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Selective activation of sar promoters with the use of green fluorescent protein transcriptional fusions as the detection system in the rabbit endocarditis model.

The global regulatory locus sar is composed of three overlapping transcripts initiated from a triple-promoter system (designated P1, P3, and P2). To explore if the individual sar promoters are differentially expressed in vitro and in vivo, we constructed a shuttle plasmid (pALC1434) containing a promoterless gfpUV gene (a gfp derivative [Clontech]) preceded by a polylinker region. Recombinant shuttle vectors containing individual sar promoters upstream of the gfpUV reporter gene were then introduced into Staphylococcus aureus RN6390. Northern and immunoblot analysis revealed that P1 is stronger than the P2 and P3 promoters in vitro. Additionally, the levels of the gfpUV transcript driven by individual sar promoters also correlated with the growth cycle dependency of these promoters in liquid cultures, thus suggesting the utility of pALC1434 as a vehicle for reporter fusion. Using the rabbit endocarditis model, we examined the expression of these three GFPUV fusions in vivo by fluorescence microscopy of infected cardiac vegetations 24 h after initial intravenous challenge. Similar to the in vitro findings, P1 was activated both in the center and on the surface of the vegetations. In contrast, the P3 promoter was silent both in vivo and in vitro as determined by fluorescence microscopy. Remarkably, P2 was silent in vitro but became highly activated in vivo. In particular, the sar P2 promoter was activated on the surface of the vegetation but not in the center of the lesion. These data imply that in vivo promoter activation of sar differed from that observed in vitro. Moreover, the individual sar promoters may be differentially expressed in different areas within the same anatomic niche, presumably reflecting the microbial physiological response to distinct host microenvironments. As the sar locus controls the synthesis of both extracellular and cell wall virulence determinants, these promoter-gfpUV constructs should be useful to characterize many aspects of S. aureus gene regulation in vivo.

Animals↗

Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic.

Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological diversity in PHA formation exists, with at least 100 different PHA constituents and at least five different dedicated PHA biosynthetic pathways. This diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic engineering to develop optimal PHA-producing organisms. Commercial processes for PHA production were initially developed by W. R. Grace in the 1960s and later developed by Imperial Chemical Industries, Ltd., in the United Kingdom in the 1970s and 1980s. Since the early 1990s, Metabolix Inc. and Monsanto have been the driving forces behind the commercial exploitation of PHA polymers in the United States. The gram-negative bacterium Ralstonia eutropha, formerly known as Alcaligenes eutrophus, has generally been used as the production organism of choice, and intracellular accumulation of PHA of over 90% of the cell dry weight have been reported. The advent of molecular biological techniques and a developing environmental awareness initiated a renewed scientific interest in PHAs, and the biosynthetic machinery for PHA metabolism has been studied in great detail over the last two decades. Because the structure and monomeric composition of PHAs determine the applications for each type of polymer, a variety of polymers have been synthesized by cofeeding of various substrates or by metabolic engineering of the production organism. Classical microbiology and modern molecular bacterial physiology have been brought together to decipher the intricacies of PHA metabolism both for production purposes and for the unraveling of the natural role of PHAs. This review provides an overview of the different PHA biosynthetic systems and their genetic background, followed by a detailed summation of how this natural diversity is being used to develop commercially attractive, recombinant processes for the large-scale production of PHAs.

Acetyl-CoA C-Acetyltransferase↗

A charmed life.

Boris Magasanik was born in Kharkoff, Ukraine, on December 19, 1919. He received his preliminary and secondary education in Vienna, Austria, and studied chemistry at the University of Vienna in 1937. He continued his studies at City College, New York (BS, 1941) and after one semester of graduate study at Pennsylvania State University, served in the US Army in England and France from 1942-1945. He obtained his PhD degree in biochemistry from Columbia University in 1948. A faculty member in the Department of Bacteriology and Immunology at Harvard Medical School from 1951 to 1960, he then continued his career as Professor of Microbiology at MIT where he served as head of the Department from 1967 to 1977. He became a member of the National Academy of Sciences USA in 1969 and received the Selman A Waksman Award in 1993. He is currently the Jacques Monod Professor Emeritus at MIT and is the author of over 240 publications dealing with microbial physiology and the regulation of gene expression in bacteria and yeast.

