Biomedical subjects

Richard M Amasino

Publications and source records attributed to Richard M Amasino.

At least 19 recordsLinked to original sources

PubMed2006

The WiscDsLox T-DNA collection: an arabidopsis community resource generated by using an improved high-throughput T-DNA sequencing pipeline.

We have developed a new community resource, called the WiscDsLox collection, for performing reverse-genetic analysis in arabidopsis. This resource is composed of 10,459 T-DNA lines generated using the Arabidopsis thaliana ecotype Columbia. The flanking sequence tag for each T-DNA insertion has been deposited in public databases, and seed for each line is currently available from the Arabidopsis Biological Resource Center. The pDsLox vector used to create this new population contains a Ds transposon and Cre/Lox recombination sites. Each WiscDsLox line therefore has the potential to serve as a launch-pad for performing local saturation mutagenesis by mobilization of the Ds element. In addition, Cre-Lox recombination between the T-DNA and a transposed Ds element should enable targeted deletion of specific genomic regions. We generated the WiscDsLox collection using an improved high-throughput pipeline that streamlines analysis of large numbers of independent Arabidopsis thaliana (L.) Hyenh. lines. In this paper we describe the details of this novel method and also provide potential users of WiscDsLox T-DNA lines with useful background information about this collection. Experiments to characterize the utility of the Ds transposon and Cre/Lox elements present in the WiscDsLox lines are in progress and will be reported in the future.

Arabidopsis↗

PubMed2006

Evolutionary conservation of the FLOWERING LOCUS C-mediated vernalization response: evidence from the sugar beet (Beta vulgaris).

In many plant species, exposure to a prolonged period of cold during the winter promotes flowering in the spring, a process termed vernalization. In Arabidopsis thaliana, the vernalization requirement of winter-annual ecotypes is caused by the MADS-box gene FLOWERING LOCUS C (FLC), which is a repressor of flowering. During the vernalization process, FLC is downregulated by alteration of its chromatin structure, thereby permitting flowering to occur. In wheat, a vernalization requirement is imposed by a different repressor of flowering, suggesting that some components of the regulatory network controlling the vernalization response differ between monocots and dicots. The extent to which the molecular mechanisms underlying vernalization have been conserved during the diversification of the angiosperms is not well understood. Using phylogenetic analysis, we identified homologs of FLC in species representing the three major eudicot lineages. FLC homologs have not previously been documented outside the plant family Brassicaceae. We show that the sugar beet FLC homolog BvFL1 functions as a repressor of flowering in transgenic Arabidopsis and is downregulated in response to cold in sugar beet. Cold-induced downregulation of an FLC-like floral repressor may be a central feature of the vernalization response in at least half of eudicot species.

Arabidopsis↗

PubMed2006

A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis.

The proper timing of flowering is critical for successful reproduction. The perception of the seasonal cues of day-length changes and exposure to cold influences flowering time in many plant species through the photoperiod and vernalization pathways, respectively. Here we show that a plant homeodomain (PHD) finger-containing protein, VIN3-LIKE 1 (VIL1), participates in both the photoperiod and vernalization pathways in Arabidopsis thaliana by regulating expression of the related floral repressors FLOWERING LOCUS C (FLC) and FLOWERING LOCUS M (FLM). In the vernalization pathway, VIL1, along with VERNALIZATION INSENSITIVE 3 (VIN3), is necessary for the modifications to FLC and FLM chromatin that are associated with an epigenetically silenced state and with acquisition of competence to flower. In addition, VIL1 regulates FLM independently of VIN3 in a photoperiod-dependent manner.

Arabidopsis↗

PubMed2006

Molecular genetic studies of the memory of winter.

Many plant species have evolved the ability to flower in the proper season by sensing environmental cues. The prolonged cold of winter is one such cue that certain plants use to acquire competence to flower the following spring. For example, biennials and winter annuals become established in one growing season and often flower quickly in the early spring of the following year to complete their life cycles. The process by which exposure to prolonged cold establishes competence to flower is known as vernalization. Many studies, starting with the classic work of Lang and Melchers, have shown that the vernalized state can be stable; i.e. after exposure to cold has ended, competence to flower, in certain species, can persist for many months and throughout many cell divisions in the shoot apical meristem. Thus, plants can exhibit a 'memory of winter' and vernalization can result in an epigenetic switch in the classic sense of the term: a change that is stable in the absence of the inducing signal. The nature of this epigenetic switch in Arabidopsis thaliana is discussed here.

