Animal and human RNA viruses: genetic variability and ability to overcome vaccines.

RNA viruses, in general, exhibit high mutation rates; this is mainly due to the low fidelity displayed by the RNA-dependent polymerases required for their replication that lack the proofreading machinery to correct misincorporated nucleotides and produce high mutation rates. This lack of replication fidelity, together with the fact that RNA viruses can undergo spontaneous mutations, results in genetic variants displaying different viral morphogenesis, as well as variation on their surface glycoproteins that affect viral antigenicity. This diverse viral population, routinely containing a variety of mutants, is known as a viral 'quasispecies'. The mutability of their virions allows for fast evolution of RNA viruses that develop antiviral resistance and overcome vaccines much more rapidly than DNA viruses. This also translates into the fact that pathogenic RNA viruses, that cause many diseases and deaths in humans, represent the major viral group involved in zoonotic disease transmission, and are responsible for worldwide pandemics.

A short voyage into the past: former misconceptions and misinterpretations in the etiology of some viral diseases.

The advancement of human knowledge has historically followed the pattern of one-step growth (the same pattern followed by microorganisms in laboratory culture conditions). In this way, each new important discovery opened the door to multiple secondary breakthroughs, eventually reaching a "plateau" when new findings emerged. Microbiology research has usually followed this pattern, but often the conclusions attained from experimentation/observation were either equivocal or altogether false, causing important delays in the advancement of this science. This mini-review deals with some of these documented scientific errors, but the aim is not to include every mistake, but to select those that are paramount to the advance of Microbiology.

Cell aggregations in yeasts and their applications.

Yeasts can display four types of cellular aggregation: sexual, flocculation, biofilm formation, and filamentous growth. These cell aggregations arise, in some yeast strains, as a response to environmental or physiological changes. Sexual aggregation is part of the yeast mating process, representing the first step of meiotic recombination. The flocculation phenomenon is a calcium-dependent asexual reversible cellular aggregation that allows the yeast to withstand adverse conditions. Biofilm formation consists of multicellular aggregates that adhere to solid surfaces and are embedded in a protein matrix; this gives the yeast strain either the ability to colonize new environments or to survive harsh environmental conditions. Finally, the filamentous growth is the ability of some yeast strains to grow in filament forms. Filamentous growth can be attained by two different means, with the formation of either hyphae or pseudohyphae. Both hyphae and pseudohyphae arise when the yeast strain is under nutrient starvation conditions and they represent a means for the microbial strain to spread over a wide area to survey for food sources, without increasing its biomass. Additionally, this filamentous growth is also responsible for the invasive growth of some yeast.

Construction of new Pichia pastoris X-33 strains for production of lycopene and ß-carotene.

In this study, we used the non-carotenogenic yeast Pichia pastoris X33 as a receptor for ß-carotene-encoding genes, in order to obtain new recombinant strains capable of producing different carotenoidic compounds. We designed and constructed two plasmids, pGAPZA-EBI* and pGAPZA-EBI*L*, containing the genes encoding lycopene and ß-carotene, respectively. Plasmid pGAPZA-EBI*, expresses three genes, crtE, crtB, and crtI*, that encode three carotenogenic enzymes, geranylgeranyl diphosphate synthase, phytoene synthase, and phytoene desaturase, respectively. The other plasmid, pGAPZA-EBI*L*, carried not only the three genes above mentioned, but also the crtL* gene, that encodes lycopene ß-cyclase. The genes crtE, crtB, and crtI were obtained from Erwinia uredovora, whereas crtL* was cloned from Ficus carica (JF279547). The plasmids were integrated into P. pastoris genomic DNA, and the resulting clones Pp-EBI and Pp-EBIL were selected for either lycopene or ß-carotene production and purification, respectively. Cells of these strains were investigated for their carotenoid contents in YPD media. These carotenoids produced by the recombinant P. pastoris clones were qualitatively and quantitatively analyzed by high-resolution liquid chromatography, coupled to photodiode array detector. These analyses confirmed that the recombinant P. pastoris clones indeed produced either lycopene or ß-carotene, according to the integrated vector, and productions of 1.141 µg of lycopene and 339 µg of ß-carotene per gram of cells (dry weight) were achieved. To the best of our knowledge, this is the first time that P. pastoris has been genetically manipulated to produce ß-carotene, thus providing an alternative source for large-scale biosynthesis of carotenoids.

Short communication: A comparative analysis of recombinant chymosins.

