Fibulins: physiological and disease perspectives

The fibulins are a family of proteins that are associated with basement membranes and elastic extracellular matrix fibres. This review summarizes findings from studies of animal models of fibulin deficiency, human fibulin gene mutations, human tumours and injury models that have advanced our understanding of the normal and pathological roles of members of this formerly obscure family.     

Autophagy in yeast: mechanistic insights and physiological function.

Unicellular eukaryotic organisms must be capable of rapid adaptation to changing environments. While such changes do not normally occur in the tissues of multicellular organisms, developmental and pathological changes in the environment of cells often require adaptation mechanisms not dissimilar from those found in simpler cells. Autophagy is a catabolic membrane-trafficking phenomenon that occurs in response to dramatic changes in the nutrients available to yeast cells, for example during starvation or after challenge with rapamycin, a macrolide antibiotic whose effects mimic starvation. Autophagy also occurs in animal cells that are serum starved or challenged with specific hormonal stimuli. In macroautophagy, the form of autophagy commonly observed, cytoplasmic material is sequestered in double-membrane vesicles called autophagosomes and is then delivered to a lytic compartment such as the yeast vacuole or mammalian lysosome. In this fashion, autophagy allows the degradation and recycling of a wide spectrum of biological macromolecules. While autophagy is induced only under specific conditions, salient mechanistic aspects of autophagy are functional in a constitutive fashion. In Saccharomyces cerevisiae, induction of autophagy subverts a constitutive membrane-trafficking mechanism called the cytoplasm-to-vacuole targeting pathway from a specific mode, in which it carries the resident vacuolar hydrolase, aminopeptidase I, to a nonspecific bulk mode in which significant amounts of cytoplasmic material are also sequestered and recycled in the vacuole. The general aim of this review is to focus on insights gained into the mechanism of autophagy in yeast and also to review our understanding of the physiological significance of autophagy in both yeast and higher organisms.     

Osmoregulation in decapod crustaceans: physiological and genomic perspectives

Aquatic plants may face resource constraints or anthropogenic pollution, and effects might be heightened under multiple stress conditions. We investigated if arsenate effects on Myriophyllum spicatum L. would be stronger under CO₂ limitation and low phosphorus availability. In a factorial design, we exposed sediment-grown plants to either CO₂ (high carbon or HC) or bicarbonate (low carbon or LC) and four levels of arsenate. We observed strong effects of arsenate exposure on growth, biomass allocation (leaf, stem and root mass fractions), pigments and phenolic compounds. CO₂ availability strongly affected the content in phenolic compounds and a few other response variables, yet overall effects were less pronounced than expected. Strong interactive effects of CO₂ availability and arsenic concentration were only observed for carotenoids, the carotenoid/chlorophyll ratio and phenolic compounds in leaves. Only the carbon content declined with increasing arsenic concentration, otherwise leaf elemental content and stoichiometry were not affected by arsenic or CO₂ availability, suggesting that plants strived to maintain leaf functions. The observed effects on biomass allocation and plant quality, specifically dry matter content and phenolic compound content of M. spicatum not only show direct changes in plant performance but suggest also indirect effects on ecological interactions such as competition or herbivory.     

Chaperone-mediated autophagy: Molecular mechanisms and physiological relevance

Chaperone-mediated autophagy (CMA) is a selective lysosomal pathway for the degradation of cytosolic proteins. We review in this work some of the recent findings on this pathway regarding the molecular mechanisms that contribute to substrate targeting, binding and translocation across the lysosomal membrane. We have placed particular emphasis on the critical role that changes in the lipid composition of the lysosomal membrane play in the regulation of CMA, as well as the modulatory effect of other novel CMA components. In the second part of this review, we describe the physiological relevance of CMA and its role as one of the cellular mechanisms involved in the response to stress. Changes with age in CMA activity and the contribution of failure of CMA to the phenotype of aging and to the pathogenesis of several age-related pathologies are also described.     

Current knowledge on mycolic acids in Corynebacterium glutamicum and their relevance for biotechnological processes

Corynebacterium glutamicum is the world’s largest producer of glutamate and lysine. Industrial glutamate overproduction is induced by empirical processes, such as biotin limitation, supplementation with specific surfactants or addition of sublethal concentration of certain antibiotics to the culture media. Although Gram-positive bacteria, C. glutamicum and related bacterial species and genera contain, in addition to the plasma membrane, an outer permeability membrane similar to that of Gram-negative microorganisms. As the amino acids have to cross both membranes, their integrity, composition and fluidity influence the export process. While the precise mechanism of the export of the amino acids by C. glutamicum is not fully understood, the excretion of amino acids through the inner membrane involved at least a major export system mechanosensitive channel MscS family (MscCG) encoded by NCgl1221. As the various industrial treatments have been shown to affect the lipid content of the bacterial cell, it is strongly believed that defects in the hallmark of the outer membrane, 2-alkyl, 3-hydroxylated long-chain fatty acids (mycolic acids), could be key factors in the glutamate overproduction. This review aims at giving an overview of the current knowledge on mycolic acids structure, biosynthesis and transfer in C. glutamicum and their relevance for amino acid biotechnological production.     

