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Chang YC, Hu Z, Rachlin J, Anton BP, Kasif S, Roberts RJ, Steffen M. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. Nucleic Acids Res 2015; 44:D330-5. [PMID: 26635392 PMCID: PMC4702925 DOI: 10.1093/nar/gkv1324] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/11/2015] [Indexed: 02/06/2023] Open
Abstract
The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue.
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Affiliation(s)
- Yi-Chien Chang
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Zhenjun Hu
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | | | | | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Martin Steffen
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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102
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Subramanian D, Natarajan J. Network analysis of S. aureus response to ramoplanin reveals modules for virulence factors and resistance mechanisms and characteristic novel genes. Gene 2015; 574:149-62. [DOI: 10.1016/j.gene.2015.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/30/2015] [Accepted: 08/03/2015] [Indexed: 12/27/2022]
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103
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Complete Genome Sequence of Coriobacteriaceae Strain 68-1-3, a Novel Mucus-Degrading Isolate from the Swine Intestinal Tract. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01143-15. [PMID: 26450725 PMCID: PMC4599084 DOI: 10.1128/genomea.01143-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A novel Coriobacteriaceae bacterium (strain 68-1-3) was isolated from the ileum of the swine intestinal tract using a selective mucus-based medium. Here we present the finished genome sequence for the swine commensal, totaling 1.97 Mb in size.
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104
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Wong DHJ, Beiko RG. Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. BMC Genomics 2015; 16:526. [PMID: 26173980 PMCID: PMC4502571 DOI: 10.1186/s12864-015-1752-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/06/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways. RESULTS The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture. CONCLUSIONS Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.
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Affiliation(s)
- Dennis H-J Wong
- Faculty of Graduate Studies, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
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105
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Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Give, Isolated from an Imported Chili Powder Product. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00726-15. [PMID: 26139723 PMCID: PMC4490851 DOI: 10.1128/genomea.00726-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report the genome sequence of Salmonella enterica subsp. enterica serovar Give (CFSAN012622), isolated from imported chili powder in 2014. This genome contains genes previously reported to be specific only to S. enterica serovar Enteritidis. This strain shows a unique pulsed-field gel electrophoresis (PFGE) pattern clustering with serovar Enteritidis (JEG X01.0005).
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106
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Serba DD, Uppalapati SR, Mukherjee S, Krom N, Tang Y, Mysore KS, Saha MC. Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0075. [PMID: 33228298 DOI: 10.3835/plantgenome2014.10.0075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/23/2014] [Indexed: 06/11/2023]
Abstract
Switchgrass rust caused by Puccinia emaculata is a major limiting factor for switchgrass (Panicum virgatum L.) production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, OK, field. To identify the differentially expressed genes during the rust infection process and the mechanisms of switchgrass rust resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F1 parents ('PV281' and 'NFGA472'), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5 × A4) × (AP13 × VS16). On average, 23.5 million reads per sample (leaf tissue was collected at 0, 24, and 60 h post-inoculation (hpi)) were obtained from paired-end (2 × 100 bp) sequencing on the Illumina HiSeq2000 platform. Mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 ver. 1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense-related genes, including the nucleotide binding site-leucine-rich repeat domain containing disease resistance gene analogs, play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can be a valuable resource for developing molecular markers for rust resistance. Furthermore, the rust-resistant genotypes and gene transcripts identified in this study can expedite rust-resistant cultivar development in switchgrass.
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Affiliation(s)
- Desalegn D Serba
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
| | - Srinivasa Rao Uppalapati
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Dupont Pioneer, Dupont Knowledge Center, Turakapally, Hyderabad, Telangana, India, 500 078
| | - Shreyartha Mukherjee
- Computing Services, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Nick Krom
- Computing Services, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Malay C Saha
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
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107
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Shen Z, Feng Y, Sheh A, Everitt J, Bertram F, Paster BJ, Fox JG. Isolation and characterization of a novel Helicobacter species, Helicobacter jaachi sp. nov., from common marmosets (Callithrix jaachus). J Med Microbiol 2015; 64:1063-1073. [PMID: 26297446 DOI: 10.1099/jmm.0.000113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Purpose-bred common marmosets from domestic sources housed in a US research facility, and used in multiple drug discovery programmes, were noted to have a high incidence of spontaneous inflammatory bowel disease and sporadic cholecystitis and cholangiohepatitis. Inflammatory infiltrates increased in incidence and severity with age. Because Helicobacter spp. have been linked to gastrointestinal diseases, samples from the gastrointestinal tracts of 39 marmosets were screened for Helicobacter spp. by culture and PCR. Helicobacter spp. were frequently detected in marmosets; 28.2% of the marmosets were positive for a proposed novel species, Helicobacter jaachi sp. nov., by culture, and 48.7% were positive by Helicobacter genus-specific PCR. Seventeen strains of Helicobacter sp. from 11 marmosets were cultured from various gastrointestinal sites. Older animals (age 6-11 years) had a higher helicobacter prevalence rate (57.1%) compared with younger animals (age 3-5 years), which had a 27.2% prevalence rate. Cells of H. jaachi sp. nov. were catalase, urease and oxidase positive and had fusiform morphology, with periplasmic fibres and multiple bipolar, sheathed flagella. All isolates had similar 16S and 23S rRNA sequences, which clustered as representatives of a novel Helicobacter species closely related to 'Helicobacter sanguini' (97%), a species isolated from cotton-top tamarins and 'Helicobacter callitrichis' (96%) isolated previously from the faeces of common marmosets. The whole genome sequence of one of the liver isolates, H. jaachi sp. nov. MIT 09-6949(T), had a 1.9 Mb genome length with a 41 mol% DNA G+C content. The type strain of Helicobacter jaachi sp. nov., MIT 09-6949(T), has been deposited in the BCCM/LMG Bacteria Collection as LMG 28613(T). These findings add to the increasing number of animal species with gastrointestinal disease in which novel enterohepatic Helicobacter spp. have been isolated.
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Affiliation(s)
- Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yan Feng
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander Sheh
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
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108
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Hoffmann M, Luo Y, Monday SR, Gonzalez-Escalona N, Ottesen AR, Muruvanda T, Wang C, Kastanis G, Keys C, Janies D, Senturk IF, Catalyurek UV, Wang H, Hammack TS, Wolfgang WJ, Schoonmaker-Bopp D, Chu A, Myers R, Haendiges J, Evans PS, Meng J, Strain EA, Allard MW, Brown EW. Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States. J Infect Dis 2015; 213:502-8. [PMID: 25995194 DOI: 10.1093/infdis/jiv297] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/01/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Using a novel combination of whole-genome sequencing (WGS) analysis and geographic metadata, we traced the origins of Salmonella Bareilly isolates collected in 2012 during a widespread food-borne outbreak in the United States associated with scraped tuna imported from India. METHODS Using next-generation sequencing, we sequenced the complete genome of 100 Salmonella Bareilly isolates obtained from patients who consumed contaminated product, from natural sources, and from unrelated historically and geographically disparate foods. Pathogen genomes were linked to geography by projecting the phylogeny on a virtual globe and produced a transmission network. RESULTS Phylogenetic analysis of WGS data revealed a common origin for outbreak strains, indicating that patients in Maryland and New York were infected from sources originating at a facility in India. CONCLUSIONS These data represent the first report fully integrating WGS analysis with geographic mapping and a novel use of transmission networks. Results showed that WGS vastly improves our ability to delimit the scope and source of bacterial food-borne contamination events. Furthermore, these findings reinforce the extraordinary utility that WGS brings to global outbreak investigation as a greatly enhanced approach to protecting the human food supply chain as well as public health in general.
