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1.
Proc Natl Acad Sci U S A ; 113(51): 14811-14816, 2016 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-27911822

RESUMO

Numerous therapeutically relevant small molecules have been identified from the screening of natural products (NPs) produced by environmental bacteria. These discovery efforts have principally focused on culturing bacteria from natural environments rich in biodiversity. We sought to assess the biosynthetic capacity of urban soil environments using a phylogenetic analysis of conserved NP biosynthetic genes amplified directly from DNA isolated from New York City park soils. By sequencing genes involved in the biosynthesis of nonribosomal peptides and polyketides, we found that urban park soil microbiomes are both rich in biosynthetic diversity and distinct from nonurban samples in their biosynthetic gene composition. A comparison of sequences derived from New York City parks to genes involved in the biosynthesis of biomedically important NPs produced by bacteria originally collected from natural environments around the world suggests that bacteria producing these same families of clinically important antibiotics, antifungals, and anticancer agents are actually present in the soils of New York City. The identification of new bacterial NPs often centers on the systematic exploration of bacteria present in natural environments. Here, we find that the soil microbiomes found in large cities likely hold similar promise as rich unexplored sources of clinically relevant NPs.


Assuntos
Bactérias/genética , Parques Recreativos , Microbiologia do Solo , Solo/química , Biodiversidade , Produtos Biológicos , Desenho de Drogas , Metagenoma , Microbiota , Cidade de Nova Iorque , Filogenia , Análise de Sequência de DNA
2.
J Microbiol Biol Educ ; 17(1): 7-12, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27047581

RESUMO

Citizen science has become a powerful force for scientific inquiry, providing researchers with access to a vast array of data points while connecting nonscientists to the authentic process of science. This citizen-researcher relationship creates an incredible synergy, allowing for the creation, execution, and analysis of research projects that would otherwise prove impossible in traditional research settings, namely due to the scope of needed human or financial resources (or both). However, citizen-science projects are not without their challenges. For instance, as projects are scaled up, there is concern regarding the rigor and usability of data collected by citizens who are not formally trained in research science. While these concerns are legitimate, we have seen examples of highly successful citizen-science projects from multiple scientific disciplines that have enhanced our collective understanding of science, such as how RNA molecules fold or determining the microbial metagenomic snapshot of an entire public transportation system. These and other emerging citizen-science projects show how improved protocols for reliable, large-scale science can realize both an improvement of scientific understanding for the general public and novel views of the world around us.

3.
Cell Syst ; 1(1): 72-87, 2015 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-26594662

RESUMO

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station's history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.

6.
J Biol Chem ; 289(7): 4417-31, 2014 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-24273168

RESUMO

The toxic subcellular accumulation of lipids predisposes several human metabolic syndromes, including obesity, type 2 diabetes, and some forms of neurodegeneration. To identify pathways that prevent lipid-induced cell death, we performed a genome-wide fatty acid sensitivity screen in Saccharomyces cerevisiae. We identified 167 yeast mutants as sensitive to 0.5 mm palmitoleate, 45% of which define pathways that were conserved in humans. 63 lesions also impacted the status of the lipid droplet; however, this was not correlated to the degree of fatty acid sensitivity. The most liposensitive yeast strain arose due to deletion of the "ARE2 required for viability" (ARV1) gene, encoding an evolutionarily conserved, potential lipid transporter that localizes to the endoplasmic reticulum membrane. Down-regulation of mammalian ARV1 in MIN6 pancreatic ß-cells or HEK293 cells resulted in decreased neutral lipid synthesis, increased fatty acid sensitivity, and lipoapoptosis. Conversely, elevated expression of human ARV1 in HEK293 cells or mouse liver significantly increased triglyceride mass and lipid droplet number. The ARV1-induced hepatic triglyceride accumulation was accompanied by up-regulation of DGAT1, a triglyceride synthesis gene, and the fatty acid transporter, CD36. Furthermore, ARV1 was identified as a transcriptional of the protein peroxisome proliferator-activated receptor α (PPARα), a key regulator of lipid homeostasis whose transcriptional targets include DGAT1 and CD36. These results implicate ARV1 as a protective factor in lipotoxic diseases due to modulation of fatty acid metabolism. In conclusion, a lipotoxicity-based genetic screen in a model microorganism has identified 75 human genes that may play key roles in neutral lipid metabolism and disease.


