1
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Jin H, Abouzaid M, Lin Y, Hull JJ, Ma W. Cloning and RNAi-mediated three lethal genes that can be potentially used for Chilo suppressalis (Lepidoptera: Crambidae) management. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 174:104828. [PMID: 33838721 DOI: 10.1016/j.pestbp.2021.104828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/27/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
RNA interference (RNAi) has gained attention in recent years as a viable pest control strategy. Here, RNAi assays were performed to screen the potential functionality of genes in Chilo suppressalis, a serious pest of rice, and to determine their potential for developing a highly targeted molecular control approach. Potential homologs of NADH dehydrogenase (ND), glycerol 3-phosphate dehydrogenase (GPDH) and male specific lethal 3 (MSL3) were cloned from C. suppressalis, and their spatiotemporal gene expression evaluated. The expression of all three genes was higher in the pupal and adult stages than the larval stages and largely higher in the larval head compared to other tissues. Newly hatched larvae exhibited high mortalities and suppressed growth when fed bacteria producing double-stranded RNAs (dsRNAs) corresponding to the three target genes. This study provides insights into the function of ND, GPDH and MSL3 during C. suppressalis larval development and suggests that all may be candidate gene targets for C. suppressalis pest management.
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Affiliation(s)
- Huihui Jin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Mostafa Abouzaid
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China
| | - J Joe Hull
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ 85138, USA
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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2
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Contreras A, Morales L, Del Olmo N, Pérez-García C. Effects of Intermittent versus Chronic-Moderate Ethanol Administration during Adolescence in the Adult Hippocampal Phosphoproteome. Chem Res Toxicol 2020; 33:448-460. [PMID: 31944673 DOI: 10.1021/acs.chemrestox.9b00359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alcohol consumption during adolescence is known to cause different impairments in the hippocampus that could lead to persistent deficits in adulthood. A common pattern of alcohol use in adolescents consists of excessive and intermittent alcohol consumption over a very short period of time (binge drinking). Protein phosphorylation is a mechanism underlying memory processes and we have previously demonstrated changes in the rat hippocampal phosphoproteome after a single dose of ethanol; however, studies showing the phosphoprotein alterations in the hippocampus after repeated exposition to alcohol are limited. This study focuses on the identification of the phosphoproteins differentially regulated in the adolescent rat hippocampus after repeated ethanol administration by comparing different patterns of alcohol treatments according to dose and frequency of administration ((i) moderate dose-chronic use, (ii) low dose-intermittent use, and (iii) high dose-intermittent use). We have used a proteomic approach, including phosphoprotein enrichment by immobilized metal affinity chromatography, which revealed 21 proteins differentially affected depending on the pattern of alcohol treatment used. Many of these proteins are included in glycolysis and glucagon signaling pathways and are also involved in neurodegeneration, which could reinforce the role of metabolic alterations in the neural damage induced by repeated alcohol exposure during adolescence.
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Affiliation(s)
- Ana Contreras
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
| | - Lidia Morales
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
| | - Nuria Del Olmo
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
| | - Carmen Pérez-García
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia , Universidad CEU-San Pablo , Madrid 28003 , Spain
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3
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Laptev IA, Raevskaya NM, Filimonova NA, Sineoky SP. The piggyBac Transposon as a Tool in Genetic Engineering. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s000368381709006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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4
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Liu J, Li L, Peters BM, Li B, Chen L, Deng Y, Xu Z, Shirtliff ME. The viable but nonculturable state induction and genomic analyses of Lactobacillus casei BM-LC14617, a beer-spoilage bacterium. Microbiologyopen 2017; 6. [PMID: 28685978 PMCID: PMC5635166 DOI: 10.1002/mbo3.506] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/14/2017] [Accepted: 05/22/2017] [Indexed: 01/05/2023] Open
Abstract
This study aimed to investigate the viable but nonculturable (VBNC) state and genomic features of a beer‐spoilage strain, Lactobacillus caseiBM‐LC14617. Induction on the VBNC state of L. casei strain BM‐LC14617 was conducted by both low‐temperature storage and continuous passage in beer, and formation of VBNC state was detected after 196 ± 3.3 days and 32 ± 1.6 subcultures, respectively. Resuscitation of VBNC cells was successfully induced by addition of catalase, and culturable, VBNC, and resuscitated cells shared similar beer‐spoilage capability. Whole genome sequencing was performed, and out of a total of 3,964 predicted genes, several potential VBNC and beer‐spoilage‐associated genes were identified. L. casei is capable of entering into and resuscitating from the VBNC state and possesses beer‐spoilage capability. The genomic characterization yield insightful elucidation of VBNC state for L. casei. This study represents the first evidence on VBNC state induction of L. casei and beer‐spoilage capability of VBNC and resuscitated cells. Also, this is the first genomic characterization of L. casei as a beer‐spoilage bacterium. The current study may aid in further study on L. casei and other beer‐spoilage bacteria, and guide the prevention and control of beer spoilage.
