24 results on '"Zelzion E"'
Search Results
2. The Staphylococcus aureus small non-coding RNA IsrR regulates TCA cycle activity and virulence.
- Author
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Rios-Delgado G, McReynolds AKG, Pagella EA, Norambuena J, Briaud P, Zheng V, Munneke MJ, Kim J, Racine H, Carroll R, Zelzion E, Skaar E, Bose JL, Parker D, Lalaouna D, and Boyd JM
- Abstract
Staphylococcus aureus has evolved mechanisms to cope with low iron (Fe) availability in host tissues. S. aureus uses the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that an S. aureus Δ fur mutant has decreased expression of acnA , which codes for the Fe-dependent enzyme aconitase. Decreased acnA expression prevented the Δ fur mutant from growing with amino acids as sole carbon and energy sources. Suppressor analysis determined that a mutation in isrR , which produces a regulatory RNA, permitted growth by decreasing isrR transcription. The decreased AcnA activity of the Δ fur mutant was partially relieved by an Δ isrR mutation. Directed mutation of bases predicted to facilitate the interaction between the acnA transcript and IsrR, decreased the ability of IsrR to control acnA expression in vivo and IsrR bound to the acnA transcript in vitro . IsrR also bound to the transcripts coding the alternate TCA cycle proteins sdhC , mqo , citZ , and citM . Whole cell metal analyses suggest that IsrR promotes Fe uptake and increases intracellular Fe not ligated by macromolecules. Lastly, we determined that Fur and IsrR promote infection using murine skin and acute pneumonia models.
- Published
- 2024
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3. Marine phytoplankton downregulate core photosynthesis and carbon storage genes upon rapid mixed layer shallowing.
- Author
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Diaz BP, Zelzion E, Halsey K, Gaube P, Behrenfeld M, and Bidle KD
- Subjects
- Phytoplankton metabolism, Carbon metabolism, Photosynthesis, Diatoms, Chlorophyta
- Abstract
Marine phytoplankton are a diverse group of photoautotrophic organisms and key mediators in the global carbon cycle. Phytoplankton physiology and biomass accumulation are closely tied to mixed layer depth, but the intracellular metabolic pathways activated in response to changes in mixed layer depth remain less explored. Here, metatranscriptomics was used to characterize the phytoplankton community response to a mixed layer shallowing (from 233 to 5 m) over the course of two days during the late spring in the Northwest Atlantic. Most phytoplankton genera downregulated core photosynthesis, carbon storage, and carbon fixation genes as the system transitioned from a deep to a shallow mixed layer and shifted towards catabolism of stored carbon supportive of rapid cell growth. In contrast, phytoplankton genera exhibited divergent transcriptional patterns for photosystem light harvesting complex genes during this transition. Active virus infection, taken as the ratio of virus to host transcripts, increased in the Bacillariophyta (diatom) phylum and decreased in the Chlorophyta (green algae) phylum upon mixed layer shallowing. A conceptual model is proposed to provide ecophysiological context for our findings, in which integrated light limitation and lower division rates during transient deep mixing are hypothesized to disrupt resource-driven, oscillating transcript levels related to photosynthesis, carbon fixation, and carbon storage. Our findings highlight shared and unique transcriptional response strategies within phytoplankton communities acclimating to the dynamic light environment associated with transient deep mixing and shallowing events during the annual North Atlantic bloom., (© 2023. The Author(s).)
- Published
- 2023
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4. Genetic Approaches to Uncover Gene Products Involved in Iron-Sulfur Protein Maturation: High-Throughput Genomic Screening Using Transposon Sequencing.
- Author
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Carabetta VJ, Esquilin-Lebron K, Zelzion E, and Boyd JM
- Subjects
- Iron metabolism, Iron-Sulfur Proteins genetics, Iron-Sulfur Proteins metabolism, Metabolic Networks and Pathways, Sulfur metabolism, Genomics
- Abstract
Iron-sulfur (Fe-S) clusters are one of the most ubiquitous and versatile prosthetic groups exploited by nature. Fe-S clusters aid in conducting redox reactions, carbon activation, and environmental sensing. This chapter presents an overview of the genetic approaches that have been useful for identifying and characterizing bacterial factors involved in Fe-S protein assembly. Traditional genetic screens that assess viability or conditional auxotrophies and bioinformatic approaches have identified the majority of the described genes utilized for Fe-S protein assembly. Herein, we expand upon this list of genetic methods by detailing the use of transposon sequencing (TnSeq) to identify gene products that are necessary for the proper function of metabolic pathways that require Fe-S enzymes. TnSeq utilizes the power of genomics and massively parallel DNA sequencing to allow researchers to quantify the necessity of individual gene products for a specific growth condition. This allows for the identification of gene products or gene networks that have a role in a given metabolic process but are not essential for the process. An advantage of this approach is that it allows researchers to identify mutants that have partial phenotypes that are often missed using traditional plate-based selections. Applying TnSeq to address questions of Fe-S protein maturation will result in a more comprehensive understanding of genetic interactions and factors utilized in Fe-S biogenesis and Fe-S protein assembly., (© 2021. Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2021
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5. Pyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment.
