Genomics and the bacterial species problem

Whether or not bacteria have species is a perennially vexatious question. Given what we now know about variation among bacterial genomes, we argue that there is no intrinsic reason why the processes driving diversification and adaptation must produce groups of individuals sufficiently coherent in their genetic and phenotypic properties to merit the designation 'species' - although sometimes they might.     

桉树基因组和功能基因组

本文就桉树基因组和功能基因组的研究进展作介绍。     

Phospholipid metabolism during bacterial growth

Haemophilus parainfluenzae incorporates glycerol and phosphate into the membrane phospholipids without lag during logarithmic growth. In phosphatidyl glycerol (PG), the phosphate and unacylated glycerol moieties turn over and incorporate radioactivity much more rapidly than does the diacylated glycerol. At least half the radioactivity is lost from the phosphate and unacylated glycerol in about 1 doubling. The total fatty acids turn over slightly faster than the diacyl glycerol. In phosphatidyl ethanolamine (PE), which is the major lipid of the bacterium, ethanolamine and phosphate turn over and incorporate radioactivity at least half as fast as the phosphate in PG. The glycerol of PE did not turn over in 4 bacterial doublings. In phosphatidic acid the glycerol turns over at one-third the rate of phosphate turnover. By means of a modified method for the quantitative recovery of 1,3-glycerol diphosphate from cardiolipin, the phosphates and middle glycerol of cardiolipin were shown to turn over more rapidly than the acylated glycerols during bacterial growth. There is no randomization of the radioactivity in the 1- and 3-positions of the glycerol in the course of 1 doubling. The fatty acids of PG turn over faster than those in PE. In both lipids the 2-fatty acids turn over much faster than the 1-fatty acids. At both positions the individual fatty acids have their own rates of turnover. The distribution of fatty acids between the 1- and 2-positions is the same as in other organisms, with more monoenoic and long-chain fatty acids at the 2-position. The different rates of turnover and incorporation of radioactivity into different parts of the lipids suggest that exchange reactions may be important to phospholipid metabolism.     

A discrete model of bacterial metabolism

This paper describes a computer model of the intermediary metabolismof bacteria during steady-state growth and during adaptations,e g. to new carbon sources. Metabolic regulation is representedas a process of optimisation, in which the trend is towardsimproved metabolic performance. The model uses linear programmingtechniques for the optimisation The implementation falls intofour phases: (i) assembly of model parameters; (ii) calculations;(iii) storage of solutions and (iv) projection of solutions.The use of a commercial database and a commercial spreadsheethas proved to be of great assistance in the first and thirdphases. A metabolic map format, with the optional addition ofconversion values, names of enzymes or co-factors has been usedto project the results in a form convenient for inspection. Received on August 22, 1985; accepted on January 3, 1985     

The bacterial metabolism of 2,4-xylenol

1. Measurements of the rates of oxidation of various compounds by a fluorescent Pseudomonas indicated that metabolism of 2,4-xylenol was initiated by oxidation of the methyl group para to the hydroxyl group. 2. 4-Hydroxy-3-methylbenzoic acid was isolated as the product of oxidation of 2,4-xylenol by cells inhibited with alphaalpha'-bipyridyl. 3. 4-Hydroxyisophthalic acid accumulated at low oxygen concentrations when either 2,4-xylenol or 4-hydroxy-3-methylbenzoic acid was oxidized by cells grown with 2,4-xylenol. 4. When supplemented with NADH, but not with NADPH, cell extracts oxidized 4-hydroxy-3-methylbenzoic acid readily. 2-Hydroxy-5-methylbenzoic acid was not oxidized. 5. Both 4-hydroxyisophthalic acid and p-hydroxybenzoic acid were oxidized to beta-oxoadipic acid by cell extracts supplemented with either NADH or NADPH. 4,5-Dihydroxyisophthalic acid was not oxidized. 6. From measurements of oxygen consumed and carbon dioxide evolved it was concluded that protocatechuic acid is an intermediate in the conversion of 4-hydroxyisophthalic acid into beta-oxoadipic acid.     

The origin of ancestral bacterial metabolism

A model for metabolism of the last bacterial common ancestor based on biomimetic analysis of the metabolic systems of phylogenetically ancient bacteria is developed. The mechanism of natural selection and evolution of the autocatalytic chemical systems under the effect of natural homeostatic parameters, such as chemical potentials, temperature, and pressure of environment is proposed. Competition between particular parts of the autocatalytic network with positive-plus-negative feedback resulted in the formation of particular systems of primary autotrophic, mixotrophic, and heterotrophic metabolism. The model of the last common ancestor as a combination of coupled metabolic cycles among population of protocells is discussed. Physicochemical features of these metabolic cycles determined the major principles of natural selection towards ancestral bacterial taxa.     

