The HOG Pathway Dictates the Short-Term Translational Response after Hyperosmotic Shock

In the global osmoshock translational response in yeast, some gene products were translationally mobilized without transcriptional up-regulation. Conversely, other transcriptionally up-regulated mRNAs were translationally inhibited. Analogous changes occurred on the protein level. These translational responses were strongly dependent on Hog1 and Rck2

Systems and synthetic biology studies in Saccharomyces cerevisiae

A fundamental property of living cells is the ability to sense and respond appropriately to changing environmental conditions. In budding yeast (Sacharomyces cerevisiae), changes in extracellular osmotic conditions are sensed by the HOG SAPK pathway, which orchestrates the cell adaptation program required to maximize cell survival upon stress. Although most of the HOG pathway components have been described, little was known about the dynamics of the response. The aim of this thesis was to analyze the dynamic behavior of the HOG pathway. By using a chemical inhibitor and extensive signal quantification we showed that the HOG pathway is controlled by high basal signaling counteracted by a negative feedback regulatory system. This property determines dynamic signaling in terms of faster response times and higher sensitivity to small variations in extracellular stimuli. This thesis also aimed to implement novel strategies for biological computation that allow increasing complexity of circuits. By engineering signaling pathways in yeast, we have shown that distribution of computation tasks among several wired cells reduces wiring constraints and allows scalability of circuit complexity. Moreover, reusability of cells permits implementation of multiple circuits. Overall, our results define novel dynamic properties of the HOG pathway and have been important to achieve a better view of signal transduction process though MAPK pathways. Moreover, we have developed and implemented novel strategies for biological computation that solved fundamental constrains in the field of synthetic biology.Una propietat cel•lular fonamental és l’habilitat de detectar estímuls i respondre coherentment a un ambient dinàmic. En cèl•lules de llevat (Saccharomyces cerevisiae), els canvis en l’osmolaritat externa són detectats per la via de senyalització de HOG que organitza tot el programa d’adaptació cel•lular, indispensable per assegurar la supervivència cel•lular en estrès osmòtic. Tot i que la gran majoria dels components de la via de HOG han estat identificats, la dinàmica del procés de senyalització és encara força desconeguda. L’objectiu d’aquest projecte de tesis ha estat analitzar el comportament dinàmic de la via de HOG. Gràcies a la utilització d’un al•lel inhibible de la MAPK Hog1 i a la quantificació sistemàtica del procés de senyalització, hem pogut demostrar que en la via de HOG existeix una intensa senyal basal reprimida constantment per un feedback negatiu depenent de la MAPK Hog1. Aquesta tesi també té com a objectiu la implementació de noves estratègies de computació biològica que permetin un increment de la complexitat dels circuits. Gràcies a la bioenginyeria de les vies de senyalització de llevat, hem demostrat que la distribució de la computació en diferents cèl•lules connectades entre elles disminueix les limitacions de connexió i permet incrementar la complexitat dels circuits a un baix cost. En conjunt, els nostres resultats defineixen noves propietats dinàmiques de la via de HOG i han estat importants per tenir una visió global millorada del procés de senyalització per vies de MAPK. A més, hem dissenyat i implementat noves estratègies de computació biològica que han resolt problemes fonamentals del camp de la biologia sintètica

3D time-lapse microscopy paired with endpoint lineage analysis in mouse blastocysts

Summary: Determining how signaling dynamics relate to gene expression and cell fate is essential to understanding multicellular development. We present a unified live imaging and lineage analysis method that allows integrated analysis of both techniques in the same mouse embryos. This protocol describes the embryo isolation, confocal imaging, immunofluorescence, and in silico alignment required to connect time-lapse and endpoint measurements. By utilizing different biosensors and fixed readouts, this method allows interrogation of signaling dynamics that specify cell fates in developing embryos.For complete details on the use and execution of this protocol, please refer to Pokrass et al. (2020)

Distributed biological computation with multicellular engineered networks

5 páginas, 4 figuras.-- Regot, Sergi et al.Ongoing efforts within synthetic and systems biology have been directed towards the building of artificial computational devices1 using engineered biological units as basic building blocks2, 3. Such efforts, inspired in the standard design of electronic circuits4, 5, 6, 7, are limited by the difficulties arising from wiring the basic computational units (logic gates) through the appropriate connections, each one to be implemented by a different molecule. Here, we show that there is a logically different form of implementing complex Boolean logic computations that reduces wiring constraints thanks to a redundant distribution of the desired output among engineered cells. A practical implementation is presented using a library of engineered yeast cells, which can be combined in multiple ways. Each construct defines a logic function and combining cells and their connections allow building more complex synthetic devices. As a proof of principle, we have implemented many logic functions by using just a few engineered cells. Of note, small modifications and combination of those cells allowed for implementing more complex circuits such as a multiplexer or a 1-bit adder with carry, showing the great potential for re-utilization of small parts of the circuit. Our results support the approach of using cellular consortia as an efficient way of engineering complex tasks not easily solvable using single-cell implementations.This work was supported by grants fromthe James McDonnell Foundation to R.S., the MICINN (BIO2009-07762 and FIS2009-12365); Consolider Ingenio 2010 programme (grant CSD2007-0015), from the ESF (ERAS-CT-2003-980409) FP6 as part of a EURYI scheme award (www.esf.org/euryi) to F.P. and the CELLCOMPUT (FP6) project to F.P., R.S. and S.H., and FP7 UNICELLSYS grant (#201142) to F.P. and S.H., and The Santa Fe Institute to R.S.; F.P. and R.S. laboratories are also supported by the Fundación Marcelino Botín (FMB). F.P. is recipient of an ICREA Acadèmia (Generalitat de Catalunya).Peer reviewe

The HOG pathway dictates the short-term translational response after hyperosmotic shock

Cellular responses to environmental changes occur on different levels. We investigated the translational response of yeast cells after mild hyperosmotic shock by isolating mRNA associated with multiple ribosomes (polysomes) followed by array analysis. Globally, recruitment of preexisting mRNAs to ribosomes (translational response) is faster than the transcriptional response. Specific functional groups of mRNAs are recruited to ribosomes without any corresponding increase in total mRNA. Among mRNAs under strong translational up-regulation upon shock, transcripts encoding membrane-bound proteins including hexose transporters were enriched. Similarly, numerous mRNAs encoding cytoplasmic ribosomal proteins run counter to the overall trend of down-regulation and are instead translationally mobilized late in the response. Surprisingly, certain transcriptionally induced mRNAs were excluded from ribosomal association after shock. Importantly, we verify, using constructs with intact 5' and 3' untranslated regions, that the observed changes in polysomal mRNA are reflected in protein levels, including cases with only translational up-regulation. Interestingly, the translational regulation of the most highly osmostress-regulated mRNAs was more strongly dependent on the stress-activated protein kinases Hog1 and Rck2 than the transcriptional regulation. Our results show the importance of translational control for fine tuning of the adaptive responses.This work was financially supported by the European Commission (QUASI; LSHG-CT2003-530203 and UNICELLSYS; LSHG-CT2007-201142) to P.S and F.P, grants from MICINN and Consolider from the Spanish government, EURYI scheme award (www.esf.org/euryi), ICREA Acadèmia (Generalitat de Catalunya) and Fundación Marcelino Botín (FMB) to F.P, and by grants from the Swedish Research Council (2007-5460) and the Swedish Cancer Fund (09-0772) to P. S