Biodegradation of phenol and its derivatives by engineered bacteria: current knowledge and perspectives

Biodegradation of phenolic compounds is a promising alternative to physical and chemical methods used to remove these toxic pollutants from the environment. The ability of various microorganisms to metabolize phenol and its derivatives (alkylphenols, nitrophenols and halogenated derivatives) has therefore been intensively studied. Knowledge of the enzymes catalyzing the individual reactions, the genes encoding these enzymes and the regulatory mechanisms involved in the expression of the respective genes in bacteria serves as a basis for the development of more efficient degraders of phenols via genetic engineering methods. Engineered bacteria which efficiently degrade phenolic compounds were constructed in laboratories using various approaches such as cloning the catabolic genes in multicopy plasmids, the introduction of heterologous genes or broadening the substrate range of key enzymes by mutagenesis. Efforts to apply the engineered strains in in situ bioremediation are problematic, since engineered strains often do not compete successfully with indigenous microorganisms. New efficient degraders of phenolic compounds may be obtained by complex approaches at the organism level, such as genome shuffling or adaptive evolution. The application of these engineered bacteria for bioremediation will require even more complex analysis of both the biological characteristics of the degraders and the physico-chemical conditions at the polluted sites.     

Phloridzin: Biosynthesis,distribution and physiological relevance in plants

The phenolic compound phloridzin (phloretin 2′-O-glucoside, phlorizin, phlorrhizin, phlorhizin or phlorizoside) is a prominent member of the chemical class of dihydrochalcones, which are phenylpropanoids. The apple tree (Malus sp.) accumulates high amounts of phloridzin, whereas few other species contain this compound only in low amounts. Additionally, Malus sp. show a species- and tissue-specific distribution of phloridzin and its derivatives. Whereas the physiological role of phloridzin in planta is not fully understood, the effect on human health – especially diabetes – and membrane permeability is well documented. The biosynthesis of phloridzin was investigated only recently with recombinant enzymes and plant protein extracts and involved a NADPH-dependent dehydrogenase, chalcone synthase and UDP-glucose:phloretin 2′-O-glycosyltransferase.     

Chemical signals in insects and other arthropods: from molecular structure to physiological functions

Chemical communication is virtually universal among terrestrial and aquatic organisms. Chemical signals control the interactions of cells and organs (hormones) as well as the intra- (pheromones) and interspecific (allelochemicals) relationships between animals. The review considers three examples for chemical communication in insects and other arthropods on different hierarchic levels of biological organization, from the intraindividual level, where hormones control development and reproduction of the animals, to the interspecific level, where semiochemicals function as defense agents against predators or may be used for finding and recognizing food resources. Knowledge of the function of these systems and of the molecular structures of the chemical compounds involved may provide the basis for highly selective techniques of pest control.     

Metabolic depression in animals: physiological perspectives and biochemical generalizations

