Biochemical consequences of the insertion of a suppressor-mutator (Spm) receptor at the bronze-1 locus in maize

Molecular insights on the origin and development of waxy genotypes in major crop plants

Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.

Deletions in a dspm insert in a maize bronze-1 allele alter RNA processing and gene expression

The bz-m13 allele of the bronze-1 (bz) locus in maize contains a 2.2-kb defective Suppressor-mutator (dSpm) transposable element inserted in the second exon. We compared bz expression in bz-m13 and five derivatives in which the dSpm insertion had sustained deletions ranging from 2 to 1300 bp. Tissues homozygous for bz-m13 in the absence of Spm-s activity were found to contain from 5 to 13% of the enzymatic activity conditioned by a wild-type allele at the bz locus. Tissues homozygous for the deletion derivatives contained enzymatic activities ranging from less than 1% to 67%. These differences are closely correlated with the steady-state level of one of two alternatively spliced transcripts. In all alleles bz transcription proceeds through the dSpm insert. Subsequent RNA processing uses the donor site of the single bz intron and either one of two alternative acceptor splice sites (AS1 and AS2) located within the dSpm sequence. Use of the AS1 removes all but 2 bp of dSpm sequence and produces the 1.8-kb transcript whose level corresponds closely to the level of enzymatic activity. Use of AS2 produces a transcript which retains more than 600 bp of dSpm sequence. Those derivatives in which AS2 is either deleted or inactivated have substantially increased levels of both the 1.8-kb transcript and enzymatic activity. We therefore document one sequence of events which began with the insertion of a transposable element and resulted in novel and stable introns which retain element-derived sequence and which in certain cases permit substantial host-gene expression.

Large tandem duplication associated with a Mu2 insertion in Zea mays B-Peru gene

The b locus of Zea mays encodes a transcriptional activator of the anthocyanin biosynthetic pathway. The B-Peru allele is expressed in the aleurone layer of the seed, which results in dark purple pigmentation of this tissue. An unstable Mutator-induced B-Peru mutant allele, b-Perum220, displays weak, variable pigment and a high germinal reversion rate not characteristic of other Mutator insertions. Characterization of relevant regions of b-Perum220 revealed a Mu2 element insertion in one copy of a 534 bp sequence. This 534 bp sequence is tandemly triplicated in the progenitor B-Peru allele, upstream of the B-Peru transcription start site. In addition to the Mu2 insertion, the b-Perum220 allele contains a newly formed large tandem duplication of 4.0 kb, which includes the promoter region and the first three exons of the B-Peru gene. The Mu2 element does not reside at any of the duplication breakpoints. The molecular study of eleven independent germinal revertants revealed five structural classes including structures in which the 4.0 kb tandem duplication is partially or completely deleted, the Mu2 element is partially or completely deleted, or a combination of these events has occurred. We hypothesize that most of the revertants arose by unequal recombination between the duplicated regions. Based on these structural analyses, models are discussed to explain the reduced b gene expression in b-Perum220.

Maize bronze 1:dSpm insertion mutations that are not fully suppressed by an active Spm

The Suppressor-mutator (Spm) family of maize transposable elements consists of autonomous Spm elements and nonautonomous defective Spm (dSpm) elements. One characteristic of this family is that the insertion of dSpm elements into a structural gene often permits some level of structural gene expression in the absence of SpM activity, and this structural gene expression is suppressed in trans by Spm activity. The Spm's subterminal repetitive regions (SRRs) contain several iterations of a 12-bp repeat motif. It had been proposed that binding of an Spm-encoded protein to these repeat motifs blocks structural gene transcriptional readthrough, thus suppressing gene expression. The bz-m13 allele of the bronze 1 locus contains a 2.24-kb dSpm insertion in the second exon of a Bz allele. In the absence of Spm activity, bz-m13 displays substantial Bz expression, and this expression is fully suppressed by Spm. Four intra-dSpm deletion derivatives are described in which this Bz expression is only partially suppressed by Spm. Each of these derivatives retains at least 12 SRR repeat motifs. Thus the presence of these repeat motifs is not sufficient to guarantee complete suppression by Spm. Some other property such as secondary structure or element size must play a role.

