Utility and distribution of conserved noncoding sequences in the grasses

Control of gene expression requires cis-acting regulatory DNA sequences. Historically these sequences have been difficult to identify. Conserved noncoding sequences (CNSs) have recently been identified in mammalian genes through cross-species genomic DNA comparisons, and some have been shown to be regulatory sequences. Using sequence alignment algorithms, we compared genomic noncoding DNA sequences of the liguleless1 (lg1) genes in two grasses, maize and rice, and found several CNSs in lg1. These CNSs are present in multiple grass species that represent phylogenetically disparate lineages. Six other maize/rice genes were compared and five contained CNSs. Based on nucleotide substitution rates, these CNSs exist because they have biological functions. Our analysis suggests that grass CNSs are smaller and far less frequent than those identified in mammalian genes and that mammalian gene regulation may be more complex than that of grasses. CNSs make excellent pan-grass PCR-based genetic mapping tools. They should be useful as characters in phylogenetic studies and as monitors of gene regulatory complexity.

Biodiversity (Communications arising): maize transgene results in Mexico are artefacts

Quist and Chapela's conclusion that the transgenes they claim to have detected in native maize in Oaxaca, Mexico, are predominantly reassorted and inserted into a "diversity of genomic contexts" seems to be based on an artefact arising from the inverse polymerase chain reaction (i-PCR) they used to amplify sequences flanking 35S transgenes from cauliflower mosaic virus (CaMV).

Mutator transposase is widespread in the grasses

Although the Mutator (Mu) system is well characterized in maize (Zea mays), very little is known about this highly mutagenic system of transposons in other grasses. Mutator is regulated by the MuDR class of elements, which encodes two genes, one of which, mudrA, has similarity to a number of bacterial transposases. Experiments in our laboratory, as well as database searches, demonstrate that mudrA sequences are ubiquitous and diverse in the grasses. In several species it is clear that multiple paralogous elements can be present in a single genome. In some species such as wheat (Triticum aestivum) and rice (Oryza sativa), mudrA-similar sequences are represented in cDNA databases, suggesting the presence of active Mu transposon systems in these species. Further, in rice and in sorghum, mudrA-like genes are flanked by long terminal inverted repeats, as well as the short host sequence direct repeats diagnostic of insertion. Thus, there is ample evidence that systems related to Mu in maize are at least potentially active in a wide variety of grasses. However, the mudrB gene, though important for Mu activity in maize, is not necessarily a component of Mu elements in other grasses.

Biomechanical analysis of the Rolled (RLD) leaf phenotype of maize

The pleiotropic effects of the Rld1-O/+ mutation of Zea mays (Poaceae) on leaf phenotype include a suppression of normal transverse unrolling, a reversed top/bottom epidermal polarity, and an apparently straighter longitudinal shape. According to engineering shell theory, there might be mechanical coupling between transverse and longitudinal habit, i.e., the leaf rolling itself might produce the longitudinal straightening. We tested this possibility with quantitative curvature measurements and mechanical uncoupling experiments. The contributions of elastic bending under self weight, mechanical coupling, and rest state of leaf parts to the longitudinal and transverse habit were assessed in Rld1-O/+ mutants and a population of sibling +/+ segregants. Elastic bending and curvature coupling are shown to be relatively unimportant. The Rld1-O/+ mutation is shown to alter not only the unrolling process, but also the developmental longitudinal curving in the growing leaf, leading to a straighter midrib and a rolled lamina. The Rld1-O/+ mutant is thus a suitable model to study the relation between tissue polarity and differential curvature development in the maize leaf. Since on the abaxial side of the leaf, more abundant sclerenchyma is found in +/+ than in Rld1-O/+, a gradient in sclerification may contribute to the development of midrib curvature.

Mutator-suppressible alleles of rough sheath1 and liguleless3 in maize reveal multiple mechanisms for suppression

Insertions of Mutator transposons into maize genes can generate suppressible alleles. Mu suppression is when, in the absence of Mu activity, the phenotype of a mutant allele reverts to that of its progenitor. Here we present the characterization of five dominant Mu-suppressible alleles of the knox (knotted1-like homeobox) genes liguleless3 and rough sheath1, which exhibit neomorphic phenotypes in the leaves. RNA blot analysis suggests that Mu suppression affects only the neomorphic aspect of the allele, not the wild-type aspect. Additionally, Mu suppression appears to be exerting its effects at the level of transcription or transcript accumulation. We show that truncated transcripts are produced by three alleles, implying a mechanism for Mu suppression of 5' untranslated region insertion alleles distinct from that which has been described previously. Additionally, it is found that Mu suppression can be caused by at least three different types of Mutator elements. Evidence presented here suggests that whether an allele is suppressible or not may depend upon the site of insertion. We cite previous work on the knox gene kn1, and discuss our results in the context of interactions between Mu-encoded products and the inherently negative regulation of neomorphic liguleless3 and rough sheath1 transcription.

