硫氧化细菌的种类及硫氧化途径的研究进展

硫,作为生物必需的大量营养元素之一,参与了细胞的能量代谢与蛋白质、维生素和抗生素等物质代谢。自然界中,硫以多种化学形态存在,包括单质硫、还原性硫化物、硫酸盐和含硫有机物。硫氧化是硫元素生物地球化学循环的重要组成部分,通常是指单质硫或还原性硫化物被微生物氧化的过程。硫氧化细菌种类繁多,其硫氧化相关基因、酶和途径也多种多样。近几年,相关方面的研究已取得很多进展,但在不同层面仍存在一些尚未解决的科学问题。本文主要围绕硫氧化细菌的种类及硫氧化途径的研究进展进行了综述。     

Expression profiling of metabolic genes in response to methyl jasmonate reveals regulation of genes of primary and secondary sulfur-related pathways in Arabidopsis thaliana

The treatment of Arabidopsis thaliana with methyl jasmonate was used to investigate the reaction of 2467 selected genes of primary and secondary metabolism by macroarray hybridization. Hierarchical cluster analysis allowed distinctions to be made between diurnally and methyl jasmonate regulated genes in a time course from 30 min to 24 h. 97 and 64 genes were identified that were up- or down-regulated more than 2–fold by methyl jasmonate, respectively. These genes belong to 18 functional categories of which sulfur-related genes were by far strongest affected. Gene expression and metabolite patterns of sulfur metabolism were analysed in detail, since numerous defense compounds contain oxidized or reduced sulfur. Genes encoding key reactions of sulfate reduction as well as of cysteine, methionine and glutathione synthesis were rapidly up-regulated, but none of the known sulfur-deficiency induced sulfate transporter genes. In addition, increased expression of genes of sulfur-rich defense proteins and of enzymes involved in glucosinolate metabolism was observed. In contrast, profiling of primary and secondary sulfur metabolites revealed only an increase in the indole glucosinolate glucobrassicin upon methyl jasmonate treatment. The observed rapid mRNA changes were thus regulated by a signal independent of the known sulfur deficiency response. These results document for the first time how comprehensively the regulation of sulfur-related genes and plant defense are connected. This interaction is discussed as a new approach to differentiate between supply- and demand-driven regulation of the sulfate assimilation pathway.     

Sulfur Metabolism in Plants: Are Trees Different?

Sulfur metabolite levels and sulfur metabolism have been studied in a significant number of herbaceous and woody plant species. However, only a limited number of datasets are comparable and can be used to identify similarities and differences between these two groups of plants. From these data, it appears that large differences in sulfur metabolite levels, as well as the genetic organization of sulfate assimilation and metabolism do not exist between herbaceous plants and trees. The general response of sulfur metabolism to internal and/or external stimuli, such as oxidative stress, seems to be conserved between the two groups of plants. Thus, it can be expected that, generally, the molecular mechanisms of regulation of sulfur metabolism will also be similar. However, significant differences have been found in fine tuning of the regulation of sulfur metabolism and in developmental regulation of sulfur metabolite levels. It seems that the homeostasis of sulfur metabolism in trees is more robust than in herbaceous plants and a greater change in conditions is necessary to initiate a response in trees. This view is consistent with the requirement for highly flexible defence strategies in woody plant species as a consequence of longevity. In addition, seasonal growth of perennial plants exerts changes in sulfur metabolite levels and regulation that currently are not understood. In this review, similarities and differences in sulfur metabolite levels, sulfur assimilation and its regulation are characterized and future areas of research are identified.     

The level of sulfane sulfur in the fungus <Emphasis Type="Italic">Aspergillus nidulans</Emphasis> wild type and mutant strains

The interdependence of the sulfane sulfur metabolism and sulfur amino acid metabolism was studied in the fungus Aspergillus nidulans wild type strain and in mutants impaired in genes encoding enzymes involved in the synthesis of cysteine (a precursor of sulfane sulfur) or in regulatory genes of the sulfur metabolite repression system. It was found that a low concentration of cellular cysteine leads to elevation of two sulfane sulfurtransferases, rhodanase and cystathionine γ-lyase, while the level of 3-mercaptopyruvate sulfurtransferase remains largely unaffected. In spite of drastic differences in the levels of biosynthetic enzymes and of sulfur amino acids due to mutations or sulfur supplementation of cultures, the level of total sulfane sulfur is fairly stable. This stability confirms the crucial role of sulfane sulfur as a fine-tuning regulator of cellular metabolism.     

