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。     

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。     

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。     

深海热液区化能自养菌Caminibacter profundus氢酶及其对H2的响应特点

化能自养菌中的氢酶在深海热液区生态系统的物质和能量转化中具有重要作用。以Caminibacter profundus为研究对象,通过设计PCR引物,克隆编码膜结合的类型I NiFe-氢酶大亚基基因序列hynL并进行生物信息学分析;研究hynL相对表达、甲基紫晶(MV)还原氢酶活性以及菌株生长对H2浓度变化的响应特点。结果表明,从C.profundus克隆获得864 bp的hynL基因片段,其编码的氨基端序列与Lebetimonas acidiphila的相似性为99%,与热液区化能自养的Epsilonproteobacteria D类群的类型I NiFe氢酶大亚基属同一分支。hynL相对表达量和MV还原的氢酶活性分别于12 h和24 h达到最高,此时菌体处于指数生长期;hynL相对表达量和MV还原的氢酶活性和菌株生长的最适H2浓度均为60%。提示C.profundus通过调控hynL的表达,响应环境中H2浓度的变化,以影响菌株能量代谢的催化过程和生长繁殖。     

四唑（Tetrazolium）对固氮鱼腥藻固氮和氢代谢的影响

固氮鱼腥藻(Anabaena azotica Ley)细胞能还原无色的TTC和NBT分别成为红色或蓝色的甲zan(formazan)沉淀。异形胞还原TTC的速率高于营养细胞。前异形胞及异形胞附近的营养细胞对NBT的还原作用最强。而异形胞对NBT不起还原作用。无论在异形胞形成红色甲zan或在营养细胞形成蓝色甲zan后都抑制固氮酶活性。NBT甲zan对固氮酶活性的抑制作用大于TTC甲zan,因为NBT氧化还原电位低于TTC。TTC和NBT两者都明显地抑制固氮鱼腥藻完整细胞的放氢。因鱼腥藻的放氢是由固氮酶催化的结果。四唑抑制放氢推想是由于它截取了固氮酶催化系统中的电子的缘故。固氮微生物(包括蓝色细菌和根瘤菌)对四唑还原与吸氢酶之间有无相关是一个争论的问题。一些学者认为分离豆科植物体的一些根瘤菌株培养于含有TTC的琼脂培养基,如还原,便可证明这些根瘤菌株能氧化氢;换言之,应用TTC的还原可作为一些根瘤菌的菌落具有吸氢酶的验证。相反,我们发现固氮鱼腥藻还原TTC和NBT之后,都没有影响吸氢的能力。因此,我们推想固氮鱼腥藻对四唑之还原与吸氢酶是没有直接的关系。     

光合细菌Chromatium vinosum可溶性氢酶的FTIR谱的研究

光合细菌Chromatium vinosum含有一种可溶性氢酶和一种膜结合态氢酶。氧化态可溶性氢酶在红外光谱区（1860－2140cm^-1）有四个特征吸收峰（2103．7,2086．2,2054．8和1962．5cm^-1）。其中1962．5cm^－1处吸收带的位置与已知的NiFe一氢酶活性中心－CO基团所产生的吸收带位置相近;另外三条吸收带的位置与已知的NiFe一氢酶活性中心－CN基团所产生的吸收带的位置相近。以2,6－二氯酚靛酚（DPIP）氧化可溶性氢酶时,四条吸收谱带的位置基本上没有发生变化。可溶性氢酶被Na2S2O4充分还原时,－CO基团的吸收带移至1946．8cm^-1,而－CN基团的三条吸收带中的两条分别移至2076．8cm^-1和2093．1cm^-1处,另一条则消失了。还原态可溶性氢酶与CO反应后,其红外光谱显示七条吸收带,在－CO基团红外光谱区和－CN基团红外光谱区各产生了两条新的吸收带。研究表明,Cuinosum可溶性氢酶的活性中心的结构类似于其它已知的NiFe－氢酶,但与活性中心金属原子相连的可能包括三个－CN基团和一个－CO基团,结合可溶性氢酶的FPR谱特征,推测C.vinosum可溶性氢酶活性中心的结构可能为Ni(CN)Fe(CN)2(CO).     