Biochemistry↗

Cell-free protein synthesis with prokaryotic combined transcription-translation.

Cell-free biology exploits and studies complex biological processes in a controlled environment without intact cells. One model system is prokaryotic cell-free protein synthesis. This technology offers an attractive and convenient approach to produce properly folded recombinant DNA (rDNA) proteins on a laboratory scale, screen PCR fragment libraries in a high-throughput format, express pharmaceutical proteins, incorporate labeled or unnatural amino acids into proteins, and activate microbial physiology to allow for investigation of biological systems. We describe the preparation of materials necessary for the expression, quantification, and purification of rDNA proteins from active Escherichia coli extracts.

Autoradiography↗

Compartmentalization of metals within the diverse colloidal matrices comprising activated sludge microbial flocs.

Activated sludge floc from a wastewater treatment system was characterized, with regard to principal structural, chemical, and microbiological components and properties, in relation to contaminant-colloid associations and settling. Multiscale analytical microscopies, in conjunction with multimethod sample preparations, were used correlatively to characterize diverse colloidal matrices within microbial floc. Transmission electron microscopy, in conjunction with energy dispersive spectroscopy (EDS), revealed specific associations of contaminant heavy metals with individual bacterial cells and with extracellular polymeric substances (EPS). Floc structure was mapped from the level of gross morphology down to the nano-scale, and flocs were described with respect to settling properties, size, shape, density, porosity, bound water content, and EPS chemical composition; gross surface properties were also measured for correlation with principal floc features. Compartmentalization results based on 171 EDS analyses and representative high-resolution images showed that nano-scale agglomerations of (i) silver (100%) and (ii) zinc (91%) were confined almost entirely to EPS matrices while (iii) Pb (100%) was confined to intracellular granules and (iv) aluminum was partitioned between EPS matrices (41%) and intracellular matrices (59%). The results suggest that engineered changes in microbial physiology and/or in macromolecular EPS composition may influence metal removal efficiencies.

Flocculation↗

Genomics in anti-infective drug discovery--getting to endgame.

Whole chromosome sequence of prokaryotes has provided the availability of multiple bacterial pathogen sequence data and it has become a widely used tool in the drug discovery process. However the sequence data in itself is merely a starting point for drug discovery of novel antibacterial targets and, eventually, drugs. In order to leverage this large amount of data it is necessary to match an understanding of the microbial physiology of pathogenic bacteria to disease processes and identifying the gene products for which intervention may reduce or eliminate the infectious state. However, to date, the application of genomics to anti-infective drug discovery has not, since 1995 with the first complete sequence of a pathogenic bacterium, led to identification of a novel antibacterial agent. Here we review the field of bacterial genomics and how it is enabling the drug discovery process. Many new molecular-based technologies (proteomics, transcriptional profiling, studies of gene expression in vivo) have originated or have expanded into wider use, and have been made possible by the availability of complete bacterial genome sequence information and subsequent bioinformatic analytic tools. Taken together, these technologies, overlaid within an established drug discovery program, now affords the opportunity for the identification, validation, and process design for high-throughput target mining at unprecedented volumes and timeframes.

Anti-Bacterial Agents↗

Defects in pyruvate kinase cause a conditional increase of thiamine synthesis in Salmonella typhimurium.

As genomic sequence data become more prevalent, the challenges in microbial physiology shift from identifying biochemical pathways to understanding the interactions that occur between them to create a robust but responsive metabolism. One of the most powerful methods to identify such interactions is in vivo phenotypic analysis. We have utilized thiamine synthesis as a model to detect subtle metabolic interactions due to the sensitivity allowed by the small cellular requirement for this vitamin. Although purine biosynthesis produces an intermediate in thiamine synthesis, mutants blocked in the first step of de novo purine biosynthesis (PurF) are able to grow in the absence of thiamine owing to an alternative synthesis. A number of general metabolic defects have been found to prevent PurF-independent thiamine synthesis. Here we report stimulation of thiamine-independent growth caused by a mutation in one or both genes encoding the pyruvate kinase isozymes. The results presented herein represent the first phenotype described for mutants defective in pykA or pykF, and thus identify metabolic interactions that exist in vivo.

Gene Expression Regulation, Bacterial↗

Robert Earle Buchanan: an unappreciated scientist.