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Affiliation(s)
- Maria Hoffmann
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition Department of Nutrition & Food Science and Joint Institute for Food Safety & Applied Nutrition, University of Maryland, College Park
| | - Yan Luo
- Division of Public Health and Biostatistics, Office of Food Defense, Communication and Emergency Response, Center for Food Safety and Nutrition, US Food and Drug Administration, College Park
| | - Steven R Monday
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | | | - Andrea R Ottesen
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - Tim Muruvanda
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - Charles Wang
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - George Kastanis
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - Christine Keys
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University North Carolina at Charlotte
| | - Izzet F Senturk
- Department of Biomedical Informatics, Ohio State University, Columbus
| | - Umit V Catalyurek
- Department of Biomedical Informatics, Ohio State University, Columbus
| | - Hua Wang
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - Thomas S Hammack
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | | | | | - Alvina Chu
- Maryland Department of Health and Mental Hygiene, Baltimore
| | - Robert Myers
- Maryland Department of Health and Mental Hygiene, Baltimore
| | | | - Peter S Evans
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - Jianghong Meng
- Department of Nutrition & Food Science and Joint Institute for Food Safety & Applied Nutrition, University of Maryland, College Park
| | - Errol A Strain
- Division of Public Health and Biostatistics, Office of Food Defense, Communication and Emergency Response, Center for Food Safety and Nutrition, US Food and Drug Administration, College Park
| | - Marc W Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
| | - Eric W Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition
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109
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Bell RL, Zheng J, Burrows E, Allard S, Wang CY, Keys CE, Melka DC, Strain E, Luo Y, Allard MW, Rideout S, Brown EW. Ecological prevalence, genetic diversity, and epidemiological aspects of Salmonella isolated from tomato agricultural regions of the Virginia Eastern Shore. Front Microbiol 2015; 6:415. [PMID: 25999938 PMCID: PMC4423467 DOI: 10.3389/fmicb.2015.00415] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/20/2015] [Indexed: 11/13/2022] Open
Abstract
Virginia is the third largest producer of fresh-market tomatoes in the United States. Tomatoes grown along the eastern shore of Virginia are implicated almost yearly in Salmonella illnesses. Traceback implicates contamination occurring in the pre-harvest environment. To get a better understanding of the ecological niches of Salmonella in the tomato agricultural environment, a 2-year study was undertaken at a regional agricultural research farm in Virginia. Environmental samples, including tomato (fruit, blossoms, and leaves), irrigation water, surface water and sediment, were collected over the growing season. These samples were analyzed for the presence of Salmonella using modified FDA-BAM methods. Molecular assays were used to screen the samples. Over 1500 samples were tested. Seventy-five samples tested positive for Salmonella yielding over 230 isolates. The most commonly isolated serovars were S. Newport and S. Javiana with pulsed-field gel electrophoresis yielding 39 different patterns. Genetic diversity was further underscored among many other serotypes, which showed multiple PFGE subtypes. Whole genome sequencing (WGS) of several S. Newport isolates collected in 2010 compared to clinical isolates associated with tomato consumption showed very few single nucleotide differences between environmental isolates and clinical isolates suggesting a source link to Salmonella contaminated tomatoes. Nearly all isolates collected during two growing seasons of surveillance were obtained from surface water and sediment sources pointing to these sites as long-term reservoirs for persistent and endemic contamination of this environment.
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Affiliation(s)
- Rebecca L. Bell
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Jie Zheng
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Erik Burrows
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Sarah Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Charles Y. Wang
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Christine E. Keys
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - David C. Melka
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Errol Strain
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Yan Luo
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
| | - Steven Rideout
- Eastern Shore Agricultural Research and Extension Center, Virginia TechPainter, VA, USA
| | - Eric W. Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCollege Park, MD, USA
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110
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Draft Genome Sequences of Histamine-Producing Photobacterium kishitanii and Photobacterium angustum, Isolated from Albacore (Thunnus alalunga) and Yellowfin (Thunnus albacares) Tuna. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00400-15. [PMID: 25931609 PMCID: PMC4417705 DOI: 10.1128/genomea.00400-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Histamine-producing bacteria are responsible for scombrotoxin (histamine) fish poisoning, a leading cause of fish poisoning in the United States. We report here the draft genome sequences of four histamine-producing (HP) Photobacterium kishitanii strains and nine HP Photobacterium angustum strains isolated from tuna.
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111
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Complete Genome Sequence of Paenibacillus polymyxa CF05, a Strain of Plant Growth-Promoting Rhizobacterium with Elicitation of Induced Systemic Resistance. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00198-15. [PMID: 25883277 PMCID: PMC4400420 DOI: 10.1128/genomea.00198-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Paenibacillus polymyxa CF05 is a Gram-positive rod-shaped bacterium isolated from the interior of an ancient tree, Cryptomeria fortunei, in China. This bacterium displays potent biocontrol effects against certain soil-borne diseases and the elicitation of induced systemic resistance in tomatoes. Here, we report the complete genome sequence of P. polymyxa CF05.
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112
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Pirone-Davies C, Hoffmann M, Roberts RJ, Muruvanda T, Timme RE, Strain E, Luo Y, Payne J, Luong K, Song Y, Tsai YC, Boitano M, Clark TA, Korlach J, Evans PS, Allard MW. Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars. PLoS One 2015; 10:e0123639. [PMID: 25860355 PMCID: PMC4393132 DOI: 10.1371/journal.pone.0123639] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N6-methyladenine (m6A) methylated motifs, one N4-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all Salmonella serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in Salmonella.
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Affiliation(s)
- Cary Pirone-Davies
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
- * E-mail:
| | - Maria Hoffmann
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | | | - Tim Muruvanda
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Ruth E. Timme
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Errol Strain
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Yan Luo
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Justin Payne
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Khai Luong
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Yi Song
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Yu-Chih Tsai
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Matthew Boitano
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Tyson A. Clark
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Peter S. Evans
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
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113
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Lüdeke CHM, Kong N, Weimer BC, Fischer M, Jones JL. Complete Genome Sequences of a Clinical Isolate and an Environmental Isolate of Vibrio parahaemolyticus. GENOME ANNOUNCEMENTS 2015; 3:e00216-15. [PMID: 25814612 PMCID: PMC4384152 DOI: 10.1128/genomea.00216-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 11/20/2022]
Abstract
Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We report complete genome sequences for two V. parahaemolyticus strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin, respectively. These two sequences might assist in the investigation of differential virulence of this organism.