Assuntos
Proteínas de Transporte/metabolismo , Ácidos Graxos/metabolismo , Metabolismo dos Lipídeos/fisiologia , Fígado/metabolismo , Proteínas de Membrana/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Triglicerídeos/metabolismo , Animais , Apoptose/fisiologia , Antígenos CD36/genética , Antígenos CD36/metabolismo , Proteínas de Transporte/genética , Linhagem Celular Tumoral , Diacilglicerol O-Aciltransferase/genética , Diacilglicerol O-Aciltransferase/metabolismo , Ácidos Graxos/genética , Estudo de Associação Genômica Ampla , Células HEK293 , Humanos , Fígado/citologia , Proteínas de Membrana/genética , Camundongos , PPAR alfa/genética , PPAR alfa/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Triglicerídeos/genética
7.
J Lipid Res ; 53(12): 2716-25, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23033213

RESUMO

STARD4, a member of the evolutionarily conserved START gene family, has been implicated in the nonvesicular intracellular transport of cholesterol. However, the direction of transport and the membranes with which this protein interacts are not clear. We present studies of STARD4 function using small hairpin RNA knockdown technology to reduce STARD4 expression in HepG2 cells. In a cholesterol-poor environment, we found that a reduction in STARD4 expression leads to retention of cholesterol at the plasma membrane, reduction of endoplasmic reticulum-associated cholesterol, and decreased ACAT synthesized cholesteryl esters. Furthermore, D4 KD cells exhibited a reduced rate of sterol transport to the endocytic recycling compartment after cholesterol repletion. Although these cells displayed normal endocytic trafficking in cholesterol-poor and replete conditions, cell surface low density lipoprotein receptor (LDLR) levels were increased and decreased, respectively. We also observed a decrease in NPC1 protein expression, suggesting the induction of compensatory pathways to maintain cholesterol balance. These data indicate a role for STARD4 in nonvesicular transport of cholesterol from the plasma membrane and the endocytic recycling compartment to the endoplasmic reticulum and perhaps other intracellular compartments as well.


Assuntos
Membrana Celular/metabolismo , Colesterol/metabolismo , Endocitose , Retículo Endoplasmático/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , RNA Interferente Pequeno/metabolismo , Membrana Celular/química , Retículo Endoplasmático/química , Células Hep G2 , Humanos , Proteínas de Membrana Transportadoras/deficiência , Proteínas de Membrana Transportadoras/genética , Células Tumorais Cultivadas
8.
J Biol Chem ; 286(33): 29074-85, 2011 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-21708942

RESUMO

The PAH1-encoded phosphatidate (PA) phosphatase in Saccharomyces cerevisiae is a pivotal enzyme that produces diacylglycerol for the synthesis of triacylglycerol (TAG) and simultaneously controls the level of PA used for phospholipid synthesis. Quantitative lipid analysis showed that the pah1Δ mutation caused a reduction in TAG mass and an elevation in the mass of phospholipids and free fatty acids, changes that were more pronounced in the stationary phase. The levels of unsaturated fatty acids in the pah1Δ mutant were unaltered, although the ratio of palmitoleic acid to oleic acid was increased with a similar change in the fatty acid composition of phospholipids. The pah1Δ mutant exhibited classic hallmarks of apoptosis in stationary phase and a marked reduction in the quantity of cytoplasmic lipid droplets. Cells lacking PA phosphatase were sensitive to exogenous fatty acids in the order of toxicity palmitoleic acid > oleic acid > palmitic acid. In contrast, the growth of wild type cells was not inhibited by fatty acid supplementation. In addition, wild type cells supplemented with palmitoleic acid exhibited an induction in PA phosphatase activity and an increase in TAG synthesis. Deletion of the DGK1-encoded diacylglycerol kinase, which counteracts PA phosphatase in controlling PA content, suppressed the defect in lipid droplet formation in the pah1Δ mutant. However, the sensitivity of the pah1Δ mutant to palmitoleic acid was not rescued by the dgk1Δ mutation. Overall, these findings indicate a key role of PA phosphatase in TAG synthesis for protection against fatty acid-induced toxicity.


Assuntos
Ácidos Graxos/metabolismo , Fosfatidato Fosfatase/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimologia , Triglicerídeos/biossíntese , Apoptose/fisiologia , Mutação , Fosfatidato Fosfatase/genética , Proteínas de Saccharomyces cerevisiae/genética , Triglicerídeos/genética
9.
J Lipid Res ; 51(5): 1134-43, 2010 May.
Artigo em Inglês | MEDLINE | ID: mdl-19965609

RESUMO

Steroidogenic acute regulatory protein (StAR)D4 is a member of the StAR related lipid transfer family. Homology comes from the approximately 210 amino acid lipid binding domain implicated in intracellular transport, cell signaling, and lipid metabolism. StARD4 was identified as a gene downregulated 2-fold by dietary cholesterol (Soccio, R. E., R. M. Adams, K. N. Maxwell, and J. L. Breslow. 2005. Differential gene regulation of StarD4 and StarD5 cholesterol transfer proteins. Activation of StarD4 by sterol regulatory element-binding protein-2 and StarD5 by endoplasmic reticulum stress. J. Biol. Chem. 280: 19410-19418). A mouse knockout was created to investigate StARD4's functionality and role in lipid metabolism. Homozygous knockout mice exhibited normal Mendelian mating genetics, but weighed less than wild-type littermates, an effect not accounted for by energy metabolism or food intake. Body composition as analyzed by DEXA scan showed no significant difference. No significant alterations in plasma or liver lipid content were observed on a chow diet, but female knockout mice showed a decrease in gallbladder bile cholesterol and phospholipid concentration. When challenged with a 0.2% lova-statin diet, StARD4 homozygous mice exhibited no changes. However, when challenged with a 0.5% cholesterol diet, female StARD4 homozygous mice showed a moderate decrease in total cholesterol, LDL, and cholesterol ester concentrations. Microarray analysis of liver RNA found few changes. However, NPC1's expression, a gene not on the microarray, was decreased approximately 2.5-fold in knockouts. These observations suggest that StARD4's role can largely be compensated for by other intracellular cholesterol transporters.


