151
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Riggs-Shute SD, Falkinham JO, Yang Z. Construction and Use of Transposon MycoTetOP 2 for Isolation of Conditional Mycobacteria Mutants. Front Microbiol 2020; 10:3091. [PMID: 32038540 PMCID: PMC6985430 DOI: 10.3389/fmicb.2019.03091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria are unique in many aspects of their biology. The development of genetic tools to identify genes critical for their growth by forward genetic analysis holds great promises to advance our understanding of their cellular, physiological and biochemical processes. Here we report the development of a novel transposon, MycoTetOP 2, to aid the identification of such genes by direct transposon mutagenesis. This mariner-based transposon contains nested anhydrotetracycline (ATc)-inducible promoters to drive transcription outward from both of its ends. In addition, it includes the Escherichia coli R6Kγ origin to facilitate the identification of insertion sites. MycoTetOP 2 was placed in a shuttle plasmid with a temperature-sensitive DNA replication origin in mycobacteria. This allows propagation of mycobacteria harboring the plasmid at a permissive temperature. The resulting population of cells can then be subjected to a temperature shift to select for transposon mutants. This transposon and its delivery system, once constructed, were tested in the fast-growing model Mycobacterium smegmatis and 13 mutants with ATc-dependent growth were isolated. The identification of the insertion sites in these mutants led to nine unique genetic loci with genes critical for essential processes in both M. smegmatis and Mycobacterium tuberculosis. These results demonstrate that MycoTetOP 2 and its delivery vector provide valuable tools for the studies of mycobacteria by forward genetics.
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Affiliation(s)
- Sarah D. Riggs-Shute
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
- Department of Biology, Tidewater Community College, Portsmouth, VA, United States
| | - Joseph O. Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Zhaomin Yang
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
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152
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Bhatta TR, Chamings A, Vibin J, Klaassen M, Alexandersen S. Detection of a Reassortant H9N2 Avian Influenza Virus with Intercontinental Gene Segments in a Resident Australian Chestnut Teal. Viruses 2020; 12:E88. [PMID: 31940999 PMCID: PMC7019556 DOI: 10.3390/v12010088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The present study reports the genetic characterization of a low-pathogenicity H9N2 avian influenza virus, initially from a pool and subsequently from individual faecal samples collected from Chestnut teals (Anas castanea) in southeastern Australia. Phylogenetic analyses of six full gene segments and two partial gene segments obtained from next-generation sequencing showed that this avian influenza virus, A/Chestnut teal/Australia/CT08.18/12952/2018 (H9N2), was a typical, low-pathogenicity, Eurasian aquatic bird lineage H9N2 virus, albeit containing the North American lineage nucleoprotein (NP) gene segment detected previously in Australian wild birds. This is the first report of a H9N2 avian influenza virus in resident wild birds in Australia, and although not in itself a cause of concern, is a clear indication of spillover and likely reassortment of influenza viruses between migratory and resident birds, and an indication that any lineage could potentially be introduced in this way.
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Affiliation(s)
- Tarka Raj Bhatta
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Jessy Vibin
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Marcel Klaassen
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- Centre for Integrative Ecology, Deakin University, Victoria 3220, Australia
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
- Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia
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153
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Maleki E, Koohi S, Kavehvash Z, Mashaghi A. OptCAM: An ultra-fast all-optical architecture for DNA variant discovery. JOURNAL OF BIOPHOTONICS 2020; 13:e201900227. [PMID: 31397961 DOI: 10.1002/jbio.201900227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/25/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both high-speed processing and operational parallelism, inherently exist in optics. The proposed method, named as OptCAM, utilizes amplitude and wavelength of the optical signals, to accurately locate mutations through three main procedures. Furthermore, an all-optical implementation of the OptCAM method is proposed consisting of three units, corresponding to the three OptCAM procedures. Performing considerably fast processes by passing optical signals through high-throughput photonic devices, OptCAM avoids various limitations of electrical implementations. Accuracy and efficiency of the OptCAM method and its optical implementation are validated through numerical simulation by a gold standard simulation benchmark. The results indicate the proposed method is significantly faster than its electrical counterparts, in both single node and grid computation.
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Affiliation(s)
- Ehsan Maleki
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Somayyeh Koohi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Zahra Kavehvash
- Department of Electrical Engineering, Sharif University of Technology, Tehran, Iran
| | - Alireza Mashaghi
- Systems Biomedicine and Pharmacology Division, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, Netherlands
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154
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Xu G, Bian C, Nie Z, Li J, Wang Y, Xu D, You X, Liu H, Gao J, Li H, Liu K, Yang J, Li Q, Shao N, Zhuang Y, Fang D, Jiang T, Lv Y, Huang Y, Gu R, Xu J, Ge W, Shi Q, Xu P. Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. Gigascience 2020; 9:giz157. [PMID: 31895412 PMCID: PMC6939831 DOI: 10.1093/gigascience/giz157] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/28/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). RESULTS In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. CONCLUSIONS We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.
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Affiliation(s)
- Gangchun Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Binhu District, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Zhijuan Nie
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
| | - Yuyu Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Dongpo Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Hongbo Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jiancao Gao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Hongxia Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jian Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Quanjie Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Nailin Shao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Yanbing Zhuang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Dian Fang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Tao Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Ruobo Gu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Binhu District, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
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155
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Wang X, Liu Z, Li X, Li D, Cai J, Yan H. SPDB: a specialized database and web-based analysis platform for swine pathogens. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5881264. [PMID: 32761141 PMCID: PMC7409514 DOI: 10.1093/database/baaa063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/07/2020] [Accepted: 07/10/2020] [Indexed: 11/12/2022]
Abstract
The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research. Database URL: http://spdatabase.com:2080/.
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Affiliation(s)
- Xiaoru Wang
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - Zongbao Liu
- Institute for Advanced Study, Shenzhen University, No. 3688, Nanhai Boulevard, Nanshan District, Shenzhen, Guangdong Province 518061, China
| | - Xiaoying Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - Danwei Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - Jiayu Cai
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
| | - He Yan
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou, Guangdong Province 510641, China
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156
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Contributions to the knowledge of Pseudolevinseniella (Trematoda: Digenea) and temnocephalans from alien crayfish in natural freshwaters of Thailand. Heliyon 2019; 5:e02990. [PMID: 31879707 PMCID: PMC6920264 DOI: 10.1016/j.heliyon.2019.e02990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/04/2018] [Accepted: 12/03/2019] [Indexed: 11/23/2022] Open
Abstract
Redclaw crayfish (Cherax quadricarinatus) is a decapod species originating from Australian freshwater. For more than two decades, these crayfish have been re-distributing to environments in many countries, including Thailand. Moreover, they can carry endosymbionts and/or ectosymbionts into new environments. The aim of this study was to introduce a morphological description of Pseudolevinseniella anenteron as a metacercaria of the endoparasites of redclaw crayfish collected from natural water sources in Thailand. The occurrence of two ectosymbiotic temnocephalans (Diceratocephala boschmai and Temnosewellia sp.) in C. quadricarinatus was also reported. The internal morphology of P. anenteron, D. boschmai and Temnosewellia were described and discussed. The surface ultrastructure of the multidentate spines on the body and the metacercarial cyst wall of P. anenteron was investigated by scanning electron microscopy (SEM). By performing a search of the GenBank nucleotide database of partial sequences of 18S, 28S rDNA and cytochrome c oxidase subunit I (cox1), P. anenteron was found to be related to Maritrema, and Temnosewellia was found to be related to T. fasciata. However, according to the cox1 gene, Temnosewellia was found to be similar to T. minor. These results reveal that redclaw crayfish that inhabit natural freshwaters in Thailand may harbour endoparasites and ecto- and endosymbionts. Furthermore, these findings may be able to monitor invasive or non-invasive species in an ecosystem.
