Gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. Although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. This review summarizes the development in the field since our previous review (H. Nikaido and M. Vaara, Microbiol. Rev. 49:1-32, 1985) was published. With the discovery of protein channels, structural knowledge enables us to understand in molecular detail how porins, specific channels, TonB-linked receptors, and other proteins function. We are now beginning to see how the export of large proteins occurs across the outer membrane. With our knowledge of the lipopolysaccharide-phospholipid asymmetric bilayer of the outer membrane, we are finally beginning to understand how this bilayer can retard the entry of lipophilic compounds, owing to our increasing knowledge about the chemistry of lipopolysaccharide from diverse organisms and the way in which lipopolysaccharide structure is modified by environmental conditions.

Molecular Basis of Bacterial Outer Membrane Permeability Revisited

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

/pdf/cell-biology-and-molecular-basis-of-denitrification-red4l5iffz.pdf

Cell biology and molecular basis of denitrification.

Publisher Summary Recent advances in the biochemistry of microorganisms have revealed that cell-component analysis can be effectively applied to bacterial systematics, providing the basis of chemotaxonomy. Analyses of cell components are coming to be essential tools not only for bacterial classification but also for identification. The sequence of chromosomal DNA holds the essential genetic information for an organism. Phylogenetic relationships are often examined using data on nucleotide sequences of ribosomal RNA. However, it is still impossible to determine the sequences of large polynucleotides for the number of organisms sufficient for taxonomic purposes. DNA (RNA) homologies, which have been applied to various kinds of bacteria, present useful information on bacterial systematics. Homology indices are values used in comparing microorganisms. DNA homology data contribute to the clarification, not only of the relatedness of two organisms, but also of the evaluation of phenotypic characteristics.

4 Lipid and Cell-Wall Analysis in Bacterial Systematics

Contents
I. Introduction  424
II. The phosphorus conundrum 424
III. Adaptations to low P 424
IV. Uptake of P  424
V. P deficiency alters root development and function 426
VI. P deficiency modifies carbon metabolism 431
VII. Acid phosphatase 436
VIII. Genetic regulation of P responsive genes 437
IX. Improving P acquisition 439
X. Synopsis  440


Summary
Phosphorus (P) is limiting for crop yield on > 30% of the world's arable land and, by some estimates, world resources of inexpensive P may be depleted by 2050. Improvement of P acquisition and use by plants is critical for economic, humanitarian and environmental reasons. Plants have evolved a diverse array of strategies to obtain adequate P under limiting conditions, including modifications to root architecture, carbon metabolism and membrane structure, exudation of low molecular weight organic acids, protons and enzymes, and enhanced expression of the numerous genes involved in low-P adaptation. These adaptations may be less pronounced in mycorrhizal-associated plants. The formation of cluster roots under P-stress by the nonmycorrhizal species white lupin (Lupinus albus), and the accompanying biochemical changes exemplify many of the plant adaptations that enhance P acquisition and use. Physiological, biochemical, and molecular studies of white lupin and other species response to P-deficiency have identified targets that may be useful for plant improvement. Genomic approaches involving identification of expressed sequence tags (ESTs) found under low-P stress may also yield target sites for plant improvement. Interdisciplinary studies uniting plant breeding, biochemistry, soil science, and genetics under the large umbrella of genomics are prerequisite for rapid progress in improving nutrient acquisition and use in plants.

/pdf/phosphorus-acquisition-and-use-critical-adaptations-by-56im8qzi8m.pdf

Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource

Complementary approaches were employed to characterize transitional episodes in Pseudomonas aeruginosa biofilm development using direct observation and whole-cell protein analysis. Microscopy and in situ reporter gene analysis were used to directly observe changes in biofilm physiology and to act as signposts to standardize protein collection for two-dimensional electrophoretic analysis and protein identification in chemostat and continuous-culture biofilm-grown populations. Using these approaches, we characterized five stages of biofilm development: (i) reversible attachment, (ii) irreversible attachment, (iii) maturation-1, (iv) maturation-2, and (v) dispersion. Biofilm cells were shown to change regulation of motility, alginate production, and quorum sensing during the process of development. The average difference in detectable protein regulation between each of the five stages of development was 35% (approximately 525 proteins). When planktonic cells were compared with maturation-2 stage biofilm cells, more than 800 proteins were shown to have a sixfold or greater change in expression level (over 50% of the proteome). This difference was higher than when planktonic P. aeruginosa were compared with planktonic cultures of Pseudomonas putida. Las quorum sensing was shown to play no role in early biofilm development but was important in later stages. Biofilm cells in the dispersion stage were more similar to planktonic bacteria than to maturation-2 stage bacteria. These results demonstrate that P. aeruginosa displays multiple phenotypes during biofilm development and that knowledge of stage-specific physiology may be important in detecting and controlling biofilm growth.

