革兰氏阴性菌TonB依赖性受体的功能与结构研究进展*

为维持生长所需,革兰氏阴性菌需要从外界摄取多种营养物质。分子量小于600 Da的分子可以通过自由扩散的方式通过革兰氏阴性菌的外膜,而大分子物质则需要特殊的转运系统才能将其转运至革兰氏阴性菌的胞内。革兰氏阴性菌对大分子营养物质的识别和转运主要由TonB依赖性受体负责完成。所有革兰氏阴性菌中均有TonB依赖性受体的存在,然而不同种类的革兰氏阴性菌拥有TonB依赖性受体的数量不同且功能各异。最近研究表明,TonB依赖性受体不仅参与了铁、血红素、锰、锌、镍、维生素、碳水化合物等多种营养物质的摄取,而且参与了蛋白酶的分泌。为对TonB依赖性受体提供更为深入和系统的理解,详细介绍了目前已知的TonB依赖性受体的功能及结构,以期为更进一步探知TonB依赖性受体未知功能提供可参考依据。     

A growing family: the expanding universe of the bacterial cytoskeleton

Cytoskeletal proteins are important mediators of cellular organization in both eukaryotes and bacteria. In the past, cytoskeletal studies have largely focused on three major cytoskeletal families, namely the eukaryotic actin, tubulin, and intermediate filament (IF) proteins and their bacterial homologs MreB, FtsZ, and crescentin. However, mounting evidence suggests that these proteins represent only the tip of the iceberg, as the cellular cytoskeletal network is far more complex. In bacteria, each of MreB, FtsZ, and crescentin represents only one member of large families of diverse homologs. There are also newly identified bacterial cytoskeletal proteins with no eukaryotic homologs, such as WACA proteins and bactofilins. Furthermore, there are universally conserved proteins, such as the metabolic enzyme CtpS, that assemble into filamentous structures that can be repurposed for structural cytoskeletal functions. Recent studies have also identified an increasing number of eukaryotic cytoskeletal proteins that are unrelated to actin, tubulin, and IFs, such that expanding our understanding of cytoskeletal proteins is advancing the understanding of the cell biology of all organisms. Here, we summarize the recent explosion in the identification of new members of the bacterial cytoskeleton and describe a hypothesis for the evolution of the cytoskeleton from self-assembling enzymes.     

Bioactive Compounds from Marine Bacteria and Fungi

Marine bacteria and fungi are of considerable importance as new promising sources of a huge number of biologically active products. Some of these marine species live in a stressful habitat, under cold, lightless and high pressure conditions. Surprisingly, a large number of species with high diversity survive under such conditions and produce fascinating and structurally complex natural products. Up till now, only a small number of microorganisms have been investigated for bioactive metabolites, yet a huge number of active substances with some of them featuring unique structural skeletons have been isolated. This review covers new biologically active natural products published recently (2007–09) and highlights the chemical potential of marine microorganisms, with focus on bioactive products as well as on their mechanisms of action.     

Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics

The availability of whole genome sequences has enabled the application of powerful tools for assaying global expression patterns in environmentally relevant bacteria such as Shewanella oneidensis MR-1. A large number of genes in prokaryote genomes, including MR-1, have been annotated as hypothetical, indicating that no similar protein has yet been identified in other organisms. Using high-sensitivity MS coupled with accurate mass and time (AMT) tag methodology, 1078 tryptic peptides were collectively detected in MR-1 cultures, 671 of which were unique to their parent protein. Using only these unique tryptic peptides and a minimum of two peptides per protein, we identified, with high confidence, the expression of 258 hypothetical proteins. These proteins ranged from 3.5 to 139 kDa, with 47 being 100 amino acid residues or less. Using a combination of information including detection in cells grown under specific culture conditions, presence within a specific cell fraction, and predictive algorithms such as PSORT and PSORT-B, possible/plausible functions are proposed for some hypothetical proteins. Further, by applying this approach a number of proteins were found not only to be expressed, but only expressed under certain culturing conditions, thereby suggesting function while at the same time isolating several proteins to distinct locales of the cell. These results demonstrate the utility of the AMT tag methodology for comprehensive profiling of the microbial proteome while confirming the expression of a large number of hypothetical genes.     