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157
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Li J, Gao X, Sang S, Liu C. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae. BMC Genomics 2019; 20:912. [PMID: 31874634 PMCID: PMC6929338 DOI: 10.1186/s12864-019-6319-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/21/2019] [Indexed: 01/19/2023] Open
Abstract
Background Euphorbiaceae is one of the largest families of flowering plants. Due to its exceptional growth form diversity and near-cosmopolitan distribution, it has attracted much interest since ancient times. SBP-box (SBP) genes encode plant-specific transcription factors that play critical roles in numerous biological processes, especially flower development. We performed genome-wide identification and characterization of SBP genes from four economically important Euphorbiaceae species. Results In total, 77 SBP genes were identified in four Euphorbiaceae genomes. The SBP proteins were divided into three length ranges and 10 groups. Group-6 was absent in Arabidopsis thaliana but conserved in Euphorbiaceae. Segmental duplication played the most important role in the expansion processes of Euphorbiaceae SBP genes, and all the duplicated genes were subjected to purify selection. In addition, about two-thirds of the Euphorbiaceae SBP genes are potential targets of miR156, and some miR-regulated SBP genes exhibited high intensity expression and differential expression in different tissues. The expression profiles related to different stress treatments demonstrated broad involvement of Euphorbiaceae SBP genes in response to various abiotic factors and hormonal treatments. Conclusions In this study, 77 SBP genes were identified in four Euphorbiaceae species, and their phylogenetic relationships, protein physicochemical characteristics, duplication, tissue and stress response expression, and potential roles in Euphorbiaceae development were studied. This study lays a foundation for further studies of Euphorbiaceae SBP genes, providing valuable information for future functional exploration of Euphorbiaceae SBP genes.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shiye Sang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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158
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Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Herrera G, Ríos-Chaparro DI, Díaz-Arévalo D, Patarroyo MA, Lawley TD, Ramírez JD. Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum. Virulence 2019; 10:657-676. [PMID: 31304854 PMCID: PMC6629180 DOI: 10.1080/21505594.2019.1637699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/23/2019] [Accepted: 06/25/2019] [Indexed: 01/23/2023] Open
Abstract
Some well-known Clostridiales species such as Clostridium difficile and C. perfringens are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as Clostridium tertium and C. paraputrificum. Three fecal isolates were identified as Clostridium tertium (Gcol.A2 and Gcol.A43) and C. paraputrificum (Gcol.A11) during public health screening for C. difficile infections in Colombia. C. paraputrificum genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the C. tertium genomes than in the C. paraputrificum genomes. C. difficile tcdA and tcdB toxins encoding homologous sequences and other potential virulence factors were also identified. EndoA interferase, a toxic component of the type II toxin-antitoxin system, was found among the C. tertium genomes. toxA was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the C. tertium genomes compared with the C. paraputrificum genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), with proteins involved in sporulation processes more highly represented in C. tertium. These finding suggest the need to advance in the study of those species with potential importance at public health level.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Posgrado Interfacultades, Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
| | - Nitin Kumar
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Animal Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Trevor D. Lawley
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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159
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Chen L, Pan X, Zeng T, Zhang YH, Zhang Y, Huang T, Cai YD. Immunosignature Screening for Multiple Cancer Subtypes Based on Expression Rule. Front Bioeng Biotechnol 2019; 7:370. [PMID: 31850330 PMCID: PMC6901955 DOI: 10.3389/fbioe.2019.00370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy (i.e., fluid biopsy) involves a series of clinical examination approaches. Monitoring of cancer immunological status by the “immunosignature” of patients presents a novel method for tumor-associated liquid biopsy. The major work content and the core technological difficulties for the monitoring of cancer immunosignature are the recognition of cancer-related immune-activating antigens by high-throughput screening approaches. Currently, one key task of immunosignature-based liquid biopsy is the qualitative and quantitative identification of typical tumor-specific antigens. In this study, we reused two sets of peptide microarray data that detected the expression level of potential antigenic peptides derived from tumor tissues to avoid the detection differences induced by chip platforms. Several machine learning algorithms were applied on these two sets. First, the Monte Carlo Feature Selection (MCFS) method was used to analyze features in two sets. A feature list was obtained according to the MCFS results on each set. Second, incremental feature selection method incorporating one classification algorithm (support vector machine or random forest) followed to extract optimal features and construct optimal classifiers. On the other hand, the repeated incremental pruning to produce error reduction, a rule learning algorithm, was applied on key features yielded by the MCFS method to extract quantitative rules for accurate cancer immune monitoring and pathologic diagnosis. Finally, obtained key features and quantitative rules were extensively analyzed.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, China.,College of Information Engineering, Shanghai Maritime University, Shanghai, China.,Shanghai Key Laboratory of Pure Mathematics and Mathematical Practice (PMMP), East China Normal University, Shanghai, China
| | - XiaoYong Pan
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China.,IDLab, Department for Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - YunHua Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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160
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Lee TH, Carpenter TS, D'haeseleer P, Savage DF, Yung MC. Encapsulin carrier proteins for enhanced expression of antimicrobial peptides. Biotechnol Bioeng 2019; 117:603-613. [PMID: 31709513 DOI: 10.1002/bit.27222] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) are regarded as attractive alternatives to conventional antibiotics, but their production in microbes remains challenging due to their inherent bactericidal nature. To address these limitations, we have developed a novel AMP fusion protein system based on an encapsulin nanocompartment protein and have demonstrated its utility in enhancing expression of HBCM2, an AMP with activity against Gram-negative bacteria. Here, HBCM2 was fused to the N-terminus of several Encapsulin monomer (Enc) variants engineered with multiple TEV protease recognition site insertions to facilitate proteolytic release of the fused HBCM2. Fusion of HBCM2 to the Enc variants, but not other common carrier proteins, enabled robust overexpression in Escherichia coli C43(DE3) cells. Interestingly, variants with a TEV site insertion following residue K71 in Enc exhibited the highest overexpression and HBCM2 release efficiencies compared to other variants but were deficient in cage formation. HBCM2 was purified from the highest expressing variant following TEV protease digestion and was found to be highly active in inhibiting E. coli growth (MIC = 5 μg/ml). Our study demonstrates the potential use of the Enc system to enhance expression of AMPs for biomanufacturing and therapeutic applications.
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Affiliation(s)
- Tek-Hyung Lee
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - Timothy S Carpenter
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - Patrik D'haeseleer
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, California
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
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161
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Jiang L, Yu M, Zhou Y, Tang Z, Li N, Kang J, He B, Huang J. AGONOTES: A Robot Annotator for Argonaute Proteins. Interdiscip Sci 2019; 12:109-116. [PMID: 31741225 DOI: 10.1007/s12539-019-00349-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/06/2019] [Accepted: 10/30/2019] [Indexed: 12/01/2022]
Abstract
The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered for gene silencing and genome editing and plays an important role in biological studies. With an increasing number of genomes and proteomes of various microbes becoming available, computational tools for identifying and annotating argonaute proteins are urgently needed. We introduce AGONOTES (Argonaute Notes). It is a web service especially designed for identifying and annotating Ago. AGONOTES uses the BLASTP similarity search algorithm to categorize all submitted proteins into three groups: prokaryotic argonaute protein (pAgo), eukaryotic argonaute protein (eAgo), and non-argonaute protein (non-Ago). Argonaute proteins can then be aligned to the corresponding standard set of Ago sequences using the multiple sequence alignment program MUSCLE. All functional domains of Ago can further be curated from the alignment results and visualized easily through Bio::Graphic modules in the BioPerl bundle. Compared with existing tools such as CD-Search and available databases such as UniProt and AGONOTES showed a much better performance on domain annotations, which is fundamental in studying the new Ago. AGONOTES can be freely accessed at http://i.uestc.edu.cn/agonotes/. AGONOTES is a friendly tool for annotating Ago domains from a proteome or a series of protein sequences.
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Affiliation(s)
- Lixu Jiang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Min Yu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Yuwei Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Zhongjie Tang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Ning Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Juanjuan Kang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Bifang He
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China.,School of Medicine, Guizhou University, Guiyang, China
| | - Jian Huang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China.
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162
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TmDorX2 positively regulates antimicrobial peptides in Tenebrio molitor gut, fat body, and hemocytes in response to bacterial and fungal infection. Sci Rep 2019; 9:16878. [PMID: 31728023 PMCID: PMC6856108 DOI: 10.1038/s41598-019-53497-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022] Open
Abstract
Dorsal, a member of the nuclear factor-kappa B (NF-κB) family of transcription factors, is a critical downstream component of the Toll pathway that regulates the expression of antimicrobial peptides (AMPs) against pathogen invasion. In this study, the full-length ORF of Dorsal was identified from the RNA-seq database of the mealworm beetle Tenebrio molitor (TmDorX2). The ORF of TmDorX2 was 1,482 bp in length, encoding a polypeptide of 493 amino acid residues. TmDorX2 contains a conserved Rel homology domain (RHD) and an immunoglobulin-like, plexins, and transcription factors (IPT) domain. TmDorX2 mRNA was detected in all developmental stages, with the highest levels observed in 3-day-old adults. TmDorX2 transcripts were highly expressed in the adult Malpighian tubules (MT) and the larval fat body and MT tissues. After challenging the larvae with Staphylococcus aureus and Escherichia coli, the TmDorX2 mRNA levels were upregulated 6 and 9 h post infection in the whole body, fat body, and hemocytes. Upon Candida albicans challenge, the TmDorX2 mRNA expression were found highest at 9 h post-infection in the fat body. In addition, TmDorX2-knockdown larvae exposed to E. coli, S. aureus, or C. albicans challenge showed a significantly increased mortality rate. Furthermore, the expression of 11 AMP genes was downregulated in the gut and fat body of dsTmDorX2-injected larvae upon E. coli challenge. After C. albicans and S. aureus challenge of dsTmDorX2-injected larvae, the expression of 11 and 10 AMPs was downregulated in the gut and fat body, respectively. Intriguingly, the expression of antifungal transcripts TmTenecin-3 and TmThaumatin-like protein-1 and -2 was greatly decreased in TmDorX2-silenced larvae in response to C. albicans challenge, suggesting that TmDorX2 regulates antifungal AMPs in the gut in response to C. albicans infection. The AMP expression profiles in the fat body, hemocytes, gut, and MTs suggest that TmDorX2 might have an important role in promoting the survival of T. molitor larvae against all mentioned pathogens.
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163
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Ge H, Lin K, Shen M, Wu S, Wang Y, Zhang Z, Wang Z, Zhang Y, Huang Z, Zhou C, Lin Q, Wu J, Liu L, Hu J, Huang Z, Zheng L. De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C. Mol Ecol Resour 2019; 19:1461-1469. [PMID: 31325912 PMCID: PMC6899872 DOI: 10.1111/1755-0998.13064] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/02/2023]
Abstract
The red-spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South-East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA-seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.