The first step in cheesemaking is the milk clotting process, in which κ-caseinolytic enzymes contribute to micelle precipitation. The best enzyme for this purpose is chymosin because of its high degree of specificity toward κ-casein. Although recombinant bovine chymosin is the most frequently used chymosin in the industry, new sources of recombinant chymosin, such as goat, camel, or buffalo, are now available. The present work represents a comparative study of 4 different recombinant chymosins (goat and buffalo chymosins expressed in Pichia pastoris, and bovine and camel chymosin expressed in Aspergillus niger). Recombinant goat chymosin exhibited the best catalytic efficiency compared with the buffalo, bovine, or camel recombinant enzymes. Moreover, recombinant goat chymosin exhibited the best specific proteolytic activity, a wider pH range of action, and a lower glycosylation degree than the other 3 enzymes. In conclusion, we propose that recombinant goat chymosin represents a serious alternative to recombinant bovine chymosin for use in the cheesemaking industry.

Synergism between outer membrane proteins and antimicrobials.

Antibiotic-resistant bacteria are becoming one of the most important problems in health care because of the number of resistant strains and the paucity of new effective antimicrobials. Since antibiotic-resistant bacteria will continue to increase, it is necessary to look for new alternative strategies to fight against them. It is generally accepted that Gram-negative bacteria are intrinsically less susceptible than Gram-positive bacteria to antimicrobials. The main reason is that Gram-negative bacteria are surrounded by a permeability barrier known as the outer membrane (OM). Hydrophilic solutes most often cross the OM through water-filled channels formed by a particular family of proteins known as porins. This work explores the possibility of using exogenous porins to lower the required amounts of antibiotics (ampicillin, ciprofloxacin, cefotaxime, clindamycin, erythromycin, and tetracycline). Porins had a bactericidal effect on Escherichia coli cultures, mainly in the logarithmic phase of growth, when combined with low antibiotic concentrations. The use of different antibiotic-porin mixtures showed a bactericidal effect greater than those of antibiotics and porins when used separately. It was possible to observe different behaviors according to the antibiotic type used.

Cloning and expression of the XPR2 gene from Yarrowia lipolytica in Pichia pastoris.

Yarrowia lipolytica is a dimorphic yeast able to secrete different types of proteases depending on the pH of the environment. At neutral pH, the production of an extracellular alkaline protease (AEP) is induced. This protease could be useful in the leather, detergent, or food industries. The XPR2 gene, coding for AEP, was extracted from the pINA154 vector and cloned into the pHIL-D2 vector to obtain a new protease-producing recombinant Pichia pastoris strain. The gene was efficiently integrated in the P. pastoris genome and expressed from the AOX1 promoter actively induced by methanol. Finally, the protease was successfully secreted by P. pastoris GS115.

Antimicrobial peptides (AMPs): Ancient compounds that represent novel weapons in the fight against bacteria.

Antimicrobial peptides (AMPs) are short peptidic molecules produced by most living creatures. They help unicellular organisms to successfully compete for nutrients with other organisms sharing their biological niche, while AMPs form part of the immune system of multicellular creatures. Thus, these molecules represent biological weapons that have evolved over millions of years as a result of an escalating arms race for survival among living organisms. All AMPs share common features, such as a small size, with cationic and hydrophobic sequences within a linear or cyclic structure. AMPs can inhibit or kill bacteria at micromolar concentrations, often by non-specific mechanisms; hence the appearance of resistance to these antimicrobials is rare. Moreover, AMPs can kill antibiotic-resistant bacteria, including insidious microbes such as Acinetobacter baumannii and the methicillin-resistant Staphylococcus aureus. This review gives a detailed insight into a selection of the most prominent and interesting AMPs with antibacterial activity. In the near future AMPs, due to their properties and despite their ancient origin, should represent a novel alternative to antibiotics in the struggle to control pathogenic microorganisms and maintain the current human life expectancy.

Antivirals against animal viruses.

Antivirals are compounds used since the 1960s that can interfere with viral development. Some of these antivirals can be isolated from a variety of sources, such as animals, plants, bacteria or fungi, while others must be obtained by chemical synthesis, either designed or random. Antivirals display a variety of mechanisms of action, and while some of them enhance the animal immune system, others block a specific enzyme or a particular step in the viral replication cycle. As viruses are mandatory intracellular parasites that use the host's cellular machinery to survive and multiply, it is essential that antivirals do not harm the host. In addition, viruses are continually developing new antiviral resistant strains, due to their high mutation rate, which makes it mandatory to continually search for, or develop, new antiviral compounds. This review describes natural and synthetic antivirals in chronological order, with an emphasis on natural compounds, even when their mechanisms of action are not completely understood, that could serve as the basis for future development of novel and/or complementary antiviral treatments.

Fluorescein thiocarbamoyl-kappa-casein assay for the specific testing of milk-clotting proteases.

