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Wang Y, Qian J, Yan F, Wang Y, Shi T, Zhang Z, Ye C, Huang H. DSEMR: A database for special environment microorganisms resource and associating them with synthetic biological parts. Synth Syst Biotechnol 2023; 8:647-653. [PMID: 37840639 PMCID: PMC10569984 DOI: 10.1016/j.synbio.2023.09.006] [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: 06/28/2023] [Revised: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Special environmental microorganisms are considered to be of great industrial application value because of their special genotypes, physiological functions and metabolites. The research and development of special environmental microorganisms will certainly bring about some innovations in biotechnology processes and change the face of bioengineering. The Special Environmental Microbial Database (DSEMR) is a comprehensive database that provides information on special environmental microbial resources and correlates them with synthetic biological parts. DSEMR aggregates information on specific environmental microbial genomes, physiological properties, culture media, biological parts, and metabolic pathways, and provides online tool analysis data, including 5268 strains from 620 genera, 31 media, and 42,126 biological parts. In short, DSEMR will become an important resource for the study of microorganisms in special environments and actively promote the development of synthetic biology.
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Affiliation(s)
- Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
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Xi H, Nie X, Gao F, Liang X, Li H, Zhou H, Cai Y, Yang C. A bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine. SCIENCE ADVANCES 2023; 9:eadj9075. [PMID: 37878710 PMCID: PMC10599626 DOI: 10.1126/sciadv.adj9075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/22/2023] [Indexed: 10/27/2023]
Abstract
Spermidine, a ubiquitous polyamine, is known to be required for critical physiological functions in bacteria. Two principal pathways are known for spermidine biosynthesis, both of which involve aminopropylation of putrescine. Here, we identified a spermidine biosynthetic pathway via a previously unknown metabolite, carboxyaminopropylagmatine (CAPA), in a model cyanobacterium Synechocystis sp. PCC 6803 through an approach combining 13C and 15N tracers, metabolomics, and genetic and biochemical characterization. The CAPA pathway starts with reductive condensation of agmatine and l-aspartate-β-semialdehyde into CAPA by a previously unknown CAPA dehydrogenase, followed by decarboxylation of CAPA to form aminopropylagmatine, and ends with conversion of aminopropylagmatine to spermidine by an aminopropylagmatine ureohydrolase. Thus, the pathway does not involve putrescine and depends on l-aspartate-β-semialdehyde as the aminopropyl group donor. Genomic, biochemical, and metagenomic analyses showed that the CAPA-pathway genes are widespread in 15 different phyla of bacteria distributed in marine, freshwater, and other ecosystems.
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Affiliation(s)
- Huachao Xi
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqun Nie
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fang Gao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Hu Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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Parra-Sánchez Á, Antequera-Zambrano L, Martínez-Navarrete G, Zorrilla-Muñoz V, Paz JL, Alvarado YJ, González-Paz L, Fernández E. Comparative Analysis of CRISPR-Cas Systems in Pseudomonas Genomes. Genes (Basel) 2023; 14:1337. [PMID: 37510242 PMCID: PMC10379622 DOI: 10.3390/genes14071337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Pseudomonas is a bacterial genus with some saprophytic species from land and others associated with opportunistic infections in humans and animals. Factors such as pathogenicity or metabolic aspects have been related to CRISPR-Cas, and in silico studies into it have focused more on the clinical and non-environmental setting. This work aimed to perform an in silico analysis of the CRISPR-Cas systems present in Pseudomonas genomes. It analyzed 275 complete genomic sequences of Pseudomonas taken from the NCBI database. CRISPR loci were obtained from CRISPRdb. The genes associated with CRISPR (cas) and CAS proteins, and the origin and diversity of spacer sequences, were identified and compared by BLAST. The presence of self-targeting sequences, PAMs, and the conservation of DRs were visualized using WebLogo 3.6. The CRISPR-like RNA secondary structure prediction was analyzed using RNAFold and MFold. CRISPR structures were identified in 19.6% of Pseudomonas species. In all, 113 typical CRISPR arrays with 18 putative cas were found, as were 2050 spacers, of which 52% showed homology to bacteriophages, 26% to chromosomes, and 22% to plasmids. No potential self-targeting was detected within the CRISPR array. All the found DRs can form thermodynamically stable secondary RNA structures. The comparison of the CRISPR/Cas system can help understand the environmental adaptability of each evolutionary lineage of clinically and environmentally relevant species, providing data support for bacterial typing, traceability, analysis, and exploration of unconventional CRISPR.
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Affiliation(s)
- Ángel Parra-Sánchez
- Genetics and Molecular Biology Laboratory, Biology Department, Faculty of Sciences, University of Zulia, Maracaibo 4001, Venezuela
- Neuroprosthesis and Visual Rehabilitation Laboratory, Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
| | - Laura Antequera-Zambrano
- Genetics and Molecular Biology Laboratory, Biology Department, Faculty of Sciences, University of Zulia, Maracaibo 4001, Venezuela
| | - Gema Martínez-Navarrete
- Neuroprosthesis and Visual Rehabilitation Laboratory, Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
| | - Vanessa Zorrilla-Muñoz
- Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
- University Institute on Gender Studies, University Carlos III of Madrid, Getafe, 28903 Madrid, Spain
| | - José Luis Paz
- Academic Department of Inorganic Chemistry, Faculty of Chemistry and Chemical Engineering, National University of San Marcos, Lima 15081, Peru
| | - Ysaias J Alvarado
- Laboratory of Theoretical and Experimental Biophysical Chemistry (LQBTE), Center for Molecular Biomedicine (CBM), Venezuelan Institute for Scientific Research (IVIC), Maracaibo 4001, Venezuela
| | - Lenin González-Paz
- Genetics and Molecular Biology Laboratory, Biology Department, Faculty of Sciences, University of Zulia, Maracaibo 4001, Venezuela
- Laboratory of Biocomputing (LB), Center for Molecular Biomedicine (CBM), Venezuelan Institute for Scientific Research (IVIC), Maracaibo 4001, Venezuela
| | - Eduardo Fernández
- Neuroprosthesis and Visual Rehabilitation Laboratory, Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain
- Biomedical Research Network Center (CIBER-BBN), 28029 Madrid, Spain
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Salwan R, Sharma V. Genomics of Prokaryotic Extremophiles to Unfold the Mystery of Survival in Extreme Environments. Microbiol Res 2022; 264:127156. [DOI: 10.1016/j.micres.2022.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
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Monteiro MR, Marshall AJ, Hawes I, Lee CK, McDonald IR, Cary SC. Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert. Front Microbiol 2022; 12:783767. [PMID: 35173689 PMCID: PMC8841834 DOI: 10.3389/fmicb.2021.783767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/15/2021] [Indexed: 11/15/2022] Open
Abstract
The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.
