Clostridium thermocellum is an anaerobic, thermophilic bacterium that utilizes on cellulose while... more Clostridium thermocellum is an anaerobic, thermophilic bacterium that utilizes on cellulose while providing its own cellulases and produces ethanol and byproducts by fermentation. C. thermocellum is a candidate industrial biocatalyst for future lignocellulosic fuel ethanol production. In the present study, we resequenced the genome of the wild-type strain and a previously described ethanol tolerant mutant using microarray and pyrosequencing-based approaches. We sequenced 106 Mb of ethanol tolerant C. thermocellum strain DNA from 451,118 reads and identified 500 SNPs in the mutant strain. The 454 reads were unable to map two large DNA regions, each spanning approximately 9 kb and 35 kb. Whole genome microarray resequencing indicated these regions contained many SNPs. Preliminary analysis was in agreement with published membrane proteome data, but also found new changes in key genes such as alcohol dehydrogenase. The type strain contained 75 SNPs compared to the version deposited in g...
Geobacillus thermoglucosidasius Y4.1MC1 was isolated from a boiling spring in the lower geyser ba... more Geobacillus thermoglucosidasius Y4.1MC1 was isolated from a boiling spring in the lower geyser basin of Yellowstone National Park. This species is of interest because of its metabolic versatility. The genome consists of one circular chromosome of 3,840,330 bp and a circular plasmid of 71,617 bp with an average GC content of 44.01%. The genome is available in the GenBank database (NC_014650.1 and NC_014651.1). In addition to the expected metabolic pathways for sugars and amino acids, the Y4.1MC1 genome codes for two separate carbon monoxide utilization pathways, an aerobic oxidation pathway and the anaerobic reductive acetyl-CoA (Wood-Ljungdahl) pathway. This is the first report of a non-anaerobic organism with the Wood-Ljungdahl pathway. This anaerobic pathway permits the strain to utilize H2 and fix CO2 present in the hot spring environment. Y4.1MC1 and its related species may play a significant role in carbon capture and sequestration in thermophilic ecosystems and may open up new routes to produce biofuels and chemicals from CO, H2 and CO2.
Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was... more Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation. Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The ...
More than 80% of the microbial genomes in GenBank are of 'draft' quality (12,553 draft vs... more More than 80% of the microbial genomes in GenBank are of 'draft' quality (12,553 draft vs. 2,679 finished, as of October, 2013). We have examined all the microbial DNA sequences available for complete, draft, and Sequence Read Archive genomes in GenBank as well as three other major public databases, and assigned quality scores for more than 30,000 prokaryotic genome sequences. Scores were assigned using four categories: the completeness of the assembly, the presence of full-length rRNA genes, tRNA composition and the presence of a set of 102 conserved genes in prokaryotes. Most (~88%) of the genomes had quality scores of 0.8 or better and can be safely used for standard comparative genomics analysis. We compared genomes across factors that may influence the score. We found that although sequencing depth coverage of over 100x did not ensure a better score, sequencing read length was a better indicator of sequencing quality. With few exceptions, most of the 30,000 genomes have...
Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. P. sojae has a narro... more Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. P. sojae has a narrow host range, whereas P. ramorum has a wide host range. A global proteomics comparison of the vegetative (mycelium) and infective (germinating cyst) life stages of P. sojae and P. ramorum was conducted to identify candidate proteins involved in host range, early infection, and vegetative growth. Sixty-two candidates for early infection, 26 candidates for vegetative growth, and numerous proteins that may be involved in defining host specificity were identified. In addition, common life stage proteomic trends between the organisms were observed. In mycelia, proteins involved in transport and metabolism of amino acids, carbohydrates, and other small molecules were up-regulated. In the germinating cysts, up-regulated proteins associated with lipid transport and metabolism, cytoskeleton, and protein synthesis were observed. It appears that the germinating cyst catabolizes lipid reserves through the beta-oxidation pathway to drive the extensive protein synthesis necessary to produce the germ tube and initiate infection. Once inside the host, the pathogen switches to vegetative growth in which energy is derived from glycolysis and utilized for synthesis of amino acids and other molecules that assist survival in the plant tissue.
Proceedings of the National Academy of Sciences of the United States of America, Jan 8, 2010
The application of systems biology tools holds promise for rational industrial microbial strain d... more The application of systems biology tools holds promise for rational industrial microbial strain development. Here, we characterize a Zymomonas mobilis mutant (AcR) demonstrating sodium acetate tolerance that has potential importance in biofuel development. The genome changes associated with AcR are determined using microarray comparative genome sequencing (CGS) and 454-pyrosequencing. Sanger sequencing analysis is employed to validate genomic differences and to investigate CGS and 454-pyrosequencing limitations. Transcriptomics, genetic data and growth studies indicate that over-expression of the sodium-proton antiporter gene nhaA confers the elevated AcR sodium acetate tolerance phenotype. nhaA over-expression mostly confers enhanced sodium (Na(+)) tolerance and not acetate (Ac(-)) tolerance, unless both ions are present in sufficient quantities. NaAc is more inhibitory than potassium and ammonium acetate for Z. mobilis and the combination of elevated Na(+) and Ac(-) ions exerts a ...
Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass a... more Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involv...
