Structural and Functional Comparison of Polysaccharide-Degrading Enzymes

Sugar molecules as well as enzymes degrading them are ubiquitously present in physiological systems, especially for vertebrates. Polysaccharides have at least two aspects to their function, one due to their mechanical properties and the second one involves multiple regulatory processes or interactions between molecules, cells, or extracellular space. Various bacteria exert exogenous pressures on their host organism to diversity glycans and their structures in order for the host organism to evade the destructive function of such microbes. Many bacterial organism produce glycan-degrading enzymes in order to facilitate their invasion of host tissues. Such polysaccharide degrading enzymes utilize mainly two modes of polysaccharide-degradation, a hydrolysis and a β-elimination process. The three-dimensional structures of several of these enzymes have been elucidated recently using X-ray crystallography. There are many common structural motifs among these enzymes, mainly the presence of an elongated cleft transversing these molecules which functions as a polysaccharide substrate binding site as well as the catalytic site for these enzymes. The detailed structural information obtained about these enzymes allowed formulation of proposed mechanisms of their action. The polysaccharide lyases utilize a proton acceptance and donation mechanism (PAD), whereas polysaccharide hydrolases use a direct double displacement (DD) mechanism to degrade their substrates.     

Function and structure of inherently disordered proteins

The application of bioinformatics methodologies to proteins inherently lacking 3D structure has brought increased attention to these macromolecules. Here topics concerning these proteins are discussed, including their prediction from amino acid sequence, their enrichment in eukaryotes compared to prokaryotes, their more rapid evolution compared to structured proteins, their organization into specific groups, their structural preferences, their half-lives in cells, their contributions to signaling diversity (via high contents of multiple-partner binding sites, post-translational modifications, and alternative splicing), their distinct functional repertoire compared to that of structured proteins, and their involvement in diseases.     

Structural and functional comparison of polysaccharide-degrading enzymes

Sugar molecules as well as enzymes degrading them are ubiquitously present in physiological systems, especially for vertebrates. Polysaccharides have at least two aspects to their function, one due to their mechanical properties and the second one involves multiple regulatory processes or interactions between molecules, cells, or extracellular space. Various bacteria exert exogenous pressures on their host organism to diversity glycans and their structures in order for the host organism to evade the destructive function of such microbes. Many bacterial organism produce glycan-degrading enzymes in order to facilitate their invasion of host tissues. Such polysaccharide degrading enzymes utilize mainly two modes of polysaccharide-degradation, a hydrolysis and a beta-elimination process. The three-dimensional structures of several of these enzymes have been elucidated recently using X-ray crystallography. There are many common structural motifs among these enzymes, mainly the presence of an elongated cleft transversing these molecules which functions as a polysaccharide substrate binding site as well as the catalytic site for these enzymes. The detailed structural information obtained about these enzymes allowed formulation of proposed mechanisms of their action. The polysaccharide lyases utilize a proton acceptance and donation mechanism (PAD), whereas polysaccharide hydrolases use a direct double displacement (DD) mechanism to degrade their substrates.     

Segment- and nest-specific determination in the histoblasts of the housefly

Summary Using a novel grafting procedure for histoblasts, we have transplanted the fifth dorsal or ventral histoblast nests to heterotopic positions in the abdomen of the prepupa of the housefly to find out how rigid are these imaginai cells in their commitment to form their respective segmental pattern. Our results clearly show that these histoblasts survive in their new positions and form patterns according to their original determined state.     

Importance of lysosomal cysteine proteases in lung disease

The human lysosomal cysteine proteases are a family of 11 proteases whose members include cathepsins B, C, H, L, and S. The biology of these proteases was largely ignored for decades because of their lysosomal location and the belief that their function was limited to the terminal degradation of proteins. In the past 10 years, this view has changed as these proteases have been found to have specific functions within cells. This review highlights some of these functions, specifically their roles in matrix remodeling and in regulating the immune response, and their relationship to lung diseases.     

Culture conditions differentially affect the translation of individual Escherichia coli mRNAs.