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Affiliation(s)
- Junyan Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Lin Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Guangzhou, China
| | - Brian M Peters
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Bing Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Guangzhou, China
| | - Lequn Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Yang Deng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Zhenbo Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Guangzhou, China.,Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland
| | - Mark E Shirtliff
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland
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5
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Park GS, Hong SJ, Jung BK, Park S, Jin H, Lee SJ, Shin JH, Lee HS. Whole genome sequence of lactic acid bacterium Pediococcus acidilactici strain S1. Braz J Microbiol 2017; 48:395-396. [PMID: 28256390 PMCID: PMC5498416 DOI: 10.1016/j.bjm.2016.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/18/2016] [Indexed: 11/11/2022] Open
Abstract
Pediococcus acidilactici strain S1, a lactic acid-fermenting bacterium, was isolated from makgeolli—a Korean traditional fermented alcoholic beverage. Here we report the 1,980,172 bp (G + C content, 42%) genome sequence of Pediococcus acidilactici strain S1 with 1,525 protein-coding sequences (CDS), of which 47% could be assigned to recognized functional genes. The genome sequence of the strain S1 might provide insights into the genetic basis of the lactic acid bacterium with alcohol-tolerant.
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Affiliation(s)
- Gun-Seok Park
- Kyungpook National University, School of Applied Biosciences, Daegu, Republic of Korea
| | - Sung-Jun Hong
- Kyungpook National University, School of Applied Biosciences, Daegu, Republic of Korea
| | - Byung Kwon Jung
- Kyungpook National University, School of Applied Biosciences, Daegu, Republic of Korea
| | - Seulki Park
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea
| | - Hyewon Jin
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea
| | - Sang-Jae Lee
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea; Silla University, The Research Center for Extremophiles and Marine Microbiology, Busan, Republic of Korea
| | - Jae-Ho Shin
- Kyungpook National University, School of Applied Biosciences, Daegu, Republic of Korea; Kyungpook National University, Institute for Phylogenomics and Evolution, Daegu, Republic of Korea.
| | - Han-Seung Lee
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea; Silla University, The Research Center for Extremophiles and Marine Microbiology, Busan, Republic of Korea.
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6
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Park GS, Hong SJ, Park S, Jin H, Lee SJ, Shin JH, Lee HS. Draft genome sequence of alcohol-tolerant bacteria Pediococcus acidilactici strain K3. Braz J Microbiol 2017; 48:1-2. [PMID: 28043774 PMCID: PMC5220627 DOI: 10.1016/j.bjm.2016.07.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/12/2015] [Indexed: 12/03/2022] Open
Abstract
Pediococcus acidilactici strain K3 is an alcohol-tolerant lactic acid bacterium isolated from nuruk, which is a traditional Korean fermentation starter for makgeolli brewing. Draft genome of this strain was approximately 1,991,399 bp (G+C content, 42.1%) with 1525 protein-coding sequences (CDS), of which 44% were assigned to recognized functional genes. This draft genome sequence data of the strain K3 will provide insights into the genetic basis of its alcohol-tolerance.
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Affiliation(s)
- Gun-Seok Park
- Kyungpook National University, School of Applied Biosciences, Daegu, Republic of Korea
| | - Sung-Jun Hong
- Kyungpook National University, School of Applied Biosciences, Daegu, Republic of Korea
| | - Seulki Park
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea
| | - Hyewon Jin
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea
| | - Sang-Jae Lee
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea; Silla University, The Research Center for Extremophiles and Marine Microbiology, Busan, Republic of Korea
| | - Jae-Ho Shin
- Kyungpook National University, School of Applied Biosciences, Daegu, Republic of Korea.
| | - Han-Seung Lee
- Silla University, College of Medical and Life Sciences, Major in Food Biotechnology, Busan, Republic of Korea; Silla University, The Research Center for Extremophiles and Marine Microbiology, Busan, Republic of Korea.
