微生物产氢机理的研究进展

微生物可以利用工业废弃物产生氢气,其产氢机理可以分成两种:光合产氢和发酵产氢。前者利用光能,后者利用代谢过程中产生的电子,分解有机物产氢。氢酶是产氢过程中的关键酶,催化氢的氧化或质子的还原。氢酶主要有[NiFe]氢酶和[Fe]氢酶两种,具有不同的结构,但催化机理是相似的。本文主要综述产氢微生物的种类、微生物产氢代谢途径和关键酶催化机理,并展望微生物产氢研究的发展方向。     

氢酶结构及催化机理研究进展

氢酶是一类催化氢的氧化或质子还原的酶,它在微生物产氢过程中扮演着重要角色。根据氢酶所含的金属元素,可分为NiFe_氢酶、Fe-氢酶和不含金属元素的metal_free氢酶。大多数氢酶含有金属原子,它们参与氢酶活性中心和[Fe_S]簇的形成。氢酶的活性中心直接催化氢的氧化与质子的还原,[Fe_S]簇则参与氢酶催化过程中电子的传输。目前已有数种NiFe_氢酶和Fe_氢酶的X射线衍射晶体结构被阐明。根据metal_free氢酶的序列特征,推断其结构与NiFe_氢酶和Fe_氢酶之间存在较大差异。对氢酶活性中心和[Fe_S]簇的深入研究,揭示了氢酶催化反应的机理。     

高等植物氢化酶活性研究进展

氢化酶作为一种可催化氢气氧化与质子还原的金属酶,在生物体的氢代谢过程中发挥着关键作用。已有研究表明,氢气干预可对植物的生长发育和抗逆性产生积极影响,同时一些高等植物的内源性产氢现象也已得到证实,然而关于催化内源性产氢的氢化酶目前了解较少。虽然已有多项研究表明,叶绿体可能是高等植物产氢的关键部位,但是鉴于多种植物在种子萌发时仍然可以产氢,而种子萌发过程中叶绿体还没有生成,加上氢化酶在进化上与线粒体复合物Ⅰ具有同源性,在对氢化酶研究现状进行概述的基础上,提出了高等植物线粒体具有氢化酶活性的猜想,并总结了线粒体存在氢化酶活性的初步实验证据,以期为后续线粒体与氢化酶的关系研究提供参考依据。     

绿藻高效制氢影响因素的研究

绿藻作为生物能源的研究和开发具有诱人的发展前景。本文概述了绿藻制氢和产氢途径的研究进展,重点介绍了绿藻高效制氢的影响因素--绿藻[Fe]-氢化酶的研究和绿藻制氢的重要控制参数,同时,对绿藻制氢作为生物能源的开发应用前景进行了展望。     

氢化酶重组表达研究进展

氢化酶催化最简单的氧化还原反应,但蛋白结构却非常复杂,对其蛋白结构和催化功能的研究牵动着生物制氢、光电产氢催化剂及氢能源电池等相关绿色能源产业的发展。氢化酶通常可逆地催化质子还原产氢的反应,对氧化还原电位非常敏感,催化活性中心易于被氧化失活,活性蛋白的分离提纯十分不易,使得对其催化机制的认识推进缓慢。为了获取更多的氢化酶活性蛋白,许多研究团队先后对氢化酶开展了大量的同源或异源重组表达研究,就这类研究工作进行了扼要的总结和分析。     

产甲烷古菌铁氢酶研究进展

根据活性中心金属原子的不同,氢酶主要分为镍铁、铁铁、铁氢酶三大类。铁氢酶是发现较晚、存在物种单一且结构较为特殊的一类氢酶。目前,铁氢酶仅发现于氢营养型产甲烷古菌中。该酶直接催化氢气异裂,还原产甲烷代谢途径中一碳载体四氢蝶呤的次甲基转化为亚甲基。与其他两类氢酶相比,铁氢酶不含传递电子的铁硫簇和双金属活性中心,在结构组成上有较大的差异。此外,铁氢酶活性中心的吡啶环被高度取代,活性中心铁原子直接与酰基碳成键,这些奇特的活性分子结构预示着氢酶全新的催化机制,以及古菌细胞在合成特殊结构大分子方面的特殊功能。本文总结了从1990年发现这类新型氢酶以来的相关研究,分别从氢酶的生理功能、结构特征、催化机制、成熟过程及应用研究等方面阐述铁氢酶的研究进展。     

