Crystalline arrays of proteinaceous subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope structures. They are ubiquitous amongst Gram-positive and Gram-negative archeaobacteria and eubacteria and, if present, account for the major protein species produced by the cells. S-layers can provide organisms with a selection advantage by providing various functions including protective coats, molecular sieves, ion traps and structures involved in cell surface interactions. S-layers were identified as contributing to virulence when present as a structural component of pathogens. In Gram-negative archaeobacteria they are involved in determining cell shape and cell division. The crystalline arrays reveal a broad-application potential in biotechnology, vaccine development and molecular nanotechnology.

Crystalline bacterial cell-surface layers.

Publisher Summary Prokaryotic cells have developed different ways to present their surfaces to the environment. One of the most remarkable features of many Gram-positive and Gram-negative eubacteria and archaebacteria is the presence of a regularly ordered protein or glycoprotein layer as the outermost component of the cell envelope, called the surface layer (S-layer). They are composed of a single molecular species, protein or glycoprotein in nature, and are endowed with the ability to assemble into 2D crystalline arrays by an entropy-driven process. S-layers possess a high degree of structural regularity, and thus they are the most abundant of all bacterial cellular proteins, they are ideal model systems for studying the dynamic process of assembly of a supramolecular structure during cell growth. S-Layers are the simplest biological protein membranes developed during evolution. The information encoded in a single S-layer protein species guarantees maintenance of a closed, highly ordered porous protein meshwork on a growing cell surface. Surface layers are an integral part of the cell envelope of a great variety of archaebacteria and eubacteria. Because of their surface location, it is evident that functions have evolved as the result of specific interactions with particular environmental and ecological conditions. Due to the increased knowledge of the structure, assembly, chemistry, biosynthesis, pathogenicity and permeability properties of S-layers, a considerable potential for various biotechnological and non-biological applications for 2D crystals have become evident in few years.

Crystalline bacterial cell surface layers

Sulfate reduction and methanogenesis in marine sediments

The 16S rRNA sequences were determined for species of Spirochaeta, Treponema, Borrelia, Leptospira, Leptonema, and Serpula, using a modified Sanger method of direct RNA sequencing. Analysis of aligned 16S rRNA sequences indicated that the spirochetes form a coherent taxon composed of six major clusters or groups. The first group, termed the treponemes, was divided into two subgroups. The first treponeme subgroup consisted of Treponema pallidum, Treponema phagedenis, Treponema denticola, a thermophilic spirochete strain, and two species of Spirochaeta, Spirochaeta zuelzerae and Spirochaeta stenostrepta, with an average interspecies similarity of 89.9%. The second treponeme subgroup contained Treponema bryantii, Treponema pectinovorum, Treponema saccharophilum, Treponema succinifaciens, and rumen strain CA, with an average interspecies similarity of 86.2%. The average interspecies similarity between the two treponeme subgroups was 84.2%. The division of the treponemes into two subgroups was verified by single-base signature analysis. The second spirochete group contained Spirochaeta aurantia, Spirochaeta halophila, Spirochaeta bajacaliforniensis, Spirochaeta litoralis, and Spirochaeta isovalerica, with an average similarity of 87.4%. The Spirochaeta group was related to the treponeme group, with an average similarity of 81.9%. The third spirochete group contained borrelias, including Borrelia burgdorferi, Borrelia anserina, Borrelia hermsii, and a rabbit tick strain. The borrelias formed a tight phylogenetic cluster, with average similarity of 97%. THe borrelia group shared a common branch with the Spirochaeta group and was closer to this group than to the treponemes. A single spirochete strain isolated fromt the shew constituted the fourth group. The fifth group was composed of strains of Serpula (Treponema) hyodysenteriae and Serpula (Treponema) innocens. The two species of this group were closely related, with a similarity of greater than 99%. Leptonema illini, Leptospira biflexa, and Leptospira interrogans formed the sixth and most deeply branching group. The average similarity within this group was 83.2%. This study represents the first demonstration that pathogenic and saprophytic Leptospira species are phylogenetically related. The division of the spirochetes into six major phylogenetic clusters was defined also by sequence signature elements. These signature analyses supported the conclusion that the spirochetes represent a monophylectic bacterial phylum.