- Author
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Wang D, Yu X, Xu K, Bi G, Cao M, Zelzion E, Fu C, Sun P, Liu Y, Kong F, Du G, Tang X, Yang R, Wang J, Tang L, Wang L, Zhao Y, Ge Y, Zhuang Y, Mo Z, Chen Y, Gao T, Guan X, Chen R, Qu W, Sun B, Bhattacharya D, and Mao Y
- Subjects
- Animal Shells chemistry, Animals, Antioxidants pharmacology, Base Composition genetics, Biological Evolution, Calcium Carbonate metabolism, Carbonic Anhydrases genetics, Carbonic Anhydrases metabolism, Cell Nucleus genetics, Gene Dosage, Gene Expression Profiling, Gene Transfer, Horizontal genetics, Mollusca, Photosynthesis drug effects, Ploidies, Rhodophyta drug effects, Superoxide Dismutase genetics, Transcription, Genetic drug effects, Carbon metabolism, Genome, Rhodophyta genetics, Rhodophyta metabolism, Water Movements
- Abstract
Changes in atmospheric CO
2 concentration have played a central role in algal and plant adaptation and evolution. The commercially important red algal genus, Pyropia (Bangiales) appears to have responded to inorganic carbon (Ci ) availability by evolving alternating heteromorphic generations that occupy distinct habitats. The leafy gametophyte inhabits the intertidal zone that undergoes frequent emersion, whereas the sporophyte conchocelis bores into mollusk shells. Here, we analyze a high-quality genome assembly of Pyropia yezoensis to elucidate the interplay between Ci availability and life cycle evolution. We find horizontal gene transfers from bacteria and expansion of gene families (e.g. carbonic anhydrase, anti-oxidative related genes), many of which show gametophyte-specific expression or significant up-regulation in gametophyte in response to dehydration. In conchocelis, the release of HCO3 - from shell promoted by carbonic anhydrase provides a source of Ci . This hypothesis is supported by the incorporation of13 C isotope by conchocelis when co-cultured with13 C-labeled CaCO3 .- Published
- 2020
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6. Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology.
- Author
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Nissimov JI, Talmy D, Haramaty L, Fredricks HF, Zelzion E, Knowles B, Eren AM, Vandzura R, Laber CP, Schieler BM, Johns CT, More KD, Coolen MJL, Follows MJ, Bhattacharya D, Van Mooy BAS, and Bidle KD
- Subjects
- Ecology, Haptophyta virology, Models, Theoretical, Phycodnaviridae enzymology, Phycodnaviridae genetics, Phycodnaviridae pathogenicity, Serine C-Palmitoyltransferase, Viral Proteins genetics, Viral Proteins metabolism, Virulence, Virus Replication, Glycosphingolipids biosynthesis, Phycodnaviridae metabolism
- Abstract
Coccolithoviruses (EhVs) are large, double-stranded DNA-containing viruses that infect the single-celled, marine coccolithophore Emiliania huxleyi. Given the cosmopolitan nature and global importance of E. huxleyi as a bloom-forming, calcifying, photoautotroph, E. huxleyi-EhV interactions play a key role in oceanic carbon biogeochemistry. Virally-encoded glycosphingolipids (vGSLs) are virulence factors that are produced by the activity of virus-encoded serine palmitoyltransferase (SPT). Here, we characterize the dynamics, diversity and catalytic production of vGSLs in an array of EhV strains in relation to their SPT sequence composition and explore the hypothesis that they are a determinant of infectivity and host demise. vGSL production and diversity was positively correlated with increased virulence, virus replication rate and lytic infection dynamics in laboratory experiments, but they do not explain the success of less-virulent EhVs in natural EhV communities. The majority of EhV-derived SPT amplicon sequences associated with infected cells in the North Atlantic derived from slower infecting, less virulent EhVs. Our lab-, field- and mathematical model-based data and simulations support ecological scenarios whereby slow-infecting, less-virulent EhVs successfully compete in North Atlantic populations of E. huxleyi, through either the preferential removal of fast-infecting, virulent EhVs during active infection or by having access to a broader host range., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2019
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7. Genome analysis of the rice coral Montipora capitata.