Milk-clotting proteases, which are widely used in the cheese-making industry, are enzymes that use soluble caseins as their preferential substrates. Here, we propose a modification to a method previously described for the specific determination of milk-clotting proteases by using kappa-casein labeled with fluorescein isothiocyanate as substrate. Validation of the modified method was confirmed using natural bacterial, fungal, plant, and animal milk-clotting proteases, as well as a milk-clotting enzyme of recombinant origin. The new modified method described here allowed specific quantification of the activity of milk-clotting proteases in a very sensitive way and permitted determination of the appropriate kinetic parameters of all the enzymes tested, consistent with their origin and degree of purity.

Draft Genome Sequence of the Bacterium Gordonia jacobaea, a New Member of the Gordonia Genus.

Gordonia jacobaea was isolated and characterized in the Department of Microbiology, University of Santiago de Compostela, in 2000. Here we present the draft genome sequence of this species, which will improve our understanding of the diversity and the relation of the cell wall proteins of G. jacobaea with other mycolata.

Cloning of genes related to exo-beta-glucanase production in Saccharomyces cerevisiae: characterization of an exo-beta-glucanase structural gene.

The EXG1 gene of Saccharomyces cerevisiae was cloned and identified by complementation of a mutant strain (exg1-2) with highly reduced extracellular exo-beta-1,3-glucanase (EXG) activity. Two recombinant plasmids containing an overlapping region of 5.2 kb were isolated from a genomic DNA library and characterized by restriction mapping. The coding region was located by subcloning the original DNA inserts in a 2.7-kb HindIII-XhoI fragment. Exg+ strains and Exg- mutants transformed with yeast multicopy plasmids containing this DNA fragment showed an EXG activity 5- to 20-fold higher than for the untransformed Exg+ wild-type (wt) strains. The overproduced EXG had the same enzymic activity on different substrates, and showed the same electrophoretic behaviour on polyacrylamide gels and identical properties upon filtration through Sephacryl S-200 as those of the main EXG from Exg+ wt strains. The EXG1 gene transformed Schizosaccharomyces pombe, yielding extracellular EXG activity which showed cross-reactivity with anti-S. cervisiae EXG antibodies. A fragment including only a part of the EXG1 region was subcloned into the integrating vector YIp5, and the resulting plasmid was used to transform an Exg+ strain. Genetic and Southern analysis of several stable Exg- transformants showed that the fragment integrated by homology with the EXG1 locus. The chromosomal DNA fragment into which the plasmid integrated has a restriction pattern identical to that of the fragment on which we had previously identified the putative EXG1 gene. Only one copy of the EXG1 gene per genome was found in several strains tested by Southern analysis. Furthermore, two additional recombinant plasmids sharing a yeast DNA fragment of about 4.1 kb, which partially complements the exg1-2 mutation but which shows no homology with the 2.7-kb fragment containing the EXG1 gene, were also identified in this study. This 4.1-kb DNA fragment does not appear to contain an extragenic suppressor and could be related in some way to EXG production in S. cerevisiae.

Heterogeneous glycosylation of the EXG1 gene product accounts for the two extracellular exo-beta-glucanases of Saccharomyces cerevisiae.

Two exo-beta-glucanases of glycoprotein nature can be detected in culture supernatants of Saccharomyces cerevisiae cells. These exo-beta-glucanases show different Mr values and kinetic properties, although they are immunologically related. Their carbohydrate content and the electrophoretic mobility of both endoglycosidase H-treated exo-beta-glucanases suggest that they share the same protein fraction. Studies at genetic level relate the production of both extracellular exo-beta-glucanases with the expression of a single-copy gene in S. cerevisiae. Expression of this gene in another yeast, Schizosaccharomyces pombe, demonstrates that it codes for a protein with exo-beta-glucanase activity whose heterogeneous N-glycosylation accounts for both extracellular exo-beta-glucanases of S. cerevisiae.

Differentiation of Candida guilliermondii varieties by lectin-like substances from marine algae.

Lectin-like substances of 54 marine algae, corresponding to 30 red algae and 24 brown algae, were studied to estimate the agglutination activity against Candida guilliermondii. Extracts of Dictyopteris membranacea, Bifurcaria bifurcata, Halidrys siliquosa, Ascophyllum nodosum, Fucus serratus and F. spiralis algae showed selective agglutinating activities for C. guilliermondii "sensu stricto" and some of its varieties. According to their response to agglutination (positive or negative), certain algal extracts enabled the differentiation of varieties of C. guilliermondii independently of the titre values. Three extracts of brown algae were sufficient to identify 4 varieties of C. guilliermondii. The results suggest that lectin-like substances from marine algae may be valuable reagents as assistant tools for the identification of yeast strains.

Production of pectic enzymes in yeasts.

