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Converting genetic network oscillations into somite spatial pattern  [PDF]
K. I. Mazzitello,C. M. Arizmendi,H. G. E. Hentschel
Quantitative Biology , 2007, DOI: 10.1103/PhysRevE.78.021906
Abstract: In most vertebrate species, the body axis is generated by the formation of repeated transient structures called somites. This spatial periodicity in somitogenesis has been related to the temporally sustained oscillations in certain mRNAs and their associated gene products in the cells forming the presomatic mesoderm. The mechanism underlying these oscillations have been identified as due to the delays involved in the synthesis of mRNA and translation into protein molecules [J. Lewis, Current Biol. {\bf 13}, 1398 (2003)]. In addition, in the zebrafish embryo intercellular Notch signalling couples these oscillators and a longitudinal positional information signal in the form of an Fgf8 gradient exists that could be used to transform these coupled temporal oscillations into the observed spatial periodicity of somites. Here we consider a simple model based on this known biology and study its consequences for somitogenesis. Comparison is made with the known properties of somite formation in the zebrafish embryo . We also study the effects of localized Fgf8 perturbations on somite patterning.
The Transcriptional Regulator CzcR Modulates Antibiotic Resistance and Quorum Sensing in Pseudomonas aeruginosa  [PDF]
Guenna?lle Dieppois, Véréna Ducret, Olivier Caille, Karl Perron
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038148
Abstract: The opportunistic pathogen Pseudomonas aeruginosa responds to zinc, cadmium and cobalt by way of the CzcRS two-component system. In presence of these metals the regulatory protein CzcR induces the expression of the CzcCBA efflux pump, expelling and thereby inducing resistance to Zn, Cd and Co. Importantly, CzcR co-regulates carbapenem antibiotic resistance by repressing the expression of the OprD porin, the route of entry for these antibiotics. This unexpected co-regulation led us to address the role of CzcR in other cellular processes unrelated to the metal response. We found that CzcR affected the expression of numerous genes directly involved in the virulence of P. aeruginosa even in the absence of the inducible metals. Notably the full expression of quorum sensing 3-oxo-C12-HSL and C4-HSL autoinducer molecules is impaired in the absence of CzcR. In agreement with this, the virulence of the czcRS deletion mutant is affected in a C. elegans animal killing assay. Additionally, chromosome immunoprecipitation experiments allowed us to localize CzcR on the promoter of several regulated genes, suggesting a direct control of target genes such as oprD, phzA1 and lasI. All together our data identify CzcR as a novel regulator involved in the control of several key genes for P. aeruginosa virulence processes.
The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor Morphogenesis  [PDF]
Mark M. Slabodnick ,J. Graham Ruby,Joshua G. Dunn,Jessica L. Feldman,Joseph L. DeRisi,Wallace F. Marshall
PLOS Biology , 2014, DOI: 10.1371/journal.pbio.1001861
Abstract: Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular. But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown. Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus. Here we show that the RNA interference (RNAi) machinery is conserved in Stentor. Using RNAi, we identify the kinase coactivator Mob1—with conserved functions in cell division and morphogenesis from plants to humans—as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor. Our studies reopen the door for Stentor as a model regeneration system.
Notch Signalling Synchronizes the Zebrafish Segmentation Clock but Is Not Needed To Create Somite Boundaries  [PDF]
Ertu?rul M ?zbudak,Julian Lewis
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.0040015
Abstract: Somite segmentation depends on a gene expression oscillator or clock in the posterior presomitic mesoderm (PSM) and on read-out machinery in the anterior PSM to convert the pattern of clock phases into a somite pattern. Notch pathway mutations disrupt somitogenesis, and previous studies have suggested that Notch signalling is required both for the oscillations and for the read-out mechanism. By blocking or overactivating the Notch pathway abruptly at different times, we show that Notch signalling has no essential function in the anterior PSM and is required only in the posterior PSM, where it keeps the oscillations of neighbouring cells synchronized. Using a GFP reporter for the oscillator gene her1, we measure the influence of Notch signalling on her1 expression and show by mathematical modelling that this is sufficient for synchronization. Our model, in which intracellular oscillations are generated by delayed autoinhibition of her1 and her7 and synchronized by Notch signalling, explains the observations fully, showing that there are no grounds to invoke any additional role for the Notch pathway in the patterning of somite boundaries in zebrafish.
