Plasmids impact on rhizobia-legumes symbiosis in diverse environments

Rhizobia are a well-known group of soil bacteria that establish symbiotic relationship with leguminous plants, fix atmospheric nitrogen, and improve soil fertility. To fulfill multiple duties in soil, rhizobia are elaborated with a large and complex multipartite genome composed of several replicons. The genetic material is divided among various replicons, in a way to cope with, and satisfy the diverse functions of rhizobia. In addition to the main chromosome, which is carrying the essential (core) genes required for sustaining cell life, the rhizobia genomes contain several extra-chromosomal plasmids, carrying the nonessential (accessory) genes. Occasionally, some mega-plasmids, denoted as secondary chromosomes or chromids, carry some essential (core) genes. Furthermore, specific accessory gene sequences (the symbiotic chromosomal islands) are incorporated in the main chromosome of some rhizobia species in Bradyrhizobium and Mesorhizobium genera. Plasmids in rhizobia are of variable sizes. All of the plasmids in a Rhizobium cell constitute about 30–50% of the genome. Rhizobia plasmids have specific characters such as miscellaneous genes, independent replication system, self-transmissibility, and instability. The plasmids regulate several cellular metabolic functions and enable the host rhizobia to survive in diverse habitats and even under stress conditions. Symbiotic plasmids in rhizobia are receiving increased attention because of their significance in the symbiotic nitrogen fixation process. They carry the symbiotic (nod, nif and fix) genes, and some non-symbiotic genes. Symbiotic plasmids are conjugally-transferred by the aid of the non-symbiotic, self-transmissible plasmids, and hence, brings about major changes in the symbiotic interactions and host specificity of rhizobia. Besides, the rhizobia cells harbor one or more accessory, non-symbiotic plasmids, carrying genes regulating various metabolic functions, rhizosphere colonization, and nodulation competitiveness. The entire rhizobia-plasmid pool interacting in harmony and provides rhizobia with substantial abilities to fulfill their complex symbiotic and non-symbiotic functions in variable environments. The above concepts are extensively reviewed and fairly discussed.     

根瘤菌分类研究进展及存在的争议

根瘤菌是一类与农业生产关系密切的细菌。近年来, 现代分子生物学技术的发展和应用使根瘤菌分类研究有了突破性进展, 新的根瘤菌资源的不断发掘, 根瘤菌的分类体系也不断地被完善。文中主要阐述了根瘤菌分类系统的演化历史、目前存在争议及相关的研究进展。     

Early interactions between legumes and rhizobia: disclosing complexity in a molecular dialogue

The exchange of chemical signals between soil bacteria (rhizobia) and legumes has been termed a molecular dialogue. As initially conceived in the early 1990s, it involved two main groups of molecules: nod gene-inducing flavonoids from plants and the mitogenic lipochito-oligosaccharide Nod factors of rhizobia. This review considers how subsequent research revealed the existence of a more complex set of interactions, featuring expanded roles for the original participants and contributions from additional plant and bacterial metabolites. Rhizobia respond to chemoattractants and growth-enhancing compounds in root exudates, and several plant nonflavonoids possess nod gene-inducing properties. Expression of non-nod genes is induced by flavonoids; these include encoders of a type I secreted protein and the entire type III, and possibly also type IV, secretion systems. Many other genes and proteins in rhizobia are flavonoid-inducible but their functions are largely unknown. Rhizobia produce far more Nod factor variants than was previously envisaged and their structures can be influenced by the pH of the environment. Other symbiotically active compounds or systems of rhizobia, some of them universally present, are: the surface polysaccharides, quorum-sensing N-acyl homoserine lactones, plant growth-promoting lumichrome and two-component regulatory systems.     

Regulation of Biotin Transport in Saccharomyces cerevisiae

The metabolic control of biotin transport in Saccharomyces cerevisiae was investigated. Nonproliferating cells harvested from cultures grown in excess biotin (25 ng/ml) took up small amounts of biotin, whereas cells grown in biotin-sufficient medium (0.25 ng/ml) accumulated large amounts of the vitamin. Transport was inhibited maximally in cells grown in medium containing 9 ng (or more) of biotin per ml. When avidin was added to biotin-excess cultures, the cells developed the ability to take up large amounts of biotin. Boiled avidin was without effect, as was treatment of cells with avidin in buffer. Avidin did not relieve transport inhibition when added to biotin-excess cultures treated with cycloheximide, suggesting that protein synthesis was required for cells to develop the capacity to take up biotin after removal of extracellular vitamin by avidin. Cycloheximide did not inhibit the activity of the preformed transport system in biotin-sufficient cells. The presence of high intracellular free biotin pools did not inhibit the activity of the transport system. The characteristics of transport in biotin-excess cells (absence of temperature or pH dependence, no stimulation by glucose, absence of iodoacetate inhibition, independence of uptake on cell concentration, and nonsaturation kinetics) indicated that biotin entered these cells by diffusion. The results suggest that the synthesis of the biotin transport system in S. cerevisiae may be repressed during growth in medium containing high concentrations of biotin.     

Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes

Rhizobia described so far belong to three distinct phylogenetic branches within the alpha-2 subclass of Proteobacteria. Here we report the discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus. Rhizobia isolated from Crotalaria legumes were assigned to a new species, "Methylobacterium nodulans," within the Methylobacterium genus on the basis of 16S ribosomal DNA analyses. We demonstrated that these rhizobia facultatively grow on methanol, which is a characteristic of Methylobacterium spp. but a unique feature among rhizobia. Genes encoding two key enzymes of methylotrophy and nodulation, the mxaF gene, encoding the alpha subunit of the methanol dehydrogenase, and the nodA gene, encoding an acyltransferase involved in Nod factor biosynthesis, were sequenced for the type strain, ORS2060. Plant tests and nodA amplification assays showed that "M. nodulans" is the only nodulating Methylobacterium sp. identified so far. Phylogenetic sequence analysis showed that "M. nodulans" NodA is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer.     

Biotin uptake by isolated rat intestinal cells

Isolated intestinal mucosa cells of rats were used to investigate the intestinal transport of biotin. This method utilizing a double-label isotope technique showed that uptake could not be saturated, even in a wide range of biotin concentrations (0.01-2 microM). A metabolic inhibitor (antimycin A) did not prevent cell uptake of biotin. The transport mechanism was independent of temperature (Q10 = 1.04). When excess biotin was added to the incubation medium, there was no efflux of the vitamin from intestinal cells. The results also showed that the cells did not concentrate the vitamin, regardless of its concentration in the incubation medium. The mechanism of biotin uptake by rat cells at physiological concentrations is thus a passive diffusion phenomenon.     

The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering

The synthesis of biotin, a vitamin required for many carboxylation reactions, is a variable trait in Saccharomyces cerevisiae. Many S. cerevisiae strains, including common laboratory strains, contain only a partial biotin synthesis pathway. We here report the identification of the first step necessary for the biotin synthesis pathway in S. cerevisiae. The biotin auxotroph strain S288c was able to grow on media lacking biotin when BIO1 and the known biotin synthesis gene BIO6 were introduced together on a plasmid vector. BIO1 is a paralog of YJR154W, a gene of unknown function and adjacent to BIO6. The nature of BIO1 illuminates the remarkable evolutionary history of the biotin biosynthesis pathway in S. cerevisiae. This pathway appears to have been lost in an ancestor of S. cerevisiae and subsequently rebuilt by a combination of horizontal gene transfer and gene duplication followed by neofunctionalization. Unusually, for S. cerevisiae, most of the genes required for biotin synthesis in S. cerevisiae are grouped in two subtelomeric gene clusters. The BIO1-BIO6 functional cluster is an example of a cluster of genes of "dispensable function," one of the few categories of genes in S. cerevisiae that are positionally clustered.     

Biotin biosynthesis in Mycobacterium tuberculosis: physiology,biochemistry and molecular intervention

Biotin is an important micronutrient that serves as an essential enzyme cofactor. Bacteria obtain biotin either through de novo synthesis or by active uptake from exogenous sources. Mycobacteria are unusual amongst bacteria in that their primary source of biotin is through de novo synthesis. Here we review the importance of biotin biosynthesis in the lifecycle of Mycobacteria. Genetic screens designed to identify key metabolic processes have highlighted a role for the biotin biosynthesis in bacilli growth, infection and survival during the latency phase. These studies help to establish the biotin biosynthetic pathway as a potential drug target for new anti-tuberculosis agents.     

Biotin uptake: influx, efflux and countertransport in Escherichia coli K12

Biotin uptake by Escherichia coli K12 has been reinvestigated. The vitamin uptake is an active process depending on energy and inhibited by uncouplers. The kinetic parameters (Km = 0.27 microM, Vmax = 6.8 pmol/min per mg dry cells) are close to those previously determined for a biotin-dependent strain E. coli C162 (Piffeteau, A., Zamboni, M. and Gaudry, M. (1982) Biochim. Biophys. Acta 688, 29-36). By use of biotin p-nitrophenyl ester, an affinity label of the biotin transport system, it was shown, under conditions of steady state, that the efflux of biotin is not energy dependent and is mainly mediated by a diffusion mechanism. Reexamination of the regulation of the biotin transport by biotin, revealed that only 50% of the biotin uptake system is under control by the vitamin.     