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Affiliation(s)
| | | | | | - Markus Fischer
- Hamburg School of Food Science, University of Hamburg, Hamburg, Germany
| | - Jessica L Jones
- Gulf Coast Seafood Laboratory, Division of Seafood Science and Technology, Food and Drug Administration, Dauphin Island, Alabama, USA
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114
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Complete Genome Sequence of Terribacillus aidingensis Strain MP602, a Moderately Halophilic Bacterium Isolated from Cryptomeria fortunei in Tianmu Mountain in China. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00126-15. [PMID: 25792050 PMCID: PMC4395062 DOI: 10.1128/genomea.00126-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Terribacillus aidingensis strain MP602, which was isolated from an ancient tree (Cryptomeria forunei) in Tianmu Mountain in China, has antagonistic activity against several certain phytopathogenic fungi. Here, we report the genome sequence of this strain. This is the first complete genome report of the Terribacillus genus.
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115
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Derbyshire MK, Gonzales NR, Lu S, He J, Marchler GH, Wang Z, Marchler-Bauer A. Improving the consistency of domain annotation within the Conserved Domain Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav012. [PMID: 25767294 PMCID: PMC4356950 DOI: 10.1093/database/bav012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
When annotating protein sequences with the footprints of evolutionarily conserved domains, conservative score or E-value thresholds need to be applied for RPS-BLAST hits, to avoid many false positives. We notice that manual inspection and classification of hits gathered at a higher threshold can add a significant amount of valuable domain annotation. We report an automated algorithm that ‘rescues’ valuable borderline-scoring domain hits that are well-supported by domain architecture (DA, the sequential order of conserved domains in a protein query), including tandem repeats of domain hits reported at a more conservative threshold. This algorithm is now available as a selectable option on the public conserved domain search (CD-Search) pages. We also report on the possibility to ‘suppress’ domain hits close to the threshold based on a lack of well-supported DA and to implement this conservatively as an option in live conserved domain searches and for pre-computed results. Improving domain annotation consistency will in turn reduce the fraction of NR sequences with incomplete DAs. URL:http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
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Affiliation(s)
- Myra K Derbyshire
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Noreen R Gonzales
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Shennan Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jane He
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Gabriele H Marchler
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Zhouxi Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
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Handelman SK, Aaronson JM, Seweryn M, Voronkin I, Kwiek JJ, Sadee W, Verducci JS, Janies DA. Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies. Comput Biol Med 2015; 58:1-13. [PMID: 25577610 PMCID: PMC4331246 DOI: 10.1016/j.compbiomed.2014.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 12/09/2014] [Accepted: 12/15/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Associations between genotype and phenotype provide insight into the evolution of pathogenesis, drug resistance, and the spread of pathogens between hosts. However, common ancestry can lead to apparent associations between biologically unrelated features. The novel method Cladograms with Path to Event (ClaPTE) detects associations between character-pairs (either a pair of mutations or a mutation paired with a phenotype) while adjusting for common ancestry, using phylogenetic trees. METHODS ClaPTE tests for character-pairs changing close together on the phylogenetic tree, consistent with an associated character-pair. ClaPTE is compared to three existing methods (independent contrasts, mixed model, and likelihood ratio) to detect character-pair associations adjusted for common ancestry. Comparisons utilize simulations on gene trees for: HIV Env, HIV promoter, and bacterial DnaJ and GuaB; and case studies for Oseltamavir resistance in Influenza, and for DnaJ and GuaB. Simulated data include both true-positive/associated character-pairs, and true-negative/not-associated character-pairs, used to assess type I (frequency of p-values in true-negatives) and type II (sensitivity to true-positives) error control. RESULTS AND CONCLUSIONS ClaPTE has competitive sensitivity and better type I error control than existing methods. In the Influenza/Oseltamavir case study, ClaPTE reports no new permissive mutations but detects associations between adjacent (in primary sequence) amino acid positions which other methods miss. In the DnaJ and GuaB case study, ClaPTE reports more frequent associations between positions both from the same protein family than between positions from different families, in contrast to other methods. In both case studies, the results from ClaPTE are biologically plausible.
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Affiliation(s)
- Samuel K Handelman
- Department of Pharmacology, Ohio State University College of Medicine, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States; Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH 43210, United States.
| | - Jacob M Aaronson
- Department of Biomedical Informatics, Ohio State University College of Medicine, 3190 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Michal Seweryn
- Mathematical Biosciences Institute, The Ohio State University, Jennings Hall 3rd Floor, 1735 Neil Avenue, Columbus, OH 43210, United States
| | - Igor Voronkin
- Department of Biomedical Informatics, Ohio State University College of Medicine, 3190 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Jesse J Kwiek
- Department of Microbial Infection & Immunity and Department of Microbiology, The Ohio State University, 788 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210, United States
| | - Wolfgang Sadee
- Department of Pharmacology, Ohio State University College of Medicine, 5072 Graves Hall, 333 West 10th Avenue, Columbus, OH 43210, United States
| | - Joseph S Verducci
- Department of Statistics, The Ohio State University, 404 Cockins Hall, 1958 Neil Avenue, Columbus, OH 43210-1247, United States
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223-0001, United States
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117
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Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport. GENOME ANNOUNCEMENTS 2015; 3:3/1/e00027-15. [PMID: 25720681 PMCID: PMC4342422 DOI: 10.1128/genomea.00027-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Newport has been a long-standing public health concern in the United States. We present the complete sequences of six IncA/C plasmids from animal-derived MDR S. Newport ranging from 80.1 to 158.5 kb. They shared a genetic backbone with S. Newport IncA/C plasmids pSN254 and pAM04528.
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118
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Whole-Genome Sequences of 12 Clinical Strains of Listeria monocytogenes. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01203-14. [PMID: 25720683 PMCID: PMC4342424 DOI: 10.1128/genomea.01203-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Listeria monocytogenes is a foodborne pathogen of global concern due to the high mortality rate among immunocompromised patients. Whole-genome sequences of 12 strains of L. monocytogenes from humans were reported. The availability of these genomes should provide useful information on the evolutionary history and genetic diversity of L. monocytogenes.
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119
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Haendiges J, Timme R, Allard MW, Myers RA, Brown EW, Gonzalez-Escalona N. Characterization of Vibrio parahaemolyticus clinical strains from Maryland (2012-2013) and comparisons to a locally and globally diverse V. parahaemolyticus strains by whole-genome sequence analysis. Front Microbiol 2015; 6:125. [PMID: 25745421 PMCID: PMC4333860 DOI: 10.3389/fmicb.2015.00125] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/02/2015] [Indexed: 11/13/2022] Open
Abstract
Vibrio parahaemolyticus is the leading cause of foodborne illnesses in the US associated with the consumption of raw shellfish. Previous population studies of V. parahaemolyticus have used Multi-Locus Sequence Typing (MLST) or Pulsed Field Gel Electrophoresis (PFGE). Whole genome sequencing (WGS) provides a much higher level of resolution, but has been used to characterize only a few United States (US) clinical isolates. Here we report the WGS characterization of 34 genomes of V. parahaemolyticus strains that were isolated from clinical cases in the state of Maryland (MD) during 2 years (2012-2013). These 2 years saw an increase of V. parahaemolyticus cases compared to previous years. Among these MD isolates, 28% were negative for tdh and trh, 8% were tdh positive only, 11% were trh positive only, and 53% contained both genes. We compared this set of V. parahaemolyticus genomes to those of a collection of 17 archival strains from the US (10 previously sequenced strains and 7 from NCBI, collected between 1988 and 2004) and 15 international strains, isolated from geographically-diverse environmental and clinical sources (collected between 1980 and 2010). A WGS phylogenetic analysis of these strains revealed the regional outbreak strains from MD are highly diverse and yet genetically distinct from the international strains. Some MD strains caused outbreaks 2 years in a row, indicating a local source of contamination (e.g., ST631). Advances in WGS will enable this type of analysis to become routine, providing an excellent tool for improved surveillance. Databases built with phylogenetic data will help pinpoint sources of contamination in future outbreaks and contribute to faster outbreak control.
