Structural features of archaebacterial cell envelopes

Regularly arrayed surface (glyco)proteins—often referred to as S layers—are a common feature of the cell envelopes of almost all archaebacteria. We have selected some examples (Halobacterium, Sulfolobus, Thermoproteus, Pyrobaculum, Staphylothermus), and we describe the structure of their surface layers as revealed primarily by electron crystallography. In spite of a considerable diversity in shapes and dimensions, some common structural features emerge from the comparison. The glycoprotein arrays are composed of oligomeric units which are anchored in the plasma membrane; extended spacer or linker domains maintain the bulk of the more or less porous surface layers at a constant distance above the membrane surface, thus creating a quasi-periplasmic compartment. Functions ascribed to surface layers, such as compartmentalization, shape maintenance and determination, and adhesion are discussed.     

Stage-specific cuticular proteins of Ostertagia circumcincta and Ostertagia ostertagi

In this study we have shown that NHS-biotin and I¹²⁵-streptavidin can detect cuticular polypeptides of Ostertagia spp. The labelled polypeptide profile of intact nematodes is simple compared to the profile obtained by labelling homogenates. None of the major internal polypeptides are labelled and the subset of proteins labelled in intact nematodes appears to be mainly surface associated. The results presented here demonstrate that NHS-biotin may be used as a reagent for the analysis of surface polypeptides. The surface polypeptide profiles of the five major developmental stages (L1, L2, L3, L4 and adult) of Ostertagia circumcincta show a series of stage-specific molecules with no polypeptides common to all stages, indicating that the cuticle is a dynamic structure which changes throughout the life cycle. Similarity comparison of Ostertagia ostertagi L3 and L4 stage surface profiles showed that each stage is clearly distinct; comparison of these stages between the two species shows an overall similarity.     

Wood excavations of three species of subterranean termites

We compared the feeding excavations on wood blocks of three species of subterranean termites, Coptotermes formosanus Shiraki, Reticulitermes flavipes (Kollar), and R. virginicus (Banks). Feeding rate followed the order C. formosanus > R. flavipes > R. virginicus. Wood surface area (mm²) exposed per unit feeding was higher for C. formosanus and R. flavipes than for R. virginicus. This was caused by the tendency of C. formosanus and R. flavipes to make internally penetrating tunnels, thereby increasing surface area, whereas R. virginicus made trough- and bowl-like depressions on the outside of blocks, sometimes decreasing the size of blocks outwardly without a corresponding high increase in surface area typical with the tunnels of the other species. Consequently, wood surface area was sometimes reduced, rather than increased as a result of feeding by R. virginicus. Different patterns of wood excavation suggest that these termites have divergent roles in wood decay processes.