Depression of metabolic rate has been recorded for virtually all major animal phyla in response to environmental stress. The extent of depression is usually measured as the ratio of the depressed metabolic rate to the normal resting metabolic rate. Metabolic rate is sometimes only depressed to approx. 80% of the resting value (i.e. a depression of approx. 20% of resting); it is more commonly 5-40 % of resting (i.e. a depression of approx. 60-95% of resting); extreme depression is to 1% or less of resting, or even to an unmeasurably low metabolic rate (i.e. a depression of approx. 99-100% of resting). We have examined the resting and depressed metabolic rate of animals as a function of their body mass, corrected to a common temperature. This allometric approach allows ready comparison of the absolute level of both resting and depressed metabolic rate for various animals, and suggests three general patterns of metabolic depression. Firstly, metabolic depression to approx. 0.05-0.4 of rest is a common and remarkably consistent pattern for various non-cryptobiotic animals (e.g. molluscs, earthworms, crustaceans, fishes, amphibians, reptiles). This extent of metabolic depression is typical for dormant animals with ‘intrinsic’ depression, i.e. reduction of metabolic rate in anticipation of adverse environmental conditions but without substantial changes to their ionic or osmotic status, or state of body water. Some of these types of animal are able to survive anoxia for limited periods, and their anaerobic metabolic depression is also to approx. 0.05-0.4 of resting. Metabolic depression to much less than 0.2 of resting is apparent for some ‘resting’, ‘over-wintering’ or diapaused eggs of these animals, but this can be due to early developmental arrest so that the egg has a low ‘metabolic mass’ of developed tissue (compared to the overall mass of the egg) with no metabolic depression, rather than having metabolic depression of the entire cell mass. A profound decrease in metabolic rate occurs in hibernating (or aestivating) mammals and birds during torpor, e.g. to less than 0.01 of pre-torpor metabolic rate, but there is often no intrinsic metabolic depression in addition to that reduction in metabolic rate due to readjustment of thermoregulatory control and a decrease in body temperature with a concommitant Q₁₀ effect. There may be a modest intrinsic metabolic depression for some species in shallow torpor (to approx. 0.86) and a more substantial metabolic depression for deep torpor (approx. 0.6), but any energy saving accruing from this intrinsic depression is small compared to the substantial savings accrued from the readjustment of thermoregulation and the Q₁₀ effect. Secondly, a more extreme pattern of metabolic depression (to < 0.05 of rest) is evident for cryptobiotic animals. For these animals there is a profound change in their internal environment-for anoxybiotic animals there is an absence of oxygen and for osmobiotic, anhydrobiotic or cryobiotic animals there is an alteration of the ionic/osmotic balance or state of body water. Some normally aerobic animals can tolerate anoxia for considerable periods, and their duration of tolerance is inversely related to their magnitude of metabolic depression; anaerobic metabolic rate can be less than 0.005 of resting. The metabolic rate of anhydrobiotic animals is often so low as to be unmeasurable, if not zero. Thus, anhydrobiosis is the ultimate strategy for eggs or other stages of the life cycle to survive extended periods of environmental stress. Thirdly, a pattern of absence of metabolism when normally hydrated (as opposed to anhydrobiotic or cryobiotic) is apparently unique to diapaused eggs of the brine-shrimp (Artemia spp., an anostracan crustacean) during anoxia. The apparent complete metabolic depression of anoxic yet hydrated cysts (and extreme metabolic depression of normoxic, hypoxic, or osmobiotic, yet hydrated cysts), is an obvious exception to the above patterns. In searching for biochemical mechanisms for metabolic depression, it is clear that there are five general characteristics at the molecular level of cells which have a depressed metabolism; a decrease in pH, the presence of latent mRNA, a change in protein phosphorylation state, the maintenance of one particular energy-utilizing process (ion pumping), and the down-regulation of another (protein synthesis). Oxygen sensing is now the focus of intense investigation and obviously plays an important role in many aspects of cell biology. Recent studies show that oxygen sensing is involved in metabolic depression and research is now being directed towards characterising the proteins and mechanisms that comprise this response. As more data accumulate, oxygen sensing as a mechanism will probably become the sixth general characteristic of depressed cells. The majority of studies on these general characteristics of metabolically depressed cells come from members of the most common group of animals that depress metabolism, those non-cryptobiotic animals that remain hydrated and depress to 0.05-0.4 of rest. These biochemical investigations are becoming more molecular and sophisticated, and directed towards defined processes, but as yet no complete mechanism has been delineated. The consistency of the molecular data within this group of animals suggests similar metabolic strategies and mechanisms associated with metabolic depression. The biochemical ‘adaptations’ of anhydrobiotic organisms would seem to be related more to surviving the dramatic reduction in cell water content and its physico-chemical state, than to molecular mechanisms for lowering metabolic rate. Metabolic depression would seem to be an almost inevitable consequence of their altered hydration state. The unique case of profound metabolic depression of hydrated Artemia spp. cysts under a variety of conditions could reflect unique mechanisms at the molecular level. However, the available data are not consistent with this possibility (with the exception of a uniquely large decrease in ATP concentration of depressed, hydrated Artemia spp. cysts) and the question remains: how do cells of anoxic and hydrated Artemia spp. differ from anoxic goldfish or turtle cells, enabling them so much more completely to depress their metabolism?     

Biodegradation of sulfamethoxazole: current knowledge and perspectives

Antibiotic compounds, like sulfamethoxazole (SMX), have become a concern in the aquatic environment due to the potential development of antibacterial resistances. Due to extensive consumption, excretion and disposal, SMX has been frequently detected in wastewaters and surface waters. This has led to numerous studies investigating the nature of SMX, with many researchers focusing on the biodegradation and persistence of SMX during wastewater treatment and in the environment. This review provides a summary of recent developments, outlines the discrepancies in observations and results, and demonstrates the need for further research to determine optimal biological removal strategies for SMX and other antibiotics.     