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Affiliation(s)
| | - Ruth Timme
- Center for Food and Applied Nutrition, Food and Drug Administration College Park, MD, USA
| | - Marc W Allard
- Center for Food and Applied Nutrition, Food and Drug Administration College Park, MD, USA
| | - Robert A Myers
- Department of Health and Mental Hygiene Baltimore, MD, USA
| | - Eric W Brown
- Center for Food and Applied Nutrition, Food and Drug Administration College Park, MD, USA
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Transoceanic spreading of pathogenic strains of Vibrio parahaemolyticus with distinctive genetic signatures in the recA gene. PLoS One 2015; 10:e0117485. [PMID: 25679989 PMCID: PMC4334540 DOI: 10.1371/journal.pone.0117485] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/23/2014] [Indexed: 01/22/2023] Open
Abstract
Vibrioparahaemolyticus is an important human pathogen whose transmission is associated with the consumption of contaminated seafood. Consistent multilocus sequence typing for V. parahaemolyticus has shown difficulties in the amplification of the recA gene by PCR associated with a lack of amplification or a larger PCR product than expected. In one strain (090–96, Peru, 1996), the produced PCR product was determined to be composed of two recA fragments derived from different Vibrio species. To better understand this phenomenon, we sequenced the whole genome of this strain. The hybrid recA gene was found to be the result of a fragmentation of the original lineage-specific recA gene resulting from a DNA insertion of approximately 30 kb in length. This insert had a G+C content of 38.8%, lower than that of the average G+C content of V. parahaemolyticus (45.2%), and contained 19 ORFs, including a complete recA gene. This new acquired recA gene deviated 24% in sequence from the original recA and was distantly related to recA genes from bacteria of the Vibrionaceae family. The reconstruction of the original recA gene (recA3) identified the precursor as belonging to ST189, a sequence type reported previously only in Asian countries. The identification of this singular genetic feature in strains from Asia reveals new evidence for genetic connectivity between V. parahaemolyticus populations at both sides of the Pacific Ocean that, in addition to the previously described pandemic clone, supports the existence of a recurrent transoceanic spreading of pathogenic V. parahaemolyticus with the corresponding potential risk of pandemic expansion.
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121
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Liljeqvist M, Ossandon FJ, González C, Rajan S, Stell A, Valdes J, Holmes DS, Dopson M. Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream. FEMS Microbiol Ecol 2015; 91:fiv011. [PMID: 25764459 DOI: 10.1093/femsec/fiv011] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 11/13/2022] Open
Abstract
An acid mine drainage (pH 2.5-2.7) stream biofilm situated 250 m below ground in the low-temperature (6-10°C) Kristineberg mine, northern Sweden, contained a microbial community equipped for growth at low temperature and acidic pH. Metagenomic sequencing of the biofilm and planktonic fractions identified the most abundant microorganism to be similar to the psychrotolerant acidophile, Acidithiobacillus ferrivorans. In addition, metagenome contigs were most similar to other Acidithiobacillus species, an Acidobacteria-like species, and a Gallionellaceae-like species. Analyses of the metagenomes indicated functional characteristics previously characterized as related to growth at low temperature including cold-shock proteins, several pathways for the production of compatible solutes and an anti-freeze protein. In addition, genes were predicted to encode functions related to pH homeostasis and metal resistance related to growth in the acidic metal-containing mine water. Metagenome analyses identified microorganisms capable of nitrogen fixation and exhibiting a primarily autotrophic lifestyle driven by the oxidation of the ferrous iron and inorganic sulfur compounds contained in the sulfidic mine waters. The study identified a low diversity of abundant microorganisms adapted to a low-temperature acidic environment as well as identifying some of the strategies the microorganisms employ to grow in this extreme environment.
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Affiliation(s)
- Maria Liljeqvist
- Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden
| | - Francisco J Ossandon
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago 7780272, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago 7780272, Chile Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Piso 14, 7550296, Chile
| | - Sukithar Rajan
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 31 Kalmar, Sweden
| | - Adam Stell
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 31 Kalmar, Sweden
| | - Jorge Valdes
- Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Piso 14, 7550296, Chile
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago 7780272, Chile
| | - Mark Dopson
- Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 392 31 Kalmar, Sweden
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122
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Persicke M, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C. Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T). Stand Genomic Sci 2015; 10:5. [PMID: 26203323 PMCID: PMC4510995 DOI: 10.1186/1944-3277-10-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/21/2014] [Indexed: 11/23/2022] Open
Abstract
Corynebacterium callunae DSM 20147(T) is a member of the genus Corynebacterium which contains Gram-positive and non-spore forming bacteria with a high G + C content. C. callunae was isolated during a screening for l-glutamic acid producing bacteria and belongs to the aerobic and non-haemolytic corynebacteria. As this is a type strain in a subgroup of industrial relevant bacteria for many of which there are also complete genome sequence available, knowledge of the complete genome sequence might enable genome comparisons to identify production relevant genetic loci. This project, describing the 2.84 Mbp long chromosome and the two plasmids, pCC1 (4.11 kbp) and pCC2 (85.02 kbp), with their 2,647 protein-coding and 82 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Marcus Persicke
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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123
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Draft genome sequences of eight enterohepatic helicobacter species isolated from both laboratory and wild rodents. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01218-14. [PMID: 25428971 PMCID: PMC4246163 DOI: 10.1128/genomea.01218-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The draft genome sequences of eight enterohepatic Helicobacter species, H. muridarum, H. trogontum, H. typhlonius, and five unnamed helicobacters, are presented here. Using laboratory mice pervasively infected with helicobacters, we characterized the presence of known virulence factors.
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124
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Abstract
Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.
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Affiliation(s)
- J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Danso Ako-Adjei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yiming Bao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Olga Blinkova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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125
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Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH. CDD: NCBI's conserved domain database. Nucleic Acids Res 2014; 43:D222-6. [PMID: 25414356 DOI: 10.1093/nar/gku1221] [Citation(s) in RCA: 2354] [Impact Index Per Article: 235.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
NCBI's CDD, the Conserved Domain Database, enters its 15(th) year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
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Affiliation(s)
- Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Myra K Derbyshire
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Noreen R Gonzales
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Shennan Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Farideh Chitsaz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lewis Y Geer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Renata C Geer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jane He
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Marc Gwadz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - David I Hurwitz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Christopher J Lanczycki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Fu Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Gabriele H Marchler
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - James S Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Narmada Thanki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Zhouxi Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Roxanne A Yamashita
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Dachuan Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Chanjuan Zheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stephen H Bryant
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
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126
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Abstract
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.