Amino Acid Sequence↗

PubMed2006

FLOWERING LOCUS C-dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways.

BACKGROUND: The circadian system drives pervasive biological rhythms in plants. Circadian clocks integrate endogenous timing information with environmental signals, in order to match rhythmic outputs to the local day/night cycle. Multiple signaling pathways affect the circadian system, in ways that are likely to be adaptively significant. Our previous studies of natural genetic variation in Arabidopsis thaliana accessions implicated FLOWERING LOCUS C (FLC) as a circadian-clock regulator. The MADS-box transcription factor FLC is best known as a regulator of flowering time. Its activity is regulated by many regulatory genes in the "autonomous" and vernalization-dependent flowering pathways. We tested whether these same pathways affect the circadian system. RESULTS: Genes in the autonomous flowering pathway, including FLC, were found to regulate circadian period in Arabidopsis. The mechanisms involved are similar, but not identical, to the control of flowering time. By mutant analyses, we demonstrate a graded effect of FLC expression upon circadian period. Related MADS-box genes had less effect on clock function. We also reveal an unexpected vernalization-dependent alteration of periodicity. CONCLUSION: This study has aided in the understanding of FLC's role in the clock, as it reveals that the network affecting circadian timing is partially overlapping with the floral-regulatory network. We also show a link between vernalization and circadian period. This finding may be of ecological relevance for developmental programming in other plant species.

Arabidopsis↗

PubMed2006

Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1.

Vernalization is the process by which sensing a prolonged exposure to winter cold leads to competence to flower in the spring. In winter annual Arabidopsis thaliana accessions, flowering is suppressed in the fall by expression of the potent floral repressor FLOWERING LOCUS C (FLC). Vernalization promotes flowering via epigenetic repression of FLC. Repression is accompanied by a series of histone modifications of FLC chromatin that include dimethylation of histone H3 at Lys9 (H3K9) and Lys27 (H3K27). Here, we report that A. thaliana LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is necessary to maintain the epigenetically repressed state of FLC upon return to warm conditions typical of spring. LHP1 is enriched at FLC chromatin after prolonged exposure to cold, and LHP1 activity is needed to maintain the increased levels of H3K9 dimethylation at FLC chromatin that are characteristic of the vernalized state.

Arabidopsis↗

PubMed2006

Defending science education against intelligent design: a call to action.

We review here the current political landscape and our own efforts to address the attempts to undermine science education in Wisconsin. To mount an effective response, expertise in evolutionary biology and in the history of the public controversy is useful but not essential. However, entering the fray requires a minimal tool kit of information. Here, we summarize some of the scientific and legal history of this issue and list a series of actions that scientists can take to help facilitate good science education and an improved atmosphere for the scientific enterprise nationally. Finally, we provide some model legislation that has been introduced in Wisconsin to strengthen the teaching of science.

Animals↗

PubMed2005

FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana.

Studies of natural variation have revealed that the winter-annual habit of many accessions of Arabidopsis is conferred by two genes, FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), whose activities impose a vernalization requirement. To better understand the mechanism underlying the winter-annual habit, a genetic screen was performed to identify mutants that suppress the late-flowering behavior of a non-vernalized winter-annual strain. We have identified a locus, FRIGIDA-ESSENTIAL 1 (FES1), which, like FRI, is specifically required for the upregulation of FLC expression. FES1 is predicted to encode a protein with a CCCH zinc finger, but the predicted sequence does not otherwise share significant similarity with other known proteins. fes1 is a complete suppressor of FRI-mediated delayed flowering, but has little effect on the late-flowering phenotype of autonomous-pathway mutants. Thus, FES1 activity is required for the FRI-mediated winter-annual habit, but not for the similar phenotype resulting from autonomous-pathway mutations. Epistasis analysis between FES1, FRI and another specific suppressor of FRI-containing lines, FRIGIDA-LIKE 1 (FRL1), indicates that these genes do not function in a linear pathway, but instead act cooperatively to promote the expression of FLC.

Amino Acid Sequence↗

PubMed2005

Vernalization and flowering time.

Vernalization is the process by which flowering is promoted by prolonged exposure to the cold of a typical winter. In certain plant species, the role of vernalization is to suppress the expression of genes that encode repressors of flowering. In Arabidopsis, this suppression is an epigenetic phenomenon in the sense that it is mitotically stable in the spring after the inducing signal, cold, is no longer perceived. This epigenetic silencing results from the modification of the chromatin of flowering repressors.

Arabidopsis↗

PubMed2005

Role of chromatin modification in flowering-time control.