Molecular genetics of sulfate assimilation in plants

The sulfate assimilation pathway is the primary route by which higher plants obtain the sulfur necessary for growth. Sulfur is involved in a myriad of processes of central importance in metabolism. In the past few years much has been learned about this pathway and its regulation through analysis'of the genes encoding the enzymes and proteins that make up the sulfate assimilation pathway. The recent molecular genetic analysis builds on the biochemical and physiological groundwork of past studies. Further, gene analysis has provided the opportunity to compare directly the evolution of sulfate assimilation in plants and other organisms.,     

Regulation and evolution of chlorophyll metabolism

Chlorophylls are the most abundant tetrapyrrole molecules essential for photosynthesis in photosynthetic organisms. After many years of intensive research, most of the genes encoding the enzymes for the pathway have been identified, and recently the underlying molecular mechanisms have been elucidated. These studies revealed that the regulation of chlorophyll metabolism includes all levels of control to allow a balanced metabolic flow in response to external and endogenous factors and to ensure adaptation to varying needs of chlorophyll during plant development. Furthermore, identification of biosynthetic genes from various organisms and genetic analysis of functions of identified genes enables us to predict the evolutionary scenario of chlorophyll metabolism. In this review, based on recent findings, we discuss the regulation and evolution of chlorophyll metabolism.     

Riding the sulfur cycle--metabolism of sulfonates and sulfate esters in gram-negative bacteria

Sulfonates and sulfate esters are widespread in nature, and make up over 95% of the sulfur content of most aerobic soils. Many microorganisms can use sulfonates and sulfate esters as a source of sulfur for growth, even when they are unable to metabolize the carbon skeleton of the compounds. In these organisms, expression of sulfatases and sulfonatases is repressed in the presence of sulfate, in a process mediated by the LysR-type regulator protein CysB, and the corresponding genes therefore constitute an extension of the cys regulon. Additional regulator proteins required for sulfonate desulfonation have been identified in Escherichia coli (the Cbl protein) and Pseudomonas putida (the AsfR protein). Desulfonation of aromatic and aliphatic sulfonates as sulfur sources by aerobic bacteria is oxygen-dependent, carried out by the alpha-ketoglutarate-dependent taurine dioxygenase, or by one of several FMNH(2)-dependent monooxygenases. Desulfurization of condensed thiophenes is also FMNH(2)-dependent, both in the rhodococci and in two Gram-negative species. Bacterial utilization of aromatic sulfate esters is catalyzed by arylsulfatases, most of which are related to human lysosomal sulfatases and contain an active-site formylglycine group that is generated post-translationally. Sulfate-regulated alkylsulfatases, by contrast, are less well characterized. Our increasing knowledge of the sulfur-regulated metabolism of organosulfur compounds suggests applications in practical fields such as biodesulfurization, bioremediation, and optimization of crop sulfur nutrition.     

Microbial metabolism of sulfurand phosphorus-containing xenobiotics

Abstract: The enzymes involved in the microbial metabolism of many important phosphorus- or sulfur-containing xenobiotics, including organophosphate insecticides and precursors to organosulfate and organosulfonate detergents and dyestuffs have been characterized. In several instances their genes have been cloned and analysed. For phosphonate xenobiotics, the enzyme system responsible for the cleavage of the carbon-phosphorus bond has not yet been observed in vitro, though much is understood on a genetic level about phosphonate degradation. Phosphonate metabolism is regulated as part of the Pho regulon, under phosphate starvation control. For organophosphorothionate pesticides the situation is not so clear, and the mode of regulation appears to depend on whether the compounds are utilized to provide phosphorus, carbon or sulfur for cell growth. The same is true for organosulfonate metabolism, where different (and differently regulated) enzymatic pathways are involved in the utilization of sulfonates as carbon and as sulfur sources, respectively. Observations at the protein level in a number of bacteria suggest that a regulatory system is present which responds to sulfate limitation and controls the synthesis of proteins involved in providing sulfur to the cell and which may reveal analogies between the regulation of phosphorus and sulfur metabolism.     

