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Wang H, Chen M, Wei X, Xia R, Pei D, Huang X, Han B. Computational tools for plant genomics and breeding. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2578-6. [PMID: 38676814 DOI: 10.1007/s11427-024-2578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024]
Abstract
Plant genomics and crop breeding are at the intersection of biotechnology and information technology. Driven by a combination of high-throughput sequencing, molecular biology and data science, great advances have been made in omics technologies at every step along the central dogma, especially in genome assembling, genome annotation, epigenomic profiling, and transcriptome profiling. These advances further revolutionized three directions of development. One is genetic dissection of complex traits in crops, along with genomic prediction and selection. The second is comparative genomics and evolution, which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant discovery. The third direction is the development of deep learning approaches for the rational design of biological sequences, especially proteins, for synthetic biology. All three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.
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Affiliation(s)
- Hai Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Mengjiao Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
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2
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Fan S, Yang S, Li G, Wan S. Genome-Wide Identification and Characterization of CDPK Gene Family in Cultivated Peanut ( Arachis hypogaea L.) Reveal Their Potential Roles in Response to Ca Deficiency. Cells 2023; 12:2676. [PMID: 38067104 PMCID: PMC10705679 DOI: 10.3390/cells12232676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
This study identified 45 calcium-dependent protein kinase (CDPK) genes in cultivated peanut (Arachis hypogaea L.), which are integral in plant growth, development, and stress responses. These genes, classified into four subgroups based on phylogenetic relationships, are unevenly distributed across all twenty peanut chromosomes. The analysis of the genetic structure of AhCDPKs revealed significant similarity within subgroups, with their expansion primarily driven by whole-genome duplications. The upstream promoter sequences of AhCDPK genes contained 46 cis-acting regulatory elements, associated with various plant responses. Additionally, 13 microRNAs were identified that target 21 AhCDPK genes, suggesting potential post-transcriptional regulation. AhCDPK proteins interacted with respiratory burst oxidase homologs, suggesting their involvement in redox signaling. Gene ontology and KEGG enrichment analyses affirmed AhCDPK genes' roles in calcium ion binding, protein kinase activity, and environmental adaptation. RNA-seq data revealed diverse expression patterns under different stress conditions. Importantly, 26 AhCDPK genes were significantly induced when exposed to Ca deficiency during the pod stage. During the seedling stage, four AhCDPKs (AhCDPK2/-25/-28/-45) in roots peaked after three hours, suggesting early signaling roles in pod Ca nutrition. These findings provide insights into the roles of CDPK genes in plant development and stress responses, offering potential candidates for predicting calcium levels in peanut seeds.
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Affiliation(s)
| | | | - Guowei Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan 250100, China; (S.F.); (S.Y.)
| | - Shubo Wan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan 250100, China; (S.F.); (S.Y.)
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3
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Mehrasa R, Cristea I, Bredrup C, Rødahl E, Bruland O. Functional characterization of all-trans retinoic acid-induced differentiation factor (ATRAID). FEBS Open Bio 2023; 13:1874-1886. [PMID: 37530719 PMCID: PMC10549228 DOI: 10.1002/2211-5463.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/09/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
All-trans retinoic acid-induced differentiation (ATRAID) factor was first identified in HL60 cells. Several mRNA isoforms exist, but the respective proteins have not been fully characterized. In transfected cells expressing Myc-Flag-tagged ATRAID Isoform (Iso) A, B, and C, Iso C was found to be expressed at high levels, Iso A was found to be expressed at low levels due to rapid degradation, and the predicted protein expressed from Iso B was not detected. Iso C was present mainly in an N-glycosylated form. In subcellular fractionation experiments, Iso C localized to the membranous and nuclear fractions, while immunofluorescence analysis revealed that Iso C is located close to the plasma membrane, mainly in cytoplasmic vesicles and in the Golgi area. We confirm that Iso C colocalizes to some extent with endosomal/lysosomal markers LAMP1 and LAMP2. Furthermore, we show that ATRAID co-localizes with RAB11, a GTPase associated with recycling endosomes and implicated in regulating vesicular trafficking.
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Affiliation(s)
- Roya Mehrasa
- Department of Clinical MedicineUniversity of BergenNorway
- Department of Medical GeneticsHaukeland University HospitalBergenNorway
| | - Ileana Cristea
- Department of Clinical MedicineUniversity of BergenNorway
- Department of OphthalmologyHaukeland University HospitalBergenNorway
| | - Cecilie Bredrup
- Department of Clinical MedicineUniversity of BergenNorway
- Department of OphthalmologyHaukeland University HospitalBergenNorway
| | - Eyvind Rødahl
- Department of Clinical MedicineUniversity of BergenNorway
- Department of OphthalmologyHaukeland University HospitalBergenNorway
| | - Ove Bruland
- Department of Medical GeneticsHaukeland University HospitalBergenNorway
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4
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Asensio-Calavia P, González-Acosta S, Otazo-Pérez A, López MR, Morales-delaNuez A, Pérez de la Lastra JM. Teleost Piscidins-In Silico Perspective of Natural Peptide Antibiotics from Marine Sources. Antibiotics (Basel) 2023; 12:antibiotics12050855. [PMID: 37237758 DOI: 10.3390/antibiotics12050855] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Fish, like all other animals, are exposed to constant contact with microbes, both on their skin and on the surfaces of their respiratory and digestive systems. Fish have a system of non-specific immune responses that provides them with initial protection against infection and allows them to survive under normal conditions despite the presence of these potential invaders. However, fish are less protected against invading diseases than other marine vertebrates because their epidermal surface, composed primarily of living cells, lacks the keratinized skin that serves as an efficient natural barrier in other marine vertebrates. Antimicrobial peptides (AMPs) are one type of innate immune protection present in all life forms. AMPs have been shown to have a broader range of biological effects than conventional antibiotics, including antibacterial, antiviral, antiprotozoal, and antifungal effects. Although other AMPs, such as defensins and hepcidins, are found in all vertebrates and are relatively well conserved, piscidins are found exclusively in Teleost fish and are not found in any other animal. Therefore, there is less information on the expression and bioactivity of piscidins than on other AMPs. Piscidins are highly effective against Gram-positive and Gram-negative bacteria that cause disease in fish and humans and have the potential to be used as pharmacological anti-infectives in biomedicine and aquaculture. To better understand the potential benefits and limitations of using these peptides as therapeutic agents, we are conducting a comprehensive study of the Teleost piscidins included in the "reviewed" category of the UniProt database using bioinformatics tools. They all have amphipathic alpha-helical structures. The amphipathic architecture of piscidin peptides and positively charged residues influence their antibacterial activity. These alpha-helices are intriguing antimicrobial drugs due to their stability in high-salt and metal environments. New treatments for multidrug-resistant bacteria, cancer, and inflammation may be inspired by piscidin peptides.
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Affiliation(s)
- Patricia Asensio-Calavia
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de La Laguna, Spain
- School of Doctoral and Graduate Studies, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-Apdo. 456, 38200 San Cristóbal de La Laguna, Spain
| | - Sergio González-Acosta
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de La Laguna, Spain
- School of Doctoral and Graduate Studies, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-Apdo. 456, 38200 San Cristóbal de La Laguna, Spain
| | - Andrea Otazo-Pérez
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de La Laguna, Spain
- School of Doctoral and Graduate Studies, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-Apdo. 456, 38200 San Cristóbal de La Laguna, Spain
| | - Manuel R López
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de La Laguna, Spain
| | - Antonio Morales-delaNuez
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de La Laguna, Spain
| | - José Manuel Pérez de la Lastra
- Biotechnology of Macromolecules Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206 San Cristóbal de La Laguna, Spain
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5
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Lim CP, Kok BH, Lim HT, Chuah C, Abdul Rahman B, Abdul Majeed AB, Wykes M, Leow CH, Leow CY. Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design. Pathog Glob Health 2023; 117:134-151. [PMID: 35550001 PMCID: PMC9970233 DOI: 10.1080/20477724.2022.2072456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally devastated public health, the economies of many countries and quality of life universally. The recent emergence of immune-escaped variants and scenario of vaccinated individuals being infected has raised the global concerns about the effectiveness of the current available vaccines in transmission control and disease prevention. Given the high rate mutation of SARS-CoV-2, an efficacious vaccine targeting against multiple variants that contains virus-specific epitopes is desperately needed. An immunoinformatics approach is gaining traction in vaccine design and development due to the significant reduction in time and cost of immunogenicity studies and increasing reliability of the generated results. It can underpin the development of novel therapeutic methods and accelerate the design and production of peptide vaccines for infectious diseases. Structural proteins, particularly spike protein (S), along with other proteins have been studied intensively as promising coronavirus vaccine targets. Numbers of promising online immunological databases, tools and web servers have widely been employed for the design and development of next generation COVID-19 vaccines. This review highlights the role of immunoinformatics in identifying immunogenic peptides as potential vaccine targets, involving databases, and prediction and characterization of epitopes which can be harnessed for designing future coronavirus vaccines.
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Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia.,Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Health Sciences, Universiti Teknologi MARA, Penang, Malaysia
| | | | | | - Michelle Wykes
- Molecular Immunology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
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6
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Strejčková B, Mazzucotelli E, Čegan R, Milec Z, Brus J, Çakır E, Mastrangelo AM, Özkan H, Šafář J. Wild emmer wheat, the progenitor of modern bread wheat, exhibits great diversity in the VERNALIZATION1 gene. FRONTIERS IN PLANT SCIENCE 2023; 13:1106164. [PMID: 36684759 PMCID: PMC9853909 DOI: 10.3389/fpls.2022.1106164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Wild emmer wheat is an excellent reservoir of genetic variability that can be utilized to improve cultivated wheat to address the challenges of the expanding world population and climate change. Bearing this in mind, we have collected a panel of 263 wild emmer wheat (WEW) genotypes across the Fertile Crescent. The genotypes were grown in different locations and phenotyped for heading date. Genome-wide association mapping (GWAS) was carried out, and 16 SNPs were associated with the heading date. As the flowering time is controlled by photoperiod and vernalization, we sequenced the VRN1 gene, the most important of the vernalization response genes, to discover new alleles. Unlike most earlier attempts, which characterized known VRN1 alleles according to a partial promoter or intron sequences, we obtained full-length sequences of VRN-A1 and VRN-B1 genes in a panel of 95 wild emmer wheat from the Fertile Crescent and uncovered a significant sequence variation. Phylogenetic analysis of VRN-A1 and VRN-B1 haplotypes revealed their evolutionary relationships and geographic distribution in the Fertile Crescent region. The newly described alleles represent an attractive resource for durum and bread wheat improvement programs.
