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Structure, Function and Regulation of the Clostridium cellulovorans Cellulosome

Description: Our major goal for this project (2004-2008) was to obtain an understanding ofthe structure, function, and regulation of the Clostridium cellulovorans cellulosomes. Our specific goals were to select genes for cellulosomal and non-cellulosomal enzymes and characterize their products, to study the synergistic action between cellulosomal and non-cellulosomal enzymes, to study the composition of cellulosomes when cells were grown with different carbon sources, continue our studies on the scaffolding protein and examine heterologous expression of cellulosomal genes in Bacillus subtilis. We fulfilled the specific goals of our proposal.
Date: June 1, 2008
Creator: Doi, Roy H.
Partner: UNT Libraries Government Documents Department

Multi-Probe Investigation of Proteomic Structure of Pathogens

Description: Complete genome sequences are available for understanding biotransformation, environmental resistance and pathogenesis of microbial, cellular and pathogen systems. The present technological and scientific challenges are to unravel the relationships between the organization and function of protein complexes at cell, microbial and pathogens surfaces, to understand how these complexes evolve during the bacterial, cellular and pathogen life cycles, and how they respond to environmental changes, chemical stimulants and therapeutics. In particular, elucidating the molecular structure and architecture of human pathogen surfaces is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance and development of countermeasures against bioterrorist agents. The objective of this project was to investigate the architecture, proteomic structure, and function of bacterial spores through a combination of high-resolution in vitro atomic force microscopy (AFM) and AFM-based immunolabeling with threat-specific antibodies. Particular attention in this project was focused on spore forming Bacillus species including the Sterne vaccine strain of Bacillus anthracis and the spore forming near-neighbor of Clostridium botulinum, C. novyi-NT. Bacillus species, including B. anthracis, the causative agent of inhalation anthrax are laboratory models for elucidating spore structure/function. Even though the complete genome sequence is available for B. subtilis, cereus, anthracis and other species, the determination and composition of spore structure/function is not understood. Prof. B. Vogelstein and colleagues at the John Hopkins University have recently developed a breakthrough bacteriolytic therapy for cancer treatment (1). They discovered that intravenously injected Clostridium novyi-NT spores germinate exclusively within the avascular regions of tumors in mice and destroy advanced cancerous lesions. The bacteria were also found to significantly improve the efficacy of chemotherapeutic drugs and radiotherapy (2,3). Currently, there is no understanding of the structure-function relationships of Clostridium novyi-NT spores. As well as their therapeutic interest, studies of Clostridium noyii spores could provide a model for further studies of ...
Date: January 24, 2008
Creator: Malkin, A J; Plomp, M; Leighton, T J; Vogelstein, B & Wheeler, K E
Partner: UNT Libraries Government Documents Department

Genetics of solvent-producing clostridia. Final technical report

Description: Specific Aims 1 and 2 of the original project proposal were specifically addressed during this project period. This involved the development of the pCAK1 phagemid delivery vector, refinement of the C. acetobutylicum electroporation protocol, selection and characterization of the engB cellulase gene from C. cellulovorans and the introduction and successful expression of this heterologous engB gene from C. cellulovorans in C. acetobutylicum. The successful expression of a heterologous engB gene from C. cellulovorans in C. acetobutylicum ATCC 824 has important industrial significance for the utilization of cellulose by this ABE fermentation microorganism. Conversion efficiency testing of the developed recombinant strains in batch and continuous culture (Specific Aim 3) will be carried out once suitable strains have been developed which can utilize cellulose as sole carbon source. The functionality of pCAK1 in the E. coli host system, especially in generating ssDNA, in the absence of impairing E. coli cell viability, together with successful introduction of pCAK1 into C. acetobutylicum and C. perfringens is the basis for the construction of a M13-like genetic system for the genus Clostridium and is expected to allow for more sophisticated molecular genetic analysis of this genus.
Date: June 1, 1997
Partner: UNT Libraries Government Documents Department

CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE B.

