TABLE 21.
Strategies and methods used to study the stress response, genes, and proteins in archaea
| Method | Stressor/conditionsa | Gene or protein and organismb | Reference(s) |
|---|---|---|---|
| Culture | |||
| Viability, acquired stress tolerance | Heat Pressure Osmotic stress Irradiation P starvation |
PES4, SSH, MSE MJA, PES4, PES1, TPE MTP, HXV PFU SAC |
33, 64, 68, 114, 129, 130, 201, 204, 221, 225, 233, 279, 281, 282 |
| Growth | Continuous culturec | MSE | 114, 255 |
| Morphology | Heat/starvation Ammonia |
MSE (membrane potential effects) MMA, MTP (cell shape) |
165a, 255 |
| DNA | |||
| Southern blot as only identifier |
hsp70: MAC, MBA, MHU, HHA pho: SAC |
10, 42, 99, 164, 221 | |
| Sequencing of gene |
hsp60: AFU, DSY, HXV, MTH, MJA, MTL, MKA, PAE, PKOD, SSH, SSP7, TKS, TAC hsp70: HCU, HMA, MTH, MMA, MTP, TAC HCU (hsp40), MMA (grpE, hsp40, trkA), MTP (hsp40), PAL585 (dinF), MBR (crx) Otherd: MJA, AFU, PAE, PHO, MTH |
3, 24, 31, 32, 45, 79, 84, 105, 110, 111, 126, 140, 141, 143, 144, 147, 151, 163, 181–183, 207, 263, 281, 288, 305, 308 | |
| Stability of DNA | Heat | PFU | 224 |
| DNA repair | UV light | SAC, PFU | 64, 301 |
| DNA (plasmid) topology | Heat and cold | Sulfolobus species | 173, 174 |
| RNA | |||
| Stress related increase in transcript (Northern/slot blot) | Heat Heat, ammonia, metal Heat and ammonia Copper |
hsp60: SSH, HXV hsp70: MMA, MTPd Others: MMA (hsp40, grpE, trkA) MBR (crx) |
42, 44, 126, 141, 147, 163, 165, 277 |
| Transcriptionally active regions of genome | Heat and osmotic stress | HXV | 77, 283 |
| Protein | |||
| 1-D electrophoresis (unidentified proteins) | Osmotic stress Pressure Heat shock Copper Starvation Cold |
HME TPE, PES4 POC, TPE, MSE, SSH MBR MSE PES4 |
33, 68, 114, 129, 130, 141, 147, 225, 230 |
| 1-D electrophoresis, radiolabelled | Osmotic stress Heat Oxidative stress Ethanol |
HXV (several), HME, MTP (betaine) SSH (Hsp60e), MVO (11f), HMA (4), SAC (4) HXV MVO MVO (11f), SAC (none) |
55, 68, 110, 119, 139, 141, 204, 233, 234, 279, 282 |
| 2-D electrophoresis (unidentified proteins) | Heat P starvation |
HXV, MSE SAC |
114, 204, 221 |
| 2-D electrophoresis, radiolabelled | Pressure | MTL | 55, 138, 204, 221 |
| Osmotic stress | HXV | ||
| P starvation | SAC | ||
| Heat | HVO | ||
| Isoelectric focusing | SSO(Hsp60) | 154 | |
| Stress-accumulation determined by NMR | Osmotic stress Heat |
PFU, MIG, PWO (inositol compounds), PFU, MIG (inositol) | 40, 41, 193, 257 |
| Cross reaction with antibodies for stress proteins | Hsp60: ABR, TTE, POC, SMA, MSE, SAC, PAB, HBU, DAM, AFU, TAC | 114, 141, 225, 230, 290 | |
| Peptide analysis/sequencing | Hsp60: SSO, TAC, SSP7, MKA Crx: MBR |
3, 147, 154, 207, 289 | |
| Purification of protein | Hsp60: SSH, TAC, MKA, PKOD, SSO, POC, SSP7, MJA, MTL, TKS sHsp: MJA Crx: MBR |
3, 65, 84, 101, 147, 148, 154, 161, 187, 207, 216, 230, 234, 281, 289, 290, 305, 308 | |
| Structure | See Table 14 | Hsp60: SSH, TAC, MKA, MTL, POC, SSP7, PBR, SSO, TKS sHsp: MJA |
3, 65, 84, 148–150, 154, 187, 207, 216, 230, 231, 234, 279, 280, 281, 289, 290, 307, 308 |
| Conformational changes | Heat or ATP | Hsp60: SSH, SSO | 101, 154, 170, 171, 234, 246, 307 |
| Stress accumulation (Western blotting/activity gels) | Hsp60: POC, MSE, AFU Hsp70: MMA Superoxide dismutase: HHA Crx: MBR |
