Stress Genes and Proteins in the Archaea

The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in the mesophilic methanogen Methanosarcina mazei S-6. The proteins possess markers typical of bacterial homologs but none of the signatures distinctive of eukaryotes. In contrast, gene expression and transcription initiation signals and factors are of the eucaryal type, which suggests a hybrid archaeal-bacterial complexion for the Hsp70 system. Another remarkable feature is that several archaeal species in different phylogenetic branches do not have the gene hsp70(dnaK), an evolutionary puzzle that raises the important question of what replaces the product of this gene, Hsp70(DnaK), in protein biogenesis and refolding and for stress resistance. Although archaea are prokaryotes like bacteria, their Hsp60 (chaperonin) family is of type (group) II, similar to that of the eukaryotic cytosol; however, unlike the latter, which has several different members, the archaeal chaperonin system usually includes only two (in some species one and in others possibly three) related subunits of ∼60 kDa. These form, in various combinations depending on the species, a large structure or chaperonin complex sometimes called the thermosome. This multimolecular assembly is similar to the bacterial chaperonin complex GroEL/S, but it is made of only the large, double-ring oligomers each with eight (or nine) subunits instead of seven as in the bacterial complex. Like Hsp70(DnaK), the archaeal chaperonin subunits are remarkable for their evolution, but for a different reason. Ubiquitous among archaea, the chaperonins show a pattern of recurrent gene duplication—hetero-oligomeric chaperonin complexes appear to have evolved several times independently. The stress response and stress tolerance in the archaea involve chaperones, chaperonins, other heat shock (stress) proteins including sHsp, thermoprotectants, the proteasome, as yet incompletely understood thermoresistant features of many molecules, and formation of multicellular structures. The latter structures include single- and mixed-species (bacterial-archaeal) types. Many questions remain unanswered, and the field offers extraordinary opportunities owing to the diversity, genetic makeup, and phylogenetic position of archaea and the variety of ecosystems they inhabit. Specific aspects that deserve investigation are elucidation of the mechanism of action of the chaperonin complex at different temperatures, identification of the partners and substitutes for the Hsp70 chaperone machine, analysis of protein folding and refolding in hyperthermophiles, and determination of the molecular mechanisms involved in stress gene regulation in archaeal species that thrive under widely different conditions (temperature, pH, osmolarity, and barometric pressure). These studies are now possible with uni- and multicellular archaeal models and are relevant to various areas of basic and applied research, including exploration and conquest of ecosystems inhospitable to humans and many mammals and plants.

本综述所涉领域尚属新兴：1991年首次报道了编码分子伴侣（molecular chaperone）Hsp70（heat shock protein 70）的基因序列，以及古菌（Archaea）中伴侣蛋白（chaperonin）的首次描述。上述发现推动了古菌以外与细菌、真核生物直接相关的诸多领域的研究，例如胁迫基因调控、伴侣蛋白复合物的结构-功能关系、基于蛋白质的生物分子系统发育研究（涵盖各类生物及真核细胞细胞器）、极端环境生命的分子生物学与生物化学研究，以及细胞与分子层面的胁迫耐受性研究。
近八年来，学界已针对古菌来源的热休克蛋白家族成员展开研究，包括Hsp70、Hsp60（伴侣蛋白）、Hsp40（DnaJ）以及小分子热休克蛋白（sHsp）。目前已分别在7种、4种和2个古菌物种中完成了hsp70(dnaK)、hsp40(dnaJ)与grpE基因（即“伴侣机器”）的测序，但仅在嗜温产甲烷菌马氏甲烷八叠球菌S-6（Methanosarcina mazei S-6）中对这些基因的表达进行了详尽研究。上述蛋白质具备细菌同源蛋白的典型标记，但无真核生物特有的特征序列。与之相对，基因表达、转录起始信号与调控因子均属于真核类型，这表明Hsp70系统兼具古菌与细菌的混合特征。
另一显著特征是，不同进化分支的多种古菌均缺失hsp70(dnaK)基因，这一进化谜题引出了关键问题：在蛋白质生物合成、复性以及胁迫抗性过程中，究竟是什么物质替代了该基因的产物Hsp70(DnaK)？
尽管古菌与细菌同属原核生物，但其Hsp60（伴侣蛋白）家族属于Ⅱ型，与真核细胞质溶胶中的同类相似；但与真核细胞质溶胶中存在多种不同亚型的伴侣蛋白不同，古菌的伴侣蛋白系统通常仅包含2个（部分物种为1个，部分可能为3个）分子量约60kDa的相关亚基。这些亚基会根据物种不同以多种组合形式形成大型多分子结构，即伴侣蛋白复合物，有时也被称为热体（thermosome）。这种多分子组装体与细菌伴侣蛋白复合物GroEL/S结构相似，但仅由大型双环寡聚体构成，每个环包含8个（或9个）亚基，而非细菌复合物中的7个亚基。与Hsp70(DnaK)类似，古菌伴侣蛋白亚基的进化过程同样引人关注，但其背后的原因却有所不同。
伴侣蛋白广泛存在于古菌中，其进化模式呈现出反复的基因复制现象——异源寡聚型伴侣蛋白复合物似乎曾多次独立演化产生。
古菌的胁迫响应与胁迫耐受性涉及多种分子系统：伴侣蛋白、伴侣蛋白复合物、包括sHsp在内的其他热休克（胁迫）蛋白、热保护剂、蛋白酶体，以及众多尚未被完全阐明的分子耐热特性，此外还包括多细胞结构的形成。这类多细胞结构包含单细胞型以及细菌-古菌混合物种型两种。
目前仍有诸多悬而未决的问题，而古菌的多样性、遗传组成与系统发育位置，加之其所栖息的生态系统种类繁多，使得该领域拥有巨大的研究潜力。值得深入探究的具体方向包括：阐明伴侣蛋白复合物在不同温度下的作用机制、鉴定Hsp70伴侣机器的互作伙伴与替代蛋白、分析超嗜热菌体内的蛋白质折叠与复性过程，以及明确在温度、pH、渗透压与气压差异悬殊的环境中生存的古菌物种的胁迫基因调控分子机制。
如今借助单细胞与多细胞古菌模型，上述研究已具备可行性，且其研究成果可应用于基础与应用研究的诸多领域，包括探索与开拓人类、多数哺乳动物与植物均无法生存的极端生态系统。