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7
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Talbert ME, Barnett B, Hoff R, Amella M, Kuczynski K, Lavington E, Koury S, Brud E, Eanes WF. Genetic perturbation of key central metabolic genes extends lifespan in Drosophila and affects response to dietary restriction. Proc Biol Sci 2016; 282:rspb.2015.1646. [PMID: 26378219 DOI: 10.1098/rspb.2015.1646] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
There is a connection between nutrient inputs, energy-sensing pathways, lifespan variation and aging. Despite the role of metabolic enzymes in energy homeostasis and their metabolites as nutrient signals, little is known about how their gene expression impacts lifespan. In this report, we use P-element mutagenesis in Drosophila to study the effect on lifespan of reductions in expression of seven central metabolic enzymes, and contrast the effects on normal diet and dietary restriction. The major observation is that for five of seven genes, the reduction of gene expression extends lifespan on one or both diets. Two genes are involved in redox balance, and we observe that lower activity genotypes significantly extend lifespan. The hexokinases also show extension of lifespan with reduced gene activity. Since both affect the ATP/ADP ratio, this connects with the role of AMP-activated protein kinase as an energy sensor in regulating lifespan and mediating caloric restriction. These genes possess significant expression variation in natural populations, and our experimental genotypes span this level of natural activity variation. Our studies link the readout of energy state with the perturbation of the genes of central metabolism and demonstrate their effect on lifespan.
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Affiliation(s)
- Matthew E Talbert
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Brittany Barnett
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Robert Hoff
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Maria Amella
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kate Kuczynski
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Erik Lavington
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Spencer Koury
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Evgeny Brud
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Walter F Eanes
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
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8
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Fry JD. Mechanisms of naturally evolved ethanol resistance in Drosophila melanogaster. J Exp Biol 2014; 217:3996-4003. [PMID: 25392459 PMCID: PMC4229365 DOI: 10.1242/jeb.110510] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/21/2014] [Indexed: 02/02/2023]
Abstract
The decaying fruit in which Drosophila melanogaster feed and breed can contain ethanol in concentrations as high as 6-7%. In this cosmopolitan species, populations from temperate regions are consistently more resistant to ethanol poisoning than populations from the tropics, but little is known about the physiological basis of this difference. I show that when exposed to low levels of ethanol vapor, flies from a tropical African population accumulated 2-3 times more internal ethanol than flies from a European population, giving evidence that faster ethanol catabolism by European flies contributes to the resistance difference. Using lines differing only in the origin of their third chromosome, however, I show that faster ethanol elimination cannot fully explain the resistance difference, because relative to African third chromosomes, European third chromosomes confer substantially higher ethanol resistance, while having little effect on internal ethanol concentrations. European third chromosomes also confer higher resistance to acetic acid, a metabolic product of ethanol, than African third chromosomes, suggesting that the higher ethanol resistance conferred by the former might be due to increased resistance to deleterious effects of ethanol-derived acetic acid. In support of this hypothesis, when ethanol catabolism was blocked with an Alcohol dehydrogenase mutant, there was no difference in ethanol resistance between flies with European and African third chromosomes.
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Affiliation(s)
- James D Fry
- Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA
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9
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Lavington E, Cogni R, Kuczynski C, Koury S, Behrman EL, O'Brien KR, Schmidt PS, Eanes WF. A small system--high-resolution study of metabolic adaptation in the central metabolic pathway to temperate climates in Drosophila melanogaster. Mol Biol Evol 2014; 31:2032-41. [PMID: 24770333 DOI: 10.1093/molbev/msu146] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In this article, we couple the geographic variation in 127 single-nucleotide polymorphism (SNP) frequencies in genes of 46 enzymes of central metabolism with their associated cis-expression variation to predict latitudinal or climatic-driven gene expression changes in the metabolic architecture of Drosophila melanogaster. Forty-two percent of the SNPs in 65% of the genes show statistically significant clines in frequency with latitude across the 20 local population samples collected from southern Florida to Ontario. A number of SNPs in the screened genes are also associated with significant expression variation within the Raleigh population from North Carolina. A principal component analysis of the full variance-covariance matrix of latitudinal changes in SNP-associated standardized gene expression allows us to identify those major genes in the pathway and its associated branches that are likely targets of natural selection. When embedded in a central metabolic context, we show that these apparent targets are concentrated in the genes of the upper glycolytic pathway and pentose shunt, those controlling glycerol shuttle activity, and finally those enzymes associated with the utilization of glutamate and pyruvate. These metabolites possess high connectivity and thus may be the points where flux balance can be best shifted. We also propose that these points are conserved points associated with coupling energy homeostasis and energy sensing in mammals. We speculate that the modulation of gene expression at specific points in central metabolism that are associated with shifting flux balance or possibly energy-state sensing plays a role in adaptation to climatic variation.
