Detlef Weigel

Bio: Detlef Weigel is an academic researcher from Max Planck Society. The author has contributed to research in topics: Arabidopsis & Arabidopsis thaliana. The author has an hindex of 142, co-authored 516 publications receiving 84670 citations. Previous affiliations of Detlef Weigel include Ludwig Maximilian University of Munich & California Institute of Technology.

Independent Regulation of Flowering by Phytochrome B and Gibberellins in Arabidopsis

Abstract: Phytochromes and gibberellins (GAs) coordinately regulate multiple aspects of Arabidopsis development. Phytochrome B (PHYB) promotes seed germination by increasing GA biosynthesis, but inhibits hypocotyl elongation by decreasing the responsiveness to GAs. Later in the life cycle of the plant, PHYB and GAs have opposite effects on flowering. PHYB delays flowering, while GAs promote flowering, particularly under noninductive photoperiods. To learn how PHYB and GAs interact in the control of flowering, we have analyzed the effect of a phyB mutation on flowering time and on the expression of the floral meristem-identity gene LFY (LEAFY). We show that the early flowering caused by phyB correlated with an increase in LFY expression, which complements our previous finding that GAs are required for activation of LFY under noninductive photoperiods (M.A. Blazquez, R. Green, O. Nilsson, M.R. Sussman, D. Weigel [1998] Plant Cell 10: 791-800). Since phyB did not change the GA responsiveness of the LFY promoter and suppressed the lack of flowering of severe GA-deficient mutants under short days, we propose that PHYB modulates flowering time at least partially through a GA-independent pathway. Interestingly, the effects of PHYB on flowering do not seem to be mediated by transcriptional up-regulation of genes such as CO (CONSTANS) and FT (Flowering locus T), which are known to mediate the effects of the photoperiod-dependent floral-induction pathway.

NFL1, a Nicotiana tabacum LEAFY-like gene, controls meristem initiation and floral structure.

Abstract: The Arabidopsis LEAFY (LFY) gene product induces cells of the shoot apical meristem to differentiate into floral primordia by acting as a master regulator of downstream floral homeotic genes. Tobacco, an allotetraploid, possesses two homologous genes, NFL1 and NFL2, which are 97% identical in amino acid sequence and share 73% amino acid sequence identity with LFY. In order to test whether the highly conserved tobacco orthologue, NFL1, shares functional identity with LFY, we created transgenic tobacco and Arabidopsis plants that constitutively express the NFL1 cDNA. Our results indicate that NFL1 plays a critical role in the allocation of meristematic cells that differentiate lateral structures such as leaves and branches, thereby determining the architecture of the wild-type tobacco shoot. NFL1 also regulates floral meristem development and does so through the control of cell proliferation as well as cell identity. Surprisingly, unlike ectopic LFY expression, which can act as a floral trigger, ectopic NFL1 expression does not promote severe precocious flowering in Nicotiana tabacum suggesting that variations in amino acid sequence among members of the LFY-like gene family have led to divergence in the functional roles of these genes.

MIGS: miRNA-induced gene silencing.

Abstract: Gene silencing is an important tool in the study of gene function. Virus-induced gene silencing (VIGS) and hairpin RNA interference (hpRNAi), both of which rely on small interfering RNAs, together with artificial microRNAs (amiRNA), are amongst the most popular methods for reduction of gene activity in plants. However, all three approaches have limitations. Here, we introduce miRNA-induced gene silencing (MIGS). This method exploits a special 22-nucleotide miRNA of Arabidopsis thaliana, miR173, which can trigger production of another class of small RNAs called trans-acting small interfering RNAs (tasiRNAs). We show that fusion of gene fragments to an upstream miR173 target site is sufficient for effective silencing of the corresponding endogenous gene. MIGS can be reliably used for the knockdown of a single gene or of multiple unrelated genes. In addition, we show that MIGS can be applied to other species by co-expression of miR173.

Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box Gene AGAMOUS-LIKE6.

Abstract: MADS-domain transcription factors play pivotal roles in various developmental processes. The lack of simple loss-of-function phenotypes provides impediments to understand the biological function of some of the MADS-box transcription factors. Here we have characterized the potential role of the Arabidopsis thaliana AGAMOUS-LIKE6 (AGL6) gene by fusing full-length coding sequence with transcriptional activator and repressor domains and suggest a role for AGL6 in lateral organ development and flowering. Upon photoperiodic induction of flowering, AGL6 becomes expressed in abaxial and proximal regions of cauline leaf primordia, as well as the cryptic bracts subtending flowers. In developing flowers, AGL6 is detected in the proximal regions of all floral organs and in developing ovules. Converting AGL6 into a strong activator through fusion to the VP16 domain triggers bract outgrowth, implicating AGL6 in the development of bractless flowers in Arabidopsis. In addition, ectopic reproductive structures form on both bracts and flowers in gAGL6::VP16 transgenic plants, which is dependent on B and C class homeotic genes, but independent of LEAFY. Overexpression of both AGL6 and its transcriptional repressor form, AGL6::EAR, causes precocious flowering and terminal flower formation, suggesting that AGL6 suppresses the function of a floral repressor.

Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression

Abstract: Flowers develop from floral meristems, which harbor stem cells that support the growth of floral organs. The MADS domain transcription factor AGAMOUS (AG) plays a central role in floral patterning and is required not only for the specification of the two reproductive organ types, but also for termination of stem cell fate. Using a highly conserved cis-regulatory motif as bait, we identified the bZIP transcription factor PERIANTHIA (PAN) as a direct regulator of AG in Arabidopsis. PAN and AG expression domains overlap, and mutations in either the PAN-binding site or PAN itself abolish the activity of a reporter devoid of redundant elements. Whereas under long-day conditions pan mutants have merely altered floral organ number, they display in addition typical AG loss-of-function phenotypes when grown under short days. Consistently, we found reduced AG RNA levels in these flowers. Finally, we show that PAN expression persists in ag mutant flowers, suggesting that PAN and AG are engaged in a negative-feedback loop, which might be mediated by the stem-cell-inducing transcription factor WUSCHEL (WUS).

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Human biochemical genetics

Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

Abstract: The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.