42 research outputs found
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An investigation of carbon and nitrogen metabolism through a genomic analysis of the genus Nitrobacter
The chemolithoautotrophic nitrite oxidizing bacteria (NOB) participate in the
biogeochemical cycling of nitrogen by catalyzing and conserving energy from the
oxidation of nitrite (NOâ-) to nitrate (NOâ-) via a nitrite oxidoreductase (NXR). The
main objective of this work was to comparatively annotate and analyze the genome
sequences of Nitrobacter winogradskyi NB255 and Nitrobacter hamburgensis X14 and
use this information to extend our understanding of nitrogen and carbon metabolism in NOB. Through the analysis of the N. winogradskyi genome, genes encoding pathways for known modes of lithotrophic and heterotrophic growth were identified, including multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism. N. winogradskyi lacked genes encoding a complete glycolysis pathway and for the active transport of sugars. The N. hamburgensis genome harbored many genes not
found in N. winogradskyi, including a complete glycolysis pathway, unique electron
transport components, and putative pathways for the catabolism of aromatic, organic
and one-carbon compounds. FAD-dependent oxidases were identified in the genome of
N. hamburgensis which suggested that lactate could be metabolized, providing reductant and carbon to the cell. Indeed, D-lactate enhanced the growth rate and yield of N. hamburgensis in the presence of NOâ- and served as a sole energy and carbon source
in the absence of NOâ-. Although lactate consumption occurred constitutively in
lithoautotrophically grown cells, evidence was obtained for physiological adaptation to
lactate. D-lactate grown cells consumed and assimilated lactate at a faster rate than NOâ- grown cells, and D-lactate-dependent Oâ uptake was significantly greater in cells grown heterotrophically or mixotrophically compared to cells grown lithoautotrophically.
However, D-lactate could not substitute for COâ as the sole carbon source(lithoheterotrophy) during growth in the presence of NOâ-. Through a comparative
analysis of the Nitrobacter 'core' genome, many genes involved in NOâ- metabolism
were identified, including a dissimilatory nitrite reductase (NirK). The putative nirK in N. winogradskyi was maximally transcribed under low oxygen in the presence of NOâ- and transcription was not detected under anaerobic conditions. Although production of
NO under aerobic conditions was not detected, NO was consumed in a cyanide sensitive process and reversibly inhibited NOâ-dependent Oâ uptake
Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants
Vampirovibrio chlorellavorus is recognized as a pathogen of commercially-relevant Chlorella species. Algal infection and total loss of productivity (biomass) often occurs when susceptible algal hosts are cultivated in outdoor open pond systems. The pathogenic life cycle of this bacterium has been inferred from laboratory and field observations, and corroborated in part by the genomic analyses for two Arizona isolates recovered from an open algal reactor. V. chlorellavorus predation has been reported to occur in geographically- and environmentally-diverse conditions. Genomic analyses of these and additional field isolates is expected to reveal new information about the extent of ecological diversity and genes involved in host-pathogen interactions. The draft genome sequences for two isolates of the predatory V. chlorellavorus (Cyanobacteria; Ca. Melainabacteria) from an outdoor cultivation system located in the Arizona Sonoran Desert were assembled and annotated. The genomes were sequenced and analyzed to identify genes (proteins) with predicted involvement in predation, infection, and cell death of Chlorella host species prioritized for biofuel production at sites identified as highly suitable for algal production in the southwestern USA. Genomic analyses identified several predicted genes encoding secreted proteins that are potentially involved in pathogenicity, and at least three apparently complete sets of virulence (Vir) genes, characteristic of the VirB-VirD type system encoding the canonical VirB1-11 and VirD4 proteins, respectively. Additional protein functions were predicted suggesting their involvement in quorum sensing and motility. The genomes of two previously uncharacterized V. chlorellavorus isolates reveal nucleotide and protein level divergence between each other, and a previously sequenced V. chlorellavorus genome. This new knowledge will enhance the fundamental understanding of trans-kingdom interactions between a unique cosmopolitan cyanobacterial pathogen and its green microalgal host, of broad interest as a source of harvestable biomass for biofuels or bioproducts.Bioenergy Technology Office within the US Department of Energy Office of Energy Efficiency and Renewable Energy [NL0029949 (WBS 1.3.1.600)]; US Department of Energy [DE-EE0006269]Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of Abrus precatorius
The sequenced genome and the leaf transcriptome of a near relative of Abrus pulchellus and Abrus precatorius was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (<1 Mbp). The Abrusprecatorius cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified, and we observed substantial diversity of genes and predicted gene products in Abrus precatorius and previously characterized toxins. This suggests diverse toxin repertoires within Abrus, potentially the results of rapid toxin evolution.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts
In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy\u27s Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels
Legionella pneumophila Type II Protein Secretion Promotes Virulence in the A/J Mouse Model of Legionnaires' Disease Pneumonia