粪产碱菌A—15氢酶的初步探讨

1931年Stephenson及其同事从异养菌中发现氢酶以来,国内外科学家们均在好气微生物和厌气微生物的氢酶方面做了大量的工作。鉴于氢酶在固氮过程中可能起节能作用,这与固氮活力有重要关系。本文就微需氧固氮的稻根联合固氮菌粪产碱菌A—15(AlcaligenesfaecalisA—15)氢酶进行了一些研究。     

蓝藻Hox氢酶催化产氢的调控

蓝藻是唯一能通过光合作用产生清洁可再生燃料氢气的原核微生物。一些蓝藻具有催化产氢活性的镍-铁Hox氢酶(双向氢酶), 由于其巨大的应用潜力受到广泛的关注。但Hox氢酶在蓝藻产氢过程中调控途径尚不清楚。本文对蓝藻Hox氢酶的结构、生态分布和表达调控的研究进展进行了总结。简单介绍了作者近来对模式蓝藻Synechocystis sp. PCC 6803 hox操纵子中两个未知功能基因ssl2420和sll1225的研究结果。     

绿藻[FeFe]氢化酶

该文介绍了绿藻[FeFe]氢化酶的研究现状,包括酶的结构、催化中心、金属簇的性质,以及对氧的敏感性和可能的解决办法。并且对已报道的绿藻[FeFe]氢化酶基因及其调控等问题作了介绍。     

贵州传统发酵豆制品中水解银杏黄酮苷的微生物β-葡萄糖苷酶筛选

[目的]微生物β-葡萄糖苷酶法水解银杏黄酮苷具有重要意义,不过目前这方面的研究极少。因此,本文目的是筛选到水解银杏黄酮苷的酶活高的微生物β-葡萄糖苷酶,并分析其底物选择性机制。[方法]以银杏叶提取物作为唯一碳源富集培养,从贵州传统发酵豆豉中筛选产对银杏黄酮苷水解酶活高的β-葡萄糖苷酶的菌株,并对该菌株进行鉴定。然后比较此β-葡萄糖苷酶对不同底物的选择性,同时测定此酶水解银杏黄酮苷反应的米氏常数Km及最大反应速率Vmax。最后,对不同的底物进行分子对接,分析其底物特异性机制。[结果]结果表明,筛选到的菌株GUXN01所产β-葡萄糖苷酶水解银杏黄酮苷的酶活最高,被鉴定为枯草芽孢杆菌。此β-葡糖糖苷酶对β构型的糖类以及苷类等具有广泛的底物特异性和不同的选择性,尤其对银杏黄酮苷具有很好的亲和性。分子对接研究表明枯草芽孢杆菌β-葡萄糖苷酶对银杏黄酮苷和其他糖苷类具有不同亲和性和选择性的原因主要是酶结构和底物分子结构的相互作用力的差异导致的。[结论]这些发现为GUXN01所产的β-葡萄糖苷酶应用于水解银杏黄酮苷类生产相应苷元奠定了良好的基础。     

Functional studies of [FeFe] hydrogenase maturation in an Escherichia coli biosynthetic system