四唑(Tetrazolium)对固氮鱼腥藻固氮和氢代谢的影响

固氮鱼腥藻(Anabaena azotica Ley)细胞能还原无色的TTC和NBT分别成为红色或蓝色的甲(月朁)(formazan)沉淀。异形胞还原TTC的速率高于营养细胞。前异形胞及异形胞附近的营养细胞对NBT的还原作用最强。而异形胞对NBT不起还原作用。无论在异形胞形成红色甲(月朁)或在营养细胞形成蓝色甲(月朁)后都抑制固氮酶活性。NBT甲(月朁)对固氮酶活性的抑制作用大于TTC甲(月朁),因为NBT氧化还原电位低于TTC。 TTC和NBT两者都明显地抑制固氮鱼腥藻完整细胞的放氢。因鱼腥藻的放氢是由固氮酶催化的结果。四唑抑制放氢推想是由于它截取了固氮酶催化系统中的电子的缘故。固氮微生物(包括蓝色细菌和根瘤菌)对四唑还原与吸氢酶之间有无相关是一个争论的问题。一些学者认为分离豆科植物体的一些根瘤菌株培养于含有TTC的琼脂培养基,如还原,便可证明这些根瘤菌株能氧化氢;换言之,应用TTC的还原可作为一些根瘤菌的菌落具有吸氢酶的验证。相反,我们发现固氮鱼腥藻还原TTC和NBT之后,都没有影响吸氢的能力。因此,我们推想固氮鱼腥藻对四唑之还原与吸氢酶是没有直接的关系。     

氧化还原伴侣工程：P450低效问题的解决方案之一

细胞色素P450酶(CYPs或P450s)可将O₂的一个原子插入有机底物同时将另一个原子还原为水，广泛参与各种合成代谢和分解代谢过程，所以一直以来都是生物技术领域关注的焦点。在催化循环底物的氧化依赖于氧化还原伴侣向血红素铁传递电子，因此电子转移是P450s催化过程中的限速步骤。利用不同方法优化蛋白质-蛋白质相互作用以提高P450系统的电子转移效率，被称为“氧化还原伴侣工程”，是目前工程化P450s的重要手段之一，并取得了卓有成效的进展。本文将着重介绍关于氧化还原伴侣组分替换组装、P450酶与氧化还原伴侣融合及P450酶与氧化还原伴侣作用界面修饰等方面的进展，期望为未来该方面的工作提供一定的指导作用。     

荚膜红假单孢菌膜结合态氢酶生理电子受体性质的研究

对光合细菌荚膜红假单孢菌F菌株的部分纯化膜结合态氢酶进行了分离,此酶虽能催化氢的可逆氧化还原反应,但主要行使吸氢功能,其吸氢活性是放氢活性的100倍左右。在吸氢反应中,对电子载体MB的Km为10．4μm;此氢酶放氢活性的最适pH为7．2,电子载体为MV,阴离子F一、Cl-、Br一、I一和SO24一对放氢活性有不同程度抑制。同时,过渡金属阳离子Fe2+、Cu2+、Hg2+以及极性溶剂Me2SO对其放氢活性也有抑制作用。细胞色素c,作为电子载体可参与氢酶放氧反应;在氢酶存在下,细胞色素c,能被分子氢还原。而在相同测定条件下,Fd支持的氢酶放氢活性却很低,并且很难被氢一氢酶体系所还原。基于这些结果,对氢酶的生理电子受体性质进行了讨论。     

Delivery of iron-sulfur clusters to the hydrogen-oxidizing [NiFe]-hydrogenases in Escherichia coli requires the A-type carrier proteins ErpA and IscA