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Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) Research Centre for Genomics and Bioinformatics via San Protaso 302, Fiorenzuola d’Arda, Italy
| | - Radim Čegan
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, ;Czechia
| | - Zbyněk Milec
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Esra Çakır
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics (CREA) Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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7
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Xu J, Wang Q, Wang S, Huang W, Xie Y, Gu X, He R, Peng X, Wu S, Yang G. Comparative genomics of Sarcoptes scabiei provide new insights into adaptation to permanent parasitism and within-host species divergence. Transbound Emerg Dis 2022; 69:3468-3484. [PMID: 36134513 DOI: 10.1111/tbed.14706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 02/04/2023]
Abstract
Sarcoptes scabiei is the causative agent of a highly contagious skin disease in humans and more than 100 mammals. Here, we reported the first chromosome-level reference genome of S. scabiei isolated from rabbits, with a contig N50 size of 5.92 Mb, a total assembled length of 57.30 Mb, ∼12.65% repetitive sequences and 9333 predicted protein-coding genes. The phylogenetic tree based on 1338 shared high-confidence single-copy orthologous genes estimated that the mammalian ectoparasite S. scabiei and the plant-feeding mite Tetranychus urticae separated ∼340 million years ago. Both neighbour-joining tree and principal component analysis of 20 mite populations isolated from four hosts (humans, pigs, dogs and rabbits) distributed in three countries (China, Australia and the USA) consistently supported genetic subdivisions according to host species rather than geographical location. The demographic history of S. scabiei reconstructed by multiple sequentially Markovian coalescent analysis suggested that S. scabiei isolated from rabbits, humans, dogs and pigs diverged ∼5000 years ago. Investigation of the homeobox (Hox) genes revealed that S. scabiei contains 8 of 10 canonical Hox genes that are present in the arthropod ancestor, and the absence of the Abd-A gene may correlate with the long gap between their front and back legs. Comparative genomics demonstrated that genes specific to scabies mites were mainly enriched in nutrition digestive systems, whereas genes in the families that involved detoxification (cytochrome P450, carboxyl/cholinesterases and the ATP-binding cassette transporter C group) were extremely contracted compared with that of other mites analysed in this study. Selective sweep analysis of mite populations from various pairs of two out of the four host species revealed that the strongest selective sweep signals were mainly enriched in cysteine-type peptidase activity and apoptosis. The results provided clues for the mechanisms of S. scabiei adaptation to a permanent parasitic lifestyle and knowledge that would enable further control of this highly contagious skin disease.
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Affiliation(s)
- Jing Xu
- Department, of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | | | - Sen Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China.,Bioinformatics Center, Beijing University of Agriculture, Beijing, China
| | | | - Yue Xie
- Department, of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaobin Gu
- Department, of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ran He
- Department, of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Guangyou Yang
- Department, of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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He F, Kuwasako K, Takizawa M, Takahashi M, Tsuda K, Nagata T, Watanabe S, Tanaka A, Kobayashi N, Kigawa T, Güntert P, Shirouzu M, Yokoyama S, Muto Y. 1H, 13C and 15N resonance assignments and solution structures of the two RRM domains of Matrin-3. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:41-49. [PMID: 34783967 DOI: 10.1007/s12104-021-10057-0] [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: 08/10/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Matrin-3 is a multifunctional protein that binds to both DNA and RNA. Its DNA-binding activity is linked to the formation of the nuclear matrix and transcriptional regulation, while its RNA-binding activity is linked to mRNA metabolism including splicing, transport, stabilization, and degradation. Correspondingly, Matrin-3 has two zinc finger domains for DNA binding and two consecutive RNA recognition motif (RRM) domains for RNA binding. Matrin-3 has been reported to cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) when its disordered region contains pathogenic mutations. Simultaneously, it has been shown that the RNA-binding activity of Matrin-3 mediated by its RRM domains, affects the formation of insoluble cytoplasmic granules, which are related to the pathogenic mechanism of ALS/FTD. Thus, the effect of the RRM domains on the phase separation of condensed protein/RNA mixtures has to be clarified for a comprehensive understanding of ALS/FTD. Here, we report the 1H, 15N, and 13C resonance assignments of the two RNA binding domains and their solution structures. The resonance assignments and the solution structures obtained in this work will contribute to the elucidation of the molecular basis of Matrin-3 in the pathogenic mechanism of ALS and/or FTD.
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Affiliation(s)
- Fahu He
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kanako Kuwasako
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Masayuki Takizawa
- Department of Pharmaceutical Sciences, Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Mari Takahashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kengo Tsuda
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Takashi Nagata
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Satoru Watanabe
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Akiko Tanaka
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Naohiro Kobayashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Yokohama NMR Facility, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takanori Kigawa
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Peter Güntert
- Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan
- Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Mikako Shirouzu
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
| | - Yutaka Muto
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- Department of Pharmaceutical Sciences, Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan.
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9
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Xu HF, Dai GZ, Wang YJ, Cheng C, Shang JL, Li RH, Liu K, Duanmu D, Qiu BS. Expansion of bilin-based red light sensors in the subaerial desert cyanobacterium Nostoc flagelliforme. Environ Microbiol 2022; 24:2047-2058. [PMID: 35172392 DOI: 10.1111/1462-2920.15932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022]
Abstract
Light is the crucial environmental signal for desiccation-tolerant cyanobacteria to activate photosynthesis and prepare for desiccation at dawn. However, the photobiological characteristics of desert cyanobacteria adaptation to one of the harshest habitats on Earth remain unresolved. In this study, we surveyed the genome of a subaerial desert cyanobacterium Nostoc flagelliforme and identified two phytochromes and seven cyanobacteriochromes (CBCRs) with one or more bilin-binding GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains. Biochemical and spectroscopic analyses of 69 purified GAF-containing proteins from recombinant phycocyanobilin (PCB), biliverdin or phycoerythrobilin-producing Escherichia coli indicated that nine of these proteins bind chromophores. Further investigation revealed that 11 GAFs form covalent adducts responsive to near-UV and visible light: eight GAFs contained PCB chromophores, three GAFs contained biliverdin chromophores and one contained the PCB isomer, phycoviolobilin. Interestingly, COO91_03972 is the first-ever reported GAF-only CBCR capable of sensing five wavelengths of light. Bioinformatics and biochemical analyses revealed that residue P132 of COO91_03972 is essential for chromophore binding to dual-cysteine CBCRs. Furthermore, the complement of N. flagelliforme CBCRs is enriched in red light sensors. We hypothesize that these sensors are critical for the acclimatization of N. flagelliforme to weak light environments at dawn.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Jie Wang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Chao Cheng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ren-Han Li
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ke Liu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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10
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Naha A, Banerjee S, Debroy R, Basu S, Ashok G, Priyamvada P, Kumar H, Preethi A, Singh H, Anbarasu A, Ramaiah S. Network metrics, structural dynamics and density functional theory calculations identified a novel Ursodeoxycholic Acid derivative against therapeutic target Parkin for Parkinson's disease. Comput Struct Biotechnol J 2022; 20:4271-4287. [PMID: 36051887 PMCID: PMC9399899 DOI: 10.1016/j.csbj.2022.08.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/23/2022] [Accepted: 08/07/2022] [Indexed: 12/03/2022] Open
Abstract
GIN analysis revealed PARK2, LRRK2, PARK7, PINK1 and SNCA as hub-genes. Topologically favoured Parkin was considered as a therapeutic target. ADMET screening identified a novel UDCA derivative as potential lead candidate. Chemical reactivity and ligand stability were analysed through DFT simulation. Docking and MDS established novel lead as potential Parkin inhibitor.
Parkinson's disease (PD) has been designated as one of the priority neurodegenerative disorders worldwide. Although diagnostic biomarkers have been identified, early onset detection and targeted therapy are still limited. An integrated systems and structural biology approach were adopted to identify therapeutic targets for PD. From a set of 49 PD associated genes, a densely connected interactome was constructed. Based on centrality indices, degree of interaction and functional enrichments, LRRK2, PARK2, PARK7, PINK1 and SNCA were identified as the hub-genes. PARK2 (Parkin) was finalized as a potent theranostic candidate marker due to its strong association (score > 0.99) with α-synuclein (SNCA), which directly regulates PD progression. Besides, modeling and validation of Parkin structure, an extensive virtual-screening revealed small (commercially available) inhibitors against Parkin. Molecule-258 (ZINC5022267) was selected as a potent candidate based on pharmacokinetic profiles, Density Functional Theory (DFT) energy calculations (ΔE = 6.93 eV) and high binding affinity (Binding energy = -6.57 ± 0.1 kcal/mol; Inhibition constant = 15.35 µM) against Parkin. Molecular dynamics simulation of protein-inhibitor complexes further strengthened the therapeutic propositions with stable trajectories (low structural fluctuations), hydrogen bonding patterns and interactive energies (>0kJ/mol). Our study encourages experimental validations of the novel drug candidate to prevent the auto-inhibition of Parkin mediated ubiquitination in PD.