When grown in the appropriate medium, several yeast species produce pectinases able to degrade pectic substances. It is mainly exocellular endopolygalacturonases that break pectins or pectate down by hydrolysis of alpha-1,4-glycosidic linkages in a random way. Biochemical characterisation of these enzymes has shown that they have an optimal pH in the acidic region and an optimal temperature between 40 and 55 degrees C. Their production by yeasts is a constitutive feature and is repressed by the glucose concentration and aeration. Pectic substances and their hydrolysis products are used as carbon sources by a limited number of yeasts and hence these enzymes must be involved in the colonisation of different parts of plants, including fruits. The first yeast pectic enzyme (encoded by the PSE3 gene) was cloned from Tichosporon penicillatum. Recently, a polygalacturonase-encoding gene from Saccharomyces cerevisiae has been cloned and overexpressed in several strains and the gene for an extracellular endopolygalacturonase from Kluyveromyces marxianus has also been described. Taking all the results together, the idea is now emerging that this type of yeast enzyme could offer an alternative to fungal enzymes for industrial applications.

Curing of the killer character of Saccharomyces cerevisiae with acridine orange.

Acridine orange, an intercalating dye usually employed in the curing of bacterial plasmids, was tested for its ability to cure K1 and K2 killer strains (laboratory and wine strains). The results showed a high curing percentage of the killer character. This was demonstrated by the loss of M1 or M2 dsRNAs (responsible for toxin production and resistance to it) and because the meiotic products exhibited non-Mendelian segregation. The curing percentages varied, depending on the strain but not on the killer type, and showed similar efficiency as compared with other known curing agents.

Cloning of a new FLO gene from the flocculating Saccharomyces cerevisiae IM1-8b strain.

A flocculation conferring gene was cloned from a genomic library of the flocculating strain Saccharomyces cerevisiae IM1-8b as a 5 kb DNA fragment. The shortest DNA fragment (XbaI-XbaI) able to confer the flocculating phenotype was 3.1 kb. Southern analysis revealed that this gene was not homologous to the already reported FLO1 gene since strong hybridization signals were obtained when chromosomes IV and XII were probed with a digoxygenin-labelled fragment and no signal at all was detected for chromosome I. Partial sequencing data unequivocally ascribed the cloned fragment to chromosome XII. The gene was detected in a variety of S. cerevisiae strains regardless of their being phenotypically flocculating. This gene which, we propose as FLO2, is able to complement the flo1 mutation and is suppressed by suppressors (fsu3) that do not affect other FLO genes.

Cloning, molecular characterization, and expression of an endo-polygalacturonase-encoding gene from Saccharomyces cerevisiae IM1-8b.

A structural polygalacturonase-encoding gene (PGU1) from Saccharomyces cerevisiae IM1-8b was cloned and sequenced. The predicted protein comprises 361 amino acids, with a signal peptide between residues 1 and 18 and two potential glycosylation points in residues 318 and 330. The putative active site is a conserved histidine in position 222. This polygalacturonase showed 54% homology with the fungal ones and only 24% homology with their plant and bacterial counterparts. The gene is present in a single gene copy per haploid genome and it is detected in all strains, regardless of their phenotype. The expression of PGU1 gene in several strains of S. cerevisiae revealed that the polygalacturonase activity depended on the plasmid used and also on the genetic background of each strain but in all cases the enzymatic activity increased.

Isolation and characterization of a mutant of Saccharomyces cerevisiae affected in the FLO1 locus.

A non-flocculent strain of Saccharomyces cerevisiae was selected after EMS mutation of a flocculent and heterozygous FLO1 locus diploid. The analysis of 25 asci from this diploid showed in all cases segregation 0F:4NF, thus confirming that it was probably affected in the desired gene. After sporulation and dissection of asci, three haploid strains were chosen, which were altered in the locus FLO1. Crossing these three strains with two other ones having markers for ADE1 and pho11::LEU2, we could map the mutation at ca. 4.3 cM and ca. 37.7 cM from the PHO11 and ADE1 loci respectively.

Characterization of killer-resistant strains of Saccharomyces cerevisiae isolated from spontaneous fermentations.

A study of 26 killer-resistant wine strains of Saccharomyces cerevisiae, isolated during spontaneous fermentations in three vineyards in NW Spain, was carried out employing several methods that included a spheroplast-killing assay and analysis of chromosomal DNA patterns by pulse-field agarose electrophoresis. The results showed that 92% of the strains were derivatives of K2 killer toxin producing wine strains isolated from the same fermentations, and that they could be grouped into four different karyotypes. The remaining strains were killer-resistant at cell-wall level and were not related to the others, as was demonstrated by the absence of L and M ds-RNAs and by their different karyotypes.