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Affiliation(s)
- Maria R. Monteiro
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Alexis J. Marshall
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian Hawes
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian R. McDonald
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Stephen Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
- *Correspondence: Stephen Craig Cary,
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6
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Batista LL, Malta SM, Guerra Silva HC, Borges LDF, Rocha LO, da Silva JR, Rodrigues TS, Venturini G, Padilha K, da Costa Pereira A, Espindola FS, Ueira-Vieira C. Kefir metabolites in a fly model for Alzheimer's disease. Sci Rep 2021; 11:11262. [PMID: 34045626 PMCID: PMC8160324 DOI: 10.1038/s41598-021-90749-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
Alzheimer's Disease (AD) is the most common cause of dementia among elderly individuals worldwide, leading to a strong motor-cognitive decline and consequent emotional distress and codependence. It is traditionally characterized by amyloidogenic pathway formation of senile plaques, and recent studies indicate that dysbiosis is also an important factor in AD's pathology. To overcome dysbiosis, probiotics-as kefir-have shown to be a great therapeutic alternative for Alzheimer's disease. In this present work, we explored kefir as a probiotic and a metabolite source as a modulator of microbiome and amyloidogenic pathway, using a Drosophila melanogaster model for AD (AD-like flies). Kefir microbiota composition was determined through 16S rRNA sequencing, and the metabolome of each fraction (hexane, dichloromethane, ethyl acetate, and n-butanol) was investigated. After treatment, flies had their survival, climbing ability, and vacuolar lesions accessed. Kefir and fraction treated flies improved their climbing ability survival rate and neurodegeneration index. In conclusion, we show that kefir in natura, as well as its fractions may be promising therapeutic source against AD, modulating amyloidogenic related pathways.
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Affiliation(s)
| | - Serena Mares Malta
- Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | | | | | - Lays Oliveira Rocha
- Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | | | | | | | - Kallyandra Padilha
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo, SP, Brazil
| | | | | | - Carlos Ueira-Vieira
- Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, Brazil.
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Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica. Microorganisms 2020; 8:microorganisms8030404. [PMID: 32183078 PMCID: PMC7143839 DOI: 10.3390/microorganisms8030404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 01/07/2023] Open
Abstract
Polar ecosystems are generally limited in nitrogen (N) nutrients, and the patchy availability of N is partly determined by biological pathways, such as nitrification, which are carried out by distinctive prokaryotic functional groups. The activity and diversity of microorganisms are generally strongly influenced by environmental conditions. However, we know little of the attributes that control the distribution and activity of specific microbial functional groups, such as nitrifiers, in extreme cold environments and how they may respond to change. To ascertain relationships between soil geochemistry and the ecology of nitrifying microbial communities, we carried out a laboratory-based manipulative experiment to test the selective effect of key geochemical variables on the activity and abundance of ammonia-oxidizing communities in soils from the McMurdo Dry Valleys of Antarctica. We hypothesized that nitrifying communities, adapted to different environmental conditions within the Dry Valleys, will have distinct responses when submitted to similar geochemical disturbances. In order to test this hypothesis, soils from two geographically distant and geochemically divergent locations, Miers and Beacon Valleys, were incubated over 2 months under increased conductivity, ammonia concentration, copper concentration, and organic matter content. Amplicon sequencing of the 16S rRNA gene and transcripts allowed comparison of the response of ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) to each treatment over time. This approach was combined with measurements of 15NH4+ oxidation rates using 15N isotopic additions. Our results showed a higher potential for nitrification in Miers Valley, where environmental conditions are milder relative to Beacon Valley. AOA exhibited better adaptability to geochemical changes compared to AOB, particularly to the increase in copper and conductivity. AOA were also the only nitrifying group found in Beacon Valley soils. This laboratorial manipulative experiment provided new knowledge on how nitrifying groups respond to changes on key geochemical variables of Antarctic desert soils, and we believe these results offer new insights on the dynamics of N cycling in these ecosystems.
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Contador CA, Veas-Castillo L, Tapia E, Antipán M, Miranda N, Ruiz-Tagle B, García-Araya J, Andrews BA, Marin M, Dorador C, Asenjo JA. Atacama Database: a platform of the microbiome of the Atacama Desert. Antonie van Leeuwenhoek 2019; 113:185-195. [PMID: 31535335 DOI: 10.1007/s10482-019-01328-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/07/2019] [Indexed: 11/30/2022]
Abstract
The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.
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Affiliation(s)
- Carolina A Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile.
| | - Luis Veas-Castillo
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Emilio Tapia
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Marcela Antipán
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Noemi Miranda
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Benjamín Ruiz-Tagle
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Jonathan García-Araya
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Mauricio Marin
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
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10
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Karlik E, Ari S, Gozukirmizi N. LncRNAs: genetic and epigenetic effects in plants. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1581085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Elif Karlik
- Department of Biotechnology Institute of Graduate Studies in Science and Engineering, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
| | - Sule Ari
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
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11
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Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, Chen IMA, Kyrpides NC, Reddy TBK. Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res 2019; 47:D649-D659. [PMID: 30357420 PMCID: PMC6323969 DOI: 10.1093/nar/gky977] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022] Open
Abstract
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project. Currently GOLD hosts information on 33 415 Studies, 49 826 Biosamples, 313 324 Organisms, 215 881 Sequencing Projects and 174 454 Analysis Projects with a total of 541 metadata fields, of which 80 are based on controlled vocabulary (CV) terms. GOLD provides a user-friendly web interface to browse sequencing projects and launch advanced search tools across four classification levels. Users submit metadata on a wide range of Sequencing and Analysis Projects in GOLD before depositing sequence data to the Integrated Microbial Genomes (IMG) system for analysis. GOLD conforms with and supports the rules set by the Genomic Standards Consortium (GSC) Minimum Information standards. The current version of GOLD (v.7) has seen the number of projects and associated metadata increase exponentially over the years. This paper provides an update on the current status of GOLD and highlights the new features added over the last two years.
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Affiliation(s)
- Supratim Mukherjee
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Dimitri Stamatis
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jon Bertsch
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Galina Ovchinnikova
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Hema Y Katta
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alejandro Mojica
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - I-Min A Chen
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nikos C Kyrpides
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - TBK Reddy
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
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12
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Palani B. Quantification of Histidine-Rich Protein 3 of Plasmodium falciparum. Monoclon Antib Immunodiagn Immunother 2018; 37:87-90. [PMID: 29634395 DOI: 10.1089/mab.2017.0068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Malaria is a life-threatening infectious disease and continues to be a major public health crisis in many parts of the tropical world. Plasmodium falciparum is responsible for the majority of mortality and morbidity associated with malaria. During the intraerythrocytic cycle, P. falciparum releases three proteins with high histidine content as follows: histidine-rich protein 1 (HRP1), histidine-rich protein 2 (HRP2), and histidine-rich protein 3 (HRP3). Currently, most of the diagnostic tests of P. falciparum infection target HRP2, and a number of monoclonal antibodies (mAbs) against HRP2 have been developed for use in HRP2 detection and quantification. When parasites have HRP2 deletions, the detection of HRP3 could augment the sensitivity of the detection system. The combination of both HRP2 and HRP3 mAbs in the detection system will enhance the test sensitivity. In the HRP quantitative enzyme-linked immunosorbent assay (ELISA), both HRP2 and HRP3 contribute to the result, but the relative contribution of HRP2 and HRP3 was unable to investigate, because of the nonavailability of HRP3 specific antibody ELISA. Hence an ELISA test system based on HRP3 is also essential for detection and quantification. There is not much documented in the literature on HRP3 antigen and HRP3 specific mAbs and polyclonal antibodies (pAbs). In the present study, recombinant HRP3 was expressed in Escherichia coli and purified with Ni-NTA agarose column. The purified rHRP3 was used for the generation and characterization of monoclonal and pAbs. The purification of monoclonal and pAbs was done using a mixed-mode chromatography sorbent, phenylpropylamine HyperCel™. With the purified antibodies, a sandwich ELISA was developed. The sandwich ELISA method was explored to detect and quantify HRP3 of P. falciparum in the spent medium. The generated mAbs could be potentially used for the detection and quantification of P. falciparum HRP3.