Maturation of [FeFe] hydrogenases requires the biosynthesis and insertion of the catalytic iron-sulfur cluster, the H cluster. Two radical S-adenosylmethionine (SAM) proteins proposed to function in H cluster biosynthesis, HydEF and HydG, were recently identified in the hydEF-1 mutant of the green alga Chlamydomonas reinhardtii (M. C. Posewitz, P. W. King, S. L. Smolinski, L. Zhang, M. Seibert, and M. L. Ghirardi, J. Biol. Chem. 279:25711-25720, 2004). Previous efforts to study [FeFe] hydrogenase maturation in Escherichia coli by coexpression of C. reinhardtii HydEF and HydG and the HydA1 [FeFe] hydrogenase were hindered by instability of the hydEF and hydG expression clones. A more stable [FeFe] hydrogenase expression system has been achieved in E. coli by cloning and coexpression of hydE, hydF, and hydG from the bacterium Clostridium acetobutylicum. Coexpression of the C. acetobutylicum maturation proteins with various algal and bacterial [FeFe] hydrogenases in E. coli resulted in purified enzymes with specific activities that were similar to those of the enzymes purified from native sources. In the case of structurally complex [FeFe] hydrogenases, maturation of the catalytic sites could occur in the absence of an accessory iron-sulfur cluster domain. Initial investigations of the structure and function of the maturation proteins HydE, HydF, and HydG showed that the highly conserved radical-SAM domains of both HydE and HydG and the GTPase domain of HydF were essential for achieving biosynthesis of active [FeFe] hydrogenases. Together, these results demonstrate that the catalytic domain and a functionally complete set of Hyd maturation proteins are fundamental to achieving biosynthesis of catalytic [FeFe] hydrogenases.     

Selenium is involved in regulation of periplasmic hydrogenase gene expression in Desulfovibrio vulgaris Hildenborough

Desulfovibrio vulgaris Hildenborough is a good model organism to study hydrogen metabolism in sulfate-reducing bacteria. Hydrogen is a key compound for these organisms, since it is one of their major energy sources in natural habitats and also an intermediate in the energy metabolism. The D. vulgaris Hildenborough genome codes for six different hydrogenases, but only three of them, the periplasmic-facing [FeFe], [FeNi]1, and [FeNiSe] hydrogenases, are usually detected. In this work, we studied the synthesis of each of these enzymes in response to different electron donors and acceptors for growth as well as in response to the availability of Ni and Se. The formation of the three hydrogenases was not very strongly affected by the electron donors or acceptors used, but the highest levels were observed after growth with hydrogen as electron donor and lowest with thiosulfate as electron acceptor. The major effect observed was with inclusion of Se in the growth medium, which led to a strong repression of the [FeFe] and [NiFe]1 hydrogenases and a strong increase in the [NiFeSe] hydrogenase that is not detected in the absence of Se. Ni also led to increased formation of the [NiFe]1 hydrogenase, except for growth with H2, where its synthesis is very high even without Ni added to the medium. Growth with H2 results in a strong increase in the soluble forms of the [NiFe]1 and [NiFeSe] hydrogenases. This study is an important contribution to understanding why D. vulgaris Hildenborough has three periplasmic hydrogenases. It supports their similar physiological role in H2 oxidation and reveals that element availability has a strong influence in their relative expression.     

Biochemical and Molecular Genetic Basis of Hydrogenases

Hydrogenases catalyse the reversible reduction of protons to molecular hydrogen. Applied research is focused on structure and catalytic function under the aspect of hydrogen formation. In this review we summarize the current knowledge about properties and physiological roles of hydrogenases in pro- and eukaryotes and compile molecular genetical data about structural features of prokaryotic hydrogenases. Finally, prospects are given for the possible application of hydrogenases or ‘hydrogenase-like catalysts’ in energy production.     