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Résumé Les organismes pionniers qui modifient le bois et le rendent acceptable par les insectes qui le perforent sont généralement des champignons du bois pourri. Cependant, une fois que les termites ou autres insectes perforant le bois ont pénétré, leurs galeries favorisent les bactéries fixatrices d'azote, permettent l'invasion d'autres organismes décomposeurs, et de ce fait régularisent la décomposition du bois (Ausmus, 1977). L'exposition de la surface à l'intérieur des perforations jouant un rôle très important dans le processus de pourrissement, il est souhaitable de pouvoir quantifier la surface des galeries dues à l'alimentation des termites. Une courbe type permettant de prédire l'aire de la surface perforée a été construite en perçant 109 morceaux de bois de trous cylindriques de différents diamètres, en calculant l'aire de la surface des morceaux de bois, en appliquant et pesant une couche de vernis pour bois au polyuréthane, et en divisant la masse de polyuréthane par l'aire de la surface. Le modèle prédictif qui en découle est: Y=0,01443×-3,51825 (P=0,0001; r=0,68), y étant la masse de polyuréthane (en g) et x la surface (en mm²) du morceau de bois. En traitant de la même façon au polyuréthane les morceaux de bois perforés par les termites, nous pourrions déduire leur surface.Une expérience a été effectuée avec 3 espèces de rhinotermitides,- Coptotermes formosanus Shiraki, Reticulitermes flavipes (Kollar) et R. virginicus (Banks). Des groupes de chaque espèce se sont alimentés pendant 11 ou 12 jours sur des morceaux de bois non contaminés par des champignons. Nous avons déterminé la survie, la consommation, la modification de la surface du morceau de bois (par utilisation du modèle prédictif) et le changement de surface par terminte.La survie est la même, mais la consommation est dans l'ordre suivant: C. formosanus > R. flavipes > R. virginicus. L'aire de la surface exposée par unité d'alimentation était plus élevée pour C. formosanus et R. flavipes que pour R. virginicus (Tab. 1). Ceci est dû à la tendance de C. formosanus et R. flavipes de creuser des galeries vers l'intérieur, tandis que R. virginicus fait des cuvettes à la surface du bois. Les attaques superficielles de R. virginicus réduisent parfois le volume du morceau de bois sans accroître proportionnellement la surface comme le font les espèces creusant des galeries. Ainsi, avec R. virginicus la surface peut être réduite au lieu d'augmenter. Des différences entre colonies s'observent avec toutes les variables (Tab. 2).Nos résultats suggèrent que C. formosanus et R. flavipes contribuent plus que R. virginicus à exposer le bois aux autres organismes décomposeurs. Cependant, ces résultats peuvent être modifiés par un conditionnement préalable du bois par des champignons.

     

Membrane surface properties of sheep erythrocytes,an immunological reagent,after different treatments as reflected by partition in two-polymer aqueous phases

Sheep erythrocytes (E) which, with or without certain treatments, are currently used as “immunological reagents” to detect cells with specific receptors (by rosette-formation) have been partitioned in two-polymer aqueousphase systems selected so as to reflect charge-associatedor lipid-related membrane surface properties. We have found that the partitioning behavior of E is not affected in these phases by reacting the cells with anti-E antibody (either IgG or IgM), forming EA. The additional binding of complement to the cell-antibody complex, forming EAC, results, however, in a marked decrease in the partition coefficient,K. Apparently both the charge-associated and hydrophobic properties reflected by partitioning remain accessible to the phase polymers when the cells are coated with antibody, but are not with the addition of complement. It is interesting that EA can still rosette with T-lymphocytes (14), a property of E, while the additional coating with complement results in EAC which does not appreciably do so (26). Neuraminidase or trypsin treatments of E, which yield Es having quite different rosetting properties with T-lymphocytes (14), cause increasedKs and unchangedKs, respectively, in phases reflecting lipid-related surface properties. Either treatment causes reducedKs of E in charged-phase systems. Neuraminidase treatment also results in a reduced electrophoretic mobility of E, while trypsin treatment is not detectable by cell electrophoresis (25). We are currently studying the possible usefulness of employing cell electrophoresis and cell partitioning in charged-phase systems jointly to obtain information on events occurring at the shear plane versus those occurring deeper in the membrane.     

A comparison of direct and indirect methods for measuring leaf and surface areas of individual bushes

Indirect estimates of leaf area from measurements with three commercially available instruments (DEMON, LAI-2000 and Sunfleck Ceptometer) were compared with directly measured areas of individual Retama sphaerocarpa bushes. The three indirect methods gave good estimates of the total surface area of individual bushes. For the DEMON, the method of log-linear averaging of transmitted radiation gave estimates closer to directly measured surface area than the method of averaging transmission linearly. For the LAI-2000, estimated surface area index multiplied by canopy projected area gave the best agreement with directly measured values. For measurements with the Sunfleck Ceptometer, values of surface area estimated from the transmission of photosynthetic quantum flux density, without correcting for diffuse radiation, gave the best agreement with directly measured values. Surface areas estimated by the three instruments were not significantly different from directly measured total (leaf + branch + stem) surface areas. Leaf surface area could be calculated from estimated total surface area minus directly measured branch surface area. Measured branch surface area was linearly related to canopy projected area.     