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Affiliation(s)
- Erik Lavington
- Department of Ecology and Evolution, Stony Brook University
| | - Rodrigo Cogni
- Department of Ecology and Evolution, Stony Brook University
| | | | - Spencer Koury
- Department of Ecology and Evolution, Stony Brook University
| | | | | | | | - Walter F Eanes
- Department of Ecology and Evolution, Stony Brook University
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10
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Wang H, Lai D, Yuan M, Xu H. Growth inhibition and differences in protein profiles in azadirachtin-treated Drosophila melanogaster larvae. Electrophoresis 2014; 35:1122-9. [PMID: 24458307 DOI: 10.1002/elps.201300318] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 12/16/2013] [Accepted: 01/12/2014] [Indexed: 11/06/2022]
Abstract
Azadirachtin A is a very effective biopesticide widely used in insect pest control. It has strong antifeeding and growth inhibitory activity against most insects, however, its mode of action is still unclear. Proteomic experiments using 2DE indicate significant effects of Azadirachtin A on the amount of proteins related to growth inhibition in Drosophila melanogaster larvae. Twenty-one spots with different intensity in azadirachtin-treated larvae were identified. These proteins are involved in cytoskeletal organization, transcription and translation, hormonal regulation, and energy metabolism. Protein network analysis reveals heat shock protein 23 to be a potential target of azadirachtin. These results provide new insights into understanding the mechanism of growth inhibition in insects in response to azadirachtin.
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Affiliation(s)
- Hao Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, P.R. China
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11
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Marden JH. Nature's inordinate fondness for metabolic enzymes: why metabolic enzyme loci are so frequently targets of selection. Mol Ecol 2013; 22:5743-64. [PMID: 24106889 DOI: 10.1111/mec.12534] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 01/01/2023]
Abstract
Metabolic enzyme loci were some of the first genes accessible for molecular evolution and ecology research. New technologies now make the whole genome, transcriptome or proteome readily accessible, allowing unbiased scans for loci exhibiting significant differences in allele frequency or expression level and associated with phenotypes and/or responses to natural selection. With surprising frequency and in many cases in proportions greater than chance relative to other genes, glycolysis and TCA cycle enzyme loci appear among the genes with significant associations in these studies. Hence, there is an ongoing need to understand the basis for fitness effects of metabolic enzyme polymorphisms. Allele-specific effects on the binding affinity and catalytic rate of individual enzymes are well known, but often of uncertain significance because metabolic control theory and in vivo studies indicate that many individual metabolic enzymes do not affect pathway flux rate. I review research, so far little used in evolutionary biology, showing that metabolic enzyme substrates affect signalling pathways that regulate cell and organismal biology, and that these enzymes have moonlighting functions. To date there is little knowledge of how alleles in natural populations affect these phenotypes. I discuss an example in which alleles of a TCA enzyme locus associate with differences in a signalling pathway and development, organismal performance, and ecological dynamics. Ultimately, understanding how metabolic enzyme polymorphisms map to phenotypes and fitness remains a compelling and ongoing need for gaining robust knowledge of ecological and evolutionary processes.
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Affiliation(s)
- James H Marden
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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12
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Chen L, Li BQ, Zheng MY, Zhang J, Feng KY, Cai YD. Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways. BIOMED RESEARCH INTERNATIONAL 2013; 2013:723780. [PMID: 24083237 PMCID: PMC3780555 DOI: 10.1155/2013/723780] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 07/24/2013] [Indexed: 12/11/2022]
Abstract
Drug combinatorial therapy could be more effective in treating some complex diseases than single agents due to better efficacy and reduced side effects. Although some drug combinations are being used, their underlying molecular mechanisms are still poorly understood. Therefore, it is of great interest to deduce a novel drug combination by their molecular mechanisms in a robust and rigorous way. This paper attempts to predict effective drug combinations by a combined consideration of: (1) chemical interaction between drugs, (2) protein interactions between drugs' targets, and (3) target enrichment of KEGG pathways. A benchmark dataset was constructed, consisting of 121 confirmed effective combinations and 605 random combinations. Each drug combination was represented by 465 features derived from the aforementioned three properties. Some feature selection techniques, including Minimum Redundancy Maximum Relevance and Incremental Feature Selection, were adopted to extract the key features. Random forest model was built with its performance evaluated by 5-fold cross-validation. As a result, 55 key features providing the best prediction result were selected. These important features may help to gain insights into the mechanisms of drug combinations, and the proposed prediction model could become a useful tool for screening possible drug combinations.