Description: The toxigenic strains of Clostridium botulinum produce seven serologically distinct types of neurotoxins labeled A - G (EC 3.4.24.69), while Clostridium tetani produces tetanus neurotoxin (EC 3.4.24.68). Botulinum and tetanus neurotoxins (BoNTs and TeNT) are produced as single inactive chains of molecular mass of approximately 150 kDa. Most of these neurotoxins are released after being cleaved into two chains, a heavy chain (HI) of 100 kDa and a light chain (L) of 50 kDa held together by an interchain disulfide bond, by tissue proteinases. BoNT/E is released as a single chain but cleaved by host proteinases [1]. Clostvidium botulinum neurotoxins are extremely poisonous proteins with their LD{sub 50} for humans in the range of 0.1 - 1 ng kg{sup -1} [2]. Botulinum neurotoxins are responsible for neuroparalytic syndromes of botulism characterized by serious neurological disorders and flaccid paralysis. BoNTs block the release of acetylcholine at the neuromuscular junction causing flaccid paralysis while TeNT blocks the release of neurotransmitters like glycine and {gamma}-aminobutyric acid (GABA) in the inhibitory interneurons of the spinal cord resulting in spastic paralysis. In spite of different clinical symptoms, their aetiological agents intoxicate neuronal cells in the same way and these toxins have similar structural organization [3].
Date: November 19, 2001
Creator: Swaminathan, S. & Eswaramoorthy, S.
Partner: UNT Libraries Government Documents Department

Pathway engineering to improve ethanol production by thermophilic bacteria

Description: Continuation of a research project jointly funded by the NSF and DOE is proposed. The primary project goal is to develop and characterize strains of C. thermocellum and C. thermosaccharolyticum having ethanol selectivity similar to more convenient ethanol-producing organisms. An additional goal is to document the maximum concentration of ethanol that can be produced by thermophiles. These goals build on results from the previous project, including development of most of the genetic tools required for pathway engineering in the target organisms. As well, we demonstrated that the tolerance of C. thermosaccharolyticum to added ethanol is sufficiently high to allow practical utilization should similar tolerance to produced ethanol be demonstrated, and that inhibition by neutralizing agents may explain the limited concentrations of ethanol produced in studies to date. Task 1 involves optimization of electrotransformation, using either modified conditions or alternative plasmids to improve upon the low but reproducible transformation, frequencies we have obtained thus far.
Date: December 1998
Creator: Lynd, L. R.
Partner: UNT Libraries Government Documents Department

Microbiology and physiology of anaerobic fermentation of cellulose. Annual report for 1990, 1992, 1993 and final report

Description: This report focuses on the bioconversion of cellulose to methane by various anaerobes. The structure and enzymatic activity of cellulosome and polycellulosome was studied in Clostridium thermocellum. The extracellular enzymes involved in the degradation of plant material and the physiology of fermentation was investigated in anaerobic fungi. Enzymes dealing with CO, CO{sub 2}, H{sub 2}, CH{sub 3}OH, as well as electron transport and energy generation coupled to the acetyl-CoA autotrophic pathway was studied in acetogenic clostridia.
Date: August 31, 1993
Creator: Ljungdahl, L.G.; Wiegel, J.; Peck, H.D. Jr. & Mortenson, L.E.
Partner: UNT Libraries Government Documents Department

Interactions of Ionic Liquids with Uranium and its Bioreduction

Description: We investigated the influence of ionic liquids (ILs) 1-butyl-3-methylimidazolium hexafluorophosphate [BMIM]{sup +}[PF{sub 6}]{sup -}, N-ethylpyridinium trifluoroacetate [EtPy]{sup +}[CF{sub 3}COO]{sup -} and N-ethylpyridinium tetrafluoroborate [Et-Py]{sup +}[BF{sub 4}]{sup -} on uranium reduction by Clostridium sp. under anaerobic conditions. Potentiometric titration, UV-vis spectrophotometry, LC-MS and EXAFS analyses showed monodentate complexation between uranyl and BF{sub 4}{sup -} PF{sub 6}{sup -}; and bidentate complexation with CF{sub 3}COO{sup -}. Ionic liquids affected the growth of Clostridium sp. as evidenced by decrease in optical density, changes in pH, gas production, and the extent of U(VI) reduction and precipitation of U(IV) from solution. Reduction of U(VI) to U(IV) was observed in the presence of [EtPy][BF{sub 4}] and [BMIM][PF{sub 6}] but not with [EtPy][CF{sub 3}COO].
Date: September 18, 2012
Creator: Zhang, C. & Francis, A.
Partner: UNT Libraries Government Documents Department

Genetic and biochemical analysis of solvent formation in Clostridium acetobutylicum. Progress report, September 1, 1992--July 31, 1996