The liguleless2 gene of maize functions during the transition from the vegetative to the reproductive shoot apex

During a maize plant's (Zea mays) development, the shoot apical meristem (SAM) generates an apex that proceeds through different phases: juvenile vegetative, adult vegetative and reproductive. During each phase the structures produced are distinguishable from structures produced during the other phases. In this paper, we demonstrate that the LIGULELESS2 (LG2) function is required for an accurate vegetative to reproductive phase transition. The maize gene liguleless2 (lg2) has been shown to encode a basic-leucine zipper (bZIP) protein and to function in narrowing the region from which the ligule and auricle develop in a typical maize leaf. Here we show that lg2 mutant plants can have reduced long tassel branches, extra vegetative leaves and extra husk leaves when compared to wild-type siblings. This indicates a role for the lg2 gene in the vegetative to reproductive phase transition of the shoot apex. We also discuss a potential role for the lg2 gene in general phase transition processes.

The maize rough sheath2 gene and leaf development programs in monocot and dicot plants

Leaves of higher plants develop in a sequential manner from the shoot apical meristem. Previously it was determined that perturbed leaf development in maize rough sheath2 (rs2) mutant plants results from ectopic expression of knotted1-like (knox) homeobox genes. Here, the rs2 gene sequence was found to be similar to the Antirrhinum PHANTASTICA (PHAN) gene sequence, which encodes a Myb-like transcription factor. RS2 and PHAN are both required to prevent the accumulation of knox gene products in maize and Antirrhinum leaves, respectively. However, rs2 and phan mutant phenotypes differ, highlighting fundamental differences in monocot and dicot leaf development programs.

Ectopic expression of the maize homeobox gene liguleless3 alters cell fates in the leaf

The semidominant mutation Liguleless3-O (Lg3-O) causes a blade-to-sheath transformation at the midrib region of the maize (Zea mays L.) leaf. We isolated a full-length lg3 cDNA containing a knotted1-like family homeobox. Six Lg3-O partial revertant alleles caused by insertion of a Mutator (Mu) transposon and two deletion derivatives were isolated and used to verify that our knotted1-like cDNA corresponds to the LG3 message. In wild-type plants the LG3 mRNA is expressed in apical regions but is not expressed in leaves. In mutant plants harboring any of three dominant lg3 alleles (Lg3-O, -Mlg, and -347), LG3 mRNA is expressed in leaf sheath tissue, indicating that the Lg3 phenotype is due to ectopic expression of the gene. The Lg3-O revertant alleles represent two classes of Lg3 phenotypes that correlate well with the level of ectopic Lg3 expression. High levels of ectopic LG3 mRNA expression results in a severe Lg3 phenotype, whereas weak ectopic Lg3 expression results in a mild Lg3 phenotype. We propose that ectopic Lg3 expression early in leaf development causes the blade-to-sheath transformation, but the level of expression determines the extent of the transformation.

Functional analysis of deletion derivatives of the maize transposon MuDR delineates roles for the MURA and MURB proteins

The regulatory transposon of the Mutator system of transposable elements in maize is MuDR. MuDR elements produce two transcripts, from genes mudrA and mudrB, encoding proteins MURA and MURB, respectively. Like many other transposons, MuDR elements often undergo deletions, usually of internal sequences. Analysis of a deletion that is restricted to the region encoding MURB demonstrates that this gene is not required to cause excisions of a reporter element, although it may be required for transposition or suppression of suppressible alleles. Conversely, a derivative that lacks the region encoding MURA but that produces MURB is nonfunctional for all aspects of Mutator activity. Northern analysis of these derivatives reveals that each of the two transcripts can be independently transcribed, and analysis using an antibody specific for MURB reveals that mudrB transcript can also be successfully translated and its product appropriately localized in the absence of mudrA. A third deletion derivative provides evidence for a source of previously reported antisense transcript.

