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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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Zhang M, Li P, Yan X, Wang J, Cheng T, Zhang Q. Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume. BMC Ecol Evol 2021; 21:32. [PMID: 33622244 PMCID: PMC7901119 DOI: 10.1186/s12862-021-01762-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/08/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees. RESULTS To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume. CONCLUSIONS We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.
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Affiliation(s)
- Man Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Xiaolan Yan
- Mei Germplasm Research Center, Wuhan, 430073, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.
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Lebedeva MA, Dodueva IE, Gancheva MS, Tvorogova VE, Kuznetsova KA, Lutova LA. The Evolutionary Aspects of Flowering Control: Florigens and Anti-Florigens. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542011006x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kaur N, Chen W, Fei Z, Wintermantel WM. Differences in gene expression in whitefly associated with CYSDV-infected and virus-free melon, and comparison with expression in whiteflies fed on ToCV- and TYLCV-infected tomato. BMC Genomics 2019; 20:654. [PMID: 31416422 PMCID: PMC6694564 DOI: 10.1186/s12864-019-5999-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 07/26/2019] [Indexed: 01/31/2023] Open
Abstract
Background Cucurbit yellow stunting disorder virus (CYSDV; genus Crinivirus, Closteroviridae) is transmitted in a semipersistent manner by the whitefly, Bemisia tabaci, and is efficiently transmitted by the widely prevalent B. tabaci cryptic species, MEAM1. In this study, we compared transcriptome profiles of B. tabaci MEAM1, after 24 h, 72 h and 7 days of acquisition feeding on melon plants infected with CYSDV (CYSDV-whiteflies) with those fed on virus-free melon, using RNA-Seq technology. We also compared transcriptome profiles with whiteflies fed on tomato plants separately infected with Tomato chlorosis virus (ToCV), a crinivirus closely related to CYSDV, and Tomato yellow leaf curl virus (TYLCV), a member of the genus Begomovirus, which has a distinctly different mode of transmission and their respective virus-free controls, to find common gene expression changes among viruliferous whiteflies feeding on different host plants infected with distinct (TYLCV) and related (CYSDV and ToCV) viruses. Results A total of 275 differentially expressed genes (DEGs) were identified in CYSDV-whiteflies, with 3 DEGs at 24 h, 221 DEGs at 72 h, and 51 DEGs at 7 days of virus acquisition. Changes in genes encoding orphan genes (54 genes), phosphatidylethanolamine-binding proteins (PEBP) (20 genes), and AAA-ATPase domain containing proteins (10 genes) were associated with the 72 h time point. Several more orphan genes (20 genes) were differentially expressed at 7 days. A total of 59 common DEGs were found between CYSDV-whiteflies and ToCV-whiteflies, which included 20 orphan genes and 6 lysosomal genes. A comparison of DEGs across the three different virus-host systems revealed 14 common DEGs, among which, eight showed similar and significant up-regulation in CYSDV-whiteflies at 72 h and TYLCV-whiteflies at 24 h, while down-regulation of the same genes was observed in ToCV-whiteflies at 72 h. Conclusions Dynamic gene expression changes occurred in CYSDV-whiteflies after 72 h feeding, with decreased gene expression changes associated with 7 days of CYSDV acquisition. Similarities in gene expression changes among CYSDV-whiteflies, ToCV-whiteflies and TYLCV-whiteflies suggest the possible involvement of common genes or pathways for virus acquisition and transmission by whiteflies, even for viruses with distinctly different modes of transmission. Electronic supplementary material The online version of this article (10.1186/s12864-019-5999-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Navneet Kaur
- USDA-ARS, Crop Improvement and Protection Research, 1636 East Alisal Street, Salinas, CA, 93905, USA.,Present Address: Driscoll's Inc., 151 Silliman Rd., Watsonville, CA, 95076, USA
| | - Wenbo Chen
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA.,USDA-ARS, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, New York, 14853-2901, USA
| | - William M Wintermantel
- USDA-ARS, Crop Improvement and Protection Research, 1636 East Alisal Street, Salinas, CA, 93905, USA.
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Dong J, Han L, Wang Y, Huang J, Wu J. Transcript expression bias of phosphatidylethanolamine binding protein gene in bumblebee, Bombus lantschouensis (Hymenoptera: Apidae). Gene 2017. [PMID: 28647560 DOI: 10.1016/j.gene.2017.06.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The phosphatidylethanolamine-binding protein (PEBP) family is a highly conserved group of proteins found in a wide range of organism. It plays an important role in innate immunity of insects. Little is known on the expression characteristic and function of PEBP in bees. In the current study, we cloned the pebp gene and investigated its expression profiles at different developmental stages and reproductive status from bumblebee, Bombus lantschouensis (Vogt), which is one of the most abundant pollinators for wild plants and crops in Northern China. Two transcripts (PEBPX1 and PEBPX2) of the pebp gene were cloned for the first time. The transcript PEBPX2 lacked a signal peptide sequence compared to PEBPX1. The full-length cDNA of these two PEBP transcripts is 1005bp and 915bp, with an open reading frame of 627bp and 549bp, respectively. Transcript PEBPX2 was one order of magnitude more expressed than transcript PEBPX1 at most of the developmental stages and different reproductive status (egg-laying versus non- egg-laying females). Both of the PEBP transcripts were highly expressed in brown-eyed with light and dark pigmented cuticle pupae stages. Quantitative PCR and Western Blot demonstrated that PEBP was significantly up-regulated in egg-laying females. In summary, we suggest that levels of these two PEBPs could be related to the regulation of reproduction in bumblebees. In addition, both transcripts likely play an important role in the metamorphosis developmental stage of bumblebee pupae.
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Affiliation(s)
- Jie Dong
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Lei Han
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Ye Wang
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Jiaxing Huang
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China.
| | - Jie Wu
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China.
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Chen W, Hasegawa DK, Kaur N, Kliot A, Pinheiro PV, Luan J, Stensmyr MC, Zheng Y, Liu W, Sun H, Xu Y, Luo Y, Kruse A, Yang X, Kontsedalov S, Lebedev G, Fisher TW, Nelson DR, Hunter WB, Brown JK, Jander G, Cilia M, Douglas AE, Ghanim M, Simmons AM, Wintermantel WM, Ling KS, Fei Z. The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. BMC Biol 2016; 14:110. [PMID: 27974049 PMCID: PMC5157087 DOI: 10.1186/s12915-016-0321-y] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/28/2016] [Indexed: 12/04/2022] Open
Abstract
Background The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop losses and poses a serious threat to global food security. Results We report the 615-Mb high-quality genome sequence of B. tabaci Middle East-Asia Minor 1 (MEAM1), the first genome sequence in the Aleyrodidae family, which contains 15,664 protein-coding genes. The B. tabaci genome is highly divergent from other sequenced hemipteran genomes, sharing no detectable synteny. A number of known detoxification gene families, including cytochrome P450s and UDP-glucuronosyltransferases, are significantly expanded in B. tabaci. Other expanded gene families, including cathepsins, large clusters of tandemly duplicated B. tabaci-specific genes, and phosphatidylethanolamine-binding proteins (PEBPs), were found to be associated with virus acquisition and transmission and/or insecticide resistance, likely contributing to the global invasiveness and efficient virus transmission capacity of B. tabaci. The presence of 142 horizontally transferred genes from bacteria or fungi in the B. tabaci genome, including genes encoding hopanoid/sterol synthesis and xenobiotic detoxification enzymes that are not present in other insects, offers novel insights into the unique biological adaptations of this insect such as polyphagy and insecticide resistance. Interestingly, two adjacent bacterial pantothenate biosynthesis genes, panB and panC, have been co-transferred into B. tabaci and fused into a single gene that has acquired introns during its evolution. Conclusions The B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0321-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenbo Chen
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel K Hasegawa
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,US Department of Agriculture-Agricultural Research Service, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Navneet Kaur
- US Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research, Salinas, CA, 93905, USA
| | - Adi Kliot
- Department of Entomology, The Volcani Center, Bet Dagan, 50250, Israel
| | - Patricia Valle Pinheiro
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,EMBRAPA Rice and Beans, Santo Antônio de Goiás, GO, 75375-000, Brazil.,Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Junbo Luan
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Wenli Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Yimin Xu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Yuan Luo
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Angela Kruse
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Xiaowei Yang
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Galina Lebedev
- Department of Entomology, The Volcani Center, Bet Dagan, 50250, Israel
| | - Tonja W Fisher
- Department of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Wayne B Hunter
- US Department of Agriculture-Agricultural Research Service, US Horticultural Laboratory, Fort Pierce, FL, 34945, USA
| | - Judith K Brown
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Michelle Cilia
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,Department of Biology, Lund University, Lund, SE-223 62, Sweden.,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Murad Ghanim
- Department of Entomology, The Volcani Center, Bet Dagan, 50250, Israel
| | - Alvin M Simmons
- US Department of Agriculture-Agricultural Research Service, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - William M Wintermantel
- US Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research, Salinas, CA, 93905, USA.
| | - Kai-Shu Ling
- US Department of Agriculture-Agricultural Research Service, US Vegetable Laboratory, Charleston, SC, 29414, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. .,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
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Bonizzoni M, Ochomo E, Dunn WA, Britton M, Afrane Y, Zhou G, Hartsel J, Lee MC, Xu J, Githeko A, Fass J, Yan G. RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs. Parasit Vectors 2015; 8:474. [PMID: 26381877 PMCID: PMC4574070 DOI: 10.1186/s13071-015-1083-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/10/2015] [Indexed: 11/30/2022] Open
Abstract
Background The extensive use of pyrethroids for control of malaria vectors, driven by their cost, efficacy and safety, has led to widespread resistance. To favor their sustainable use, the World Health Organization (WHO) formulated an insecticide resistance management plan, which includes the identification of the mechanisms of resistance and resistance surveillance. Recognized physiological mechanisms of resistance include target site mutations in the para voltage-gated sodium channel, metabolic detoxification and penetration resistance. Such understanding of resistance mechanisms has allowed the development of resistance monitoring tools, including genotyping of the kdr mutation L1014F/S in the para gene. Methods The sequence-based technique RNA-seq was applied to study changes in the transcriptome of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from the Western Province of Kenya. The resulting gene expression profiles were compared to data in the most recent literature to derive a list of candidate resistance genes. RNA-seq data were analyzed also to identify sequence polymorphisms linked to resistance. Results A total of five candidate-resistance genes (AGAP04177, AGAP004572, AGAP008840, AGAP007530 and AGAP013036) were identified with altered expression between resistant and susceptible mosquitoes from West and East Africa. A change from G to C at position 36043997 of chromosome 3R resulting in A101G of the sulfotransferase gene AGAP009551 was significantly associated with the resistance phenotype (odds ratio: 5.10). The kdr L1014S mutation was detected at similar frequencies in both phenotypically resistant and susceptible mosquitoes, suggesting it is no longer fully predictive of the resistant phenotype. Conclusions Overall, these results support the conclusion that resistance to pyrethroids is a complex and evolving phenotype, dependent on multiple gene functions including, but not limited to, metabolic detoxification. Functional convergence among metabolic detoxification genes may exist, with the role of each gene being modulated by the life history and selection pressure on mosquito populations. As a consequence, biochemical assays that quantify overall enzyme activity may be a more suitable method for predicting metabolic resistance than gene-based assays. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-1083-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mariangela Bonizzoni
- Program in Public Health, University of California, Irvine, CA, USA. .,Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| | - Eric Ochomo
- Centre for Global health Research, Kenya Medical Research Institute, Kisumu, Kenya.