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127
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Hoppe S, Bier FF, von Nickisch-Rosenegk M. Identification of antigenic proteins of the nosocomial pathogen Klebsiella pneumoniae. PLoS One 2014; 9:e110703. [PMID: 25333280 PMCID: PMC4205017 DOI: 10.1371/journal.pone.0110703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 09/24/2014] [Indexed: 12/17/2022] Open
Abstract
The continuous expansion of nosocomial infections around the globe has become a precarious situation. Key challenges include mounting dissemination of multiple resistances to antibiotics, the easy transmission and the growing mortality rates of hospital-acquired bacterial diseases. Thus, new ways to rapidly detect these infections are vital. Consequently, researchers around the globe pursue innovative approaches for point-of-care devices. In many cases the specific interaction of an antigen and a corresponding antibody is pivotal. However, the knowledge about suitable antigens is lacking. The aim of this study was to identify novel antigens as specific diagnostic markers. Additionally, these proteins might be aptly used for the generation of vaccines to improve current treatment options. Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After screening 1536 clones, 14 previously unknown immunogenic proteins were identified. Subsequently, each protein was expressed in full-length and its immunodominant character examined by ELISA and microarray analyses. Consequently, six proteins were selected for epitope mapping and three thereof possessed linear epitopes. After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. pneumoniae. The remaining epitopes showed ambiguous results regarding the specificity for K. pneumoniae. The approach adopted herein has been successfully utilized to discover novel antigens of Campylobacter jejuni and Salmonella enterica antigens before. Now, we have transferred this knowledge to the key nosocomial agent, K. pneumoniae. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen.
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Affiliation(s)
- Sebastian Hoppe
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocess (IZI-BB), Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
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128
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Draft Genome Sequences of Clinical Vibrio parahaemolyticus Strains Isolated in Maryland (2010 to 2013). GENOME ANNOUNCEMENTS 2014; 2:2/4/e00776-14. [PMID: 25103764 PMCID: PMC4125775 DOI: 10.1128/genomea.00776-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Vibrio parahaemolyticus is the leading cause of food-borne illnesses associated with the consumption of raw shellfish worldwide. Here, we report 45 draft genomes of V. parahaemolyticus. Thirty-five of them are strains that were isolated from clinical cases in the state of Maryland from 2010 to 2013. The remaining 10 strains were historical isolates, isolated mostly from the West Coast of the United States during the period of 1988 to 2004. The availability of these genomes will allow for future phylogenetic analyses with other V. parahaemolyticus strains.
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129
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Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00501-14. [PMID: 25013133 PMCID: PMC4110765 DOI: 10.1128/genomea.00501-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen. Here, we report the draft whole-genome sequences of nine STEC strains isolated from clinical cases in the United States. This is the first report of such information for STEC of serotypes O69, H11, O145:H25, O118:H16, O91:H21, O146:H21, O45:H2, O128:H2, and O121:H19.
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130
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Rückert C, Albersmeier A, Al-Dilaimi A, Bednarz H, Niehaus K, Szczepanowski R, Kalinowski J. Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)). Stand Genomic Sci 2014; 9:505-13. [PMID: 25197436 PMCID: PMC4149027 DOI: 10.4056/sigs.4588337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium, which contains Gram-positive and non-spore forming bacteria with a high G+C content. C. terpenotabidum was isolated from soil based on its ability to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria. It displays tolerance to salts (up to 8%) and is related to Corynebacterium variabile involved in cheese ripening. As this is a type strain of Corynebacterium, this project describing the 2.75 Mbp long chromosome with its 2,369 protein-coding and 72 RNA genes will aid the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Arwa Al-Dilaimi
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | | | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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131
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Everard A, Lazarevic V, Gaïa N, Johansson M, Ståhlman M, Backhed F, Delzenne NM, Schrenzel J, François P, Cani PD. Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity. ISME JOURNAL 2014; 8:2116-30. [PMID: 24694712 PMCID: PMC4163056 DOI: 10.1038/ismej.2014.45] [Citation(s) in RCA: 433] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 02/27/2014] [Indexed: 12/25/2022]
Abstract
The gut microbiota is involved in metabolic and immune disorders associated with obesity and type 2 diabetes. We previously demonstrated that prebiotic treatment may significantly improve host health by modulating bacterial species related to the improvement of gut endocrine, barrier and immune functions. An analysis of the gut metagenome is needed to determine which bacterial functions and taxa are responsible for beneficial microbiota-host interactions upon nutritional intervention. We subjected mice to prebiotic (Pre) treatment under physiological (control diet: CT) and pathological conditions (high-fat diet: HFD) for 8 weeks and investigated the production of intestinal antimicrobial peptides and the gut microbiome. HFD feeding significantly decreased the expression of regenerating islet-derived 3-gamma (Reg3g) and phospholipase A2 group-II (PLA2g2) in the jejunum. Prebiotic treatment increased Reg3g expression (by ∼50-fold) and improved intestinal homeostasis as suggested by the increase in the expression of intectin, a key protein involved in intestinal epithelial cell turnover. Deep metagenomic sequencing analysis revealed that HFD and prebiotic treatment significantly affected the gut microbiome at different taxonomic levels. Functional analyses based on the occurrence of clusters of orthologous groups (COGs) of proteins also revealed distinct profiles for the HFD, Pre, HFD-Pre and CT groups. Finally, the gut microbiota modulations induced by prebiotics counteracted HFD-induced inflammation and related metabolic disorders. Thus, we identified novel putative taxa and metabolic functions that may contribute to the development of or protection against the metabolic alterations observed during HFD feeding and HFD-Pre feeding.
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Affiliation(s)
- Amandine Everard
- Université catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life sciences and BIOtechnology), Metabolism and Nutrition Research Group, Brussels, Belgium
| | - Vladimir Lazarevic
- Geneva University Hospitals, Division of Infectious Diseases, Genomic Research Lab, Geneva, Switzerland
| | - Nadia Gaïa
- Geneva University Hospitals, Division of Infectious Diseases, Genomic Research Lab, Geneva, Switzerland
| | - Maria Johansson
- 1] Wallenberg Laboratory/Sahlgrenska Center for Cardiovascular and Metabolic Research, Sahlgrenska University Hospital, Gothenburg, Sweden [2] Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Marcus Ståhlman
- 1] Wallenberg Laboratory/Sahlgrenska Center for Cardiovascular and Metabolic Research, Sahlgrenska University Hospital, Gothenburg, Sweden [2] Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Backhed
- 1] Wallenberg Laboratory/Sahlgrenska Center for Cardiovascular and Metabolic Research, Sahlgrenska University Hospital, Gothenburg, Sweden [2] Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Nathalie M Delzenne
- Université catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life sciences and BIOtechnology), Metabolism and Nutrition Research Group, Brussels, Belgium
| | - Jacques Schrenzel
- 1] Geneva University Hospitals, Division of Infectious Diseases, Genomic Research Lab, Geneva, Switzerland [2] Geneva University Hospitals, Laboratory of Bacteriology, Geneva, Switzerland
| | - Patrice François
- Geneva University Hospitals, Division of Infectious Diseases, Genomic Research Lab, Geneva, Switzerland
| | - Patrice D Cani
- Université catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life sciences and BIOtechnology), Metabolism and Nutrition Research Group, Brussels, Belgium
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132
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Li W, Ma B, Zhang K. Optimizing Spaced k-mer Neighbors for Efficient Filtration in Protein Similarity Search. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:398-406. [PMID: 26355786 DOI: 10.1109/tcbb.2014.2306831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Large-scale comparison or similarity search of genomic DNA and protein sequence is of fundamental importance in modern molecular biology. To perform DNA and protein sequence similarity search efficiently, seeding (or filtration) method has been widely used where only sequences sharing a common pattern or "seed" are subject to detailed comparison. Therefore these methods trade search sensitivity with search speed. In this paper, we introduce a new seeding method, called spaced k-mer neighbors, which provides a better tradeoff between the sensitivity and speed in protein sequence similarity search. With the method of spaced k-mer neighbors, for each spaced k-mer, a set of spaced k-mers is selected as its neighbors. These pre-selected spaced k-mer neighbors are then used to detect hits between query sequence and database sequences. We propose an efficient heuristic algorithm for the spaced neighbor selection. Our computational experimental results demonstrate that the method of spaced k-mer neighbors can improve the overall tradeoff efficiency over existing seeding methods.