Assuntos
Técnicas de Inativação de Genes , Metabolismo dos Lipídeos/genética , Proteínas de Membrana Transportadoras/deficiência , Proteínas de Membrana Transportadoras/genética , Perda de Peso/genética , Absorciometria de Fóton , Animais , Índice de Massa Corporal , Colesterol/farmacologia , Gorduras na Dieta , Ingestão de Alimentos/genética , Feminino , Fertilidade/genética , Vesícula Biliar/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Teste de Tolerância a Glucose , Fígado/metabolismo , Lovastatina/farmacologia , Masculino , Proteínas de Membrana Transportadoras/química , Proteínas de Membrana Transportadoras/metabolismo , Camundongos , Tamanho do Órgão/genética , Estrutura Terciária de Proteína , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Esteróis/metabolismo , Fatores de Tempo
10.
J Biol Chem ; 284(45): 30994-1005, 2009 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-19690167

RESUMO

Deletion of the acyltransferases responsible for triglyceride and steryl ester synthesis in Saccharomyces cerevisiae serves as a genetic model of diseases where lipid overload is a component. The yeast mutants lack detectable neutral lipids and cytoplasmic lipid droplets and are strikingly sensitive to unsaturated fatty acids. Expression of human diacylglycerol acyltransferase 2 in the yeast mutants was sufficient to reverse these phenotypes. Similar to mammalian cells, fatty acid-mediated death in yeast is apoptotic and presaged by transcriptional induction of stress-response pathways, elevated oxidative stress, and activation of the unfolded protein response. To identify pathways that protect cells from lipid excess, we performed genetic interaction and transcriptional profiling screens with the yeast acyltransferase mutants. We thus identified diacylglycerol kinase-mediated phosphatidic acid biosynthesis and production of phosphatidylcholine via methylation of phosphatidylethanolamine as modifiers of lipotoxicity. Accordingly, the combined ablation of phospholipid and triglyceride biosynthesis increased sensitivity to saturated fatty acids. Similarly, normal sphingolipid biosynthesis and vesicular transport were required for optimal growth upon denudation of triglyceride biosynthesis and also mediated resistance to exogenous fatty acids. In metazoans, many of these processes are implicated in insulin secretion thus linking lipotoxicity with early aspects of pancreatic beta-cell dysfunction, diabetes, and the metabolic syndrome.


Assuntos
Diacilglicerol O-Aciltransferase/deficiência , Ácidos Graxos/toxicidade , Saccharomyces cerevisiae/citologia , Saccharomyces cerevisiae/enzimologia , Esteróis/metabolismo , Morte Celular/efeitos dos fármacos , Diacilglicerol O-Aciltransferase/genética , Diacilglicerol O-Aciltransferase/metabolismo , Ácidos Graxos/metabolismo , Regulação Fúngica da Expressão Gênica , Humanos , Viabilidade Microbiana , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética
11.
Curr Opin Clin Nutr Metab Care ; 12(2): 110-6, 2009 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-19202381

RESUMO

PURPOSE OF REVIEW: To present current perspectives on the mediators and mechanisms of cyto-lipotoxic events and their relevance to human health. RECENT FINDINGS: The relatively recent isolation of lipid acyltransferase genes from yeast to mice and humans has resulted in a paradigm shift that now establishes all fatty acids as toxic, albeit in tissue specific patterns and by different mechanisms. Furthermore, the dysregulation of glucose homeostasis in combination with excess fatty acids provides a synergistic effect leading to glucolipotoxicity and cell death. These findings are relevant to the development of disease states associated with the pathogenesis of the metabolic syndrome. SUMMARY: In an era when an astounding number of people are diagnosed with metabolic disorders, it is imperative that we understand the consequences of a chronic metabolic surplus. Excessive fat, saturated or otherwise, has to be accommodated. Multiple aspects of this homeostasis are emerging, some of which are described here.


Assuntos
Tecido Adiposo/metabolismo , Gorduras na Dieta/efeitos adversos , Ácidos Graxos/metabolismo , Hiperlipidemias/metabolismo , Metabolismo dos Lipídeos , Morte Celular/fisiologia , Glucose/metabolismo , Homeostase , Humanos , Síndrome Metabólica/metabolismo , Obesidade/metabolismo
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