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Affiliation(s)
- Hui Ge
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Kebing Lin
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Mi Shen
- Nextomics Biosciences InstituteWuhanChina
| | - Shuiqing Wu
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Ziping Zhang
- College of Animal SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries CollegeJimei UniversityXiamenChina
| | - Yong Zhang
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic AnimalsSun Yat‐Sen UniversityGuangzhouChina
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic AdministrationFujian Normal UniversityFuzhouChina
| | - Chen Zhou
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Qi Lin
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Jianshao Wu
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Lei Liu
- Nextomics Biosciences InstituteWuhanChina
| | - Jiang Hu
- Nextomics Biosciences InstituteWuhanChina
| | - Zhongchi Huang
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
| | - Leyun Zheng
- Key Laboratory of Cultivation and High‐value Utilization of Marine Organisms in Fujian ProvinceFisheries Research Institute of FujianXiamenChina
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164
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Madusanka RK, Priyathilaka TT, Janson ND, Kasthuriarachchi TDW, Jung S, Tharuka MDN, Lee J. Molecular, transcriptional and functional delineation of Galectin-8 from black rockfish (Sebastes schlegelii) and its potential immunological role. FISH & SHELLFISH IMMUNOLOGY 2019; 93:449-462. [PMID: 31352119 DOI: 10.1016/j.fsi.2019.07.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/18/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Galectins are β-galactoside-binding lectins, which are involved in pattern recognition, cell adhesion, and stimulation of the host innate immune responses against microbial pathogens. In spite of several functional studies on different galectins isolated from vertebrates and invertebrates, this is the first report to present functional studies for galectin-8 from the marine teleost tissues. In the present study, we characterized galectin-8 homolog from black rockfish (Sebastes schlegelii), in molecular and functional aspects. Rockfish galectin-8 (SsGal8) was found to consist of a 969 bp long open reading frame (ORF), encoding a protein of 322 amino acids and the predicted molecular weight was 35.82 kDa. In silico analysis of SsGal8 revealed the presence of two carbohydrate binding domains (CRDs), at both N and C-termini and a linker peptide of 40 amino acids, in between the two domains. As expected, the phylogenetic tree categorized SsGal8 as a tandem-repeat galectin, and ultimately positioned it in the sub-clade of fish galectin-8. rSsGal8 was able to strongly agglutinate fish erythrocytes and the inhibition of agglutination was successfully exhibited by lactose and d-galactose. Bacterial agglutination assay resulted in agglutination of both Gram (+) and Gram (-) bacteria, including Escherichia coli, Vibrio harveyi, Vibrio parahaemolyticus, Streptococcus parauberis, Lactococcus garvieae, Streptococcus iniae and Vibrio tapetis. The tissue distribution analysis based on qPCR assays, revealed a ubiquitous tissue expression of SsGal8 for the examined rockfish tissues, with the most pronounced expression in blood, followed by brain, intestine, head kidney and kidney. Furthermore, the mRNA transcription level of SsGal8 was significantly up-regulated in spleen, liver and head kidney, upon immune challenges with Streptococcus iniae, LPS and poly I:C, in a time dependent manner. Taken together, these findings strongly suggest the contribution of SsGal8 in regulating innate immune responses to protect the rockfish from bacterial infections.
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Affiliation(s)
- Rajamanthrilage Kasun Madusanka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Thanthrige Thiunuwan Priyathilaka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - N D Janson
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - T D W Kasthuriarachchi
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Sumi Jung
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - M D Neranjan Tharuka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea.
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165
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Huang W, Wang G, Yin C, Chen D, Dhand A, Chanza M, Dimitrova N, Fallon JT. Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections. Microorganisms 2019; 7:microorganisms7100388. [PMID: 31554234 PMCID: PMC6843764 DOI: 10.3390/microorganisms7100388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 11/16/2022] Open
Abstract
The surveillance of health care-associated infection (HAI) is an essential element of the infection control program. While whole-genome sequencing (WGS) has widely been adopted for genomic surveillance, its data processing remains to be improved. Here, we propose a three-level data processing pipeline for the precision genomic surveillance of microorganisms without prior knowledge: species identification, multi-locus sequence typing (MLST), and sub-MLST clustering. The former two are closely connected to what have widely been used in current clinical microbiology laboratories, whereas the latter one provides significantly improved resolution and accuracy in genomic surveillance. Comparing to a broadly used reference-dependent alignment/mapping method and an annotation-dependent pan-/core-genome analysis, we implemented our reference- and annotation-independent, k-mer-based, simplified workflow to a collection of Acinetobacter and Enterococcus clinical isolates for tests. By taking both single nucleotide variants and genomic structural changes into account, the optimized k-mer-based pipeline demonstrated a global view of bacterial population structure in a rapid manner and discriminated the relatedness between bacterial isolates in more detail and precision. The newly developed WGS data processing pipeline would facilitate WGS application to the precision genomic surveillance of HAI. In addition, the results from such a WGS-based analysis would be useful for the precision laboratory diagnosis of infectious microorganisms.
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Affiliation(s)
- Weihua Huang
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA.
| | - Guiqing Wang
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA.
- Department of Pathology and Clinical Laboratories, Westchester Medical Center, Valhalla, NY 10595, USA.
| | - Changhong Yin
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA.
| | - Donald Chen
- Department of Medicine, New York Medical College, Valhalla, NY 10595, USA.
- Department of Infection Prevention and Control, Westchester Medical Center, Valhalla, NY 10595, USA.
| | - Abhay Dhand
- Department of Medicine, New York Medical College, Valhalla, NY 10595, USA.
| | - Melissa Chanza
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA.
| | | | - John T Fallon
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA.
- Department of Pathology and Clinical Laboratories, Westchester Medical Center, Valhalla, NY 10595, USA.
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166
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Wei Y, Xiao D, Zhang C, Hou X. The Expanded SWEET Gene Family Following Whole Genome Triplication in Brassica rapa. Genes (Basel) 2019; 10:E722. [PMID: 31540414 PMCID: PMC6771021 DOI: 10.3390/genes10090722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 01/15/2023] Open
Abstract
The SWEET family, which includes transcripts of a cohort of plant hexose and sucrose transporters, is considered key to improving crop stress tolerance and yield through its role in manipulating the carbohydrate partitioning process. The functions and regulatory roles of this gene family are variable among different species; thus, to determine these roles, more species-specific information is needed. Brassica rapa displays complicated regulation after a whole-genome triplication (WGT) event, which provides enormous advantages for use in genetic studies, thus it is an ideal model for exploring the functional and regulatory roles of SWEETs from a genetic perspective. In this study, the results of a homology search and phylogenetic relationship analysis revealed the evolutionary footprint of SWEETs among different plant taxa, which showed that plant SWEETs may have originated from Clade II and then expanded from vascular plants. The amino acid sequence characteristics and an analysis of the exon-intron structure of BrSWEETs duplicates clarified that SWEETs retention occurred after a WGT event in B. rapa. An analysis of the transcriptional levels of BrSWEETs in different tissues identified the expression differences among duplicated co-orthologs. In addition, qRT-PCR indicated that the BrSWEETs' co-orthologs were varied in their stress responses. This study greatly enriches our knowledge of SWEETs in the B. rapa species, which will contribute to future studies on the Brassica-specific regulatory pathways and to creating genetic innovations.
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Affiliation(s)
- Yanping Wei
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
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167
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Minervini G, Quaglia F, Tabaro F, Tosatto SCE. Insights into the molecular features of the von Hippel-Lindau-like protein. Amino Acids 2019; 51:1461-1474. [PMID: 31485743 DOI: 10.1007/s00726-019-02781-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/28/2019] [Indexed: 12/19/2022]
Abstract
We present an in silico characterization of the von Hippel-Lindau-like protein (VLP), the only known human paralog of the von Hippel-Lindau tumor suppressor protein (pVHL). Phylogenetic investigation showed VLP to be mostly conserved in upper mammals and specifically expressed in brain and testis. Structural analysis and molecular dynamics simulations show VLP to be very similar to pVHL three-dimensional organization and binding dynamics. In particular, conservation of elements at the protein interfaces suggests VLP to be a functional pVHL homolog potentially possessing multiple functions beyond HIF-1α-dependent binding activity. Our findings show that VLP may share at least seven interactors with pVHL, suggesting novel functional roles for this understudied human protein. These may occur at precise hypoxia levels where functional overlap with pVHL may permit a finer modulation of pVHL functions.
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Affiliation(s)
- Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy
| | - Francesco Tabaro
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy.,Institute of Biosciences and Medical Technology, Tampere, Finland
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121, Padua, Italy. .,CNR Institute of Neuroscience, Padua, Italy.
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168
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Li D, Huang W, Wang C, Qiu S. The complete genome sequence of the thermophilic bacterium Laceyella sacchari FBKL4.010 reveals the basis for tetramethylpyrazine biosynthesis in Moutai-flavor Daqu. Microbiologyopen 2019; 8:e922. [PMID: 31482696 PMCID: PMC6925174 DOI: 10.1002/mbo3.922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/29/2022] Open
Abstract
The genus Laceyella consists of a thermophilic filamentous bacteria. The pure isolate of Laceyella sacchari FBKL4.010 was isolated from Moutai‐flavor Daqu, Guizhou Province, China. In this study, the whole genome was sequenced and analyzed. The complete genome consists of one 3,374,379‐bp circular chromosome with 3,145 coding sequences (CDSs), seven clustered regularly interspaced short palindromic repeat (CRISPR) regions of 12 CRISPRs. Moreover, we identified that the genome contains genes encoding key enzymes such as proteases, peptidases, and acetolactate synthase (ALS) of the tetramethylpyrazine metabolic pathway. Metabolic pathways relevant to tetramethylpyrazine synthesis were also reconstructed based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) PATHWAY database. Annotation and syntenic analyses using antiSMASH 4.0 also revealed the presence of two gene clusters in this strain that differ from known tetramethylpyrazine synthesis clusters, with one encoding amino acid dehydrogenase (ADH) and the other encoding transaminase in tetramethylpyrazine metabolism. The results of this study provide flavor and genomic references for further research on the flavor‐producing functions of strain FBKL4.010 in the Moutai liquor‐making process.