Robert Earle Buchanan (1883-1973), 19th President of the Society of American Bacteriologists (later American Society for Microbiology), was one of the more important 20th century microbiologists. He was a dominant force in creating the field of bacterial systematics and made significant contributions to microbial physiology. He also numbered a number of influential textbooks. A reasonable conclusion is that Buchanan was a major cultivator of modern microbiology. To justify that assertion, I have four major objectives in this essay: i) a brief biographical review of Buchanan's early life; ii) a brief review of his scientific contributions, many of which go beyond his recognized contributions to bacterial systematics; iii) Buchanan was an important academic administrator who created the microbiology program and fostered a strong graduate education program at Iowa State, iv)finally, I close the essay with a focus on Buchanan's "moral character."

Bacteriology↗

NMR and microorganisms.

This article is an introduction to the use of NMR for the investigation of microbial physiology and metabolism. NMR parameters which determine the sensitivity and resolving power of the method are reviewed. A broad survey of current applications follows. Qualitative uses are described first; they include compound identification and localisation. Quantitative aspects, such as pH, concentration and flux measurements are then examined, as well as the corresponding experimental constraints. The review ends with suggestions of possible future developments in instrument capabilities aimed at improving sensitivity: higher fields, spectroscopic and imaging microprobes.

Cell Membrane↗

The human nasolacrimal ducts.

The human nasolacrimal ducts are a borderland of the disciplines ophthalmology and otorhinolaryngology, which work close together in the treatment of nasolacrimal disorders. However, little knowledge exists concerning the physiology of the nasolacrimal system and, therefore, its pathophysiology. The aim of the present investigations was to obtain a better understanding of tear flow physiology, microbial defence strategies and pathophysiological processes by analysing the nasolacrimal system, thus opening new perspectives against existing therapeutical concepts of diseases of the nasolacrimal ducts. The human nasolacrimal ducts consist of the upper and the lower lacrimal canaliculus, the lacrimal sac and the nasolacrimal duct. They drain the tear fluid from the ocular surface into the lower meatus of the nose. The lining epithelium of the lacrimal sac and the nasolacrimal duct is faced by microvilli, and animal experiments in rabbits support the hypothesis that tear fluid components are absorbed in the human nasolacrimal system. Evidence of seromucous glands, intraepithelial lipids and a specific mucus layer leads to the conclusion that the normal three-layering of the tear film is also present in the nasolacrimal ducts. Based on its composition, the mucus layer, which is mainly synthesised by goblet cells and intraepithelial mucus glands, functionally serves as a simplified drainage of tear fluid, and it is attributed similar properties to epithelia of the gastrointestinal tract. Further defence mechanisms are represented by antimicrobial peptides IgA and immunocompetent cells (lymphocytes and macrophages) which show intraepithelially and subepithelially a special distribution. Moreover, organised lymphoid tissue is present, which reveals the cytomorphologic and immunophenotypic characteristics of mucosa-associated lymphoid tissue. The wall of the lacrimal sac and the nasolacrimal duct are made up of a helical system of different connective tissue fibres. Wide luminal vascular plexus are embedded in this helical system, which is comparable to a cavernous body. Caudally, the vascular system is connected to the cavernous body of the inferior turbinate. With distension the system may be "wrung out" due to its medial attachment and helically arranged fibrillar structures. Thereby, tear fluid is drained distally. The embedded blood vessels underlie vegetative control. By means of this innervation, the specialised blood vessels permit regulation of blood flow by opening and closing the lumen of the lacrimal passage as effected by the engorgement and subsidence of the cavernous body, at the same time regulating tear outflow. Related functions, such as a role in the occurrence of epiphora related to emotional responses, are relevant. Moreover, malfunctions in the cavernous body and in its innervation may lead to disturbances in the tear outflow cycle, ocular congestion or total occlusion of the lacrimal passage. Thus, the pathophysiology of primary acquired dacryostenosis can be explained: Descending inflammation from the eye or ascending inflammation from the nose initiates swelling of the mucous membrane, remodelling of the helical arrangement of connective tissue fibres, malfunctions in the subepithelial cavernous body with reactive hyperaemia, and temporary occlusion of the lacrimal passage. In the follow-up, repeated isolated occurrence of dacryocystitis leads to structural epithelial and sub-epithelial changes, which may lead either to a total fibrous closure of the lumen of the efferent tear duct or to a non-functional segment in the lacrimal passage that is manifest on syringing. The normally constant absorption of tear fluid components into the blood vessels of the surrounding cavernous body that are connected to the blood vessels of the outer eye could be a feedback signal for tear fluid production, which comes to a halt if these tear components are not absorbed. Thus, dry eye could be initiated. Defective stimulation of tear duct-associated lymphoid tissue (TALT) could result in abnormal immune deviation at the ocular surface leading to an autoimmunologic response that could cause dry eye pathology.