The regulation of the FLC locus provides a plant model of how chromatin-modifying systems have emerged as important components in the control of a major developmental switch, the transition to flowering. Genetic and molecular studies have revealed that three systems of FLC regulation (vernalization, FRI and the autonomous pathway) all influence the state of FLC chromatin. Histone H3 trimethylation at lysine 4 and histone acetylation are associated with active FLC expression, whereas histone deacetylation and histone H3 dimethylation at lysines 9 and 27 are involved in FLC repression. These chromatin modifications provide an additional level of regulation of gene expression beyond that of the transcription factors that recruit RNA polymerase to target genes.

Arabidopsis↗

PubMed2005

HUA2 is required for the expression of floral repressors in Arabidopsis thaliana.

The HUA2 gene acts as a repressor of floral transition. Lesions in hua2 were identified through a study of natural variation and through two mutant screens. An allele of HUA2 from Landsberg erecta (Ler) contains a premature stop codon and acts as an enhancer of early flowering 4 (elf4) mutants. hua2 single mutants, in the absence of the elf4 lesion, flower earlier than wild type under short days. hua2 mutations partially suppress late flowering in FRIGIDA (FRI )-containing lines, autonomous pathway mutants, and a photoperiod pathway mutant. hua2 mutations suppress late flowering by reducing the expression of several MADS genes that act as floral repressors including FLOWERING LOCUS C (FLC ) and FLOWERING LOCUS M (FLM ).

Arabidopsis↗

PubMed2005

Senescence-associated vacuoles with intense proteolytic activity develop in leaves of Arabidopsis and soybean.

Vacuolar compartments associated with leaf senescence and the subcellular localization of the senescence-specific cysteine-protease SAG12 (senescence-associated gene 12) were studied using specific fluorescent markers, the expression of reporter genes, and the analysis of high-pressure frozen/freeze-substituted samples. Senescence-associated vacuoles (SAVs) with intense proteolytic activity develop in the peripheral cytoplasm of mesophyll and guard cells in Arabidopsis and soybean. The vacuolar identity of these compartments was confirmed by immunolabeling with specific antibody markers. SAVs and the central vacuole differ in their acidity and tonoplast composition: SAVs are more acidic than the central vacuole and, whereas the tonoplast of central vacuoles is highly enriched in gamma-TIP (tonoplast intrinsic protein), the tonoplast of SAVs lacks this aquaporin. The expression of a SAG12-GFP fusion protein in transgenic Arabidopsis plants shows that SAG12 localizes to SAVs. The analysis of Pro(SAG12):GUS transgenic plants indicates that SAG12 expression in senescing leaves is restricted to SAV-containing cells, for example, mesophyll and guard cells. A homozygous sag12 Arabidopsis mutant develops SAVs and does not show any visually detectable phenotypical alteration during senescence, indicating that SAG12 is not required either for SAV formation or for progression of visual symptoms of senescence. The presence of two types of vacuoles in senescing leaves could provide different lytic compartments for the dismantling of specific cellular components. The possible origin and functions of SAVs during leaf senescence are discussed.

Arabidopsis↗

PubMed2005

Remembering winter: toward a molecular understanding of vernalization.

Exposure to the prolonged cold of winter is an important environmental cue that favors flowering in the spring in many types of plants. The process by which exposure to cold promotes flowering is known as vernalization. In Arabidopsis and certain cereals, the block to flowering in plants that have not been vernalized is due to the expression of flowering repressors. The promotion of flowering is due to the cold-mediated suppression of these repressors. Recent work has demonstrated that covalent modifications of histones in the chromatin of target loci are part of the molecular mechanism by which certain repressors are silenced during vernalization.

Adaptation, Physiological↗

PubMed2004

Integration of flowering signals in winter-annual Arabidopsis.

Photoperiod is the primary environmental factor affecting flowering time in rapid-cycling accessions of Arabidopsis (Arabidopsis thaliana). Winter-annual Arabidopsis, in contrast, have both a photoperiod and a vernalization requirement for rapid flowering. In winter annuals, high levels of the floral inhibitor FLC (FLOWERING LOCUS C) suppress flowering prior to vernalization. FLC acts to delay flowering, in part, by suppressing expression of the floral promoter SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1). Vernalization leads to a permanent epigenetic suppression of FLC. To investigate how winter-annual accessions integrate signals from the photoperiod and vernalization pathways, we have examined activation-tagged alleles of FT and the FT homolog, TSF (TWIN SISTER OF FT), in a winter-annual background. Activation of FT or TSF strongly suppresses the FLC-mediated late-flowering phenotype of winter annuals; however, FT and TSF overexpression does not affect FLC mRNA levels. Rather, FT and TSF bypass the block to flowering created by FLC by activating SOC1 expression. We have also found that FLC acts as a dosage-dependent inhibitor of FT expression. Thus, the integration of flowering signals from the photoperiod and vernalization pathways occurs, at least in part, through the regulation of FT, TSF, and SOC1.