- Author
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Shumaker A, Putnam HM, Qiu H, Price DC, Zelzion E, Harel A, Wagner NE, Gates RD, Yoon HS, and Bhattacharya D
- Subjects
- Animals, Anthozoa genetics, Anthozoa metabolism, Genome, Stress, Physiological physiology, Transcription, Genetic physiology
- Abstract
Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai'i. Our work provides insights into the architecture of coral genomes and shows how they differ in size and gene inventory, putatively due to population size variation. We describe a recent example of foreign gene acquisition via a bacterial gene transfer agent and illustrate the major pathways of stress response that can be used to predict regulatory components of the transcriptional networks in M. capitata. These genomic resources provide insights into the adaptive potential of these sessile, long-lived species in both natural and human influenced environments and facilitate functional and population genomic studies aimed at Hawaiian reef restoration and conservation.
- Published
- 2019
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8. Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals.
- Author
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Qiu H, Zelzion E, Putnam HM, Gates RD, Wagner NE, Adams DK, and Bhattacharya D
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- Animals, Anthozoa classification, Conserved Sequence, DNA chemistry, Evolution, Molecular, Gene Expression Regulation, Gene Transfer, Horizontal, Multigene Family, Nucleic Acid Conformation, Phylogeny, Anthozoa genetics, Gene Expression Profiling methods, Sequence Analysis, DNA methods, Sequence Analysis, RNA methods
- Abstract
Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA. These repeat families have undergone frequent duplication and degradation, suggesting a 'boom and bust' cycle of invasion and loss. We speculate that due to their surprisingly high sequence identities across deeply diverged corals, physical association with genes, and dynamic evolution, SCORs might have adaptive functions in corals that need to be explored using population genomic and function-based approaches., (Copyright © 2017 Elsevier Inc. All rights reserved.)
- Published
- 2017
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9. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata .
- Author
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Putnam HM, Adams DK, Zelzion E, Wagner NE, Qiu H, Mass T, Falkowski PG, Gates RD, and Bhattacharya D
- Abstract
We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major ( M. capitata ) and a minor ( M. flabellata ) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2-3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata , whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers., Competing Interests: The authors declare there are no competing interests.
- Published
- 2017
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10. High phenolics Rutgers Scarlet Lettuce improves glucose metabolism in high fat diet-induced obese mice.
- Author
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Cheng DM, Roopchand DE, Poulev A, Kuhn P, Armas I, Johnson WD, Oren A, Ribnicky D, Zelzion E, Bhattacharya D, and Raskin I
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- Animals, Carbohydrate Metabolism, Diet, Fat-Restricted, Dietary Fats metabolism, Gastrointestinal Tract microbiology, Glucose metabolism, Glucose Tolerance Test, Hyperglycemia metabolism, Liver metabolism, Male, Metabolic Syndrome metabolism, Mice, Mice, Inbred C57BL, Mice, Obese, Obesity metabolism, Quercetin analogs & derivatives, Triglycerides metabolism, Weight Gain, Diet, High-Fat adverse effects, Lactuca chemistry
- Abstract
Scope: The ability of high phenolic Rutgers Scarlet Lettuce (RSL) to attenuate metabolic syndrome and gut dysbiosis was studied in very high fat diet (VHFD)-fed mice. Phenolic absorption was assessed in vivo and in a gastrointestinal tract model., Methods and Results: Mice were fed VHFD, VHFD supplemented with RSL (RSL-VHFD) or store-purchased green lettuce (GL-VHFD), or low-fat diet (LFD) for 13 weeks. Compared to VHFD or GL-VHFD-fed groups, RSL-VHFD group showed significantly improved oral glucose tolerance (p<0.05). Comparison of VHFD, RSL-VHFD, and GL-VHFD groups revealed no significant differences with respect to insulin tolerance, hepatic lipids, body weight gain, fat mass, plasma glucose, triglycerides, free fatty acid, and lipopolysaccharide levels, as well as relative abundances of major bacterial phyla from 16S rDNA amplicon data sequences (from fecal and cecal samples). However, RSL and GL-supplementation increased abundance of several taxa involved in plant polysaccharide degradation/fermentation. RSL phenolics chlorogenic acid, quercetin-3-glucoside, and quercetin-malonyl-glucoside were bioaccessible in the TIM-1 digestion model, but had relatively low recovery., Conclusions: RSL phenolics contributed to attenuation of post-prandial hyperglycemia. Changes in gut microbiota were likely due to microbiota accessible carbohydrates in RSL and GL rather than RSL phenolics, which may be metabolized, absorbed, or degraded before reaching the colon., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2016
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11. Comparative genomics explains the evolutionary success of reef-forming corals.