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11
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Xu D, Zhang W, Chen R, Song H, Tian L, Tan P, Wang L, Zhu Q, Wu B, Lou B, Min J, Zhou J. Chromosome-scale assembly and high-density genetic map of the yellow drum, Nibea albiflora. Sci Data 2021; 8:268. [PMID: 34654820 PMCID: PMC8521588 DOI: 10.1038/s41597-021-01045-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/18/2021] [Indexed: 11/15/2022] Open
Abstract
The yellow drum (Nibea albiflora) is an economically important sciaenid fish in East Asian countries. In this study, we sequenced and assembled a near-complete gynogenetic yellow drum genome. We generated 45.63 Gb of Illumina short-reads and 80.27 Gb of PacBio long-reads and assembled them into a 628.01-Mb genome with a contig N50 of 4.42 Mb. Twenty-four chromosomes with a scaffold N50 of 26.73 Mb were obtained using the Hi-C analysis. We predicted a set of 27,069 protein-coding genes, of which 1,581 and 2,583 were expanded and contracted gene families, respectively. The most expanded genes were categorised into the protein binding, zinc-ion binding and ATP binding functional pathways. We built a high-density genetic linkage map that spanned 4,300.2 cM with 24 linkage groups and a resolution of 0.69 cM. The high-quality reference genome and annotated profiles that we produced will not only increase our understanding of the genetic architecture of economic traits in the yellow drum, but also help us explore the evolution and unique biological characteristics of sciaenid fishes.
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Affiliation(s)
- Dongdong Xu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, 316100, Zhoushan, China.
| | - Wanchang Zhang
- Key Lab of Aquatic Resources and Utilization of Jiangxi Province, School of Life Sciences, Nanchang University, 999 Xuefu Avenue, Nanchang, 330031, China
| | - Ruiyi Chen
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, 316100, Zhoushan, China
| | - Hongbin Song
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, 316100, Zhoushan, China
| | - Lu Tian
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, 316100, Zhoushan, China
| | - Peng Tan
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, 316100, Zhoushan, China
| | - Ligai Wang
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, 316100, Zhoushan, China
| | - Qihui Zhu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, 316100, Zhoushan, China
| | - Bin Wu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Bao Lou
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Jiumeng Min
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Juhong Zhou
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
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12
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Shirasawa K, Chahota R, Hirakawa H, Nagano S, Nagasaki H, Sharma T, Isobe S. A chromosome-scale draft genome sequence of horsegram ( Macrotyloma uniflorum). GIGABYTE 2021; 2021:gigabyte30. [PMID: 36824333 PMCID: PMC9650294 DOI: 10.46471/gigabyte.30] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
Horsegram (Macrotyloma uniflorum [Lam.] Verdc.) is an underutilized warm-season diploid legume (2n = 20, 22). Because of its ability to grow under water-deficient and marginal soil conditions, horsegram is a preferred choice in the era of global climate change. In recognition of its potential as a crop species, we generated and analyzed a draft genome sequence for a horsegram variety, HPK-4. Ten chromosome-scale pseudomolecules were created by aligning Illumina scaffold sequences onto a linkage map. The total length of the ten pseudomolecules was 259.2 Mbp, covering 89% of the total length of the assembled sequences. A total of 36,105 genes were predicted on the assembled sequences. Diversity analysis of 89 horsegram accessions by dd-RAD-Seq identified 277 single nucleotide polymorphisms (SNPs), suggesting narrow genetic diversity among the horsegram accessions. This is the first attempt to generate a draft genome sequence of horsegram and will provide a reference for sequence-based analysis of horsegram germplasm.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Rakesh Chahota
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh 176062, India
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Soichiro Nagano
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan,Forest Tree Breeding Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan
| | - Hideki Nagasaki
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tilak Sharma
- ICAR – Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand 834010, India
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan, Corresponding author. E-mail:
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13
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Gonzales-Vigil E, vonLoessl ME, Chen JY, Li S, Haslam TM, Kunst L, Mansfield SD. Understanding the Role of Populus ECERIFERUM2-Likes in the Biosynthesis of Very-Long-Chain Fatty Acids for Cuticular Waxes. PLANT & CELL PHYSIOLOGY 2021; 62:827-838. [PMID: 33749753 DOI: 10.1093/pcp/pcab040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/28/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Cuticular waxes are derived from very-long-chain fatty acid (VLCFA) precursors made by the concerted action of four enzymes that form the fatty acid (FA) elongation complex. The condensing enzyme of the complex confers specificity to substrates of different chain lengths, yet on its own cannot account for the biosynthesis of VLCFAs longer than 28 carbons (C28). Recent evidence from Arabidopsis thaliana points to a synergistic role of clade II BAHD acyltransferases and condensing enzymes in the elongation of VLCFAs beyond C28. In Populus trichocarpa, clade II is composed of seven uncharacterized paralogous genes (PtCER2-like1-7). In the present study, five of these genes were heterologously expressed in yeast and their respective FA profiles were determined. PtCER2-likes differentially altered the accumulation of C28 and C30 FAs when expressed in the presence of the condensing enzyme AtCER6. Among these, PtCER2-like5 produced the highest levels of C28 FAs in yeast and its expression was localized to the epidermis in β-glucuronidase-reporter poplar lines, consistent with a role in cuticular wax biosynthesis. Complementation of the A. thaliana cer2-5 mutant with PtCER2-like5 increased the levels of C28-derived cuticular waxes at the expense of C30-derived components. Together, these results demonstrate that the role of CER2-likes in cuticular wax biosynthesis is conserved in Populus clade II BAHD acyltransferases.
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Affiliation(s)
- Eliana Gonzales-Vigil
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Michelle E vonLoessl
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jeff Y Chen
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Sitong Li
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Tegan M Haslam
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ljerka Kunst
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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14
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Chen Z, Shang JL, Hou S, Li T, Li Q, Yang YW, Hess WR, Qiu BS. Genomic and transcriptomic insights into the habitat adaptation of the diazotrophic paddy-field cyanobacterium Nostoc sphaeroides. Environ Microbiol 2021; 23:5802-5822. [PMID: 33848055 DOI: 10.1111/1462-2920.15521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Nitrogen-fixing cyanobacteria are common in paddy fields, one of the most productive wetland ecosystems. Here, we present the complete genome of Nostoc sphaeroides, a paddy-field diazotroph used for food and medicine for more than 1700 years and deciphered the transcriptional regulation during the developmental transition from hormogonia to vegetative filaments with heterocysts. The genome of N. sphaeroides consists of one circular chromosome (6.48 Mb), one of the largest ever reported megaplasmids (2.34 Mb), and seven plasmids. Multiple gene families involved in the adaption to high solar radiation and water fluctuation conditions were found expanded, while genes involved in anoxic adaptation and phosphonate utilization are located on the megaplasmid, suggesting its indispensable role in environmental adaptation. Distinct gene expression patterns were observed during the light-intensity-regulated transition from hormogonia to vegetative filaments, specifically, genes encoding proteins involved in photosynthetic light reaction, carbon fixation, nitrogen metabolism and heterocyst differentiation were significantly upregulated, whereas genes related to cell motility were down-regulated. Our results provide genomic and transcriptomic insights into the adaptation of a filamentous nitrogen-fixing cyanobacterium to the highly dynamic paddy-field habitat, suggesting N. sphaeroides as an excellent system to understand the transition from aquatic to terrestrial habitats and to support sustainable rice production.
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Affiliation(s)
- Zhen Chen
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.,Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jin-Long Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, CA, Los Angeles, 90089, USA
| | - Tao Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Qi Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Yi-Wen Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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15
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He F, Endo R, Kuwasako K, Takahashi M, Tsuda K, Nagata T, Watanabe S, Tanaka A, Kobayashi N, Kigawa T, Güntert P, Shirouzu M, Yokoyama S, Muto Y. 1H, 13C and 15N resonance assignment of the YTH domain of YTHDC2. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:1-7. [PMID: 32930954 DOI: 10.1007/s12104-020-09974-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
In humans, YTH (YT521-B homology) domain containing protein 2 (YTHDC2) plays a crucial role in the phase-shift from mitosis to meiosis. YTH domains bind to methylated adenosine nucleotides such as m6A. In a phylogenic tree, the YTH domain of YTHDC2 (YTH2) and that of the YTH containing protein YTHDC1 (YTH1) belong to the same sub-group. However, the binding affinity of m6A differs between these proteins. Here, we report 1H, 13C and 15N resonance assignment of YTH2 and its solution structure to examine the difference of the structural architecture and the dynamic properties of YTH1 and YTH2. YTH2 adopts a β1-α1-β2-α2-β3-β4-β5-α3-β6-α4 topology, which was also observed in YTH1. However, the β4-β5 loops of YTH1 and YTH2 are distinct in length and amino acid composition. Our data revealed that, unlike in YTH1, the structure of m6A-binding pocket of YTH2 formed by the β4-β5 loop is stabilized by electrostatic interaction. This assignment and the structural information for YTH2 will provide the insight on the further functional research of YTHDC2.
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Affiliation(s)
- Fahu He
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Ryuta Endo
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kanako Kuwasako
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan
| | - Mari Takahashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kengo Tsuda
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Takashi Nagata
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611 -0011, Japan
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Satoru Watanabe
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Akiko Tanaka
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Naohiro Kobayashi
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN SPring-8 Center, Yokohama, 230-0045, Japan
| | - Takanori Kigawa
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Peter Güntert
- Tatsuo Miyazawa Memorial Program, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan
- Institute of Biophysical Chemistry and Frankfurt Institute of Advanced Studies, Goethe-University Frankfurt, Max- von-Laue-Str.9, 60438, Frankfurt am Main, Germany
- Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Mikako Shirouzu
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Yutaka Muto
- RIKEN Center for Life Science and Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- RIKEN, Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
- Faculty of Pharmacy and Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, 202-8585, Japan.