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Affiliation(s)
- Dounan Li
- College of Life Sciences, Guizhou University, Guiyang, China.,The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
| | - Wei Huang
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China.,School of Liquor-Making and Food Engineering, Guizhou University, Guiyang, China
| | - Chunxiao Wang
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China.,School of Liquor-Making and Food Engineering, Guizhou University, Guiyang, China
| | - Shuyi Qiu
- College of Life Sciences, Guizhou University, Guiyang, China.,The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China.,School of Liquor-Making and Food Engineering, Guizhou University, Guiyang, China
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169
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Whole Genome Sequencing of Chinese White Dolphin ( Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. Mar Drugs 2019; 17:md17090504. [PMID: 31466310 PMCID: PMC6780146 DOI: 10.3390/md17090504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 01/17/2023] Open
Abstract
Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases.
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170
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Wang Z, Miao H, Liu J, Xu B, Yao X, Xu C, Zhao S, Fang X, Jia C, Wang J, Zhang J, Li J, Xu Y, Wang J, Ma W, Wu Z, Yu L, Yang Y, Liu C, Guo Y, Sun S, Baurens FC, Martin G, Salmon F, Garsmeur O, Yahiaoui N, Hervouet C, Rouard M, Laboureau N, Habas R, Ricci S, Peng M, Guo A, Xie J, Li Y, Ding Z, Yan Y, Tie W, D'Hont A, Hu W, Jin Z. Musa balbisiana genome reveals subgenome evolution and functional divergence. NATURE PLANTS 2019; 5:810-821. [PMID: 31308504 PMCID: PMC6784884 DOI: 10.1038/s41477-019-0452-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
Banana cultivars (Musa ssp.) are diploid, triploid and tetraploid hybrids derived from Musa acuminata and Musa balbisiana. We presented a high-quality draft genome assembly of M. balbisiana with 430 Mb (87%) assembled into 11 chromosomes. We identified that the recent divergence of M. acuminata (A-genome) and M. balbisiana (B-genome) occurred after lineage-specific whole-genome duplication, and that the B-genome may be more sensitive to the fractionation process compared to the A-genome. Homoeologous exchanges occurred frequently between A- and B-subgenomes in allopolyploids. Genomic variation within progenitors resulted in functional divergence of subgenomes. Global homoeologue expression dominance occurred between subgenomes of the allotriploid. Gene families related to ethylene biosynthesis and starch metabolism exhibited significant expansion at the pathway level and wide homoeologue expression dominance in the B-subgenome of the allotriploid. The independent origin of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) homoeologue gene pairs and tandem duplication-driven expansion of ACO genes in the B-subgenome contributed to rapid and major ethylene production post-harvest in allotriploid banana fruits. The findings of this study provide greater context for understanding fruit biology, and aid the development of tools for breeding optimal banana cultivars.
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Affiliation(s)
- Zhuo Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hongxia Miao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Juhua Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Biyu Xu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Chunyan Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | | | - Caihong Jia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jingyi Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianbin Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jingyang Li
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yi Xu
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashui Wang
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weihong Ma
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Lili Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Silong Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frederic Salmon
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Guadeloupe, France
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Nathalie Laboureau
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Remy Habas
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Sebastien Ricci
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Guadeloupe, France
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Zhiqiang Jin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China.
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171
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Genome Sequencing of the Japanese Eel ( Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes. Mar Drugs 2019; 17:md17070426. [PMID: 31330852 PMCID: PMC6669545 DOI: 10.3390/md17070426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/08/2023] Open
Abstract
Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.
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172
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Rashid I, Pathak AK, Kumar R, Srivastava P, Singh M, Murali S, Kushwaha B. Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements. Front Genet 2019; 10:659. [PMID: 31379925 PMCID: PMC6660265 DOI: 10.3389/fgene.2019.00659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 06/21/2019] [Indexed: 12/20/2022] Open
Abstract
Cyprinus carpio is world's most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (-4,900 to +100) sequences of 31,466 protein coding genes was downloaded from "Gene" and "RefSeq" databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.
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Affiliation(s)
- Iliyas Rashid
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India.,AMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow, India
| | - Ajey Kumar Pathak
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Prachi Srivastava
- AMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - S Murali
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
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173
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Lineage-Specific Evolved MicroRNAs Regulating NB-LRR Defense Genes in Triticeae. Int J Mol Sci 2019; 20:ijms20133128. [PMID: 31248042 PMCID: PMC6651130 DOI: 10.3390/ijms20133128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023] Open
Abstract
Disease resistance genes encoding proteins with nucleotide binding sites and Leucine-Rich Repeat (NB-LRR) domains include many members involved in the effector-triggered immunity pathway in plants. The transcript levels of these defense genes are negatively regulated by diverse microRNAs (miRNAs) in angiosperms and gymnosperms. In wheat, using small RNA expression datasets and degradome datasets, we identified five miRNA families targeting NB-LRR defense genes in monocots, some of which arose in the Triticeae species era. These miRNAs regulate different types of NB-LRR genes, most of them with coil-coiled domains, and trigger the generation of secondary small interfering RNAs (siRNA) as a phased pattern in the target site regions. In addition to acting in response to biotic stresses, they are also responsive to abiotic stresses such as heat, drought, salt, and light stress. Their copy number and expression variation in Triticeae suggest a rapid birth and death frequency. Altogether, non-conserved miRNAs as conserved transcriptional regulators in gymnosperms and angiosperms regulating the disease resistance genes displayed quick plasticity including the variations of sequences, gene copy number, functions, and expression level, which accompanied with NB-LRR genes may be tune-regulated to plants in natural environments with various biotic and abiotic stresses.
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174
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Bayer B, Pelikan C, Bittner MJ, Reinthaler T, Könneke M, Herndl GJ, Offre P. Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. mSystems 2019; 4:e00181-19. [PMID: 31239395 PMCID: PMC6593220 DOI: 10.1128/msystems.00181-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/09/2019] [Indexed: 01/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2 However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.
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Affiliation(s)
- Barbara Bayer
- Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, Austria
| | - Claus Pelikan
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Meriel J Bittner
- Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, Austria
| | - Thomas Reinthaler
- Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, Austria
| | - Martin Könneke
- Marine Archaea Group, MARUM-Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Texel, The Netherlands
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Texel, The Netherlands
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175
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Shamanskiy VA, Timonina VN, Popadin KY, Gunbin KV. ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation. BMC Genomics 2019; 20:295. [PMID: 31284879 PMCID: PMC6614062 DOI: 10.1186/s12864-019-5536-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA. RESULTS We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats. CONCLUSIONS ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/ . It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research.
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Affiliation(s)
- Viktor A Shamanskiy
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Valeria N Timonina
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Konstantin Yu Popadin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Konstantin V Gunbin
- Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal University, Kaliningrad, Russia. .,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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176
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Bustamante D, Segarra S, Tortajada M, Ramón D, del Cerro C, Auxiliadora Prieto M, Iglesias JR, Rojas A. In silico prospection of microorganisms to produce polyhydroxyalkanoate from whey: Caulobacter segnis DSM 29236 as a suitable industrial strain. Microb Biotechnol 2019; 12:487-501. [PMID: 30702206 PMCID: PMC6465232 DOI: 10.1111/1751-7915.13371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 12/20/2018] [Accepted: 12/26/2018] [Indexed: 11/29/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are polyesters of microbial origin that can be synthesized by prokaryotes from noble sugars or lipids and from complex renewable substrates. They are an attractive alternative to conventional plastics because they are biodegradable and can be produced from renewable resources, such as the surplus of whey from dairy companies. After an in silico screening to search for ß-galactosidase and PHA polymerase genes, several bacteria were identified as potential PHA producers from whey based on their ability to hydrolyse lactose. Among them, Caulobacter segnis DSM 29236 was selected as a suitable strain to develop a process for whey surplus valorization. This microorganism accumulated 31.5% of cell dry weight (CDW) of poly(3-hydroxybutyrate) (PHB) with a titre of 1.5 g l-1 in batch assays. Moreover, the strain accumulated 37% of CDW of PHB and 9.3 g l-1 in fed-batch mode of operation. This study reveals this species as a PHA producer and experimentally validates the in silico bioprospecting strategy for selecting microorganisms for waste re-valorization.