Changes in state of the Wx-m5 allele of maize are due to intragenic transposition of Ds

The molecular basis for the unusual phenotype conditioned by the waxy(Wx)-m5 Ds allele has been elucidated. Unlike most Ds alleles, Wx-m5 is phenotypically wild-type in the absence of Ac. We find that the Wx-m5 gene contains a 2-kb Ds element at -470 relative to the start of Wx transcription, representing the most 5' insertion of any transposable element allele characterized to date in plants. Despite its wild type phenotype, Wx-m5 has reduced levels of Wx enzymatic activity indicating that Ds insertion influences Wx gene expression. In the presence of Ac, Wx-m5 kernels have sectors of null expression on a wild-type background and give rise to stable wx and unstable wx-m germinal derivatives. Seventeen of 20 derivatives examined are wx-m alleles and at least 15 of these appear to result from intragenic transposition of Ds from -470 to new sites within the Wx gene. Three wx-m alleles contain two Ds elements, one at -470 and a second in Wx coding sequences. Surprisingly, only 3 out of 20 derivatives are stable wx mutants and these have sustained gross rearrangements of Wx and flanking sequences. For most other maize transposable element alleles somatic sectors and germinal derivatives usually arise following element excision or deletions of element sequences. In contrast, element insertion following intragenic transposition is apparently responsible for most of the somatic sectors and germinal derivatives of Wx-m5.

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.

Tissue-specific effects of maize bronze gene promoter mutations induced by Ds1 insertion and excision

Bz-wm is an allele of the Bz locus of maize isolated by McClintock (1962) as a derivative of bz-m2. It contains a Ds1 insertion 63 bp upstream of the start of transcription and a 3 bp insertion in the coding region at the site of the Ac element that was present in bz-m2. Bz-wm produces, in the aleurone layer of the endosperm, low amounts (approximately 1% of wild-type) of a Bz-gene encoded UDP-glucose: flavoid 3-0-glucosyltransferase (UFGT) polypeptide with altered thermal stability. Three phenotypically wild-type derivatives, Bz' (wm)-1, Bz' (wm)-2 and Bz' (wm)-3, were isolated in the presence of Ac and shown to have excised the Ds1 element but not fully restored UFGT activity in endosperm assays. In the studies reported here, we have further analyzed these Bz' derivatives of Bz-wm by determining the DNA sequences left behind on Ds1 excision, and by measuring the amount of UFGT activity and/or Bz mRNA conditioned by Bz-wm and the Bz' derivatives in different tissues. The data indicate that tissue-specific differences in expression of the Bz gene have been produced in alleles with mutations caused by transposable elements Ac and Ds. These mutations may affect either the amount of Bz transcription or the stability of the UFGT polypeptide. The sequence or spacing in the -63 region of the Bz promoter appears to be critical for maximum expression in aleurone and husk but not in pollen and pigmented seedling tissue.

Two mutations in a maize bronze-1 allele caused by transposable elements of the Ac-Ds family alter the quantity and quality of the gene product

The Dissociation (Ds) mutant, Bz-wm, of the maize bronze-1 (bz) locus conditions a leaky phenotype. Plants carrying this mutant allele synthesize a low amount of an altered Bz gene product, which leads to reduced anthocyanin pigmentation in the seed. The molecular analysis reported here shows that the Bz-wm mutant has a 406-bp Ds1 insertion located 63 bp 5' to the start of Bz transcription. Furthermore, the Bz-wm allele contains three additional base pairs within the second exon, relative to the wild-type Bz allele. These additional nucleotides are believed to be derived from the 8-bp target site duplication created by an Activator (Ac) element in a previous allele in the series. The biochemical and molecular analyses of Bz-wm and revertants of Bz-wm indicate that the three additional nucleotides are responsible for the altered enzyme stability, while the Ds1 element affects the steady-state level of Bz-specific protein and RNA. Since the two mutations present in the Bz-wm mutant were each caused by the action of the Ac-Ds transposable element system, these results provide new insights into the ways that transposable elements can modify maize gene expression.