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Affiliation(s)
- Balraj Palani
- Department of Zoology, Government Thirumagal Mills College , Gudiyattam, India
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Cai M, Ng SK, Lim CK, Lu H, Jia Y, Lee PKH. Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification. Front Microbiol 2018. [PMID: 29535685 PMCID: PMC5835065 DOI: 10.3389/fmicb.2018.00280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nitrification plays a crucial role in global nitrogen cycling and treatment processes. However, the relationships between the nitrifier guilds of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) are still poorly understood, especially in freshwater habitats. This study examined the physiological interactions between the AOB and NOB present in a freshwater aquarium biofilter by culturing them, either together or separately, in a synthetic medium. Metagenomic and 16S rRNA gene sequencing revealed the presence and the draft genomes of Nitrosomonas-like AOB as well as Nitrobacter-like NOB in the cultures, including the first draft genome of Nitrobacter vulgaris. The nitrifiers exhibited different growth rates with different ammonium (NH4+) or nitrite concentrations (50-1,500 μM) and the growth rates were elevated under a high bicarbonate (HCO3-) concentration. The half-saturation constant (Ks for NH4+), the maximum growth rate (μmax), and the lag duration indicated a strong dependence on the synergistic relationships between the two guilds. Overall, the ecophysiological and metagenomic results in this study provided insights into the phylogeny of the key nitrifying players in a freshwater biofilter and showed that interactions between the two nitrifying guilds in a microbial community enhanced nitrification.
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Affiliation(s)
- Mingwei Cai
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Siu-Kin Ng
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Yangyang Jia
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
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14
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Aylward J, Steenkamp ET, Dreyer LL, Roets F, Wingfield BD, Wingfield MJ. A plant pathology perspective of fungal genome sequencing. IMA Fungus 2017; 8:1-15. [PMID: 28824836 PMCID: PMC5493528 DOI: 10.5598/imafungus.2017.08.01.01] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/19/2017] [Indexed: 10/26/2022] Open
Abstract
The majority of plant pathogens are fungi and many of these adversely affect food security. This mini-review aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.
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Affiliation(s)
- Janneke Aylward
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0002, South Africa
| | - Léanne L. Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | | | - Michael J. Wingfield
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0002, South Africa
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15
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Vieira LM, Grativol C, Thiebaut F, Carvalho TG, Hardoim PR, Hemerly A, Lifschitz S, Ferreira PCG, Walter MEMT. PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants. Noncoding RNA 2017; 3:ncrna3010011. [PMID: 29657283 PMCID: PMC5831995 DOI: 10.3390/ncrna3010011] [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: 12/29/2016] [Revised: 02/19/2017] [Accepted: 02/24/2017] [Indexed: 12/17/2022] Open
Abstract
Non-coding RNAs (ncRNAs) constitute an important set of transcripts produced in the cells of organisms. Among them, there is a large amount of a particular class of long ncRNAs that are difficult to predict, the so-called long intergenic ncRNAs (lincRNAs), which might play essential roles in gene regulation and other cellular processes. Despite the importance of these lincRNAs, there is still a lack of biological knowledge and, currently, the few computational methods considered are so specific that they cannot be successfully applied to other species different from those that they have been originally designed to. Prediction of lncRNAs have been performed with machine learning techniques. Particularly, for lincRNA prediction, supervised learning methods have been explored in recent literature. As far as we know, there are no methods nor workflows specially designed to predict lincRNAs in plants. In this context, this work proposes a workflow to predict lincRNAs on plants, considering a workflow that includes known bioinformatics tools together with machine learning techniques, here a support vector machine (SVM). We discuss two case studies that allowed to identify novel lincRNAs, in sugarcane (Saccharum spp.) and in maize (Zea mays). From the results, we also could identify differentially-expressed lincRNAs in sugarcane and maize plants submitted to pathogenic and beneficial microorganisms.
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Affiliation(s)
- Lucas Maciel Vieira
- Departamento de Ciência da Computação, Universidade de Brasília, Brasília-DF 70910-900, Brasil.
| | - Clicia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes-RJ 28013-602, Brazil.
| | - Flavia Thiebaut
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ 21941-901, Brazil.
| | - Thais G Carvalho
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ 21941-901, Brazil.
| | - Pablo R Hardoim
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ 21941-901, Brazil.
| | - Adriana Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ 21941-901, Brazil.
| | - Sergio Lifschitz
- Departamento de Informática, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro-RJ 22451-900, Brazil.
| | - Paulo Cavalcanti Gomes Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro-RJ 21941-901, Brazil.
| | - Maria Emilia M T Walter
- Departamento de Ciência da Computação, Universidade de Brasília, Brasília-DF 70910-900, Brasil.
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16
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Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Verezemska O, Isbandi M, Thomas AD, Ali R, Sharma K, Kyrpides NC, Reddy TBK. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. Nucleic Acids Res 2017; 45:D446-D456. [PMID: 27794040 PMCID: PMC5210664 DOI: 10.1093/nar/gkw992] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/11/2016] [Accepted: 10/19/2016] [Indexed: 01/28/2023] Open
Abstract
The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. This paper describes the data updates and additional features added during the last two years.