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Affiliation(s)
- Lei Chen
- Institute of Systems Biology, Shanghai University, Shanghai 200444, China
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Bi-Qing Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Yue Zheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai 201203, China
| | - Jian Zhang
- Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Kai-Yan Feng
- Beijing Genomics Institute, Shenzhen Beishan Industrial Zone, Shenzhen 518083, China
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai 200444, China
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13
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Kondrashov FA. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci 2012; 279:5048-57. [PMID: 22977152 PMCID: PMC3497230 DOI: 10.1098/rspb.2012.1108] [Citation(s) in RCA: 383] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/21/2012] [Indexed: 01/13/2023] Open
Abstract
A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.
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Affiliation(s)
- Fyodor A Kondrashov
- Institució Catalana de Recerca i Estudis Avançats, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, 88 Dr Aiguader, Barcelona 08003, Spain.
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14
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Quantitative trait loci for response to ethanol in an intercontinental set of recombinant inbred lines of Drosophila melanogaster. Alcohol 2012; 46:737-45. [PMID: 22925826 DOI: 10.1016/j.alcohol.2012.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 07/12/2012] [Accepted: 07/19/2012] [Indexed: 11/23/2022]
Abstract
Alcohol, a drug widely abused, impacts the central nervous system functioning of diverse organisms. The behavioral responses to acute alcohol exposure are remarkably similar among humans and fruit flies. In its natural environment, rich in fermentation products, the fruit fly Drosophila melanogaster encounters relatively high levels of ethanol. The effects of ethanol and its metabolites on Drosophila have been studied for decades, as a model for adaptive evolution. Although extensive work has been done for elucidating patterns of genetic variation, substantially less is known about the genomic regions or genes that underlie the genetic variation of this important trait. To identify regions containing genes involved in the responses to ethanol, we used a mapping population of recombinant inbred (RIL) lines to map quantitative trait loci (QTL) that affect variation in resistance and recovery from ethanol sedation in adults and ethanol resistance in larvae. We mapped fourteen QTL affecting the response to ethanol on the three chromosomes. Seven of the QTL influence the resistance to ethanol in adults, two QTL are related to ethanol-coma recovery in adults and five affect the survival to ethanol in larvae. Most of the QTL were trait specific, suggesting that overlapping but generally unique genetic architectures underlie each trait. Each QTL explained up to 16.8% of the genetic variance among lines. Potential candidate loci contained within our QTL regions were identified and analyzed.
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15
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Yampolsky LY, Glazko GV, Fry JD. Evolution of gene expression and expression plasticity in long-term experimental populations of Drosophila melanogaster maintained under constant and variable ethanol stress. Mol Ecol 2012; 21:4287-99. [PMID: 22774776 PMCID: PMC3654693 DOI: 10.1111/j.1365-294x.2012.05697.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene expression responds to the environment and can also evolve rapidly in response to altered selection regimes. Little is known, however, about the extent to which evolutionary adaptation to a particular type of stress involves changes in the within-generation ('plastic') responses of gene expression to the stress. We used microarrays to quantify gene expression plasticity in response to ethanol in laboratory populations of Drosophila melanogaster differing in their history of ethanol exposure. Two populations ('R' populations) were maintained on regular medium, two ('E') were maintained on medium supplemented with ethanol, and two ('M') were maintained in a mixed regime in which half of the population was reared on one medium type, and half on the other, each generation. After more than 300 generations, embryos from each population were collected and exposed to either ethanol or water as a control, and RNA was extracted from the larvae shortly after hatching. Nearly 2000 transcripts showed significant within-generation responses to ethanol exposure. Evolutionary history also affected gene expression: the E and M populations were largely indistinguishable in expression, but differed significantly in expression from the R populations for over 100 transcripts, the majority of which did not show plastic responses. Notably, in no case was the interaction between selection regime and ethanol exposure significant after controlling for multiple comparisons, indicating that adaptation to ethanol in the E and M populations did not involve substantial changes in gene expression plasticity. The results give evidence that expression plasticity evolves considerably more slowly than mean expression.
