951
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Kohan-Baghkheirati E, Geisler-Lee J. Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. NANOMATERIALS (BASEL, SWITZERLAND) 2015; 5:436-467. [PMID: 28347022 PMCID: PMC5312895 DOI: 10.3390/nano5020436] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 12/14/2022]
Abstract
Silver nanoparticles (AgNPs) have been widely used in industry due to their unique physical and chemical properties. However, AgNPs have caused environmental concerns. To understand the risks of AgNPs, Arabidopsis microarray data for AgNP, Ag⁺, cold, salt, heat and drought stresses were analyzed. Up- and down-regulated genes of more than two-fold expression change were compared, while the encoded proteins of shared and unique genes between stresses were subjected to differential enrichment analyses. AgNPs affected the fewest genes (575) in the Arabidopsis genome, followed by Ag⁺ (1010), heat (1374), drought (1435), salt (4133) and cold (6536). More genes were up-regulated than down-regulated in AgNPs and Ag⁺ (438 and 780, respectively) while cold down-regulated the most genes (4022). Responses to AgNPs were more similar to those of Ag⁺ (464 shared genes), cold (202), and salt (163) than to drought (50) or heat (30); the genes in the first four stresses were enriched with 32 PFAM domains and 44 InterPro protein classes. Moreover, 111 genes were unique in AgNPs and they were enriched in three biological functions: response to fungal infection, anion transport, and cell wall/plasma membrane related. Despite shared similarity to Ag⁺, cold and salt stresses, AgNPs are a new stressor to Arabidopsis.
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Affiliation(s)
- Eisa Kohan-Baghkheirati
- Department of Plant Biology, Southern Illinois University Carbondale, Carbondale, IL 62901, USA.
- Department of Biology, Golestan University, Gorgan 49138-15739, Iran.
| | - Jane Geisler-Lee
- Department of Plant Biology, Southern Illinois University Carbondale, Carbondale, IL 62901, USA.
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952
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Davis RM, Muller RY, Haynes KA. Can the natural diversity of quorum-sensing advance synthetic biology? Front Bioeng Biotechnol 2015; 3:30. [PMID: 25806368 PMCID: PMC4354409 DOI: 10.3389/fbioe.2015.00030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/21/2015] [Indexed: 12/12/2022] Open
Abstract
Quorum-sensing networks enable bacteria to sense and respond to chemical signals produced by neighboring bacteria. They are widespread: over 100 morphologically and genetically distinct species of eubacteria are known to use quorum sensing to control gene expression. This diversity suggests the potential to use natural protein variants to engineer parallel, input-specific, cell-cell communication pathways. However, only three distinct signaling pathways, Lux, Las, and Rhl, have been adapted for and broadly used in engineered systems. The paucity of unique quorum-sensing systems and their propensity for crosstalk limits the usefulness of our current quorum-sensing toolkit. This review discusses the need for more signaling pathways, roadblocks to using multiple pathways in parallel, and strategies for expanding the quorum-sensing toolbox for synthetic biology.
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Affiliation(s)
- René Michele Davis
- Ira A. Fulton School of Biological and Health Systems Engineering, Arizona State University , Tempe, AZ , USA ; Biological Design Graduate Program, Arizona State University , Tempe, AZ , USA
| | - Ryan Yue Muller
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, AZ , USA ; School of Life Sciences, Arizona State University , Tempe, AZ , USA
| | - Karmella Ann Haynes
- Ira A. Fulton School of Biological and Health Systems Engineering, Arizona State University , Tempe, AZ , USA
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953
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Liu JL, Peng Y, Fu YS. Efficient prediction of progesterone receptor interactome using a support vector machine model. Int J Mol Sci 2015; 16:4774-85. [PMID: 25741764 PMCID: PMC4394448 DOI: 10.3390/ijms16034774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/20/2015] [Accepted: 02/25/2015] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interaction (PPI) is essential for almost all cellular processes and identification of PPI is a crucial task for biomedical researchers. So far, most computational studies of PPI are intended for pair-wise prediction. Theoretically, predicting protein partners for a single protein is likely a simpler problem. Given enough data for a particular protein, the results can be more accurate than general PPI predictors. In the present study, we assessed the potential of using the support vector machine (SVM) model with selected features centered on a particular protein for PPI prediction. As a proof-of-concept study, we applied this method to identify the interactome of progesterone receptor (PR), a protein which is essential for coordinating female reproduction in mammals by mediating the actions of ovarian progesterone. We achieved an accuracy of 91.9%, sensitivity of 92.8% and specificity of 91.2%. Our method is generally applicable to any other proteins and therefore may be of help in guiding biomedical experiments.