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Affiliation(s)
- Supratim Mukherjee
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Dimitri Stamatis
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Jon Bertsch
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Galina Ovchinnikova
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Olena Verezemska
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Michelle Isbandi
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Alex D Thomas
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Rida Ali
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Kaushal Sharma
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
| | - Nikos C Kyrpides
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - T B K Reddy
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, 94598 CA, USA
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17
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Angly FE, Pantos O, Morgan TC, Rich V, Tonin H, Bourne DG, Mercurio P, Negri AP, Tyson GW. Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon. PeerJ 2016; 4:e1758. [PMID: 26989611 PMCID: PMC4793316 DOI: 10.7717/peerj.1758] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 02/13/2016] [Indexed: 11/25/2022] Open
Abstract
Diuron is a herbicide commonly used in agricultural areas where excess application causes it to leach into rivers, reach sensitive marine environments like the Great Barrier Reef (GBR) lagoon and pose risks to marine life. To investigate the impact of diuron on whole prokaryotic communities that underpin the marine food web and are integral to coral reef health, GBR lagoon water was incubated with diuron at environmentally-relevant concentration (8 µg/L), and sequenced at specific time points over the following year. 16S rRNA gene amplicon profiling revealed no significant short- or long-term effect of diuron on microbiome structure. The relative abundance of prokaryotic phototrophs was not significantly altered by diuron, which suggests that they were largely tolerant at this concentration. Assembly of a metagenome derived from waters sampled at a similar location in the GBR lagoon did not reveal the presence of mutations in the cyanobacterial photosystem that could explain diuron tolerance. However, resident phages displayed several variants of this gene and could potentially play a role in tolerance acquisition. Slow biodegradation of diuron was reported in the incubation flasks, but no correlation with the relative abundance of heterotrophs was evident. Analysis of metagenomic reads supports the hypothesis that previously uncharacterized hydrolases carried by low-abundance species may mediate herbicide degradation in the GBR lagoon. Overall, this study offers evidence that pelagic phototrophs of the GBR lagoon may be more tolerant of diuron than other tropical organisms, and that heterotrophs in the microbial seed bank may have the potential to degrade diuron and alleviate local anthropogenic stresses to inshore GBR ecosystems.
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Affiliation(s)
- Florent E. Angly
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Olga Pantos
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
- Global Change Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Thomas C. Morgan
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Virginia Rich
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States of America
- Microbiology Department, The Ohio State University, Columbus, OH, United States of America
| | - Hemerson Tonin
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - David G. Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Philip Mercurio
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- National Research Centre for Environmental Toxicology, The University of Queensland, Coopers Plains, Queensland, Australia
| | - Andrew P. Negri
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
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18
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Angly FE, Heath C, Morgan TC, Tonin H, Rich V, Schaffelke B, Bourne DG, Tyson GW. Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ 2016; 4:e1511. [PMID: 26839738 PMCID: PMC4734448 DOI: 10.7717/peerj.1511] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/25/2015] [Indexed: 12/15/2022] Open
Abstract
The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.
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Affiliation(s)
- Florent E Angly
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
| | - Candice Heath
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
| | - Thomas C Morgan
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
| | - Hemerson Tonin
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | - Virginia Rich
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States of America; Microbiology Department, Ohio State University, Columbus, OH, United States of America
| | - Britta Schaffelke
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | - David G Bourne
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, University of Queensland , St Lucia, Queensland , Australia
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19
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Pert PL, Ens EJ, Locke J, Clarke PA, Packer JM, Turpin G. An online spatial database of Australian Indigenous Biocultural Knowledge for contemporary natural and cultural resource management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 534:110-121. [PMID: 25682266 DOI: 10.1016/j.scitotenv.2015.01.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/07/2015] [Accepted: 01/22/2015] [Indexed: 06/04/2023]
Abstract
With growing international calls for the enhanced involvement of Indigenous peoples and their biocultural knowledge in managing conservation and the sustainable use of physical environment, it is timely to review the available literature and develop cross-cultural approaches to the management of biocultural resources. Online spatial databases are becoming common tools for educating land managers about Indigenous Biocultural Knowledge (IBK), specifically to raise a broad awareness of issues, identify knowledge gaps and opportunities, and to promote collaboration. Here we describe a novel approach to the application of internet and spatial analysis tools that provide an overview of publically available documented Australian IBK (AIBK) and outline the processes used to develop the online resource. By funding an AIBK working group, the Australian Centre for Ecological Analysis and Synthesis (ACEAS) provided a unique opportunity to bring together cross-cultural, cross-disciplinary and trans-organizational contributors who developed these resources. Without such an intentionally collaborative process, this unique tool would not have been developed. The tool developed through this process is derived from a spatial and temporal literature review, case studies and a compilation of methods, as well as other relevant AIBK papers. The online resource illustrates the depth and breadth of documented IBK and identifies opportunities for further work, partnerships and investment for the benefit of not only Indigenous Australians, but all Australians. The database currently includes links to over 1500 publically available IBK documents, of which 568 are geo-referenced and were mapped. It is anticipated that as awareness of the online resource grows, more documents will be provided through the website to build the database. It is envisaged that this will become a well-used tool, integral to future natural and cultural resource management and maintenance.
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Affiliation(s)
- Petina L Pert
- CSIRO Land and Water Flagship, Cairns, Qld 4870, Australia; Division of Tropical Environments and Societies, Centre for Tropical Environmental Sustainability Science, James Cook University - Cairns Campus, Smithfield, Qld 4878, Australia.
| | - Emilie J Ens
- Department of Environment and Geography, Macquarie University, NSW 2109, Australia
| | - John Locke
- Biocultural Consulting Pty Ltd, Maroochydore, Qld 4000, Australia
| | - Philip A Clarke
- School of Environment, Griffith University, Nathan, Qld 4111, Australia
| | - Joanne M Packer
- National Institute of Complementary Medicine, University of Western Sydney, NSW 2751, Australia
| | - Gerry Turpin
- Tropical Indigenous Ethnobotany Centre, Cairns, Qld 4970, Australia; Department of Science, Information Technology, Innovation, and the Arts, Cairns, Qld 4870, Australia
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20
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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21
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Kang K, Dzakah EE, Li W, Xie M, Luo X, Liu H. Novel monoclonal antibodies against Plasmodium falciparum histidine-rich protein 2: development and application in rapid diagnostic tests of malaria in hyperendemic regions of China and Myanmar. BMC Microbiol 2015; 15:98. [PMID: 25962879 PMCID: PMC4427986 DOI: 10.1186/s12866-015-0429-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria presents a considerable threat to public health. Histidine-rich protein 2 (HRP 2) is the major protein released into human blood upon infection by Plasmodium falciparum. In this study, we aimed to evaluate the immunogenicity of HRP 2 exon II and the efficacy of novel monoclonal antibodies (mAbs) against HRP 2 for Point-of-Care Test (POCT). METHODS The recombinant protein was expressed in soluble form in E. coli and used to immunize mice for mAb production. Two IgG1 mAbs (1A5 and 1C10) with high affinity, specificity and sensitivity for both native and recombinant HRP 2 were selected after fusion of mouse spleen with myeloma cells. The affinity constant of 1A5 and 1C10 were 7.15 and 4.91 × 10-7 L/mol, respectively. Subsequently, an immunochromatograhic assay was used for screening of clinical samples in endemic regions of China and Myanmar. RESULTS The immunochromatographic test retrospectively showed an overall sensitivity of 99.07%, and specificity of 100%. Sensitivity at parasite densities < 200, 200-2000, and > 2000 parasites/μL was 87.5, 98.7, and 100%, respectively. CONCLUSIONS These results suggest that HRP 2 exon II contains immunogenic sites similar to those of the native antigen and can be used for the development of mAbs suitable for malaria diagnosis in endemic communities.