万座嗜酸两面菌硫代谢相关膜蛋白基因的筛选

活性巯基在浸矿微生物硫代谢的过程中起着重要的作用,半胱氨酸残基作为蛋白质中活性巯基的提供者,为筛选硫代谢相关蛋白质基因提供了依据。本研究以极端嗜酸热古菌万座嗜酸两面菌Acidianus manzaensis为研究对象,基于其全基因组注释信息,筛选出编码富半胱氨酸残基的潜在硫代谢相关膜蛋白基因,并通过RT-qPCR实验对筛选出来的基因进行表达水平验证,同时利用生物信息学方法对其进一步分析。研究表明,与在亚铁中生长的细胞相比,单质硫培养下的细菌中与能量代谢相关的β-葡糖苷酶,与电子传递相关的ATP合成酶、NADH-辅酶Q氧化还原酶基因均表达上调,说明硫代谢途径可能与能量代谢和电子传递有着重要的联系。此外,还有三个假定蛋白基因表达上调,这三个假定膜蛋白中,ARM75161.1、ARM75436.1中的半胱氨酸都位于保守区域,且均有一个半胱氨酸残基暴露于膜外,而ARM75580.1中的半光氨酸不位于保守区域。其中ARM75436.1具有CXXXC结构域,且该结构域中半胱氨酸残基处于同一个β-折叠中。这些假定蛋白可能参与A. manzaensis中硫代谢途径。     

Computational identification of a new SelD-like family that may participate in sulfur metabolism in hyperthermophilic sulfur-reducing archaea

Background

Selenium (Se) and sulfur (S) are closely related elements that exhibit similar chemical properties. Some genes related to S metabolism are also involved in Se utilization in many organisms. However, the evolutionary relationship between the two utilization traits is unclear.

Results

In this study, we conducted a comparative analysis of the selenophosphate synthetase (SelD) family, a key protein for all known Se utilization traits, in all sequenced archaea. Our search showed a very limited distribution of SelD and Se utilization in this kingdom. Interestingly, a SelD-like protein was detected in two orders of Crenarchaeota: Sulfolobales and Thermoproteales. Sequence and phylogenetic analyses revealed that SelD-like protein contains the same domain and conserved functional residues as those of SelD, and might be involved in S metabolism in these S-reducing organisms. Further genome-wide analysis of patterns of gene occurrence in different thermoproteales suggested that several genes, including SirA-like, Prx-like and adenylylsulfate reductase, were strongly related to SelD-like gene. Based on these findings, we proposed a simple model wherein SelD-like may play an important role in the biosynthesis of certain thiophosphate compound.

Conclusions

Our data suggest novel genes involved in S metabolism in hyperthermophilic S-reducing archaea, and may provide a new window for understanding the complex relationship between Se and S metabolism in archaea.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-908) contains supplementary material, which is available to authorized users.     

Molecular characterization of four genes involved in sulfur metabolism in <Emphasis Type="Italic">Porphyra purpurea</Emphasis> (Roth) C. Agardh

Sulfated polysaccharides (carrageenans and agars) are among the most important products of red algae that are used as food additives as well as in molecular biology research. The quality and value of the product is greatly dependent on the levels and sites of sulfation of the polysaccharides. Little information is currently available on the molecular details of sulfur metabolism in red algae. Considering the economic importance of sulfated polysaccharide, elucidating the molecular details of sulfur metabolism in these organisms could help in future endeavors to improve algal commercial value, e.g., through genetic engineering. A cDNA library from the red alga Porphyra purpurea (Roth) C. Agardh was used to isolate four cDNAs with homology to genes encoding known sulfur assimilation enzymes: sulfate adenyltransferase (ATP sulfurylase), adenosine 5′-phosphosulfate kinase (APSK), sulfite reductase, and cysteine synthase. These cDNAs were characterized with respect to their molecular properties and a cDNA with homology to APSK was used to functionally complement an Escherichia coli auxotroph APSK⁻ mutant. The other cDNAs are being similarly characterized with respect to their ability to produce functional enzymes. Elucidation of the regulation of expression of these genes will aid in future research to determine the biochemical and genetic details of the sulfate assimilation pathway as well as its genetic manipulation in red algae.     