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16
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Alsamri MT, Alabdouli A, Alkalbani AM, Iram D, Tawil MI, Antony P, Vijayan R, Souid AK. Genetic variants of small airways and interstitial pulmonary disease in children. Sci Rep 2021; 11:2715. [PMID: 33526882 PMCID: PMC7851163 DOI: 10.1038/s41598-021-81280-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic variants of small airways and interstitial pulmonary disease have not been comprehensively studied. This cluster of respiratory disorders usually manifests from early infancy (‘lung disease in utero’). In this study, 24 variants linked to these entities are described. The variants involved two genes associated with surfactant metabolism dysfunction (ABCA3 and CSF2RB), two with pulmonary fibrosis (MUC5B and SFTP), one with bronchiectasis (SCNN1B), and one with alpha-1-antitrypsin deficiency (SERPINA1). A nonsense variant, MUC5B:c.16861G > T, p.Glu5621*, was found in homozygous state in two siblings with severe respiratory disease from birth. One of the siblings also had heterozygous SFTPA1:c.675C > G, p.Asn225Lys, which resulted in a more severe respiratory disease. The sibling with only the homozygous MUC5B variant had lung biopsy, which showed alveolar simplification, interstitial fibrosis, intra-alveolar lipid-laden macrophages, and foci of foreign body giant cell reaction in distal airspaces. Two missense variants, MUC5B:c.14936 T > C, p.Ile4979Thr (rs201287218) and MUC5B:c.16738G > A, p.Gly5580Arg (rs776709402), were also found in compound heterozygous state in two siblings with severe respiratory disease from birth. Overall, the results emphasize the need for genetic studies for patients with complex respiratory problems. Identifying pathogenic variants, such as those presented here, assists in effective family counseling aimed at genetic prevention. In addition, results of genetic studies improve the clinical care and provide opportunities for participating in clinical trials, such as those involving molecularly-targeted therapies.
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Affiliation(s)
| | | | | | - Durdana Iram
- Departments of Pediatrics, Tawam Hospital, Al Ain, UAE
| | - Mohamed I Tawil
- Department of Radiology, Sheikh Khalifa Medical City, Abu Dhabi, UAE
| | - Priya Antony
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, UAE
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, UAE.
| | - Abdul-Kader Souid
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE.
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17
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Karaman Mayack B, Sippl W. Current In Silico Drug Repurposing Strategies. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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18
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Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 2020; 11:6014. [PMID: 33293529 PMCID: PMC7723042 DOI: 10.1038/s41467-020-19813-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition. A new donkey reference genome and comparisons with wild asses yields insights into the evolutionary history of donkey domestication and identifies a genetic variant that results in the non-Dun coat colours of domestic donkeys.
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Engineering and application of a biosensor with focused ligand specificity. Nat Commun 2020; 11:4851. [PMID: 32978386 PMCID: PMC7519686 DOI: 10.1038/s41467-020-18400-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/20/2020] [Indexed: 02/01/2023] Open
Abstract
Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering approach using a FACS-based screening/counterscreening strategy to generate an l-lysine insensitive LysG-based biosensor. This biosensor can be used to isolate l-histidine-producing strains by FACS, showing that TR engineering towards a more focused ligand spectrum can expand the scope of application of such metabolite sensors. Transcriptional biosensors represent powerful tools for the screening of vast strain libraries, but the broad ligand specificity of some transcriptional regulators (TRs) can prohibit such applications. Here authors present the engineering of a LysG-based biosensor with a focused ligand specificity to isolate L-histidine-producing strains.
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20
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Weldenegodguad M, Pokharel K, Ming Y, Honkatukia M, Peippo J, Reilas T, Røed KH, Kantanen J. Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. Sci Rep 2020; 10:8980. [PMID: 32488117 PMCID: PMC7265531 DOI: 10.1038/s41598-020-65487-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/05/2020] [Indexed: 12/24/2022] Open
Abstract
Reindeer are semi-domesticated ruminants that have adapted to the challenging northern Eurasian environment characterized by long winters and marked annual fluctuations in daylight. We explored the genetic makeup behind their unique characteristics by de novo sequencing the genome of a male reindeer and conducted gene family analyses with nine other mammalian species. We performed a population genomics study of 23 additional reindeer representing both domestic and wild populations and several ecotypes from various geographic locations. We assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, comprising 27,332 genes. The results from the demographic history analysis suggested marked changes in the effective population size of reindeer during the Pleistocene period. We detected 160 reindeer-specific and expanded genes, of which zinc finger proteins (n = 42) and olfactory receptors (n = 13) were the most abundant. Comparative genome analyses revealed several genes that may have promoted the adaptation of reindeer, such as those involved in recombination and speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these characteristic reindeer genes have been reported for the first time here. Moreover, our population genomics analysis suggested at least two independent reindeer domestication events with genetic lineages originating from different refugial regions after the Last Glacial Maximum. Taken together, our study has provided new insights into the domestication, evolution and adaptation of reindeer and has promoted novel genomic research of reindeer.
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Affiliation(s)
- Melak Weldenegodguad
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70201, Kuopio, Finland
| | - Kisun Pokharel
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Mervi Honkatukia
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
- Nordic Genetic Resource Centre - NordGen, c/o NMBU - Biovit Box 5003, Ås, NO-1432, Norway
| | - Jaana Peippo
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Tiina Reilas
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, P.O.Box 369 Centrum, 0102, Oslo, Norway
| | - Juha Kantanen
- Natural Resources Institute Finland, FI-31600, Jokioinen, Finland.
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Vascon S, Frasca M, Tripodi R, Valentini G, Pelillo M. Protein function prediction as a graph-transduction game. Pattern Recognit Lett 2020. [DOI: 10.1016/j.patrec.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Tang M, Lu Y, Xiong Z, Chen M, Qin Y. The Grass Carp Genomic Visualization Database (GCGVD): an informational platform for genome biology of grass carp. Int J Biol Sci 2019; 15:2119-2127. [PMID: 31592084 PMCID: PMC6775296 DOI: 10.7150/ijbs.32860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/27/2019] [Indexed: 11/25/2022] Open
Abstract
With the release of the draft genome of the grass carp, researches on the grass carp from the genetic level and the further molecular mechanisms of economically valuable physiological behaviors have gained great attention. In this paper, we integrated a large number of genomic, genetic and some other data resources and established a web-based grass carp genomic visualization database (GCGVD). To view these data more effectively, we visualized grass carp and zebrafish gene collinearity and genetic linkage map using Scalable Vector Graphics (SVG) format in the browser, and genomic annotations by JBrowse. Furthermore, we carried out some preliminary study on a whole-genome alternative splicing (AS)of the grass carp. The RNA-seq reads of 15 samples were aligned to the reference genome of the grass carp by Bowtie2 software. RNA-seq reads of each sample and density map of reads were also exhibited in JBrowse. Additionally, we designed a universal grass carp genome annotation data model to improve the retrieval speed and scalability. Compared with the published database GCGD previously, we newly added the visualization of some more genomic annotations, conserved domain and RNA-seq reads aligned to the reference genome. GCGVD can be accessed at http://122.112.216.104.
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Affiliation(s)
- Min Tang
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Ying Lu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhongmin Xiong
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Ming Chen
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Yufang Qin
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
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HajSalah El Beji I, Mouzeyar S, Bouzidi MF, Roche J. Expansion and Functional Diversification of SKP1-Like Genes in Wheat ( Triticum aestivum L.). Int J Mol Sci 2019; 20:ijms20133295. [PMID: 31277523 PMCID: PMC6650978 DOI: 10.3390/ijms20133295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/06/2019] [Accepted: 07/02/2019] [Indexed: 01/17/2023] Open
Abstract
The ubiquitin proteasome 26S system (UPS), involving monomeric and multimeric E3 ligases is one of the most important signaling pathways in many organisms, including plants. The SCF (SKP1/Cullin/F-box) multimeric complex is particularly involved in response to development and stress signaling. The SKP1 protein (S-phase kinase-associated protein 1) is the core subunit of this complex. In this work, we firstly identified 92 and 87 non-redundant Triticum aestivumSKP1-like (TaSKP) genes that were retrieved from the latest release of the wheat genome database (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0) and the genome annotation of the TGAC v1 respectively. We then investigated the structure, phylogeny, duplication events and expression patterns of the SKP1-like gene family in various tissues and environmental conditions using a wheat expression platform containing public data. TaSKP1-like genes were expressed differentially in response to stress conditions, displaying large genomic variations or short insertions/deletions which suggests functional specialization within TaSKP1-like genes. Finally, interactions between selected wheat FBX (F-box) proteins and putative ancestral TaSKP1-like proteins were tested using the yeast two-hybrid (Y2H) system to examine the molecular interactions. These observations suggested that six Ta-SKP1 genes are likely to be ancestral genes, having similar functions as ASK1 and ASK2 in Arabidopsis, OSK1 and OSK20 in rice and PpSKP1 and PpSKP2 in Physcomitrella patens.
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Affiliation(s)
- Imen HajSalah El Beji
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France
| | - Said Mouzeyar
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France
| | - Mohammed-Fouad Bouzidi
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France
| | - Jane Roche
- UMR INRA/UCA 1095 GDEC, Université Clermont Auvergne, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA 60026 AUBIERE, France.