The rough sheath2 gene negatively regulates homeobox gene expression during maize leaf development

Leaves of higher plants are produced in a sequential manner through the differentiation of cells that are derived from the shoot apical meristem. Current evidence suggests that this transition from meristematic to leaf cell fate requires the down-regulation of knotted1-like homeobox (knox) gene expression. If knox gene expression is not repressed, overall leaf shape and cellular differentiation within the leaf are perturbed. In order to identify genes that are required for the aquisition of leaf cell fates, we have genetically screened for recessive mutations that confer phenotypes similar to dominant mutations (e.g. Knotted1 and Rough sheath1) that result in the ectopic expression of class I knox genes. Independently derived mutations at the rough sheath2 (rs2) locus condition a range of pleiotropic leaf, node and internode phenotypes that are sensitive to genetic background and environment. Phenotypes include dwarfism, leaf twisting, disorganized differentiation of the blade-sheath boundary, aberrant vascular patterning and the generation of semi-bladeless leaves. knox genes are initially repressed in rs2 mutants as leaf founder cells are recruited in the meristem. However, this repression is often incomplete and is not maintained as the leaf progresses through developement. Expression studies indicate that three knox genes are ectopically or over-expressed in developing primordia and in mature leaves. We therefore propose that the rs2 gene product acts to repress knox gene expression (either directly or indirectly) and that rs2 gene action is essential for the elaboration of normal leaf morphology.

Lax midrib1-O, a systemic, heterochronic mutant of maize

Lxm1-O, a dominant EMS (ethyl methanesulfonate) induced mutation in maize (Zea mays, Poaceae), was originally reported to affect the blade/sheath boundary over the midrib region of the leaf. Here we present a more extensive analysis of the Lxm phenotype in nine different inbred lines. Lxm leaves are longer and narrower, and can initiate ectopic leaves. Additionally, Lxm1-O affects all plant organs observed. Compared to wild-type siblings, Lxm plants have fewer nodes, basal displacement of reproductive structures, and advance more quickly to the reproductive phase. We address questions as to whether Lxm1-O abbreviates a specific developmental phase, using hair, wax, and ear node data. We found that each phase was affected, although to varying degrees, depending on the inbred line. We interpret Lxm1-O to be a heterochronic mutation, causing the developmental acceleration of each phase of the shoot. Lxm1-O is novel, since other systemic heterochronic maize mutants prolong the juvenile phase, thereby extending shoot development. We discuss the importance of heterochronic mutations in the context of morphological evolution.

The maize gene liguleless2 encodes a basic leucine zipper protein involved in the establishment of the leaf blade-sheath boundary

The blade and sheath of a maize leaf are separated by a linear epidermal fringe, the ligule, and two wedge-like structures, the auricles. In plants homozygous for the null mutation, liguleless2-reference (lg2-R), the ligule and auricles are often absent or positioned incorrectly and the blade-sheath boundary is diffuse. This phenotype is in contrast to that of liguleless1-reference (lgl-R) mutant plants, which have a more defined boundary even in the absence of the ligule and auricles. Additionally, mosaic analysis indicates the lg2-R phenotype is cell-nonautonomous and the lg1-R phenotype is cell-autonomous. Using scanning electron microscopy we show that lg2-R mutant plants are affected before the first visible sign of ligule and auricle formation. We have cloned the Lg2+ gene through a Mutator-8 transposon insertion allele, and verified it with five independently derived alleles. The comparison of genomic DNA and cDNA sequences reveals an open reading frame encoding a protein of 531 amino acids with partial homology to a subclass of plant basic leucine zipper (bZIP) transcription factors. Although a large body of molecular and biochemical characterization exists on this subclass of bZIP proteins, our work represents the first report of a mutant phenotype within this group. A specific reverse transcriptase (RT)-PCR assay shows LG2 mRNA expression in meristem/developing ligule regions. RT-PCR also shows that LG2 mRNA accumulation precedes that of LG1 mRNA. The mutant phenotype and expression analysis of lg2 suggest an early role in initiating an exact blade-sheath boundary within the young leaf primordia.