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133
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Danckert L, Hoppe S, Bier FF, von Nickisch-Rosenegk M. Rapid identification of novel antigens of Salmonella Enteritidis by microarray-based immunoscreening. Mikrochim Acta 2014; 181:1707-1714. [PMID: 25253911 PMCID: PMC4167438 DOI: 10.1007/s00604-014-1197-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/30/2014] [Indexed: 01/13/2023]
Abstract
We report on an approach to rapidly screen thousands of Salmonella Enteritidis proteins with the goal of identifying novel immunodominant proteins. We used a microarray-based system that warrants high throughput and easy handling. Seven immunogenic candidates were selected after screening. Comparative analyses by ELISA and microarrays manifested their immunodominant character. The large repetitive protein (SEN4030) that plays a role as a putative adhesin in initial cell surface interaction and is highly specific to Salmonella is considered to be the most suitable protein for a diagnostic approach. The results further demonstrate that the strategy applied herein is convenient for specifically identifying immunogenic proteins of pathogenic microorganisms. Consequently, it enables a sound assessment of promising candidates for diagnostic applications and vaccine development. Moreover, the elucidation of immunogenic proteins may assist in unveiling unknown virulence-associated factors, thus furthering the understanding of the underlying pathogenicity of Salmonella in general, and of S. Enteritidis, one of the most frequently detected serovars of this pathogen, in particular. FigureThe microarray-based approach was aimed at identifying novel immunodominant proteins of S. Enteritidis. Seven antigens were revealed by screening a cDNA expression library. SEN4030, a large repetitive protein specific for salmonella, is considered an optimal candidate for future applications.
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Affiliation(s)
- Lena Danckert
- Fraunhofer IBMT, Am Mühlenberg 13., 14476 Potsdam, Germany
| | | | - Frank F. Bier
- Fraunhofer IBMT, Am Mühlenberg 13., 14476 Potsdam, Germany
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134
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Genome Sequence of a Helicobacter pylori Strain Isolated from a Mexican Patient with Intestinal Gastric Cancer. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01214-13. [PMID: 24459275 PMCID: PMC3900907 DOI: 10.1128/genomea.01214-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Helicobacter pylori strains are the major risk factor for gastric cancer. Strains vary in their content of disease-associated genes, so genome-wide analysis of cancer-isolated strains will help elucidate their pathogenesis and genetic diversity. We present the draft genome sequence of H. pylori isolated from a Mexican patient with intestinal gastric cancer.
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135
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Mueller TJ, Berla BM, Pakrasi HB, Maranas CD. Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. BMC SYSTEMS BIOLOGY 2013; 7:142. [PMID: 24369854 PMCID: PMC3880981 DOI: 10.1186/1752-0509-7-142] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/19/2013] [Indexed: 12/02/2022]
Abstract
Background Cyanobacteria are photoautotrophic prokaryotes that exhibit robust growth under diverse environmental conditions with minimal nutritional requirements. They can use solar energy to convert CO2 and other reduced carbon sources into biofuels and chemical products. The genus Cyanothece includes unicellular nitrogen-fixing cyanobacteria that have been shown to offer high levels of hydrogen production and nitrogen fixation. The reconstruction of quality genome-scale metabolic models for organisms with limited annotation resources remains a challenging task. Results Here we reconstruct and subsequently analyze and compare the metabolism of five Cyanothece strains, namely Cyanothece sp. PCC 7424, 7425, 7822, 8801 and 8802, as the genome-scale metabolic reconstructions iCyc792, iCyn731, iCyj826, iCyp752, and iCyh755 respectively. We compare these phylogenetically related Cyanothece strains to assess their bio-production potential. A systematic workflow is introduced for integrating and prioritizing annotation information from the Universal Protein Resource (Uniprot), NCBI Protein Clusters, and the Rapid Annotations using Subsystems Technology (RAST) method. The genome-scale metabolic models include fully traced photosynthesis reactions and respiratory chains, as well as balanced reactions and GPR associations. Metabolic differences between the organisms are highlighted such as the non-fermentative pathway for alcohol production found in only Cyanothece 7424, 8801, and 8802. Conclusions Our development workflow provides a path for constructing models using information from curated models of related organisms and reviewed gene annotations. This effort lays the foundation for the expedient construction of curated metabolic models for organisms that, while not being the target of comprehensive research, have a sequenced genome and are related to an organism with a curated metabolic model. Organism-specific models, such as the five presented in this paper, can be used to identify optimal genetic manipulations for targeted metabolite overproduction as well as to investigate the biology of diverse organisms.
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Affiliation(s)
| | | | | | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA.
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136
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Draft Genome Sequence of Shewanella decolorationis S12, a Dye-Degrading Bacterium Isolated from a Wastewater Treatment Plant. GENOME ANNOUNCEMENTS 2013; 1:1/6/e00993-13. [PMID: 24309738 PMCID: PMC3853061 DOI: 10.1128/genomea.00993-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Shewanella decolorationis is a valuable microorganism for degrading diverse synthetic textile dyes. Here, we present an annotated draft genome sequence of S. decolorationis S12, which contains 4,219 protein-coding genes and 86 structural RNAs. This information regarding the genetic basis of this bacterium can greatly advance our understanding of the physiology of this species.
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137
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Abstract
In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page.
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Affiliation(s)
- NCBI Resource Coordinators
- *To whom correspondence should be addressed. Eric W. Sayers. Tel: +1 301 496 2475; Fax: +1 301 480 9241;
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138
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McMurry LM, Levy SB. Amino acid residues involved in inactivation of the Escherichia coli multidrug resistance repressor MarR by salicylate, 2,4-dinitrophenol, and plumbagin. FEMS Microbiol Lett 2013; 349:16-24. [PMID: 24111786 DOI: 10.1111/1574-6968.12291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/27/2013] [Accepted: 09/12/2013] [Indexed: 11/28/2022] Open
Abstract
MarR is the dedicated autorepressor of the marRAB operon found in seven genera of the Enterobacteraceae. The MarA transcriptional regulator directly activates numerous genes involved in multidrug resistance and other environmental responses. MarR is inactivated by certain phenolic ligands, such as salicylate, by an unknown mechanism. Our recent work has shown that several amino acid residues of Escherichia coli MarR affecting ligand binding are located between the dimerization and DNA-binding domains. To further characterize the ligand-binding region of MarR, we have now examined 7 point mutants generated by random mutagenesis and 11 site-directed alanine replacement mutants for inactivation by three ligands: salicylate, 2,4-dinitrophenol, and plumbagin. Inactivation of MarR was quantitated in intact cells by loss of MarR-mediated repression of a chromosomal mar-lacZ transcriptional fusion. The results showed that most of the residues important for ligand effectiveness lay in the α1 and α2 helices of MarR, between the putative DNA-binding domain and the dimerization domain of MarR, reinforcing our earlier findings. Moreover, the three ligands had different, but overlapping, sets of residues impacting their effects on MarR.