Arabidopsis↗

PubMed2004

PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis.

The winter-annual habit (which typically involves a requirement for exposure to the cold of winter to flower in the spring) in Arabidopsis thaliana is mainly due to the repression of flowering by relatively high levels of FLC expression. Exposure to prolonged cold attenuates FLC expression through a process known as vernalization and thus permits flowering to occur in the spring. Here we show that the elevated FLC expression characteristic of nonvernalized winter annuals requires two genes, EARLY FLOWERING 7 (ELF7) and EARLY FLOWERING 8 (ELF8), that are homologs of components of the PAF1 complex of Saccharomyces cerevisiae. Furthermore, ELF7 and ELF8 are also required for the expression of other genes in the FLC clade of flowering repressors such as MAF2 and FLM. FLC, FLM, and MAF2 are involved in multiple flowering pathways that account for the broad effects of elf7 and elf8 mutations on flowering behavior. ELF7 and ELF8 are required for the enhancement of histone 3 trimethylation at Lys 4 in FLC chromatin. This modification of FLC chromatin appears to be required to elevate FLC expression to levels that can delay flowering in plants that have not been vernalized. A model of the role of ELF7, ELF8, and other previously described genes in the modification of the chromatin of flowering repressors is presented.

Acclimatization↗

PubMed2004

Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time.

Flowering in Arabidopsis thaliana is controlled by multiple pathways, including the photoperiod pathway and the FLOWERING LOCUS C (FLC)-dependent pathway. Here, we report that a pair of related jumonji-class transcription factors, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play divergent roles in the regulation of Arabidopsis flowering. ELF6 acts as a repressor in the photoperiod pathway, whereas REF6, which has the highest similarity to ELF6, is an FLC repressor. Ectopic expression studies and expression pattern analyses show that ELF6 and REF6 have different cellular roles and are also regulated differentially despite their sequence similarities. Repression of FLC expression by REF6 accompanies histone modifications in FLC chromatin, indicating that the transcriptional regulatory activity of this class of proteins includes chromatin remodeling. This report demonstrates the in vivo functions of this class of proteins in higher eukaryotes.

Amino Acid Sequence↗

PubMed2004

FRIGIDA-related genes are required for the winter-annual habit in Arabidopsis.

In temperate climates, the prolonged cold temperature of winter serves as a seasonal landmark for winter-annual and biennial plants. In these plants, flowering is blocked before winter. In Arabidopsis thaliana, natural variation in the FRIGIDA (FRI) gene is a major determinate of the rapid-cycling vs. winter-annual flowering habits. In winter-annual accessions of Arabidopsis, FRI activity blocks flowering through the up-regulation of the floral inhibitor FLOWERING LOCUS C (FLC). Most rapid-flowering accessions, in contrast, contain null alleles of FRI. By performing a mutant screen in a winter-annual strain, we have identified a locus, FRIGIDA LIKE 1 (FRL1), that is specifically required for the up-regulation of FLC by FRI. Cloning of FRL1 revealed a gene with a predicted protein sequence that is 23% identical to FRI. Despite sequence similarity, FRI and FRL1 do not have redundant functions. FRI and FRL1 belong to a seven-member gene family in Arabidopsis, and FRI, FRL1, and at least one additional family member, FRIGIDA LIKE 2 (FRL2), are in a clade of this family that is required for the winter-annual habit in Arabidopsis.

Amino Acid Sequence↗

PubMed2004

Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3.

In biennials and winter annuals, flowering is typically blocked in the first growing season. Exposure to the prolonged cold of winter, through a process called vernalization, is required to alleviate this block and permit flowering in the second growing season. In winter-annual types of Arabidopsis thaliana, a flowering repressor, FLOWERING LOCUS C (FLC), is expressed at levels that inhibit flowering in the first growing season. Vernalization promotes flowering by causing a repression of FLC that is mitotically stable after return to warm growing conditions. Here we identify a gene with a function in the measurement of the duration of cold exposure and in the establishment of the vernalized state. We show that this silencing involves changes in the modification of histones in FLC chromatin.

Acetylation↗