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Affiliation(s)
- Lev Y. Yampolsky
- Department of Biology, University of Rochester, Rochester, NY 14627 U.S.A
| | - Galina V. Glazko
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642 U.S.A
| | - James D. Fry
- Department of Biology, University of Rochester, Rochester, NY 14627 U.S.A
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Experimental approaches to evaluate the contributions of candidate protein-coding mutations to phenotypic evolution. Methods Mol Biol 2012; 772:377-96. [PMID: 22065450 DOI: 10.1007/978-1-61779-228-1_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identifying mechanisms of molecular adaptation can provide important insights into the process of phenotypic evolution, but it can be exceedingly difficult to quantify the phenotypic effects of specific mutational changes. To verify the adaptive significance of genetically based changes in protein function, it is necessary to document functional differences between the products of derived and wild-type alleles and to demonstrate that such differences impinge on higher-level physiological processes (and ultimately, fitness). In the case of metabolic enzymes, this requires documenting in vivo differences in reaction rate that give rise to differences in flux through the pathway in which the enzymes function. These measured differences in pathway flux should then give rise to differences in cellular or systemic physiology that affect fitness-related variation in whole-organism performance. Efforts to establish these causal connections between genotype, phenotype, and fitness require experiments that carefully control for environmental variation and background genetic variation. Here, we discuss experimental approaches to evaluate the contributions of amino-acid mutations to adaptive phenotypic change. We discuss conceptual and methodological issues associated with in vitro and in vivo studies of protein function, and the evolutionary insights that can be gleaned from such studies. We also discuss the importance of isolating the effects of individual mutations to distinguish between positively selected substitutions that directly contribute to improvements in protein function versus positively selected, compensatory substitutions that mitigate negative pleiotropic effects of antecedent changes.
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Hernández-Tobías A, Julián-Sánchez A, Piña E, Riveros-Rosas H. Natural alcohol exposure: Is ethanol the main substrate for alcohol dehydrogenases in animals? Chem Biol Interact 2011; 191:14-25. [DOI: 10.1016/j.cbi.2011.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 01/30/2023]
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Size matters: versatile use of PiggyBac transposons as a genetic manipulation tool. Mol Cell Biochem 2011; 354:301-9. [PMID: 21516337 DOI: 10.1007/s11010-011-0832-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 04/15/2011] [Indexed: 12/16/2022]
Abstract
Transposons have been promising elements for gene integration, and the Sleeping Beauty (SB) system has been the major one for many years, although there have been several other transposon systems available, for example, Tol2. However, recently another system known as PiggyBac (PB) has been introduced and developed for fulfilling the same purposes, for example, mutagenesis, transgenesis and gene therapy and in some cases with improved transposition efficiency and advantages over the Sleeping Beauty transposon system, although improved hyperactive transposase has highly increased the transposition efficacy for SB. The PB systems have been used in many different scientific research fields; therefore, the purpose of this review is to describe some of these versatile uses of the PiggyBac system to give readers an overview on the usage of PiggyBac system.
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Eanes WF. Molecular population genetics and selection in the glycolytic pathway. ACTA ACUST UNITED AC 2011; 214:165-71. [PMID: 21177937 DOI: 10.1242/jeb.046458] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this review, I discuss the evidence for differential natural selection acting across enzymes in the glycolytic pathway in Drosophila. Across the genome, genes evolve at very different rates and possess markedly varying levels of molecular polymorphism, codon bias and expression variation. Discovering the underlying causes of this variation has been a challenge in evolutionary biology. It has been proposed that both the intrinsic properties of enzymes and their pathway position have direct effects on their molecular evolution, and with the genomic era the study of adaptation has been taken to the level of pathways and networks of genes and their products. Of special interest have been the energy-producing pathways. Using both population genetic and experimental approaches, our laboratory has been engaged in a study of molecular variation across the glycolytic pathway in Drosophila melanogaster and its close relatives. We have observed a pervasive pattern in which genes at the top of the pathway, especially around the intersection at glucose 6-phosphate, show evidence for both contemporary selection, in the form of latitudinal allele clines, and inter-specific selection, in the form of elevated levels of amino acid substitutions between species. To further explore this question, future work will require corroboration in other species, expansion into tangential pathways, and experimental work to better characterize metabolic control through the pathway and to examine the pleiotropic effects of these genes on other traits and fitness components.
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Affiliation(s)
- Walter F Eanes
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11790, USA.
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