17, 42, 74, 114, 147, 230 | |
| Analytical gel filtration and ultrafiltration; spectral analysis | Recombinant proteins tested in vitro | Hsp60 (α and β subunits) | 202 |
| Refolding experiments | Hsp60: SSP7, SSH, SSO, MTL, PKOD, TKS, MJA | 84, 101, 161, 207, 234, 305, 308 | |
| ATP-binding site in sequence | Hsp60: TAC, MKA, MJA, SSH, PKOD, HXV, MTL, TKS | 3, 65, 84, 141, 161, 163, 289, 305, 308 | |
| ATPase activity as indicator of chaperonin action | Hsp 60: PKOD, SSO, SSH, SSP7, POC, TAC, MKA (negative result), MJA, MTL, TKS | 3, 65, 84, 101, 154, 161, 207, 230, 234, 281, 289, 305, 308 | |
| Stabilization of proteins | Pressure Heat |
MIG, MJA (protease) POC, MJA (protease), PKOD, MJA (Hsp60) |
121, 161, 200, 230, 305 |
| Recombinant expression of stress proteins in E. coli | TAC, MJA, PKOD, PAL585 (dinF), HXV, MTL, TKS, AFU | 24, 74, 84, 148, 163, 216, 290, 305, 308 | |
| Binding of denatured proteins | SSH, TAC, SSO, PKOD, MJA | 101, 161, 234, 289, 305 | |
| Proteasome function | TAC | 248 | |
| Thermostability of protein | MJA, POC | 200, 230 | |
| Reassembly | Hsp60: SSO, SSH, TAC | 141, 154, 234, 290 | |
| Filament formation | Hsp60: MTL, SSH | 84, 280, 307 | |
| RNA binding and processing | Hsp60: SSO | 249 | |
| Protein modification | P starvation | SAC (phosphorylation) SSO (methylation) |
13, 221 |
Blanks in this column indicate absence of information.
Organisms (in capitals) are: ABR, Acidianus brierleyi; AFU, Archaeoglobus fulgidus; DAM, Desulfurolobus ambivalens; DMO, Desulforococcus mobilis; DSY, Desulforococcus strain SY; HBU, Hyperthermus butyricus; HCU, Halobacterium cutirubrum; HHA, Halobacterium halobium; HMA, Haloarcula marismortui; HME, Haloferax mediterranei; HXV, Haloferax volcanii; MAC, Methanosarcina acetivorans; MBA, Methanosarcina barkeri; MBR, Methanobacterium bryantii; MFE, Methanothermus fervidus; MHU; Methanospirillum hungateii; MIG, Methanococcus igneus; MJA, Methanococcus jannaschii; MMA, Methanosarcina mazei S-6; MKA, Methanopyrus kandleri; MSE, Metallosphaera sedula; MTH, Methanobacterium thermoautotrophicum ΔH; MTL, Methanococcus thermolithotrophicus; MTP, Methanosarcina thermophila TM-1; MVO, Methanococcus voltae; PAB, Pyrodictium abyssi; PAE, Pyrobaculum aerophilum; PAL585, Pyrococcus strain IFREMER585; PBR, Pyrodictium brockii; PES1, Pyrococcus strain ES1; PES4, Pyrococcus strain ES4; PFU, Pyrococcus furiosus; PHO, Pyrococcus horikoshii OT3; POC, Pyrodictium occultum; PKOD, Pyrococcus st. KOD; PWO, Pyrococcus woesei; SAC, Sulfolobus acidocaldarius; SMA, Staphylothermus marimus; SSP7, Sulfolobus Sp. strain 7; SSH, Sulfolobus shibatae; SSO, Sulfolobus solfataricus; TAC, Thermoplasma acidophilum; TPE, Thermococcus peptonophilus; TKS, Thermococcus strain KS-1; TTE, Thermoproteus tenax. DNA (genes) and RNA (transcripts) are shown in italics.
All others are batch experiments.
Part of whole-genome projects.
Protein (first letter in capital and rest in lower case); Hsp60/hsp60, heat shock protein 60/gene belonging to the chaperonins; Hsp70/hsp70, heat shock protein 70/gene belonging to the Hsp70(DnaK) chaperone system; Crx/crx, copper-responsive protein/gene.
Number of induced proteins within parentheses.