During anaerobic growth Escherichia coli synthesizes two membrane-associated hydrogen-oxidizing [NiFe]-hydrogenases, termed hydrogenase 1 and hydrogenase 2. Each enzyme comprises a catalytic subunit containing the [NiFe] cofactor, an electron-transferring small subunit with a particular complement of [Fe-S] (iron-sulfur) clusters and a membrane-anchor subunit. How the [Fe-S] clusters are delivered to the small subunit of these enzymes is unclear. A-type carrier (ATC) proteins of the Isc (iron-sulfur-cluster) and Suf (sulfur mobilization) [Fe-S] cluster biogenesis pathways are proposed to traffic pre-formed [Fe-S] clusters to apoprotein targets. Mutants that could not synthesize SufA had active hydrogenase 1 and hydrogenase 2 enzymes, thus demonstrating that the Suf machinery is not required for hydrogenase maturation. In contrast, mutants devoid of the IscA, ErpA or IscU proteins of the Isc machinery had no detectable hydrogenase 1 or 2 activities. Lack of activity of both enzymes correlated with the absence of the respective [Fe-S]-cluster-containing small subunit, which was apparently rapidly degraded. During biosynthesis the hydrogenase large subunits receive their [NiFe] cofactor from the Hyp maturation machinery. Subsequent to cofactor insertion a specific C-terminal processing step occurs before association of the large subunit with the small subunit. This processing step is independent of small subunit maturation. Using western blotting experiments it could be shown that although the amount of each hydrogenase large subunit was strongly reduced in the iscA and erpA mutants, some maturation of the large subunit still occurred. Moreover, in contrast to the situation in Isc-proficient strains, these processed large subunits were not membrane-associated. Taken together, our findings demonstrate that both IscA and ErpA are required for [Fe-S] cluster delivery to the small subunits of the hydrogen-oxidizing hydrogenases; however, delivery of the Fe atom to the active site might have different requirements.     

Reduction of unusual iron-sulfur clusters in the H2-sensing regulatory Ni-Fe hydrogenase from Ralstonia eutropha H16

The regulatory Ni-Fe hydrogenase (RH) from Ralstonia eutropha functions as a hydrogen sensor. The RH consists of the large subunit HoxC housing the Ni-Fe active site and the small subunit HoxB containing Fe-S clusters. The heterolytic cleavage of H(2) at the Ni-Fe active site leads to the EPR-detectable Ni-C state of the protein. For the first time, the simultaneous but EPR-invisible reduction of Fe-S clusters during Ni-C state formation was demonstrated by changes in the UV-visible absorption spectrum as well as by shifts of the iron K-edge from x-ray absorption spectroscopy in the wild-type double dimeric RH(WT) [HoxBC](2) and in a monodimeric derivative designated RH(stop) lacking the C-terminal 55 amino acids of HoxB. According to the analysis of iron EXAFS spectra, the Fe-S clusters of HoxB pronouncedly differ from the three Fe-S clusters in the small subunits of crystallized standard Ni-Fe hydrogenases. Each HoxBC unit of RH(WT) seems to harbor two [2Fe-2S] clusters in addition to a 4Fe species, which may be a [4Fe-3S-3O] cluster. The additional 4Fe-cluster was absent in RH(stop). Reduction of Fe-S clusters in the hydrogen sensor RH may be a first step in the signal transduction chain, which involves complex formation between [HoxBC](2) and tetrameric HoxJ protein, leading to the expression of the energy converting Ni-Fe hydrogenases in R. eutropha.     

Hydrogenases in sulfate-reducing bacteria function as chromium reductase

The ability of sulfate-reducing bacteria (SRB) to reduce chromate VI has been studied for possible application to the decontamination of polluted environments. Metal reduction can be achieved both chemically, by H₂S produced by the bacteria, and enzymatically, by polyhemic cytochromes c₃. We demonstrate that, in addition to low potential polyheme c-type cytochromes, the ability to reduce chromate is widespread among [Fe], [NiFe], and [NiFeSe] hydrogenases isolated from SRB of the genera Desulfovibrio and Desulfomicrobium. Among them, the [Fe] hydrogenase from Desulfovibrio vulgaris strain Hildenborough reduces Cr(VI) with the highest rate. Both [Fe] and [NiFeSe] enzymes exhibit the same K_m towards Cr(VI), suggesting that Cr(VI) reduction rates are directly correlated with hydrogen consumption rates. Electron paramagnetic resonance spectroscopy enabled us to probe the oxidation by Cr(VI) of the various metal centers in both [NiFe] and [Fe] hydrogenases. These experiments showed that Cr(VI) is reduced to paramagnetic Cr(III), and revealed inhibition of the enzyme at high Cr(VI) concentrations. The significant decrease of both hydrogenase and Cr(VI)-reductase activities in a mutant lacking [Fe] hydrogenase demonstrated the involvement of this enzyme in Cr(VI) reduction in vivo. Experiments with [3Fe-4S] ferredoxin from Desulfovibrio gigas demonstrated that the low redox [Fe-S] (non-heme iron) clusters are involved in the mechanism of metal reduction by hydrogenases.     