- Author
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Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, Kamel B, Lesser MP, Levy O, Liew YJ, MacManes M, Mass T, Medina M, Mehr S, Meyer E, Price DC, Putnam HM, Qiu H, Shinzato C, Shoguchi E, Stokes AJ, Tambutté S, Tchernov D, Voolstra CR, Wagner N, Walker CW, Weber AP, Weis V, Zelzion E, Zoccola D, and Falkowski PG
- Subjects
- Animals, Anthozoa classification, Anthozoa growth & development, Anthozoa metabolism, Biological Evolution, Calcium Carbonate chemistry, Calcium Carbonate metabolism, Coral Reefs, Gene Transfer, Horizontal, Hydrogen-Ion Concentration, Light, Photosynthesis physiology, Phylogeny, Reactive Nitrogen Species metabolism, Reactive Oxygen Species metabolism, Stress, Physiological, Symbiosis physiology, Temperature, Adaptation, Physiological genetics, Anthozoa genetics, Calcification, Physiologic genetics, Genome, Genomics methods, Metabolic Networks and Pathways genetics
- Abstract
Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.
- Published
- 2016
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12. Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis.
- Author
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Mass T, Putnam HM, Drake JL, Zelzion E, Gates RD, Bhattacharya D, and Falkowski PG
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- Animals, Anthozoa genetics, Calcification, Physiologic, Coral Reefs, Gene Expression Regulation, Developmental, Immunohistochemistry, Proteins genetics, Proteins metabolism, Transcriptome, Anthozoa growth & development, Anthozoa metabolism
- Abstract
Reef-building corals begin as non-calcifying larvae that, upon settling, rapidly begin to accrete skeleton and a protein-rich skeletal organic matrix that attach them to the reef. Here, we characterized the temporal and spatial expression pattern of a suite of biomineralization genes during three stages of larval development in the reef-building coral Pocillopora damicornis: stage I, newly released; stage II, oral-aborally compressed and stage III, settled and calcifying spat. Transcriptome analysis revealed 3882 differentially expressed genes that clustered into four distinctly different patterns of expression change across the three developmental stages. Immunolocalization analysis further reveals the spatial arrangement of coral acid-rich proteins (CARPs) in the overall architecture of the emerging skeleton. These results provide the first analysis of the timing of the biomineralization 'toolkit' in the early life history of a stony coral., (© 2016 The Author(s).)
- Published
- 2016
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13. Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis.
- Author
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Méheust R, Zelzion E, Bhattacharya D, Lopez P, and Bapteste E
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- Eukaryota genetics, Gene Fusion, Genome, Plant, Models, Genetic, Multigene Family, Oxidation-Reduction, Photosynthesis genetics, Phylogeny, Plants genetics, Sequence Homology, Amino Acid, Evolution, Molecular, Plastids genetics, Proteins genetics, Symbiosis genetics
- Abstract
The integration of foreign genetic information is central to the evolution of eukaryotes, as has been demonstrated for the origin of the Calvin cycle and of the heme and carotenoid biosynthesis pathways in algae and plants. For photosynthetic lineages, this coordination involved three genomes of divergent phylogenetic origins (the nucleus, plastid, and mitochondrion). Major hurdles overcome by the ancestor of these lineages were harnessing the oxygen-evolving organelle, optimizing the use of light, and stabilizing the partnership between the plastid endosymbiont and host through retargeting of proteins to the nascent organelle. Here we used protein similarity networks that can disentangle reticulate gene histories to explore how these significant challenges were met. We discovered a previously hidden component of algal and plant nuclear genomes that originated from the plastid endosymbiont: symbiogenetic genes (S genes). These composite proteins, exclusive to photosynthetic eukaryotes, encode a cyanobacterium-derived domain fused to one of cyanobacterial or another prokaryotic origin and have emerged multiple, independent times during evolution. Transcriptome data demonstrate the existence and expression of S genes across a wide swath of algae and plants, and functional data indicate their involvement in tolerance to oxidative stress, phototropism, and adaptation to nitrogen limitation. Our research demonstrates the "recycling" of genetic information by photosynthetic eukaryotes to generate novel composite genes, many of which function in plastid maintenance.
- Published
- 2016
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14. An RNA interference knock-down of nitrate reductase enhances lipid biosynthesis in the diatom Phaeodactylum tricornutum.