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Affiliation(s)
- Daniel Bustamante
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Silvia Segarra
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Marta Tortajada
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Daniel Ramón
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Carlos del Cerro
- Microbial and Plant Biotechnology DepartmentCentro de Investigaciones BiológicasMadridSpain
- Present address:
National Renewable Energy Laboratory (NREL)15013 Denver West ParkwayGoldenCO80401USA
| | | | - José Ramón Iglesias
- Corporación Alimentaria Peñasanta (CAPSA) Polígono Industrial0, 33199Granda, AsturiasSpain
| | - Antonia Rojas
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
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177
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Simon AH, Liebscher S, Aumüller TH, Treblow D, Bordusa F. Application of a Dual Internally Quenched Fluorogenic Substrate in Screening for D-Arginine Specific Proteases. Front Microbiol 2019; 10:711. [PMID: 31001242 PMCID: PMC6456654 DOI: 10.3389/fmicb.2019.00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Abstract
The application of D-stereospecific proteases (DSPs) in resolution of racemic amino acids and in the semisynthesis of proteins has been a successful strategy. The main limitation for a broader application is, however, the accessibility of suitable DSPs covering multiple substrate specificities. To identify DSPs with novel primary substrate preferences, a fast specificity screening method using the easily accessible internally quenched fluorogenic substrate aminobenzoyl-D-arginyl-D-alanyl-p-nitroanilide was developed. By monitoring both UV/vis-absorbance and fluorescence signals at the same time it allows to detect two distinct D-amino acid substrate specificities simultaneously and separately with respect to the individual specificities. In order to identify novel DSP specificities for synthesis applications, DSPs specific for D-arginine were of special interest due to their potential ability as catalysts for substrate mimetics-mediated peptide and protein ligations. D-alanine in the substrate served as positive control and reference based on its known acceptance by numerous DSPs. In silico analysis suggested that DSPs are predominantly present in gram-positive microorganisms, therefore this study focused on the bacilli strains Bacillus thuringiensis and Bacillus subtilis as potential hosts of D-Arg-specific DSPs. While protease activities toward D-alanine were found in both organisms, a novel and so far unknown D-arginine specific DSP was detected within the culture supernatant of B. thuringiensis. Enrichment of this activity via cation exchange and size exclusion chromatography allowed isolation and further characterization of this novel enzyme consisting of a molecular mass of 37.7 kDa and an enzymatic activity of 8.3 U mg-1 for cleaving the D-Arg|D-Ala bond in the detecting substrate. Independent experiments also showed that the identified enzyme shows similarities to the class of penicillin binding proteins. In future applications this enzyme will be a promising starting point for the development of novel strategies for the semisynthesis of all-L-proteins.
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Affiliation(s)
- Andreas H Simon
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Sandra Liebscher
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Tobias H Aumüller
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
| | - Dennis Treblow
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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178
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Luo G, Li B, Yang C, Wang Y, Bian X, Li W, Liu F, Huo G. Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts. Front Microbiol 2019; 10:712. [PMID: 31024492 PMCID: PMC6465617 DOI: 10.3389/fmicb.2019.00712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/21/2019] [Indexed: 12/26/2022] Open
Abstract
Modulating gut microbiota to promote host health is well recognized. Therefore, people consume dietary products containing traditional probiotics in wishing to improve their health, and they need more research-based advices on how to select products with suitable probiotic species. Probiotic designers are sometimes confused about how to design precision products for different consumers by taking advantages of different probiotic species’ strengths. Additionally, large-scale analyses on traditional probiotic complementarity potentials and their roles in gut microbiome related to common diseases are not well understood. Here, we comprehensively analyzed 444 genomes of major traditional probiotic (sub) species (MTPS, n = 15) by combining one newly sequenced genome with all of the public NCBI-available MTPS-related genomes. The public human fecal metagenomic data (n = 1,815) of eight cohorts were used to evaluate the roles of MTPS, compared to other main gut bacteria, in disease association by examining the species enrichment direction in disease group or the control group. Our work provided a comprehensive genetic landscape and complementarity relations for MTPS and shed light on personalized probiotic supplements for consumers with different health status and the necessity that researchers and manufactures could explore novel probiotics as well as traditional ones.
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Affiliation(s)
- Guangwen Luo
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Bailiang Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Cailu Yang
- Department of Ultrasound, Maternal and Child Health Hospital of Dapeng New District, Shenzhen, China
| | - Yutang Wang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xin Bian
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Wan Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Fei Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Guicheng Huo
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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179
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New insights into the origin and evolution of α-amylase genes in green plants. Sci Rep 2019; 9:4929. [PMID: 30894656 PMCID: PMC6426938 DOI: 10.1038/s41598-019-41420-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/05/2018] [Indexed: 01/16/2023] Open
Abstract
Gene duplication is a source of genetic materials and evolutionary changes, and has been associated with gene family expansion. Functional divergence of duplicated genes is strongly directed by natural selections such as organism diversification and novel feature acquisition. We show that, plant α-amylase gene family (AMY) is comprised of six subfamilies (AMY1-AMY6) that fell into two ancient phylogenetic lineages (AMY3 and AMY4). Both AMY1 and AMY2 are grass-specific and share a single-copy ancestor, which is derived from grass AMY3 genes that have undergone massive tandem and whole-genome duplications during evolution. Ancestral features of AMY4 and AMY5/AMY6 genes have been retained among four green algal sequences (Chrein_08.g362450, Vocart_0021s0194, Dusali_0430s00012 and Monegl_16464), suggesting a gene duplication event following Chlorophyceae diversification. The observed horizontal gene transfers between plant and bacterial AMYs, and chromosomal locations of AMY3 and AMY4 genes in the most ancestral green body (C. reinhardtii), provide evidences for the monophyletic origin of plant AMYs. Despite subfamily-specific sequence divergence driven by natural selections, the active site and SBS1 are well-conserved across different AMY isoforms. The differentiated electrostatic potentials and hydrogen bands-forming residue polymorphisms, further imply variable digestive abilities for a broad substrates in particular tissues or subcellular localizations.
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180
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Bhatta TR, Chamings A, Vibin J, Alexandersen S. Detection and characterisation of canine astrovirus, canine parvovirus and canine papillomavirus in puppies using next generation sequencing. Sci Rep 2019; 9:4602. [PMID: 30872719 PMCID: PMC6418273 DOI: 10.1038/s41598-019-41045-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/27/2019] [Indexed: 12/22/2022] Open
Abstract
Gastroenteritis in young animals is a clinical presentation with many infectious and non- infectious aetiologies. We used next generation sequencing (NGS) to investigate the possible infectious causes of gastroenteritis in puppies from a dog kennel in Victoria, Australia. The near complete genome of a canine astrovirus was obtained from pooled faecal samples, and was found to be 94.7% identical with a canine astrovirus detected in the United Kingdom in 2012. The phylogenetic analysis of the capsid gene found similarities to those of canine astroviruses identified in Italy in 2005 and in UK and Hungary in 2012, but distant from that of a canine astrovirus previously identified in Australia in 2012. Thus, different serotypes of canine astrovirus are likely circulating in Australia. The close relationship to European astroviruses also suggested that there had been recent movements of ancestor canine astroviruses between Australia and Europe. NGS also detected other infections in the puppies including several canine papillomaviruses and a canine parvovirus (vaccine strain) as well as a very low level of campylobacter. Canine astrovirus was the probable cause of diarrhoea in these puppies, with the possible involvement of campylobacter bacteria. NGS was effective as a non-targeted method to determine the likely infectious cause of gastroenteritis.
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Affiliation(s)
- Tarka Raj Bhatta
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia
| | - Jessy Vibin
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia. .,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia. .,Barwon Health, University Hospital Geelong, Geelong, VIC, 3220, Australia.
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181
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Xu J, Li Y, Lv Y, Bian C, You X, Endoh D, Teraoka H, Shi Q. Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey. Genes (Basel) 2019; 10:E203. [PMID: 30857219 PMCID: PMC6470480 DOI: 10.3390/genes10030203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 02/02/2023] Open
Abstract
Serotonin is a neurotransmitter involved in various physiological processes in the central and peripheral nervous systems. Serotonin is also a precursor for melatonin biosynthesis, which mainly occurs in the pineal gland of vertebrates. Tryptophan hydroxylase (TPH) acts as the rate-limiting enzyme in serotonin biosynthesis and is the initial enzyme involved in the synthesis of melatonin. Recently, two enzymes-TPH1 and TPH2-were reported to form the TPH family in vertebrates and to play divergent roles in serotonergic systems. Here, we examined the evolution of the TPH family from 70 vertebrate genomes. Based on the sequence similarity, we extracted 184 predicted tph homologs in the examined vertebrates. A phylogenetic tree, constructed on the basis of these protein sequences, indicated that tph genes could be divided into two main clades (tph1 and tph2), and that the two clades were further split into two subgroups of tetrapods and Actinopterygii. In tetrapods, and some basal non-teleost ray-finned fishes, only two tph isotypes exist. Notably, tph1 in most teleosts that had undergone the teleost-specific genome duplication could be further divided into tph1a and tph1b. Moreover, protein sequence comparisons indicated that TPH protein changes among vertebrates were concentrated at the NH₂-terminal. The tertiary structures of TPH1 and TPH2 revealed obvious differences in the structural elements. Five positively selected sites were characterized in TPH2 compared with TPH1; these sites may reflect the functional divergence in enzyme activity and substrate specificity. In summary, our current work provides novel insights into the evolution of tph genes in vertebrates from a comprehensive genomic perspective.