Trehalose and its applications in plant biotechnology

Trehalose, a nonreducing disaccharide of glucose, is one of the most effective osmoprotectants. Several strategies leading to its accumulation have been envisaged in both model and crop plants using genes of bacterial, yeast and, more recently, plant origin. Significant levels of trehalose accumulation have been shown to cause abiotic stress tolerance in transgenic plants. In this review, we describe the most biologically relevant features of trehalose: chemical and biological properties; occurrence and metabolism in organisms with special reference to plants; protective role in stabilizing molecules; physiological role in plants with special reference to carbohydrate metabolism. The emphasis of this review, however, will be on manipulation of trehalose metabolism to improve abiotic stress tolerance in plants.     

<Emphasis Type="Italic">Bd</Emphasis> oxidase homologue of photosynthetic purple sulfur bacterium <Emphasis Type="Italic">Allochromatium vinosum</Emphasis> is co-transcribed with a nitrogen fixation related gene

Purple sulfur bacteria, which are known to be the most ancient among anoxygenic phototrophs, play an important role in the global sulfur cycle. Allochromatium vinosum oxidizes reduced sulfur compounds such as hydrogen sulfide, elemental sulfur and thiosulfide. At low oxygen concentrations, A. vinosum can grow chemotrophically using oxygen as the terminal electron acceptor. Being also a nitrogen fixer, A. vinosum is faced with the paradox of co-existence of aerobic metabolism and nitrogen fixation. Due to growth difficulties, only a few studies have dealt with the aerobic metabolism of the organism and, until now, there has been no information about the genes involved in the respiratory metabolism of purple sulfur bacteria. In this article we show the first terminal oxidase gene for A. vinosum. The presence of a Bd type of quinol oxidase is necessary to protect nitrogenases against the inhibitory effects of oxygen. In this case, a nitrogen fixation related gene is part of the cyd operon and this gene is co-transcribed with cydAB genes. Bd oxidase of A. vinosum may be the earliest form of oxidase where the function of the enzyme is to scavenge the contaminant oxygen during nitrogen fixation. This may be an important clue about the early evolution of oxygenic photosynthesis, perhaps as a protective mechanism for nitrogen fixation.     

Microbial desulfurization of organic sulfur compounds in petroleum

Sulfur removal from petroleum is important from the standpoint of the global environment because the combustion of sulfur compounds leads to the production of sulfur oxides, which are the source of acid rain. As the regulations for sulfur in fuels become more stringent, the existing chemical desulfurizations are coming inadequate for the "deeper desulfurization" to produce lower-sulfur fuels without new and innovative processes. Biodesulfurization is rising as one of the candidates. Several microorganisms were found to desulfurize dibenzothiophene (DBT), a representative of the organic sulfur compounds in petroleum, forming a sulfur-free compound, 2-hydroxybiphenyl. They are promising as biocatalysts in the microbial desulfurization of petroleum because without assimilation of the carbon content, they remove only sulfur from the heterocyclic compounds which is refractory to conventional chemical desulfurization. Both enzymological and molecular genetic studies are now in progress for the purpose of obtaining improved desulfurization activity of organisms. The genes involved in the sulfur-specific DBT desulfurization were identified and the corresponding enzymes have been investigated. From the practical point of view, it has been proved that the microbial desulfurization proceeds in the presence of high concentrations of hydrocarbons, and more complicated DBT analogs are also desulfurized by the microorganisms. This review outlines the progress in the studies of the microbial desulfurization from the basic and practical point of view.