The growth strategy of the Gram-positive rod

Abstract Bacteria grow by enlarging their envelope in such a way that osmotic pressure does not normally cause physical rupture. The strategy of Bacillus subtilis for both cylindrical elongation and pole formation is now substantially defined. Side-wall growth takes place by laying down new peptidoglycan, which is then displaced outwards, stretched and discarded; cross walls are laid down in the absence of stress, and then stretched and bulged outward as the septum is split and the pole is formed.     

Tertiary motifs as building blocks for the design of protein‐binding peptides

Despite advances in protein engineering, the de novo design of small proteins or peptides that bind to a desired target remains a difficult task. Most computational methods search for binder structures in a library of candidate scaffolds, which can lead to designs with poor target complementarity and low success rates. Instead of choosing from pre‐defined scaffolds, we propose that custom peptide structures can be constructed to complement a target surface. Our method mines tertiary motifs (TERMs) from known structures to identify surface‐complementing fragments or “seeds.” We combine seeds that satisfy geometric overlap criteria to generate peptide backbones and score the backbones to identify the most likely binding structures. We found that TERM‐based seeds can describe known binding structures with high resolution: the vast majority of peptide binders from 486 peptide‐protein complexes can be covered by seeds generated from single‐chain structures. Furthermore, we demonstrate that known peptide structures can be reconstructed with high accuracy from peptide‐covering seeds. As a proof of concept, we used our method to design 100 peptide binders of TRAF6, seven of which were predicted by Rosetta to form higher‐quality interfaces than a native binder. The designed peptides interact with distinct sites on TRAF6, including the native peptide‐binding site. These results demonstrate that known peptide‐binding structures can be constructed from TERMs in single‐chain structures and suggest that TERM information can be applied to efficiently design novel target‐complementing binders.     

Dictyostelium discoideum as Expression Host: Isotopic Labeling of a Recombinant Glycoprotein for NMR Studies

The advantages of the organism Dictyostelium discoideum as an expression host for recombinant glycoproteins have been exploited for the production of an isotopically labeled cell surface protein for NMR structure studies. Growth medium containing [¹⁵N]NH₄Cl and [¹³C]glycerol was used to generate isotopically labeled Escherichia coli, which was subsequently introduced to D. discoideum cells in simple Mes buffer. A variety of growth conditions were screened to establish minimal amounts of nitrogen and carbon metabolites for a cost-effective protocol. Following single-step purification by anion-exchange chromatography, 8 mg of uniformly ¹³C,¹⁵N-labeled protein secreted by approximately 10¹⁰D. discoideum cells was isolated from 3.3 liters of supernatant. Mass spectrometry showed the recombinant protein of 16 kDa to have incorporated greater than 99.9% isotopic label. The two-dimensional ¹H-¹³C HSQC spectrum confirms ¹³C labeling of both glycan and amino acid residues of the glycoprotein. All heteronuclear NMR spectra showed a good dispersion of cross-peaks essential for high-quality structure determination.     

Multi-domain, cell-envelope proteinases of lactic acid bacteria

The multi-domain, cell-envelope proteinases encoded by the genes prtB of Lactobacillus delbrueckii subsp. bulgaricus, prtH of Lactobacillus helveticus, prtP of Lactococcus lactis, scpA of Streptococcus pyogenes and csp of Streptococcus agalactiae have been compared using multiple sequence alignment, secondary structure prediction and database homology searching methods. This comparative analysis has led to the prediction of a number of different domains in these cell-envelope proteinases, and their homology, characteristics and putative function are described. These domains include, starting from the N-terminus, a pre-pro-domain for secretion and activation, a serine protease domain (with a smaller inserted domain), two large middle domains A and B of unknown but possibly regulatory function, a helical spacer domain, a hydrophilic cell-wall spacer or attachment domain, and a cell-wall anchor domain. Not all domains are present in each cell-envelope proteinase, suggesting that these multi-domain proteins are the result of gene shuffling and domain swapping during evolution.