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Affiliation(s)
- Junmin Xu
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Yanping Li
- BGI-Shenzhen, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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182
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Ju L, Deng G, Liang J, Zhang H, Li Q, Pan Z, Yu M, Long H. Structural organization and functional divergence of high isoelectric point α-amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). BMC Genet 2019; 20:25. [PMID: 30845909 PMCID: PMC6404323 DOI: 10.1186/s12863-019-0732-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND High isoelectric point α-amylase genes (Amy1) play major roles during cereal seed germination, and are associated with unacceptable high residual α-amylase activities in ripe wheat grains. However, in wheat and barley, due to extremely high homology of duplicated copies, and large and complex genome background, the knowledge on this multigene family is limited. RESULTS In the present work, we identified a total of 41 Amy1 genes among 13 investigated grasses. By using genomic resources and experimental validation, the exact copy numbers and chromosomal locations in wheat and barley were determined. Phylogenetic and syntenic analyses revealed tandem gene duplication and chromosomal rearrangement leading to separation of Amy1 into two distinct loci, Amy1θ and Amy1λ. The divergence of Amy1λ from Amy1θ was driven by adaptive selection pressures performed on two amino acids, Arg97 and Asn233 (P > 0.95*). The predicted protein structural alteration caused by substitution of Asp233Asn in the conserved starch binding surface site, and significantly expressional differentiation during seed germination and grain development provided evidence of functional divergence between Amy1θ and Amy1λ genes. We screened out candidate copies (TaAmy1-A1/A2 and TaAmy1-D1) associated with high residual α-amylase activities in ripe grains. Furthermore, we proposed an evolutionary model for expansion dynamics of Amy1 genes. CONCLUSIONS Our study provides comprehensive analyses of the Amy1 multigene family, and defines the fixation of two spatially structural Amy1 loci in wheat and barley. Potential functional divergence between them is reflected by their sequence features and expressional patterns, and driven by gene duplication, chromosome rearrangement and natural selections during gene family evolution. Furthermore, the discrimination of differentially effective copies during seed germination and/or grain development will provide guidance to manipulation of α-amylase activity in wheat and barley breeding for better yield and processing properties.
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Affiliation(s)
- Liangliang Ju
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
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183
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Shi G, Chen L, Chen G, Zou C, Li J, Li M, Fang C, Li C. Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs. Front Genet 2019; 10:160. [PMID: 30886630 PMCID: PMC6409335 DOI: 10.3389/fgene.2019.00160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/19/2022] Open
Abstract
An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat development. Here, we used published RNA-seq data from subcutaneous adipose tissue of Italian Large White pigs and identified 252 putative lincRNAs, wherein 34 were unannotated. These lincRNAs had relatively shorter length, lower number of exons, and lower expression level compared with protein-coding transcripts. Gene ontology and pathway analysis indicated that the adjacent genes of lincRNAs were involved in lipid metabolism. In addition, differentially expressed lincRNAs (DELs) between low and high backfat thickness pigs were identified. Through the detection of quantitative trait locus (QTL), DELs were mainly located in QTLs related to adipose development. Based on the expression correlation of DEL genes and their differentially expressed potential target genes, we constructed a co-expression network and a potential pathway of DEL's effect on lipid metabolism. Our study identified and analyzed lincRNAs in subcutaneous adipose tissue, and results suggested that lincRNAs may be involved in the regulation of subcutaneous fat development. Our findings provided new insights into the biological function of porcine lincRNAs.
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Affiliation(s)
- Gaoli Shi
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lin Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jingxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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184
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Mathews SL, Epps MJ, Blackburn RK, Goshe MB, Grunden AM, Dunn RR. Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180748. [PMID: 31031986 PMCID: PMC6458430 DOI: 10.1098/rsos.180748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/07/2019] [Indexed: 05/04/2023]
Abstract
A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder 'what good are they anyway?' and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle (Dermestes maculatus) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified that were capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.
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Affiliation(s)
- Stephanie L. Mathews
- Department of Biological Sciences, Campbell University, Buies Creek, NC 27506, USA
| | - Mary Jane Epps
- Department of Biology, Mary Baldwin University, Staunton, VA 24401, USA
| | - R. Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Amy M. Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, 2100Denmark
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185
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Identification and Characterization of a Dominant Sulfolane-Degrading Rhodoferax sp. via Stable Isotope Probing Combined with Metagenomics. Sci Rep 2019; 9:3121. [PMID: 30816276 PMCID: PMC6395730 DOI: 10.1038/s41598-019-40000-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/05/2019] [Indexed: 01/06/2023] Open
Abstract
Sulfolane is an industrial solvent and emerging organic contaminant affecting groundwater around the world, but little is known about microbes capable of biodegrading sulfolane or the pathways involved. We combined DNA-based stable isotope probing (SIP) with genome-resolved metagenomics to identify microorganisms associated with sulfolane biodegradation in a contaminated subarctic aquifer. In addition to 16S rRNA gene amplicon sequencing, we performed shotgun metagenomics on the 13C-labeled DNA to obtain functional and taxonomic information about the active sulfolane-degrading community. We identified the primary sulfolane degrader, comprising ~85% of the labeled community in the amplicon sequencing dataset, as closely related to Rhodoferax ferrireducens strain T118. We obtained a 99.8%-complete metagenome-assembled genome for this strain, allowing us to identify putative pathways of sulfolane biodegradation. Although the 4S dibenzothiophene desulfurization pathway has been proposed as an analog for sulfolane biodegradation, we found only a subset of the required genes, suggesting a novel pathway specific to sulfolane. DszA, the enzyme likely responsible for opening the sulfolane ring structure, was encoded on both the chromosome and a plasmid. This study demonstrates the power of integrating DNA-SIP with metagenomics to characterize emerging organic contaminant degraders without culture bias and expands the known taxonomic distribution of sulfolane biodegradation.
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186
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Miravet-Verde S, Ferrar T, Espadas-García G, Mazzolini R, Gharrab A, Sabido E, Serrano L, Lluch-Senar M. Unraveling the hidden universe of small proteins in bacterial genomes. Mol Syst Biol 2019; 15:e8290. [PMID: 30796087 PMCID: PMC6385055 DOI: 10.15252/msb.20188290] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Identification of small open reading frames (smORFs) encoding small proteins (≤ 100 amino acids; SEPs) is a challenge in the fields of genome annotation and protein discovery. Here, by combining a novel bioinformatics tool (RanSEPs) with “‐omics” approaches, we were able to describe 109 bacterial small ORFomes. Predictions were first validated by performing an exhaustive search of SEPs present in Mycoplasma pneumoniae proteome via mass spectrometry, which illustrated the limitations of shotgun approaches. Then, RanSEPs predictions were validated and compared with other tools using proteomic datasets from different bacterial species and SEPs from the literature. We found that up to 16 ± 9% of proteins in an organism could be classified as SEPs. Integration of RanSEPs predictions with transcriptomics data showed that some annotated non‐coding RNAs could in fact encode for SEPs. A functional study of SEPs highlighted an enrichment in the membrane, translation, metabolism, and nucleotide‐binding categories. Additionally, 9.7% of the SEPs included a N‐terminus predicted signal peptide. We envision RanSEPs as a tool to unmask the hidden universe of small bacterial proteins.
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Affiliation(s)
- Samuel Miravet-Verde
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tony Ferrar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guadalupe Espadas-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rocco Mazzolini
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anas Gharrab
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eduard Sabido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain .,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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187
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Finding an Optimal Corneal Xenograft Using Comparative Analysis of Corneal Matrix Proteins Across Species. Sci Rep 2019; 9:1876. [PMID: 30755666 PMCID: PMC6372616 DOI: 10.1038/s41598-018-38342-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/19/2018] [Indexed: 11/08/2022] Open
Abstract
Numerous animal species have been proposed as sources of corneal tissue for obtaining decellularized xenografts. The selection of an appropriate animal model must take into consideration the differences in the composition and structure of corneal proteins between humans and other animal species in order to minimize immune response and improve outcome of the xenotransplant. Here, we compared the amino-acid sequences of 16 proteins present in the corneal stromal matrix of 14 different animal species using Basic Local Alignment Search Tool, and calculated a similarity score compared to the respective human sequence. Primary amino acid structures, isoelectric point and grand average of hydropathy (GRAVY) values of the 7 most abundant proteins (i.e. collagen α-1 (I), α-1 (VI), α-2 (I) and α-3 (VI), as well as decorin, lumican, and keratocan) were also extracted and compared to those of human. The pig had the highest similarity score (91.8%). All species showed a lower proline content compared to human. Isoelectric point of pig (7.1) was the closest to the human. Most species have higher GRAVY values compared to human except horse. Our results suggest that porcine cornea has a higher relative suitability for corneal transplantation into humans compared to other studied species.
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188
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Pan J, Chen Y, Wang Y, Zhou Z, Li M. Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6. MICROBIAL ECOLOGY 2019; 77:417-428. [PMID: 30612184 DOI: 10.1007/s00248-018-1309-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.