A model system for [NiFe] hydrogenase maturation studies: Purification of an active site-containing hydrogenase large subunit without small subunit

The large subunit HoxC of the H2-sensing [NiFe] hydrogenase from Ralstonia eutropha was purified without its small subunit. Two forms of HoxC were identified. Both forms contained iron but only substoichiometric amounts of nickel. One form was a homodimer of HoxC whereas the second also contained the Ni-Fe site maturation proteins HypC and HypB. Despite the presence of the Ni-Fe active site in some of the proteins, both forms, which lack the Fe-S clusters normally present in hydrogenases, cannot activate hydrogen. The incomplete insertion of nickel into the Ni-Fe site provides direct evidence that Fe precedes Ni in the course of metal center assembly.     

The hows and whys of aerobic H2 metabolism

The bacterial [NiFe]-hydrogenases have been classified as either 'standard' or 'O2-tolerant' based on their ability to function in the presence of O2. Typically, these enzymes contain four redox-active metal centers: a Ni-Fe-CO-2CN- active site and three electron-transferring Fe-S clusters. Recent research suggests that, rather than differences at the catalytic active site, it is a novel Fe-S cluster electron transfer (ET) relay that controls how [NiFe]-hydrogenases recover from O2 attack. In light of recent structural data and mutagenic studies this article reviews the molecular mechanism of O2-tolerance in [NiFe]-hydrogenases and discusses the biosynthesis of the unique Fe-S relay.     

Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution

Background

Photosynthetic microorganisms that directly channel solar energy to the production of molecular hydrogen are a potential future biofuel system. Building such a system requires installation of a hydrogenase in the photosynthetic organism that is both tolerant to oxygen and capable of hydrogen production. Toward this end, we have identified the [NiFe] hydrogenase from the marine bacterium Alteromonas macleodii “Deep ecotype” that is able to be heterologously expressed in cyanobacteria and has tolerance to partial oxygen. The A. macleodii enzyme shares sequence similarity with the uptake hydrogenases that favor hydrogen uptake activity over hydrogen evolution. To improve hydrogen evolution from the A. macleodii hydrogenase, we examined the three Fe-S clusters found in the small subunit of many [NiFe] uptake hydrogenases that presumably act as a molecular wire to guide electrons to or from the active site of the enzyme. Studies by others altering the medial cluster of a Desulfovibrio fructosovorans hydrogenase from 3Fe-4S to 4Fe-4S resulted in two-fold improved hydrogen evolution activity.

Results

We adopted a strategy of screening for improved hydrogenase constructs using an Escherichia coli expression system before testing in slower growing cyanobacteria. From the A. macleodii enzyme, we created a mutation in the gene encoding the hydrogenase small subunit that in other systems is known to convert the 3Fe-4S medial cluster to 4Fe-4S. The medial cluster substitution did not improve the hydrogen evolution activity of our hydrogenase. However, modifying both the medial cluster and the ligation of the distal Fe-S cluster improved in vitro hydrogen evolution activity relative to the wild type hydrogenase by three- to four-fold. Other properties of the enzyme including thermostability and tolerance to partial oxygen did not appear to be affected by the substitutions.

Conclusions

Our results show that substitution of amino acids altering the ligation of Fe-S clusters in the A. macleodii [NiFe] uptake hydrogenase resulted in increased hydrogen evolution activity. This activity can be recapitulated in multiple host systems and with purified protein. These results validate the approach of using an E. coli-cyanobacteria shuttle system for enzyme expression and improvement.