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Affiliation(s)
- Keren Kang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China. .,National Engineering Laboratory of Point-of-Care Tests, Guangzhou Wondfo Biotech Co. Ltd, Guangzhou, 510663, China.
| | - Emmanuel E Dzakah
- National Engineering Laboratory of Point-of-Care Tests, Guangzhou Wondfo Biotech Co. Ltd, Guangzhou, 510663, China. .,Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana.
| | - Wenmei Li
- National Engineering Laboratory of Point-of-Care Tests, Guangzhou Wondfo Biotech Co. Ltd, Guangzhou, 510663, China.
| | - Mingquan Xie
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China.
| | - Xiaochun Luo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China.
| | - Hui Liu
- Yunnan Provincial Center for Parasitic Diseases Control and Prevention (NIPD), Yunnan, 650000, China.
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22
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Bowman JS, Deming JW. Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis. BMC Genomics 2014; 15:1120. [PMID: 25515036 PMCID: PMC4320567 DOI: 10.1186/1471-2164-15-1120] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/11/2014] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Psychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. In this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. To identify possible mechanisms of low temperature optimization we compared putative alkane hydroxylases from these psychrophiles with homologues from nineteen taxonomically related mesophilic strains. RESULTS Seven of the analyzed psychrophile genomes contained a total of 27 candidate alkane hydroxylase genes, only two of which are currently annotated as alkane hydroxylase. These candidates were mostly related to the AlkB and cytochrome p450 alkane hydroxylases, but several homologues of the LadA and AlmA enzymes, significant for their ability to degrade long-chain alkanes, were also detected. These putative alkane hydroxylases showed significant differences in primary structure from their mesophile homologues, with preferences for specific amino acids and increased flexibility on loops, bends, and α-helices. CONCLUSION A focused analysis on psychrophile genomes led to discovery of numerous candidate alkane hydroxylase genes not currently annotated as alkane hydroxylase. Gene products show signs of optimization to low temperature, including regions of increased flexibility and amino acid preferences typical of psychrophilic proteins. These findings are consistent with observations of microbial degradation of crude oil in cold environments and identify proteins that can be targeted in rate studies and in the design of molecular tools for low temperature bioremediation.
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Affiliation(s)
- Jeff S Bowman
- />School of Oceanography and Astrobiology Program, University of Washington, Box 357940, Seattle, WA 98105-7940 USA
- />Blue Marble Space Institute of Science, Seattle, USA
| | - Jody W Deming
- />Blue Marble Space Institute of Science, Seattle, USA
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23
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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Reddy TBK, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res 2014; 43:D1099-106. [PMID: 25348402 DOI: 10.1093/nar/gku950] [Citation(s) in RCA: 259] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19,200 studies, 56,000 Biosamples, 56,000 sequencing projects and 39,400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.
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Affiliation(s)
- T B K Reddy
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alex D Thomas
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Dimitri Stamatis
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jon Bertsch
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Michelle Isbandi
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jakob Jansson
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jyothi Mallajosyula
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Ioanna Pagani
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Elizabeth A Lobos
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nikos C Kyrpides
- Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 2014; 12:3516-59. [PMID: 24918453 PMCID: PMC4071589 DOI: 10.3390/md12063516] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.
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Relative amino acid composition signatures of organisms and environments. PLoS One 2013; 8:e77319. [PMID: 24204807 PMCID: PMC3808408 DOI: 10.1371/journal.pone.0077319] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/09/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment. METHODOLOGIES/PRINCIPAL FINDINGS To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny. CONCLUSIONS Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.
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Sousa FL, Shavit-Grievink L, Allen JF, Martin WF. Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis. Genome Biol Evol 2013; 5:200-16. [PMID: 23258841 PMCID: PMC3595025 DOI: 10.1093/gbe/evs127] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
An open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (RC) types, Type I reaction center (RCI) and Type II reaction center (RCII). The two main competing theories in the foreground of current thinking on this issue are that either 1) RCI and RCII are related via lineage divergence among anoxygenic photosynthetic bacteria and became merged in cyanobacteria via an event of large-scale lateral gene transfer (also called "fusion" theories) or 2) the two RC types are related via gene duplication in an ancestral, anoxygenic but protocyanobacterial phototroph that possessed both RC types before making the transition to using water as an electron donor. To distinguish between these possibilities, we studied the evolution of the core (bacterio)chlorophyll biosynthetic pathway from protoporphyrin IX (Proto IX) up to (bacterio)chlorophyllide a. The results show no dichotomy of chlorophyll biosynthesis genes into RCI- and RCII-specific chlorophyll biosynthetic clades, thereby excluding models of fusion at the origin of cyanobacteria and supporting the selective-loss hypothesis. By considering the cofactor demands of the pathway and the source genes from which several steps in chlorophyll biosynthesis are derived, we infer that the cell that first synthesized chlorophyll was a cobalamin-dependent, heme-synthesizing, diazotrophic anaerobe.
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Affiliation(s)
- Filipa L Sousa
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany.
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ExtremeDB: a unified web repository of extremophilic archaea and bacteria. PLoS One 2013; 8:e63083. [PMID: 23696792 PMCID: PMC3656046 DOI: 10.1371/journal.pone.0063083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 04/01/2013] [Indexed: 11/19/2022] Open
Abstract
Extremophiles are the microorganisms which can survive under extreme conditions of temperature, pressure, pH, salinity etc. They have gained much attention for their potential role in biotechnological and industrial applications. The large amount of experimental data in the literature is so diverse, that it becomes difficult and time consuming for the researcher to implement it in various areas of research. Therefore, a systematic arrangement of data and redirection in a similar fashion through web interface can assist researchers in analyzing the data as per their requirement. ExtremeDB is a freely available web based relational database which integrates general characteristics, genome-proteome information, industrial applications and recent scientific investigations of the seven major groups of 865 extremophillic microorganisms. The search options are user friendly and analyses tools such as Compare and Extreme BLAST have been incorporated for comparative analysis of two or more extremophiles and determining the sequence similarity of a given protein/nucleotide in relation to other extremophiles respectively. The effort put forth herein in the form of database, would open up new avenues on the potential utility of extremophiles in applied research. ExtremeDB is freely accessible via http://extrem.igib.res.in.