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Affiliation(s)
- Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yulian Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yongming Wang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
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Baig MH, Rashid I, Srivastava P, Ahmad K, Jan AT, Rabbani G, Choi D, Barreto GE, Ashraf GM, Lee EJ, Choi I. NeuroMuscleDB: a Database of Genes Associated with Muscle Development, Neuromuscular Diseases, Ageing, and Neurodegeneration. Mol Neurobiol 2019; 56:5835-5843. [PMID: 30684219 DOI: 10.1007/s12035-019-1478-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/10/2019] [Indexed: 12/25/2022]
Abstract
Skeletal muscle is a highly complex, heterogeneous tissue that serves a multitude of biological functions in living organisms. With the advent of methods, such as microarrays, transcriptome analysis, and proteomics, studies have been performed at the genome level to gain insight of changes in the expression profiles of genes during different stages of muscle development and of associated diseases. In the present study, a database was conceived for the straightforward retrieval of information on genes involved in skeletal muscle formation, neuromuscular diseases (NMDs), ageing, and neurodegenerative disorders (NDs). The resulting database named NeuroMuscleDB ( http://yu-mbl-muscledb.com/NeuroMuscleDB ) is the result of a wide literature survey, database searches, and data curation. NeuroMuscleDB contains information of genes in Homo sapiens, Mus musculus, and Bos Taurus, and their promoter sequences and specified roles at different stages of muscle development and in associated myopathies. The database contains information on ~ 1102 genes, 6030 mRNAs, and 5687 proteins, and embedded analytical tools that can be used to perform tasks related to gene sequence usage. The authors believe NeuroMuscleDB provides a platform for obtaining desired information on genes related to myogenesis and their associations with various diseases (NMDs, ageing, and NDs). NeuroMuscleDB is freely available on the web at http://yu-mbl-muscledb.com/NeuroMuscleDB and supports all major browsers.
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Affiliation(s)
- Mohammad Hassan Baig
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Iliyas Rashid
- Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, 226 028, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University, Lucknow, Uttar Pradesh, 226 028, India
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, 185236, India
| | - Gulam Rabbani
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Dukhwan Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá D.C., Colombia.,Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
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190
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Thermal Stability of a Mercuric Reductase from the Red Sea Atlantis II Hot Brine Environment as Analyzed by Site-Directed Mutagenesis. Appl Environ Microbiol 2019; 85:AEM.02387-18. [PMID: 30446558 DOI: 10.1128/aem.02387-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 11/11/2018] [Indexed: 01/28/2023] Open
Abstract
The lower convective layer (LCL) of the Atlantis II brine pool of the Red Sea is a unique environment in terms of high salinity, temperature, and high concentrations of heavy metals. Mercuric reductase enzymes functional in such extreme conditions could be considered a potential tool in the environmental detoxification of mercurial poisoning and might alleviate ecological hazards in the mining industry. Here, we constructed a mercuric reductase library from Atlantis II, from which we identified genes encoding two thermostable mercuric reductase (MerA) isoforms: one is halophilic (designated ATII-LCL) while the other is not (designated ATII-LCL-NH). The ATII-LCL MerA has a short motif composed of four aspartic acids (4D414-417) and two characteristic signature boxes that played a crucial role in its thermal stability. To further understand the mechanism behind the thermostability of the two studied enzymes, we mutated the isoform ATII-LCL-NH and found that the substitution of 2 aspartic acids (2D) at positions 415 and 416 enhanced the thermal stability, while other mutations had the opposite effect. The 2D mutant showed superior thermal tolerance, as it retained 81% of its activity after 10 min of incubation at 70°C. A three-dimensional structure prediction revealed newly formed salt bridges and H bonds in the 2D mutant compared to the parent molecule. To the best of our knowledge, this study is the first to rationally design a mercuric reductase with enhanced thermal stability, which we propose to have a strong potential in the bioremediation of mercurial poisoning.IMPORTANCE The Red Sea is an attractive environment for bioprospecting. There are 25 brine-filled deeps in the Red Sea. The Atlantis II brine pool is the biggest and hottest of such hydrothermal ecosystems. We generated an environmental mercuric reductase library from the lowermost layer of the Atlantis II brine pool, in which we identified two variants of the mercuric reductase enzyme (MerA). One is the previously described halophilic and thermostable ATII-LCL MerA and the other is a nonhalophilic relatively less thermostable enzyme, designated ATII-LCL-NH MerA. We used the ATII-LCL-NH enzyme as a parent molecule to locate the amino acid residues involved in the noticeably higher thermotolerance of the homolog ATII-LCL MerA. Moreover, we designed a novel enzyme with superior thermal stability. This enzyme might have strong potential in the bioremediation of mercuric toxicity.
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191
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Luo Q, Bian C, Tao M, Huang Y, Zheng Y, Lv Y, Li J, Wang C, You X, Jia B, Xu J, Li J, Li Z, Shi Q, Hu Z. Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga, Haematococcus pluvialis. Genome Biol Evol 2019; 11:166-173. [PMID: 30496415 PMCID: PMC6330051 DOI: 10.1093/gbe/evy263] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 01/25/2023] Open
Abstract
Haematococcus pluvialis is a freshwater species of Chlorophyta, family Haematococcaceae. It is well known for its capacity to synthesize high amounts of astaxanthin, which is a strong antioxidant that has been utilized in aquaculture and cosmetics. To improve astaxanthin yield and to establish genetic resources for H. pluvialis, we performed whole-genome sequencing, assembly, and annotation of this green microalga. A total of 83.1 Gb of raw reads were sequenced. After filtering the raw reads, we subsequently generated a draft assembly with a genome size of 669.0 Mb, a scaffold N50 of 288.6 kb, and predicted 18,545 genes. We also established a robust phylogenetic tree from 14 representative algae species. With additional transcriptome data, we revealed some novel potential genes that are involved in the synthesis, accumulation, and regulation of astaxanthin production. In addition, we generated an isoform-level reference transcriptome set of 18,483 transcripts with high confidence. Alternative splicing analysis demonstrated that intron retention is the most frequent mode. In summary, we report the first draft genome of H. pluvialis. These genomic resources along with transcriptomic data provide a solid foundation for the discovery of the genetic basis for theoretical and commercial astaxanthin enrichment.
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Affiliation(s)
- Qiulan Luo
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
- These authors contributed equally to this work
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
- These authors contributed equally to this work
| | - Ming Tao
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
- These authors contributed equally to this work
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
- These authors contributed equally to this work
| | - Yihong Zheng
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- These authors contributed equally to this work
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
- These authors contributed equally to this work
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
| | - Chaogang Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
| | - Bin Jia
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
| | - Jiancheng Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Ze Li
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Qiong Shi
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
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192
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Promising New Antifungal Treatment Targeting Chorismate Synthase from Paracoccidioides brasiliensis. Antimicrob Agents Chemother 2018; 63:AAC.01097-18. [PMID: 30348661 DOI: 10.1128/aac.01097-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/13/2018] [Indexed: 12/24/2022] Open
Abstract
Paracoccidioidomycosis (PCM), caused by Paracoccidioides, is a systemic mycosis with granulomatous character and a restricted therapeutic arsenal. The aim of this work was to search for new alternatives to treat largely neglected tropical mycosis, such as PCM. In this context, the enzymes of the shikimate pathway constitute excellent drug targets for conferring selective toxicity because this pathway is absent in humans but essential for the fungus. In this work, we have used a homology model of the chorismate synthase (EC 4.2.3.5) from Paracoccidioides brasiliensis (PbCS) and performed a combination of virtual screening and molecular dynamics testing to identify new potential inhibitors. The best hit, CP1, successfully adhered to pharmacological criteria (adsorption, distribution, metabolism, excretion, and toxicity) and was therefore used in in vitro experiments. Here we demonstrate that CP1 binds with a dissociation constant of 64 ± 1 μM to recombinant chorismate synthase from P. brasiliensis and inhibits enzymatic activity, with a 50% inhibitory concentration (IC50) of 47 ± 5 μM. As expected, CP1 showed no toxicity in three cell lines. On the other hand, CP1 reduced the fungal burden in lungs from treated mice, similar to itraconazole. In addition, histopathological analysis showed that animals treated with CP1 displayed less lung tissue infiltration, fewer yeast cells, and large areas with preserved architecture. Therefore, CP1 was able to control PCM in mice with a lower inflammatory response and is thus a promising candidate and lead structure for the development of drugs useful in PCM treatment.
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193
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Zhang QL, Zhang GL, Yuan ML, Dong ZX, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus. Front Physiol 2018; 9:1833. [PMID: 30618839 PMCID: PMC6305399 DOI: 10.3389/fphys.2018.01833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (∼104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guan-Ling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun-Yuan Chen
- Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China.,State Key Laboratory of Palaeobiology and Stratigraphy (LPS), Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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194
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Zhang Z, Zhang K, Chen S, Zhang Z, Zhang J, You X, Bian C, Xu J, Jia C, Qiang J, Zhu F, Li H, Liu H, Shen D, Ren Z, Chen J, Li J, Gao T, Gu R, Xu J, Shi Q, Xu P. Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii. Gigascience 2018; 7:1-7. [PMID: 29659813 PMCID: PMC5893958 DOI: 10.1093/gigascience/giy012] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/12/2018] [Indexed: 01/08/2023] Open
Abstract
Background As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii), also known as the blackhead seabream, has some attractive characteristics such as fast growth rate, good meat quality, resistance to diseases, and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphroditism. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon. Findings We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. We identified 19 465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found 3 types of genes potentially associated with sex change, which are useful for studying the genetic basis of the protandrous hermaphroditism. Conclusions We provide a draft genome assembly of the Chinese black porgy and discuss the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and for facilitating breeding of this economically important fish.