Phylogenetic analysis of the spirochetes.

ZnO nanomaterials of different morphologies are synthesized by different methodologies. These semiconductor photocatalysts are potentially explored for self-sensitized photodegradation of malachite green (MG) dye in water in a batch reactor. The effects of various parameters like initial dye concentration, catalyst loading, solution pH, light source on degradation efficiency was also investigated. The experimental results showed substantial reduction of COD, besides removal of colour. The photodegradation of MG dye followed the pseudo first order kinetics of Langmuir–Hinshelwood model. The hydrothermally synthesized flower shaped homocentric pencil like ZnO nanorod bundles exhibit excellent photocatalytic activity under solar light. A comparative study of photodegradation efficiency among ZnO nanoparticles, ZnO nanoparticles (hydrothermal) and flower shaped homocentric pencil like ZnO nanorod bundles were also performed. Semiconductor photocatalysis often leads to partial or complete mineralization of organic pollutants. The CO 2 gas evolved due to mineralization of MG was determined using Warburg manometric method under solar light. The possible mechanism of photodegradation under both solar and UV light were also proposed.

http://www.neist.res.in/publication/App_Cat-2015.pdf

Photocatalytic performance of ZnO nanomaterials for self sensitized degradation of malachite green dye under solar light

A strictly anaerobic spirochete was isolated from a sample of marine mud. The organism possessed two axial fibrils entwined with the regularly coiled protoplasmic cylinder. An outer envelope or sheath enclosed both protoplasmic cylinder and axial fibrils. The spirochete grew in chemically defined media containing glucose, amino acids or NH4Cl, sulfide, NaCl, vitamins, coenzyme A, and in-organic salts. A reducing agent, such as sodium sulfide or l-cysteine, as well as exogenous supplements of biotin, niacin and coenzyme A were required for growth. Pantothenate replaced coenzyme A as an exogenous growth factor, but the resulting cell yields were low. The spirochete grew in media prepared with sea water, but not in fresh water media containing less than 0.05 M NaCl (optimum concentration 0.35 M). Both Na+ and Cl- were required. Carbohydrates served as fermentable substrates. Amino acids, sugar alcohols, tricarboxylic acid cycle intermediates, and other organic acids and alcohols were not fermented. Glucose was fermented to ethyl alcohol, acetate, CO2, H2, and small amounts of lactate, formate and pyruvate. The guanine + cytosine content of the DNA of the spirochete was 50.5 moles-% (buoyant density). It is proposed that the marine isolate be considered a new species and that it be named Spirochaeta litoralis.

Spirochaeta litoralis sp. n., a strictly anaerobic marine spirochete

Treponema denticola was grown in serum-containing media to which 14C-labelled compounds were added. Determinations of radioactivity in the products formed indicated that the organism fermented alanine, cysteine, glycine, serine, and glucose. Fermentation products included acetate, lactate, succinate, formate, pyruvate, ethanol, CO2, H2S, and NH3. The products formed from glucose constituted a small portion of the total products. Assays of enzymatic activities in cell extracts indicated that the organism degraded glucose via the Embden-Meyerhof pathway. T. denticola possessed a coenzyme A-dependent CO2-pyruvate exchange activity associated with a clostridial-type clastic system for pyruvate metabolism. Phosphotransacetylase and acetate kinase activities were present in cell extracts. Acetyl phosphate formation and benzyl viologen reduction were detected when cell extracts were incubated with pyruvate, serine or cysteine. The data indicate that T. denticola is an amino acid fermenter and that it possesses the enzymes needed for the fermentation of glucose. However, glucose does not serve as the primary substrate when the organism grows in media including both this carbohydrate and amino acids.