Pseudomonas aeruginosa Displays Multiple Phenotypes during Development as a Biofilm

Strain SY1, identified as a Corynebacterium sp., was isolated on the basis of the ability to utilize dibenzothiophene (DBT) as a sole source of sulfur. Strain SY1 could utilize a wide range of organic and inorganic sulfur compounds, such as DBT sulfone, dimethyl sulfide, dimethyl sulfoxide, dimethyl sulfone, CS2, FeS2, and even elemental sulfur. Strain SY1 metabolized DBT to dibenzothiophene-5-oxide, DBT sulfone, and 2-hydroxybiphenyl, which was subsequently nitrated to produce at least two different hydroxynitrobiphenyls during cultivation. These metabolites were separated by silica gel column chromatography and identified by nuclear magnetic resonance, UV, and mass spectral techniques. Resting cells of SY1 desulfurized toluenesulfonic acid and released sulfite anion. On the basis of these results, a new DBT degradation pathway is proposed.

https://aem.asm.org/content/aem/58/3/911.full.pdf

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1

Six strains of strictly thermophilic, obligately chemolithotrophic, hydrogen-oxidizing bacteria were isolated from hot springs located in Izu and Kyushu, Japan. The bacterial strains which we tested were gram negative, nonmotile, nonsporeforming, long, straight, and rod shaped. The cell size was 0.3 to 0.5 by 2.0 to 3.0 μm. The deoxyribonucleic acid guanine-plus-cytosine contents of the six strains were between 43.5 and 43.9 mol%. The optimal temperature for autotrophic growth on H2-O2-CO2 was between 70 and 75°C. None of the strains grew at 37 or 80°C. The neutral pH range was suitable for growth. No strain showed heterotrophic growth at the expense of 48 organic compounds or on complex media, in contrast to all other known aerobic hydrogen-oxidizing bacteria which are facultative autotrophs. The major cellular fatty acids were a straight-chain saturated C18:0 acid and a straight-chain unsaturated C20:1 acid with one double bond. C16:0 and C18:1 fatty acids and a C21:0 cyclopropane acid were minor components. Cytochromes b and c were found in all of the strains. The polyacrylamide gel electrophoretic patterns of the total soluble proteins of all of the strains were essentially the same. The name Hydrogenobacter thermophilus gen. nov., sp. nov., is proposed for the six new isolates, and type strain TK-6 has been deposited with the culture collection of the Institute of Applied Microbiology, University of Tokyo, as strain IAM 12695.

Hydrogenobacter thermophilus gen. Nov., sp. Nov., an extremely thermophilic, aerobic, hydrogen-oxidizing bacterium

The incorporation of 14CO2 by the cell suspensions of an extremely thermophilic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus was studied. After short time incubation of the cell suspensions with 14CO2, the radiactivity was initially present in aspartate, glutamate, succinate, phosphorylated compounds, citrate, malate and fumarate. All of these compounds except phosphorylated compounds were related to the members of the tricarboxylic acid cycle. The proportion of labelled aspartate onglutamate in total radioactivity on each chromatogram decreased with incubation time, while the percentage of the radioactivity incorporated in phosphorylated compounds increased with time up to 10 s. These indicated that aspartate and glutamate is derived from primary products of CO2 fixation.

The CO2 assimilation via the reductive tricarboxylic acid cycle in an obligately autotrophic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus

Staphylococcus auriculans DBF63, which can grow on dibenzofuran (DBF) or fluorene (FN) as the sole source of carbon and energy, was isolated. Salicylic acid and gentisic acid accumulated in the culture broth of this strain when DBF was supplied as a growth substrate. Also, the formation of 9-fluorenol, 9-fluorenone, 4-hydroxy-9-fluorenone, and 1-hydroxy-9-fluorenone was demonstrated, and accumulation of 1,1a-dihydroxy-1-hydro-9-fluorenone was observed when this strain grew on FN. On the basis of these results, the degradation pathways of DBF and FN were proposed. The analogous oxidation products of dibenzo-p-dioxin were obtained by incubation with DBF-grown S. auriculans DBF63 cells.

Microbial degradation of dibenzofuran, fluorene, and dibenzo-p-dioxin by Staphylococcus auriculans DBF63.

A large amount of anthocyanin was accumulated in the callus tissues of Vitis hybrids without light irradiation.Culture conditions for the production of anthocyanins by Vitis cells in suspension cultures were investigated. High sucrose and low phosphate concentrations brought about a marked increase of anthocyanin formation, while high concentrations of nitrate, phosphate, and 2, 4-D repressed the pigment formation. The effects of these nutrients depended on the concentrations of coexistent ones.Regulation of the aeration rate was important for anthocyanin formation in submerged aerated cultures and light irradiation enhanced anthocyanin formation in cultured cells.

Tohru Kodama

Papers

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1

Hydrogenobacter thermophilus gen. Nov., sp. Nov., an extremely thermophilic, aerobic, hydrogen-oxidizing bacterium

The CO2 assimilation via the reductive tricarboxylic acid cycle in an obligately autotrophic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus

Microbial degradation of dibenzofuran, fluorene, and dibenzo-p-dioxin by Staphylococcus auriculans DBF63.

Production of Anthocyanins by Vitis Cells in Suspension Culture