Functional specificity of extracellular nucleases of Shewanella oneidensis MR-1

Bacterial species such as Shewanella oneidensis MR-1 require extracellular nucleolytic activity for the utilization of extracellular DNA (eDNA) as a source of nutrients and for the turnover of eDNA as a structural matrix component during biofilm formation. We have previously characterized two extracellular nucleases of S. oneidensis MR-1, ExeM and ExeS. Although both are involved in biofilm formation, they are not specifically required for the utilization of eDNA as a nutrient. Here we identified and characterized EndA, a third extracellular nuclease of Shewanella. The heterologously overproduced and purified protein was highly active and rapidly degraded linear and supercoiled DNAs of various origins. Divalent metal ions (Mg(2+) or Mn(2+)) were required for function. endA is cotranscribed with phoA, an extracellular phosphatase, and is not upregulated upon phosphostarvation. Deletion of endA abolished both extracellular degradation of DNA by S. oneidensis MR-1 and the ability to use eDNA as a sole source of phosphorus. PhoA is not strictly required for the exploitation of eDNA as a nutrient. The activity of EndA prevents the formation of large cell aggregates during planktonic growth. However, in contrast to the findings for ExeM, endA deletion had only minor effects on biofilm formation. The findings strongly suggest that the extracellular nucleases of S. oneidensis exert specific functions required under different conditions.     

Production of extracellular debranching activity by amylolytic yeasts

Summary The production of extracellular pullulan-degrading enzymes by several amylolytic yeast strains was studied. The highest activity was obtained with species of Endomycopsis, Lipomyces, Filobasidium, Leucosporidium, and Trichosporon, and also with some amylase-hyperproducing mutants. The most active strains are potentially valuable partners for intergeneric protoplast fusion.     

Isolation and characterization of cell-associated nucleases related to streptococcal extracellular deoxyribonuclease D.

A group of at least four distinct nucleases designated DcI through DcIV were isolated from cellular extracts of group A streptococcal strain S43 and shown to be antigenically similar to streptococcal extracellular deoxyribonuclease (DNase) D. These cellular endonucleases degraded single- and double-stranded deoxyribonucleic acid (DNA) as well as ribonucleic acid (RNA) to acid-soluble oligonucleotides. The products of digestion of DNA bore 5'-terminal phosphates, and in partial digests pdX-pdG linkages were most susceptible and pdA-pdX linkages were most resistant to nuclease action. The enzymes had pH optima of 8.0 to 8.5, were inhibited by NaCl, were unaffected by sulfhydryl modifying reagents, and absolutely required a divalent cation. Nucleases DcIII and DcIV were apparently hydrophobic in nature since they required the presence of detergents for migration on nondenaturing polyacrylamide gels. All four nucleases were electrophoretically distinct on such gels, from each other, and from DNase D. Molecular weights of DcI and DcII were similar to that of DNase D, suggesting that the mobility differences of these enzymes at least are reflections of differing net charges. It is suggested that the cellular nucleases represent a group of processing intermediates in the maturation and excretion of DNase D.     

Extracellular nucleases and extracellular DNA play important roles in Vibrio cholerae biofilm formation

Biofilms are a preferred mode of survival for many microorganisms including Vibrio cholerae, the causative agent of the severe secretory diarrhoeal disease cholera. The ability of the facultative human pathogen V. cholerae to form biofilms is a key factor for persistence in aquatic ecosystems and biofilms act as a source for new outbreaks. Thus, a better understanding of biofilm formation and transmission of V. cholerae is an important target to control the disease. So far the Vibrio exopolysaccharide was the only known constituent of the biofilm matrix. In this study we identify and characterize extracellular DNA as a component of the Vibrio biofilm matrix. Furthermore, we show that extracellular DNA is modulated and controlled by the two extracellular nucleases Dns and Xds. Our results indicate that extracellular DNA and the extracellular nucleases are involved in diverse processes including the development of a typical biofilm architecture, nutrient acquisition, detachment from biofilms and the colonization fitness of biofilm clumps after ingestion by the host. This study provides new insights into biofilm development and transmission of biofilm-derived V. cholerae.     