Clostridium thermocellum is an anaerobic, thermophilic bacterium that utilizes on cellulose while... more Clostridium thermocellum is an anaerobic, thermophilic bacterium that utilizes on cellulose while providing its own cellulases and produces ethanol and byproducts by fermentation. C. thermocellum is a candidate industrial biocatalyst for future lignocellulosic fuel ethanol production. In the present study, we resequenced the genome of the wild-type strain and a previously described ethanol tolerant mutant using microarray and pyrosequencing-based approaches. We sequenced 106 Mb of ethanol tolerant C. thermocellum strain DNA from 451,118 reads and identified 500 SNPs in the mutant strain. The 454 reads were unable to map two large DNA regions, each spanning approximately 9 kb and 35 kb. Whole genome microarray resequencing indicated these regions contained many SNPs. Preliminary analysis was in agreement with published membrane proteome data, but also found new changes in key genes such as alcohol dehydrogenase. The type strain contained 75 SNPs compared to the version deposited in g...
Geobacillus thermoglucosidasius Y4.1MC1 was isolated from a boiling spring in the lower geyser ba... more Geobacillus thermoglucosidasius Y4.1MC1 was isolated from a boiling spring in the lower geyser basin of Yellowstone National Park. This species is of interest because of its metabolic versatility. The genome consists of one circular chromosome of 3,840,330 bp and a circular plasmid of 71,617 bp with an average GC content of 44.01%. The genome is available in the GenBank database (NC_014650.1 and NC_014651.1). In addition to the expected metabolic pathways for sugars and amino acids, the Y4.1MC1 genome codes for two separate carbon monoxide utilization pathways, an aerobic oxidation pathway and the anaerobic reductive acetyl-CoA (Wood-Ljungdahl) pathway. This is the first report of a non-anaerobic organism with the Wood-Ljungdahl pathway. This anaerobic pathway permits the strain to utilize H2 and fix CO2 present in the hot spring environment. Y4.1MC1 and its related species may play a significant role in carbon capture and sequestration in thermophilic ecosystems and may open up new routes to produce biofuels and chemicals from CO, H2 and CO2.
Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was... more Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation. Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The ...
More than 80% of the microbial genomes in GenBank are of 'draft' quality (12,553 draft vs... more More than 80% of the microbial genomes in GenBank are of 'draft' quality (12,553 draft vs. 2,679 finished, as of October, 2013). We have examined all the microbial DNA sequences available for complete, draft, and Sequence Read Archive genomes in GenBank as well as three other major public databases, and assigned quality scores for more than 30,000 prokaryotic genome sequences. Scores were assigned using four categories: the completeness of the assembly, the presence of full-length rRNA genes, tRNA composition and the presence of a set of 102 conserved genes in prokaryotes. Most (~88%) of the genomes had quality scores of 0.8 or better and can be safely used for standard comparative genomics analysis. We compared genomes across factors that may influence the score. We found that although sequencing depth coverage of over 100x did not ensure a better score, sequencing read length was a better indicator of sequencing quality. With few exceptions, most of the 30,000 genomes have...
Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. P. sojae has a narro... more Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. P. sojae has a narrow host range, whereas P. ramorum has a wide host range. A global proteomics comparison of the vegetative (mycelium) and infective (germinating cyst) life stages of P. sojae and P. ramorum was conducted to identify candidate proteins involved in host range, early infection, and vegetative growth. Sixty-two candidates for early infection, 26 candidates for vegetative growth, and numerous proteins that may be involved in defining host specificity were identified. In addition, common life stage proteomic trends between the organisms were observed. In mycelia, proteins involved in transport and metabolism of amino acids, carbohydrates, and other small molecules were up-regulated. In the germinating cysts, up-regulated proteins associated with lipid transport and metabolism, cytoskeleton, and protein synthesis were observed. It appears that the germinating cyst catabolizes lipid reserves through the beta-oxidation pathway to drive the extensive protein synthesis necessary to produce the germ tube and initiate infection. Once inside the host, the pathogen switches to vegetative growth in which energy is derived from glycolysis and utilized for synthesis of amino acids and other molecules that assist survival in the plant tissue.
Proceedings of the National Academy of Sciences of the United States of America, Jan 8, 2010
The application of systems biology tools holds promise for rational industrial microbial strain d... more The application of systems biology tools holds promise for rational industrial microbial strain development. Here, we characterize a Zymomonas mobilis mutant (AcR) demonstrating sodium acetate tolerance that has potential importance in biofuel development. The genome changes associated with AcR are determined using microarray comparative genome sequencing (CGS) and 454-pyrosequencing. Sanger sequencing analysis is employed to validate genomic differences and to investigate CGS and 454-pyrosequencing limitations. Transcriptomics, genetic data and growth studies indicate that over-expression of the sodium-proton antiporter gene nhaA confers the elevated AcR sodium acetate tolerance phenotype. nhaA over-expression mostly confers enhanced sodium (Na(+)) tolerance and not acetate (Ac(-)) tolerance, unless both ions are present in sufficient quantities. NaAc is more inhibitory than potassium and ammonium acetate for Z. mobilis and the combination of elevated Na(+) and Ac(-) ions exerts a ...
Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass a... more Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involv...
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Papers by Miriam L Land