Humans↗

The era of microbiology: a golden phoenix.

The discoveries over the last decade have demonstrated that microbiology is a central scientific discipline with practical applications in agriculture, medicine, bioremediation, biotechnology, engineering, and other fields. It is clear that the roles of microbes in nature are so diverse that the process of mining this genetic variation for new applications will continue long into the future. Moreover, the rapid rate of microbial evolution ensures that there will be no permanent solution to agricultural, medical, or environmental problems caused by microbes. These problems will demand a continual stream of creative new approaches that evolve along with the microbes. Thus, the excitement of this field will continue long into the future. However, these opportunities and imperatives demand a deep understanding of basic microbial physiology, genetics, and ecology. Major challenges that lay ahead are to impart the broad training needed to entice and enable the next generation of microbiologists, and to educate the public and government representatives about the continued and critical importance of this field for health and the economy.

Biological Evolution↗

Microbial cell-wall contaminants in peptides: a potential source of physiological artifacts.

Microbial cell-wall products (MCWP) such as endotoxins are easily introduced into peptides produced under standard laboratory conditions. Because these products stimulate the induction of cytokines and other mediators, which, in turn, trigger a broad range of physiological responses. MCWP in peptide preparations are potential sources of artifacts. This brief tutorial outlines the physical/chemical nature of MCWP, some of their sources, their physiological effects, and a simple method to control for them in some peptide preparations.

Artifacts↗

Thermal inactivation of Enterococcus faecium: effect of growth temperature and physiological state of microbial cells.

AIMS: To provide data on the effects on culture temperature and physiological state of cells on heat resistance of Enterococcus faecium, which may be useful in establishing pasteurization procedures. METHODS AND RESULTS: The heat resistance of this Ent. faecium (ATCC 49624 strain) grown at different temperatures was monitored at various stages of growth. In all cases, the bacterial cells in the logarithmic phase of growth were more heat sensitive. For cells which had entered in the stationary phase, D70 values of 0.53 min at 5 degrees C, 0.74 min at 10 degrees C, 0.83 min at 20 degrees C, 0.79 min at 30 degrees C, 0.63 min at 37 degrees C, 0.48 min at 40 degrees C and 0.41 min at 45 degrees C were found. By extending the incubation times cells were more heat resistant as stationary phase progressed, although a different pattern was observed for cells grown at different temperatures. At the lower temperatures heat resistance increased progressively, reaching D70 values of 1.73 min for cells incubated at 5 degrees C for 50 days and 1.04 min for those grown at 10 degrees C for 16 days. At other temperatures assayed heat resistance became stable for late stationary phase cells, reaching D70 values of 1.05, 1.08 and 1.01 min for cultures incubated at 20, 30 and 37 degrees C. Heat resistance of cells obtained at higher temperatures, 40 and 45 degrees C, was significantly lower, with D70 values of 0.76 and 0.67 min, respectively. Neither the growth temperature nor the growth phase modified the z-values significantly. CONCLUSIONS: D70 values obtained for Ent. faecium (ATCC 49624) varies from 0.33 to 1.73 min as a function of culture temperature and physiological state of cells. However, z values calculated were not significantly influenced by these factors. A mean value of 4.50 +/- 0.39 degrees C was found. SIGNIFICANCE AND IMPACT OF THE STUDY: Overall results strongly suggest that, to establish heat processing conditions of pasteurized foods ensuring elimination of Ent. faecium, it is advisable to take into account the complex interaction of growth temperature and growth phase of cells acting on bacterial thermal resistance.

Colony Count, Microbial↗

Physiological attributes of microbial BTEX degradation in oxygen-limited environments.