Class IIa bacteriocins: biosynthesis, structure and activity

In the last decade, a variety of ribosomally synthesized antimicrobial peptides or bacteriocins produced by lactic acid bacteria have been identified and characterized. As a result of these studies, insight has been gained into fundamental aspects of biology and biochemistry such as producer self protection, membrane-protein interactions, and protein modification and secretion. Moreover, it has become evident that these peptides may be developed into useful antimicrobial additives. Class IIa bacteriocins can be considered as the major subgroup of bacteriocins from lactic acid bacteria, not only because of their large number, but also because of their activities and potential applications. They have first attracted particular attention as listericidal compounds and are now believed to be the next in line if more bacteriocins are to be approved in the future. The present review attempts to provide an insight into general knowledge available for class IIa bacteriocins and discusses common features and recent findings concerning these substances.     

The association of Western flower thrips, Frankliniella occidentalis, with a near Erwinia species gut bacteria: transient or permanent?

Associations between insects and gut bacteria are ubiquitous. It is possible to make a distinction between permanent associations (called symbiosis), in which the same type of bacteria is present in more than one generation of the insect, and transient associations. Transient bacteria are ingested together with food but do not settle in the insect gut in such a way that they will be passed on to the next generation. In this study, we describe the permanent association between Western flower thrips (Frankliniella occidentalis), a polyphagous insect species that is a major pest worldwide, and one type of gut bacteria. On the basis of direct microscopic observations and counts of bacteria, it was found that thrips from the populations studied contained large numbers of bacteria in their hindgut. Bacteria were isolated from their host and grown on 10 different agar media. The number of bacteria isolated on agar media equaled the number of direct counts. All isolates had the same colony morphology. On the basis of their 16S rDNA sequence these bacteria were identified as Enterobacteriaceae, closely related to Escherichia coli. Isolates tested with API 20E biochemical tests were Erwinia species. This was the only type of bacteria found in all thrips individuals on any of the 10 different agar media. Universal primers, which would potentially pick up DNA from any bacterium present in the insect, were applied on crude DNA extracts from thrips with bacteria. We only found 16S rDNA sequences similar to those of the isolated thrips gut bacteria. The same type of bacteria was present in all life stages of the thrips and was found to persist in the thrips populations for at least 2 years (more than 50 generations).     

Distribution of sulphur-cycle bacteria in the Ems-Dollard estuary

Summary A quantitative study of the sulphur cycle in the tidal flat-sediments of the Eems-Dollard estuary was started by determining the distribution of two physiologically different groups of bacteria: sulphate-reducing and sulphide-oxidizing bacteria. Viable counts of these bacterial groups were determined by most probable number techniques.The highest numbers of aerobic sulphide-oxidizing bacteria were found in the upper 2 cm of the sediment. A rapid decrease was observed with increasing depth.The anaerobic sulphate-reducing bacteria showed different distribution-patterns with depth. Frequently high numbers of these bacteria were found above the redox-discontinuity-layer. This may be attributed to the presence of anaerobic micro-pockets in this largely aerobic top-layer of the sediment.The horizontal distribution of the sulphide-oxidizing bacteria appeared to be highly correlated with sediment parameters such as organic carbon and clay content of the sediment. The sulphate-reducing bacteria showed only a small linear correlation with these parameters.By means of polyfactor-analysis mathematical models were made with bacterial numbers as the dependent variables and with some environmental parameters as independent variables. The parameters used in this models could explain the variance of the viable counts for approximately 70%. The clay content of the sediment and the number of sulphate reducing bacteria appeared to determine to a large extent the variance in numbers of sulphide-oxidizing bacteria. There are indications that a great deal of the sulphide-oxidizing bacteria might be mixotrophic.For the explanation of the variance in numbers of sulphate-reducing bacteria the most important parameters were the clay content of the sediment, the number of aerobic heterotrophic bacteria and temperature (or season). Therefore the numbers of these organisms were varying throughout the year. It is assumed that the heterotrophic bacteria supply the sulphate-reducing bacteria with organic substrates.     

