Solving the problem of how to eat something as big as yourself: Diverse bacterial strategies for degrading polysaccharides

Polysaccharide digestion by bacteria is an important activity in many ecosystems, and a number of bacterial genera can perform this function. Although many papers have been published about the properties of isolated polysaccharide-degrading enzymes, relatively little is known about how intact bacteria degrade polysaccharides. This review summarizes recent findings suggesting that there are at least three different strategies. the most familiar one is the excretion of extracellular polysaccharidases, which diffuse to and degrade nearby polysaccharides. An example of this type of strategy is provided by the plant pathogen,Erwinia spp. A second strategy is to have the enzyme exposed to the extracellular medium but attached to the surface of the cell. Examples of this strategy are provided by the pullulanase system ofKlebsiella oxytoca and the cellulosomes ofClostridium thermocellum. A strategy that could be seen as a combination of the extracellular enzyme strategy and the surface organelle strategy is provided byVibrio harveyi, which attaches to its substrate, chitin, via proteins that appear to be specialized for attachment and produces extracellular enzymes that attack the chitin. A third strategy is to import the polysaccharide, as appears to be done byBacteroides spp. In this instance, the polysaccharide is bound to an outer membrane receptor, then passes into the periplasm where the degradative enzymes are located. The ecological advantages and disadvantages of these systems are discussed, and areas where further research is needed are defined.     

Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population

Rice is a leading grain crop and the staple food for over half of the world population. Rice is also an ideal species for genetic and biological studies of cereal crops and other monocotyledonous plants because of its small genome and well developed genetic system. To facilitate rice genome analysis leading to physical mapping, the identification of molecular markers closely linked to economic traits, and map-based cloning, we have constructed two rice bacterial artificial chromosome (BAC) libraries from the parents of a permanent mapping population (Lemont and Teqing) consisting of 400 F9 recombinant inbred lines (RILs). Lemont (japonica) and Teqing (indica) represent the two major genomes of cultivated rice, both are leading commercial varieties and widely used germplasm in rice breeding programs. The Lemont library contains 7296 clones with an average insert size of 150 kb, which represents 2.6 rice haploid genome equivalents. The Teqing library contains 14208 clones with an average insert size of 130 kb, which represents 4.4. rice haploid genome equivalents. Three single-copy DNA probes were used to screen the libraries and at least two overlapping BAC clones were isolated with each probe from each library, ranging from 45 to 260 kb in insert size. Hybridization of BAC clones with chloroplast DNA probes and fluorescent in situ hybridization using BAC DNA as probes demonstrated that both libraries contain very few clones of chloroplast DNA origin and are likely free of chimeric clones. These data indicate that both BAC libraries should be suitable for map-based cloning of rice genes and physical mapping of the rice genome.     

Cloning,expression, and crystallization of the V delta domain of a human gamma delta T-cell receptor.

T-lymphocytes recognize a wide variety of antigens through highly diverse cell-surface glycoproteins known as T-cell receptors (TCRs). These disulfide-linked heterodimers are composed of alpha and beta or gamma and delta polypeptide chains consisting of variable (V) and constant (C) domains non-covalently associated with at least four invariant chains to form the TCR-CD3 complex. It is well established that alpha beta TCRs recognize antigen in the form of peptides bound to molecules of the major histocompatibility complex (MHC); furthermore, information on the three-dimensional structure of alpha beta TCRs has recently become available through X-ray crystallography. In contrast, the antigen specificity of gamma delta TCRs is much less well understood and their three-dimensional structure is unknown. We have cloned the delta chain of a human TCR specific for the MHC class I HLA-A2 molecule and expressed the V domain as a secreted protein in the periplasmic space of Escherichia coli. Following affinity purification using a nickel chelate adsorbent, the recombinant V delta domain was crystallized in a form suitable for X-ray diffraction analysis. The crystals are orthorhombic, space group P2(1)2(1)2 with unit cell dimensions a = 69.9, b = 49.0, c = 61.6 A. and diffract to beyond 2.3 A resolution. The ability of a V delta domain produced in bacteria to form well-ordered crystals strongly suggests that the periplasmic space can provide a suitable environment for the correct in vivo folding of gamma delta TCRs.     

Cellular responses to enteropathogenicEscherichia coli infection

EnteropathogenicEscherichia coli (EPEC), first described in the 1940's and 1950's, remain an important cause of severe infantile diarrhoea in many parts of the developing world. EPEC do not produce enterotoxins and are not invasive; instead their virulence depends upon exploitation of host cell signalling pathways and the host cell cytoskeleton both as a means of colonizing mucosal surfaces of the small intestine and causing diarrhoea. Following initial mucosal attachment, EPEC secrete signalling proteins and expresss a surface adhesin, intimin, to produce attaching & effacing lesions in the enterocyte brush border membrane characterised by localised destruction of brush border microvilli, intimate bacterial adhesion and cytoskeletal reorganisation and accretion beneath attached bacteria. The pathophysiology of EPEC diarrhoea is also complex and probably results from a combination of epithelial cell responses including both electrolyte secretion and structural damage.     

Seleno-lactobacillus

Lactic acid bacteria are nonpathogenic bacteria commonly used in food processing. An evaluation was made of the capacity to concentrate selenium in species of Lactobacillus. A selenium concentration of 1 μg/mL in the culture medium yielded in a bacterial content of 400 μg/g dry biomass. Dialysis and TCA precipitation experiments of a native intracellular extract proved that at least 80% of the total selenium is associated with organic molecules. Seleno-cysteine was identified as the only seleno-amino acid present in the intracellular selenoproteins. This study shows that species of the lactic acid bacteria are able to concentrate selenium intracellular as seleno-cysteine, which could be applied in supplementation studies.     