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Affiliation(s)
- Laura M McMurry
- Department of Molecular Biology and Microbiology, Center for Adaptation Genetics and Drug Resistance, Tufts University School of Medicine, Boston, MA, USA
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139
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GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696-701. [PMID: 24096415 DOI: 10.1128/aem.02411-13] [Citation(s) in RCA: 615] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
GET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles, or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain composition of proteins using the HMMER3 package, by imposing desired pairwise alignment coverage cutoffs, or by selecting only syntenic genes. The resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation, and graphical display of core genome and pangenome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core genome and pangenome sizes, and high-quality graphics can be generated. Furthermore, pangenome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50 Streptococcus genomes annotated in the Orthologous Matrix (OMA) browser as a benchmark case. The package can be downloaded at http://www.eead.csic.es/compbio/soft/gethoms.php and http://maya.ccg.unam.mx/soft/gethoms.php.
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140
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Draft Genome Sequences of Two Salmonella Strains from the SARA Collection, SARA64 (Muenchen) and SARA33 (Heidelberg), Provide Insight into Their Antibiotic Resistance. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00806-13. [PMID: 24092796 PMCID: PMC3790100 DOI: 10.1128/genomea.00806-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Salmonella enterica strains that are representatives of the S. enterica serovar Typhimurium complex in reference collection A (SARA) are closely related but exhibit differences in antibiotic resistance, which could have public health consequences. To better understand the mechanisms behind these resistances, we sequenced the genomes of two multidrug-resistant strains: SARA64 (Muenchen) and SARA33 (Heidelberg).
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141
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Draft Genome Sequences of Helicobacter pylori Strains Isolated from Regions of Low and High Gastric Cancer Risk in Colombia. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00736-13. [PMID: 24051318 PMCID: PMC3778201 DOI: 10.1128/genomea.00736-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The draft genome sequences of six Colombian Helicobacter pylori strains are presented. These strains were isolated from patients from regions of high and low gastric cancer risk in Colombia and were characterized by multilocus sequence typing. The data provide insights into differences between H. pylori strains of different phylogeographic origins.
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142
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Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. The COMBREX project: design, methodology, and initial results. PLoS Biol 2013; 11:e1001638. [PMID: 24013487 PMCID: PMC3754883 DOI: 10.1371/journal.pbio.1001638] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Brian P. Anton
- New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail: (BPA); (SK)
| | - Yi-Chien Chang
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Peter Brown
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Han-Pil Choi
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Lina L. Faller
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Jyotsna Guleria
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Zhenjun Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Niels Klitgord
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Ami Levy-Moonshine
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Almaz Maksad
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Varun Mazumdar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Mark McGettrick
- Diatom Software LLC, Holliston, Massachusetts, United States of America
| | - Lais Osmani
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Revonda Pokrzywa
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - John Rachlin
- Diatom Software LLC, Holliston, Massachusetts, United States of America
| | - Rajeswari Swaminathan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Benjamin Allen
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Genevieve Housman
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Caitlin Monahan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Krista Rochussen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Kevin Tao
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Ashok S. Bhagwat
- Department of Chemistry, Wayne State University, Detroit, Michigan, United States of America
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Donald Ferguson
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Alexey Fomenkov
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, United States of America
| | - Richard D. Morgan
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Andrei L. Osterman
- Bioinformatics and Systems Biology, Sanford Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Dmitry A. Rodionov
- Bioinformatics and Systems Biology, Sanford Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Irina A. Rodionova
- Bioinformatics and Systems Biology, Sanford Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Kenneth E. Rudd
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, Florida, United States of America
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - James Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Shuang-yong Xu
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alex Bateman
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Robert M. Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, University of Toledo, Toledo, Ohio, United States of America
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Woo-Suk Chang
- Department of Biology, University of Texas-Arlington, Arlington, Texas, United States of America
| | - Manuel Ferrer
- Spanish National Research Council (CSIC), Institute of Catalysis, Madrid, Spain
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Michael Y. Galperin
- National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Julien Gobeill
- Department of Library and Information Sciences, University of Applied Sciences Western Switzerland, Geneva, Switzerland
- Bibliomics and Text Mining Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Daniel Haft
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - John Hunt
- Biological Sciences, Columbia University, New York, New York, United States of America
| | - Peter Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, California, United States of America
| | - William Klimke
- National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dana Macelis
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Ramana Madupu
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Maria J. Martin
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Jeffrey H. Miller
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Claire O'Donovan
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Patrick Ruch
- Department of Library and Information Sciences, University of Applied Sciences Western Switzerland, Geneva, Switzerland
- Bibliomics and Text Mining Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Aaron Setterdahl
- Department of Chemistry, Indiana University Southeast, New Albany, Indiana, United States of America
| | - Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - John Tate
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Alexander Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Dmitri Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Germán Plata
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, Structural, and Genetic Studies, Columbia University, New York, New York, United States of America
| | - Jie Hu
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Russell Greiner
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - David Horn
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Kimmen Sjölander
- Berkeley Phylogenomics Group, University of California, Berkeley, California, United States of America
| | - Steven L. Salzberg
- Departments of Medicine and Biostatistics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dennis Vitkup
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Stanley Letovsky
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Charles DeLisi
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Richard J. Roberts
- New England Biolabs, Ipswich, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Martin Steffen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- * E-mail: (BPA); (SK)
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143
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Genome Sequence of Staphylococcus massiliensis Strain S46, Isolated from the Surface of Healthy Human Skin. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00553-13. [PMID: 23929469 PMCID: PMC3738885 DOI: 10.1128/genomea.00553-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Staphylococcus massiliensis strain S46 was isolated from the surface of healthy human skin. Here, we report the draft genome sequence of S. massiliensis S46 (2,447,110 bp, with a G+C content of 36.3%).
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144
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Schaffert L, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C. Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)). Stand Genomic Sci 2013; 8:516-24. [PMID: 24501635 PMCID: PMC3910691 DOI: 10.4056/sigs.4057796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium maris Coryn-1(T) Ben-Dov et al. 2009 is a member of the genus Corynebacterium which contains Gram-positive, non-spore forming bacteria with a high G+C content. C. maris was isolated from the mucus of the Scleractinian coral Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It displays tolerance to salts (up to 10%) and is related to the soil bacterium Corynebacterium halotolerans. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project, describing the 2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584 protein-coding and 67 RNA genes, will aid the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Lena Schaffert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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145
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Complete Genome Sequences of Helicobacter pylori Rifampin-Resistant Strains. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00446-13. [PMID: 23833139 PMCID: PMC3703600 DOI: 10.1128/genomea.00446-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here we present the complete genome sequences of two Helicobacter pylori rifampin-resistant (Rifr) strains (Rif1 and Rif2). Rifr strains were obtained by in vitro selection of H. pylori 26695 on agar plates with 20 µg/ml rifampin. The genome data provide insights on the genomic diversity of H. pylori under selection by rifampin.