Legionella pneumophila, the gram-negative agent of Legionnaires' disease, possesses type IV pili and a type II protein secretion (Lsp) system, both of which are dependent upon the PilD prepilin peptidase. By analyzing multiple pilD mutants and various types of Lsp mutants as well as performing trans-complementation of these mutants, we have confirmed that PilD and type II secretion genes are required for L. pneumophila infection of both amoebae and human macrophages. Based upon a complete analysis of lspDE, lspF, and lspG mutants, we found that the type II system controls the secretion of protease, RNase, lipase, phospholipase A, phospholipase C, lysophospholipase A, and tartrate-sensitive and tartrate-resistant acid phosphatase activities and influences the appearance of colonies. Examination of the developing L. pneumophila genome database indicated that the organism has two other loci (lspC and lspLM) that are predicted to promote secretion and thus a set of genes that is comparable to the type II secretion genes in other gram-negative bacteria. In contrast to lsp mutants, L. pneumophila pilus mutants lacking either the PilQ secretin, the PspA pseudopilin, or pilin were not defective for colonial growth, secreted activities, or intracellular replication. L. pneumophila dot/icm mutants were also not impaired for type II-dependent exoenzymes. Upon intratracheal inoculation into A/J mice, lspDE, lspF, and pilD mutants, but not pilus mutants, exhibited a reduced ability to grow in the lung, as measured by competition assays. The lspF mutant was also defective in an in vivo kinetic assay. Examination of infected mouse sera revealed that type II secreted proteins are expressed in vivo. Thus, the L. pneumophila Lsp system is a virulence factor and the only type II secretion system linked to intracellular infection
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D-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis
Nitrobacter hamburgensis X14 is a facultative lithoautotroph that conserves energy from the
oxidation of nitrite (NO
2 ) and fixes carbon dioxide (CO2) as its sole source of carbon. The
availability of the N. hamburgensis X14 genome sequence initiated a re-examination of its
mixotrophic and organotrophic potential, as genes encoding three flavin-dependent oxidases
were identified that may function to oxidize lactate, providing energy and carbon for growth. The
response of N. hamburgensis to D- and L-lactate in the presence (mixotrophy) and absence
(organotrophy) of NO
2 was examined. L-Lactate did not support organotrophic growth or
stimulate mixotrophic growth. In contrast, D-lactate enhanced the growth rate and yield of N.
hamburgensis in the presence of NO
2 , and served as the sole carbon and energy source for
growth in the absence of NO
2 with ammonium as the sole nitrogen source. Lithoautotrophically
grown cells immediately consumed D-lactate, suggesting that a lactate metabolic pathway is
constitutively expressed. Nevertheless, a physiological adaptation to lactate occurred, as Dlactate-
grown cells consumed and assimilated lactate at a faster rate than NO
2 -grown cells, and
the D-lactate-dependent O2 uptake rate was significantly greater in cells grown either
organotrophically or mixotrophically compared with cells grown lithoautotrophically. Although
D-lactate was assimilated and metabolized to CO2 in the presence or absence of NO
2 , exposure
to atmospheric CO2 or the addition of 0.75 mM sodium carbonate was required for mixotrophic
growth and for optimum organotrophic growth on D-lactate.Keywords: Nitrobacter hamburgensi
Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information
Abstract Background Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. Results Using these simulations, we monitored the behavior of several correlation statistics, including the Pearsonâs R and Spearmanâs Ï coefficients as well as Kendallâs Ï and TopâDown correlation. We also test the behavior of association measures, including the coefficient of determination R 2 , Kendallâs W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spearmanâs Ï , Kendallâs Ï , and Kendallâs W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R 2 coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. Conclusions Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays
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RNA-Binding Protein RBP-P Is Required for Glutelin and Prolamine mRNA Localization in Rice Endosperm Cells
In developing rice (
) endosperm, mRNAs of the major storage proteins, glutelin and prolamine, are transported and anchored to distinct subdomains of the cortical endoplasmic reticulum. RNA binding protein RBP-P binds to both glutelin and prolamine mRNAs, suggesting a role in some aspect of their RNA metabolism. Here, we show that rice lines expressing mutant RBP-P mislocalize both glutelin and prolamine mRNAs. Different mutant RBP-P proteins exhibited varying degrees of reduced RNA binding and/or protein-protein interaction properties, which may account for the mislocalization of storage protein RNAs. In addition, partial loss of RBP-P function conferred a broad phenotypic variation ranging from dwarfism, chlorophyll deficiency, and sterility to late flowering and low spikelet fertility. Transcriptome analysis highlighted the essential role of RBP-P in regulating storage protein genes and several essential biological processes during grain development. Overall, our data demonstrate the significant roles of RBP-P in glutelin and prolamine mRNA localization and in the regulation of genes important for plant growth and development through its RNA binding activity and cooperative regulation with interacting proteins