Ultrasonic velocity assay of extracellular invertase in living yeasts

Being the largest family of cell surface receptors, G-protein-coupled receptors (GPCRs) are among the most frequent targets. The functions of many GPCRs are unknown, and it is both time-consuming and expensive to determine their ligands and signaling pathways by experimental methods. It is of great practical significance to develop an automated and reliable method for classification of GPCRs. In this study, a novel method based on the concept of Chou’s pseudo amino acid composition has been developed for predicting and recognizing GPCRs. The discrete wavelet transform was used to extract feature vectors from the hydrophobicity scales of amino acid to construct pseudo amino acid (PseAA) composition for training support vector machine. The prediction accuracies by the current method among the major families of GPCRs, subfamilies of class A, and types of amine receptors were 99.72%, 97.64%, and 99.20%, respectively, showing 9.4% to 18.0% improvement over other existing methods and indicating that the proposed method is a useful automated tool in identifying GPCRs.     

Ultrasonic velocity assay of extracellular invertase in living yeasts

The use of a low-intensity ultrasonic technique (noninvasive, nondestructive, on-line, and able to assess opaque samples) to monitor the kinetics of invertase hydrolysis is presented. Adiabatic compressibility has been shown to be sensitive to sugar species: ultrasonic velocity increasing as saccharose is transformed into glucose and fructose. The influence of initial sucrose mass concentration (2−60%), temperature (25−55 °C), pH (3.5−6.5), and number of microorganisms (10⁵−10⁹ yeasts/ml) on the reaction rate, catalyzed by the extracellular invertases of intact Saccharomyces cerevisiae cells, has been measured. The results were proven to be in strict agreement with the optimal kinetic parameters of the enzyme. Ultrasonic velocity variations are explained in terms of changes of the solute concentrations in the mixture water-saccharose-glucose/fructose and calculated from the velocity of ultrasound in the corresponding pure sugar solutions. A linear relationship between the initial rate of ultrasonic velocity and the number of yeasts (enzymes) is pointed out.     

Makeup of the extracellular lipids in Rhodotorula glutinis yeasts

The fractional composition of extracellular lipids extracted with hexane and ethanol was studied in the yeast Rhodotorula glutinis 35 by thin-layer chromatography. The two extracts of extracellular lipids were found to be similar in composition though differing in the quantitative content of individual fractions. The fractional composition of extracellular lipids differed from that of intracellular lipids. The peculiarity of the fractional composition of extracellular lipids can be accounted for by the specificity of its fatty acid and alcohol composition.     

云南程海湖冬季酵母菌多样性及胞外酶活性研究

采用过滤涂皿的方法对云南程海湖冬季湖水样品中的酵母菌进行分离,通过26S r DNA D1/D2区域序列分析并结合形态观察和生理生化测试对分离获得的菌株进行鉴定,同时采用胞外酶定性筛选培养基进行产酶活性筛选,分析冬季程海湖酵母菌的多样性及胞外酶活性。结果从程海湖中分离获得171株酵母菌,鉴定为14个属22个种和2个潜在的新分类单元;优势属是红冬孢酵母属Rhodosporidium、红酵母属Rhodotorula和隐球酵母属Cryptococcus;优势种是红冬孢酵母Rhodosporidium kratochvilovae和斯鲁菲亚红酵母Rhodotorula slooffiae;湖北半部的样点CH2的多样性指数(H′=1.5945)和丰富度指数(R=2.7576)均最高,均匀度指数较高的是湖北部的样点CH1(J=0.8531);样点之间种群差异大,相似性低。大多数酵母菌株具有产1种以上的胞外酶。     

Production of extracellular higher fatty acids by yeasts grown on hexadecanoic acid

Production of exocellular higher fatty acids by Candida yeasts was studied during their growth in a mineral medium with hexadecane. The qualitative and quantitative composition of exocellular higher fatty acids was investigated during cultivation of Candida lipolytica VCM Y 2378(695) under the conditions of different aeration (5 and 80% saturation of the medium with oxygen). Palmitic (C16:0), palmitooleic (C16:1), oleic (C18:1) and linoleic (C18:2) acids predominated among other higher fatty acids. The overall amount of fatty acids increased and the content of unsaturated fatty acids decreased when the yeast growth was limited with oxygen.     