Sectors expressing the homeobox gene liguleless3 implicate a time-dependent mechanism for cell fate acquisition along the proximal-distal axis of the maize leaf

The longitudinal axis of the maize leaf is composed of, in proximal to distal order, sheath, ligule, auricle and blade. The semidominant Liguleless3-O (Lg3-O) mutation disrupts leaf development at the ligular region of the leaf midrib by transforming blade to sheath. In a previous study, we showed that leaf sectors of Lg3 mutant activity are cell nonautonomous in the transverse dimension and can confer several alternative developmental fates (Fowler, Muehlbauer and Freeling (1996) Genetics 143, 489–503). In our present study we identify five Lg3 sector types in the leaf: sheath-like with displaced ligule (sheath-like), sheath-like with ectopic ligule (ectopic ligule), auricle-like, macro-hairless blade and wild-type blade. The acquisition of a specific sector fate depends on the timing of Lg3 expression. Early Lg3 expression results in adoption of the sheath-like phenotype at the ligule position (a proximal cell fate), whereas later Lg3 expression at the same position results in one of the more distal cell fates. Furthermore, sheath-like Lg3 sectors exhibit a graded continuum of phenotypes in the transformed blade region from the most proximal (sheath) to the most distal (wild-type blade), suggesting that cell fate acquisition is a gradual process. We propose a model for leaf cell fate acquisition based on a timing mechanism whereby cells of the leaf primordium progress through a maturation schedule of competency stages which eventually specify the cell types along the proximal to distal axis of the leaf. In addition, the lateral borders between Lg3 ‘on’ sectors and wild-type leaf sometimes provide evidence of no spreading of the transformed phenotype. In these cases, competency stages are inherited somatically.

Induction of leaves directly from leaves in the maize mutant Lax midrib1-O

One of the several phenes specified by the maize dominant mutation Lax midrib1-O (Lxm1-O on 3L) is the proliferation of leaf "flaps" usually paired around veins on the abaxial leaf surface. Using histology and scanning electron microscopy, we show these flaps to be authentic leaf structures; in rare instances, complete ectopic leaves are found. The first divisions preceding flap emergence occur between plastochrons 4 and 7, stages when the course of leaf differentiation is well under way. No sign of meristem or any small, densely cytoplasmic primordium-like cells were seen at the sites of flap initiation. In addition, the sites of ectopic leaf initiation do not express KNOX (Knotted-like homeobox) proteins, a molecular marker for shoot apical meristem cell identity. Thus, the cells that proliferate into ectopic leaves do not arise from a meristem or a primordium. A similar phenomenon has been described in several dicots, but in no other monocots. The details of flap morphology compared to the morphology of the leaf proper suggest a model whereby cells in regions of the leaf proper maintain the competence they acquired in the meristem. These cells then respond properly, in a regulated manner, to a delayed signal emanating from veins denoting "make the organ you are competent to make."

liguleless1 encodes a nuclear-localized protein required for induction of ligules and auricles during maize leaf organogenesis

The maize ligule and auricle are structures on the maize leaf that develop at the boundary of the sheath and blade. In the absence of liguleless1 (Ig1) gene expression, ligule and auricle are not formed, and the blade-sheath boundary does not develop as an exact line between sheath and blade. By using the Activator (Ac) transposable element as a molecular tag, a novel Ig1 allele, Ig1-m1, was isolated and cloned. Analysis of somatic revertant sectors confirmed that the LG1 gene product functions in a cell-autonomous fashion. cDNA cloning as well as RT-PCR analysis of the LG1 mRNA indicate that the Ig1 gene is expressed at very low levels in the ligular region of developing maize leaf primordia, perhaps as early as plastochron 6 or earlier. Cellular localization studies in a heterologous system indicate that the LG1 product localizes exclusively to the nucleus. The predicted amino acid sequence of the LG1 protein is largely novel but contains an internal domain of 77 amino acids with significant similarity to a domain present in two recently identified SQUAMOSA PROMOTER-BINDING proteins 1 and 2 (SBP1 and SBP2) in Antirhinum majus.

