Max Planck Institute for Developmental Biology

Tubingen, Germany

Max Planck Institute for Developmental Biology

Tubingen, Germany

The Max Planck Institute for Developmental Biology is located in Tübingen, Germany; it was founded in 1954 as an offshoot of the Tübingen-based Max Planck Institute for Biology. The main topics of scientific research conducted by the Max Planck Institute for Developmental Biology focus on the molecular mechanisms underlying spatial information within the embryo, communication between cells in the induction process, as well as the formation and differentiation of tissues and organs. Wikipedia.

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Jekely G.,Max Planck Institute for Developmental Biology
Cold Spring Harbor Perspectives in Biology | Year: 2014

The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing "active gel, " the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming. © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Todesco M.,Max Planck Institute for Developmental Biology
PLoS genetics | Year: 2010

Many targets of plant microRNAs (miRNAs) are thought to play important roles in plant physiology and development. However, because plant miRNAs are typically encoded by medium-size gene families, it has often been difficult to assess their precise function. We report the generation of a large-scale collection of knockdowns for Arabidopsis thaliana miRNA families; this has been achieved using artificial miRNA target mimics, a recently developed technique fashioned on an endogenous mechanism of miRNA regulation. Morphological defects in the aerial part were observed for approximately 20% of analyzed families, all of which are deeply conserved in land plants. In addition, we find that non-cleavable mimic sites can confer translational regulation in cis. Phenotypes of plants expressing target mimics directed against miRNAs involved in development were in several cases consistent with previous reports on plants expressing miRNA-resistant forms of individual target genes, indicating that a limited number of targets mediates most effects of these miRNAs. That less conserved miRNAs rarely had obvious effects on plant morphology suggests that most of them do not affect fundamental aspects of development. In addition to insight into modes of miRNA action, this study provides an important resource for the study of miRNA function in plants.

Sommer R.J.,Max Planck Institute for Developmental Biology | Streit A.,Max Planck Institute for Developmental Biology
Annual Review of Genetics | Year: 2011

Nematodes are found in virtually all habitats on earth. Many of them are parasites of plants and animals, including humans. The free-living nematode, Caenorhabditis elegans, is one of the genetically best-studied model organisms and was the first metazoan whose genome was fully sequenced. In recent years, the draft genome sequences of another six nematodes representing four of the five major clades of nematodes were published. Compared to mammalian genomes, all these genomes are very small. Nevertheless, they contain almost the same number of genes as the human genome. Nematodes are therefore a very attractive system for comparative genetic and genomic studies, with C. elegans as an excellent baseline. Here, we review the efforts that were made to extend genetic analysis to nematodes other than C. elegans, and we compare the seven available nematode genomes. One of the most striking findings is the unexpectedly high incidence of gene acquisition through horizontal gene transfer (HGT). © 2011 by Annual Reviews. All rights reserved.

Jekely G.,Max Planck Institute for Developmental Biology
Proceedings of the Royal Society B: Biological Sciences | Year: 2011

Behaviour evolved before nervous systems. Various single-celled eukaryotes (protists) and the ciliated larvae of sponges devoid of neurons can display sophisticated behaviours, including phototaxis, gravitaxis or chemotaxis. In single-celled eukaryotes, sensory inputs directly influence the motor behaviour of the cell. In swimming sponge larvae, sensory cells influence the activity of cilia on the same cell, thereby steering the multicellular larva. In these organisms, the efficiency of sensory-to-motor transformation (defined as the ratio of sensory cells to total cell number) is low. With the advent of neurons, signal amplification and fast, long-range communication between sensory and motor cells became possible. This may have first occurred in a ciliated swimming stage of the first eumetazoans. The first axons may have had en passant synaptic contacts to several ciliated cells to improve the efficiency of sensory-to-motor transformation, thereby allowing a reduction in the number of sensory cells tuned for the same input. This could have allowed the diversification of sensory modalities and of the behavioural repertoire. I propose that the first nervous systems consisted of combined sensory-motor neurons, directly translating sensory input into motor output on locomotor ciliated cells and steering muscle cells. Neuronal circuitry with low levels of integration has been retained in cnidarians and in the ciliated larvae of some marine invertebrates. This parallel processing stage could have been the starting point for the evolution of more integrated circuits performing the first complex computations such as persistence or coincidence detection. The sensory-motor nervous systems of cnidarians and ciliated larvae of diverse phyla show that brains, like all biological structures, are not irreducibly complex. © 2010 The Royal Society.

Zeth K.,Max Planck Institute for Developmental Biology
Biochimica et Biophysica Acta - Bioenergetics | Year: 2010

Gram-negative bacteria are the ancestors of mitochondrial organelles. Consequently, both entities contain two surrounding lipid bilayers known as the inner and outer membranes. While protein synthesis in bacteria is accomplished in the cytoplasm, mitochondria import 90-99% of their protein ensemble from the cytosol in the opposite direction. Three protein families including Sam50, VDAC and Tom40 together with Mdm10 compose the set of integral β-barrel proteins embedded in the mitochondrial outer membrane in S. cerevisiae (MOM). The 16-stranded Sam50 protein forms part of the sorting and assembly machinery (SAM) and shows a clear evolutionary relationship to members of the bacterial Omp85 family. By contrast, the evolution of VDAC and Tom40, both adopting the same fold cannot be traced to any bacterial precursor. This finding is in agreement with the specific function of Tom40 in the TOM complex not existent in the enslaved bacterial precursor cell. Models of Tom40 and Sam50 have been developed using X-ray structures of related proteins. These models are analyzed with respect to properties such as conservation and charge distribution yielding features related to their individual functions. © 2010 Elsevier B.V.