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Shang JL, Chen M, Hou S, Li T, Yang YW, Li Q, Jiang HB, Dai GZ, Zhang ZC, Hess WR, Qiu BS. Genomic and transcriptomic insights into the survival of the subaerial cyanobacterium Nostoc flagelliforme
in arid and exposed habitats. Environ Microbiol 2019; 21:845-863. [DOI: 10.1111/1462-2920.14521] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/05/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Hubei 430079 People's Republic of China
| | - Min Chen
- School of Life and Environmental Sciences; University of Sydney; Sydney New South Wales 2006 Australia
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology; University of Freiburg; Freiburg 79104 Germany
| | - Tao Li
- Key Laboratory of Algal Biology; Institute of Hydrobiology, Chinese Academy of Science; Hubei 430072 People's Republic of China
| | - Yi-Wen Yang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Hubei 430079 People's Republic of China
| | - Qi Li
- Key Laboratory of Algal Biology; Institute of Hydrobiology, Chinese Academy of Science; Hubei 430072 People's Republic of China
| | - Hai-Bo Jiang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Hubei 430079 People's Republic of China
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Hubei 430079 People's Republic of China
| | - Zhong-Chun Zhang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Hubei 430079 People's Republic of China
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology; University of Freiburg; Freiburg 79104 Germany
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Hubei 430079 People's Republic of China
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25
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Identifying differentially expressed proteins in sorghum cell cultures exposed to osmotic stress. Sci Rep 2018; 8:8671. [PMID: 29875393 PMCID: PMC5989219 DOI: 10.1038/s41598-018-27003-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/15/2018] [Indexed: 11/28/2022] Open
Abstract
Drought stress triggers remarkable physiological changes and growth impediments, which significantly diminish plant biomass and crop yield. However, certain plant species show notable resilience, maintaining nearly normal yields under severe water deficits. For example, sorghum is a naturally drought-tolerant crop, which is ideal for studying plant adaptive responses to drought. Here we used sorbitol treatments to simulate drought-induced osmotic stress in sorghum cell suspension cultures and analysed fractions enriched for extracellular matrix proteins using isobaric tags for relative and absolute quantification technology. Sorbitol induced an overall increase in protein secretion, with putative redox proteins, proteases, and glycosyl hydrolases featuring prominently among the responsive proteins. Gene expression analysis of selected candidates revealed regulation at the transcriptional level. There was a notable differential gene expression between drought-tolerant and drought-sensitive sorghum varieties for some of the candidates. This study shows that protein secretion is a major component of the sorghum response to osmotic stress. Additionally, our data provide candidate genes, which may have putative functions in sorghum drought tolerance, and offer a pool of genes that could be developed as potential biomarkers for rapid identification of drought tolerant lines in plant breeding programs.
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26
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Kumar R, Acharya V, Singh D, Kumar S. Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01. Stand Genomic Sci 2018; 13:11. [PMID: 29721151 PMCID: PMC5909252 DOI: 10.1186/s40793-018-0313-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/04/2018] [Indexed: 11/10/2022] Open
Abstract
A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole genome-based multilocus sequence analysis clustering, in silico DDH similarity value of 95.1% and, the ANI value of 99.25% established the identity of the strain ERGS5:01 (MCC 2953) as a non-violacein producing J. lividum. The genome comparisons across genus Janthinobacterium revealed an open pan-genome with the scope of the addition of new orthologous cluster to complete the genomic inventory. The genomic insight provided the genetic basis of freezing and frequent freeze-thaw cycle tolerance and, for industrially important enzymes. Extended insight into the genome provided clues of crucial genes associated with adaptation in the harsh aquatic ecosystem of high altitude.
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Affiliation(s)
- Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post BoxNo.06, Palampur, Himachal Pradesh 176 061 India
| | - Vishal Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post BoxNo.06, Palampur, Himachal Pradesh 176 061 India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post BoxNo.06, Palampur, Himachal Pradesh 176 061 India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post BoxNo.06, Palampur, Himachal Pradesh 176 061 India
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Predicting Alpha Helical Transmembrane Proteins Using HMMs. Methods Mol Biol 2018; 1552:63-82. [PMID: 28224491 DOI: 10.1007/978-1-4939-6753-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Alpha helical transmembrane (TM) proteins constitute an important structural class of membrane proteins involved in a wide variety of cellular functions. The prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes, is of great importance for the elucidation of their structure and function. Several methods have been applied for the prediction of the transmembrane segments and the topology of alpha helical transmembrane proteins utilizing different algorithmic techniques. Hidden Markov Models (HMMs) have been efficiently used in the development of several computational methods used for this task. In this chapter we give a brief review of different available prediction methods for alpha helical transmembrane proteins pointing out sequence and structural features that should be incorporated in a prediction method. We then describe the procedure of the design and development of a Hidden Markov Model capable of predicting the transmembrane alpha helices in proteins and discriminating them from globular proteins.
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28
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Shirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H, Isobe S. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Res 2017; 24:499-508. [PMID: 28541388 PMCID: PMC5737369 DOI: 10.1093/dnares/dsx020] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site–associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kanji Isuzugawa
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Mitsunobu Ikenaga
- Central Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan
| | - Yutaro Saito
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8605, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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29
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Gardiner M, Bournazos AM, Maturana-Martinez C, Zhong L, Egan S. Exoproteome Analysis of the Seaweed Pathogen Nautella italica R11 Reveals Temperature-Dependent Regulation of RTX-Like Proteins. Front Microbiol 2017; 8:1203. [PMID: 28706511 PMCID: PMC5489592 DOI: 10.3389/fmicb.2017.01203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/13/2017] [Indexed: 12/29/2022] Open
Abstract
Climate fluctuations have been linked to an increased prevalence of disease in seaweeds, including the red alga Delisea pulchra, which is susceptible to a bleaching disease caused by the bacterium Nautella italica R11 under elevated seawater temperatures. To further investigate the role of temperature in the induction of disease by N. italica R11, we assessed the effect of temperature on the expression of the extracellular proteome (exoproteome) in this bacterium. Label-free quantitative mass spectrometry was used to identify 207 proteins secreted into supernatant fraction, which is equivalent to 5% of the protein coding genes in the N. italica R11 genome. Comparative analysis demonstrated that expression of over 30% of the N. italica R11 exoproteome is affected by temperature. The temperature-dependent proteins include traits that could facilitate the ATP-dependent transport of amino acid and carbohydrate, as well as several uncharacterized proteins. Further, potential virulence determinants, including two RTX-like proteins, exhibited significantly higher expression in the exoproteome at the disease inducing temperature of 24°C relative to non-inducing temperature (16°C). This is the first study to demonstrate that temperature has an influence exoproteome expression in a macroalgal pathogen. The results have revealed several temperature regulated candidate virulence factors that may have a role in macroalgal colonization and invasion at elevated sea-surface temperatures, including novel RTX-like proteins.
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Affiliation(s)
- Melissa Gardiner
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
| | - Adam M Bournazos
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
| | - Claudia Maturana-Martinez
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, SydneyNSW, Australia
| | - Suhelen Egan
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
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30
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Palonen EK, Raina S, Brandt A, Meriluoto J, Keshavarz T, Soini JT. Melanisation of Aspergillus terreus-Is Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of Pigments in Submerged Culture? Microorganisms 2017; 5:microorganisms5020022. [PMID: 28471414 PMCID: PMC5488093 DOI: 10.3390/microorganisms5020022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/13/2017] [Accepted: 04/28/2017] [Indexed: 12/22/2022] Open
Abstract
Pigments and melanins of fungal spores have been investigated for decades, revealing important roles in the survival of the fungus in hostile environments. The key genes and the encoded enzymes for pigment and melanin biosynthesis have recently been found in Ascomycota, including Aspergillus spp. In Aspergillus terreus, the pigmentation has remained mysterious with only one class of melanin biogenesis being found. In this study, we examined an intriguing, partially annotated gene cluster of A. terreus strain NIH2624, utilizing previously sequenced transcriptome and improved gene expression data of strain MUCL 38669, under the influence of a suggested quorum sensing inducing metabolite, butyrolactone I. The core polyketide synthase (PKS) gene of the cluster was predicted to be significantly longer on the basis of the obtained transcriptional data, and the surrounding cluster was positively regulated by butyrolactone I at the late growth phase of submerged culture, presumably during sporulation. Phylogenetic analysis of the extended PKS revealed remarkable similarity with a group of known pigments of Fusarium spp., indicating a similar function for this PKS. We present a hypothesis of this PKS cluster to biosynthesise a 1,8-dihydroxynaphthalene (DHN)-type of pigment during sporulation with the influence of butyrolactone I under submerged culture.
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Affiliation(s)
- Elina K Palonen
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Artillerigatan 6, Åbo FI-20520, Finland.
| | - Sheetal Raina
- Department of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Annika Brandt
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Artillerigatan 6, Åbo FI-20520, Finland.
| | - Jussi Meriluoto
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Artillerigatan 6, Åbo FI-20520, Finland.
| | - Tajalli Keshavarz
- Department of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Juhani T Soini
- Faculty of Life Sciences and Business, Turku University of Applied Sciences, Lemminkäinengatan 30, Åbo FI-20520, Finland.
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31
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Palonen EK, Raina S, Brandt A, Meriluoto J, Keshavarz T, Soini JT. Transcriptomic Complexity of Aspergillus terreus Velvet Gene Family under the Influence of Butyrolactone I. Microorganisms 2017; 5:E12. [PMID: 28335447 PMCID: PMC5374389 DOI: 10.3390/microorganisms5010012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/01/2017] [Accepted: 03/09/2017] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi of the Ascomycota phylum are known to contain a family of conserved conidiation regulating proteins with distinctive velvet domains. In Aspergilli, this velvet family includes four proteins, VeA, VelB, VelC and VosA, and is involved in conidiation and secondary metabolism along with a global regulator LaeA. In A. terreus, the overexpression of LaeA has been observed to increase the biogenesis of the pharmaceutically-important secondary metabolite, lovastatin, while the role of the velvet family has not been studied. The secondary metabolism and conidiation of A. terreus have also been observed to be increased by butyrolactone I in a quorum-sensing manner. An enlightenment of the interplay of these regulators will give potential advancement to the industrial use of this fungus, as well as in resolving the pathogenic features. In this study, the Aspergillus terreus MUCL 38669 transcriptome was strand-specifically sequenced to enable an in-depth gene expression analysis to further investigate the transcriptional role of butyrolactone I in these processes. The sequenced transcriptome revealed intriguing properties of the velvet family transcripts, including the regulator laeA, and uncovered the velC gene in A. terreus. The reliability refining microarray gene expression analysis disclosed a positive regulatory role for butyrolactone I in laeA expression, as well as an influence on the expression of the canonical conidiation-regulating genes under submerged culture. All of this supports the suggested regulative role of butyrolactone I in A. terreus secondary metabolism, as well as conidiation.