Clonal sectors reveal that a specific meristematic domain is not utilized in the maize mutant narrow sheath

The narrow leaf and shortened stem phenotypes of the maize mutant narrow sheath (ns) are postulated to result from the lack of founder cell initialization in a region of the meristem that gives rise to leaf and stem margins. To test this model, a lineage map of the maize meristem is presented which compares the development of leaf margins in the narrow leaf mutant, narrow sheath (ns), and wild-type sibling plants. X-irradiation of mature seeds produced aneuploid albino sectors in wild-type and ns mutant plants. Of particular interest are sectors occurring in more than one leaf, which reflect a meristematic albino cell lineage. Analyses of these sectors indicated that: (1) a region of the ns meristem does not contribute to the founder cell population of the incipient leaf; (2) the margins of ns mutant leaves are derived from a lateral region of the meristem different from those in wild-type siblings; (3) founder cells in wild-type, juvenile-staged vegetative meristems encircle the meristem to a greater extent than do founder cells in adult-staged meristems; and (4) meristematic leaf founder cells may be subdivided into specific lateral domains, such that the position of a sector on the meristem correlates with a particular cell lineage. These data support our model for ns gene function in a specific domain of the meristem.

Interactions of liguleless1 and liguleless2 function during ligule induction in maize

The maize ligule is an adaxial membranous structure on the leaf that develops at the boundary of the sheath and blade. The ligule and the associated auricle are dispensable structures, amenable to genetic manipulation. We present here a genetic analysis of liguleless1 (lg1) and liguleless2 (lg2), the two genes known to be uniquely necessary for ligule and auricle development. We show that both reference mutant alleles, lg1-R and lg2-R, are null alleles. The double mutant phenotype suggests that lg1 and lg2 act in the same pathway. Indeed, the dosage of a functional allele at either gene affects the null phenotype of the other. While lg1 function has previously been shown to be cell-autonomous, here we show that the lg2-R phenotype is cell-nonautonomous, suggesting lg1 and lg2 play different roles in the ligule-auricle induction mechanism. We present a model in which early lg2 function specifies the precise position where ligule and auricle will develop. Later lg2 function interacts with lg1 function (either directly or indirectly) to transmit and receive a make-ligule-make-auricle inductive signal.

Acquisition of identity in the developing leaf

Leaves are produced repeatedly from the shoot apical meristem of plants. Molecular and cellular evidence show that identity of the leaf and its parts is acquired progressively and that the underlying process changes as the leaf matures. The relative importance of cell lineage compared with a position-dependent model for specifying cell fates is discussed.

The maize mutant narrow sheath fails to establish leaf margin identity in a meristematic domain

The maize mutant narrow sheath (ns) displays a leaf shape and plant stature phenotype that suggests the preprimordial deletion of a leaf domain. The ns mutant phenotype is inherited as a recessive, duplicate-factor trait, conditioned upon homozygosity for each of the two unlinked mutations narrow sheath-1 (ns1) and narrow sheath-2 (ns2). Mutant leaves are missing a large domain including the leaf margin, and mutant internodes are shortened on the marginal side of the stem. This domain deletion extends from the internode to beyond the longitudinal mid-length of the blade, and corresponds to an alteration in the organization of a specific region of the shoot apical meristem. The premargin region of mutant founder cells fail to down-regulate expression of Knox genes, markers of nonleaf meristematic identity. Our results indicate that leaf domains may acquire identity in the meristem itself, and that the subdivision of preprimordial developmental fields into differential domains is a common feature of both plant and animal organogenesis.

Mosaic analysis of the liguleless3 mutant phenotype in maize by coordinate suppression of mutator-insertion alleles

Liguleless3-O (Lg3-O) transforms the leaf blade, auricle and ligule into sheath around the midrib region. We conducted a genetic mosaic analysis of the Lg3 phenotype to determine the site of Lg3 gene action. Combining the Mutator (Mu) suppressible Lg3-Or211 and a1-mum2 alleles in a Mu-active background generated a stock wherein somatic loss of Mu activity resulted in anthocyanin-marked clonal sectors expressing Lg3 in the leaf. Lg3-Or211 plants appear wild type in a Mu-active line, but Mu-inactive plants express a severe Lg3 phenotype. We observed four sector classes: wild type, sheath-like with ligule displacement, sheath-like with ectopic ligule, and auricle-like. The mutation does not cause transformation to a specific cell or regional identity. Lg3-Or211 activity in the mesophyll alters wild-type epidermal cell fates; activity in epidermis seems functionless. Lg3 mutant activity has a nonautonomous, cell-layer-specific function in the transverse dimension. In the lateral dimension, sectors of Lg3 mutant phenotype can exhibit either cell-autonomous or nonautonomous effects. Our work demonstrates that mosaic analysis by coordinate suppression of Mu-induced alleles is useful for analyzing the cell autonomy of genetically defined functions.