Igreja C.,Max Planck Institute for Developmental Biology | Izaurralde E.,Max Planck Institute for Developmental Biology
Genes and Development | Year: 2011

CUP is an eIF4E-binding protein (4E-BP) that represses the expression of specific maternal mRNAs prior to theirposterior localization. Here, we show that CUP employs multiple mechanisms to repress the expression of targetmRNAs. In addition to inducing translational repression, CUP maintains mRNA targets in a repressed stateby promoting their deadenylation and protects deadenylated mRNAs from further degradation. Translationalrepression and deadenylation are independent of eIF4E binding and require both the middle and C-terminal regionsof CUP, which collectively we termed the effector domain. This domain associates with the deadenylase complex CAF1-CCR4-NOT and decapping activators. Accordingly, in isolation, the effector domain is a potent trigger ofmRNA degradation and promotes deadenylation, decapping and decay. However, in the context of the full-lengthCUP protein, the decapping and decay mediated by the effector domain are inhibited, and target mRNAs aremaintained in a deadenylated, repressed form. Remarkably, an N-terminal regulatory domain containing a noncanonicaleIF4E-binding motif is required to protect CUP-associated mRNAs from decapping and furtherdegradation, suggesting that this domain counteracts the activity of the effector domain. Our findings indicate thatthe mode of action of CUP is more complex than previously thought and provide mechanistic insight into theregulation of mRNA expression by 4E-BPs. © 2011 by Cold Spring Harbor Laboratory Press.

Neher R.A.,Max Planck Institute for Developmental Biology
Annual Review of Ecology, Evolution, and Systematics | Year: 2013

To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetics inferences are based on frameworks assuming that adaptive evolution is rare. But if positive selection operates on many loci simultaneously, as has recently been suggested for many species, including animals such as flies, then a different approach is necessary. In this review, I discuss recent progress in characterizing and understanding evolution in rapidly adapting populations, in which random associations of mutations with genetic backgrounds of different fitness, i.e., genetic draft, dominate over genetic drift. As a result, neutral genetic diversity depends weakly on population size but strongly on the rate of adaptation or more generally the variance in fitness. Coalescent processes with multiple mergers, rather than Kingman's coalescent, are appropriate genealogical models for rapidly adapting populations, with important implications for population genetics inference. © Copyright ©2013 by Annual Reviews. All rights reserved.

Hocker B.,Max Planck Institute for Developmental Biology
Current Opinion in Structural Biology | Year: 2014

Nature has generated an impressive set of proteins with diverse folds and functions. It has been able to do so using mechanisms such as duplication and fusion as well as recombination of smaller protein fragments that serve as building blocks. These evolutionary mechanisms provide a template for the rational design of new proteins from fragments of existing proteins. Design by duplication and fusion has been explored for a number of symmetric protein folds, while design by rational recombination has just emerged. First experiments in recombining fragments from the same and different folds are proving successful in building new proteins that harbor easily evolvable properties originating from the parents. Overall, duplication and recombination of smaller fragments shows much potential for future applications in the design of proteins. © 2014 Elsevier Ltd.

Jonas S.,Max Planck Institute for Developmental Biology | Izaurralde E.,Max Planck Institute for Developmental Biology
Nature Reviews Genetics | Year: 2015

MicroRNAs (miRNAs) are a conserved class of small non-coding RNAs that assemble with Argonaute proteins into miRNA-induced silencing complexes (miRISCs) to direct post-transcriptional silencing of complementary mRNA targets. Silencing is accomplished through a combination of translational repression and mRNA destabilization, with the latter contributing to most of the steady-state repression in animal cell cultures. Degradation of the mRNA target is initiated by deadenylation, which is followed by decapping and 5′-to-3′ exonucleolytic decay. Recent work has enhanced our understanding of the mechanisms of silencing, making it possible to describe in molecular terms a continuum of direct interactions from miRNA target recognition to mRNA deadenylation, decapping and 5′-to-3′ degradation. Furthermore, an intricate interplay between translational repression and mRNA degradation is emerging. © 2015 Macmillan Publishers Limited. All rights reserved.

Jonas S.,Max Planck Institute for Developmental Biology | Izaurralde E.,Max Planck Institute for Developmental Biology
Genes and Development | Year: 2013

The removal of the 5′ cap structure by the decapping enzyme DCP2 inhibits translation and generally commits the mRNA to irreversible 5′-to-3′ exonucleolytic degradation by XRN1. DCP2 catalytic activity is stimulated by DCP1, and these proteins form the conserved core of the decapping complex. Additional decapping factors orchestrate the recruitment and activity of this complex in vivo. These factors include enhancer of decapping 3 (EDC3), EDC4, like Sm14A (LSm14A), Pat, the LSm1-7 complex, and the RNA helicase DDX6. Decapping factors are often modular and feature folded domains flanked or connected by low-complexity disordered regions. Recent studies have made important advances in understanding how these disordered regions contribute to the assembly of decapping complexes and promote phase transitions that drive RNP granule formation. These studies have also revealed that the decapping network is governed by interactions mediated by short linear motifs (SLiMs) in these disordered regions. Consequently, the network has rapidly evolved, and although decapping factors are conserved, individual interactions between orthologs have been rewired during evolution. The plasticity of the network facilitates the acquisition of additional subunits or domains in pre-existing subunits, enhances opportunities for regulating mRNA degradation, and eventually leads to the emergence of novel functions. © 2013 Jonas and Izaurralde.

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