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146
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Wu WL, Liao JH, Lin GH, Lin MH, Chang YC, Liang SY, Yang FL, Khoo KH, Wu SH. Phosphoproteomic analysis reveals the effects of PilF phosphorylation on type IV pilus and biofilm formation in Thermus thermophilus HB27. Mol Cell Proteomics 2013; 12:2701-13. [PMID: 23828892 DOI: 10.1074/mcp.m113.029330] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Thermus thermophilus HB27 is an extremely thermophilic eubacteria with a high frequency of natural competence. This organism is therefore often used as a thermophilic model to investigate the molecular basis of type IV pili-mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. In this study, the phosphoproteome of T. thermophilus HB27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. According to this analysis, the ATPase motor PilF, a type IV pili-related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in nonpiliated and nontwitching phenotypes, whereas nonphosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with a higher initial attachment rate, caused by increasing exopolysaccharide production. In summary, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production.
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Affiliation(s)
- Wan-Ling Wu
- Institute of Biochemical Sciences, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
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147
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Choi HP, Juarez S, Ciordia S, Fernandez M, Bargiela R, Albar JP, Mazumdar V, Anton BP, Kasif S, Ferrer M, Steffen M. Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PLoS One 2013; 8:e66605. [PMID: 23825549 PMCID: PMC3688963 DOI: 10.1371/journal.pone.0066605] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/08/2013] [Indexed: 12/16/2022] Open
Abstract
The functional characterization of Open Reading Frames (ORFs) from sequenced genomes remains a bottleneck in our effort to understand microbial biology. In particular, the functional characterization of proteins with only remote sequence homology to known proteins can be challenging, as there may be few clues to guide initial experiments. Affinity enrichment of proteins from cell lysates, and a global perspective of protein function as provided by COMBREX, affords an approach to this problem. We present here the biochemical analysis of six proteins from Helicobacter pylori ATCC 26695, a focus organism in COMBREX. Initial hypotheses were based upon affinity capture of proteins from total cellular lysate using derivatized nano-particles, and subsequent identification by mass spectrometry. Candidate genes encoding these proteins were cloned and expressed in Escherichia coli, and the recombinant proteins were purified and characterized biochemically and their biochemical parameters compared with the native ones. These proteins include a guanosine triphosphate (GTP) cyclohydrolase (HP0959), an ATPase (HP1079), an adenosine deaminase (HP0267), a phosphodiesterase (HP1042), an aminopeptidase (HP1037), and new substrates were characterized for a peptidoglycan deacetylase (HP0310). Generally, characterized enzymes were active at acidic to neutral pH (4.0–7.5) with temperature optima ranging from 35 to 55°C, although some exhibited outstanding characteristics.
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Affiliation(s)
- Han-Pil Choi
- Dept of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Silvia Juarez
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Sergio Ciordia
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Marisol Fernandez
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Rafael Bargiela
- Spanish National Research Council (CSIC), Institute of Catalysis, Madrid, Spain
| | - Juan P. Albar
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain
| | - Varun Mazumdar
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Brian P. Anton
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Simon Kasif
- Dept of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Manuel Ferrer
- Spanish National Research Council (CSIC), Institute of Catalysis, Madrid, Spain
- * E-mail: (MS); (MF)
| | - Martin Steffen
- Dept of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Dept of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail: (MS); (MF)
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148
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Bykova NA, Favorov AV, Mironov AA. Hidden Markov models for evolution and comparative genomics analysis. PLoS One 2013; 8:e65012. [PMID: 23762278 PMCID: PMC3676395 DOI: 10.1371/journal.pone.0065012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 04/23/2013] [Indexed: 12/21/2022] Open
Abstract
The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for example, if the states for extant species are predicted by some program and thus are known only with some level of reliability; it is common for bioinformatics field. The main idea is formulation of the problem as a hidden Markov model on a tree (tree HMM, tHMM), where the basic continuous-time Markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. Our tHMM decoding algorithm allows us to predict states at the ancestral nodes as well as to refine states at the leaves on the basis of quantitative comparative genomics. The test on the simulated data shows that the tHMM approach applied to the continuous variable reflecting the probabilities of the states (i.e. prediction score) appears to be more accurate then the reconstruction from the discrete states assignment defined by the best score threshold. We provide examples of applying our model to the evolutionary analysis of N-terminal signal peptides and transcription factor binding sites in bacteria. The program is freely available at http://bioinf.fbb.msu.ru/~nadya/tHMM and via web-service at http://bioinf.fbb.msu.ru/treehmmweb.
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Affiliation(s)
- Nadezda A Bykova
- A.A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia.
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149
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Hoppe S, Bier FF, Nickisch-Rosenegk MV. Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni. PLoS One 2013; 8:e65837. [PMID: 23734261 PMCID: PMC3667084 DOI: 10.1371/journal.pone.0065837] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 04/30/2013] [Indexed: 01/03/2023] Open
Abstract
Campylobacter jejuni remains one of the major gut pathogens of our time. Its zoonotic nature and wide-spread distribution in industrialized countries calls for a quick and reliable diagnostic tool. Antibody-based detection presents a suitable means to identify pathogenic bacteria. However, the knowledge about immunodominant targets is limited. Thus, an approach is presented, which allows for the rapid screening of numerous cDNA derived expression clones to identify novel antigens. The deeper understanding of immunodominant proteins assists in the design of diagnostic tools and furthers the insight into the bacterium's pathogenicity as well as revealing potential candidates for vaccination. We have successfully screened 1536 clones of an expression library to identify 22 proteins that have not been described as immunodominant before. After subcloning the corresponding 22 genes and expression of full-length proteins, we investigated the immunodominant character by microarrays and ELISA. Subsequently, seven proteins were selected for epitope mapping. For cj0669 and cj0920c linear epitopes were identified. For cj0669, specificity assays revealed a specific linear epitope site. Consequently, an eleven amino acid residue sequence TLIKELKRLGI was analyzed via alanine scan, which revealed the glycine residue to be significant for binding of the antibody. The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. The findings of a specific linear epitope pave the way for a plethora of future research and the potential use in diagnostic applications such as serological screenings. Moreover, the current approach is easily adaptable to other highly relevant bacteria making it a formidable tool for the future discovery of antigens and potential biomarkers. Consequently, it is desirable to simplify the identification of structural epitopes, as this would extend the spectrum of novel epitopes to be detected.
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Affiliation(s)
- Sebastian Hoppe
- Fraunhofer Institute for Biomedical Engineering, Am Muehlenberg, Potsdam, Germany
| | - Frank F. Bier
- Fraunhofer Institute for Biomedical Engineering, Am Muehlenberg, Potsdam, Germany
- University Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
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150
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Genome Sequences of Two Emerging Non-O157 Shiga Toxin-Producing Escherichia coli Strains. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00200-13. [PMID: 23682138 PMCID: PMC3656200 DOI: 10.1128/genomea.00200-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) causes severe illness in humans, including hemorrhagic colitis and hemolytic uremic syndrome. A parallel evolutionary model was proposed in which E. coli strains of distinct phylogenies independently integrate Shiga toxin-encoding genes and evolve into STEC. We report the draft genomes of two emerging non-O157 STEC strains.
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