- Author
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Levitan O, Dinamarca J, Zelzion E, Gorbunov MY, and Falkowski PG
- Subjects
- Carbon metabolism, Diatoms genetics, Gene Expression Profiling, Gene Expression Regulation, Gene Knockdown Techniques, Glutamic Acid metabolism, Glutamine metabolism, Malonyl Coenzyme A metabolism, Metabolic Networks and Pathways, NADP metabolism, Nitrate Reductase genetics, Nitrate Reductase metabolism, Nitrates pharmacology, Nitrogen metabolism, Oxidation-Reduction, Photosynthesis, RNA Interference, Stress, Physiological, Diatoms metabolism, Lipid Metabolism genetics, Nitrate Reductase physiology
- Abstract
When diatoms are stressed for inorganic nitrogen they remodel their intermediate metabolism and redirect carbon towards lipid biosynthesis. However, this response comes at a significant cost reflected in decreased photosynthetic energy conversion efficiency and growth. Here we explore a molecular genetics approach to restrict the assimilation of inorganic nitrogen by knocking down nitrate reductase (NR). The transformant strain, NR21, exhibited about 50% lower expression and activity of the enzyme but simultaneously accumulated over 40% more fatty acids. However, in contrast to nitrogen-stressed wild-type (WT) cells, which grow at about 20% of the rate of nitrogen-replete cells, growth of NR21 was only reduced by about 30%. Biophysical analyses revealed that the photosynthetic energy conversion efficiency of photosystem II was unaffected in NR21; nevertheless, the plastoquinone pool was reduced by 50% at the optimal growth irradiance while in the WT it was over 90% oxidized. Further analyses reveal a 12-fold increase in the glutamate/glutamine ratio and an increase NADPH and malonyl-CoA pool size. Transcriptomic analyses indicate that the knock down resulted in changes in the expression of genes for lipid biosynthesis, as well as the expression of specific transcription factors. Based on these observations, we hypothesize that the allocation of carbon and reductants in diatoms is controlled by a feedback mechanism between intermediate metabolites, the redox state of the plastid and the expression and binding of transcription factors related to stress responses., (© 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.)
- Published
- 2015
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15. Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress.
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Levitan O, Dinamarca J, Zelzion E, Lun DS, Guerra LT, Kim MK, Kim J, Van Mooy BA, Bhattacharya D, and Falkowski PG
- Subjects
- Diatoms genetics, Gene Expression Profiling, Gene Knockdown Techniques, Lipid Metabolism, Metabolic Flux Analysis, Metabolic Networks and Pathways, Models, Biological, Nitrate Reductase antagonists & inhibitors, Nitrate Reductase genetics, Nitrate Reductase metabolism, Stress, Physiological, Diatoms metabolism, Nitrogen metabolism
- Abstract
Diatoms are unicellular algae that accumulate significant amounts of triacylglycerols as storage lipids when their growth is limited by nutrients. Using biochemical, physiological, bioinformatics, and reverse genetic approaches, we analyzed how the flux of carbon into lipids is influenced by nitrogen stress in a model diatom, Phaeodactylum tricornutum. Our results reveal that the accumulation of lipids is a consequence of remodeling of intermediate metabolism, especially reactions in the tricarboxylic acid and the urea cycles. Specifically, approximately one-half of the cellular proteins are cannibalized; whereas the nitrogen is scavenged by the urea and glutamine synthetase/glutamine 2-oxoglutarate aminotransferase pathways and redirected to the de novo synthesis of nitrogen assimilation machinery, simultaneously, the photobiological flux of carbon and reductants is used to synthesize lipids. To further examine how nitrogen stress triggers the remodeling process, we knocked down the gene encoding for nitrate reductase, a key enzyme required for the assimilation of nitrate. The strain exhibits 40-50% of the mRNA copy numbers, protein content, and enzymatic activity of the wild type, concomitant with a 43% increase in cellular lipid content. We suggest a negative feedback sensor that couples photosynthetic carbon fixation to lipid biosynthesis and is regulated by the nitrogen assimilation pathway. This metabolic feedback enables diatoms to rapidly respond to fluctuations in environmental nitrogen availability.
- Published
- 2015
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16. The American cranberry: first insights into the whole genome of a species adapted to bog habitat.
- Author
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Polashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, and Vorsa N
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- DNA Transposable Elements genetics, Disease Resistance genetics, Genetic Markers genetics, Inbreeding, Microsatellite Repeats genetics, Mitochondria genetics, Phylogeny, Plant Diseases genetics, Polymorphism, Single Nucleotide genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Species Specificity, Transcriptome genetics, Adaptation, Physiological genetics, Genome, Plant, Vaccinium macrocarpon genetics, Wetlands
- Abstract
Background: The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear., Results: The genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%)., Conclusions: Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.
- Published
- 2014
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17. Evolution of salt tolerance in a laboratory reared population of Chlamydomonas reinhardtii.