Our work has focused on the determination of physiological traits that may facilitate in situ degradation of xenobiotic compounds by indigenous microorganisms. For this our interests center on the following questions: What are the ambient conditions in a benzene, toluene, ethylbenzene, and xylene (BTEX)-contaminated aquifer? What is the behavior of indigenous bacteria under these conditions? What are the attributes of bacterial strains that are functional under hypoxic conditions? How do these strains compare with other BTEX-degrading strains?

Bacteria↗

Fluorometric determination of adenosine nucleotide derivatives as measures of the microfouling, detrital, and sedimentary microbial biomass and physiological status.

Adenosine, adenine, cyclic adenosine monophosphate (AMP), AMP, nicotinamide adenine dinucleotide, adenosine diphosphate, and adenosine triphosphate (ATP) were recovered quantitatively from aqueous portions of lipid extracts of microfouling, detrital, and sedimentary microbial communities. These could be detected quantitatively in the picomolar range by forming their 1-N-etheno derivatives and analyzing by high-pressure liquid chromatography with fluorescence detection. Lipid extraction and subsequent analysis allowed the simultaneous measurement of the microbial community structure, total microbial biomass with the quantitative recovery of the adenine-containing cellular components, which were protected from enzymatic destruction. This extraction and fluorescent derivatization method showed equivalency with the luciferin-luciferase method for bacterial ATP measurements. Quick-freezing samples in the field with dry ice-acetone preserved the ATP and energy charge (a ratio of adenosine nucleotides) for analysis at remote laboratories. The metabolic lability of ATP in estuarine detrital and microfouling communities, as well as bacterial monocultures of constant biomass, showed ATP to be a precarious measure of biomass under some conditions. Combinations of adenosine and adenine nucleotides gave better correlations with microbial biomass measured as extractable lipid phosphate in the detrital and microfouling microbial communities than did ATP alone. Stresses such as anoxia or filtration are reflected in the rapid accumulation of intracellular adenosine and the excretion of adenosine and AMP into the surrounding milieu. Increases in AMP and adenosine may prove to be more sensitive indicators of metabolic status than the energy charge.

Journal Article↗

Microbial nitrogen cycles: physiology, genomics and applications.

Genes and pathways involved in inorganic nitrogen cycles have been found in traditional as well as unusual microorganisms. These pathways or enzymes play a very important role in the adaptation or survival of these microorganisms under a variety of environmental conditions. Microbial nitrogen metabolism has industrial applications ranging from wastewater treatment to bioremediation and potential future use in biocatalysis for chemical production.

Ammonia↗

Probing the molecular physiology of the microbial organism, Escherichia coli using proteomics.

Genomics and proteomics technologies have yielded volumes of data for more than 20 years, and they continues to produce data at an astounding rate. Has all of this data helped us understand more about life, or it is just bogging us down in details that cannot be assembled into meaningful ideas? This review of the proteomics efforts over the last couple of decades is meant to emphasize that a new scientific discipline has emerged, Molecular Physiology, and that, indeed, this discipline is contributing to our understanding of life. Molecular physiology offers the reductionisms details of individual cellular molecules and offers the systems biology multivariant and high-dimensional datasets of cellular molecules.

Bacterial Proteins↗

Siderophores: diverse roles in microbial and human physiology.

Siderophores, defined as high affinity iron(III) ion transport agents, and their cognate membrane-bound receptor complexes, occur in the enteric bacteria Escherichia coli and Salmonella typhimurium. The total system is tightly regulated by iron repression. The transport properties of the specific siderophores enterobactin and ferrichrome (which is not made by these particular enteric bacteria) have been examined in detail. In E. coli the outer membrane receptor for ferrichrome is programmed by the tonA gene; the receptor also serves as the binding site for T1, T5, phi80, albomycin and colicin M. Similarly, in S. typhimurium phage ES18, ferrichrome and albomycin compete for the genetic equivalent of the tonA locus. The ability of ascorbic acid to protect against atherosclerosis as well as rhinovirus infection in humans may be related to the role of the vitamin in iron metabolism. Deferrisiderophores are clinically useful in the treatment of acute and chronic iron poisoning but, on the other hand, they could constitute a natural hazard by transporting actinides, such as 239Pu, through the food chain.

Arteriosclerosis↗