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Bianco AM, Marcuzzi A, Zanin V, Girardelli M, Vuch J, Crovella S. Database tools in genetic diseases research. Genomics 2013; 101:75-85. [DOI: 10.1016/j.ygeno.2012.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 10/26/2012] [Accepted: 11/01/2012] [Indexed: 01/22/2023]
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Pandey A, Kumar A, Purohit R. Sequencing Closterium moniliferum: Future prospects in nuclear waste disposal. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2013. [DOI: 10.1016/j.ejmhg.2012.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Small oversights that led to the Great Plague of Marseille (1720-1723): lessons from the past. INFECTION GENETICS AND EVOLUTION 2012; 14:169-85. [PMID: 23246639 DOI: 10.1016/j.meegid.2012.11.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 11/20/2012] [Indexed: 01/14/2023]
Abstract
In recent decades, the issue of emerging and re-emerging infectious diseases has become an increasingly important area of concern in public health. Today, like centuries ago, infectious diseases confront us with the fear of death and have heavily influenced social behaviors and policy decisions at local, national and international levels. Remarkably, an infectious disease such as plague, which is disseminated from one country to another mainly by commercial transportation, remains today, as it was in the distant past, a threat for human societies. Throughout history, plague outbreaks prevailed on numerous occasions in Mediterranean harbors, including Marseille in the south of France. A few months ago, the municipal authorities of the city of Marseille, announced the archaeological discovery of the last remnants of a "lazaretto" or "lazaret" (http://20.minutes.fr, March 3th, 2012), a place equipped with an infirmary and destined to isolate ship passengers quarantined for health reasons. More recently, on September 16th, 2012, the anchor of the ship "Grand Saint Antoine" responsible for bringing the plague to Marseille in 1720, was recovered and it will be restored before being presented to the public in 2013 (http://www.libemarseille.fr/henry/2012/09/lancre-du-bateau-qui-amena-la-grande-peste-%C3%A0-marseille.html). In the light of these recent archaeological discoveries, it is quite instructive to revisit the sequence of events and decisions that led to the outbreak of the Great Plague of Marseille between 1720 and 1723. It comes to the evidence that although the threat was known and health surveillance existed with quite effective preventive measures such as quarantine, the accumulation of small negligence led to one of the worst epidemics in the city (about 30% of casualties among the inhabitants). This is an excellent model to illustrate the issues we are facing with emerging and re-emerging infectious diseases today and to define how to improve biosurveillance and response tomorrow. Importantly, the risk of plague dissemination by transport trade is negligible between developed countries, however, this risk still persists in developing countries. In addition, the emergence of antibiotic resistant strains of Yersinia pestis, the infectious agent of plague, is raising serious concerns for public health.
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Teeling H, Glöckner FO. Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. Brief Bioinform 2012; 13:728-42. [PMID: 22966151 PMCID: PMC3504927 DOI: 10.1093/bib/bbs039] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/09/2012] [Indexed: 12/21/2022] Open
Abstract
Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space. Recently, a new type of holistic ecosystem study has emerged that seeks to combine metagenomics with biodiversity, meta-expression and contextual data. Such 'ecosystems biology' approaches bear the potential to not only advance our understanding of environmental microbes to a new level but also impose challenges due to increasing data complexities, in particular with respect to bioinformatic post-processing. This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and bioinformaticians alike.
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Dini-Andreote F, Andreote FD, Araújo WL, Trevors JT, van Elsas JD. Bacterial genomes: habitat specificity and uncharted organisms. MICROBIAL ECOLOGY 2012; 64:1-7. [PMID: 22395783 PMCID: PMC3375415 DOI: 10.1007/s00248-012-0017-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 01/25/2012] [Indexed: 05/06/2023]
Abstract
The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.
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Affiliation(s)
- Francisco Dini-Andreote
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, Brazil
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Fernando Dini Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Jack T. Trevors
- School of Environmental Sciences, University of Guelph, Guelph, ON Canada N1G 2W1
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Kim WC, Lee KH, Shin KS, You RN, Lee YK, Cho K, Cho DH. REMiner-II: a tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query. Genomics 2012; 100:131-40. [PMID: 22750555 DOI: 10.1016/j.ygeno.2012.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 06/04/2012] [Accepted: 06/12/2012] [Indexed: 01/17/2023]
Abstract
Genes occupy ~3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study, REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes.
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Affiliation(s)
- Woo-Chan Kim
- Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Abstract
With plague being not only a subject of interest for historians, but still a disease of public health concern in several countries, mainly in Africa, there were hopes that analyses of the Yersinia pestis genomes would put an end to this deadly epidemic pathogen. Genomics revealed that Y. pestis isolates evolved from Yersinia pseudotuberculosis in Central Asia some millennia ago, after the acquisition of two Y. pestis-specific plasmids balanced genomic reduction parallel with the expansion of insertion sequences, illustrating the modern concept that, except for the acquisition of plasmid-borne toxin-encoding genes, the increased virulence of Y. pestis resulted from gene loss rather than gene acquisition. The telluric persistence of Y. pestis reminds us of this close relationship, and matters in terms of plague epidemiology. Whereas biotype Orientalis isolates spread worldwide, the Antiqua and Medievalis isolates showed more limited expansion. In addition to animal ectoparasites, human ectoparasites such as the body louse may have participated in this expansion and in devastating historical epidemics. The recent analysis of a Black Death genome indicated that it was more closely related to the Orientalis branch than to the Medievalis branch. Modern Y. pestis isolates grossly exhibit the same gene content, but still undergo micro-evolution in geographically limited areas by differing in the genome architecture, owing to inversions near insertion sequences and the stabilization of the YpfPhi prophage in Orientalis biotype isolates. Genomics have provided several new molecular tools for the genotyping and phylogeographical tracing of isolates and description of plague foci. However, genomics and post-genomics approaches have not yet provided new tools for the prevention, diagnosis and management of plague patients and the plague epidemics still raging in some sub-Saharan countries.
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Affiliation(s)
- M Drancourt
- URMITE UMR CNRS 6236 IRD 98, IFR48, Méditerranée Infection, Aix-Marseille-Université, Marseille, France.
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Karpinets TV, Park BH, Uberbacher EC. Analyzing large biological datasets with association networks. Nucleic Acids Res 2012; 40:e131. [PMID: 22638576 PMCID: PMC3458522 DOI: 10.1093/nar/gks403] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Due to advances in high-throughput biotechnologies biological information is being collected in databases at an amazing rate, requiring novel computational approaches that process collected data into new knowledge in a timely manner. In this study, we propose a computational framework for discovering modular structure, relationships and regularities in complex data. The framework utilizes a semantic-preserving vocabulary to convert records of biological annotations of an object, such as an organism, gene, chemical or sequence, into networks (Anets) of the associated annotations. An association between a pair of annotations in an Anet is determined by the similarity of their co-occurrence pattern with all other annotations in the data. This feature captures associations between annotations that do not necessarily co-occur with each other and facilitates discovery of the most significant relationships in the collected data through clustering and visualization of the Anet. To demonstrate this approach, we applied the framework to the analysis of metadata from the Genomes OnLine Database and produced a biological map of sequenced prokaryotic organisms with three major clusters of metadata that represent pathogens, environmental isolates and plant symbionts.