- Author
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Perrineau MM, Zelzion E, Gross J, Price DC, Boyd J, and Bhattacharya D
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- Acclimatization, Biological Evolution, Endoplasmic Reticulum metabolism, Gene Expression, Gene Expression Regulation, Plant, Glycerophospholipids metabolism, Lipid Metabolism genetics, Photosynthesis genetics, Plant Proteins metabolism, Stress, Physiological, Transcriptome, Chlamydomonas reinhardtii physiology, Salt Tolerance
- Abstract
Understanding the genetic underpinnings of adaptive traits in microalgae is important for the study of evolution and for applied uses. We used long-term selection under a regime of serial transfers with haploid populations of the green alga Chlamydomonas reinhardtii raised in liquid TAP medium containing 200 mM NaCl. After 1255 generations, evolved salt (ES) populations could grow as rapidly in high salt medium as progenitor cells (progenitor light [PL]). Transcriptome data were analysed to elucidate the basis of salt tolerance in ES cells when compared with PL cells and to cells incubated for 48 h in high salt medium (progenitor salt [PS], the short-term acclimation response). These data demonstrate that evolved and short-term acclimation responses to salt stress differ fundamentally from each other. Progenitor salt cells exhibit well-known responses to salt stress such as reduction in photosynthesis, upregulation of glycerophospholipid signaling, and upregulation of the transcription and translation machinery. In contrast, ES cells show downregulation of genes involved in the stress response and in transcription/translation. Our results suggest that gene-rich mixotrophic lineages such as C. reinhardtii may be able to adapt rapidly to abiotic stress engendered either by a rapidly changing climate or physical vicariance events that isolate populations in stressful environments., (© 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2014
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18. Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii.
- Author
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Perrineau MM, Gross J, Zelzion E, Price DC, Levitan O, Boyd J, and Bhattacharya D
- Subjects
- Adaptation, Physiological genetics, Chlamydomonas reinhardtii metabolism, Polymorphism, Single Nucleotide, Chlamydomonas reinhardtii genetics, Chlamydomonas reinhardtii growth & development, Selection, Genetic
- Abstract
Improving feedstock is critical to facilitate the commercial utilization of algae, in particular in open pond systems where, due to the presence of competitors and pests, high algal growth rates and stress tolerance are beneficial. Here we raised laboratory cultures of the model alga Chlamydomonas reinhardtii under serial dilution to explore the potential of crop improvement using natural selection. The alga was evolved for 1,880 generations in liquid medium under continuous light (EL population). At the end of the experiment, EL cells had a growth rate that was 35% greater than the progenitor population (PL). The removal of acetate from the medium demonstrated that EL growth enhancement largely relied on efficient usage of this organic carbon source. Genome re-sequencing uncovered 1,937 polymorphic DNA regions in the EL population with 149 single nucleotide polymorphisms resulting in amino acid substitutions. Transcriptome analysis showed, in the EL population, significant up regulation of genes involved in protein synthesis, the cell cycle and cellular respiration, whereas the DNA repair pathway and photosynthesis were down regulated. Like other algae, EL cells accumulated neutral lipids under nitrogen depletion. Our work demonstrates transcriptome and genome-wide impacts of natural selection on algal cells and points to a useful strategy for strain improvement.
- Published
- 2014
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19. Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa.
- Author
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Gross J, Wajid S, Price DC, Zelzion E, Li J, Chan CX, and Bhattacharya D
- Subjects
- Cluster Analysis, Cyanophora metabolism, Gene Expression Profiling, Open Reading Frames, RNA Stability, RNA, Messenger genetics, RNA, Messenger metabolism, RNA, Small Interfering metabolism, Cyanophora genetics, Exons, RNA, Plant, RNA, Small Interfering genetics
- Abstract
RNAi (RNA interference) relies on the production of small RNAs (sRNAs) from double-stranded RNA and comprises a major pathway in eukaryotes to restrict the propagation of selfish genetic elements. Amplification of the initial RNAi signal by generation of multiple secondary sRNAs from a targeted mRNA is catalyzed by RNA-dependent RNA polymerases (RdRPs). This phenomenon is known as transitivity and is particularly important in plants to limit the spread of viruses. Here we describe, using a genome-wide approach, the distribution of sRNAs in the glaucophyte alga Cyanophora paradoxa. C. paradoxa is a member of the supergroup Plantae (also known as Archaeplastida) that includes red algae, green algae, and plants. The ancient (>1 billion years ago) split of glaucophytes within Plantae suggests that C. paradoxa may be a useful model to learn about the early evolution of RNAi in the supergroup that ultimately gave rise to plants. Using next-generation sequencing and bioinformatic analyses we find that sRNAs in C. paradoxa are preferentially associated with mRNAs, including a large number of transcripts that encode proteins arising from different functional categories. This pattern of exonic sRNAs appears to be a general trend that affects a large fraction of mRNAs in the cell. In several cases we observe that sRNAs have a bias for a specific strand of the mRNA, including many instances of antisense predominance. The genome of C. paradoxa encodes four sequences that are homologous to RdRPs in Arabidopsis thaliana. We discuss the possibility that exonic sRNAs in the glaucophyte may be secondarily derived from mRNAs by the action of RdRPs. If this hypothesis is confirmed, then transitivity may have had an ancient origin in Plantae.
