Cell Calcium (2002) 32(2), 83–91 0143-4160/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved. doi:10.1016/S0143-4160(02)00110-0, available online at http://www.idealibrary.com on Genome-Wide analysis of yeast transcription upon calcium shortage L. J. Lombard´ ıa, 1 M. Becerra, 1 E. Rodr´ ıguez-Belmonte, 1 N. C. Hauser, 2 M. E. Cerdán 1 1 Dpto. Biolog´ ıa Celular y Molecular, Universidad de La Coruña, F. Ciencias, Campus de La Zapateira s/n 15075, La Coruña, Spain 2 Molecular-Genetic Genome Analysis Group, Deutsches Krebsforschungszentrum, Heidelberg, Germany Summary Several regulatory circuits related to important functions, like membrane excitation, immunoresponse, replica- tion, control of the cell cycle and differentiation, among others, cause an increase in intracellular calcium level that finally has a consequence upon transcription of specific genes. The sequencing of the whole genome of eukaryotic cells enables genome-wide analysis of gene expression under many conditions not yet assessed by conventional methods. Using the array technology, the effect of calcium shortage in yeast cells was studied. Correspondence analysis of data showed that there is a response in transcription that is correlated to calcium shortage. The distribution of up-regulated-genes in functional categories suggests a regulatory connection between the cell-cycle progression and the energetic metabolic requirements for growth and division. In silico analysis of promoters reveals the frequent appearance of the Mlu I cell cycle box (MCB) cis element that binds the transcriptional regulatory factor Mcm1. © 2002 Elsevier Science Ltd. All rights reserved. INTRODUCTION Calcium signalling mechanisms are used by differenced eukaryotic cells in a wide range of regulated processes as diverse as neuronal excitation [1], activation of T cells during immunoresponse [2], regulation of replicative en- zymes [3,4] and other nuclear functions like regulation of nuclear kinases which control cell cycle, transcription me- diated by Pol III and pre-mRNA splicing, as well as riboso- mal assembly and protein translation [5]. Calmodulin is the major calcium-binding protein in most eukaryotic cells and Ca 2+ signals can regulate gene expression through the calmodulin-dependent pro- tein phosphatase known as calcineurin and through calmodulin-dependent protein kinases. In the yeast Sac- charomyces cerevisiae functional homologues of calmod- ulin [6], calcineurin [7] and calmodulin-dependent protein kinases have been described [8]. There are several physi- Received 3 January 2002 Revised 27 March 2002 Accepted 14 May 2002 Correspondence to: Professor M. Esperanza Cerdán, Dpto. de Biolog´ ıa Celular y Molecular, F. Ciencias, Universidad de A Coruña Campus de A Zapateira s/n, A Coruña 15071, Spain. Tel.: +34-9-81-167000; fax: +34-9-81-167065; e-mail: n.hauser@dkfz-heidelberg.de, bmanamrt@udc.es ological conditions, which generate Ca 2+ signals in yeast. The first one is the long-term stimulus caused by mating pheromones. After pheromone signalling, there is an in- crease in intracellular Ca 2+ levels that activate calcineurin and calmodulin-dependent kinases [9,10]. The second physiological condition to be cited is the regulation of cation homeostasis, caused by high salt or high Ca 2+ in the medium, which is very complex and includes the stim- ulation of P-type ion pumps [11], Ca-pumping ATPases in the vacuole, Pmc1 [12], or the Golgi complex, Pmr1 [13], as well as inhibition of a vacuolar H + /Ca 2+ exchanger Vcx1/Hum1 [14]. The Ca 2+ signals commented earlier cause gene regulation through the specific transcriptional factor Tcn1/Crz1 [15] that is only targeted to the nucleus after dephosphorylation regulated by calcineurin [16]. The regulatory circuits mentioned earlier are all related to signals that cause an increase in intracellular calcium levels but there are no data available about the effect of calcium shortage. The sequencing of the whole genome of the yeast eukaryotic cell enables genome-wide anal- ysis of gene expression and anticipates to similar and near-coming studies carried out in human cells. In this report we describe a genome-wide survey of changes in gene expression in S. cerevisiae cells grown under three conditions with different Ca 2+ levels. 83