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Affiliation(s)
- Tatiana V Karpinets
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Lee CC, Lo WC, Lai SM, Chen YPP, Tang CY, Lyu PC. Metabolic classification of microbial genomes using functional probes. BMC Genomics 2012; 13:157. [PMID: 22537274 PMCID: PMC3355368 DOI: 10.1186/1471-2164-13-157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 04/27/2012] [Indexed: 11/29/2022] Open
Abstract
Background Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable to perform thorough analyses of difficult-to-culture microorganisms due to limitations in sequencing technology. As modern techniques have dramatically increased sequencing rates and rapidly expanded the number of sequenced genomes, in addition to traditional taxonomic classifications which focus on the evolutionary relationships of organisms, classifications of the genomes based on alternative points of view may help advance our understanding of the delicate relationships of organisms. Results We have developed a proteome-based method for classifying microbial species. This classification method uses a set of probes comprising short, highly conserved amino acid sequences. For each genome, in silico translation is performed to obtained its proteome, based on which a probe-set frequency pattern is generated. Then, the probe-set frequency patterns are used to cluster the proteomes/genomes. Conclusions Features of the proposed method include a high running speed in challenge of a large number of genomes, and high applicability for classifying organisms with incomplete genome sequences. Moreover, the probe-set clustering method is sensitive to the metabolic phenotypic similarities/differences among species and is thus supposed potential for the classification or differentiation of closely-related organisms.
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Affiliation(s)
- Chi-Ching Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
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Unique profile of ordered arrangements of repetitive elements in the C57BL/6J mouse genome implicating their functional roles. PLoS One 2012; 7:e35156. [PMID: 22529984 PMCID: PMC3329453 DOI: 10.1371/journal.pone.0035156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 03/09/2012] [Indexed: 12/18/2022] Open
Abstract
The entirety of all protein coding sequences is reported to represent a small fraction (∼2%) of the mouse and human genomes; the vast majority of the rest of the genome is presumed to be repetitive elements (REs). In this study, the C57BL/6J mouse reference genome was subjected to an unbiased RE mining to establish a whole-genome profile of RE occurrence and arrangement. The C57BL/6J mouse genome was fragmented into an initial set of 5,321 units of 0.5 Mb, and surveyed for REs using unbiased self-alignment and dot-matrix protocols. The survey revealed that individual chromosomes had unique profiles of RE arrangement structures, named RE arrays. The RE populations in certain genomic regions were arranged into various forms of complexly organized structures using combinations of direct and/or inverse repeats. Some of these RE arrays spanned stretches of over 2 Mb, which may contribute to the structural configuration of the respective genomic regions. There were substantial differences in RE density among the 21 chromosomes, with chromosome Y being the most densely populated. In addition, the RE array population in the mouse chromosomes X and Y was substantially different from those of the reference human chromosomes. Conversion of the dot-matrix data pertaining to a tandem 13-repeat structure within the Ch7.032 genome unit into a line map of known REs revealed a repeat unit of ∼11.3 Kb as a mosaic of six different RE types. The data obtained from this study allowed for a comprehensive RE profiling, including the establishment of a library of RE arrays, of the reference mouse genome. Some of these RE arrays may participate in a spectrum of normal and disease biology that are specific for mice.
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Xie J, Wang M, Dai D, Zhang H, Zhang W. A network clustering algorithm for detection of protein families. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2012; 2012:6329-6332. [PMID: 23367376 DOI: 10.1109/embc.2012.6347441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Detection of protein families in large scale database is a difficult but important biological problem. Computational clustering methods can effectively address the problem. Although there exist many clustering algorithms, most of them are just based on the threshold. Their computational performances are affected by the weight distribution greatly, and they are only valid for some special networks. A new network clustering algorithm, Markov Finding and Clustering (MFC), is proposed to cluster the proteins into their functionally specific families accurately in this paper. The MFC algorithm makes an improvement in the random walk process and reduces the affection of the noise on the clustering result. It has a good performance on these networks which are not well addressed by existing algorithms sensitive to the noise. Finally, experiments on the protein sequence datasets demonstrate that the algorithm is effective in the detection of protein families and has a better performance than the current algorithms.
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Affiliation(s)
- Jiang Xie
- School of Computer Engineering and Science, Shanghai University, Shanghai 200072, China
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40
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Gorbacheva MA, Yarosh AG, Dorovatovskii PV, Rakitina TV, Boiko KM, Korzhenevskii DA, Lipkin AV, Popov VO, Shumilin IA. A novel approach to studying the structural and functional properties of proteins with unknown functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 38:99-105. [DOI: 10.1134/s1068162012010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pagani I, Liolios K, Jansson J, Chen IMA, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012; 40:D571-9. [PMID: 22135293 PMCID: PMC3245063 DOI: 10.1093/nar/gkr1100] [Citation(s) in RCA: 375] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/02/2011] [Accepted: 11/03/2011] [Indexed: 12/03/2022] Open
Abstract
The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11,472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond.
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Affiliation(s)
- Ioanna Pagani
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
| | - Konstantinos Liolios
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
| | - Jakob Jansson
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
| | - I-Min A. Chen
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
| | - Tatyana Smirnova
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
| | - Bahador Nosrat
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
| | - Victor M. Markowitz
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, 2800 Mitchell Drive, Walnut Creek, Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley and Department of Energy Joint Genome Institute, Genome Portals Group, 2800 Mitchell Drive, Walnut Creek, CA, USA
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Pini F, Galardini M, Bazzicalupo M, Mengoni A. Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria? Genes (Basel) 2011; 2:1017-32. [PMID: 24710303 PMCID: PMC3927591 DOI: 10.3390/genes2041017] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/01/2022] Open
Abstract
Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions.
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Affiliation(s)
- Francesco Pini
- Department of Evolutionary Biology, University of Florence, via Romana 17, 50125 Firenze, Italy.
| | - Marco Galardini
- Department of Evolutionary Biology, University of Florence, via Romana 17, 50125 Firenze, Italy.
| | - Marco Bazzicalupo
- Department of Evolutionary Biology, University of Florence, via Romana 17, 50125 Firenze, Italy.
| | - Alessio Mengoni
- Department of Evolutionary Biology, University of Florence, via Romana 17, 50125 Firenze, Italy.
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Chung BI, Lee KH, Shin KS, Kim WC, Kwon DN, You RN, Lee YK, Cho K, Cho DH. REMiner: a tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes. Genomics 2011; 98:381-9. [PMID: 21803149 DOI: 10.1016/j.ygeno.2011.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/21/2011] [Accepted: 07/15/2011] [Indexed: 11/18/2022]
Abstract
Repetitive elements (REs) constitute a substantial portion of the genomes of human and other species; however, the RE profiles (type, density, and arrangement) within the individual genomes have not been fully characterized. In this study, we developed an RE analysis tool, called REMiner, for a chromosome-wide investigation into the occurrence of individual REs and arrangement of clusters of REs, and REMiner's functional features were examined using the human chromosome Y. The algorithm implemented by REMiner focused on unbiased mining of REs in large chromosomes and data interface within a viewer. The data from the chromosome demonstrated that REMiner is an efficient tool in regard to its capacity for a large query size and the availability of a high-resolution viewer, featuring instant retrieval of alignment data and control of magnification and identity ratio. The chromosome-wide survey identified a diverse population of ordered RE arrangements, which may participate in the genome biology.