Molecular Mechanism of Somite Development  [cached]
Gulfidan Coskun,Hulya Ozgur,Sait Polat
Arsiv Kaynak Tarama Dergisi , 2013,
Abstract: From third week of gestation, notochord and the neural folds begin to gather at the center of the embryo to form the paraxial mesoderm. Paraxial mesoderm separates into blocks of cells called somitomers at the lateral sides of the neural tube of the head region. At the beginning of the third week somitomeres take ring shapes and form blocks of somites from occipital region to caudal region. Although somites are transient structures, they are extremely important in organizing the segmental pattern of vertebrate embryos. Somites give rise to the cells that form the vertebrae and ribs, the dermis of the dorsal skin, the skeletal muscles of the back, and the skeletal muscles of the body wall and limbs. Somitogenesis are formed by a genetic mechanism that is regulated by cyclical expression of genes in the Notch, Wnt and fibroblast growth factor signaling pathways. The prevailing model of the mechanism governing somitogenesis is the clock and wave front . Somitogenesis has components of periodicity, separation, epithelialization and axial specification. According to this model, the clock causes cells to undergo repeated oscillations, with a particular phase of each oscillation defining the competency of cells in the presomitic mesoderm to form a somite. Any disruption in this mechanism can be cause of severe segmentation defects of the vertebrae and congenital anomalies. In this review, we discuss the molecular mechanisms underlying the somitogenesis which is an important part of morphogenesis. [Archives Medical Review Journal 2013; 22(3.000): 362-376]
Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation
Daniel ST Hughes, Roger J Keynes, David Tannahill
BMC Developmental Biology , 2009, DOI: 10.1186/1471-213x-9-30
Abstract: Several hundred genes are differentially-expressed between the two sclerotome halves, showing that a marked degree of molecular heterogeneity underpins the development of somite polarity.We have identified a set of genes that warrant further investigation as regulators of somite polarity and vertebral morphogenesis, as well as repellents of spinal axon growth. Moreover the results indicate that, unlike the posterior half-sclerotome, the central region of the anterior-half-sclerotome does not contribute bone and cartilage to the vertebral column, being associated instead with the development of the segmented spinal nerves.The subdivision of embryonic tissues into serial repeat-units, or segments, is a fundamental patterning process in early vertebrate development, and is most prominent in the formation of the mesodermal somites. Somites arise as paired epithelial spheres that bud off from the undifferentiated paraxial mesoderm (presomite mesoderm, PSM) flanking the notochord, and subsequently give rise to several tissues including the segmented axial skeleton and epaxial musculature of the adult organism [1,2].The formation and development of somites involves the superposition of two orthogonal patterning systems acting within the paraxial mesoderm. The first operates along the anterior-posterior (A-P) axis and is intrinsic to the paraxial mesoderm, resulting in individuation of the somites and their concomitant polarization into anterior and posterior halves (Figure 1). Somite formation is dependent on a molecular 'clock' within the PSM that generates periodic expression of genes including the notch, wnt and fibroblast growth factor (FGF) signalling pathways [3-5]. These cyclical gene expression patterns are superimposed on a regressing, longitudinal gradient of FGF expression along the A-P axis that results in the co-ordinated maturation of groups of PSM cells into each successive somite. Somite polarity is determined within the anterior PSM by a complex feedback m
A Dynamic Response Regulator Protein Modulates G-Protein–Dependent Polarity in the Bacterium Myxococcus xanthus  [PDF]
Yong Zhang,Mathilde Guzzo,Adrien Ducret,Yue-Zhong Li,Tam Mignot
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002872
Abstract: Migrating cells employ sophisticated signal transduction systems to respond to their environment and polarize towards attractant sources. Bacterial cells also regulate their polarity dynamically to reverse their direction of movement. In Myxococcus xanthus, a GTP-bound Ras-like G-protein, MglA, activates the motility machineries at the leading cell pole. Reversals are provoked by pole-to-pole switching of MglA, which is under the control of a chemosensory-like signal transduction cascade (Frz). It was previously known that the asymmetric localization of MglA at one cell pole is regulated by MglB, a GTPase Activating Protein (GAP). In this process, MglB specifically localizes at the opposite lagging cell pole and blocks MglA localization at that pole. However, how MglA is targeted to the leading pole and how Frz activity switches the localizations of MglA and MglB synchronously remained unknown. Here, we show that MglA requires RomR, a previously known response regulator protein, to localize to the leading cell pole efficiently. Specifically, RomR-MglA and RomR-MglB complexes are formed and act complementarily to establish the polarity axis, segregating MglA and MglB to opposite cell poles. Finally, we present evidence that Frz signaling may regulate MglA localization through RomR, suggesting that RomR constitutes a link between the Frz-signaling and MglAB polarity modules. Thus, in Myxococcus xanthus, a response regulator protein governs the localization of a small G-protein, adding further insight to the polarization mechanism and suggesting that motility regulation evolved by recruiting and combining existing signaling modules of diverse origins.