Biotin in microbes,the genes involved in its biosynthesis,its biochemical role and perspectives for biotechnological production

Biotin (vitamin H) is one of the most fascinating cofactors involved in central pathways in pro- and eukaryotic cell metabolism. Since its original discovery in 1901, research has led to the discovery of the complete biotin biosynthesis pathways in many different microbes and much work has been done on the highly intriguing and complex biochemistry of biotin biosynthesis. While humans and animals require several hundred micrograms of biotin per day, most microbes, plants and fungi appear to be able to synthesize the cofactor themselves. Biotin is added to many food, feed and cosmetic products, creating a world market of 10-30 t/year. However, the majority of the biotin sold is synthesized in a chemical process. Since the chemical synthesis is linked with a high environmental burden, much effort has been put into the development of biotin-overproducing microbes. A summary of biotin biosynthesis and its biological role is presented; and current strategies for the improvement of microbial biotin production using modern biotechnological techniques are discussed.     

Characteristics of rhizobia nodulating beans in the central region of Minnesota

Until recently, beans (Phaseolus vulgaris L.) grown in Minnesota were rarely inoculated. Because of this, we hypothesized that bean rhizobia collected in Minnesota would either share characteristics identifiable with Rhizobium etli of Mesoamerican or Andean origin, introduced into the region as seed-borne contaminants, or be indigenous rhizobia from prairie species, such as Dalea spp. The latter organisms have been shown to nodulate and fix N2 with Phaseolus vulgaris. Rhizobia recovered from the Staples, Verndale, and Park Rapids areas of Minnesota were grouped according to the results of BOXA1R-PCR fingerprint analysis into 5 groups, with only one of these having banding patterns similar to 2 of 4 R. etli reference strains. When representative isolates were subject to fatty acid - methyl ester analysis and 16S rRNA gene sequence analysis, the results obtained differed. 16S rRNA gene sequences of half the organisms tested were most similar to Rhizobium leguminosarum. Rhizobia from Dalea spp., an important legume in the prairie ecosystem, did not play a significant role as the microsymbiont of beans in this area. This appears to be due to the longer time needed for them to initiate infection in Phaseolus vulgaris. Strains of Rhizobium tropici IIB, including UMR1899, proved tolerant to streptomycin and captan, which are commonly applied as seed treatments for beans. Local rhizobia appeared to have very limited tolerance to these compounds.     

Dicarboxylate transport by rhizobia

Soil bacteria collectively known as rhizobia are able to convert atmospheric dinitrogen to ammonia while participating in a symbiotic association with legume plants. This capability has made the bacteria an attractive research subject at many levels of investigation, especially since physiological and metabolic specialization are central to this ecological niche. Dicarboxylate transport plays an important role in the operation of an effective, nitrogen-fixing symbiosis and considerable evidence suggests that dicarboxylates are a major energy and carbon source for the nitrogen-fixing rhizobia. The dicarboxylate transport (Dct) system responsible for importing these compounds generally consists of a dicarboxylate carrier protein, DctA, and a two component kinase regulatory system, DctB/DctD. DctA and DctB/D differ in the substrates that they recognize and a model for substrate recognition by DctA and DctB is discussed. In some rhizobia, DctA expression can be induced during symbiosis in the absence of DctB/DctD by an alternative, uncharacterized, mechanism. The DctA protein belongs to a subgroup of the glutamate transporter family now thought to have an unusual structure that combines aspects of permeases and ion channels. While the structure of C(4)-dicarboxylate transporters has not been analyzed in detail, mutagenesis of S. meliloti DctA has produced results consistent with the alignment of the rhizobial protein with the more characterized bacterial and eukaryotic glutamate transporters in this family.     

Plants need their vitamins too

Over recent years, the pathways for the biosynthesis of many vitamins have been elucidated at the molecular level in plants, and several unique features are emerging. One is that the mitochondrion plays an important role in the synthesis of folate (vitamin B9), biotin (B7), pantothenate (B5), ascorbate (C), and possibly thiamin (B1). Second, the production of some of these cofactors is regulated by developmental cues, and perhaps more surprisingly, by environmental signals such as high light and salinity. Moreover, the biosynthesis of thiamin in Arabidopsis may be negatively regulated by a riboswitch, a novel method of gene regulation that is characteristic of cofactor biosynthesis in bacteria. Vitamin B12 is unique in that it is not found in vascular plants, but is abundant in algae; recent molecular work has revealed that algae do not synthesise the vitamin but instead obtain it from bacteria.     

Rhizobium giardinii is the microsymbiont of Illinois bundleflower (Desmanthus illinoensis (Michx.) Macmillan) in midwestern prairies

Illinois bundleflower (Desmanthus illinoensis (Michx.) Macmillan) has potential as a grain and forage legume for the American Midwest. Inoculant-quality rhizobia for this legume have been identified but not previously characterized. Rhizobia trapped from 20 soils in the natural range of the Illinois bundleflower had characteristics that placed them overwhelmingly within the species Rhizobium giardinii, one of the few occasions this species has been recovered from legumes, raising questions on the biogeography and spread of midwestern prairie rhizobia.