- Published
- 2013
- Full Text
- View/download PDF
20. Cloning and characterization of four novel coral acid-rich proteins that precipitate carbonates in vitro.
- Author
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Mass T, Drake JL, Haramaty L, Kim JD, Zelzion E, Bhattacharya D, and Falkowski PG
- Subjects
- Amino Acid Sequence, Animals, Anthozoa cytology, Anthozoa genetics, Calcium Carbonate chemistry, Cloning, Molecular, Extracellular Matrix metabolism, Molecular Sequence Data, Phylogeny, Proteins classification, Proteins genetics, Sequence Alignment, Anthozoa metabolism, Calcification, Physiologic, Calcium Carbonate metabolism, Proteins metabolism
- Abstract
Biomineralization is a widely dispersed and highly regulated but poorly understood process by which organisms precipitate minerals from a wide variety of elements [1]. For many years, it has been hypothesized that the biological precipitation of carbonates is catalyzed by and organized on an extracellular organic matrix containing a suite of proteins, lipids, and polysaccharides [2, 3]. The structures of these molecules, their evolutionary history, and the biophysical mechanisms responsible for calcification remain enigmatic. Despite the recognition that mineralized tissues contain proteins that are unusually rich in aspartic and glutamic acids [4-6], the role of these proteins in biomineralization remains elusive [5, 6]. Here we report, for the first time, the identification, cloning, amino acid sequence, and characterization of four highly acidic proteins, derived from expression of genes obtained from the common stony coral, Stylophora pistillata. Each of these four proteins can spontaneously catalyze the precipitation of calcium carbonate in vitro. Our results demonstrate that coral acid-rich proteins (CARPs) not only bind Ca(2+) stoichiometrically but also precipitate aragonite in vitro in seawater at pH 8.2 and 7.6, via an electrostatic interaction with protons on bicarbonate anions. Phylogenetic analysis suggests that at least one of the CARPs arose from a gene fusion. Similar, highly acidic proteins appear to have evolved several times independently in metazoans through convergence. Based purely on thermodynamic grounds, the predicted change in surface ocean pH in the next decades would appear to have minimal effect on the capacity of these acid-rich proteins to precipitate carbonates., (Copyright © 2013 Elsevier Ltd. All rights reserved.)
- Published
- 2013
- Full Text
- View/download PDF
21. Reply to Ramos-Silva et al.: Regarding coral skeletal proteome.
- Author
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Drake JL, Massa T, Haramaty L, Zelzion E, Bhattacharya D, and Falkowski PG
- Subjects
- Animals, Anthozoa genetics, Anthozoa metabolism
- Published
- 2013
- Full Text
- View/download PDF
22. Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata.
- Author
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Drake JL, Mass T, Haramaty L, Zelzion E, Bhattacharya D, and Falkowski PG
- Subjects
- Amino Acid Sequence, Animals, Cadherins genetics, Cadherins metabolism, Calcium Carbonate metabolism, Carbonic Anhydrases genetics, Carbonic Anhydrases metabolism, Conserved Sequence, Minerals metabolism, Models, Molecular, Molecular Sequence Data, Proteome genetics, Proteome metabolism, Proteomics, Sequence Homology, Amino Acid, Tandem Mass Spectrometry, Anthozoa genetics, Anthozoa metabolism
- Abstract
It has long been recognized that a suite of proteins exists in coral skeletons that is critical for the oriented precipitation of calcium carbonate crystals, yet these proteins remain poorly characterized. Using liquid chromatography-tandem mass spectrometry analysis of proteins extracted from the cell-free skeleton of the hermatypic coral, Stylophora pistillata, combined with a draft genome assembly from the cnidarian host cells of the same species, we identified 36 coral skeletal organic matrix proteins. The proteome of the coral skeleton contains an assemblage of adhesion and structural proteins as well as two highly acidic proteins that may constitute a unique coral skeletal organic matrix protein subfamily. We compared the 36 skeletal organic matrix protein sequences to genome and transcriptome data from three other corals, three additional invertebrates, one vertebrate, and three single-celled organisms. This work represents a unique extensive proteomic analysis of biomineralization-related proteins in corals from which we identify a biomineralization "toolkit," an organic scaffold upon which aragonite crystals can be deposited in specific orientations to form a phenotypically identifiable structure.