N-nitrosamines: bacterial mutagenesis and in vitro metabolism

Many nitrosamines are potent mutagens. The rate-limiting step in their in vitro metabolism to mutagens is usually a single enzymatic reaction catalyzed by one or more of the many cytochrome P-450-dependent mixed-function oxidases present in the microsomal cell fraction. Current evidence indicates that this reaction activates nitrosamines to alpha-hydroxynitrosamines, which have half-lives on the order of seconds. This product decomposes to an aldehyde and a much shorter-lived ultimate metabolite which is probably an alkyl diazonium ion or an alkyl carbocation. This may react with DNA leading to premutagenic adducts. Such adducts represent a very small fraction of the ultimate mutagen, with the rest reacting with water to yield the corresponding alcohol. Evidence for this pathway includes (1) the observation of deuterium isotope effects in metabolism and mutagenesis, (2) products (aldehydes, alcohols, and N2) consistent with this pathway, (3) studies on metabolism of nitrosamines using purified cytochrome P-450, (4) formation of DNA adducts such as O6-alkylguanines which are consistent with those expected from the ultimate mutagen, (5) expected products and genotoxic effects of other sources of activated nitrosamines, e.g., alpha-acetoxynitrosamines, alkanediazotates and related compounds. Hydroxylation of nitrosamines at other positions also occurs in vitro (usually to a lesser extent), but these products are generally stable and must be further metabolized to exert mutagenic effects (with the exception of N-nitrosoalkyl(formylmethyl)amines, which are direct-acting mutagens). Because only low percentages of nitrosamines are metabolized in vitro, the contribution to mutagenesis by secondary metabolism is small. In this respect, in vitro metabolism can differ significantly from in vivo metabolism. Bacterial mutagenesis by nitrosamines has most often been studied in Salmonella typhimurium and to a lesser extent E. coli. Mutagenesis by nitrosamines generally requires a source of microsomes (a 9000 X g supernatant fraction is often used), and NADPH. Liver fractions from Aroclor-1254- or PB-induced rodents have been most frequently employed but liver fractions from untreated animals, and homogenates of other organs (lung, kidney, nasal mucosa, and pancreas) have also been utilized. Liver homogenates from humans are generally similar to those from untreated rats in metabolizing nitrosamines to mutagens but large interindividual variations are observed. Mutagenesis is often most effective using a liquid preincubation, a slightly acidic incubation mixture and hamster liver fractions.(ABSTRACT TRUNCATED AT 400 WORDS)     

Microbial metabolism of aliphatic glycols bacterial metabolism of ethylene glycol

A species of Flavobacterium isolated from pond water by its ability to grow aerobically on ethylene glycol as the role source of carbon initially oxidised the diol to glyoxylate via glycollate. The glyoxylate was metabolised by the glycerate pathway to acetyl-CoA. The acetyl-CoA was further metabolised by the tricarboxylic acid cycle plus malate synthase acting anaplerotically.     

The ins and outs of bacterial iron metabolism

Iron is a critical nutrient for the growth and survival of most bacterial species. Accordingly, much attention has been paid to the mechanisms by which host organisms sequester iron from invading bacteria and how bacteria acquire iron from their environment. However, under oxidative stress conditions such as those encountered within phagocytic cells during the host immune response, iron is released from proteins and can act as a catalyst for Fenton chemistry to produce cytotoxic reactive oxygen species. The transitory efflux of free intracellular iron may be beneficial to bacteria under such conditions. The recent discovery of putative iron efflux transporters in Salmonella enterica serovar Typhimurium is discussed in the context of cellular iron homeostasis.     

Genomics,evolution, and crystal structure of a new family of bacterial spore kinases

Bacterial spore formation is a complex process of fundamental relevance to biology and human disease. The spore coat structure is complex and poorly understood, and the roles of many of the protein components remain unclear. We describe a new family of spore coat proteins, the bacterial spore kinases (BSKs), and the first crystal structure of a BSK, YtaA (CotI) from Bacillus subtilis. BSKs are widely distributed in spore‐forming Bacillus and Clostridium species, and have a dynamic evolutionary history. Sequence and structure analyses indicate that the BSKs are CAKs, a prevalent group of small molecule kinases in bacteria that is distantly related to the eukaryotic protein kinases. YtaA has substantial structural similarity to CAKs, but also displays distinctive features that broaden our understanding of the CAK group. Evolutionary constraint analysis of the protein surfaces indicates that members of the BSK family have distinct clade‐conserved patterns in the substrate binding region, and probably bind and phosphorylate distinct targets. Several classes of BSKs have apparently independently lost catalytic activity to become pseudokinases, indicating that the family also has a major noncatalytic function. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria

The field of microbiology has in recent years been transformed by the ever increasing number of publicly available whole-genome sequences. This sequence information has significantly enhanced our understanding of the physiology, genetics and evolutionary development of bacteria. Among the latter group of microorganisms, bifidobacteria represent important human commensals because of their perceived contribution to maintaining a balanced gastrointestinal tract microbiota. In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For this reason, these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. Recent genome sequencing of a number of bifidobacterial species has allowed access to the complete genetic make-up of these bacteria. In this review we will discuss how genomic data has allowed us to understand bifidobacterial evolution, while also revealing genetic functions that explains their presence in the particular ecological environment of the gastrointestinal tract. An erratum to this article can be found at     

细菌培养基中营养物质的代谢及优化方法

细菌培养基是细菌体外生长的基质,其中营养物质是细菌生长、繁殖的基本成分。因此,探索培养基中营养物质的代谢,优化培养基配方,对细菌体外培养的研究及规模化生产有着重要的指导意义。现就细菌培养基分类、营养物质、细菌在营养物质中的代谢及培养基优化方法等方面予以总结。     

从结构基因组学到功能基因组学

基因组学研究随着模式生物基因组全序列测定的完成由结构基因组学阶段发展到功能基因组学阶段,基因组学成为当今最为活跃、最有影响的前沿学科.以结构基因组学的研究成果为基础,功能基因组学中各学科因其原理不同及其关键技术的特点和优势,具有各自的应用范畴和发展趋势.功能基因组学不断渗透入现代科学的各领域,促成了适用于不同研究目的新兴学科的诞生.     

Genome-scale models of bacterial metabolism: reconstruction and applications

Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities.