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Tsujimoto H, Metz HC, Smith AA, Sakamoto JM, Pal U, Rasgon JL. Function and evolution of the aquaporin IsAQP1 in the Lyme disease vector Ixodes scapularis. INSECT MOLECULAR BIOLOGY 2023. [PMID: 36680546 DOI: 10.1111/imb.12833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Ticks are important vectors of pathogenic viruses, bacteria, and protozoans to humans, wildlife, and domestic animals. Due to their life cycles, ticks face significant challenges related to water homeostasis. When blood-feeding, they must excrete water and ions, but when off-host (for stretches lasting several months), they must conserve water to avoid desiccation. Aquaporins (AQPs), a family of membrane-bound water channels, are key players in osmoregulation in many animals but remain poorly characterized in ticks. Here, we bioinformatically identified AQP-like genes from the deer tick Ixodes scapularis and used phylogenetic approaches to map the evolution of the aquaporin gene family in arthropods. Most arachnid AQP-like sequences (including those of I. scapularis) formed a monophyletic group clustered within aquaglycerolporins (GLPs) from bacteria to vertebrates. This gene family is absent from insects, revealing divergent evolutionary paths for AQPs in different hematophagous arthropods. Next, we sequenced the full-length cDNA of I. scapularis aquaporin 1 (IsAQP1) and expressed it heterologously in Xenopus oocytes to functionally characterize its permeability to water and solutes. Additionally, we examined IsAQP1 expression across different life stages and adult female organs. We found IsAQP1 is an efficient water channel with high expression in salivary glands prior to feeding, suggesting it plays a role in osmoregulation before or during blood feeding. Its functional properties are unique: unlike most GLPs, IsAQP1 has low glycerol permeability, and unlike most AQPs, it is insensitive to mercury. Together, our results suggest IsAQP1 plays an important role in tick water balance physiology and that it may hold promise as a target of novel vector control efforts.
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Affiliation(s)
- Hitoshi Tsujimoto
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Hillery C Metz
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Alexis A Smith
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Joyce M Sakamoto
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Jason L Rasgon
- Department of Entomology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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2
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Xu Y, Li H, Xu D, Li J, Yu F, Wang M, Wang Q, Wu Y, Zhang Q, Tang Y, Yu J. Identification, expression and enzyme activity of the group III sPLA 2 s in Cyprinus carpio L. JOURNAL OF FISH BIOLOGY 2021; 99:25-36. [PMID: 33534139 DOI: 10.1111/jfb.14694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Five group III secreted phospholipase (pla2g3s) homologous genes located on different linkage groups were identified from common carp (Cyprinus carpio), which we named Ccpla2g3a1, Ccpla2g3a2, Ccpla2g3b, Ccpla2g3c1 and Ccpla2g3c2. The five genes encode 530, 525, 461, 752 and 753 amino acids, respectively. Sequence analysis showed that the Ccpla2g3as contain seven exons and the others contain four exons. Synteny analysis of fish pla2g3s indicated that pla2g3a and pla2g3b were from the same ancestor gene, and Ccpla2g3a1, Ccpla2g3a2, Ccpla2g3c1 and Ccpla2g3c2 were from the specific genome duplication of common carp. Due to the significant variation of the pla2g3bs from common carp and zebrafish (Danio rerio), they formed a separate group in the phylogenetic tree. The tissue distributions of Ccpla2g3s coincided with their expression profiles during the embryo stages. The expression levels of Ccpla2g3as and Ccpla2g3cs were low at the embryo stages, and they were abundant in the liver and brain, respectively, whereas the expression of Ccpla2g3b was high at 0.5 h after fertilization and in the ovary. We obtained three soluble recombinant proteins of the bee venom-like PLA2 (BVLP) from Ccpla2g3 and evaluated their PLA2 enzyme properties. The optimum pHs of MBP-a1-BVLP, MBP-b-BVLP and MBP-c1-BVLP were 7.5, 7.0 and 8.0, respectively, and specific activities were 7.68 ± 0.66, 4.155 ± 0.158 and 1.93 ± 0.05 U μmol-1 , respectively. The Kd for Ca2+ of MBP-b-BVLP was the lowest (2.6 μM), whereas the values for both MBP-a1-BVLP and MBP-c1-BVLP were about 15 μM. The Km values of three proteins ranged from 31.9 to 41.91 μM.
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Affiliation(s)
- Yuxin Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Hongxia Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Dihui Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jianlin Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Fan Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Meiyao Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Qin Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yunsheng Wu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Qiyuan Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Juhua Yu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
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3
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Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. MOLECULAR PLANT 2020; 13:1194-1202. [PMID: 32585190 DOI: 10.1016/j.molp.2020.06.009] [Citation(s) in RCA: 5671] [Impact Index Per Article: 1417.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/04/2020] [Accepted: 06/10/2020] [Indexed: 05/18/2023]
Abstract
The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
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Affiliation(s)
- Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Hao Chen
- Oilseed Crops Institute, Hunan Agricultural University, Changsha 410128, China
| | - Yi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Hannah R Thomas
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Margaret H Frank
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Yehua He
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou, Guangdong 510640, China; College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510640, China.
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4
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Sun Y, Liu C, Huang M, Huang J, Liu C, Zhang J, Postlethwait JH, Wang H. The Molecular Evolution of Circadian Clock Genes in Spotted Gar ( Lepisosteus oculatus). Genes (Basel) 2019; 10:genes10080622. [PMID: 31426485 PMCID: PMC6723592 DOI: 10.3390/genes10080622] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022] Open
Abstract
Circadian rhythms are biological rhythms with a period of approximately 24 h. While canonical circadian clock genes and their regulatory mechanisms appear highly conserved, the evolution of clock gene families is still unclear due to several rounds of whole genome duplication in vertebrates. The spotted gar (Lepisosteus oculatus), as a non-teleost ray-finned fish, represents a fish lineage that diverged before the teleost genome duplication (TGD), providing an outgroup for exploring the evolutionary mechanisms of circadian clocks after whole-genome duplication. In this study, we interrogated the spotted gar draft genome sequences and found that spotted gar contains 26 circadian clock genes from 11 families. Phylogenetic analysis showed that 9 of these 11 spotted gar circadian clock gene families have the same number of genes as humans, while the members of the nfil3 and cry families are different between spotted gar and humans. Using phylogenetic and syntenic analyses, we found that nfil3-1 is conserved in vertebrates, while nfil3-2 and nfil3-3 are maintained in spotted gar, teleost fish, amphibians, and reptiles, but not in mammals. Following the two-round vertebrate genome duplication (VGD), spotted gar retained cry1a, cry1b, and cry2, and cry3 is retained in spotted gar, teleost fish, turtles, and birds, but not in mammals. We hypothesize that duplication of core clock genes, such as (nfil3 and cry), likely facilitated diversification of circadian regulatory mechanisms in teleost fish. We also found that the transcription factor binding element (Ahr::Arnt) is retained only in one of the per1 or per2 duplicated paralogs derived from the TGD in the teleost fish, implicating possible subfuctionalization cases. Together, these findings help decipher the repertoires of the spotted gar’s circadian system and shed light on how the vertebrate circadian clock systems have evolved.
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Affiliation(s)
- Yi Sun
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China.
| | - Chao Liu
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
| | - Moli Huang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Jian Huang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Changhong Liu
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
| | - Jiguang Zhang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
| | | | - Han Wang
- School of Biology & Basic Medical Sciences, Medical College of Soochow University, Suzhou 215123, China.
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China.
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5
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Ren J, Chung-Davidson YW, Jia L, Li W. Genomic sequence analyses of classical and non-classical lamprey progesterone receptor genes and the inference of homologous gene evolution in metazoans. BMC Evol Biol 2019; 19:136. [PMID: 31262250 PMCID: PMC6604198 DOI: 10.1186/s12862-019-1463-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 06/18/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Nuclear progesterone receptor (nPR) is an evolutionary innovation in vertebrates that mediates genomic responses to progesterone. Vertebrates also respond to progesterone via membrane progesterone receptors (mPRs) or membrane associated progesterone receptors (MAPRs) through rapid nongenomic mechanisms. Lampreys are extant agnathan vertebrates, residing at the evolutionary juncture where vertebrates diverged from invertebrates. A survey of the progesterone receptor (PR) gene sequences in lamprey genomes would inform PR gene evolutionary events during the transition from invertebrates to vertebrates. RESULTS In this study, we annotated sequences of one nPR, four mPR (β, γ, δ and ε) and four MAPR genes from genomes of two lamprey species (Petromyzon marinus and Lethenteron japonicum). To infer the origin and evolutionary history of PR genes, we constructed phylogenetic trees of PR homologous sequences across representative species of metazoans. Phylogenetic analyses revealed that the mPRγ gene first appeared in non-bilaterians, and the mPRβ gene likely arose from a duplication of mPRγ. On the other hand, the mPRγ gene gave rise to the mPRδ and ε genes much later in the vertebrate lineage. In addition, the mPRα gene first appeared in cartilaginous fishes, likely derived from duplication of mPRβ after the agnathan-gnathostome divergence. All known MAPR genes were present in the lamprey genomes. Progesterone receptor membrane component 1 (PGRMC1), neudesin and neuferricin genes probably evolved in parallel in non-bilaterians, whereas two copies of PGRMC genes probably derived from duplication of ancestral PGRMC1 sequence and appeared before the speciation of lampreys. CONCLUSIONS Non-classical mPR and MAPR genes first evolved in non-bilaterians and classical nPR genes evolved later in basal vertebrates. Sequence repertoires for membrane progesterone receptor genes in vertebrates likely originated from an ancestral metazoan sequence and expanded via several duplication events.
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Affiliation(s)
- Jianfeng Ren
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Liang Jia
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA.
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6
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Wolfstetter G, Dahlitz I, Pfeifer K, Töpfer U, Alt JA, Pfeifer DC, Lakes-Harlan R, Baumgartner S, Palmer RH, Holz A. Characterization of Drosophila Nidogen/ entactin reveals roles in basement membrane stability, barrier function and nervous system patterning. Development 2019; 146:dev.168948. [PMID: 30567930 DOI: 10.1242/dev.168948] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022]
Abstract
Basement membranes (BMs) are specialized layers of extracellular matrix (ECM) mainly composed of Laminin, type IV Collagen, Perlecan and Nidogen/entactin (NDG). Recent in vivo studies challenged the initially proposed role of NDG as a major ECM linker molecule by revealing dispensability for viability and BM formation. Here, we report the characterization of the single Ndg gene in Drosophila. Embryonic Ndg expression was primarily observed in mesodermal tissues and the chordotonal organs, whereas NDG protein localized to all BMs. Although loss of Laminin strongly affected BM localization of NDG, Ndg-null mutants exhibited no overt changes in the distribution of BM components. Although Drosophila Ndg mutants were viable, loss of NDG led to ultrastructural BM defects that compromised barrier function and stability in vivo Moreover, loss of NDG impaired larval crawling behavior and reduced responses to vibrational stimuli. Further morphological analysis revealed accompanying defects in the larval peripheral nervous system, especially in the chordotonal organs and the neuromuscular junction (NMJ). Taken together, our analysis suggests that NDG is not essential for BM assembly but mediates BM stability and ECM-dependent neural plasticity during Drosophila development.
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Affiliation(s)
- Georg Wolfstetter
- Justus-Liebig-Universitaet Giessen, Institut für Allgemeine und Spezielle Zoologie, Allgemeine Zoologie und Entwicklungsbiologie, Stephanstraße 24, 35390 Gießen, Germany.,The Sahlgrenska Academy at the University of Gothenburg, Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Medicinaregatan 9A, 41390 Gothenburg, Sweden
| | - Ina Dahlitz
- Justus-Liebig-Universitaet Giessen, Institut für Allgemeine und Spezielle Zoologie, Allgemeine Zoologie und Entwicklungsbiologie, Stephanstraße 24, 35390 Gießen, Germany
| | - Kathrin Pfeifer
- The Sahlgrenska Academy at the University of Gothenburg, Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Medicinaregatan 9A, 41390 Gothenburg, Sweden
| | - Uwe Töpfer
- Justus-Liebig-Universitaet Giessen, Institut für Allgemeine und Spezielle Zoologie, Allgemeine Zoologie und Entwicklungsbiologie, Stephanstraße 24, 35390 Gießen, Germany
| | - Joscha Arne Alt
- Justus-Liebig-Universitaet Giessen, Institut für Tierphysiologie, Integrative Sinnesphysiologie, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
| | - Daniel Christoph Pfeifer
- Justus-Liebig-Universitaet Giessen, Institut für Allgemeine und Spezielle Zoologie, Allgemeine Zoologie und Entwicklungsbiologie, Stephanstraße 24, 35390 Gießen, Germany
| | - Reinhard Lakes-Harlan
- Justus-Liebig-Universitaet Giessen, Institut für Tierphysiologie, Integrative Sinnesphysiologie, Heinrich-Buff-Ring 26, 35392 Gießen, Germany
| | - Stefan Baumgartner
- Lund University, Department of Experimental Medical Sciences, BMC D10, 22184 Lund, Sweden
| | - Ruth H Palmer
- The Sahlgrenska Academy at the University of Gothenburg, Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Medicinaregatan 9A, 41390 Gothenburg, Sweden
| | - Anne Holz
- Justus-Liebig-Universitaet Giessen, Institut für Allgemeine und Spezielle Zoologie, Allgemeine Zoologie und Entwicklungsbiologie, Stephanstraße 24, 35390 Gießen, Germany
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7
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Zuo W, Li C, Luan Y, Zhang H, Tong X, Han M, Gao R, Hu H, Song J, Dai F, Lu C. Genome-wide identification and analysis of elongase of very long chain fatty acid genes in the silkworm, Bombyx mori. Genome 2018; 61:167-176. [PMID: 29505281 DOI: 10.1139/gen-2017-0224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Very long chain fatty acids (VLCFAs), such as sphingolipids, are components of cellular lipids, which are essential for cell proliferation. Mutations in the genes that encode proteins participating in VLCFA biosynthesis may cause inherited diseases, such as macular degeneration. Elongases of very long chain fatty acid (ELOVL) are enzymes that are involved in the biosynthesis of VLCFAs. Here, a total of 13 ELOVL genes, distributed across three chromosomes, were identified in the silkworm genome; all the ELOVL members contain a distinct ELO domain and a conserved HXXHH motif. Phylogenetic reconstruction was performed to analyze the evolutionary relationships among different species and to predict gene functions. The 13 ELOVL genes were assigned to the ELOVL3/6, ELOVL1/7, and ELOVL4 clades. Microarray and semiquantitative PCR analyses indicated that these genes are differentially expressed among various tissues, in turn suggesting functional divergence in the growth and development of each tissue. Further investigation showed that the expression level of the BGIBMGA000424 gene is significantly negatively correlated with the cocoon-shell weight among different silkworm strains. Taken together, the present study is the first comprehensive analysis of ELOVL genes in silkworm, and the results may serve as a foundation for further analysis of the physiological functions of ELOVL genes in silkworm.
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Affiliation(s)
- Weidong Zuo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Chunlin Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Yue Luan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Hao Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Minjin Han
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Rui Gao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiangbo Song
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Key Laboratory of Sericulture Biology and Genetic Breeding, Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
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8
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Wolfstetter G, Pfeifer K, van Dijk JR, Hugosson F, Lu X, Palmer RH. The scaffolding protein Cnk binds to the receptor tyrosine kinase Alk to promote visceral founder cell specification inDrosophila. Sci Signal 2017; 10:10/502/eaan0804. [DOI: 10.1126/scisignal.aan0804] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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Structure and function of the alternatively spliced isoforms of the ecdysone receptor gene in the Chinese mitten crab, Eriocheir sinensis. Sci Rep 2017; 7:12993. [PMID: 29021633 PMCID: PMC5636884 DOI: 10.1038/s41598-017-13474-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/26/2017] [Indexed: 11/10/2022] Open
Abstract
Alternative splicing is an essential molecular mechanism that increase the protein diversity of a species to regulate important biological processes. Ecdysone receptor (EcR), an essential nuclear receptor, is essential in the molting, growth, development, reproduction, and regeneration of crustaceans. In this study, the whole sequence of EcR gene from Eriocheir sinensis was obtained. The sequence was 45,481 bp in length with 9 exons. Moreover, four alternatively spliced EcR isoforms (Es-EcR-1, Es-EcR-2, Es-EcR-3 and Es-EcR-4) were identified. The four isoforms harbored a common A/B domain and a DNA-binding region but different D domains and ligand-binding regions. Three alternative splicing patterns (alternative 5′ splice site, exon skipping, and intron retention) were identified in the four isoforms. Functional studies indicated that the four isoforms have specific functions. Es-EcR-3 may play essential roles in regulating periodic molting. Es-EcR-2 may participate in the regulation of ovarian development. Our results indicated that Es-EcR has broad regulatory functions in molting and development and established the molecular basis for the investigation of ecdysteroid signaling related pathways in E. sinensis.
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PrLPAAT4, a Putative Lysophosphatidic Acid Acyltransferase from Paeonia rockii, Plays an Important Role in Seed Fatty Acid Biosynthesis. Molecules 2017; 22:molecules22101694. [PMID: 28994730 PMCID: PMC6151692 DOI: 10.3390/molecules22101694] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/03/2017] [Indexed: 11/16/2022] Open
Abstract
Lysophosphatidic acid acyltransferases (LPAATs) are essential for the acylation of lysophosphatidic acid (LPA) and the synthesis of phosphatidic acid (PA), a key intermediate in the synthesis of membrane phospholipids and storage lipids. Here, a putative lysophosphatidic acid acyltransferase gene, designated PrLPAAT4, was isolated from seed unsaturated fatty acid (UFA)-rich P. rockii. The complete PrLPAAT4 cDNA contained a 1116-bp open reading frame (ORF), encoding a 42.9 kDa protein with 371 amino acid residues. Bioinformatic analysis indicates that PrLPAAT4 is a plasma membrane protein belonging to acyl-CoA:1-acylglycerol-sn-3-phosphate acyltranferases (AGPAT) family. PrLPAAT4 shared high sequence similarity with its homologs from Citrus clementina, Populus trichocarpa, Manihot esculenta, and Ricinus communis. In Arabidopsis, overexpression of PrLPAAT4 resulted in a significant increase in the content of oleic acid (OA) and total fatty acids (FAs) in seeds. AtDGAT1, AtGPAT9, and AtOleosin, involved in TAG assembly, were upregulated in PrLPAAT4-overexpressing lines. These results indicated that PrLPAAT4 functions may be as a positive regulator in seed FA biosynthesis.
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11
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Nepal MP, Andersen EJ, Neupane S, Benson BV. Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. Genes (Basel) 2017; 8:E249. [PMID: 28973974 PMCID: PMC5664099 DOI: 10.3390/genes8100249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.
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Affiliation(s)
- Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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12
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Daudu D, Allion E, Liesecke F, Papon N, Courdavault V, Dugé de Bernonville T, Mélin C, Oudin A, Clastre M, Lanoue A, Courtois M, Pichon O, Giron D, Carpin S, Giglioli-Guivarc’h N, Crèche J, Besseau S, Glévarec G. CHASE-Containing Histidine Kinase Receptors in Apple Tree: From a Common Receptor Structure to Divergent Cytokinin Binding Properties and Specific Functions. FRONTIERS IN PLANT SCIENCE 2017; 8:1614. [PMID: 28979279 PMCID: PMC5611679 DOI: 10.3389/fpls.2017.01614] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/04/2017] [Indexed: 05/07/2023]
Abstract
Cytokinin signaling is a key regulatory pathway of many aspects in plant development and environmental stresses. Herein, we initiated the identification and functional characterization of the five CHASE-containing histidine kinases (CHK) in the economically important Malus domestica species. These cytokinin receptors named MdCHK2, MdCHK3a/MdCHK3b, and MdCHK4a/MdCHK4b by homology with Arabidopsis AHK clearly displayed three distinct profiles. The three groups exhibited architectural variations, especially in the N-terminal part including the cytokinin sensing domain. Using a yeast complementation assay, we showed that MdCHK2 perceives a broad spectrum of cytokinins with a substantial sensitivity whereas both MdCHK4 homologs exhibit a narrow spectrum. Both MdCHK3 homologs perceived some cytokinins but surprisingly they exhibited a basal constitutive activity. Interaction studies revealed that MdCHK2, MdCHK4a, and MdCHK4b homodimerized whereas MdCHK3a and MdCHK3b did not. Finally, qPCR analysis and bioinformatics approach pointed out contrasted expression patterns among the three MdCHK groups as well as distinct sets of co-expressed genes. Our study characterized for the first time the five cytokinin receptors in apple tree and provided a framework for their further functional studies.
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Affiliation(s)
- Dimitri Daudu
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Elsa Allion
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Franziska Liesecke
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Nicolas Papon
- EA 3142 Groupe d’Etude des Interactions Hôte-Pathogène, Université AngersAngers, France
| | - Vincent Courdavault
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | | | - Céline Mélin
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Audrey Oudin
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Marc Clastre
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Arnaud Lanoue
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Martine Courtois
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Olivier Pichon
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - David Giron
- UMR 7261 Institut de Recherche sur la Biologie de l’Insecte, Centre National de la Recherche Scientifique (CNRS), Université François-RabelaisTours, France
| | - Sabine Carpin
- EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’OrléansOrléans, France
| | | | - Joël Crèche
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Sébastien Besseau
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
| | - Gaëlle Glévarec
- EA 2106 Biomolécules et Biotechnologies Végétales, Université François-RabelaisTours, France
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13
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Evolutionarily Conserved Alternative Splicing Across Monocots. Genetics 2017; 207:465-480. [PMID: 28839042 DOI: 10.1534/genetics.117.300189] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splice-factor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.
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Terracciano I, Cantarella C, Fasano C, Cardi T, Mennella G, D'Agostino N. Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway. Sci Rep 2017; 7:5616. [PMID: 28717173 PMCID: PMC5514110 DOI: 10.1038/s41598-017-06120-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
Tomato (Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent’s SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis- and trans-lycopene. We targeted 230 kb of genomic regions including all exons and regulatory regions and observed ~40% of on-target capture. We found ample genetic variation among all the genotypes under study and generated an extensive catalog of SNPs/InDels located in both genic and regulatory regions. SNPs/InDels were also classified based on genomic location and putative biological effect. With our work we contributed to the identification of allelic variations possibly underpinning a key agronomic trait in tomato. Results from this study can be exploited for the promotion of novel studies on tomato bio-fortification as well as of breeding programs related to carotenoid accumulation in fruits.
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Affiliation(s)
- Irma Terracciano
- CREA-OF, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Orticoltura e Florovivaismo, via Cavalleggeri 25, 84098, Pontecagnano Faiano (SA), Italy
| | - Concita Cantarella
- CREA-OF, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Orticoltura e Florovivaismo, via Cavalleggeri 25, 84098, Pontecagnano Faiano (SA), Italy
| | - Carlo Fasano
- CREA-OF, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Orticoltura e Florovivaismo, via Cavalleggeri 25, 84098, Pontecagnano Faiano (SA), Italy
| | - Teodoro Cardi
- CREA-OF, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Orticoltura e Florovivaismo, via Cavalleggeri 25, 84098, Pontecagnano Faiano (SA), Italy
| | - Giuseppe Mennella
- CREA-OF, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Orticoltura e Florovivaismo, via Cavalleggeri 25, 84098, Pontecagnano Faiano (SA), Italy
| | - Nunzio D'Agostino
- CREA-OF, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Orticoltura e Florovivaismo, via Cavalleggeri 25, 84098, Pontecagnano Faiano (SA), Italy.
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15
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Hall MR, Kocot KM, Baughman KW, Fernandez-Valverde SL, Gauthier MEA, Hatleberg WL, Krishnan A, McDougall C, Motti CA, Shoguchi E, Wang T, Xiang X, Zhao M, Bose U, Shinzato C, Hisata K, Fujie M, Kanda M, Cummins SF, Satoh N, Degnan SM, Degnan BM. The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest. Nature 2017; 544:231-234. [PMID: 28379940 DOI: 10.1038/nature22033] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/05/2017] [Indexed: 01/02/2023]
Abstract
The crown-of-thorns starfish (COTS, the Acanthaster planci species group) is a highly fecund predator of reef-building corals throughout the Indo-Pacific region. COTS population outbreaks cause substantial loss of coral cover, diminishing the integrity and resilience of reef ecosystems. Here we sequenced genomes of COTS from the Great Barrier Reef, Australia and Okinawa, Japan to identify gene products that underlie species-specific communication and could potentially be used in biocontrol strategies. We focused on water-borne chemical plumes released from aggregating COTS, which make the normally sedentary starfish become highly active. Peptide sequences detected in these plumes by mass spectrometry are encoded in the COTS genome and expressed in external tissues. The exoproteome released by aggregating COTS consists largely of signalling factors and hydrolytic enzymes, and includes an expanded and rapidly evolving set of starfish-specific ependymin-related proteins. These secreted proteins may be detected by members of a large family of olfactory-receptor-like G-protein-coupled receptors that are expressed externally, sometimes in a sex-specific manner. This study provides insights into COTS-specific communication that may guide the generation of peptide mimetics for use on reefs with COTS outbreaks.
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Affiliation(s)
- Michael R Hall
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, Queensland 4810, Australia
| | - Kevin M Kocot
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kenneth W Baughman
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Selene L Fernandez-Valverde
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marie E A Gauthier
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - William L Hatleberg
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Arunkumar Krishnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, Queensland 4810, Australia
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Xueyan Xiang
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Min Zhao
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Utpal Bose
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, Queensland 4810, Australia.,Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Sandie M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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16
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Thitisaksakul M, Arias MC, Dong S, Beckles DM. Overexpression of GSK3-like Kinase 5 (OsGSK5) in rice (Oryza sativa) enhances salinity tolerance in part via preferential carbon allocation to root starch. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:705-719. [PMID: 32480600 DOI: 10.1071/fp16424] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 04/01/2017] [Indexed: 05/26/2023]
Abstract
Rice (Oryza sativa L.) is very sensitive to soil salinity. To identify endogenous mechanisms that may help rice to better survive salt stress, we studied a rice GSK3-like isoform (OsGSK5), an orthologue of a Medicago GSK3 previously shown to enhance salinity tolerance in Arabidopsis by altering carbohydrate metabolism. We wanted to determine whether OsGSK5 functions similarly in rice. OsGSK5 was cloned and sequence, expression, evolutionary and functional analyses were conducted. OsGSK5 was expressed highest in rice seedling roots and was both salt and sugar starvation inducible in this tissue. A short-term salt-shock (150mM) activated OsGSK5, whereas moderate (50mM) salinity over the same period repressed the transcript. OsGSK5 response to salinity was due to an ionic effect since it was unaffected by polyethylene glycol. We engineered a rice line with 3.5-fold higher OsGSK5 transcript, which better tolerated cultivation on saline soils (EC=8 and 10dSm-2). This line produced more panicles and leaves, and a higher shoot biomass under high salt stress than the control genotypes. Whole-plant 14C-tracing and correlative analysis of OsGSK5 transcript with eco-physiological assessments pointed to the accelerated allocation of carbon to the root and its deposition as starch, as part of the tolerance mechanism.
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Affiliation(s)
- Maysaya Thitisaksakul
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Maria C Arias
- Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Unité Mixte de Recherche du Centre National de la Recherche Scientifique no. 8576, 59655 Villeneuve D'Ascq cedex, France
| | - Shaoyun Dong
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Diane M Beckles
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
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17
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Zhang QY, Niu LX, Yu R, Zhang XX, Bai ZZ, Duan K, Gao QH, Zhang YL. Cloning, Characterization, and Expression Analysis of a Gene Encoding a Putative Lysophosphatidic Acid Acyltransferase from Seeds of Paeonia rockii. Appl Biochem Biotechnol 2016; 182:721-741. [PMID: 27987185 DOI: 10.1007/s12010-016-2357-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/05/2016] [Indexed: 11/29/2022]
Abstract
Tree peony (Paeonia section Moutan DC.) is an excellent woody oil crop, and the cloning and functional analysis of genes related to fatty acid (FA) metabolism from this organism has not been reported. Lysophosphatidic acid acyltransferase (LPAAT), which converts lysophosphatidic acid (LPA) to phosphatidic acid (PA), catalyzes the addition of fatty acyl moieties to the sn-2 position of the LPA glycerol backbone in triacylglycerol (TAG) biosynthesis. This project reports a putative lysophosphatidic acid acyltransferase gene PrLPAAT1 isolated from Paeonia rockii. Our data indicated that PrLPAAT1 has 1047 nucleotides and encodes a putative 38.8 kDa protein with 348 amino acid residues. Bioinformatic analysis demonstrated that PrLPAAT1 contains two transmembrane domains (TMDs). Subcellular localization analysis confirmed that PrLPAAT1 is a plasma membrane protein. Phylogenetic analysis revealed that PrLPAAT1 shared 74.3 and 65.5% amino acid sequence identities with the LPAAT1 sequences from columbine and grape, respectively. PrLPAAT1 belongs to AGPAT family, and may have acyltransferase activity. PrLPAAT1 was ubiquitously expressed in diverse tissues, and PrLPAAT1 expression was higher in the flower and developing seed. PrLPAAT1 is probably an important component in the FA accumulation process, especially during the early stages of seed development. PrLPAAT1 overexpression using a seed-specific promoter increased total FA content and the main FA accumulation in Arabidopsis transgenic plants.
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Affiliation(s)
- Qing-Yu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li-Xin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rui Yu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiao-Xiao Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhang-Zhen Bai
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ke Duan
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, 201403, China
| | - Qing-Hua Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai, 201403, China
| | - Yan-Long Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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18
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Mirali M, Purves RW, Stonehouse R, Song R, Bett K, Vandenberg A. Genetics and Biochemistry of Zero-Tannin Lentils. PLoS One 2016; 11:e0164624. [PMID: 27788158 PMCID: PMC5082924 DOI: 10.1371/journal.pone.0164624] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022] Open
Abstract
The zero-tannin trait in lentil is controlled by a single recessive gene (tan) that results in a phenotype characterized by green stems, white flowers, and thin, transparent, or translucent seed coats. Genes that result in zero-tannin characteristics are useful for studies of seed coat pigmentation and biochemical characters because they have altered pigmentation. In this study, one of the major groups of plant pigments, phenolic compounds, was compared among zero-tannin and normal phenotypes and genotypes of lentil. Biochemical data were obtained by liquid chromatography-mass spectrometry (LC-MS). Genomic sequencing was used to identify a candidate gene for the tan locus. Phenolic compound profiling revealed that myricetin, dihydromyricetin, flavan-3-ols, and proanthocyanidins are only detected in normal lentil phenotypes and not in zero-tannin types. The molecular analysis showed that the tan gene encodes a bHLH transcription factor, homologous to the A gene in pea. The results of this study suggest that tan as a bHLH transcription factor interacts with the regulatory genes in the biochemical pathway of phenolic compounds starting from flavonoid-3',5'-hydroxylase (F3'5'H) and dihydroflavonol reductase (DFR).
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Affiliation(s)
- Mahla Mirali
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Randy W. Purves
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rob Stonehouse
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rui Song
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirstin Bett
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
| | - Albert Vandenberg
- Plant Sciences Department, University of Saskatchewan, Saskatoon, SK, Canada
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19
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Mehta S, Tsai P, Lasham A, Campbell H, Reddel R, Braithwaite A, Print C. A Study of TP53 RNA Splicing Illustrates Pitfalls of RNA-seq Methodology. Cancer Res 2016; 76:7151-7159. [PMID: 27913434 DOI: 10.1158/0008-5472.can-16-1624] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/02/2016] [Accepted: 09/27/2016] [Indexed: 11/16/2022]
Abstract
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to infer isoform abundance. In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The Cancer Genome Atlas to analyze TP53 splice variant expression. All three methods detected expression of the FL/40TP53α_T1 variant in most human tumors and cell lines. However, other less abundant variants were only detected with PCR-based methods. Using RNA-seq simulation analysis, we determined why RNA-seq is unable to detect less abundant TP53 transcripts and discuss the implications of these findings for the general interpretation of RNA-seq data. Cancer Res; 76(24); 7151-9. ©2016 AACR.
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Affiliation(s)
- Sunali Mehta
- Department of Pathology, University of Otago, Dunedin, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Peter Tsai
- Department of Molecular Medicine and Pathology, Faculty of Medicine, University of Auckland, Auckland, New Zealand.,Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Annette Lasham
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.,Department of Molecular Medicine and Pathology, Faculty of Medicine, University of Auckland, Auckland, New Zealand
| | - Hamish Campbell
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Roger Reddel
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Antony Braithwaite
- Department of Pathology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.,Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Cristin Print
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.,Department of Molecular Medicine and Pathology, Faculty of Medicine, University of Auckland, Auckland, New Zealand.,Bioinformatics Institute, University of Auckland, Auckland, New Zealand
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20
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Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Res 2016; 45:1015-1020. [PMID: 27742820 PMCID: PMC5210635 DOI: 10.1093/nar/gkw935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.
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Affiliation(s)
- Yi Wang
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Roger Thilmony
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden R6M 1Y5 MB, Canada
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA .,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
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21
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Zhang Q, Jia M, Xing Y, Qin L, Li B, Jia W. Genome-Wide Identification and Expression Analysis of MRLK Family Genes Associated with Strawberry (Fragaria vesca) Fruit Ripening and Abiotic Stress Responses. PLoS One 2016; 11:e0163647. [PMID: 27685863 PMCID: PMC5042409 DOI: 10.1371/journal.pone.0163647] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/12/2016] [Indexed: 11/19/2022] Open
Abstract
Malectin-like domain-containing receptor-like kinases (MRLK) constitute a large and divergent family of proteins in plants; however, little is known about the role of MRLKs in fruit growth and development. In this study, we characterized MRLK family genes in diploid strawberry, Fragaria vesca. Based on an analysis of malectin-like domain and a search in the strawberry genome and NCBI database, we identified 62 FvMRLKs in the strawberry genome, and classified these genes into six subfamilies with distinct malectin domains in the extracellular regions of the encoded proteins. Gene expression analysis indicated that more than 80% of the FvMRLKs were expressed in various tissues, with higher levels in roots than in other organs. Thirty-three FvMRLKs were found to be expressed in fruits during the early stages of development, and over 60% of these exhibited dramatic decreases in expression during fruit growth and development. Moreover, the expression of some FvMRLKs was sensitive to both environmental and internal cues that play critical roles in regulating strawberry fruit development and ripening. Collectively, this study provides valuable insight into the FvMRLKs gene family and its role in regulating strawberry fruit development and ripening.
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Affiliation(s)
- Qing Zhang
- College of Horticulture, China Agriculture University, Beijing, China
- College of Plant Science and Technology, Beijing University of Agriculture, Key Laboratory of New Technology in Agricultural Application of Beijing, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative innovation center for eco-environmental improvement with forestry and fruit trees, Beijing, China
| | - Meiru Jia
- College of Horticulture, China Agriculture University, Beijing, China
| | - Yu Xing
- College of Plant Science and Technology, Beijing University of Agriculture, Key Laboratory of New Technology in Agricultural Application of Beijing, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative innovation center for eco-environmental improvement with forestry and fruit trees, Beijing, China
| | - Ling Qin
- College of Plant Science and Technology, Beijing University of Agriculture, Key Laboratory of New Technology in Agricultural Application of Beijing, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative innovation center for eco-environmental improvement with forestry and fruit trees, Beijing, China
- * E-mail: (WJ); (LQ)
| | - Bingbing Li
- College of Horticulture, China Agriculture University, Beijing, China
- College of Plant Science and Technology, Beijing University of Agriculture, Key Laboratory of New Technology in Agricultural Application of Beijing, Beijing University of Agriculture, Beijing, China
| | - Wensuo Jia
- College of Horticulture, China Agriculture University, Beijing, China
- * E-mail: (WJ); (LQ)
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22
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Chrismas NAM, Barker G, Anesio AM, Sánchez-Baracaldo P. Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401. BMC Genomics 2016; 17:533. [PMID: 27485510 PMCID: PMC4971617 DOI: 10.1186/s12864-016-2846-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria are major primary producers in extreme cold ecosystems. Many lineages of cyanobacteria thrive in these harsh environments, but it is not fully understood how they survive in these conditions and whether they have evolved specific mechanisms of cold adaptation. Phormidesmis priestleyi is a cyanobacterium found throughout the cold biosphere (Arctic, Antarctic and alpine habitats). Genome sequencing of P. priestleyi BC1401, an isolate from a cryoconite hole on the Greenland Ice Sheet, has allowed for the examination of genes involved in cold shock response and production of extracellular polymeric substances (EPS). EPSs likely enable cyanobacteria to buffer the effects of extreme cold and by identifying mechanisms for EPS production in P. priestleyi BC1401 this study lays the way for investigating transcription and regulation of EPS production in an ecologically important cold tolerant cyanobacterium. RESULTS We sequenced the draft genome of P. priestleyi BC1401 and implemented a new de Bruijn graph visualisation approach combined with BLAST analysis to separate cyanobacterial contigs from a simple metagenome generated from non-axenic cultures. Comparison of known cold adaptation genes in P. priestleyi BC1401 with three relatives from other environments revealed no clear differences between lineages. Genes involved in EPS biosynthesis were identified from the Wzy- and ABC-dependent pathways. The numbers of genes involved in cell wall and membrane biogenesis in P. priestleyi BC1401 were typical relative to the genome size. A gene cluster implicated in biofilm formation was found homologous to the Wps system, although the intracellular signalling pathways by which this could be regulated remain unclear. CONCLUSIONS Results show that the genomic characteristics and complement of known cold shock genes in P. priestleyi BC1401 are comparable to related lineages from a wide variety of habitats, although as yet uncharacterised cold shock genes in this organism may still exist. EPS production by P. priestleyi BC1401 likely contributes to its ability to survive efficiently in cold environments, yet this mechanism is widely distributed throughout the cyanobacterial phylum. Discovering how these EPS related mechanisms are regulated may help explain why P. priestleyi BC1401 is so successful in cold environments where related lineages are not.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK.
| | - Gary Barker
- Cereal Genomics, School of Biological Sciences, University of Bristol, Bristol, BS8 1SS, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK
| | - Patricia Sánchez-Baracaldo
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK.
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23
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Watanabe KA, Ma K, Homayouni A, Rushton PJ, Shen QJ. Transcript structure and domain display: a customizable transcript visualization tool. Bioinformatics 2016; 32:2024-5. [PMID: 27153680 DOI: 10.1093/bioinformatics/btw095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/12/2016] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. AVAILABILITY AND IMPLEMENTATION TSDD is freely available for non-commercial users at http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html CONTACT : jeffery.shen@unlv.nevada.edu.
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Affiliation(s)
- Kenneth A Watanabe
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Kaiwang Ma
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA School of Medical Technology & Engineering, Henan University of Science & Technology, Luoyang, 471003, China
| | - Arielle Homayouni
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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24
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Stepniak B, Kästner A, Poggi G, Mitjans M, Begemann M, Hartmann A, Van der Auwera S, Sananbenesi F, Krueger-Burg D, Matuszko G, Brosi C, Homuth G, Völzke H, Benseler F, Bagni C, Fischer U, Dityatev A, Grabe HJ, Rujescu D, Fischer A, Ehrenreich H. Accumulated common variants in the broader fragile X gene family modulate autistic phenotypes. EMBO Mol Med 2016; 7:1565-79. [PMID: 26612855 PMCID: PMC4693501 DOI: 10.15252/emmm.201505696] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Fragile X syndrome (FXS) is mostly caused by a CGG triplet expansion in the fragile X mental retardation 1 gene (FMR1). Up to 60% of affected males fulfill criteria for autism spectrum disorder (ASD), making FXS the most frequent monogenetic cause of syndromic ASD. It is unknown, however, whether normal variants (independent of mutations) in the fragile X gene family (FMR1, FXR1, FXR2) and in FMR2 modulate autistic features. Here, we report an accumulation model of 8 SNPs in these genes, associated with autistic traits in a discovery sample of male patients with schizophrenia (N = 692) and three independent replicate samples: patients with schizophrenia (N = 626), patients with other psychiatric diagnoses (N = 111) and a general population sample (N = 2005). For first mechanistic insight, we contrasted microRNA expression in peripheral blood mononuclear cells of selected extreme group subjects with high‐ versus low‐risk constellation regarding the accumulation model. Thereby, the brain‐expressed miR‐181 species emerged as potential “umbrella regulator”, with several seed matches across the fragile X gene family and FMR2. To conclude, normal variation in these genes contributes to the continuum of autistic phenotypes.
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Affiliation(s)
- Beata Stepniak
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Anne Kästner
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Giulia Poggi
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Marina Mitjans
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Martin Begemann
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Annette Hartmann
- Department of Psychiatry and Psychotherapy, University of Halle, Halle, Germany
| | - Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Farahnaz Sananbenesi
- Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Dilja Krueger-Burg
- Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Gabriela Matuszko
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Cornelia Brosi
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Fritz Benseler
- Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Claudia Bagni
- KU Leuven, Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases, Leuven, Belgium Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Utz Fischer
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Alexander Dityatev
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Hans-Jörgen Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, University of Halle, Halle, Germany
| | - Andre Fischer
- Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany Department of Psychiatry & Psychotherapy, University of Göttingen, Göttingen, Germany
| | - Hannelore Ehrenreich
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
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25
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Geiger JT, Ding J, Crain B, Pletnikova O, Letson C, Dawson TM, Rosenthal LS, Pantelyat A, Gibbs JR, Albert MS, Hernandez DG, Hillis AE, Stone DJ, Singleton AB, Hardy JA, Troncoso JC, Scholz SW. Next-generation sequencing reveals substantial genetic contribution to dementia with Lewy bodies. Neurobiol Dis 2016; 94:55-62. [PMID: 27312774 DOI: 10.1016/j.nbd.2016.06.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/08/2016] [Accepted: 06/11/2016] [Indexed: 11/15/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is the second most common neurodegenerative dementia after Alzheimer's disease. Although an increasing number of genetic factors have been connected to this debilitating condition, the proportion of cases that can be attributed to distinct genetic defects is unknown. To provide a comprehensive analysis of the frequency and spectrum of pathogenic missense mutations and coding risk variants in nine genes previously implicated in DLB, we performed exome sequencing in 111 pathologically confirmed DLB patients. All patients were Caucasian individuals from North America. Allele frequencies of identified missense mutations were compared to 222 control exomes. Remarkably, ~25% of cases were found to carry a pathogenic mutation or risk variant in APP, GBA or PSEN1, highlighting that genetic defects play a central role in the pathogenesis of this common neurodegenerative disorder. In total, 13% of our cohort carried a pathogenic mutation in GBA, 10% of cases carried a risk variant or mutation in PSEN1, and 2% were found to carry an APP mutation. The APOE ε4 risk allele was significantly overrepresented in DLB patients (p-value <0.001). Our results conclusively show that mutations in GBA, PSEN1, and APP are common in DLB and consideration should be given to offer genetic testing to patients diagnosed with Lewy body dementia.
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Affiliation(s)
- Joshua T Geiger
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Barbara Crain
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher Letson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ted M Dawson
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Solomon H. Synder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Department of Pharmacology and Molecular Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Neuroregeneration Program, Institute of Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liana S Rosenthal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander Pantelyat
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Argye E Hillis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David J Stone
- Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, PA, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - John A Hardy
- Department of Molecular Neuroscience, University College London, London, UK
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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26
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Impact of Wild Loci on the Allergenic Potential of Cultivated Tomato Fruits. PLoS One 2016; 11:e0155803. [PMID: 27182705 PMCID: PMC4868316 DOI: 10.1371/journal.pone.0155803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/14/2016] [Indexed: 11/21/2022] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most extensively consumed vegetables but, unfortunately, it is also able to induce allergic reactions. In the past, it has been shown that the choice of tomato cultivar significantly influenced the allergic reaction of tomato allergic subjects. In this study we investigated the allergenic potential of the cultivated tomato line M82 and of two selected lines carrying small chromosome regions from the wild species Solanum pennellii (i.e. IL7-3 and IL12-4). We evaluated the positive interactions of IgEs of allergic subjects in order to investigate the different allergenic potential of the lines under investigation. We used proteomic analyses in order to identify putative tomato allergens. In addition, bioinformatic and transcriptomic approaches were applied in order to analyse the structure and the expression profiles of the identified allergen-encoding genes. These analyses demonstrated that fruits harvested from the two selected introgression lines harbour a different allergenic potential as those from the cultivated genotype M82. The different allergenicity found within the three lines was mostly due to differences in the IgE recognition of a polygalacturonase enzyme (46 kDa), one of the major tomato allergens, and of a pectin methylesterase (34 kDa); both the proteins were more immunoreactive in IL7-3 compared to IL12-4 and M82. The observed differences in the allergenic potential were mostly due to line-dependent translational control or post-translational modifications of the allergens. We demonstrated, for the first time, that the introgression from a wild species (S. pennellii) in the genomic background of a cultivated tomato line influences the allergenic properties of the fruits. Our findings could support the isolation of favorable wild loci promoting low allergenic potential in tomato.
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27
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Andersen EJ, Ali S, Reese RN, Yen Y, Neupane S, Nepal MP. Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.). Evol Bioinform Online 2016; 12:99-108. [PMID: 27168720 PMCID: PMC4857794 DOI: 10.4137/ebo.s38085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 11/05/2022] Open
Abstract
Plant disease resistance genes (R-genes) play a critical role in the defense response to pathogens. Barley is one of the most important cereal crops, having a genome recently made available, for which the diversity and evolution of R-genes are not well understood. The main objectives of this research were to conduct a genome-wide identification of barley Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) genes and elucidate their evolutionary history. We employed a Hidden Markov Model using 52 Arabidopsis thaliana CNL reference sequences and analyzed for phylogenetic relationships, structural variation, and gene clustering. We identified 175 barley CNL genes nested into three clades, showing (a) evidence of an expansion of the CNL-C clade, primarily due to tandem duplications; (b) very few members of clade CNL-A and CNL-B; and (c) a complete absence of clade CNL-D. Our results also showed that several of the previously identified mildew locus A (MLA) genes may be allelic variants of two barley CNL genes, MLOC_66581 and MLOC_10425, which respond to powdery mildew. Approximately 23% of the barley CNL genes formed 15 gene clusters located in the extra-pericentromeric regions on six of the seven chromosomes; more than half of the clustered genes were located on chromosomes 1H and 7H. Higher average numbers of exons and multiple splice variants in barley relative to those in Arabidopsis and rice may have contributed to a diversification of the CNL-C members. These results will help us understand the evolution of R-genes with potential implications for developing durable resistance in barley cultivars.
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Affiliation(s)
- Ethan J. Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Shaukat Ali
- Department of Plant Science, South Dakota State University, Brookings, SD, USA
| | - R. Neil Reese
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Madhav P. Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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28
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Körbes AP, Kulcheski FR, Margis R, Margis-Pinheiro M, Turchetto-Zolet AC. Molecular evolution of the lysophosphatidic acid acyltransferase (LPAAT) gene family. Mol Phylogenet Evol 2016; 96:55-69. [DOI: 10.1016/j.ympev.2015.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 10/21/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
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29
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Campos MD, Nogales A, Cardoso HG, Kumar SR, Nobre T, Sathishkumar R, Arnholdt-Schmitt B. Stress-Induced Accumulation of DcAOX1 and DcAOX2a Transcripts Coincides with Critical Time Point for Structural Biomass Prediction in Carrot Primary Cultures (Daucus carota L.). Front Genet 2016; 7:1. [PMID: 26858746 PMCID: PMC4731517 DOI: 10.3389/fgene.2016.00001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/07/2016] [Indexed: 11/18/2022] Open
Abstract
Stress-adaptive cell plasticity in target tissues and cells for plant biomass growth is important for yield stability. In vitro systems with reproducible cell plasticity can help to identify relevant metabolic and molecular events during early cell reprogramming. In carrot, regulation of the central root meristem is a critical target for yield-determining secondary growth. Calorespirometry, a tool previously identified as promising for predictive growth phenotyping has been applied to measure the respiration rate in carrot meristem. In a carrot primary culture system (PCS), this tool allowed identifying an early peak related with structural biomass formation during lag phase of growth, around the 4th day of culture. In the present study, we report a dynamic and correlated expression of carrot AOX genes (DcAOX1 and DcAOX2a) during PCS lag phase and during exponential growth. Both genes showed an increase in transcript levels until 36 h after explant inoculation, and a subsequent down-regulation, before the initiation of exponential growth. In PCS growing at two different temperatures (21°C and 28°C), DcAOX1 was also found to be more expressed in the highest temperature. DcAOX genes' were further explored in a plant pot experiment in response to chilling, which confirmed the early AOX transcript increase prior to the induction of a specific anti-freezing gene. Our findings point to DcAOX1 and DcAOX2a as being reasonable candidates for functional marker development related to early cell reprogramming. While the genomic sequence of DcAOX2a was previously described, we characterize here the complete genomic sequence of DcAOX1.
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Affiliation(s)
- M. Doroteia Campos
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Amaia Nogales
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Hélia G. Cardoso
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Sarma R. Kumar
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
- Molecular Plant Biology and Biotechnology Division, Council of Scientific and Industrial Research–Central Institute of Medicinal and Aromatic Plants Research CentreBangalore, India
| | - Tânia Nobre
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar UniversityCoimbatore, India
| | - Birgit Arnholdt-Schmitt
- EU Marie Curie Chair, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de ÉvoraÉvora, Portugal
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Li S, Li K, Ju Z, Cao D, Fu D, Zhu H, Zhu B, Luo Y. Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening. BMC Genomics 2016; 17:36. [PMID: 26742635 PMCID: PMC4705811 DOI: 10.1186/s12864-015-2334-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Fruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses. Results In this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm. Conclusions In this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2334-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Ka Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Zheng Ju
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Dongyan Cao
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, No. 17 Tsinghua East Road, Beijing, 100083, Peoples Republic of China.
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Zhu W, Zuo R, Zhou R, Huang J, Tang M, Cheng X, Liu Y, Tong C, Xiang Y, Dong C, Liu S. Vacuolar Iron Transporter BnMEB2 Is Involved in Enhancing Iron Tolerance of Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1353. [PMID: 27679642 DOI: 10.3389/fpls201601353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/24/2016] [Indexed: 05/22/2023]
Abstract
Iron toxicity is a nutrient disorder that severely affects crop development and yield in some soil conditions. Vacuolar detoxification of metal stress is an important strategy for plants to survive and adapt to this adverse environment. Vacuolar iron transporter (VIT) members are involved in this process and play essential roles in iron storage and transport. In this study, we identified a rapeseed VIT gene BnMEB2 (BnaC07g30170D) homologs to Arabidopsis MEB2 (At5g24290). Transient expression analysis revealed that BnMEB2 was localized to the vacuolar membrane. Q-PCR detection showed a high expression of BnMEB2 in mature (60-day-old) leaves and could be obviously induced by exogenous iron stress in both roots and leaves. Over-expressed BnMEB2 in both Arabidopsis wild type and meb2 mutant seedlings resulted in greatly improved iron tolerability with no significant changes in the expression level of other VIT genes. The mutant meb2 grew slowly and its root hair elongation was inhibited under high iron concentration condition while BnMEB2 over-expressed transgenic plants of the mutant restored the phenotypes with apparently higher iron storage in roots and dramatically increased iron content in the whole plant. Taken together, these results suggested that BnMEB2 was a VIT gene in rapeseed which was necessary for safe storage and vacuole detoxification function of excess iron to enhance the tolerance of iron toxicity. This research sheds light on a potentially new strategy for attenuating hazardous metal stress from environment and improving iron biofortification in Brassicaceae crops.
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Affiliation(s)
- Wei Zhu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences Wuhan, China
| | - Rong Zuo
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
| | - Rongfang Zhou
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences Wuhan, China
| | - Junyan Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
| | - Minqiang Tang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences Wuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences Wuhan, China
| | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture Sciences Wuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences Guiyang, China
| | - Caihua Dong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
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Zhu W, Zuo R, Zhou R, Huang J, Tang M, Cheng X, Liu Y, Tong C, Xiang Y, Dong C, Liu S. Vacuolar Iron Transporter BnMEB2 Is Involved in Enhancing Iron Tolerance of Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1353. [PMID: 27679642 PMCID: PMC5020681 DOI: 10.3389/fpls.2016.01353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/24/2016] [Indexed: 05/05/2023]
Abstract
Iron toxicity is a nutrient disorder that severely affects crop development and yield in some soil conditions. Vacuolar detoxification of metal stress is an important strategy for plants to survive and adapt to this adverse environment. Vacuolar iron transporter (VIT) members are involved in this process and play essential roles in iron storage and transport. In this study, we identified a rapeseed VIT gene BnMEB2 (BnaC07g30170D) homologs to Arabidopsis MEB2 (At5g24290). Transient expression analysis revealed that BnMEB2 was localized to the vacuolar membrane. Q-PCR detection showed a high expression of BnMEB2 in mature (60-day-old) leaves and could be obviously induced by exogenous iron stress in both roots and leaves. Over-expressed BnMEB2 in both Arabidopsis wild type and meb2 mutant seedlings resulted in greatly improved iron tolerability with no significant changes in the expression level of other VIT genes. The mutant meb2 grew slowly and its root hair elongation was inhibited under high iron concentration condition while BnMEB2 over-expressed transgenic plants of the mutant restored the phenotypes with apparently higher iron storage in roots and dramatically increased iron content in the whole plant. Taken together, these results suggested that BnMEB2 was a VIT gene in rapeseed which was necessary for safe storage and vacuole detoxification function of excess iron to enhance the tolerance of iron toxicity. This research sheds light on a potentially new strategy for attenuating hazardous metal stress from environment and improving iron biofortification in Brassicaceae crops.
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Affiliation(s)
- Wei Zhu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
| | - Rong Zuo
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
| | - Rongfang Zhou
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
| | - Junyan Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
| | - Minqiang Tang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
| | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural SciencesGuiyang, China
| | - Caihua Dong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
- *Correspondence: Caihua Dong,
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agriculture SciencesWuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei UniversityWuhan, China
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Velada I, Cardoso HG, Ragonezi C, Nogales A, Ferreira A, Valadas V, Arnholdt-Schmitt B. Alternative Oxidase Gene Family in Hypericum perforatum L.: Characterization and Expression at the Post-germinative Phase. FRONTIERS IN PLANT SCIENCE 2016; 7:1043. [PMID: 27563303 PMCID: PMC4980395 DOI: 10.3389/fpls.2016.01043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/04/2016] [Indexed: 05/05/2023]
Abstract
Alternative oxidase (AOX) protein is located in the inner mitochondrial membrane and is encoded in the nuclear genome being involved in plant response upon a diversity of environmental stresses and also in normal plant growth and development. Here we report the characterization of the AOX gene family of Hypericum perforatum L. Two AOX genes were identified, both with a structure of four exons (HpAOX1, acc. KU674355 and HpAOX2, acc. KU674356). High variability was found at the N-terminal region of the protein coincident with the high variability identified at the mitochondrial transit peptide. In silico analysis of regulatory elements located at intronic regions identified putative sequences coding for miRNA precursors and trace elements of a transposon. Simple sequence repeats were also identified. Additionally, the mRNA levels for the HpAOX1 and HpAOX2, along with the ones for the HpGAPA (glyceraldehyde-3-phosphate dehydrogenase A subunit) and the HpCAT1 (catalase 1), were evaluated during the post-germinative development. Gene expression analysis was performed by RT-qPCR with accurate data normalization, pointing out HpHYP1 (chamba phenolic oxidative coupling protein 1) and HpH2A (histone 2A) as the most suitable reference genes (RGs) according to GeNorm algorithm. The HpAOX2 transcript demonstrated larger stability during the process with a slight down-regulation in its expression. Contrarily, HpAOX1 and HpGAPA (the corresponding protein is homolog to the chloroplast isoform involved in the photosynthetic carbon assimilation in other plant species) transcripts showed a marked increase, with a similar expression pattern between them, during the post-germinative development. On the other hand, the HpCAT1 (the corresponding protein is homolog to the major H2O2-scavenging enzyme in other plant species) transcripts showed an opposite behavior with a down-regulation during the process. In summary, our findings, although preliminary, highlight the importance to investigate in more detail the participation of AOX genes during the post-germinative development in H. perforatum, in order to explore their functional role in optimizing photosynthesis and in the control of reactive oxygen species (ROS) levels during the process.