Molecular characterization of suppressor-mutator (Spm)-induced mutations at the bronze-1 locus in maize: the bz-m13 alleles

The bz-m13 allele of maize contains a defective Suppressor-mutator (dSpm) transposable element and gives rise to a variety of stable and unstable derivatives in the presence of an autonomous Suppressor-mutator (Spm) element. The dSpm-13 element of bz-m13 consists of 2,241 base pairs (bp) and is located within the second exon of the bronze-1 (bz) gene. A number of the stable derivatives, both functional and nonfunctional, derived from bz-m13 were characterized molecularly. Results from genomic DNA blotting experiments indicate that the dSpm-13 element had excised from the locus in each stable derivative analyzed. The unstable derivatives bz-m13CS9 and bz-m13CS6 contain dSpm elements in the same position and orientation as the dSpm-13 element, but they differ in the length of the element. The dSpm-13CS9 element is 902 bp and arose via a deletion between two 5-bp direct repeats within the dSpm-13 element. The dSpm-13CS6 element is 2,239 bp and only differs from dSpm-13 by a 2-bp deletion at the end of one of the 13-bp terminal inverted repeats. The effect of these deletions on the frequency and timing of Spm-induced excision is discussed herein. In the absence of Spm, each of the bz-m13 alleles conditions a nonmutant phenotype despite the presence of the insertions in the second exon. The role of RNA splicing in this phenomenon and the recent finding of an acceptor splice site within the terminal inverted repeat are also discussed.

RNA splicing permits expression of a maize gene with a defective Suppressor-mutator transposable element insertion in an exon

The bz-m13CS9 allele of the bronze-1 gene in maize contains a 902-base-pair defective Suppressor-mutator (dSpm) transposable element in the second exon. Nevertheless, 40-50% of the enzymatic activity conditioned by a nonmutant allele at the bronze-1 locus is routinely recovered in crude extracts prepared from plants carrying bz-m13CS9 in the absence of an autonomous Suppressor-mutator element. Analyses of RNAs produced by such plants show that transcription proceeds through the dSpm. The dSpm sequence of the messenger RNA precursor is then removed by RNA splicing using the donor site of the single bronze-1 intron and an acceptor site within the inverted terminal repeat of the dSpm. This results in a messenger RNA with the proper reading frame that could produce a functional enzyme. These data demonstrate that this dSpm insertion in an exon of a structural gene has produced a functional allele with a novel intron consisting, in part, of the dSpm. This mechanism appears to allow dSpm elements to reduce the impact of their insertions on gene expression.

Deletions within a defective suppressor-mutator element in maize affect the frequency and developmental timing of its excision from the bronze locus

Six independent derivatives of the bz-m13 allele, which contains a 2.2-kilobase-pair defective Suppressor-mutator (dSpm) insertion at the bronze (bz) locus, have been isolated and analyzed. The derivatives were selected for alterations in the frequency and timing of somatic reversion; such derivatives have previously been analyzed genetically and designated "changes in state" by McClintock [McClintock, B. (1955) Carnegie Inst. Washington, Yearb. 54, 245-255]. All of the derivatives analyzed in the present study revert substantially later in development than the original insertion mutation and some show a very low frequency of reversion as well. All of the derivatives contain insertions at the same site as the parent bz-m13 allele. Deletions of 400-1300 base pairs were found in the dSpm elements in four of the six derivatives; the remaining derivatives could not be distinguished structurally from the original mutant allele. The results suggest that changes in the frequency and developmental timing of excision are attributable to alterations in the dSpm element. Furthermore, these data suggest that DNA sequences near the ends of the element are important for responding to the two transacting functions supplied by the transposition-competent Suppressor-mutator (Spm) element.