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Affiliation(s)
- Zhiyong Zhang
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Kai Zhang
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Shuyin Chen
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Zhiwei Zhang
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Jinyong Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430000, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Jin Xu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Chaofeng Jia
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Jun Qiang
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Fei Zhu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Hongxia Li
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Hailin Liu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Dehua Shen
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Zhonghong Ren
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Jieming Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Tianheng Gao
- College of Oceanography, Hohhai University, Nanjing, Jiangsu 210098, China
| | - Ruobo Gu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Pao Xu
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
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195
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Li F, Tao D, Feng X, Wong MCM, Lu H. Establishment and Development of Oral Microflora in 12-24 Month-Old Toddlers Monitored by High-Throughput Sequencing. Front Cell Infect Microbiol 2018; 8:422. [PMID: 30564560 PMCID: PMC6288402 DOI: 10.3389/fcimb.2018.00422] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/20/2018] [Indexed: 12/18/2022] Open
Abstract
A cohort study was conducted to evaluate oral microbial diversity among toddlers aged 12-24 months, and to describe the dynamic processes of colonization, development, and stabilization of the oral microflora during tooth eruption using high-throughput sequencing technology. A total of 20 healthy toddlers aged 12 months were included at baseline and followed up through 18-24 months. Clinical oral examinations of dental caries status and visible plaque index were carried out at three follow-up time points. Pooled supragingival plaque biofilm samples were also collected at ages 12, 18, and 24 months. Plaque biofilm DNA was extracted and analyzed by MiSeq sequencing. A total of 18 toddlers completed three follow-ups. At 12 months of age, all the toddlers only had eruption of the anterior teeth, without dental caries. At ages 18 and 24 months, one and two toddlers showed two and three teeth with carious white spots, respectively. Depth, Good's coverage, and sample size of sequencing were reasonable. The dominant bacterial genera in the oral cavity of 12-month-old toddlers were Capnocytophaga, Neisseria, Streptococcus, Kingella, and Leptotrichia; the oral microflora composition was relatively stable by 18 months of age and included unclassified Enterobacteriaceae, Selenomonas, Prevotella, Leptotrichia, and Veillonella as the dominant genera; unclassified Enterobacteriaceae, Streptococcus, Neisseria, Leptotrichia, and Selenomonas were the dominant genera by 24 months. There were significant differences among microbial compositions in the oral cavities of 12, 18, and 24-month-old toddlers, with relatively small differences observed between the 18 and 24 months samples. In conclusion, oral microbial community of toddlers showed a trend of dynamic development. Significant differences in oral microbial diversity among toddlers aged 12-24 months were observed, while the microbial diversity differences among toddlers aged 18-24 months tended to be more similar. The findings indicated that the oral microbial community gradually matures and tends to stabilize with the growth and development of toddlers.
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Affiliation(s)
- Fei Li
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Danying Tao
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xiping Feng
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - May Chun Mei Wong
- Dental Public Health, Faculty of Dentistry, University of Hong Kong, Hong Kong, China
| | - Haixia Lu
- Department of Preventive Dentistry, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
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196
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Jiang W, Qiu Y, Pan X, Zhang Y, Wang X, Lv Y, Bian C, Li J, You X, Chen J, Yang K, Yang J, Sun C, Liu Q, Cheng L, Yang J, Shi Q. Genome Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. Front Genet 2018; 9:614. [PMID: 30564274 PMCID: PMC6288284 DOI: 10.3389/fgene.2018.00614] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/21/2018] [Indexed: 11/26/2022] Open
Abstract
A Yunnan-Guizhou Plateau fish, the Kanglang white minnow (Anabarilius grahami), is a typical “3E” (Endangered, Endemic, and Economic) species in China. Its distribution is limited to Fuxian Lake, the nation’s second deepest lake, with a significant local economic value but a drastically declining wild population. This species has been evaluated as VU (Vulnerable) in the China Species Red List. As one of the “Four Famous Fish” in Yunnan province, the artificial breeding has been achieved since 2003. It has not only re-established its wild natural populations by reintroduction of the artificial breeding stocks, but also brought a wide and popular utilization of this species to the local fish farms. A. grahami has become one of the main native aquaculture species in Yunnan province, and the artificial production has been emerging in steady growth each year. To promote the conservation and sustainable utilization of this fish, we initiated its whole genome sequencing project using an Illumina Hiseq2500 platform. The assembled genome size of A. grahami is 1.006 Gb, accounting for 98.63% of the estimated genome size (1.020 Gb), with contig N50 and scaffold N50 values of 26.4 kb and 4.41 Mb, respectively. Approximately about 50.38% of the genome was repetitive. A total of 25,520 protein-coding genes were subsequently predicted. A phylogenetic tree based on 4,580 single-copy genes from A. grahami and 18 other cyprinids revealed three well-supported subclades within the Cyprinidae. This is the first inter-subfamily relationship of cyprinids at genome level, providing a simple yet useful framework for understanding the traditional but popular subfamily classification systems. Interestingly, a further population demography of A. grahami uncovered a historical relationship between this fish and Fuxian Lake, suggesting that range expansion or shrinkage of the habitat has had a remarkable impact on the population size of endemic plateau fishes. Additionally, a total of 33,836 simple sequence repeats (SSR) markers were identified, and 11 loci were evaluated for a preliminary genetic diversity analysis in this study, thus providing another useful genetic resource for studying this “3E” species.
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Affiliation(s)
- Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Qiu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yunyun Lv
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Chao Bian
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Jieming Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Kunfeng Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Chao Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qian Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Le Cheng
- BGI-Yunnan, BGI-Shenzhen, Kunming, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
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197
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Zhao X, Luo M, Li Z, Zhong P, Cheng Y, Lai F, Wang X, Min J, Bai M, Yang Y, Cheng H, Zhou R. Chromosome-scale assembly of the Monopterus genome. Gigascience 2018; 7:4982940. [PMID: 29688346 PMCID: PMC5946948 DOI: 10.1093/gigascience/giy046] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 04/16/2018] [Indexed: 01/10/2023] Open
Abstract
Background The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available. Findings Here, we sequenced and de novo assembled the genome of M. albus and report the de novochromosome assembly by FISH walking assisted by conserved synteny (Cafs). Using Cafs, 328 scaffolds were assembled into 12 chromosomes, which covered genomic sequences of 555 Mb, accounting for 81.3% of the sequences assembled in scaffolds (∼689 Mb). A total of 18 ,660 genes were mapped on the chromosomes and showed a nonrandom distribution along chromosomes. Conclusions We report the first reference genome of the Monopterus and provide an efficient Cafs strategy for a de novo chromosome-level assembly of the Monopterus genome, which provides a valuable resource, not only for further studies in genetics, evolution, and development, particularly sex determination, but also for breed improvement of the species.
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Affiliation(s)
- Xueya Zhao
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Majing Luo
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Zhigang Li
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Pei Zhong
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yibin Cheng
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fengling Lai
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jiumeng Min
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, P. R. China
| | - Mingzhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, P. R. China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, P. R. China
| | - Hanhua Cheng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, P. R. China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
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198
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Fu X, Li J, Tian Y, Quan W, Zhang S, Liu Q, Liang F, Zhu X, Zhang L, Wang D, Hu J. Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome. Gigascience 2018; 6:1-7. [PMID: 29186486 PMCID: PMC5751067 DOI: 10.1093/gigascience/gix112] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/15/2017] [Indexed: 01/27/2023] Open
Abstract
Background Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis. Findings Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions. Conclusions We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution.
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Affiliation(s)
- Xinhua Fu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430000, China
| | - Jingjing Li
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Yu Tian
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Weipeng Quan
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Shu Zhang
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Qian Liu
- Institute for Genomic Medicine, Columbia University, 116th Street and Broadway, New York, NY 10032, USA
| | - Fan Liang
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Xinlei Zhu
- Firefly Conservation Research Centre, Shizishan Street, Hongshan District, Wuhan, Hubei 430000, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Depeng Wang
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Jiang Hu
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
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Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis. Sci Data 2018; 5:180222. [PMID: 30398469 PMCID: PMC6219407 DOI: 10.1038/sdata.2018.222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/21/2018] [Indexed: 12/20/2022] Open
Abstract
Because of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-time (SMRT) analysis. Protein-coding genes, rRNAs and tRNAs were predicted. Functional annotations of the genome using different databases revealed several genes related to pathogenicity including antibiotic resistance genes and prophages. Our work demonstrates that whole genome sequencing can enhance the resolution of clinical investigations and our data can be used as a reference genome during the rapid diagnosis of C. kerstersii infections in the future.
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200
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Maleki E, Babashah H, Koohi S, Kavehvash Z. All-optical DNA variant discovery utilizing extended DV-curve-based wavelength modulation. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2018; 35:1929-1940. [PMID: 30461853 DOI: 10.1364/josaa.35.001929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/03/2018] [Indexed: 06/09/2023]
Abstract
This paper presents a novel optical processing approach for exploring genome sequences built upon an optical correlator for global alignment and the extended dual-vector-curve (DV-curve) method for local alignment. To overcome the problem of the traditional DV-curve method for presenting an accurate and simplified output, we propose the hybrid amplitude wavelength polarization optical DV-curve (HAWPOD) method, built upon the DV-curve method, to analyze genome sequences in three steps: DNA coding, alignment, and post-analysis. For this purpose, a tunable graphene-based color filter is designed for wavelength modulation of optical signals. Moreover, all-optical implementation of the HAWPOD method is developed, while its accuracy is validated through numerical simulations in LUMERICAL FDTD. The results express that the proposed method is much faster than its electrical counterparts.
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