the-use-of-chemostats-in-microbial-systems-biology

The Use of Chemostats in Microbial Systems Biology

Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated ...

New York University 

An essential property of all cells is the ability to exit from active cell division and persist in a quiescent state. For single-celled microbes this primarily occurs in response to nutrient deprivation. We studied the genetic requirements for survival of Saccharomyces cerevisiae when starved for either of two nutrients: phosphate or leucine. We measured the survival of nearly all nonessential haploid null yeast mutants in mixed populations using a quantitative sequencing method that estimates the abundance of each mutant on the basis of frequency of unique molecular barcodes. Starvation for phosphate results in a population half-life of 337 hr whereas starvation for leucine results in a half-life of 27.7 hr. To measure survival of individual mutants in each population we developed a statistical framework that accounts for the multiple sources of experimental variation. From the identities of the genes in which mutations strongly affect survival, we identify genetic evidence for several cellular processes affecting survival during nutrient starvation, including autophagy, chromatin remodeling, mRNA processing, and cytoskeleton function. In addition, we found evidence that mitochondrial and peroxisome function is required for survival. Our experimental and analytical methods represent an efficient and quantitative approach to characterizing genetic functions and networks with unprecedented resolution and identified genotype-by-environment interactions that have important implications for interpretation of studies of aging and quiescence in yeast.

System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.

Une propri&eacute;t&eacute; essentielle de toutes les cellules est la capacit&eacute; &agrave; sortir de la division cellulaire active et de persister dans un &eacute;tat de repos. Pour les microorganismes unicellulaires, cela se produit principalement en r&eacute;ponse &agrave; la privation des &eacute;l&eacute;ments nutritifs. Nous avons &eacute;tudi&eacute; les conditions g&eacute;n&eacute;tiques pour la survie de Saccharomyces cerevisiae quand priv&eacute;es ou l&#39;autre des deux &eacute;l&eacute;ments nutritifs : phosphate ou leucine. Nous avons mesur&eacute; la survie de presque tous les mutants de levure haplo&iuml;de de null dans une population mixte &agrave; l&#39;aide d&#39;une m&eacute;thode de s&eacute;quen&ccedil;age quantitative qui permet d&#39;estimer l&#39;abondance de chaque mutant sur la base de la fr&eacute;quence des codes-barres mol&eacute;culaires uniques. Famine au phosphate se traduit par une demi-vie de population de 337 h alors que la famine pour la leucine se traduit par une demi-vie de 27,7 hr. Pour mesurer la survie des mutants individuels dans chaque population, nous avons d&eacute;velopp&eacute; un cadre statistique qui prend en compte les multiples sources de variation exp&eacute;rimentale. De l&#39;identit&eacute; des g&egrave;nes dont les mutations affectent fortement la survie, nous identifions des preuves g&eacute;n&eacute;tiques pour plusieurs processus cellulaires affectant la survie durant le je&ucirc;ne en &eacute;l&eacute;ments nutritifs, y compris d&#39;autophagie, remodelage, ARNm traitement et fonction du cytosquelette de la chromatine. En outre, nous avons trouv&eacute; des preuves que mitochondriale et peroxysomes fonction est n&eacute;cessaire pour la survie. Nos m&eacute;thodes exp&eacute;rimentales et analytiques repr&eacute;sentent une approche quantitative et efficace pour caract&eacute;riser les fonctions g&eacute;n&eacute;tiques et r&eacute;seaux avec une r&eacute;solution sans pr&eacute;c&eacute;dent et identifi&eacute; des interactions g&eacute;notype-par-environnement qui ont des implications importantes pour l&#39;interpr&eacute;tation des &eacute;tudes de vieillissement et de la quiescence chez la levure.

Au niveau du syst&egrave;me analyse des g&egrave;nes et fonctions affectant la survie durant le je&ucirc;ne en nutriments chez Saccharomyces cerevisiae.

Una propriet&agrave; essenziale di tutte le cellule &egrave; la capacit&agrave; di uscire dalla divisione cellulare attivo e persistere in uno stato quiescente. Per i singoli-celled microbi questo si verifica principalmente in risposta alla privazione dei nutrienti. Abbiamo studiato i requisiti genetici per la sopravvivenza di Saccharomyces cerevisiae quando fame per una delle due sostanze nutritive: fosfato o leucina. Abbiamo misurato la sopravvivenza di quasi tutti i non essenziali mutanti aploide lievito null in popolazioni miste, utilizzando un metodo di sequenziamento quantitativa che le stime di abbondanza di ogni mutante sulla base della frequenza di unico Molekulare codici a barre. Fame per fosfato risultati in un tempo di dimezzamento popolazione di 337 hr mentre fame per la leucina si traduce in un tempo di dimezzamento di 27,7 hr. Per misurare la sopravvivenza dei singoli mutanti in ogni popolazione abbiamo sviluppato un quadro statistico che rappresenta le molteplici fonti di variazione sperimentale. Dalle identit&agrave; dei geni in cui mutazioni fortemente influenzano la sopravvivenza, identifichiamo le prove genetiche per diversi processi cellulari che influenzano la sopravvivenza durante l&#39;inedia dei nutrienti, tra cui autophagy, chromatin che ritocca, mRNA di elaborazione e la funzione del citoscheletro. Inoltre, abbiamo trovato prove che mitocondriale e dei perossisomi funzione &egrave; necessaria per la sopravvivenza. I nostri metodi analitici e sperimentali rappresentano un approccio efficace e quantitativo per la caratterizzazione genetiche funzioni e reti con risoluzione senza precedenti e identificate interazioni genotipo-da-ambiente che hanno importanti implicazioni per l&#39;interpretazione degli studi di invecchiamento e di quiescenza in lievito.

Nathan J. Brandt

Center for Genomics and Systems Biology,
Department of Biology,
Center for Genomics and Systems Biology, Department of Biology

New York University

The Use of Chemostats in Microbial Systems Biology

Nathan J. Brandt

Center for Genomics and Systems Biology,Department of Biology,Center for Genomics and Systems Biology, Department of Biology

New York University

The Use of Chemostats in Microbial Systems Biology

Center for Genomics and Systems Biology,
Department of Biology,
Center for Genomics and Systems Biology, Department of Biology