Other white flowering mutant lines, line 17 (genotype ee) and line 19 (gg) with a late block in the flavonoid biosynthesis pathway, exhibit a concomitant reduction of CHS enzyme activity and protein content in comparison to anthocyanin-producing lines with the f(+)f(+)e(+)e(+)g(+)g(+)-genotype.

Genetic analysis of instability in Petunia hybrida : 1. A highly unstable mutation induced by a transposable element inserted at the An1 locus for flower colour

A hypothesis is proposed to interpret the results of crossing experiments with unstable mutants of Petunia hybrida having variegated flowers and showing variation in the colour intensity and the degree of spotting of the corolla. It is postulated that the An1 locus, which is involved in anthocyanin synthesis, is composed of a structural gene with an adjoining regulatory region, the latter in turn comprising two components, viz., the 'mutator', responsible for the activation of the structural gene, and the 'expressor', controlling the rate of activity. Unstable An1 alleles originate from deletions induced by a transposable element inserted within the regulatory region. Such deletions extend from one of the ends of the inserted element across the adjacent DNA and thus may include parts of the 'expressor' and the 'mutator'. Reversions result from repair of the deletions, the inserted element not necessarily becoming lost in the process.