Our aim is to investigate whether changes in growth conditions can differentially affect the initiation of translation from individual Escherichia coli mRNAs that are not subjected to specific translational control. As a model system, we have constructed a series of point-mutated lacZ genes which differ in their Shine-Dalgarno (SD) sequence, their initiator codon, or the secondary structure around these elements. Alterations in growth conditions produced large (up to 8-fold) changes in the relative expression from these genes, which, we argue, stem from changes in their relative efficiencies of translation initiation. In particular, compared to genes bearing mutations outside the SD or initiator codon, genes mutated in these elements experience a significant decrease in their expression when cells are grown in minimal rather than rich medium; at 42 degrees C rather than 37 degrees C; or under amino acid starvation. We discuss the mechanisms underlying these effects, and evocate their possible generality.     

Multidrug resistance in Gram-negative bacteria

Broadly specific, so-called multidrug, efflux mechanisms are now known to contribute significantly to intrinsic and acquired multidrug resistance in a number of Gram-negative bacteria, and the boom in bacterial genomics has confirmed the distribution of these systems in all bacteria. This broad distribution of multidrug transporters lends a certain credibility to suggestions that they play a housekeeping role in the cell, beyond any contributions they may make to antimicrobial efflux and resistance. In many instances, these transporters are dispensable, arguing against their carrying out essential cellular functions; nevertheless, the multiplicity of these broadly specific export systems within a given microorganism, often with overlapping substrate specificity, may explain the dispensability of individual exporters. Whatever their intended function, however, their conservation in so many organisms highlights their probable general importance in antimicrobial resistance, particularly in Gram-negative bacteria whose outer membranes work synergistically with many of these export systems to promote drug exclusion.     

Rab and Arf Proteins in Genetic Diseases

Rab and ADP‐ribosylation factor (Arf) family proteins are master regulators of membrane trafficking and are involved in all steps of vesicular transport. These families of small guanine‐nucleotide‐binding (G) proteins are well suited to regulate membrane trafficking processes since their nucleotide state determines their conformation and the capacity to bind to a multitude of effectors, which mediate their functions. In recent years, several inherited diseases have been associated with mutations in genes encoding proteins belonging to these two families or in proteins that regulate their GTP‐binding cycle. The genetic diseases that are caused by defects in Rabs, Arfs or their regulatory proteins are heterogeneous and display diverse symptoms. However, these diseases mainly affect two types of subcellular compartments, namely lysosome‐related organelles and cilia. Also, several of these diseases affect the nervous system. Thus, the study of these diseases represents an opportunity to understand their etiology and the molecular mechanisms involved, as well as to develop novel therapeutic strategies .     

Tsetse--A haven for microorganisms

Arthropods are involved in the transmission of parasitic and viral agents that cause devastating diseases in animals and plants. Effective control strategies for many of these diseases still rely on the elimination or reduction of vector insect populations. In addition to these pathogenic organisms, arthropods are rich in microbes that are symbiotic in their associations and are often necessary for the fecundity and viability of their hosts. Because the viability of the host often depends on these obligate symbionts, and because these organisms often live in close proximity to disease-causing pathogens, they have been of interest to applied biologists as a potential means to genetically manipulate populations of pest species. As knowledge on these symbiotic associations accumulates from distantly related insect taxa, conserved mechanisms for their transmission and evolutionary histories are beginning to emerge. Here, Serap Aksoy summarizes current knowledge on the functional and evolutionary biology of the multiple symbionts harbored in the medically and agriculturally important insect group, tsetse, and their potential role in the control of trypanosomiasis.     

Ecophysiology of the <Emphasis Type="Italic">Actinobacteria</Emphasis> in activated sludge systems

This review considers what is known about the Actinobacteria in activated sludge systems, their abundance and their functional roles there. Participation in processes leading to the microbiological removal of phosphate and in the operational problems of bulking and foaming are discussed in terms of their ecophysiological traits. We consider critically whether elucidation of their nutritional requirements and other physiological properties allow us to understand better what might affect their survival capabilities in these highly competitive systems. Furthermore, how this information might allow us to improve how these processes work is discussed.     