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Affiliation(s)
- Isabel Velada
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Laboratório de Biologia Molecular, Universidade de ÉvoraPólo da Mitra, Évora, Portugal
| | - Hélia G. Cardoso
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Laboratório de Biologia Molecular, Universidade de ÉvoraPólo da Mitra, Évora, Portugal
- *Correspondence: Hélia G. Cardoso
| | - Carla Ragonezi
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Laboratório de Biologia Molecular, Universidade de ÉvoraPólo da Mitra, Évora, Portugal
| | - Amaia Nogales
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia-Universidade de LisboaLisboa, Portugal
| | - Alexandre Ferreira
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Laboratório de Biologia Molecular, Universidade de ÉvoraPólo da Mitra, Évora, Portugal
| | - Vera Valadas
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Laboratório de Biologia Molecular, Universidade de ÉvoraPólo da Mitra, Évora, Portugal
| | - Birgit Arnholdt-Schmitt
- EU Marie Curie Chair, ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de ÉvoraPólo da Mitra, Évora, Portugal
- Birgit Arnholdt-Schmitt
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da Silva DC, da Silveira Falavigna V, Fasoli M, Buffon V, Porto DD, Pappas GJ, Pezzotti M, Pasquali G, Revers LF. Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development. HORTICULTURE RESEARCH 2016; 3:16042. [PMID: 27610237 PMCID: PMC5005469 DOI: 10.1038/hortres.2016.42] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 05/19/2023]
Abstract
The Dof (DNA-binding with one finger) protein family spans a group of plant transcription factors involved in the regulation of several functions, such as plant responses to stress, hormones and light, phytochrome signaling and seed germination. Here we describe the Dof-like gene family in grapevine (Vitis vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico characterization of the VviDofL gene family was performed. Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine sequences with those of Arabidopsis, tomato, poplar and already described Dof genes in other species allowed us to identify several duplicated genes. The diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological roles. Furthermore, distinct expression patterns were identified between samples analyzed, corroborating such hypothesis. Our expression results indicate that several VviDofL genes perform their functional roles mainly during flower, berry and seed development, highlighting their importance for grapevine growth and production. The identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.
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Affiliation(s)
- Danielle Costenaro da Silva
- Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Vítor da Silveira Falavigna
- Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Marianna Fasoli
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona 37134, Italy
| | - Vanessa Buffon
- Embrapa Uva e Vinho, Bento Gonçalves, RS 95701-008, Brazil
| | | | | | - Mario Pezzotti
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona 37134, Italy
| | - Giancarlo Pasquali
- Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
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Hellewell AL, Adams JC. Insider trading: Extracellular matrix proteins and their non-canonical intracellular roles. Bioessays 2015; 38:77-88. [PMID: 26735930 DOI: 10.1002/bies.201500103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In metazoans, the extracellular matrix (ECM) provides a dynamic, heterogeneous microenvironment that has important supportive and instructive roles. Although the primary site of action of ECM proteins is extracellular, evidence is emerging for non-canonical intracellular roles. Examples include osteopontin, thrombospondins, IGF-binding protein 3 and biglycan, and relate to roles in transcription, cell-stress responses, autophagy and cancer. These findings pose conceptual problems on how proteins signalled for secretion can be routed to the cytosol or nucleus, or can function in environments with diverse redox, pH and ionic conditions. We review evidence for intracellular locations and functions of ECM proteins, and current knowledge of the mechanisms by which they may enter intracellular compartments. We evaluate the experimental methods that are appropriate to obtain rigorous evidence for intracellular localisation and function. Better insight into this under-researched topic is needed to decipher the complete spectrum of physiological and pathological roles of ECM proteins.
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Du K, He S. Evolutionary fate and implications of retrocopies in the African coelacanth genome. BMC Genomics 2015; 16:915. [PMID: 26555943 PMCID: PMC4641402 DOI: 10.1186/s12864-015-2178-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The coelacanth is known as a "living fossil" because of its morphological resemblance to its fossil ancestors. Thus, it serves as a useful model that provides insight into the fish that first walked on land. Retrocopies are a type of novel genetic element that are likely to contribute to genome or phenotype innovations. Thus, investigating retrocopies in the coelacanth genome can determine the role of retrocopies in coelacanth genome innovations and perhaps even water-to-land adaptations. RESULTS We determined the dS values, dN/dS ratios, expression patterns, and enrichment of functional categories for 472 retrocopies in the African coelacanth genome. Of the retrocopies, 85-355 were shown to be potentially functional (i.e., retrogenes). The distribution of retrocopies based on their dS values revealed a burst pattern of young retrocopies in the genome. The retrocopy birth pattern was shown to be more similar to that in tetrapods than ray-finned fish, which indicates a genomic transformation that accompanied vertebrate evolution from water to land. Among these retrocopies, retrogenes were more prevalent in old than young retrocopies, which indicates that most retrocopies may have been eliminated during evolution, even though some retrocopies survived, attained biological function as retrogenes, and became old. Transcriptome data revealed that many retrocopies showed a biased expression pattern in the testis, although the expression was not specifically associated with a particular retrocopy age range. We identified 225 Ensembl genes that overlapped with the coelacanth genome retrocopies. GO enrichment analysis revealed different overrepresented GO (gene ontology) terms between these "retrocopy-overlapped genes" and the retrocopy parent genes, which indicates potential genomic functional organization produced by retrotranspositions. Among the 225 retrocopy-overlapped genes, we also identified 46 that were coelacanth-specific, which could represent a potential molecular basis for coelacanth evolution. CONCLUSIONS Our study identified 472 retrocopies in the coelacanth genome. Sequence analysis of these retrocopies and their parent genes, transcriptome data, and GO annotation information revealed novel insight about the potential role of genomic retrocopies in coelacanth evolution and vertebrate adaptations during the evolutionary transition from water to land.
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Affiliation(s)
- Kang Du
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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Pisanu C, Caproni S, Congiu D, Cupini LM, Squassina A, Patrinos GP, Corbelli I, Calabresi P, Del Zompo M, Sarchielli P. HDAC3 role in medication consumption in medication overuse headache patients: a pilot study. Hum Genomics 2015; 9:30. [PMID: 26542778 PMCID: PMC4635554 DOI: 10.1186/s40246-015-0051-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/26/2015] [Indexed: 12/13/2022] Open
Abstract
Background Medication overuse headache (MOH) is a common and debilitating disorder characterized by generation, perpetuation, and persistence of intense chronic migraine, caused by overuse of analgesics, triptans, or other acute headache compounds. It has been suggested that MOH could share some pathogenetic mechanisms with other kinds of drug addiction. In this regard, histone deacetylases 3 (HDAC3) seems to have a role in the memory processes involved in extinction of drug-seeking behavior in animal models. HDAC3 is inhibited by sodium valproate, a drug with proven efficacy in MOH. Recent evidence suggests an involvement of genetic factors in predisposition to medication overuse. Results In this association study, we sequenced all exons, intron/exon junctions, and 3′-5′UTR regions of HDAC3 in 23 MOH patients to investigate its role in medication overuse. Associations between genotypes with continuous and dichotomous clinical characteristics were tested by multivariate analysis and Fisher’s exact test, respectively. Sequencing of HDAC3 revealed six single-nucleotide polymorphisms. The G allele of rs2530223 was significantly associated with the number of acute medications/month used and with the number of days/month in which medications were used (p = 0.006 and p = 0.007, respectively), but neither with headache frequency or intensity. None of the single-nucleotide polymorphisms (SNPs) was associated with clinical characteristics or response to sodium valproate. Conclusions HDAC3 could be implicated in excessive medication consumption in MOH patients. Our preliminary findings provide support for the need of further investigation on larger independent samples to confirm and extend the role of HDAC3 in medication overuse headache.
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Affiliation(s)
- Claudia Pisanu
- Section of Neurosciences and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, SP8 Km. 0,700, 09042, Monserrato (CA), Italy
| | | | - Donatella Congiu
- Section of Neurosciences and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, SP8 Km. 0,700, 09042, Monserrato (CA), Italy
| | - Letizia M Cupini
- Headache and Cerebrovascular Diseases Center, Ospedale S. Eugenio, Rome, Italy
| | - Alessio Squassina
- Section of Neurosciences and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, SP8 Km. 0,700, 09042, Monserrato (CA), Italy
| | - George P Patrinos
- Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece.
| | | | - Paolo Calabresi
- Neurologic Clinic, University of Perugia, Perugia, Italy.,IRCCS Fondazione "S. Lucia", Rome, Italy
| | - Maria Del Zompo
- Section of Neurosciences and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, SP8 Km. 0,700, 09042, Monserrato (CA), Italy. .,Institute of Neuroscience, CNR, Cagliari, Italy.
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Katz TA, Liao SG, Palmieri VJ, Dearth RK, Pathiraja TN, Huo Z, Shaw P, Small S, Davidson NE, Peters DG, Tseng GC, Oesterreich S, Lee AV. Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition. Cancer Prev Res (Phila) 2015; 8:1000-9. [PMID: 26290394 PMCID: PMC4677681 DOI: 10.1158/1940-6207.capr-15-0178] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/05/2015] [Indexed: 02/06/2023]
Abstract
The most effective natural prevention against breast cancer is an early first full-term pregnancy. Understanding how the protective effect is elicited will inform the development of new prevention strategies. To better understand the role of epigenetics in long-term protection, we investigated parity-induced DNA methylation in the mammary gland. FVB mice were bred or remained nulliparous and mammary glands harvested immediately after involution (early) or 6.5 months following involution (late), allowing identification of both transient and persistent changes. Targeted DNA methylation (109 Mb of Ensemble regulatory features) analysis was performed using the SureSelectXT Mouse Methyl-seq assay and massively parallel sequencing. Two hundred sixty-nine genes were hypermethylated and 128 hypomethylated persistently at both the early and late time points. Pathway analysis of the persistently differentially methylated genes revealed Igf1r to be central to one of the top identified signaling networks, and Igf1r itself was one of the most significantly hypermethylated genes. Hypermethylation of Igf1r in the parous mammary gland was associated with a reduction of Igf1r mRNA expression. These data suggest that the IGF pathway is regulated at multiple levels during pregnancy and that its modification might be critical in the protective role of pregnancy. This supports the approach of lowering IGF action for prevention of breast cancer, a concept that is currently being tested clinically.
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Affiliation(s)
- Tiffany A Katz
- Department of Pharmacology and Chemical Biology, Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Serena G Liao
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Vincent J Palmieri
- Department of Pharmacology and Chemical Biology, Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Robert K Dearth
- Department of Biology, University of Texas-Rio Grande Valley, Edinburg, Texas
| | - Thushangi N Pathiraja
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Zhiguang Huo
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patricia Shaw
- Department of Obstetrics. Gynecology, and Reproductive Sciences, University of Pittsburgh, Pennsylvania
| | - Sarah Small
- Department of Pharmacology and Chemical Biology, Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Nancy E Davidson
- Department of Pharmacology and Chemical Biology, Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - David G Peters
- Department of Obstetrics. Gynecology, and Reproductive Sciences, University of Pittsburgh, Pennsylvania
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania.
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania.