Modulation of the mutagenic response in prokaryotes.

Short-term tests investigating genetic end-points in prokaryotes have been extensively used worldwide not only for risk assessment purposes but also for evaluating the modulation of the mutagenic response. In spite of some intrinsic limitations, such as the lack of cell compartmentalization or the need for an exogenous metabolic system working extracellularly, experimental systems in bacteria can provide useful preliminary indications and some information on the mechanisms involved. In the large majority of studies the putative modulator is mixed with a known mutagen and then assayed in target bacteria, with suitable controls. However, under natural conditions exposure of target cells to modulators may either precede, co-exist with, or follow exposure to mutagens. Therefore, a variety of methodological variations, involving pre-treatment, co-treatment, or post-treatment of bacteria with the putative modulator, have been designed. Application of these procedures showed that the effects of modulators can be completely upset, from inhibition to enhancement, or vice versa, by changing the experimental conditions. Use of methodological variations may provide more complete information on the spectrum of possible effects in bacteria as well as a better insight into modulation mechanisms. Several examples illustrating the flexibility of the Salmonella test in this field of research are available. On the other hand, the widespread use of these relatively simple techniques, yet requiring skillfulness and experience, may lead to some misuse or oversimplifications. A rather common inadequacy is to use excessive amounts of test mutagens, or to express the results in terms of revertants/survivors, rather than revertants/plate. In fact, in the Salmonella test the number of revertants is rather unrelated to the initial number of plated bacteria, provided a normal background lawn of bacterial growth is formed. Thus, a 50% killing of bacteria will not appreciably influence the number of revertants/plate, but expressed as revertants/survivors the effect will look twice as large.     

Uncommon pathways of metabolism among lactic acid bacteria

A small number of lactic acid bacteria possess the ability to derive energy from organic molecules not utilized by the vast majority of representatives of this large group of microorganisms. Thus, strains of Lactobacillus casei and enterococci readily grow at the expense of substrates such as gluconate, malate and pentitols. Transport of gluconate and pentitols is catalysed by phosphotransferase systems unique to these bacteria. Similarly, the initial steps in pentitol dissimilation are mediated by enzymes found only in Lb. casei and Streptococcus avium.     

Uncommon pathways of metabolism among lactic acid bacteria

Abstract A small number of lactic acid bacteria possess the ability to derive energy from organic molecules not utilized by the vast majority of representatives of this large group of microorganisms. Thus, strains of Lactobacillus casei and enterococci readily grow at the expense of substrates such as gluconate, malate and pentitols. Transport of gluconate and pentitols is catalysed by phosphotransferase systems unique to these bacteria. Similarly, the initial steps in pentitol dissimilation are mediated by enzymes found only in Lb. casei and Streptococcus avium .     

Santa Rosalia revisited: Why are there so many species of bacteria?

The diversity of bacteria in the world is very poorly known. Usually less than one percent of the bacteria from natural communities can be grown in the laboratory. This has caused us to underestimate bacterial diversity and biased our view of bacterial communities. The tools are now available to estimate the number of bacterial species in a community and to estimate the difference between communities. Using what data are available, I have estimated that thirty grams of forest soil contains over half a million species. The species difference between related communities suggests that the number of species of bacteria may be more than a thousand million. I suppose that the explanation for such a large number of bacterial species is simply that speciation in bacteria is easy and extinction difficult, giving a rate of speciation higher than the rate of extinction, leading to an ever increasing number of species over time. The idea that speciation is easy is justified from the results of recent experimental work in bacterial evolution.     