Amino acid and glucose fermentation by Treponema denticola.

The pathways of glucose and pyruvate metabolism in Spirochaeta litoralis, a free-living, strictly anaerobic marine spirochete, were studied. Addition of 0.2 to 0.4 M NaCl (final concentration) to suspending buffers prevented cell lysis and was necessary for gas evolution from various substrates by cell suspensions. The organism fermented glucose mainly to ethanol, acetate, CO2, and H2. Determination of radioactivity in products formed from 14C-labeled glucose and assays of enzymatic activities in cell extracts indicated that S. litoralis catabolized glucose via the Embden-Meyerhof pathway. A clostridial-type clastic reaction was utilized by the spirochete to degrade pyruvate to acetyl-coenzyme A, CO2, and H2. Formation of acetate from acetyl-coenzyme A was catalyzed by phosphotransacetylase and acetate kinase. Nicotinamide adenine dinucleotide-dependent acetaldehyde and alcohol dehydrogenases converted acetyl-coenzyme A to ethanol. A reversible hydrogenase activity was detected in cell extracts. S. litoralis cell extracts contained a rubredoxin similar in spectral properties to other bacterial rubredoxins.

Glucose and pyruvate metabolism of Spirochaeta litoralis, an anaerobic marine spirochete.

Various bacteria which degrade pyruvate by the phosphoroclastic reaction were examined with respect to the role of coenzyme A (CoA) in this reaction. The strictly anaerobic bacteria, which cleave pyruvate by the phosphoroclastic reaction characteristic of Clostridia, required catalytic levels of CoA for the CO2-pyruvate exchange and acetoin-forming portions of the phosphoroclastic reaction. These reactions were reversibly inhibited by the CoA analogue, desulfo-CoA. In contrast, using cell-free extracts of bacteria which degrade pyruvate by the coliform phosphoroclastic reaction (pyruvate formate-lyase), no requirement for CoA could be observed for the formate-pyruvate exchange reaction. It is suggested that CoA serves a regulatory function in the early portion of the clostridal type of phosphoroclastic reaction.

Requirement for Coenzyme A in the Phosphoroclastic Reaction of Anaerobic Bacteria

The pathways of carbohydrate metabolism in Spirochaeta stenostrepta, a free-living, strictly anaerobic spirochete, were studied. The organism fermented glucose to ethyl alcohol, acetate, lactate, CO(2), and H(2). Assays of enzymatic activities in cell extracts, and determinations of radioactivity distribution in products formed from (14)C-labeled glucose indicated that S. stenostrepta degraded glucose via the Embden-Meyerhof pathway. The spirochete utilized a clostridial-type clastic reaction to metabolize pyruvate to acetyl-coenzyme A, CO(2), and H(2), without production of formate. Acetyl-coenzyme A was converted to ethyl alcohol by nicotinamide adenine dinucleotide-dependent acetaldehyde and alcohol dehydrogenase activities. Phosphotransacetylase and acetate kinase catalyzed the formation of acetate from acetyl-coenzyme A. Hydrogenase and lactate dehydrogenase activities were detected in cell extracts. A rubredoxin was isolated from cell extracts of S. stenostrepta. Preparations of this rubredoxin stimulated acetyl phosphate formation from pyruvate by diethylaminoethyl cellulose-treated extracts of S. stenostrepta, an indication that rubredoxin may participate in pyruvate cleavage by this spirochete. Nutritional studies showed that S. stenostrepta fermented a variety of carbohydrates, but did not ferment amino acids or other organic acids. An unidentified growth factor present in yeast extract was required by the organism. Exogenous supplements of biotin, riboflavin, and vitamin B(12) were either stimulatory or required for growth.

Carbohydrate Metabolism in Spirochaeta stenostrepta

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