| | | | - Monica Britton
- Bioinformatics Core of the UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
| | - Yaw Afrane
- School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya.
| | - Guofa Zhou
- Program in Public Health, University of California, Irvine, CA, USA.
| | | | - Ming-Chieh Lee
- Program in Public Health, University of California, Irvine, CA, USA.
| | - Jiabao Xu
- Program in Public Health, University of California, Irvine, CA, USA.
| | - Andrew Githeko
- Centre for Global health Research, Kenya Medical Research Institute, Kisumu, Kenya.
| | - Joseph Fass
- Bioinformatics Core of the UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, CA, USA.
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He K, Xiao W, Lv W. Comprehensive identification of essential pathways and transcription factors related to epilepsy by gene set enrichment analysis on microarray datasets. Int J Mol Med 2014; 34:715-24. [PMID: 25016997 PMCID: PMC4121356 DOI: 10.3892/ijmm.2014.1843] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/30/2014] [Indexed: 11/06/2022] Open
Abstract
Epilepsy is a common chronic neurological disorder characterized by seizures or convulsions, and is known to affect patients with primary brain tumors. The etiology of epilepsy is superficially thought to be multifactorial; however, the genetic factors which may be involved in the pathogenesis of seizures have not yet been elucidated, particularly at the pathway level. In the present study, in order to systematically investigate the gene regulatory networks involved in epilepsy, we employed a microarray dataset from the public database library of Gene Expression Omnibus (GEO) associated with tumor-induced epileptogenesis and applied gene set enrichment analysis (GSEA) on these data sets and performed candidate transcription factor (TF) selection. As a result, 68 upregulated pathways, including the extracellular matrix (ECM)-receptor interaction (P=0.004) and peroxisome proliferator-activated receptor (PPAR) signaling pathways (P=0.045), as well as 4 downregulated pathways, including the GnRH signaling pathway (P=0.029) and gap junction (P=0.034) were identified as epileptogenesis-related pathways. The majority of these pathways identified have been previously reported and our results were in accordance with those reports. However, some of these pathways identified were novel. Finally, co-expression networks of the related pathways were constructed with the significant core genes and TFs, such as PPAR-γ and phosphatidylethanolamine-binding protein. The results of our study may contribute to the improved understanding of the molecular mechanisms of epileptogenesis on a genome-wide level.
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Affiliation(s)
- Kan He
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui 230601, P.R. China
| | - Weizhong Xiao
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Pudong, Shanghai 201399, P.R. China
| | - Wenwen Lv
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui 230601, P.R. China
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Benning UF, Tamot B, Guelette BS, Hoffmann-Benning S. New aspects of Phloem-mediated long-distance lipid signaling in plants. FRONTIERS IN PLANT SCIENCE 2012; 3:53. [PMID: 22639651 PMCID: PMC3355628 DOI: 10.3389/fpls.2012.00053] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/29/2012] [Indexed: 05/08/2023]
Abstract
Plants are sessile and cannot move to appropriate hiding places or feeding grounds to escape adverse conditions. As a consequence, they evolved mechanisms to detect changes in their environment, communicate these to different organs, and adjust development accordingly. These adaptations include two long-distance transport systems which are essential in plants: the xylem and the phloem. The phloem serves as a major trafficking pathway for assimilates, viruses, RNA, plant hormones, metabolites, and proteins with functions ranging from synthesis to metabolism to signaling. The study of signaling compounds within the phloem is essential for our understanding of plant communication of environmental cues. Determining the nature of signals and the mechanisms by which they are communicated through the phloem will lead to a more complete understanding of plant development and plant responses to stress. In our analysis of Arabidopsis phloem exudates, we had identified several lipid-binding proteins as well as fatty acids and lipids. The latter are not typically expected in the aqueous environment of sieve elements. Hence, lipid transport in the phloem has been given little attention until now. Long-distance transport of hydrophobic compounds in an aqueous system is not without precedence in biological systems: a variety of lipids is found in human blood and is often bound to proteins. Some lipid-protein complexes are transported to other tissues for storage, use, modification, or degradation; others serve as messengers and modulate transcription factor activity. By simple analogy it raises the possibility that lipids and the respective lipid-binding proteins in the phloem serve similar functions in plants and play an important role in stress and developmental signaling. Here, we introduce the lipid-binding proteins and the lipids we found in the phloem and discuss the possibility that they may play an important role in developmental and stress signaling.
