Swi/SNF‐GCN5‐dependent chromatin remodelling determines induced expression of GDH3, one of the paralogous genes responsible for ammonium assimilation and glutamate biosynthesis in Saccharomyces cerevisiae

Abstract

SummaryIt is accepted that Saccharomyces cerevisiae genome arose from complete duplication of eight ancestral chromosomes; functionally normal ploidy was recovered because of the massive loss of 90% of duplicated genes. There is evidence that indicates that part of this selective conservation of gene pairs is compelling to yeast facultative metabolism. As an example, the duplicated NADP-glutamate dehydrogenase pathway has been maintained because of the differential expression of the paralogous GDH1 and GDH3 genes, and the biochemical specialization of the enzymes they encode. The present work has been aimed to the understanding of the regulatory mechanisms that modulate GDH3 transcriptional activation. Our results show that GDH3 expression is repressed in glucose-grown cultures, as opposed to what has been observed for GDH1 , and induced under respiratory conditions, or under stationary phase. Although GDH3 pertains to the nitrogen metabolic network, and its expression is Gln3p-regulated, complete derepression is ultimately determined by the carbon source through the action of the SAGA and SWI/SNF chromatin remodelling complexes. GDH3 carbonmediated regulation is over-imposed to that exerted by the nitrogen source, highlighting the fact that operation of facultative metabolism requires strict control of enzymes, like Gdh3p, involved in biosynthetic pathways that use tricarboxylic acid cycle intermediates.

Diversification of Paralogous α-Isopropylmalate Synthases by Modulation of Feedback Control and Hetero-Oligomerization in Saccharomyces cerevisiae

“…Formation of paralogous isozymes with different enzymatic capacities had already been observed, and it had been proposed that the various enzymatic properties were due to the existence of multiple homo-and hetero-oligomeric isoforms. Accordingly, it was considered that the NADP-Gdh1-Gdh3 isozyme activity could provide the pacemaker mechanism, ensuring optimum glutamate biosynthesis and operation of the energyyielding metabolism under either fermentative or respiratory conditions (18,19). The study presented here analyzed the existence and role of hetero-oligomeric organization in LEU4 and LEU9 functional diversification.…”

“…Normal ploidy was recovered through the massive loss of 90% of the duplicated genes and the selective retention and further diversification of 8% of the retained paralogous copies (17). Diversification of paralogous genes whose products are involved in amino acid metabolism has led to the separation and specialization of the ancestral function of the two duplicated genes, the retention of both copies fulfilling the function carried out by the original and unique ancestral gene (10,(18)(19)(20). Subfunctionalization of paralogous pairs can be achieved through various nonexclusive molecular mechanisms, i.e., (i) modifications of the coding sequence leading to paralogous proteins with particular kinetic properties (18), (ii) modifications of the regulatory region determining the differential expression of each copy (20), or (iii) different subcellular localization (21).…”

“…In particular, it has been proposed that retention of GDH1/GDH3 and LYS20/LYS21 has afforded mechanisms allowing ␣-ketoglutarate (␣-KG) utilization without impairing the integrity of the tricarboxylic acid cycle as an energyproviding system. The relative abundance of each one of the Gdh1/Gdh3 and Lys20/Lys21 isoforms under fermentative or respiratory conditions modulates the rate at which ␣-KG is channeled to glutamate and lysine biosynthesis (18,19).…”

TheNeurospora crassaWhite Collar-1 dependent Blue Light Response Requires Acetylation of Histone H3 Lysine 14 by NGF-1

“…Conidia (10 6 ) were used as inocula, and cultures were incubated in liquid medium for 2 d in the dark at 28°C. Darkand light-induced mycelia were collected by filtration under a red safety light and in vivo cross-linked (Avendano et al, 2005). Cross-linked chromatinprotein complexes were immunoprecipitated with antibodies against unmodified histone H3 (06 -755; Upstate Biotechnology, Charlottesville, VA), acetylated H3 (06 -599; Upstate Biotechnology), or acetylated H3 K14 (07-353, Upstate Biotechnology).…”

“…ChIP assays were performed according to a yeast protocol (Avendano et al, 2005) with some modifications. Conidia (10 6 ) were used as inocula, and cultures were incubated in liquid medium for 2 d in the dark at 28°C.…”