Antimicrobial peptides: clinical relevance and therapeutic implications

Antimicrobial peptides (AMPs) are molecules that provide protection against environmental pathogens, acting against a large number of microorganisms, including bacteria, fungi, yeast, virus and others. Two major groups of antimicrobial peptides are found in humans: cathelicidins and defensins. Recently, several studies have furnished information that besides their role in infection diseases, antimicrobial peptides play a role in diseases as diverse as inflammatory disorders, autoimmunity and cancer. Here, we discuss the role of antimicrobial peptides and vitamin D have in such complex diseases and propose their use should be more explored in the diagnosis and treatment of such conditions.     

Aerobic Phototrophic Bacteria: New Evidence for the Diversity,Ecological Importance and Applied Potential of this Previously Overlooked Group

The aerobic phototrophic bacteria are a recently discovered group capable of producing a photosynthetic apparatus similar to that of purple phototrophic bacteria. However, this apparatus, in contrast to that of their anaerobic counterparts, is functional in terms of photoinduced electron transport only under aerobic conditions. Although these bacteria have been widely studied, little is yet known about their ecological importance, and why they differ from other anoxygenic phototrophs with respect to oxygen requirements. In recent years a large number of new genera and species have been described from a wide variety of habitats, and evidence has been presented to support their important ecological role. This minireview focuses on recent discoveries regarding taxonomy, ecology and physiology, as well as the latest advances in the understanding of their photosynthetic apparatus and its genetic regulation.This revised version was published online in October 2005 with corrections to the Cover Date.     

Subcutaneous Bacteria in Turkey Carcasses

Two methods were employed to quantitate the subcutaneous bacteria in fresh, refrigerated, and frozen turkey carcasses. Relatively few bacteria were detected in the skin-flesh interface and in the flesh as compared with the number of bacteria on the skin surface and in the skin layer. No subcutaneous bacteria were detected in 49% of the skin-flesh interface and flesh samples. The number of bacteria detected in skin samples from carcasses chemically disinfected to kill skin surface bacteria was smaller than that in nondisinfected skin samples. These results indicate that the skin blending method used to quantify microorganisms on poultry carcass skin measures the skin layer flora and that the number of subcutaneous membrane or flesh bacteria measured is not normally large enough to have a significant influence on the results.     

Distribution and physiology of ABC-type transporters contributing to multidrug resistance in bacteria.

Membrane proteins responsible for the active efflux of structurally and functionally unrelated drugs were first characterized in higher eukaryotes. To date, a vast number of transporters contributing to multidrug resistance (MDR transporters) have been reported for a large variety of organisms. Predictions about the functions of genes in the growing number of sequenced genomes indicate that MDR transporters are ubiquitous in nature. The majority of described MDR transporters in bacteria use ion motive force, while only a few systems have been shown to rely on ATP hydrolysis. However, recent reports on MDR proteins from gram-positive organisms, as well as genome analysis, indicate that the role of ABC-type MDR transporters in bacterial drug resistance might be underestimated. Detailed structural and mechanistic analyses of these proteins can help to understand their molecular mode of action and may eventually lead to the development of new strategies to counteract their actions, thereby increasing the effectiveness of drug-based therapies. This review focuses on recent advances in the analysis of ABC-type MDR transporters in bacteria.     