The IleL229 → Met mutation impairs the quinone binding to the QB-pocket in reaction centers of Rhodobacter sphaeroides

A spontaneous mutant (R/89) of photosynthetic purple bacterium Rhodobacter sphaeroides R-26 was selected for resistance to 200 M atrazin. It showed increased resistance to interquinone electron transfer inhibitors of o-phenanthroline (resistance factor, RF=20) in UQ_o reconstituted isolated reaction centers and terbutryne in reaction centers (RF=55) and in chromatophores (RF=85). The amino acid sequence of the Q_B binding protein of the photosynthetic reaction center (the L subunit) was determined by sequencing the corresponding pufL gene and a single mutation was found (Ile^L229 Met). The changed amino acid of the mutant strain is in van der Waals contact with the secondary quinone Q_B. The binding and redox properties of Q_B in the mutant were characterized by kinetic (charge recombination) and multiple turnover (cytochrome oxidation and semiquinone oscillation) assays of the reaction center. The free energy for stabilization of Q_AQ_B ^– with respect to Q_A ^–Q_B was G_AB=–60 meV and 0 meV in reaction centers and G_AB=–85 meV and –46 meV in chromatophores of R-26 and R/89 strains at pH 8, respectively. The dissociation constants of the quinone UQ_o and semiquinone UQ_o ^– in reaction centers from R-26 and R/89 showed significant and different pH dependence. The observed changes in binding and redox properties of quinones are interpreted in terms of differential effects (electrostatics and mesomerism) of mutation on the oxidized and reduced states of Q_B.Abbreviations BChl bacteriochlorophyll - Ile isoleucine - Met methionin - P primary donor - Q_A primary quinone acceptor - Q_B secondary quinone acceptor - RC reaction center protein - UQ_o 2,3-dimethoxy-5-methyl benzoquinone - UQ₁₀ ubiquinone 50 This work is dedicated to the memory of Randall Ross Stein (1954–1994) and is, in a small way, a testament to the impact which Randy's ideas have had on the development of the field of competitive herbicide binding.     

Protein recovery from cell debris using rotary and tangential crossflow microfiltration

Protein recovery from a bacterial lysate was accomplished using microfiltration membranes in a flat crossflow filter and in a cylindrical rotary filter. Severe membrane fouling yielded relatively low long-term permeate flux values of 10(-4)-10(-3) cm/s (where I cm/s = 3.6 x 10(4) L/m(2) - h). The permeate flux was found to be nearly independent of transmembrane pressure and to increase with increasing shear rate and decreasing solids concentration. The flux increased with shear to approximately the one-third power or greater for the flat filter and the one-half power or greater for the rotary filter; the stronger dependence for the rotary filter is thought to result from Taylor vortices enhancing the back transport of debris carried to the membrane surface by the permeate flow. The average protein transmission or sieving coefficient was measured at approximately 0.6, but considerable scatter in the transmission data was observed. The largest sieving coefficients were obtained for dilute suspensions at high shear rate. The rotary filter provided higher fluxes than did the flat filter for dilute suspensions, but not for concentrated suspensions. (c) 1995 John Wiley & Sons, Inc.     

Stimulative and inhibitory effects of bacteria on the growth of microalgae

Several examples of stimulative and inhibitoryeffects of bacteria on microalgal growth areintroduced, and the importance of bacteria in algalmass culture is investigated. Diatoms are often usedas live food for planktonic larvae of sea urchin andbivalves. Monodispersed Chaetoceros ceratosporum hasbeen cultivated by using clean, high nutrient content,deep seawater (DSW). However, the growth rate and cellyield of diatoms fluctuated, to relatively largeextent, with the season that DSW was collected. Whensome bacterial strains isolated from DSW were added tothe culture, diatom growth was often stimulated and arelatively constant cell yield was obtained. Anotherdiatom species, C. gracilis, was also stimulated byadding some bacterial strains to cultures. Thepositive effect of bacteria on diatoms was observednot only for planktonic species, but also on attachedspecies. A benthic diatom, Nitzschia sp., wasstimulated by a bacterial film of Alcaligenes on thesurface of the substratum. On the other hand, a strainof Flavobacterium sp. isolated from natural seawaterduring the decline period of an algal bloom had a strongalgicidal effect on the red tide plankton,Gymnodinium mikimotoi. Recent reports demonstratethat many bacterial strains have significantalgicidal effects on many species of red tideplankton. These results indicate that bacterialeffects should be taken into account to obtain stablemass culture of food microalgae.     

Crystallization and X-ray analysis of a single fab binding domain from protein L of Peptostreptococcus magnus

Protein L is a multi domain cell wall constituent of certain strains of Peptostreptococcus magnus which binds to the variable domain of immunoglobulin κ-light chains. A single immunoglobulin-binding domain of M_r = 9000 from this protein has been isolated and crystallized. The crystals are of space group P4₂2₁2, with cell dimensions a = b = 66.9 Å, c = 68.3 Å, and diffract to at least 2.2 Å resolution. The asymmetric unit of the crystal contains two molecules of the protein L domain, related by a noncrystallographic 2-fold axis, as revealed by a self-rotation function calculated with native diffraction data. © 1995 Wiley-Liss, Inc.