Elevated histone expression promotes life span extension

Abstract

Changes to the chromatin structure accompany aging, but the molecular mechanisms underlying aging and the accompanying changes to the chromatin are unclear. Here, we report a mechanism whereby altering chromatin structure regulates life span. We show that normal aging is accompanied by a profound loss of histone proteins from the genome. Indeed, yeast lacking the histone chaperone Asf1 or acetylation of histone H3 on lysine 56 are short lived, and this appears to be at least partly due to their having decreased histone levels. Conversely, increasing the histone supply by inactivation of the histone information regulator (Hir) complex or overexpression of histones dramatically extends life span via a pathway that is distinct from previously known pathways of life span extension. This study indicates that maintenance of the fundamental chromatin structure is critical for slowing down the aging process and reveals that increasing the histone supply extends life span.

Figure 1. Asf1 is required for normal lifespan

A. Replicative lifespan of isogenic strains BY4741 (“WT”) or BY4747asf1 (“asf1”). B. Replicative lifespan of isogenic strains that were wild type (DBY746) or deleted for ASF1 (JFY022) in the DBY746 background often used for aging studies. C. Replicative aging analysis of isogenic yeast strains BY4741 (“WT”), BY4747asf1 (“asf1”), BY4747sir2 (“sir2”), and BY4747asf1sir2 (“asf1sir2”).

Figure 2. Genetic identification of the pathway through which Asf1 regulates replicative lifespan

A. Replicative aging analysis of wild type W303 yeast (“WT”) or this strain deleted for ASF1 (“asf1”), CAC1 (“cac1”) or both ASF1 and CAC1 (“asf1cac1”). B. Isogenic strains that were wild type (BY4741) or deleted for ASF1 or MRC1 from the genome wide deletion collection in the S288c strain background were analyzed for replicative lifespan. C. Replicative aging analysis of yeast strains YB (“WT”), ZGY608 (“asf1”), ZGY906 (“rtt109”), and ZGY964 (“asf1rtt109”). D. Replicative aging analysis of yeast strains HMY152 (“WT”), JFY004 (“asf1”), HMY139 (“H3 K56Q”), HMY140 (“H3 K56R”), JFY005 (“H3 K56Q asf1”), and JFY006 (“H3 K56R asf1”). E. Replicative aging analysis of isogenic yeast strains BY4741 (“WT”) and YNML7 (“hst3hst4”). F. Replicative aging analysis of isogenic yeast strains SHY0015 (“WT”) and SHY0014 (“pGALAsf1”). 0.5% galactose leads to endogenous levels of Asf1, while 1% galactose leads to higher than endogenous levels of Asf1 (Zabaronick and Tyler, 2005).

Figure 3. Aging cells have reduced histone protein levels

A. RNA levels for H3 (HHT2 and HHT1), H4 (HHF2 and HHF1), H2A (HTA1, HTA2), H2B (HTB1, HTB2) and tubulin (TUB) from strain BY4741 (“WT”) or this strain deleted for ASF1 (“asf1Δ”), or RTT109 (“rtt109Δ”). RNA levels were normalized to total DNA content, and the RNA levels were normalized to 1 for young WT RNA (data prior to normalizing to 1 are given in Suppl. Fig. 3C). Representative results are shown. B. Histone H3 protein and tubulin levels in wild type strain BY4741 were measured by western analysis of equivalent amounts of total protein extracts from biochemically separated wild type yeast. Below is shown a Coomassie stained gel of the same amounts of the same total yeast protein extracts analyzed in the western analyses. The western analyses used infrared secondary antibodies and the images were taken in the linear range of detection. C. Total (T), soluble (S) and pellet (P) proteins were isolated from strain UCC5181 (“WT”) or this strain deleted for HIR1 (“hir1Δ”), ASF1 (“asf1 Δ”), or RTT109 (“rtt109Δ”), that were growing asynchronously of mixed age or were aged via the “mother enrichment program”. The same DNA equivalents of each fraction were analyzed for histone H3 protein levels by western blotting, where non-chromatin bound histones reside in the soluble fraction and chromatinized histones reside in the pellet fraction. “*” denotes a likely proteolytic cleavage product of H3 that arises upon over-handling of the protein. Tubulin was assayed to demonstrate the efficiency of the fractionation. Below are shown amido black staining of the membranes used for the western analyses. The western analyses used infrared secondary antibodies and the images were taken in the linear range of detection. D. Cells of mixed age (“Asynch”) or following aging via the mother enrichment program (“aged”) from strain UCC5181 were subject to ChIP analysis for histone H3 occupancy at the indicated DNA regions. Data shown are the average of two independent experiments, whose results are shown individually in Suppl. Fig. S6A and B. E. Replicative lifespan of strain JFY047 and JFY048 (“asf1”) carrying the empty vector pRS426 or the 2 micron vector pFB1156 carrying the HHF1/HHT1 and HTB1/HTA1 genes. The pvalue indicates the significance of the lifespan extension. F. Replicative lifespan of strains JFY056 and JFY050 (“asf1”) carrying the empty vector pRS315 or the vector pRO689 carrying the pGAL driven HTB1/HTA1 genes. G. Replicative lifespan of isogenic strains with the indicated gene encoding subunits of the Hir complex deleted.

Figure 4. Increased histone supply does not extend lifespan by the same pathways as Sir2 or ERCs

A. Replicative lifespan of isogenic strains with the indicated genes deleted or containing an extra copy of Sir2 (Sir2OX). B. Replicative lifespan of isogenic strains with the indicated genes deleted. C. Replicative lifespan of isogenic strains with the indicated genes deleted and/or containing an extra copy of Sir2 (Sir2OX).

Figure 5. Epistasis analysis with the Tor1 pathway or CR

A. Replicative lifespan of isogenic strains with the indicated genes deleted. B. Replicative lifespan of isogenic strains with or without HIR1 deleted, grown on either 0.5% glucose to induce CR or on 2% glucose. C. Schematic of the dual luciferase reporter plasmid used to measure Gcn4 translation levels. The ratio of the signal from the GCN4-firefly luciferase to renilla luciferase is shown for isogenic strains from the genome wide deletion collection in the S288c strain background. D. Polysome profiles of the indicated isogenic strains from the genome wide deletion collection in the S288c strain background. The position of the 60S, 40S, 80S ribosome and the polysomes are indicated. E. Histone H3 protein and tubulin levels were measured by western analysis of equivalent amounts of total protein extracts from biochemically separated young and old wild type and tor1 mutant yeast. Below is shown the amido black stained membrane to show equivalent total protein loading. The western analyses used infrared secondary antibodies and the images were taken in the linear range of detection. F. As for E, but with wild type yeast grown in normal conditions (2% glucose) or calorie restricted conditions (0.5% glucose).

Figure 6. Overexpression of histones H3/H4 extends lifespan

A. Replicative lifespan of isogenic strains that are wild type (“WT”) or carrying an extra copy of either HHT2/HHF2 or HTB1/HTA1 driven from the galactose inducible pGAL1/10 divergent promoter integrated into the genome grown on 1% galactose and B. on 2% galactose. C. Model for lifespan extension by increasing histone supply.