The glycerophosphoinositols and their cellular functions

Interest in the glycerophosphoinositols has been increasing recently, on the basis of their biological activities. The cellular metabolism of these water-soluble bioactive phosphoinositide metabolites has been clarified, with the identification of the specific enzyme involved in their synthesis, PLA2IVα (phospholipase A2 IVα), and the definition of their phosphodiesterase-based catabolism, and thus inactivation. The functional roles and mechanisms of action of these compounds have been investigated in different cellular contexts. This has led to their definition in the control of various cell functions, such as cell proliferation in the thyroid and actin cytoskeleton organization in fibroblasts and lymphocytes. Roles for the glycerophosphoinositols in immune and inflammatory responses are also being defined. In addition to these physiological functions, the glycerophosphoinositols have potential anti-metastatic activities that should lead to their pharmacological exploitation.     

The role of lipid anchors for small G proteins in membrane trafficking

Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. In order to perform these functions, the proteins must associate with specific donor vesicles and be recycled after fusion of these vesicles with their acceptor membrane target. Recent results have identified a number of lipid modifications of these proteins, occurring at the N- or C-termini, that contribute to their membrane binding. Recycling appears, in some cases, to be mediated by soluble proteins that bind the lipid-modified tails, removing them from the membrane and allowing their reutilization via the cytosol.     

Persistent yeast single-stranded RNA viruses exist in vivo as genomic RNA.RNA polymerase complexes in 1:1 stoichiometry

Yeast narnavirus 20 S and 23 S RNAs encode RNA-dependent RNA polymerases p91 and p104, respectively, but do not encode coat proteins. Both RNAs form ribonucleoprotein complexes with their cognate polymerases. Here we show that these complexes are not localized in mitochondria, unlike the closely related mitoviruses, which reside in these organelles. Cytoplasmic localization of these polymerases was demonstrated by immunofluorescence and by fluorescence emitted from green fluorescent protein-fused polymerases. These fusion proteins were able to form ribonucleoprotein complexes as did the wild-type polymerases. Fluorescent observations and cell fractionation experiments suggested that the polymerases were stabilized by complex formation with their viral RNA genomes. Immunoprecipitation experiments with anti-green fluorescent protein antibodies demonstrated that a single polymerase molecule binds to a single viral RNA genome in the complex. Moreover, the majority (if not all) of 20 S and 23 S RNA molecules were found to form complexes with their cognate RNA polymerases. Since these viral RNAs were not encapsidated, ribonucleoprotein complex formation with their cognate RNA polymerases appears to be their strategy to survive in the host as persistent viruses.     

The cellular machineries responsible for the division of endosymbiotic organelles

Chloroplasts (plastids) and mitochondria evolved from endosymbiotic bacteria. These organelles perform vital functions in photosynthetic eukaryotes, such as harvesting and converting energy for use in biological processes. Consistent with their evolutionary origins, plastids and mitochondria proliferate by the binary fission of pre-existing organelles. Here, I review the structures and functions of the supramolecular machineries driving plastid and mitochondrial division, which were discovered and first studied in the primitive red alga Cyanidioschyzon merolae. In the past decade, intact division machineries have been isolated from plastids and mitochondria and examined to investigate their underlying structure and molecular mechanisms. A series of studies has elucidated how these division machineries assemble and transform during the fission of these organelles, and which of the component proteins generate the motive force for their contraction. Plastid- and mitochondrial-division machineries have important similarities in their structures and mechanisms despite sharing no component proteins, implying that these division machineries evolved in parallel. The establishment of these division machineries might have enabled the host eukaryotic ancestor to permanently retain these endosymbiotic organelles by regulating their binary fission and the equal distribution of resources to daughter cells. These findings provide key insights into the establishment of endosymbiotic organelles and have opened new avenues of research into their evolution and mechanisms of proliferation.     

Conservation Value of Landscape Supplementation for Howler Monkeys Living in Forest Patches

Many animal populations are forced to inhabit very small forest patches, which may threaten their long-term survival. In some cases, animals in these forest remnants are able to supplement their diet by using resources outside of their home patch, a process named 'landscape supplementation'. Although this is probably a key process for population survival in fragmented landscapes, little is known about the ability of most animal species to move through the matrix and feed from different landscape elements. In this paper we report several cases of landscape supplementation by two groups of Mexican mantled howler monkeys Alouatta palliata mexicana inhabiting two different forest patches in Los Tuxtlas, Mexico. Our observations show that howler monkeys used several landscape elements, such as isolated trees, live fences and neighboring forest patches to supplement their diet. These observations underline the importance of these landscape elements for the survival of forest-dependent animals in highly fragmented landscapes, as they can provide important food resources and, hence, can be considered as potential extensions of their home range. However, the degree of protection the landowner provides to howler monkeys and proper management of these landscape elements are key aspects in determining the use of these elements by these animals.     