Screening for the production of extracellular hydrolytic enzymes by non-Saccharomyces wine yeasts

AIMS: The objective of this study was to investigate what types of enzymes are being produced by non-Saccharomyces yeasts isolated from grapes in South Africa vineyards and clarified grape juice. These enzyme profiles could pave the way for attributing specific effects in wine to some of these enzymes produced by so-called wild yeasts associated with grape must. METHODS AND RESULTS: In this study 245 yeast isolates, belonging to the genera Kloeckera, Candida, Debaryomyces, Rhodotorula, Pichia, Zygosaccharomyces, Hanseniaspora and Kluyveromyces were screened for the production of extracellular pectinases, proteases beta-glucanases, lichenases, beta-glucosidases, cellulases, xylanases, amylases and sulphite reductase activity. These yeasts, representing 21 species, were previously isolated from grapes and clarified grape juice. The production of all extracellular hydrolytic enzymes screened for was observed except beta-glucosidase activity. The amount and range of enzymes produced varied with different isolates of the same species. CONCLUSION: This study clearly revealed the potential of non-Saccharomyces wine yeasts to produce a wide range of useful extracellular enzymes during the initial phase of wine fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY: Enzymes produced by indigenous yeasts associated with grapes and juice might be harnessed to catalyse desired biotransformations during wine fermentation.     

Single-strand-specific nucleases

Single-strand-specific nucleases are multifunctional enzymes and widespread in distribution. Their ability to act selectively on single-stranded nucleic acids and single-stranded regions in double-stranded nucleic acids has led to their extensive application as probes for the structural determination of nucleic acids. Intracellularly, they have been implicated in recombination, repair and replication, whereas extracellular enzymes have a role in nutrition. Although more than 30 single-strand-specific nucleases from various sources have been isolated till now, only a few enzymes (S1 nuclease from Aspergillus oryzae, P1 nuclease from Penicillium citrinum and nucleases from Alteromonas espejiana, Neurospora crassa, Ustilago maydis and mung bean) have been characterized to a significant extent. Recently, some of these enzymes have been cloned, their crystal structures solved and their interactions with different substrates have been established. The detection, purification, characteristics, structure-function correlations, biological role and applications of single-strand-specific nucleases are reviewed.     

The adherence of Candida yeasts to human and bovine vascular endothelium and subendothelial extracellular matrix

Abstract The adherence of Candida albicans yeasts and other Candida species to human umbilical vein endothelial cells (HUVEC), bovine aortic endothelial cells (BAEC) and their respective subendothelial extracellular matrices (ECM) was studied. Yeast adherence to confluent HUVEC and BAEC appeared to occur at intercellular junctions and edges of endothelial cells in preference to the contoured surface of the endothelial cell. Both endothelial cell lines characteristically resisted yeast adherence. The resistance of endothelium to yeast adherence was especially pronounced in the presence of serum. On the other hand, there was avid yeast binding to the subendothelial ECMs, on the order of 200–500% greater than to monolayers of syngeneic endothelial cells.     

Antistress cross-effects of extracellular metabolites of bacteria, archaea, and yeasts: A review

This paper reviews examples of specific and global responses of microorganisms and the characteristics of stress responses involving extracellular signaling metabolites. Information regarding the protective and reactivating effects produced by active exometabolites of representatives of domains of bacteria, archaea, and eukaryotes is summarized, and interdomain cross-responses to stressors are demonstrated.