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Affiliation(s)
- Urs Florian Benning
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Banita Tamot
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Brandon Scott Guelette
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Susanne Hoffmann-Benning
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
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10
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Mutti NS, Dolezal AG, Wolschin F, Mutti JS, Gill KS, Amdam GV. IRS and TOR nutrient-signaling pathways act via juvenile hormone to influence honey bee caste fate. J Exp Biol 2011; 214:3977-84. [PMID: 22071189 PMCID: PMC3212421 DOI: 10.1242/jeb.061499] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2011] [Indexed: 11/20/2022]
Abstract
Regardless of genetic makeup, a female honey bee becomes a queen or worker depending on the food she receives as a larva. For decades, it has been known that nutrition and juvenile hormone (JH) signaling determine the caste fate of the individual bee. However, it is still largely unclear how these factors are connected. To address this question, we suppressed nutrient sensing by RNA interference (RNAi)-mediated gene knockdown of IRS (insulin receptor substrate) and TOR (target of rapamycin) in larvae reared on queen diet. The treatments affected several layers of organismal organization that could play a role in the response to differential nutrition between castes. These include transcript profiles, proteomic patterns, lipid levels, DNA methylation response and morphological features. Most importantly, gene knockdown abolished a JH peak that signals queen development and resulted in a worker phenotype. Application of JH rescued the queen phenotype in either knockdown, which demonstrates that the larval response to JH remains intact and can drive normal developmental plasticity even when IRS or TOR transcript levels are reduced. We discuss our results in the context of other recent findings on honey bee caste and development and propose that IRS is an alternative substrate for the Egfr (epidermal growth factor receptor) in honey bees. Overall, our study describes how the interplay of nutritional and hormonal signals affects many levels of organismal organization to build different phenotypes from identical genotypes.
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Affiliation(s)
- Navdeep S. Mutti
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Adam G. Dolezal
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Florian Wolschin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Jasdeep S. Mutti
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Kulvinder S. Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Gro V. Amdam
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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11
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Rautureau GJP, Vovelle F, Schoentgen F, Decoville M, Locker D, Damblon C, Jouvensal L. NMR structure of a phosphatidyl-ethanolamine binding protein fromDrosophila. Proteins 2010; 78:1606-10. [DOI: 10.1002/prot.22682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Minami M, Kureha O, Mori M, Kamitsuji H, Suzuki K, Irie T. Long serial analysis of gene expression for transcriptome profiling during the initiation of ligninolytic enzymes production in Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2007; 75:609-18. [PMID: 17308906 DOI: 10.1007/s00253-007-0850-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 01/18/2007] [Accepted: 01/21/2007] [Indexed: 11/29/2022]
Abstract
To analyze the transcriptome profile during the initiation of manganese peroxidase (MnP) and lignin peroxidase (LiP) production in Phanerochaete chrysosporium, we constructed long serial analysis of gene expression (LongSAGE) libraries. A total of 13,666 tags (the number of cumulative counted tags) that included 6,945 unique tags (the number of distinct tags) were isolated from the day-3 culture, which just started the enzymes production and was 24 h after veratryl alcohol addition and oxygen-purge into the culture (day-2 culture). A total of 12,402 tags that included 6,396 unique tags were isolated from the day-2 culture, in which the activity of enzymes is not detected. The comparison of the two libraries suggested that 38 genes showed significant (p < or = 0.01) fourfold or greater upregulation; this included the MnP gene (mnp2, mnp3) and LiP H8 gene. On the other hand, 43 genes showed significant (p < or = 0.01) fourfold or greater downregulation. This LongSAGE analysis found many new candidate genes regulating the enzymes production.