Description: Several degenerate strains were isolated and characterized by sporulation, motility and growth properties. Cell appearance and colony morphology were also recorded. Enzymatic assays revealed reduced butyraldehyde dehydrogenase and Co-A transferase enzyme activities in the degenerates. DNA analysis revealed that in complete degenerate strains the genes of the solvent locus were absent. Gyrase inhibitors slightly reduced the growth rate and decreased acetone formation preferentially. In an effort to analyze the role of sporulation sigma factors in solvent gene expression, recombination experiments were conducted and led to strains with increased solvent production. Analysis of redox systems has resulted in the sequence analysis of a cluster encoding formyl transferase proteins and an oxidoreductase-like gene. The genes for the two subunits of an apparent electron transfer flavoprotein were sequenced and suggest this factor acts to carry electrons to the butyryl-CoA dehydrogenase. The genes encoding the Fo subunits of the membrane ATPase have been sequenced.
Date: January 1, 1997
Creator: Bennett, G.N. & Rudolph, F.B.
Partner: UNT Libraries Government Documents Department

Engineered Microbial Consortium for the Efficient Conversion of Biomass to Biofuels

Description: Current energy and environmental challenges are driving the use of cellulosic materials for biofuel production. A major obstacle in this pursuit is poor ethanol tolerance among cellulolytic Clostridium species. The first objective of this work was to establish a potential upper boundary of ethanol tolerance for the cellulosome itself. The hydrolytic function of crude cellulosome extracts from C. cellulolyticum on carboxymethyl cellulose (CMC) with 0, 5, 10, 15, 20 and 25% (v/v) ethanol was determined. Results indicated that the endoglucanase activity of the cellulosome incubated in 5% and 10% ethanol was significantly different from a control without ethanol addition. Furthermore a significant difference was observed in endoglucanase activity for cellulosome incubated in 5%, 10%, 15%, 20% and 25% ethanol in a standalone experiment. Endoglucanase activity continued to be observed for up to 25% ethanol, indicating that cellulosome function in ethanol will not be an impediment to future efforts towards engineering increasing production titers to levels at least as high as the current physiological limits of the most tolerant ethanologenic microbes. The second objective of this work was to study bioethanol production by a microbial co-culture involving Clostridium cellulolyticum and a recombinant Zymomonas mobilis engineered for the utilization of oligodextrans. The recombinant Z. mobilis ZM4 pAA1 and wild type ZM4 were first tested on RM medium (ATCC 1341) containing 2% cellobiose as the carbon source. Ethanol production from the recombinant Z. mobilis was three times that observed from the wild type Z. mobilis. Concomitant with ethanol production was the reduction in OD from 2.00 to 1.580, indicating the consumption of cellobiose. No such change in OD was observed from the wild type. The recombinant ZM4 was then co-cultured with C. cellulolyticum using cellobiose and microcrystalline cellulose respectively as carbon sources. Results indicate that the recombinant ZM4 acted synergistically with C. cellulolyticum ...
Date: August 2014
Creator: Anieto, Ugochukwu Obiakornobi
Partner: UNT Libraries

Annotation of the Clostridium Acetobutylicum Genome

Description: The genome sequence of the solvent producing bacterium Clostridium acetobutylicum ATCC824, has been determined by the shotgun approach. The genome consists of a 3.94 Mb chromosome and a 192 kb megaplasmid that contains the majority of genes responsible for solvent production. Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of gene order, which has not been seen in comparisons of other genomes with similar, or, in some cases, closer, phylogenetic proximity. This conservation allows the prediction of many previously undetected operons in both bacteria.
Date: June 9, 2004
Creator: Daly, M. J.
Partner: UNT Libraries Government Documents Department

Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol

Description: BackgroundIncreasing energy costs and environmental concerns have motivated engineering microbes for the production of ?second generation? biofuels that have better properties than ethanol.Results& ConclusionsSaccharomyces cerevisiae was engineered with an n-butanol biosynthetic pathway, in which isozymes from a number of different organisms (S. cerevisiae, Escherichia coli, Clostridium beijerinckii, and Ralstonia eutropha) were substituted for the Clostridial enzymes and their effect on n-butanol production was compared. By choosing the appropriate isozymes, we were able to improve production of n-butanol ten-fold to 2.5 mg/L. The most productive strains harbored the C. beijerinckii 3-hydroxybutyryl-CoA dehydrogenase, which uses NADH as a co-factor, rather than the R. eutropha isozyme, which uses NADPH, and the acetoacetyl-CoA transferase from S. cerevisiae or E. coli rather than that from R. eutropha. Surprisingly, expression of the genes encoding the butyryl-CoA dehydrogenase from C. beijerinckii (bcd and etfAB) did not improve butanol production significantly as previously reported in E. coli. Using metabolite analysis, we were able to determine which steps in the n-butanol biosynthetic pathway were the most problematic and ripe for future improvement.
Date: November 25, 2008
Creator: Steen, EricJ.; Chan, Rossana; Prasad, Nilu; Myers, Samuel; Petzold, Christopher; Redding, Alyssa et al.
Partner: UNT Libraries Government Documents Department

Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains

Description: Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees of interrelatedness and recombination as has been previously noted for the NTNH gene which is linked to BoNT. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for treatment of botulism.
Date: July 6, 2006
Creator: Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svennson, R T et al.
Partner: UNT Libraries Government Documents Department

CLOSTRIDIUM SPORE ATTACHMENT TO HUMAN CELLS

Description: This paper uses high resolution scanning electron microscopy (SEM) with a LaB6 gun and the newest commercial field emission guns, to obtain high magnification images of intact clostridial spores throughout the activation/germination/outgrowth process. By high resolution SEM, the clostridial exosporial membrane can be seen to produce numerous delicate projections (following activation), that extend from the exosporial surface to a nutritive substrate (agar), or cell surface when anaerobically incubated in the presence of human cells (embryonic fibroblasts and colon carcinoma cells). Magnifications of 20,000 to 200,000Xs at accelerating voltages low enough to minimize or eliminate specimen damage (1--5 kV) have permitted the entire surface of C.sporogenes and C.difficile endospores to be examined during all stages of germination. The relationships between the spore and the agar or human cell surface were also clearly visible.
Date: August 10, 1997
Creator: PANESSA-WARREN,B.; TORTORA,G. & WARREN,J.
Partner: UNT Libraries Government Documents Department

THERMOPHILE ENDOSPORES HAVE RESPONSIVE EXOSPORIUM FOR ATTACHMENT

Description: Recently studies examining the colonization of Clostridial pathogens on agar and human tissue culture cells, demonstrated that (C. sporogenes ATCC 3584, C. difficile ATCC 43594 [patient isolate], C. difficile ATCC 9689 [non-clinical], C. clostridioforme [patient isolate]) bacterial spores (endospores) of the genus Clostridia have an outer membrane that becomes responsive at activation and exhibits extensions of the exosporial membrane that facilitate and maintain spore attachment to a nutritive substrate during germination and initial outgrowth of the newly developed bacterial cell. Therefore this attachment phenomenon plays an important role in insuring bacterial colonization of a surface and the initial stages of the infective process. To see if other non-clinical members of this genus also have this ability to attach to a substrate or food-source during spore germination, and how this attachment process in environmental thermophiles compares to the clinical paradigm (in relation to time sequence, exosporial membrane structure, type of attachment structures, composition of the membrane etc...), sediment samples were collected in sterile transport containers at 4 geothermal sites at Yellowstone National Park in Wyoming. Because spore forming bacteria will produce spores when conditions are unfavorable for growth, the samples were sealed and stored at 4 C. After 8 months the samples were screened for the presence of spores by light microscope examination using malachite green/safranin, and traditional endospores were identified in significant quantities from the Terrace Spring site (a 46 C lake with bacterial mats and a rapidly moving run-off channel leading to a traditional hot spring). The highest spore population was found in the top sediment and benthic water of the run-off channel, pH 8.1.
Date: August 1, 1999
Creator: PANESSA-WARREN,B.; TORTORA,G.T.; WARREN,J. & SABATINI,R.
Partner: UNT Libraries Government Documents Department

Microbiology and physiology of anaerobic fermentation of cellulose. Progress report (4/30/91--4/30/92) and outline of work for the period 9/1/92--9/1/93

Description: The authors are continuing their efforts to partly dissociate the cellulolytic enzyme complex of C. thermocellum. This complex named cellulosome (also existing as polycellulosome) consists of perhaps as many as 26 different subunits. It is extremely resistant to dissociation and denaturation. Treatments with urea and SDS have little effect unless the latter treatment is at high temperature. Significantly, some of the subunits after SDS dissociation have CMCase (endoglucanase) activity but no activity toward crystalline cellulose. The only reported success of hydrolysis of crystalline cellulose by cellulosomal subunits is by Wu et al. who isolated two protein fractions labeled SL and SS which when combined exhibit a low (about 1% of the original cellulosome) activity toward crystalline cellulose. The long standing goal is still to determine the activities of the individual subunits, to characterize them, to find out how they are associated in the cellulosome, and to establish the minimum number of subunits needed for efficient hydrolysis of crystalline cellulose. This report also presents the results of experiments on cellulose hydrolysis in aerobic fungi, as well as other anaerobic bacteria.
Date: December 31, 1992
Creator: Ljungdahl, L.G.
Partner: UNT Libraries Government Documents Department