Def6 Is Required for Convergent Extension Movements during Zebrafish Gastrulation Downstream of Wnt5b Signaling  [PDF]
Katerina Goudevenou, Paul Martin, Yu-Jung Yeh, Peter Jones, Fred Sablitzky
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026548
Abstract: During gastrulation, convergent extension (CE) cell movements are regulated through the non-canonical Wnt signaling pathway. Wnt signaling results in downstream activation of Rho GTPases that in turn regulate actin cytoskeleton rearrangements essential for co-ordinated CE cell movement. Rho GTPases are bi-molecular switches that are inactive in their GDP-bound stage but can be activated to bind GTP through guanine nucleotide exchange factors (GEFs). Here we show that def6, a novel GEF, regulates CE cell movement during zebrafish gastrulation. Def6 morphants exhibit broadened and shortened body axis with normal cell fate specification, reminiscent of the zebrafish mutants silberblick and pipetail that lack Wnt11 or Wnt5b, respectively. Indeed, def6 morphants phenocopy Wnt5b mutants and ectopic overexpression of def6 essentially rescues Wnt5b morphants, indicating a novel role for def6 as a central GEF downstream of Wnt5b signaling. In addition, by knocking down both def6 and Wnt11, we show that def6 synergises with the Wnt11 signaling pathway.
Analysis of her1 and her7 Mutants Reveals a Spatio Temporal Separation of the Somite Clock Module  [PDF]
Suma Choorapoikayil, Bernd Willems, Peter Str?hle, Martin Gajewski
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039073
Abstract: Somitogenesis is controlled by a genetic network consisting of an oscillator (clock) and a gradient (wavefront). The “hairy and Enhancer of Split”- related (her) genes act downstream of the Delta/Notch (D/N) signaling pathway, and are crucial components of the segmentation clock. Due to genome duplication events, the zebrafish genome, possesses two gene copies of the mouse Hes7 homologue: her1 and her7. To better understand the functional consequences of this gene duplication, and to determine possible independent roles for these two genes during segmentation, two zebrafish mutants her1hu2124 and her7hu2526 were analyzed. In the course of embryonic development, her1hu2124 mutants exhibit disruption of the three anterior-most somite borders, whereas her7hu2526 mutants display somite border defects restricted to somites 8 (+/?3) to 17 (+/?3) along the anterior-posterior axis. Analysis of the molecular defects in her1hu2124 mutants reveals a her1 auto regulatory feedback loop during early somitogenesis that is crucial for correct patterning and independent of her7 oscillation. This feedback loop appears to be restricted to early segmentation, as cyclic her1 expression is restored in her1hu2124 embryos at later stages of development. Moreover, only the anterior deltaC expression pattern is disrupted in the presomitic mesoderm of her1hu2124 mutants, while the posterior expression pattern of deltaC remains unaltered. Together, this data indicates the existence of an independent and genetically separable anterior and posterior deltaC clock modules in the presomitic mesdorm (PSM).
Regulation of Hoxb4 induction after neurulation by somite signal and neural competence
Gayana S Amirthalingam, Sara Howard, Susana Alvarez, Angel R de Lera, Nobue Itasaki
BMC Developmental Biology , 2009, DOI: 10.1186/1471-213x-9-17
Abstract: We show that somites are required for the up-regulation of Hoxb4 in the neural tube at the level of somites 1 to 5, the anterior-most domain of expression. However, each somite immediately adjacent to the neural tube is not sufficient at each level; planar signaling is additionally required particularly at the anterior-most segments of the expression domain. We also show that the dorsal side of the neural tube has a greater susceptibility to expressing Hoxb4 than the ventral region, a feature associated with dorsalization of the neural tube by BMP signals. BMP4 is additionally able to up-regulate Hoxb4 ventrally, but the effect is restricted to the axial levels at which Hoxb4 is normally expressed, and only in the presence of retinoic acid (RA) or somites, suggesting a role for BMP in rendering the neural tube competent to express Hoxb4 in response to RA or somite signals.In identifying the collaboration between somites and neural tube competence in the induction of Hoxb4, this study demonstrates interplay between A-P and dorsal-ventral (D-V) patterning systems, whereby a specific feature of D-V polarity may be a prerequisite for proper A-P patterning by Hox genes.The anterior-posterior (A-P) identity of the body axis at the level of the hindbrain and the spinal cord is largely dependent upon the regulated expression of Hox gene clusters [1,2]. At early embryogenesis, Hox genes are up-regulated sequentially in the epiblast and establish their ordered expression patterns along the A-P axis [3,4]. They also play an instructive role in distributing cells in an ordered manner along the A-P axis during ingression of epiblast cells [5]. As a consequence, Hox gene expression exhibits nested patterns in the paraxial mesoderm as well as in the neuroepithelium. One unique feature of conferring A-P identity by Hox genes is that these nested expression patterns display sharp anterior boundaries, creating codes of expression along the A-P axis [6,7]. For example, expression of p
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