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Dudzic JP, Kondo S, Ueda R, Bergman CM, Lemaitre B. Drosophila innate immunity: regional and functional specialization of prophenoloxidases. BMC Biol 2015; 13:81. [PMID: 26437768 PMCID: PMC4595066 DOI: 10.1186/s12915-015-0193-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/17/2015] [Indexed: 01/08/2023] Open
Abstract
Background The diversification of immune systems during evolution involves the expansion of particular gene families in given phyla. A better understanding of the metazoan immune system requires an analysis of the logic underlying such immune gene amplification. This analysis is now within reach due to the ease with which we can generate multiple mutations in an organism. In this paper, we analyze the contribution of the three Drosophila prophenoloxidases (PPOs) to host defense by generating single, double and triple mutants. PPOs are enzymes that catalyze the production of melanin at the site of infection and around parasites. They are the rate-limiting enzymes that contribute to the melanization reaction, a major immune mechanism of arthropods. The number of PPO-encoding genes is variable among insects, ranging from one in the bee to ten in the mosquito. Results By analyzing mutations alone and in combination, we ascribe a specific function to each of the three PPOs of Drosophila. Our study confirms that two PPOs produced by crystal cells, PPO1 and PPO2, contribute to the bulk of melanization in the hemolymph, upon septic or clean injury. In contrast, PPO3, a PPO restricted to the D. melanogaster group, is expressed in lamellocytes and contributes to melanization during the encapsulation process. Interestingly, another overlapping set of PPOs, PPO2 and PPO3, achieve melanization of the capsule upon parasitoid wasp infection. Conclusions The use of single or combined mutations allowed us to show that each PPO mutant has a specific phenotype, and that knocking out two of three genes is required to abolish fully a particular function. Thus, Drosophila PPOs have partially overlapping functions to optimize melanization in at least two conditions: following injury or during encapsulation. Since PPO3 is restricted to the D. melanogaster group, this suggests that production of PPO by lamellocytes emerged as a recent defense mechanism against parasitoid wasps. We conclude that differences in spatial localization, immediate or late availability, and mode of activation underlie the functional diversification of the three Drosophila PPOs, with each of them having non-redundant but overlapping functions. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0193-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan P Dudzic
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.
| | - Shu Kondo
- Invertebrate Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Ryu Ueda
- Invertebrate Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.
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Harrison S, Lewis SJ, Hall AJ, Vuckovic D, Girotto G, Martin RM, Adams JC. Association of SNPs in LCP1 and CTIF with hearing in 11 year old children: findings from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort and the G-EAR consortium. BMC Med Genomics 2015; 8:48. [PMID: 26264041 PMCID: PMC4533938 DOI: 10.1186/s12920-015-0112-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 07/02/2015] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The genetic basis of hearing loss in humans is relatively poorly understood. In recent years, experimental approaches including laboratory studies of early onset hearing loss in inbred mouse strains, or proteomic analyses of hair cells or hair bundles, have suggested new candidate molecules involved in hearing function. However, the relevance of these genes/gene products to hearing function in humans remains unknown. We investigated whether single nucleotide polymorphisms (SNPs) in the human orthologues of genes of interest arising from the above-mentioned studies correlate with hearing function in children. METHODS 577 SNPs from 13 genes were each analysed by linear regression against averaged high (3, 4 and 8 kHz) or low frequency (0.5, 1 and 2 kHz) audiometry data from 4970 children in the Avon Longitudinal Study of Parents and Children (ALSPAC) birth-cohort at age eleven years. Genes found to contain SNPs with low p-values were then investigated in 3417 adults in the G-EAR study of hearing. RESULTS Genotypic data were available in ALSPAC for a total of 577 SNPs from 13 genes of interest. Two SNPs approached sample-wide significance (pre-specified at p = 0.00014): rs12959910 in CBP80/20-dependent translation initiation factor (CTIF) for averaged high frequency hearing (p = 0.00079, β = 0.61 dB per minor allele); and rs10492452 in L-plastin (LCP1) for averaged low frequency hearing (p = 0.00056, β = 0.45 dB). For low frequencies, rs9567638 in LCP1 also enhanced hearing in females (p = 0.0011, β = -1.76 dB; males p = 0.23, β = 0.61 dB, likelihood-ratio test p = 0.006). SNPs in LCP1 and CTIF were then examined against low and high frequency hearing data for adults in G-EAR. Although the ALSPAC results were not replicated, a SNP in LCP1, rs17601960, is in strong LD with rs9967638, and was associated with enhanced low frequency hearing in adult females in G-EAR (p = 0.00084). CONCLUSIONS There was evidence to suggest that multiple SNPs in CTIF may contribute a small detrimental effect to hearing, and that a sex-specific locus in LCP1 is protective of hearing. No individual SNPs reached sample-wide significance in both ALSPAC and G-EAR. This is the first report of a possible association between LCP1 and hearing function.
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Affiliation(s)
- Sean Harrison
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2PS, UK.
| | - Sarah J Lewis
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2PS, UK.
| | - Amanda J Hall
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2PS, UK.
| | - Dragana Vuckovic
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34100, Trieste, Italy.
| | - Giorgia Girotto
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34100, Trieste, Italy.
| | - Richard M Martin
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2PS, UK.
| | - Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
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Zhao ZX, Cao DC, Xu J, Xu R, Li JT, Zhang Y, Xu P, Sun XW. Diversification of the duplicated Rab1a genes in a hypoxia-tolerant fish, common carp (Cyprinus carpio). Comp Biochem Physiol B Biochem Mol Biol 2015; 188:54-62. [PMID: 26129846 DOI: 10.1016/j.cbpb.2015.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 11/25/2022]
Abstract
Common carp is a widely cultivated fish with longer than 2,000 years domestication history, due to its strong environmental adaptabilities, especially hypoxia tolerance. The common carp genome has experienced a very recent whole genome duplication (WGD) event. Among a large number of highly similar duplicated genes, a pair of Ras-associated binding-GTPase 1a (Rab1a) genes were found fast diverging. Four analogous Rab1a genes were identified in the common carp genome. Comparisons of gene structures and sequences indicated Rab1a-1 and Rab1a-2 was a pair of fast diverging duplicates, while Rab1a-3 and Rab1a-4 was a pair of less diverged duplicates. All putative Rab1a proteins shared conserved GTPase domain, which enabled the proteins serve as molecular switches for vesicular trafficking. Rab1a-1 and Rab1a-2 proteins varied in their C-terminal sequences, which were generally considered to encode the membrane localization signals. Differential expression patterns were observed between Rab1a-1 and Rab1a-2 genes. In blood, muscle, spleen, and heart, the mRNA level of Rab1a-1 was higher than that of Rab1a-2. In liver and intestine, the mRNA level of Rab1a-2 was higher. Expression of Rab1a-1 and Rab1a-2 showed distinct hypoxia responses. Under severe hypoxia, Rab1a-1 expression was down-regulated in blood, while Rab1a-2 expression was up-regulated in liver. Compared with the less diverged Rab1a-3/4 gene pair, common carp Rab1a-1/2 gene pair exhibited strong characteristics of sub-functionalization, which might contribute to a sophisticated and efficient Ras-dependent regulating network for the hypoxia-tolerant fish.
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Affiliation(s)
- Zi-Xia Zhao
- CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
| | - Ding-Chen Cao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Jian Xu
- CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Ru Xu
- CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Jiong-Tang Li
- CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Yan Zhang
- CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Peng Xu
- CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Xiao-Wen Sun
- CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
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Soler M, Camargo ELO, Carocha V, Cassan-Wang H, San Clemente H, Savelli B, Hefer CA, Paiva JAP, Myburg AA, Grima-Pettenati J. The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function. THE NEW PHYTOLOGIST 2015; 206:1364-77. [PMID: 25250741 DOI: 10.1111/nph.13039] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/05/2014] [Indexed: 05/19/2023]
Abstract
The R2R3-MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide. A total of 141 predicted R2R3-MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR. We found some R2R3-MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed. In Eucalyptus, R2R3-MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth.
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Affiliation(s)
- Marçal Soler
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Eduardo Leal Oliveira Camargo
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Victor Carocha
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal
| | - Hua Cassan-Wang
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Hélène San Clemente
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Bruno Savelli
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Charles A Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Jorge A Pinto Paiva
- Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal
- Instituto de Investigaçao Científica e Tropical (IICT/MNE) Palacio Burnay - Rua da Junqueira, 30, 1349-007, Lisboa, Portugal
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Jacqueline Grima-Pettenati
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
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Lee PT, Zou J, Holland JW, Martin SAM, Scott CJW, Kanellos T, Secombes CJ. Functional characterisation of a TLR accessory protein, UNC93B1, in Atlantic salmon (Salmo salar). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 50:38-48. [PMID: 25576824 DOI: 10.1016/j.dci.2014.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 06/04/2023]
Abstract
Toll-like receptors (TLRs) are indispensable components of the innate immune system, which recognise conserved pathogen associated molecular patterns (PAMPs) and induce a series of defensive immune responses to protect the host. Biosynthesis, localisation and activation of TLRs are dependent on TLR accessory proteins. In this study, we identified the accessory protein, UNC93B1, from Atlantic salmon (Salmo salar) whole-genome shotgun (WGS) contigs aided by the conserved gene synteny of genes flanking UNC93B1 in fish, birds and mammals. Phylogenetic analysis showed that salmon UNC93B1 grouped with other vertebrate UNC93B1 molecules, and had highest amino acid identity and similarity to zebrafish UNC93B1. The salmon UNC93B1 gene organisation was also similar in structure to mammalian UNC93B1. Our gene expression studies revealed that salmon UNC93B1 was more highly expressed in spleen, liver and gill tissues but was expressed at a lower level in head kidney tissue in post-smolts relative to parr. Moreover, salmon UNC93B1 mRNA transcripts were up-regulated in vivo in spleen tissue from polyI:C treated salmon and in vitro in polyI:C or IFNγ stimulated Salmon Head Kidney-1 (SHK-1) cells. Initial studies into the functional role of salmon UNC93B1 in fish TLR signalling found that both wild type salmon UNC93B1 and a molecule with a site-directed mutation (H424R) co-immunoprecipitated with salmon TLR19, TLR20a and TLR20d. Overall, these data illustrate the potential importance of UNC93B1 as an accessory protein in fish TLR signalling.
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Affiliation(s)
- P T Lee
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - J Zou
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - J W Holland
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - S A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - C J W Scott
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - T Kanellos
- Animal Health Division, Zoetis, 23-25 avenue du Dr. Lannelongue, Paris Cedex 14 75668, France
| | - C J Secombes
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom.
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Altmann S, Rebl A, Kühn C, Goldammer T. Identification and de novo sequencing of housekeeping genes appropriate for gene expression analyses in farmed maraena whitefish (Coregonus maraena) during crowding stress. FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:397-412. [PMID: 25249196 DOI: 10.1007/s10695-014-9991-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/15/2014] [Indexed: 06/03/2023]
Abstract
Maraena whitefish (Coregonus maraena; synonym Coregonus lavaretus f. balticus) is a high-quality food fish in the Southern Baltic Sea belonging to the group of salmonid fishes. Coregonus sp. is successfully kept in aquaculture throughout northern Europe (e.g. in Finland, Germany, Russia) and North America. In this regard, the molecular and immunological characterisation of stress response in maraena whitefish contributes to the development of robust and fast-growing maraena whitefish breeding strains for aquaculture. Thus, in the present study, the potential housekeeping genes beta actin (ACTB), elongation factor 1 alpha (EEF1A1), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), ribosomal protein 9 (RPL9), ribosomal protein 32 (RPL32) and ribosomal protein S20 (RPS20) were de novo sequenced and tested concerning their applicability as reference genes in quantitative real-time PCR (qPCR) in maraena whitefish under different stocking densities. For this purpose, tissue samples of liver, kidney, gills, head kidney, skin, adipose tissue, heart and dorsal fin were investigated. qPCR data were analysed with Normfinder tool to determine gene expression stability. DNA sequencing exposed transcribed paralogous EEF1A1A and EEF1A1B genes differing in their putative protein structure. Normfinder analysis revealed RPL9 and RPL32 as most stable, GAPDH and ACTB as least stable genes for qPCR analyses, respectively. This is the first study that provides a subset of seven de novo sequenced housekeeping genes usable as reference genes in studies of stress response in maraena whitefish.