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Affiliation(s)
- Ji-Long Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Ying Peng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Yong-Sheng Fu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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954
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Blumer-Schuette SE, Alahuhta M, Conway JM, Lee LL, Zurawski JV, Giannone RJ, Hettich RL, Lunin VV, Himmel ME, Kelly RM. Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose. J Biol Chem 2015; 290:10645-56. [PMID: 25720489 DOI: 10.1074/jbc.m115.641480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Indexed: 11/06/2022] Open
Abstract
A variety of catalytic and noncatalytic protein domains are deployed by select microorganisms to deconstruct lignocellulose. These extracellular proteins are used to attach to, modify, and hydrolyze the complex polysaccharides present in plant cell walls. Cellulolytic enzymes, often containing carbohydrate-binding modules, are key to this process; however, these enzymes are not solely responsible for attachment. Few mechanisms of attachment have been discovered among bacteria that do not form large polypeptide structures, called cellulosomes, to deconstruct biomass. In this study, bioinformatics and proteomics analyses identified unique, discrete, hypothetical proteins ("tāpirins," origin from Māori: to join), not directly associated with cellulases, that mediate attachment to cellulose by species in the noncellulosomal, extremely thermophilic bacterial genus Caldicellulosiruptor. Two tāpirin genes are located directly downstream of a type IV pilus operon in strongly cellulolytic members of the genus, whereas homologs are absent from the weakly cellulolytic Caldicellulosiruptor species. Based on their amino acid sequence, tāpirins are specific to these extreme thermophiles. Tāpirins are also unusual in that they share no detectable protein domain signatures with known polysaccharide-binding proteins. Adsorption isotherm and trans vivo analyses demonstrated the carbohydrate-binding module-like affinity of the tāpirins for cellulose. Crystallization of a cellulose-binding truncation from one tāpirin indicated that these proteins form a long β-helix core with a shielded hydrophobic face. Furthermore, they are structurally unique and define a new class of polysaccharide adhesins. Strongly cellulolytic Caldicellulosiruptor species employ tāpirins to complement substrate-binding proteins from the ATP-binding cassette transporters and multidomain extracellular and S-layer-associated glycoside hydrolases to process the carbohydrate content of lignocellulose.
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Affiliation(s)
- Sara E Blumer-Schuette
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Markus Alahuhta
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Jonathan M Conway
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Laura L Lee
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Jeffrey V Zurawski
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905
| | - Richard J Giannone
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Robert L Hettich
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Vladimir V Lunin
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Michael E Himmel
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Robert M Kelly
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905,
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955
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Zou D, Ma L, Yu J, Zhang Z. Biological databases for human research. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:55-63. [PMID: 25712261 PMCID: PMC4411498 DOI: 10.1016/j.gpb.2015.01.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 01/01/2023]
Abstract
The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation.
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Affiliation(s)
- Dong Zou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lina Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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956
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Harty BL, Krishnan A, Sanchez NE, Schiöth HB, Monk KR. Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish. BMC Genomics 2015; 16:62. [PMID: 25715737 PMCID: PMC4335454 DOI: 10.1186/s12864-015-1296-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/29/2015] [Indexed: 01/03/2023] Open
Abstract
Background Adhesion G protein-coupled receptors (aGPCRs) are the second largest of the five GPCR families and are essential for a wide variety of physiological processes. Zebrafish have proven to be a very effective model for studying the biological functions of aGPCRs in both developmental and adult contexts. However, aGPCR repertoires have not been defined in any fish species, nor are aGPCR expression profiles in adult tissues known. Additionally, the expression profiles of the aGPCR family have never been extensively characterized over a developmental time-course in any species. Results Here, we report that there are at least 59 aGPCRs in zebrafish that represent homologs of 24 of the 33 aGPCRs found in humans; compared to humans, zebrafish lack clear homologs of GPR110, GPR111, GPR114, GPR115, GPR116, EMR1, EMR2, EMR3, and EMR4. We find that several aGPCRs in zebrafish have multiple paralogs, in line with the teleost-specific genome duplication. Phylogenetic analysis suggests that most zebrafish aGPCRs cluster closely with their mammalian homologs, with the exception of three zebrafish-specific expansion events in Groups II, VI, and VIII. Using quantitative real-time PCR, we have defined the expression profiles of 59 zebrafish aGPCRs at 12 developmental time points and 10 adult tissues representing every major organ system. Importantly, expression profiles of zebrafish aGPCRs in adult tissues are similar to those previously reported in mouse, rat, and human, underscoring the evolutionary conservation of this family, and therefore the utility of the zebrafish for studying aGPCR biology. Conclusions Our results support the notion that zebrafish are a potentially useful model to study the biology of aGPCRs from a functional perspective. The zebrafish aGPCR repertoire, classification, and nomenclature, together with their expression profiles during development and in adult tissues, provides a crucial foundation for elucidating aGPCR functions and pursuing aGPCRs as therapeutic targets. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1296-8) contains supplementary material, which is available to authorized users.
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957
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Vogt JHM, Schippers JHM. Setting the PAS, the role of circadian PAS domain proteins during environmental adaptation in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:513. [PMID: 26217364 PMCID: PMC4496561 DOI: 10.3389/fpls.2015.00513] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The per-ARNT-sim (PAS) domain represents an ancient protein module that can be found across all kingdoms of life. The domain functions as a sensing unit for a diverse array of signals, including molecular oxygen, small metabolites, and light. In plants, several PAS domain-containing proteins form an integral part of the circadian clock and regulate responses to environmental change. Moreover, these proteins function in pathways that control development and plant stress adaptation responses. Here, we discuss the role of PAS domain-containing proteins in anticipation, and adaptation to environmental changes in plants.
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Affiliation(s)
- Julia H. M. Vogt
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jos H. M. Schippers
- Institute for Biology I, RWTH Aachen University, Aachen, Germany
- *Correspondence: Jos H. M. Schippers, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany,
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