     

Insights into [FeFe]-hydrogenase structure, mechanism, and maturation

Hydrogenases are metalloenzymes that are key to energy metabolism in a variety of microbial communities. Divided into three classes based on their metal content, the [Fe]-, [FeFe]-, and [NiFe]-hydrogenases are evolutionarily unrelated but share similar nonprotein ligand assemblies at their active site metal centers that are not observed elsewhere in biology. These nonprotein ligands are critical in tuning enzyme reactivity, and their synthesis and incorporation into the active site clusters require a number of specific maturation enzymes. The wealth of structural information on different classes and different states of hydrogenase enzymes, biosynthetic intermediates, and maturation enzymes has contributed significantly to understanding the biochemistry of hydrogen metabolism. This review highlights the unique structural features of hydrogenases and emphasizes the recent biochemical and structural work that has created a clearer picture of the [FeFe]-hydrogenase maturation pathway.     

Redox intermediates of Desulfovibrio gigas [NiFe] hydrogenase generated under hydrogen. M?ssbauer and EPR characterization of the metal centers

The hydrogenase (EC 1.2.2.1) of Desulfovibrio gigas is a complex enzyme containing one nickel center, one [3Fe-4S] and two [4Fe-4S] clusters. Redox intermediates of this enzyme were generated under hydrogen (the natural substrate) using a redox-titration technique and were studied by EPR and M?ssbauer spectroscopy. In the oxidized states, the two [4Fe-4S]2+ clusters exhibit a broad quadrupole doublet with parameters (apparent delta EQ = 1.10 mm/s and delta = 0.35 mm/s) typical for this type of cluster. Upon reduction, the two [4Fe-4S]1+ clusters are spectroscopically distinguishable, allowing the determination of their midpoint redox potentials. The cluster with higher midpoint potential (-290 +/- 20 mV) was labeled Fe-S center I and the other with lower potential (-340 +/- 20 mV), Fe-S center II. Both reduced clusters show atypical magnetic hyperfine coupling constants, suggesting structural differences from the clusters of bacterial ferredoxins. Also, an unusually broad EPR signal, labeled Fe-S signal B', extending from approximately 150 to approximately 450 mT was observed concomitantly with the reduction of the [4Fe-4S] clusters. The following two EPR signals observed at the weak-field region were tentatively attributed to the reduced [3Fe-4S] cluster: (i) a signal with crossover point at g approximately 12, labeled the g = 12 signal, and (ii) a broad signal at the very weak-field region (approximately 3 mT), labeled the Fe-S signal B. The midpoint redox potential associated with the appearance of the g = 12 signal was determined to be -70 +/- 10 mV. At potentials below -250 mV, the g = 12 signal began to decrease in intensity, and simultaneously, the Fe-S signal B appeared. The transformation of the g = 12 signal into the Fe-S signal B was found to parallel the reduction of the two [4Fe-4S] clusters indicating that the [3Fe-4S]o cluster is sensitive to the redox state of the [4Fe-4S] clusters. Detailed redox profiles for the previously reported Ni-signal C and the g = 2.21 signal were obtained in this study, and evidence was found to indicate that these two signals represent two different oxidation states of the enzyme. Finally, the mechanistic implications of our results are discussed.     

Molecular biology of microbial hydrogenases

Hydrogenases (H2ases) are metalloproteins. The great majority of them contain iron-sulfur clusters and two metal atoms at their active center, either a Ni and an Fe atom, the [NiFe]-H2ases, or two Fe atoms, the [FeFe]-H2ases. Enzymes of these two classes catalyze the reversible oxidation of hydrogen gas (H2 <--> 2 H+ + 2 e-) and play a central role in microbial energy metabolism; in addition to their role in fermentation and H2 respiration, H2ases may interact with membrane-bound electron transport systems in order to maintain redox poise, particularly in some photosynthetic microorganisms such as cyanobacteria. Recent work has revealed that some H2ases, by acting as H2-sensors, participate in the regulation of gene expression and that H2-evolving H2ases, thought to be involved in purely fermentative processes, play a role in membrane-linked energy conservation through the generation of a protonmotive force. The Hmd hydrogenases of some methanogenic archaea constitute a third class of H2ases, characterized by the absence of Fe-S cluster and the presence of an iron-containing cofactor with catalytic properties different from those of [NiFe]- and [FeFe]-H2ases. In this review, we emphasise recent advances that have greatly increased our knowledge of microbial H2ases, their diversity, the structure of their active site, how the metallocenters are synthesized and assembled, how they function, how the synthesis of these enzymes is controlled by external signals, and their potential use in biological H2 production.