Cassava mosaic geminiviruses: actual knowledge and perspectives

Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) is one of the most devastating crop diseases and a major constraint for cassava cultivation. CMD has been reported only from the African continent and Indian subcontinent despite the large-scale cultivation of cassava in Latin America and several South-East Asian countries. Seven CMG species have been reported from Africa and two from the Indian subcontinent and, in addition, several strains have been recognized. Recombination and pseudo-recombination between CMGs give rise not only to different strains, but also to members of novel virus species with increased virulence and a new source of biodiversity, causing severe disease epidemics. CMGs are known to trigger gene silencing in plants and, in order to counteract this natural host defence, geminiviruses have evolved suppressor proteins. Temperature and other environmental factors can affect silencing and suppression, and thus modulate the symptoms. In the case of mixed infections of two or more CMGs, there is a possibility for a synergistic interaction as a result of the presence of differential and combinatorial suppressor proteins. In this article, we provide the status of recent research findings with regard to the CMD complex, present the molecular biology knowledge of CMGs with reference to other geminiviruses, and highlight the mechanisms by which CMGs have exploited nature to their advantage.     

Osteoclastogenesis--current knowledge and future perspectives

The strength and integrity of the human skeleton depends on a delicate equilibrium between bone resorption by osteoclasts and bone formation by osteoblasts. This equilibrium is continuously compromised by a variety of genetic, humoral, and mechanical alterations. In osteoporosis, this balance shifts in favor of osteoclasts, and bone resorption exceeds bone formation. More detailed knowledge of the biology of osteoclasts and osteoclastogenesis has shown that the involved procedures can provide opportunities for developing therapeutic agents. Osteoclastogenesis is a multi-complex procedure that includes many stages, and each one of them presents as a potential target for therapeutic intervention, except for the stage of commitment of pre-osteoclasts,at least for the time being. Because the osteoclast is derived from the pluripotent hematopoietic stem cell, any intervention in this stage could result in serious adverse effects from the hematopoietic system. On the contrary, intervention in the later stages of differentiation, multi-nucleation, and activation, has proved to be very promising in the development of novel potent anti-resorptive agents. In the present review we summarized the current knowledge related to osteoclast differentiation and the new developing targets of pharmacological intervention in each stage of this extremely complicated and not completely elucidated process.     

Protease expression by microorganisms and its relevance to crucial physiological/pathological events

The treatment of infections caused by fungi and trypanosomatids is difficult due to the eukaryotic nature of these microbial cells,which are similar in several biochemical and genetic aspects to host cells.Aggravating this scenario,very few antifungal and anti-trypanosomatidal agents are in clinical use and,therefore,therapy is limited by drug safety considerations and their narrow spectrum of activity,efficacy and resistance. The search for new bioactive agents against fungi and trypanosomatids has been expanded because progress in biochemistry and molecular biology has led to a better understanding of important and essential pathways in these microorganisms including nutrition,growth, proliferation,signaling,differentiation and death.In this context,proteolytic enzymes produced by these eukaryotic microorganisms are appointed and,in some cases,proven to be excellent targets for searching novel natural and/or synthetic pharmacological compounds,in order to cure or prevent invasive fungal/trypanosomatid diseases.With this task in mind,our research group and others have focused on aspartic-type proteases,since the activity of this class of hydrolytic enzymes is directly implicated in several facets of basic biological processes of both fungal and trypanosomatid cells as well as due to the participation in numerous events of interaction between these microorganisms and host structures.In the present paper,a concise revision of the beneficial effects of aspartic protease inhibitors,with emphasis on the aspartic protease inhibitors used in the anti-human immunodeficiency virus therapy,will be presented and discussed using our experience with the following microbial models:the yeast Candida albicans,the filamentous fungus Fonsecaea pedrosoi and the protozoan trypanosomatid Leishmania amazonensis.     

Autophagy deregulation in neurodegenerative diseases - recent advances and future perspectives

Autophagy is an evolutionarily conserved homeostatic process for the turnover of cellular contents, organelles and misfolded proteins through the lysosomal machinery. Recently, the involvement of autophagy in the pathophysiology of neurodegenerative diseases has attracted considerable interest because autophagy deregulation has been linked to some of these neurodegenerative disorders. This interest is further heightened by the demonstration that various autophagic pathways, including macroautophagy and chaperone-mediated autophagy, are implicated in the turnover of proteins that are prone to aggregation in cellular or animal disease models. These observations have stimulated new awareness in the pivotal role of the autophagic pathways in neurodegenerative disease pathophysiology, and have sparked extensive research aimed at deciphering the mechanisms by which autophagy is altered in these disorders. Here, we summarize the latest advances in our understanding of the role of autophagy deregulation in Parkinson's, Alzheimer's and Huntington's disease.