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Affiliation(s)
- Simone Altmann
- Fish Genetics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
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Passarini MRZ, Ottoni CA, Santos C, Lima N, Sette LD. Induction, expression and characterisation of laccase genes from the marine-derived fungal strains Nigrospora sp. CBMAI 1328 and Arthopyrenia sp. CBMAI 1330. AMB Express 2015; 5:19. [PMID: 25852996 PMCID: PMC4385153 DOI: 10.1186/s13568-015-0106-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/26/2015] [Indexed: 11/10/2022] Open
Abstract
The capability of the fungi Nigrospora sp. CBMAI 1328 and Arthopyrenia sp. CBMAI 1330 isolated from marine sponge to synthesise laccases (Lcc) in the presence of the inducer copper (1–10 μM) was assessed. In a liquid culture medium supplemented with 5 μM of copper sulphate after 5 days of incubation, Nigrospora sp. presented the highest Lcc activity (25.2 U·L−1). The effect of copper on Lcc gene expression was evaluated by reverse transcriptase polymerase chain reaction. Nigrospora sp. showed the highest gene expression of Lcc under the same conditions of Lcc synthesis. The highest Lcc expression by the Arthopyrenia sp. was detected at 96 h of incubation in absence of copper. Molecular approaches allowed the detection of Lcc isozymes and suggest the presence of at least two undescribed putative genes. Additionally, Lcc sequences from the both fungal strains clustered with other Lcc sequences from other fungi that inhabit marine environments.
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Berman JM, Brand C, Awayda MS. A long isoform of the epithelial sodium channel alpha subunit forms a highly active channel. Channels (Austin) 2015; 9:30-43. [PMID: 25517724 DOI: 10.4161/19336950.2014.985478] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A long isoform of the human Epithelial Sodium Channel (ENaC) α subunit has been identified, but little data exist regarding the properties or regulation of channels formed by α728. The baseline whole cell conductance of oocytes expressing trimeric α728βγ channels was 898.1±277.2 and 49.59±13.2 µS in low and high sodium solutions, respectively, and was 11 and 2 fold higher than the conductances of α669βγ in same solutions. α728βγ channels were also 2 to 5 fold less sensitive to activation by the serine proteases subtilisin and trypsin than α669βγ in low and high Na+ conditions. The long isoform exhibited lower levels of full length and cleaved protein at the plasma membrane and a rightward shifted sensitivity to inhibition by increases of [Na+]i. Both channels displayed similar single channel conductances of 4 pS, and both were activated to a similar extent by reducing temperature, altogether indicating that activation of baseline conductance of α728βγ was likely mediated by enhanced channel activity or open probability. Expression of α728 in native kidneys was validated in human urinary exosomes. These data demonstrate that the long isoform of αENaC forms the structural basis of a channel with different activity and regulation, which may not be easily distinguishable in native tissue, but may underlie sodium hyperabsorption and salt sensitive differences in humans.
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Affiliation(s)
- Jonathan M Berman
- a Department of Physiology and Biophysics ; State University of New York at Buffalo ; Buffalo , NY USA
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Hou Q, Bartels D. Comparative study of the aldehyde dehydrogenase (ALDH) gene superfamily in the glycophyte Arabidopsis thaliana and Eutrema halophytes. ANNALS OF BOTANY 2015; 115:465-79. [PMID: 25085467 PMCID: PMC4332599 DOI: 10.1093/aob/mcu152] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 05/28/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Stresses such as drought or salinity induce the generation of reactive oxygen species, which subsequently cause excessive accumulation of aldehydes in plant cells. Aldehyde dehydrogenases (ALDHs) are considered as 'aldehyde scavengers' to eliminate toxic aldehydes caused by oxidative stress. The completion of the genome sequencing projects of the halophytes Eutrema parvulum and E. salsugineum has paved the way to explore the relationships and the roles of ALDH genes in the glycophyte Arabidopsis thaliana and halophyte model plants. METHODS Protein sequences of all plant ALDH families were used as queries to search E. parvulum and E. salsugineum genome databases. Evolutionary analyses compared the phylogenetic relationships of ALDHs from A. thaliana and Eutrema. Expression patterns of several stress-associated ALDH genes were investigated under different salt conditions using reverse transcription-PCR. Putative cis-elements in the promoters of ALDH10A8 from A. thaliana and E. salsugineum were compared in silico. KEY RESULTS Sixteen and 17 members of ten ALDH families were identified from E. parvulum and E. salsugineum genomes, respectively. Phylogenetic analysis of ALDH protein sequences indicated that Eutrema ALDHs are closely related to those of Arabidopsis, and members within these species possess nearly identical exon-intron structures. Gene expression analysis under different salt conditions showed that most of the ALDH genes have similar expression profiles in Arabidopsis and E. salsugineum, except for ALDH7B4 and ALDH10A8. In silico analysis of promoter regions of ALDH10A8 revealed different distributions of cis-elements in E. salsugineum and Arabidopsis. CONCLUSIONS Genomic organization, copy number, sub-cellular localization and expression profiles of ALDH genes are conserved in Arabidopsis, E. parvulum and E. salsugineum. The different expression patterns of ALDH7B4 and ALDH10A8 in Arabidopsis and E. salsugineum suggest that E. salsugineum uses modified regulatory pathways, which may contribute to salinity tolerance.
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Affiliation(s)
- Quancan Hou
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, D-53315 Bonn, Germany
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, D-53315 Bonn, Germany
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Przysiecka Ł, Książkiewicz M, Wolko B, Naganowska B. Structure, expression profile and phylogenetic inference of chalcone isomerase-like genes from the narrow-leafed lupin (Lupinus angustifolius L.) genome. FRONTIERS IN PLANT SCIENCE 2015; 6:268. [PMID: 25954293 PMCID: PMC4404975 DOI: 10.3389/fpls.2015.00268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/03/2015] [Indexed: 05/20/2023]
Abstract
Lupins, like other legumes, have a unique biosynthesis scheme of 5-deoxy-type flavonoids and isoflavonoids. A key enzyme in this pathway is chalcone isomerase (CHI), a member of CHI-fold protein family, encompassing subfamilies of CHI1, CHI2, CHI-like (CHIL), and fatty acid-binding (FAP) proteins. Here, two Lupinus angustifolius (narrow-leafed lupin) CHILs, LangCHIL1 and LangCHIL2, were identified and characterized using DNA fingerprinting, cytogenetic and linkage mapping, sequencing and expression profiling. Clones carrying CHIL sequences were assembled into two contigs. Full gene sequences were obtained from these contigs, and mapped in two L. angustifolius linkage groups by gene-specific markers. Bacterial artificial chromosome fluorescence in situ hybridization approach confirmed the localization of two LangCHIL genes in distinct chromosomes. The expression profiles of both LangCHIL isoforms were very similar. The highest level of transcription was in the roots of the third week of plant growth; thereafter, expression declined. The expression of both LangCHIL genes in leaves and stems was similar and low. Comparative mapping to reference legume genome sequences revealed strong syntenic links; however, LangCHIL2 contig had a much more conserved structure than LangCHIL1. LangCHIL2 is assumed to be an ancestor gene, whereas LangCHIL1 probably appeared as a result of duplication. As both copies are transcriptionally active, questions arise concerning their hypothetical functional divergence. Screening of the narrow-leafed lupin genome and transcriptome with CHI-fold protein sequences, followed by Bayesian inference of phylogeny and cross-genera synteny survey, identified representatives of all but one (CHI1) main subfamilies. They are as follows: two copies of CHI2, FAPa2 and CHIL, and single copies of FAPb and FAPa1. Duplicated genes are remnants of whole genome duplication which is assumed to have occurred after the divergence of Lupinus, Arachis, and Glycine.
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Affiliation(s)
- Łucja Przysiecka
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
- NanoBioMedical Centre, Adam Mickiewicz UniversityPoznań, Poland
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
- *Correspondence: Michał Książkiewicz, Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań 60-479, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of SciencesPoznań, Poland
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Kuderová A, Gallová L, Kuricová K, Nejedlá E, Čurdová A, Micenková L, Plíhal O, Šmajs D, Spíchal L, Hejátko J. Identification of AHK2- and AHK3-like cytokinin receptors in Brassica napus reveals two subfamilies of AHK2 orthologues. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:339-53. [PMID: 25336686 DOI: 10.1093/jxb/eru422] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cytokinin (CK) signalling is known to play key roles in the regulation of plant growth and development, crop yields, and tolerance to both abiotic stress and pathogen defences, but the mechanisms involved are poorly characterized in dicotyledonous crops. Here the identification and functional characterization of sensor histidine kinases homologous to Arabidopsis CK receptors AHK2 and AHK3 in winter oilseed rape are presented. Five CHASE-containing His kinases were identified in Brassica napus var. Tapidor (BnCHK1-BnCHK5) by heterologous hybridization of its genomic library with gene-specific probes from Arabidopsis. The identified bacterial artificial chromosome (BAC) clones were fingerprinted and representative clones in five distinct groups were sequenced. Using a bioinformatic approach and cDNA cloning, the precise gene and putative protein domain structures were determined. Based on phylogenetic analysis, four AHK2 (BnCHK1-BnCHK4) homologues and one AHK3 (BnCHK5) homologue were defined. It is further suggested that BnCHK1 and BnCHK3, and BnCHK5 are orthologues of AHK2 and AHK3, originally from the B. rapa A genome, respectively. BnCHK1, BnCHK3, and BnCHK5 displayed high affinity for trans-zeatin (1-3nM) in a live-cell competitive receptor assay, but not with other plant hormones (indole acetic acid, GA3, and abscisic acid), confirming the prediction that they are genuine CK receptors. It is shown that BnCHK1 and BnCHK3, and BnCHK5 display distinct preferences for various CK bases and metabolites, characteristic of their AHK counterparts, AHK2 and AHK3, respectively. Interestingly, the AHK2 homologues could be divided into two subfamilies (BnCHK1/BnCK2 and BnCHK3/BnCHK4) that differ in putative transmembrane domain topology and CK binding specificity, thus implying potential functional divergence.
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Affiliation(s)
- Alena Kuderová
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lucia Gallová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Katarína Kuricová
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eliška Nejedlá
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Anna Čurdová
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lenka Micenková
- Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ondřej Plíhal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - David Šmajs
- Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lukáš Spíchal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
| | - Jan Hejátko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. ACTA ACUST UNITED AC 2014; 31:1296-7. [PMID: 25504850 PMCID: PMC4393523 DOI: 10.1093/bioinformatics/btu817] [Citation(s) in RCA: 2232] [Impact Index Per Article: 223.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/07/2014] [Indexed: 11/16/2022]
Abstract
Summary: Visualizing genes’ structure and annotated features helps biologists to investigate their function and evolution intuitively. The Gene Structure Display Server (GSDS) has been widely used by more than 60 000 users since its first publication in 2007. Here, we reported the upgraded GSDS 2.0 with a newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure. Moreover, a user-specified phylogenetic tree can be added to facilitate further evolutionary analysis. The full source code is also available for downloading. Availability and implementation: Web server and source code are freely available at http://gsds.cbi.pku.edu.cn. Contact: gaog@mail.cbi.pku.edu.cn or gsds@mail.cbi.pku.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bo Hu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Jinpu Jin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - An-Yuan Guo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - He Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Jingchu Luo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
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