Iron hydrogenases and the evolution of anaerobic eukaryotes

Hydrogenases, oxygen-sensitive enzymes that can make hydrogen gas, are key to the function of hydrogen-producing organelles (hydrogenosomes), which occur in anaerobic protozoa scattered throughout the eukaryotic tree. Hydrogenases also play a central role in the hydrogen and syntrophic hypotheses for eukaryogenesis. Here, we show that sequences related to iron-only hydrogenases ([Fe] hydrogenases) are more widely distributed among eukaryotes than reports of hydrogen production have suggested. Genes encoding small proteins which contain conserved structural features unique to [Fe] hydrogenases were identified on all well-surveyed aerobic eukaryote genomes. Longer sequences encoding [Fe] hydrogenases also occur in the anaerobic eukaryotes Entamoeba histolytica and Spironucleus barkhanus, both of which lack hydrogenosomes. We also identified a new [Fe] hydrogenase sequence from Trichomonas vaginalis, bringing the total of [Fe] hydrogenases reported for this organism to three, all of which may function within its hydrogenosomes. Phylogenetic analysis and hypothesis testing using likelihood ratio tests and parametric bootstrapping suggest that the [Fe] hydrogenases in anaerobic eukaryotes are not monophyletic. Iron-only hydrogenases from Entamoeba, Spironucleus, and Trichomonas are plausibly monophyletic, consistent with the hypothesis that a gene for [Fe] hydrogenase was already present on the genome of the common, perhaps also anaerobic, ancestor of these phylogenetically distinct eukaryotes. Trees where the [Fe] hydrogenase from the hydrogenosomal ciliate Nyctotherus was constrained to be monophyletic with the other eukaryote sequences were rejected using a likelihood ratio test of monophyly. In most analyses, the Nyctotherus sequence formed a sister group with a [Fe] hydrogenase on the genome of the eubacterium Desulfovibrio vulgaris. Thus, it is possible that Nyctotherus obtained its hydrogenosomal [Fe] hydrogenase from a different source from Trichomonas for its hydrogenosomes. We find no support for the hypothesis that components of the Nyctotherus [Fe] hydrogenase fusion protein derive from the mitochondrial respiratory chain.     

Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.

BACKGROUND: Many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. These reactions are catalyzed by two unrelated enzymes: the Ni-Fe hydrogenases and the Fe-only hydrogenases. RESULTS: We report here the structure of the heterodimeric Fe-only hydrogenase from Desulfovibrio desulfuricans - the first for this class of enzymes. With the exception of a ferredoxin-like domain, the structure represents a novel protein fold. The so-called H cluster of the enzyme is composed of a typical [4Fe-4S] cubane bridged to a binuclear active site Fe center containing putative CO and CN ligands and one bridging 1, 3-propanedithiol molecule. The conformation of the subunits can be explained by the evolutionary changes that have transformed monomeric cytoplasmic enzymes into dimeric periplasmic enzymes. Plausible electron- and proton-transfer pathways and a putative channel for the access of hydrogen to the active site have been identified. CONCLUSIONS: The unrelated active sites of Ni-Fe and Fe-only hydrogenases have several common features: coordination of diatomic ligands to an Fe ion; a vacant coordination site on one of the metal ions representing a possible substrate-binding site; a thiolate-bridged binuclear center; and plausible proton- and electron-transfer pathways and substrate channels. The diatomic coordination to Fe ions makes them low spin and favors low redox states, which may be required for catalysis. Complex electron paramagnetic resonance signals typical of Fe-only hydrogenases arise from magnetic interactions between the [4Fe-4S] cluster and the active site binuclear center. The paucity of protein ligands to this center suggests that it was imported from the inorganic world as an already functional unit.     

The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.