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Affiliation(s)
- Masahiko Minami
- Department of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
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13
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Pucci-Minafra I, Cancemi P, Fontana S, Minafra L, Feo S, Becchi M, Freyria AM, Minafra S. Expanding the protein catalogue in the proteome reference map of human breast cancer cells. Proteomics 2006; 6:2609-25. [PMID: 16526084 DOI: 10.1002/pmic.200500627] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this report we present a catalogue of 162 proteins (including isoforms and variants) identified in a prototype of proteomic map of breast cancer cells. This work represents the prosecution of previous studies describing the protein complement of breast cancer cells of the line 8701-BC, which has been well characterized for several parameters, providing to be a useful model for the study of breast cancer-associated candidate biomarkers. In particular, 110 spots were identified ex novo by PMF, or validated following previous gel matching identification method; 30 were identified by N-terminal microsequencing and the remaining by gel matching with maps available from our former work. As a consequence of the expanded number of proteins, we have updated our previous classification extending the number of protein groups from 4 to 13. In order to facilitate comparative proteome studies of different kinds of breast cancers, in this report we provide the whole complement of proteins so far identified and grouped into the new classification. A consistent number of them were not described before in other proteomic maps of breast cancer cells or tissues, and therefore they represent a valuable contribution for breast cancer protein databases and for future application in basic and clinical researches.
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Affiliation(s)
- Ida Pucci-Minafra
- Dipartimento di Oncologia Sperimentale ed Applicazioni Cliniche (DOSAC), Via San Lorenzo Colli, Palermo, Italy.
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14
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Rautureau G, Jouvensal L, Decoville M, Locker D, Vovelle F, Schoentgen F. Cloning, high yield over-expression, purification, and characterization of CG18594, a new PEBP/RKIP family member from Drosophila melanogaster. Protein Expr Purif 2006; 48:90-7. [PMID: 16529946 DOI: 10.1016/j.pep.2006.01.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Revised: 01/18/2006] [Accepted: 01/27/2006] [Indexed: 11/22/2022]
Abstract
The phosphatidylethanolamine-binding protein (PEBP) family is widely distributed in various species, from bacteria to mammals. These proteins seem to modulate important cell mechanisms: they control heterotrimeric G-proteins, inhibit the MAP-kinase and NFkappaB signaling pathways, and also serine proteases (thrombin, neuropsin, and chymotrypsin). In order to establish structure-function relationships for this family of proteins, our study focuses on PEBPs expressed within a single organism: Drosophila melanogaster, which constitutes a model system that lends itself well to establishing links between genes' expression and the corresponding proteins' functions, and to studying physiological mechanisms such as development. Here, we describe an optimized protocol for high level over-expression and high yield/high purity production of CG18594, one of Drosophila six putative PEBPs, for biophysical studies. The yield of the purified 15N labeled protein is estimated to be 60 mg/L of M9 minimal medium. Analysis of the secondary structure using circular dichroism indicates that the protein comprises mainly beta-sheets at pH 7. The good dispersion of the crosspeaks on the 1H-15N HSQC spectrum provides evidence of a proper folding of the purified protein, though its time evolution suggests a tendency to denature. Taken together, these data are consistent with the assumption that the CG18594 protein belongs to the PEPB family.
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Affiliation(s)
- Gilles Rautureau
- Centre de Biophysique Moléculaire, UPR 4301 CNRS affiliated to Orléans University and to INSERM, Rue Charles Sadron, 45071 Orléans cedex 2, France
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