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Affiliation(s)
- Byung-Ik Chung
- Division of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Bradley BJ, Lawler RR. Linking genotypes, phenotypes, and fitness in wild primate populations. Evol Anthropol 2011; 20:104-19. [DOI: 10.1002/evan.20306] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Haft DH. Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. BMC Genomics 2011; 12:21. [PMID: 21223593 PMCID: PMC3023750 DOI: 10.1186/1471-2164-12-21] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 01/11/2011] [Indexed: 11/10/2022] Open
Abstract
Background Enzymes in the radical SAM (rSAM) domain family serve in a wide variety of biological processes, including RNA modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. Evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rSAM-containing system, shaping patterns in results obtained through various comparative genomics analyses. Results An uncharacterized gene cluster found in many Actinobacteria and sporadically in Firmicutes, Chloroflexi, Deltaproteobacteria, and one Archaeal plasmid contains a PqqE-like rSAM protein family that includes Rv0693 from Mycobacterium tuberculosis. Members occur clustered with a strikingly well-conserved small polypeptide we designate "mycofactocin," similar in size to bacteriocins and PqqA, precursor of pyrroloquinoline quinone (PQQ). Partial Phylogenetic Profiling (PPP) based on the distribution of these markers identifies the mycofactocin cluster, but also a second tier of high-scoring proteins. This tier, strikingly, is filled with up to thirty-one members per genome from three variant subfamilies that occur, one each, in three unrelated classes of nicotinoproteins. The pattern suggests these variant enzymes require not only NAD(P), but also the novel gene cluster. Further study was conducted using SIMBAL, a PPP-like tool, to search these nicotinoproteins for subsequences best correlated across multiple genomes to the presence of mycofactocin. For both the short chain dehydrogenase/reductase (SDR) and iron-containing dehydrogenase families, aligning SIMBAL's top-scoring sequences to homologous solved crystal structures shows signals centered over NAD(P)-binding sites rather than over substrate-binding or active site residues. Previous studies on some of these proteins have revealed a non-exchangeable NAD cofactor, such that enzymatic activity in vitro requires an artificial electron acceptor such as N,N-dimethyl-4-nitrosoaniline (NDMA) for the enzyme to cycle. Conclusions Taken together, these findings suggest that the mycofactocin precursor is modified by the Rv0693 family rSAM protein and other enzymes in its cluster. It becomes an electron carrier molecule that serves in vivo as NDMA and other artificial electron acceptors do in vitro. Subclasses from three different nicotinoprotein families show "only-if" relationships to mycofactocin because they require its presence. This framework suggests a segregated redox pool in which mycofactocin mediates communication among enzymes with non-exchangeable cofactors.
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Affiliation(s)
- Daniel H Haft
- J Craig Venter Institute, 9704 Rockville, MD 20850, USA.
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46
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Stark JL, Powers R. Application of NMR and molecular docking in structure-based drug discovery. Top Curr Chem (Cham) 2011; 326:1-34. [PMID: 21915777 DOI: 10.1007/128_2011_213] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drug discovery is a complex and costly endeavor, where few drugs that reach the clinical testing phase make it to market. High-throughput screening (HTS) is the primary method used by the pharmaceutical industry to identify initial lead compounds. Unfortunately, HTS has a high failure rate and is not particularly efficient at identifying viable drug leads. These shortcomings have encouraged the development of alternative methods to drive the drug discovery process. Specifically, nuclear magnetic resonance (NMR) spectroscopy and molecular docking are routinely being employed as important components of drug discovery research. Molecular docking provides an extremely rapid way to evaluate likely binders from a large chemical library with minimal cost. NMR ligand-affinity screens can directly detect a protein-ligand interaction, can measure a corresponding dissociation constant, and can reliably identify the ligand binding site and generate a co-structure. Furthermore, NMR ligand affinity screens and molecular docking are perfectly complementary techniques, where the combination of the two has the potential to improve the efficiency and success rate of drug discovery. This review will highlight the use of NMR ligand affinity screens and molecular docking in drug discovery and describe recent examples where the two techniques were combined to identify new and effective therapeutic drugs.
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Affiliation(s)
- Jaime L Stark
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA
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In silico subtractive genomics for target identification in human bacterial pathogens. Drug Dev Res 2010. [DOI: 10.1002/ddr.20413] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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de Souza GA, Arntzen MØ, Fortuin S, Schürch AC, Målen H, McEvoy CRE, van Soolingen D, Thiede B, Warren RM, Wiker HG. Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Mol Cell Proteomics 2010; 10:M110.002527. [PMID: 21030493 PMCID: PMC3013451 DOI: 10.1074/mcp.m110.002527] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Precise annotation of genes or open reading frames is still a difficult task that results in divergence even for data generated from the same genomic sequence. This has an impact in further proteomic studies, and also compromises the characterization of clinical isolates with many specific genetic variations that may not be represented in the selected database. We recently developed software called multistrain mass spectrometry prokaryotic database builder (MSMSpdbb) that can merge protein databases from several sources and be applied on any prokaryotic organism, in a proteomic-friendly approach. We generated a database for the Mycobacterium tuberculosis complex (using three strains of Mycobacterium bovis and five of M. tuberculosis), and analyzed data collected from two laboratory strains and two clinical isolates of M. tuberculosis. We identified 2561 proteins, of which 24 were present in M. tuberculosis H37Rv samples, but not annotated in the M. tuberculosis H37Rv genome. We were also able to identify 280 nonsynonymous single amino acid polymorphisms and confirm 367 translational start sites. As a proof of concept we applied the database to whole-genome DNA sequencing data of one of the clinical isolates, which allowed the validation of 116 predicted single amino acid polymorphisms and the annotation of 131 N-terminal start sites. Moreover we identified regions not present in the original M. tuberculosis H37Rv sequence, indicating strain divergence or errors in the reference sequence. In conclusion, we demonstrated the potential of using a merged database to better characterize laboratory or clinical bacterial strains.
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Affiliation(s)
- Gustavo A de Souza
- The Gade Institute, Section for Microbiology and Immunology, University of Bergen, N-5021 Bergen, Norway
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Deshayes C, Bach H, Euphrasie D, Attarian R, Coureuil M, Sougakoff W, Laval F, Av-Gay Y, Daffé M, Etienne G, Reyrat JM. MmpS4 promotes glycopeptidolipids biosynthesis and export in Mycobacterium smegmatis. Mol Microbiol 2010; 78:989-1003. [DOI: 10.1111/j.1365-2958.2010.07385.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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50
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Wynne C, Edwards NJ, Fenselau C. Phyloproteomic classification of unsequenced organisms by top-down identification of bacterial proteins using capLC-MS/MS on an Orbitrap. Proteomics 2010; 10:3631-43. [DOI: 10.1002/pmic.201000172] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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