BACKGROUND: [NiFeSe] hydrogenases are metalloenzymes that catalyze the reaction H2<-->2H+ + 2e-. They are generally heterodimeric, contain three iron-sulfur clusters in their small subunit and a nickel-iron-containing active site in their large subunit that includes a selenocysteine (SeCys) ligand. RESULTS: We report here the X-ray structure at 2.15 A resolution of the periplasmic [NiFeSe] hydrogenase from Desulfomicrobium baculatum in its reduced, active form. A comparison of active sites of the oxidized, as-prepared, Desulfovibrio gigas and the reduced D. baculatum hydrogenases shows that in the reduced enzyme the nickel-iron distance is 0.4 A shorter than in the oxidized enzyme. In addition, the putative oxo ligand, detected in the as-prepared D. gigas enzyme, is absent from the D. baculatum hydrogenase. We also observe higher-than-average temperature factors for both the active site nickel-selenocysteine ligand and the neighboring Glu18 residue, suggesting that both these moieties are involved in proton transfer between the active site and the molecular surface. Other differences between [NiFeSe] and [NiFe] hydrogenases are the presence of a third [4Fe4S] cluster replacing the [3Fe4S] cluster found in the D. gigas enzyme, and a putative iron center that substitutes the magnesium ion that has already been described at the C terminus of the large subunit of two [NiFe] hydrogenases. CONCLUSIONS: The heterolytic cleavage of molecular hydrogen seems to be mediated by the nickel center and the selenocysteine residue. Beside modifying the catalytic properties of the enzyme, the selenium ligand might protect the nickel atom from oxidation. We conclude that the putative oxo ligand is a signature of inactive 'unready' [NiFe] hydrogenases.     

Characterization of a cyanobacterial-like uptake [NiFe] hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans

Electron paramagnetic resonance (EPR) and Fourier transform IR studies on the soluble hydrogenase from Acidithiobacillus ferrooxidans are presented. In addition, detailed sequence analyses of the two subunits of the enzyme have been performed. They show that the enzyme belongs to a group of uptake [NiFe] hydrogenases typical for Cyanobacteria. The sequences have also a close relationship to those of the H₂-sensor proteins, but clearly differ from those of standard [NiFe] hydrogenases. It is concluded that the structure of the catalytic centre is similar, but not identical, to that of known [NiFe] hydrogenases. The active site in the majority of oxidized enzyme molecules, 97% in cells and more than 50% in the purified enzyme, is EPR-silent. Upon contact with H₂ these sites remain EPR-silent and show only a limited IR response. Oxidized enzyme molecules with an EPR-detectable active site show a Ni_r*-like EPR signal which is light-sensitive at cryogenic temperatures. This is a novelty in the field of [NiFe] hydrogenases. Reaction with H₂ converts these active sites to the well-known Ni_a-C* state. Illumination below 160 K transforms this state into the Ni_a-L* state. The reversal, in the dark at 200 K, proceeds via an intermediate Ni EPR signal only observed with the H₂-sensor protein from Ralstonia eutropha. The EPR-silent active sites in as-isolated and H₂-treated enzyme are also light-sensitive as observed by IR spectra at cryogenic temperatures. The possible origin of the light sensitivity is discussed. This study represents the first spectral characterization of an enzyme of the group of cyanobacterial uptake hydrogenases. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Analyses of the large subunit histidine-rich motif expose an alternative proton transfer pathway in [NiFe] hydrogenases

A highly conserved histidine-rich region with unknown function was recognized in the large subunit of [NiFe] hydrogenases. The HxHxxHxxHxH sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. Site-directed mutagenesis of the His-rich region of the T. roseopersicina membrane-attached Hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the His104 residue. Computational analysis of the hydrogen bond network in the large subunits indicated that the second histidine of this motif might be a component of a proton transfer pathway including Arg487, Asp103, His104 and Glu436. Substitutions of the conserved amino acids of the presumed transfer route impaired the activity of the Hyn hydrogenase. Western hybridization was applied to demonstrate that the cellular level of the mutant hydrogenases was similar to that of the wild type. Mostly based on theoretical modeling, few proton transfer pathways have already been suggested for [NiFe] hydrogenases. Our results propose an alternative route for proton transfer between the [NiFe] active center and the surface of the protein. A novel feature of this model is that this proton pathway is located on the opposite side of the large subunit relative to the position of the small subunit. This is the first study presenting a systematic analysis of an in silico predicted proton translocation pathway in [NiFe] hydrogenases by site-directed mutagenesis.