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Affiliation(s)
- Elina K Palonen
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Åbo, Finland.
| | - Sheetal Raina
- Department of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Annika Brandt
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Åbo, Finland.
| | - Jussi Meriluoto
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Åbo, Finland.
| | - Tajalli Keshavarz
- Department of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Juhani T Soini
- Faculty of Life Sciences and Business, Turku University of Applied Sciences, FI-20520 Åbo, Finland.
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Ur Rehman H, Azam N, Yao J, Benso A. A three-way approach for protein function classification. PLoS One 2017; 12:e0171702. [PMID: 28234929 PMCID: PMC5325230 DOI: 10.1371/journal.pone.0171702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/06/2017] [Indexed: 12/04/2022] Open
Abstract
The knowledge of protein functions plays an essential role in understanding biological cells and has a significant impact on human life in areas such as personalized medicine, better crops and improved therapeutic interventions. Due to expense and inherent difficulty of biological experiments, intelligent methods are generally relied upon for automatic assignment of functions to proteins. The technological advancements in the field of biology are improving our understanding of biological processes and are regularly resulting in new features and characteristics that better describe the role of proteins. It is inevitable to neglect and overlook these anticipated features in designing more effective classification techniques. A key issue in this context, that is not being sufficiently addressed, is how to build effective classification models and approaches for protein function prediction by incorporating and taking advantage from the ever evolving biological information. In this article, we propose a three-way decision making approach which provides provisions for seeking and incorporating future information. We considered probabilistic rough sets based models such as Game-Theoretic Rough Sets (GTRS) and Information-Theoretic Rough Sets (ITRS) for inducing three-way decisions. An architecture of protein functions classification with probabilistic rough sets based three-way decisions is proposed and explained. Experiments are carried out on Saccharomyces cerevisiae species dataset obtained from Uniprot database with the corresponding functional classes extracted from the Gene Ontology (GO) database. The results indicate that as the level of biological information increases, the number of deferred cases are reduced while maintaining similar level of accuracy.
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Affiliation(s)
- Hafeez Ur Rehman
- Department of Computer Science, National University of Computer and Emerging Sciences, Peshawar Pakistan
| | - Nouman Azam
- Department of Computer Science, National University of Computer and Emerging Sciences, Peshawar Pakistan
| | - JingTao Yao
- Department of Computer Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Alfredo Benso
- Department of Computer & Control Engineering, Politecnico di Torino, I-10129, Torino, Italy
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33
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Zou M, Lu C, Zhang S, Chen Q, Sun X, Ma P, Hu M, Peng M, Ma Z, Chen X, Zhou X, Wang H, Feng S, Fang K, Xie H, Li Z, Liu K, Qin Q, Pei J, Wang S, Pan K, Hu W, Feng B, Fan D, Zhou B, Wu C, Su M, Xia Z, Li K, Wang W. Epigenetic map and genetic map basis of complex traits in cassava population. Sci Rep 2017; 7:41232. [PMID: 28120898 PMCID: PMC5264614 DOI: 10.1038/srep41232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/16/2016] [Indexed: 11/13/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important tropical starchy root crop that is adapted to drought but extremely cold sensitive. A cold-tolerant, high-quality, and robust supply of cassava is urgently needed. Here, we clarify genome-wide distribution and classification of CCGG hemi-methylation and full-methylation, and detected 77 much candidate QTLsepi for cold stress and 103 much candidate QTLsepi for storage root quality and yield in 186 cassava population, generated by crossing two non-inbred lines with female parent KU50 and male parent SC124 (KS population). We developed amplified-fragment single nucleotide polymorphism and methylation (AFSM) genetic map in this population. We also constructed the AFSM QTL map, identified 260 much candidate QTL genes for cold stress and 301 much candidate QTL genes for storage root quality and yield, based on the years greenhouse and field trials. This may accounted for a significant amount of the variation in the key traits controlling cold tolerance and the high quality and yield of cassava.
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Affiliation(s)
- Meiling Zou
- Huazhong Agricultural University, Wuhan, China.,The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Cheng Lu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Shengkui Zhang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Qing Chen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Xianglai Sun
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Pingan Ma
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Meizhen Hu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Ming Peng
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Zilong Ma
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Xin Chen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Xincheng Zhou
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Haiyan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Subin Feng
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Kaixin Fang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Hairong Xie
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Zaiyun Li
- Huazhong Agricultural University, Wuhan, China
| | - Kede Liu
- Huazhong Agricultural University, Wuhan, China
| | - Qiongyao Qin
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Jinli Pei
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Shujuan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Kun Pan
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Wenbin Hu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Binxiao Feng
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Dayong Fan
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Bin Zhou
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Chunling Wu
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Ming Su
- Guangxi Academy of Agricultural Sciences, Guilin, China
| | - Zhiqiang Xia
- Huazhong Agricultural University, Wuhan, China.,The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Kaimian Li
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Wenquan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
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Roppongi RT, Karimi B, Siddiqui TJ. Role of LRRTMs in synapse development and plasticity. Neurosci Res 2016; 116:18-28. [PMID: 27810425 DOI: 10.1016/j.neures.2016.10.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 12/19/2022]
Abstract
Leucine-rich-repeat transmembrane neuronal proteins (LRRTMs) are a family of four synapse organizing proteins critical for the development and function of excitatory synapses. The genes encoding LRRTMs and their binding partners, neurexins and HSPGs, are strongly associated with multiple psychiatric disorders. Here, we review the literature covering their structural features, expression patterns in the developing and adult brains, evolutionary origins, and discovery as synaptogenic proteins. We also discuss their role in the development and plasticity of excitatory synapses as well as their disease associations.
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Affiliation(s)
- Reiko T Roppongi
- Department of Physiology and Pathophysiology, College of Medicine, University of Manitoba, Winnipeg, MB, Canada; Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Health Sciences Centre, 710 William Avenue, Winnipeg R3Y 0Z3, MB, Canada
| | - Benyamin Karimi
- Department of Physiology and Pathophysiology, College of Medicine, University of Manitoba, Winnipeg, MB, Canada; Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Health Sciences Centre, 710 William Avenue, Winnipeg R3Y 0Z3, MB, Canada
| | - Tabrez J Siddiqui
- Department of Physiology and Pathophysiology, College of Medicine, University of Manitoba, Winnipeg, MB, Canada; Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Health Sciences Centre, 710 William Avenue, Winnipeg R3Y 0Z3, MB, Canada.
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35
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Chen Z, Chen D, Chu W, Zhu D, Yan H, Xiang Y. Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants. Front Genet 2016; 7:176. [PMID: 27746812 PMCID: PMC5043136 DOI: 10.3389/fgene.2016.00176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/16/2016] [Indexed: 11/13/2022] Open
Abstract
Whole-genome duplication events have occurred more than once in the genomes of some rosids and played a significant role over evolutionary time. Lipoxygenases (LOXs) are involved in many developmental and resistance processes in plants. Our study concerns the subject of the LOX gene family; we tracked the evolutionary process of ancestral LOX genes in four modern rosids. Here we show that some members of the LOX gene family in the Arabidopsis genome are likely to be lost during evolution, leading to a smaller size than that in Populus, Vitis, and Carica. Strong purifying selection acted as a critical role in almost all of the paralogous and orthologous genes. The structure of LOX genes in Carica and Populus are relatively stable, whereas Vitis and Arabidopsis have a difference. By searching conserved motifs of LOX genes, we found that each sub-family shared similar components. Research on intraspecies gene collinearity show that recent duplication holds an important position in Populus and Arabidopsis. Gene collinearity analysis within and between these four rosid plants revealed that all LOX genes in each modern rosid were the offspring from different ancestral genes. This study traces the evolution of LOX genes which have been differentially retained and expanded in rosid plants. Our results presented here may aid in the selection of special genes retained in the rosid plants for further analysis of biological function.
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Affiliation(s)
- Zhu Chen
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Danmei Chen
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Wenyuan Chu
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Dongyue Zhu
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, Anhui Agricultural UniversityHefei, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture UniversityHefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, Anhui Agricultural UniversityHefei, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture UniversityHefei, China
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36
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Hirakawa H, Kaur P, Shirasawa K, Nichols P, Nagano S, Appels R, Erskine W, Isobe SN. Draft genome sequence of subterranean clover, a reference for genus Trifolium. Sci Rep 2016; 6:30358. [PMID: 27545089 PMCID: PMC4992838 DOI: 10.1038/srep30358] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/04/2016] [Indexed: 11/26/2022] Open
Abstract
Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover (T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover (T. pratense) and white clover (T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.
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Affiliation(s)
- Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Parwinder Kaur
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Phillip Nichols
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA 6151, Australia.,School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Soichiro Nagano
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Rudi Appels
- Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Sachiko N Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
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37
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Spetale FE, Tapia E, Krsticevic F, Roda F, Bulacio P. A Factor Graph Approach to Automated GO Annotation. PLoS One 2016; 11:e0146986. [PMID: 26771463 PMCID: PMC4714749 DOI: 10.1371/journal.pone.0146986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/23/2015] [Indexed: 12/19/2022] Open
Abstract
As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.