Effect of antituberculous calixarenes on phospholipase A2 susceptibility and on fusion of phospholipid bilayers.

Some homologous calixarenes or polyoxyethylene ethers that are known to suppress or enhance experimental tuberculous infection (depending on their polyoxyethylene chain lengths) were examined for their effects on phospholipid bilayers. The effect of these solutes is seen at 0.5-50p.p.m., and their effect depends upon their structure as well as that of the phospholipid substrate. The antituberculous compound HOC-12.5 (Macrocyclon) inhibits susceptibility to pig pancreatic phospholipase A2 action and to aggregation/fusion of the ternary co-dispersions of dimyristoyl phosphatidylcholine + 1-palmitoyl lysophosphatidylcholine + palmitic acid (50:11:11 molar proportions). In contrast, the protuberculous compound HOC-60 stimulates these effects. Differential scanning calorimetry suggests that these effects are probably due to modulation of the phase equilibrium in substrate bilayers by these polyethers.     

Speed versus accuracy in collective decision making

We demonstrate a speed versus accuracy trade-off in collective decision making. House-hunting ant colonies choose a new nest more quickly in harsh conditions than in benign ones and are less discriminating. The errors that occur in a harsh environment are errors of judgement not errors of omission because the colonies have discovered all of the alternative nests before they initiate an emigration. Leptothorax albipennis ants use quorum sensing in their house hunting. They only accept a nest, and begin rapidly recruiting members of their colony, when they find within it a sufficient number of their nest-mates. Here we show that these ants can lower their quorum thresholds between benign and harsh conditions to adjust their speed-accuracy trade-off. Indeed, in harsh conditions these ants rely much more on individual decision making than collective decision making. Our findings show that these ants actively choose to take their time over judgements and employ collective decision making in benign conditions when accuracy is more important than speed.     

Suitable areas for the invasion expansion of Xylocopa bees in South America

The introduction of exotic species into native ecosystems can be a cause for concern when those species are invasive. Invasive species cause ecological problems and have socio-cultural impacts on human health and the economy; for example, invasive bees may negatively impact their introduced ecosystem by spreading diseases or outcompeting native pollinators. Xylocopa spp. bees are diverse and distributed throughout the Neotropics. However, Xylocopa augusti (Lepeletier, 1841) and Xylocopa splendidula (Lepeletier, 1841) are not native to Mediterranean Chile. This study aimed to evaluate the invasive potential of these exotic species and predict the potential macroecological effects of their invasions. We also aimed to pinpoint possible distributions for these species throughout South America. We correlated biogeographic occurrence data with climatic variables for each species to model their potential distribution in both current and future scenarios. The models provide strong evidence that both species are changing their distributions: their ranges are expanding towards western South America, particularly Bolivia, Chile and Peru. We demonstrate an increase in niche overlap between these species and show there are new geographic areas vulnerable to the establishment of these invasive bees under current and future climate conditions. These data suggest that these bees may adapt their geographic distribution as the climate changes and pose a threat to native pollinators in new geographic areas.     

Local adaptation of the trematode Fasciola hepatica to the snail Galba truncatula

Experimental infections of six riverbank populations of Galba truncatula with Fasciola hepatica were carried out to determine if the poor susceptibility of these populations to this digenean might be due to the scarcity or the absence of natural encounters between these snails and the parasite. The first three populations originated from banks frequented by cattle in the past (riverbank group) whereas the three others were living on islet banks without any known contact with local ruminants (islet group). After their exposure, all snails were placed in their natural habitats from the end of October up to their collection at the beginning of April. Compared to the riverbank group, snails, which died without cercarial shedding clearly predominated in the islet group, while the other infected snails were few in number. Most of these last snails released their cercariae during a single shedding wave. In islet snails dissected after their death, the redial and cercarial burdens were significantly lower than those noted in riverbank G. truncatula. Snails living on these islet banks are thus able to sustain larval development of F. hepatica. The modifications noted in the characteristics of snail infection suggest the existence of an incomplete adaptation between these G. truncatula and the parasite, probably due to the absence of natural contact between host and parasite.