Dynamic Metabolic Adjustments and Genome Plasticity Are Implicated in the Heat Shock Response of the Extremely Thermoacidophilic ArchaeonSulfolobus solfataricus

Abstract

Approximately one-third of the open reading frames encoded in the Sulfolobus solfataricus genome were differentially expressed within 5 min following an 80 to 90°C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response.The ability to cope with environmental stress is essential to microorganisms (1, 34, 39), including those thriving in extreme environments relative to temperature (4, 10, 21, 28, 42, 45, 50, 52), pressure (9, 31, 35, 44, 51), ionic strength (47), acidity (30, 53), alkalinity (26), metals (15, 37), and radiation (25,36,43). Certain crenarchaea, such as members of the Sulfolobales, occupy niches that are biologically extreme in two respects: low pH and elevated temperature (19). Key to their physiological function is a transmembrane proton gradient that renders intracellular pH close to neutral. As such, maintaining cytosolic pH in the face of thermal stress-induced cellular damage involves complex genetic and metabolic strategies (40). To examine such mechanisms for extreme thermoacidophiles at supraoptimal temperatures, the heat shock response of Sulfolobus solfataricus (49, 55) was studied using genome-wide transcriptional response.A whole-genome oligonucleotide microarray for Sulfolobus solfataricus P2 (DSMZ, Germany) was developed (49). Probes were designed in OligoArray 2.0 (46), custom synthesized (Integrated DNA Technologies, Coralville, IA), and printed onto arrays following protocols previously developed for other hyperthermophiles (14, 20, 50); five replicates per probe were spotted on each array to fortify statistical analysis. S. solfataricus was routinely grown at 80°C and pH 4.0 on DSMZ 182 medium; cells were enumerated using epifluorescence microscopy with acridine orange stain (13). The heat shock time course experiment was carried out as described in the legend for Fig. 1A. RNA was extracted from chilled culture samples (12). cDNA synthesis, microarray hybridizations (Fig. 1B), and data collection were performed as described previously (12), with minor adjustments for long oligonucleotide platforms. Data from each experiment were analyzed with SAS 9.0 (SAS, Cary, NC) (42), using a mixed linear analysis of variance model (54). A Ϯ2.0-fold change (FC) or higher defined differential expression.Transcriptional response to heat stress. When S. solfataricus was shifted from 80 to 90°C at pH 4.0, approximately one-third of the genome responded (1,088 genes, 551 up/537 down) within 5 min after the culture reached 90°C. Differential expression was less pronounced after this initial period; ϳ300 genes (161 up/144 down) changed between 5 and 30 min, and only 30 genes (18 up/12 down) changed between 30 and 60 min (Table 1 and Fig. 2). Table 2 lists selected heat shock (HS)-responsive genes involved in basic metabolic functions and regulation. S. solfataricus relies on HSP20 family small heat shock proteins (sHSPs) (27), the thermosome/rosetta...

Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius

“…5), whereas cells arrested by acetate showed elevated levels of Orc1-2 and low levels of Orc1-1 and Orc1-3 (1); resumption of growth after arrest resulted in elevated Orc1-1 and -3 and greatly reduced Orc1-2. Several laboratories have reported microarray analyses of the response of the Sulfolobus transcriptome to a range of physiological stresses such as UV treatment, viral infection, and heat shock (21)(22)(23)(24). Interestingly, these studies have revealed modulation of Orc1 gene transcript and/or protein levels; similar to that seen with microarray analysis of acetate-treated cells (25).…”

Role of the β1 Subunit in the Function and Stability of the 20S Proteasome in the Hyperthermophilic ArchaeonPyrococcus furiosus

“…In yeast, a heat shock transcription factor was found to coordinate expression of proteasome proteins to control proteasome synthesis under thermal stress, although the impact on this on CP constitution was not determined (18). Recent results from our lab showed that when S. solfataricus was shifted from optimal (80°C) to supraoptimal (90°C) temperatures, the transcription of ORFs encoding CP proteins (␣, ␤1, and ␤2) was unaffected throughout the 60-min period following the temperature shift (40). It was also noted that the transcriptional levels of CP proteins in S. solfataricus were much higher than in P. furiosus under normal or stressed conditions, although the ORF encoding S. solfataricus PAN decreased significantly following the temperature shift.…”

VapC6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote Sulfolobus solfataricus

“…Additional components of the heat-shock (HS) response in this organism include adaptive heat resistance by pre-treatment (Trent et al 1990) and heat-induced shifts in the proteome (Cerchia et al 2000). In a related species, Sulfolobus solfataricus, the HS response transcriptome associated with a nonlethal temperature shift involved approximately one-third of the genome (Tachdjian and Kelly 2006). However, transcription factors that control thermotolerance are missing in crenarchaeotal genomes such as those characterized in the other major archaeal phylum, the Euryarchaeota (Thompson et al 1999;Vierke et al 2003;Liu et al 2007).…”

“…Finally, while VapC5 from several species of Mycobacteria have undergone structural (Miallau et al 2009) and in vivo characterization, a biologic function has yet to be identified (Robson et al 2009). In S. solfataricus, the strong and rapid heat-shock induction of certain vapBC loci (Tachdjian and Kelly 2006), combined with preliminary information on an uncomplemented vapBC mutant (Cooper et al 2009), provided the impetus to investigate the function of the toxin and antitoxin belonging to a single family member, vapBC6, and a role in thermotolerance.…”

“…In archaea, there are three toxin-antitoxin families that have been identified: RelBE, Phd/Doc, and VapBC . The Vap (Virulence associated protein) family make up z40% of all TAs in prokaryotes , with at least 26 identified in S. solfataricus (Tachdjian and Kelly 2006;Jorgensen et al 2009). While the target and cognate protease have been identified for E. coli RelBE and Phd/Doc families, the VapBC family, although the most abundant of all the TAs, has no known targets nor proteases .…”