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Affiliation(s)
- Flavio E. Spetale
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad de Cs. Exactas, Ingeniería y Agrimensura, National University of Rosario, Rosario, Argentina
| | - Elizabeth Tapia
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad de Cs. Exactas, Ingeniería y Agrimensura, National University of Rosario, Rosario, Argentina
| | - Flavia Krsticevic
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad Regional San Nicolás, National Technological University, San Nicolás, Argentina
| | | | - Pilar Bulacio
- CIFASIS-Conicet Institute, Rosario, Argentina
- Facultad de Cs. Exactas, Ingeniería y Agrimensura, National University of Rosario, Rosario, Argentina
- Facultad Regional San Nicolás, National Technological University, San Nicolás, Argentina
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38
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Uchino Y, Miura T, Hosoyama A, Ohji S, Yamazoe A, Ito M, Takahata Y, Suzuki KI, Fujita N. Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method. Stand Genomic Sci 2015; 10:102. [PMID: 26568785 PMCID: PMC4644273 DOI: 10.1186/s40793-015-0095-9] [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: 05/15/2015] [Accepted: 11/02/2015] [Indexed: 11/10/2022] Open
Abstract
A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.
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Affiliation(s)
- Yoshihito Uchino
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Takamasa Miura
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Akira Hosoyama
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Shoko Ohji
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Atsushi Yamazoe
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Masako Ito
- />Taisei Corporation, 344-1 Nase, Kanagawa, 245-0051 Japan
| | - Yoh Takahata
- />Taisei Corporation, 344-1 Nase, Kanagawa, 245-0051 Japan
| | - Ken-ichiro Suzuki
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Nobuyuki Fujita
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
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Solute Carrier Family 26 Member a2 (slc26a2) Regulates Otic Development and Hair Cell Survival in Zebrafish. PLoS One 2015; 10:e0136832. [PMID: 26375458 PMCID: PMC4573323 DOI: 10.1371/journal.pone.0136832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 08/10/2015] [Indexed: 12/16/2022] Open
Abstract
Hearing loss is one of the most prevalent human birth defects. Genetic factors contribute to the pathogenesis of deafness. It is estimated that one-third of deafness genes have already been identified. The current work is an attempt to find novel genes relevant to hearing loss using guilt-by-profiling and guilt-by-association bioinformatics analyses of approximately 80 known non-syndromic hereditary hearing loss (NSHL) genes. Among the 300 newly identified candidate deafness genes, slc26a2 were selected for functional studies in zebrafish. The slc26a2 gene was knocked down using an antisense morpholino (MO), and significant defects were observed in otolith patterns, semicircular canal morphology, and lateral neuromast distributions in morphants. Loss-of-function defects are caused primarily by apoptosis, and morphants are insensitive to sound stimulation and imbalanced swimming behaviours. Morphant defects were found to be partially rescued by co-injection of human SLC26A2 mRNA. All the results suggest that bioinformatics is capable of predicting new deafness genes and this showed slc26a2 is to be a critical otic gene whose dysfunction may induce hearing impairment.
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40
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Rhee DB, Croken MM, Shieh KR, Sullivan J, Micklem G, Kim K, Golden A. toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav066. [PMID: 26130662 PMCID: PMC4485433 DOI: 10.1093/database/bav066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/09/2015] [Indexed: 01/09/2023]
Abstract
Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it is still not fully known which genetic or epigenetic factors are involved in regulating virulence traits of T. gondii. There are on-going efforts to elucidate the mechanisms regulating the stage transition process via the application of high-throughput epigenomics, genomics and proteomics techniques. Given the range of experimental conditions and the typical yield from such high-throughput techniques, a new challenge arises: how to effectively collect, organize and disseminate the generated data for subsequent data analysis. Here, we describe toxoMine, which provides a powerful interface to support sophisticated integrative exploration of high-throughput experimental data and metadata, providing researchers with a more tractable means toward understanding how genetic and/or epigenetic factors play a coordinated role in determining pathogenicity of T. gondii. As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward user interaction. Furthermore, toxoMine allows users to define their own parameters during the search process that gives users near-limitless search and query capabilities. The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine complements the major community database ToxoDB by providing a data warehouse that enables more extensive integrative studies for T. gondii. Given all these factors, we believe it will become an indispensable resource to the greater infectious disease research community. Database URL:http://toxomine.org
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Affiliation(s)
- David B Rhee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA,
| | - Matthew McKnight Croken
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kevin R Shieh
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Julie Sullivan
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK and
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK and
| | - Kami Kim
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA,
| | - Aaron Golden
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA, Department of Mathematical Sciences, Yeshiva University, New York, NY 10033, USA
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41
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Frasca M, Bassis S, Valentini G. Learning node labels with multi-category Hopfield networks. Neural Comput Appl 2015. [DOI: 10.1007/s00521-015-1965-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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42
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Xiao L, Yang G, Zhang L, Yang X, Zhao S, Ji Z, Zhou Q, Hu M, Wang Y, Chen M, Xu Y, Jin H, Xiao X, Hu G, Bao F, Hu Y, Wan P, Li L, Deng X, Kuang T, Xiang C, Zhu JK, Oliver MJ, He Y. The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. Proc Natl Acad Sci U S A 2015; 112:5833-7. [PMID: 25902549 PMCID: PMC4426394 DOI: 10.1073/pnas.1505811112] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
"Drying without dying" is an essential trait in land plant evolution. Unraveling how a unique group of angiosperms, the Resurrection Plants, survive desiccation of their leaves and roots has been hampered by the lack of a foundational genome perspective. Here we report the ∼1,691-Mb sequenced genome of Boea hygrometrica, an important resurrection plant model. The sequence revealed evidence for two historical genome-wide duplication events, a compliment of 49,374 protein-coding genes, 29.15% of which are unique (orphan) to Boea and 20% of which (9,888) significantly respond to desiccation at the transcript level. Expansion of early light-inducible protein (ELIP) and 5S rRNA genes highlights the importance of the protection of the photosynthetic apparatus during drying and the rapid resumption of protein synthesis in the resurrection capability of Boea. Transcriptome analysis reveals extensive alternative splicing of transcripts and a focus on cellular protection strategies. The lack of desiccation tolerance-specific genome organizational features suggests the resurrection phenotype evolved mainly by an alteration in the control of dehydration response genes.
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Affiliation(s)
- Lihong Xiao
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ge Yang
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Liechi Zhang
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xinhua Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Shuang Zhao
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Zhongzhong Ji
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qing Zhou
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Min Hu
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Yu Wang
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ming Chen
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Yu Xu
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Haijing Jin
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xuan Xiao
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Guipeng Hu
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Fang Bao
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yong Hu
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ping Wan
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Legong Li
- School of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xin Deng
- Key Laboratory of Plant Resources and
| | - Tingyun Kuang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chengbin Xiang
- School of Life Sciences, University of Science and Technology of China, Hefei 230022, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907; and
| | - Melvin J Oliver
- Plant Genetics Research Unit, Midwest Area, Agricultural Research Service, United State Department of Agriculture, University of Missouri, Columbia, MO 65211
| | - Yikun He
- School of Life Sciences, Capital Normal University, Beijing 100048, China;
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Kaneko J, Yamada-Narita S, Abe N, Onodera T, Kan E, Kojima S, Miyazaki T, Yamamoto Y, Oguchi A, Ankai A, Ichikawa N, Nakazawa H, Fukui S, Takahashi M, Yamazaki S, Fujita N, Kamio Y. Complete genome sequence of Selenomonas ruminantium subsp. lactilytica will accelerate further understanding of the nature of the class Negativicutes. FEMS Microbiol Lett 2015; 362:fnv050. [PMID: 25837814 DOI: 10.1093/femsle/fnv050] [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] [Accepted: 03/29/2015] [Indexed: 01/14/2023] Open
Abstract
Selenomonas ruminantium subsp. lactilytica, a strictly anaerobic ruminal bacterium, possesses typical Gram-negative cell surface structure comprising cytoplasmic membrane, peptidoglycan layer and outer membrane, whereas its 16S rRNA-based taxonomy shows that the bacteria belongs to Gram-positive Firmicutes. Complete genome analysis showed that genes or gene clusters involved in Gram-negative cell structure were scattered in the S. ruminantium genome, and might provide the new insight of phylogenetic relationship between the bacterium and other bacterial species.
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Affiliation(s)
- Jun Kaneko
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Sachiko Yamada-Narita
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Naoki Abe
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Tomoko Onodera
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Eiichiro Kan
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Seiji Kojima
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Takao Miyazaki
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
| | - Yuji Yamamoto
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 23-35-1 Higashi, Towada 034-8628, Japan
| | - Akio Oguchi
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Akiho Ankai
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Natsuko Ichikawa
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Hidekazu Nakazawa
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Shigehiro Fukui
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Mikio Takahashi
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Syuji Yamazaki
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Nobuyuki Fujita
- Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-49-10 Nishihara, Shinjuku-ku, Tokyo 151-0066, Japan
| | - Yoshiyuki Kamio
- Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori, Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan Department of Human Health and Nutrition, Graduate School of Comprehensive Human Sciences, Shokei Gakuin University, 4-10-1 Yurigaoka, Natori 981-1295, Japan
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Hirakawa H, Okada Y, Tabuchi H, Shirasawa K, Watanabe A, Tsuruoka H, Minami C, Nakayama S, Sasamoto S, Kohara M, Kishida Y, Fujishiro T, Kato M, Nanri K, Komaki A, Yoshinaga M, Takahata Y, Tanaka M, Tabata S, Isobe SN. Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Res 2015; 22:171-9. [PMID: 25805887 PMCID: PMC4401327 DOI: 10.1093/dnares/dsv002] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/17/2015] [Indexed: 12/21/2022] Open
Abstract
Ipomoea trifida (H. B. K.) G. Don. is the most likely diploid ancestor of the hexaploid sweet potato, I. batatas (L.) Lam. To assist in analysis of the sweet potato genome, de novo whole-genome sequencing was performed with two lines of I. trifida, namely the selfed line Mx23Hm and the highly heterozygous line 0431-1, using the Illumina HiSeq platform. We classified the sequences thus obtained as either ‘core candidates’ (common to the two lines) or ‘line specific’. The total lengths of the assembled sequences of Mx23Hm (ITR_r1.0) was 513 Mb, while that of 0431-1 (ITRk_r1.0) was 712 Mb. Of the assembled sequences, 240 Mb (Mx23Hm) and 353 Mb (0431-1) were classified into core candidate sequences. A total of 62,407 (62.4 Mb) and 109,449 (87.2 Mb) putative genes were identified, respectively, in the genomes of Mx23Hm and 0431-1, of which 11,823 were derived from core sequences of Mx23Hm, while 28,831 were from the core candidate sequence of 0431-1. There were a total of 1,464,173 single-nucleotide polymorphisms and 16,682 copy number variations (CNVs) in the two assembled genomic sequences (under the condition of log2 ratio of >1 and CNV size >1,000 bases). The results presented here are expected to contribute to the progress of genomic and genetic studies of I. trifida, as well as studies of the sweet potato and the genus Ipomoea in general.