- Published
- 2013
- Full Text
- View/download PDF
23. A single disulfide bond disruption in the β3 integrin subunit promotes thiol/disulfide exchange, a molecular dynamics study.
- Author
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Levin L, Zelzion E, Nachliel E, Gutman M, Tsfadia Y, and Einav Y
- Subjects
- Cluster Analysis, Computational Biology, Humans, Integrin beta3 genetics, Molecular Dynamics Simulation, Mutation genetics, Protein Subunits chemistry, Cell Communication physiology, Disulfides chemistry, Integrin beta3 chemistry, Sulfhydryl Compounds chemistry
- Abstract
The integrins are a family of membrane receptors that attach a cell to its surrounding and play a crucial function in cell signaling. The combination of internal and external stimuli alters a folded non-active state of these proteins to an extended active configuration. The β3 subunit of the platelet αIIbβ3 integrin is made of well-structured domains rich in disulfide bonds. During the activation process some of the disulfides are re-shuffled by a mechanism requiring partial reduction of some of these bonds; any disruption in this mechanism can lead to inherent blood clotting diseases. In the present study we employed Molecular Dynamics simulations for tracing the sequence of structural fluctuations initiated by a single cysteine mutation in the β3 subunit of the receptor. These simulations showed that in-silico protein mutants exhibit major conformational deformations leading to possible disulfide exchange reactions. We suggest that any mutation that prevents Cys560 from reacting with one of the Cys(567)-Cys(581) bonded pair, thus disrupting its ability to participate in a disulfide exchange reaction, will damage the activation mechanism of the integrin. This suggestion is in full agreement with previously published experiments. Furthermore, we suggest that rearrangement of disulfide bonds could be a part of a natural cascade of thiol/disulfide exchange reactions in the αIIbβ3 integrin, which are essential for the native activation process.
- Published
- 2013
- Full Text
- View/download PDF
24. Unique disulfide bonds in epidermal growth factor (EGF) domains of β3 affect structure and function of αIIbβ3 and αvβ3 integrins in different manner.
- Author
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Mor-Cohen R, Rosenberg N, Einav Y, Zelzion E, Landau M, Mansour W, Averbukh Y, and Seligsohn U
- Subjects
- Amino Acid Sequence, Animals, Cell Line, Cricetinae, Disulfides metabolism, Epidermal Growth Factor genetics, Humans, Integrin alphaVbeta3 genetics, Molecular Sequence Data, Platelet Glycoprotein GPIIb-IIIa Complex genetics, Protein Binding, Protein Structure, Tertiary, Disulfides chemistry, Epidermal Growth Factor metabolism, Integrin alphaVbeta3 chemistry, Integrin alphaVbeta3 metabolism, Platelet Glycoprotein GPIIb-IIIa Complex chemistry, Platelet Glycoprotein GPIIb-IIIa Complex metabolism
- Abstract
The β3 subunit of αIIbβ3 and αvβ3 integrins contains four epidermal growth factor (EGF)-like domains. Each domain harbors four disulfide bonds of which one is unique for integrins. We previously discerned a regulatory role of the EGF-4 Cys-560-Cys-583 unique bond for αIIbβ3 activation. In this study we further investigated the role of all four integrin unique bonds in both αIIbβ3 and αvβ3. We created β3 mutants harboring serine substitutions of each or both cysteines that disrupt the four unique bonds (Cys-437-Cys-457 in EGF-1, Cys-473-Cys-503 in EGF-2, Cys-523-Cys-544 in EGF-3, and Cys-560-Cys-583 in EGF-4) and transfected them into baby hamster kidney cells together with normal αv or αIIb. Flow cytometry was used to measure surface expression of αIIbβ3 and αvβ3 and their activity state by soluble fibrinogen binding. Most cysteine substitutions caused similarly reduced surface expression of both receptors. Disrupting all four unique disulfide bonds by single cysteine substitutions resulted in variable constitutive activation of αIIbβ3 and αvβ3. In contrast, whereas double C437S/C457S and C473S/C503S mutations yielded constitutively active αIIbβ3 and αvβ3, the C560S/C583S mutation did not, and the C523S/C544S mutation only yielded constitutively active αIIbβ3. Activation of C523S/C544S αvβ3 mutant by activating antibody and dithiothreitol was also impaired. Molecular dynamics of C523S/C544S β3 in αIIbβ3 but not in αvβ3 displayed an altered stable conformation. Our findings indicate that unique disulfide bonds in β3 differently affect the function of αIIbβ3 and αvβ3 and suggest a free sulfhydryl-dependent regulatory role for Cys-560-Cys-583 in both αIIbβ3 and αvβ3 and for Cys-523-Cys-544 only in αvβ3.
- Published
- 2012
- Full Text
- View/download PDF
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