The microbial community of Vetiver root and its involvement into essential oil biogenesis

Vetiver is the only grass cultivated worldwide for the root essential oil, which is a mixture of sesquiterpene alcohols and hydrocarbons, used extensively in perfumery and cosmetics. Light and transmission electron microscopy demonstrated the presence of bacteria in the cortical parenchymatous essential oil-producing cells and in the lysigen lacunae in close association with the essential oil. This finding and the evidence that axenic Vetiver produces in vitro only trace amounts of oil with a strikingly different composition compared with the oils from in vivo Vetiver plants stimulated the hypothesis of an involvement of these bacteria in the oil metabolism. We used culture-based and culture-independent approaches to analyse the microbial community of the Vetiver root. Results demonstrate a broad phylogenetic spectrum of bacteria, including alpha-, beta- and gamma-Proteobacteria, high-G+C-content Gram-positive bacteria, and microbes belonging to the Fibrobacteres/Acidobacteria group. We isolated root-associated bacteria and showed that most of them are able to grow by using oil sesquiterpenes as a carbon source and to metabolize them releasing into the medium a large number of compounds typically found in commercial Vetiver oils. Several bacteria were also able to induce gene expression of a Vetiver sesquiterpene synthase. These results support the intriguing hypothesis that bacteria may have a role in essential oil biosynthesis opening the possibility to use them to manoeuvre the Vetiver oil molecular structure.     

Bacterial genes induced within the nodule during the Rhizobium–legume symbiosis

During the symbiosis between the bacterium Rhizobium meliloti and plants such as alfalfa, the bacteria elicit the formation of nodules on the roots of host plants. The bacteria infect the nodule, enter the cytoplasm of plant cells and differentiate into a distinct cell type called a bacteroid, which is capable of fixing atmospheric nitrogen. To discover bacterial genes involved in the infection and differentiation stages of symbiosis, we obtained genes expressed at the appropriate time and place in the nodule by identifying promoters that are able to direct expression of the bacA gene, which is required for bacteroid differentiation. We identified 230 fusions that are expressed predominantly in the nodule. Analysis of 23 sequences indicated that only three encode proteins known to be involved in the Rhizobium-legume symbiosis, six encode proteins with homology to proteins not previously associated with symbiosis, and 14 have no significant similarity to proteins of known function. Disruption of a locus that encodes a protein with homology to a cell adhesion molecule led to a defect in the formation of nitrogen-fixing nodules, resulting in an increased number of nitrogen-starved plants. Our isolation of a large number of nodule-expressed genes will help to open the intermediate stages of nodulation to molecular analysis.     

Unravelling the drivers of aquatic communities using disparate organismal groups and different taxonomic levels

Bioassessment and monitoring methods should be as cost-efficient as possible. Limiting the number of sites is not a practical solution to face the financial challenges related to bioassessment. Hence, it is highly important to find inexpensive ways to assess and monitor human-impacted environments. Suggestions have been made to use coarser taxonomic levels because they require less expertise and time, or to use single surrogate taxonomic groups that indicate the overall state of ecosystems. In this study, we examined the level of within-taxon and cross-taxon congruence of aquatic bacterial, diatom and macroinvertebrate communities, while simultaneously assessing the chemical, physical and spatial drivers of community structure in these organismal groups. Our study area was an extensively sampled large lake system with high connectivity between sites. Thus, we ensured that spatial processes, if they existed, were well portrayed in our data. Our aim was to find out the taxonomic levels sufficient for the purposes of bioassessment and to detect possible surrogate taxonomic groups. We found that bacterial communities were best associated with pure effects of water chemistry, whereas diatom and macroinvertebrate communities were varyingly related to chemical, physical and spatial variables. Macroinvertebrates were the only group related to small-scale spatial variables, while bacteria and diatoms were associated with variables illustrating spatial relations among sites at large and intermediate scales. Overall, the three organismal groups were mainly related to different chemical parameters. Also, the three organismal groups showed only weak, if any, congruent patterns in their community structure. Thus, we do not recommend the use of only one biological group as a surrogate in bioassessment. However, we found that higher taxonomic levels of all three studied organismal groups could be used as surrogates for finer-level taxonomic assignments. Our findings are promising for the possible use of bacteria in future bioassessment and monitoring. Owing to the characteristics of very large lake systems, our findings may be applied to similarly highly connected ecosystems, such as marine coastal systems.