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Affiliation(s)
- Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yoshihiro Okada
- Crop and Agribusiness Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Itoman, Okinawa 901-0336, Japan
| | - Hiroaki Tabuchi
- Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akiko Watanabe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hisano Tsuruoka
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Chiharu Minami
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | | | | | - Mitsuyo Kohara
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yoshie Kishida
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | | | - Midori Kato
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Keiko Nanri
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akiko Komaki
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masaru Yoshinaga
- Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan
| | - Yasuhiro Takahata
- Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan
| | - Masaru Tanaka
- Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko N Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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Wlodarchak N, Tariq R, Striker R. Comparative analysis of the human and zebrafish kinomes: focus on the development of kinase inhibitors. TRENDS IN CELL & MOLECULAR BIOLOGY 2015; 10:49-75. [PMID: 27011661 PMCID: PMC4801344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Targeting kinases with semi-selective kinase inhibitors is one of the most successful drug development strategies of the 21st century. Zebrafish have become an increasingly useful model for pharmaceutical development. Water-soluble compounds can be screened for zebrafish phenotypes in a high throughput format against a living vertebrate, and cell-signaling events can be imaged in transparent living fish. Despite zebrafish being a more relevant model than more distantly related systems such as the well-annotated kinome of yeast and drosophila, there is no comparative analysis of the human and zebrafish kinome. Furthermore most approved kinase inhibitors, often called 'DFG in' ATP competitive inhibitors, act on conserved active site residues in the kinase. Since the active site residues can be identified by examining the primary sequence, primary sequence identity can be a rough guide as to whether a particular inhibitor will have activity against another kinase. There is a need to evaluate the utility of zebrafish as a drug development model for active site inhibitors of kinases. Here we offer a systematic comparison of the catalytic domains of classical human kinases with the catalytic domains of all annotated zebrafish kinases. We found a high degree of identity between the catalytic domains of most human kinases and their zebrafish homologs, and we ranked 504 human kinase catalytic domains by order of similarity. We found only 23 human kinases with no easily recognizable homologous zebrafish catalytic domain. On the other hand we found 78 zebrafish kinase catalytic domains with no close human counterpart. These 'additional kinase active sites' could represent potential mediators of zebrafish toxicity that may not be relevant to human kinase inhibitors. We used two clinically approved human kinase inhibitors, one targeting a highly homologous target and one targeting a lesser homologous target, and we compared the known human kinase target structures with modeled zebrafish target structures. As expected, the homologous target had high structural identity, but even the less homologous target had high structural identity in residues contacted by the inhibitor. Overall this analysis should help guide researchers interested in studying human kinases and their inhibitors in more tractable systems.
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Affiliation(s)
- Nathan Wlodarchak
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
| | - Rehan Tariq
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
| | - Rob Striker
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
- W. S. Middleton Memorial Veteran’s Administration Hospital, 2500 Overlook Terrace, Madison, WI 53705, USA
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46
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Sabetian S, Shamsir MS, Abu Naser M. Functional features and protein network of human sperm-egg interaction. Syst Biol Reprod Med 2014; 60:329-37. [PMID: 25222562 DOI: 10.3109/19396368.2014.955896] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidation of the sperm-egg interaction at the molecular level is one of the unresolved problems in sexual reproduction, and understanding the molecular mechanism is crucial in solving problems in infertility and failed in vitro fertilization (IVF). Many molecular interactions in the form of protein-protein interactions (PPIs) mediate the sperm-egg membrane interaction. Due to the complexity of the problem such as difficulties in analyzing in vivo membrane PPIs, many efforts have failed to comprehensively elucidate the fusion mechanism and the molecular interactions that mediate sperm-egg membrane fusion. The main purpose of this study was to reveal possible protein interactions and associated molecular function during sperm-egg interaction using a protein interaction network approach. Different databases have been used to construct the human sperm-egg interaction network. The constructed network revealed new interactions. These included CD151 and CD9 in human oocyte that interact with CD49 in sperm, and CD49 and ITGA4 in sperm that interact with CD63 and CD81, respectively, in the oocyte. These results showed that the different integrins in sperm may be involved in human sperm-egg interaction. It was also suggested that sperm ADAM2 plays a role as a protein candidate involved in sperm-egg membrane interaction by interacting with CD9 in the oocyte. Interleukin-4 receptor activity, receptor signaling protein tyrosine kinase activity, and manganese ion transmembrane transport activity are the major molecular functions in sperm-egg interaction protein network. The disease association analysis indicated that sperm-egg interaction defects are also reflected in other disease networks such as cardiovascular, hematological, and breast cancer diseases. By analyzing the network, we identified the major molecular functions and disease association genes in sperm-egg interaction protein. Further experimental studies will be required to confirm the significance of these new computationally resolved interactions and the genetic links between sperm-egg interaction abnormalities and the associated disease.
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Affiliation(s)
- Soudabeh Sabetian
- Department of Biological and Health Sciences, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia , Johor , Malaysia
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47
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Guo L, Chen Y, Ye N, Dai X, Yang W, Yin T. Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family. BMC Genomics 2014. [PMID: 25047956 DOI: 10.1186/1471-2229-12-612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods. RESULTS The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene. CONCLUSIONS Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.
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Affiliation(s)
| | | | | | | | | | - Tongming Yin
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, 159#, Longpan Road, Nanjing 210037, China.
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48
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Guo L, Chen Y, Ye N, Dai X, Yang W, Yin T. Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family. BMC Genomics 2014; 15:612. [PMID: 25047956 PMCID: PMC4117974 DOI: 10.1186/1471-2164-15-612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 07/07/2014] [Indexed: 12/03/2022] Open
Abstract
Background All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods. Results The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene. Conclusions Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-612) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Tongming Yin
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, 159#, Longpan Road, Nanjing 210037, China.
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Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T. Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res 2014; 21:481-90. [PMID: 24848699 PMCID: PMC4195494 DOI: 10.1093/dnares/dsu014] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
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Affiliation(s)
- Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Feng Li
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Zhongwei Zou
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Yoichi Hasegawa
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Kaoru Tonosaki
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Sachiko Shirasawa
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Aki Fukushima
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Shuji Yokoi
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Yoshihito Takahata
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Tomohiro Kakizaki
- National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Masahiko Ishida
- National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Shunsuke Okamoto
- Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan
| | - Koji Sakamoto
- Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
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50
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Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O'Connell MJ, McInerney JO, Born EW, Dalén L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R, Willerslev E, Wang J. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 2014; 157:785-94. [PMID: 24813606 PMCID: PMC4089990 DOI: 10.1016/j.cell.2014.03.054] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/20/2013] [Accepted: 03/04/2014] [Indexed: 12/22/2022]
Abstract
Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.
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Affiliation(s)
- Shiping Liu
- BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510641, China
| | - Eline D Lorenzen
- Department of Integrative Biology, 3060 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA; Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Matteo Fumagalli
- Department of Integrative Biology, 3060 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA
| | - Bo Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Kelley Harris
- Department of Mathematics, 970 Evans Hall, University of California, Berkeley, CA 94720, USA
| | | | - Long Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Thorfinn Sand Korneliussen
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Mehmet Somel
- Department of Integrative Biology, 3060 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA
| | - Courtney Babbitt
- Department of Biology, 124 Science Drive, Duke Box # 90338, Duke University, Durham, NC 27708, USA; Institute for Genome Sciences & Policy, 101 Science Drive, DUMC Box 3382, Duke University, Durham, NC 27708, USA
| | - Greg Wray
- Department of Biology, 124 Science Drive, Duke Box # 90338, Duke University, Durham, NC 27708, USA; Institute for Genome Sciences & Policy, 101 Science Drive, DUMC Box 3382, Duke University, Durham, NC 27708, USA
| | | | - Weiming He
- BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510641, China
| | - Zhuo Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Xueyan Xiang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Claire C Morgan
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Aoife Doherty
- Bioinformatics and Molecular Evolution Unit, Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - James O McInerney
- Bioinformatics and Molecular Evolution Unit, Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Erik W Born
- Greenland Institute of Natural Resources, c/o Government of Greenland Representation in Denmark, Strandgade 91, 3. Floor, PO Box 2151, 1016 Copenhagen K, Denmark
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 10405, Stockholm, Sweden
| | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, Frederiksborgvej 399, PO Box 358, 4000 Roskilde, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Christian Sonne
- Department of Bioscience, Arctic Research Centre, Aarhus University, Frederiksborgvej 399, PO Box 358, 4000 Roskilde, Denmark
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Rasmus Nielsen
- BGI-Shenzhen, Shenzhen 518083, China; Department of Integrative Biology, 3060 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA; Department of Statistics, 367 Evans Hall, University of California, Berkeley, CA 94720, USA; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen Ø, Denmark.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen Ø, Denmark; Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau 999078, China; Department of Medicine, University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong.
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