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Nguyen HN, Markin A, Friedberg I, Eulenstein O. Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it. Bioinformatics 2021; 36:i668-i674. [PMID: 33381825 PMCID: PMC7773486 DOI: 10.1093/bioinformatics/btaa794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 11/25/2022] Open
Abstract
Motivation The evolution of complexity is one of the most fascinating and challenging problems in modern biology, and tracing the evolution of complex traits is an open problem. In bacteria, operons and gene blocks provide a model of tractable evolutionary complexity at the genomic level. Gene blocks are structures of co-located genes with related functions, and operons are gene blocks whose genes are co-transcribed on a single mRNA molecule. The genes in operons and gene blocks typically work together in the same system or molecular complex. Previously, we proposed a method that explains the evolution of orthologous gene blocks (orthoblocks) as a combination of a small set of events that take place in vertical evolution from common ancestors. A heuristic method was proposed to solve this problem. However, no study was done to identify the complexity of the problem. Results Here, we establish that finding the homologous gene block problem is NP-hard and APX-hard. We have developed a greedy algorithm that runs in polynomial time and guarantees an O(lnn) approximation. In addition, we formalize our problem as an integer linear program problem and solve it using the PuLP package and the standard CPLEX algorithm. Our exploration of several candidate operons reveals that our new method provides more optimal results than the results from the heuristic approach, and is significantly faster. Availability and implementation The software and data accompanying this paper are available under the GPLv3 and CC0 license respectively on: https://github.com/nguyenngochuy91/Relevant-Operon.
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Affiliation(s)
- Huy N Nguyen
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.,Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Alexey Markin
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.,Interdepartmental Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Oliver Eulenstein
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA.,Interdepartmental Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
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2
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Miskovic L, Béal J, Moret M, Hatzimanikatis V. Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties. PLoS Comput Biol 2019; 15:e1007242. [PMID: 31430276 PMCID: PMC6716680 DOI: 10.1371/journal.pcbi.1007242] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/30/2019] [Accepted: 07/03/2019] [Indexed: 11/18/2022] Open
Abstract
A persistent obstacle for constructing kinetic models of metabolism is uncertainty in the kinetic properties of enzymes. Currently, available methods for building kinetic models can cope indirectly with uncertainties by integrating data from different biological levels and origins into models. In this study, we use the recently proposed computational approach iSCHRUNK (in Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models), which combines Monte Carlo parameter sampling methods and machine learning techniques, in the context of Bayesian inference. Monte Carlo parameter sampling methods allow us to exploit synergies between different data sources and generate a population of kinetic models that are consistent with the available data and physicochemical laws. The machine learning allows us to data-mine the a priori generated kinetic parameters together with the integrated datasets and derive posterior distributions of kinetic parameters consistent with the observed physiology. In this work, we used iSCHRUNK to address a design question: can we identify which are the kinetic parameters and what are their values that give rise to a desired metabolic behavior? Such information is important for a wide variety of studies ranging from biotechnology to medicine. To illustrate the proposed methodology, we performed Metabolic Control Analysis, computed the flux control coefficients of the xylose uptake (XTR), and identified parameters that ensure a rate improvement of XTR in a glucose-xylose co-utilizing S. cerevisiae strain. Our results indicate that only three kinetic parameters need to be accurately characterized to describe the studied physiology, and ultimately to design and control the desired responses of the metabolism. This framework paves the way for a new generation of methods that will systematically integrate the wealth of available omics data and efficiently extract the information necessary for metabolic engineering and synthetic biology decisions. Kinetic models are the most promising tool for understanding the complex dynamic behavior of living cells. The primary goal of kinetic models is to capture the properties of the metabolic networks as a whole, and thus we need large-scale models for dependable in silico analyses of metabolism. However, uncertainty in kinetic parameters impedes the development of kinetic models, and uncertainty levels increase with the model size. Tools that will address the issues with parameter uncertainty and that will be able to reduce the uncertainty propagation through the system are therefore needed. In this work, we applied a method called iSCHRUNK that combines parameter sampling and machine learning techniques to characterize the uncertainties and uncover intricate relationships between the parameters of kinetic models and the responses of the metabolic network. The proposed method allowed us to identify a small number of parameters that determine the responses in the network regardless of the values of other parameters. As a consequence, in future studies of metabolism, it will be sufficient to explore a reduced kinetic space, and more comprehensive analyses of large-scale and genome-scale metabolic networks will be computationally tractable.
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Affiliation(s)
- Ljubisa Miskovic
- Laboratory of Computational Systems Biology (LCSB), EPFL, CH, Lausanne, Switzerland
| | - Jonas Béal
- Master's Program in Life Sciences and Technology, EPFL, CH, Lausanne, Switzerland
| | - Michael Moret
- Master's Program in Life Sciences and Technology, EPFL, CH, Lausanne, Switzerland
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Ream DC, Bankapur AR, Friedberg I. An event-driven approach for studying gene block evolution in bacteria. ACTA ACUST UNITED AC 2015; 31:2075-83. [PMID: 25717195 PMCID: PMC4481853 DOI: 10.1093/bioinformatics/btv128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/20/2015] [Indexed: 11/24/2022]
Abstract
Motivation: Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria. Results: We show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures. Availability and implementation: The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolution Contact:i.friedberg@miamioh.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David C Ream
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
| | - Asma R Bankapur
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
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Abstract
Omics, including genomics, proteomics, and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. The central task is to transform molecular catalogs of genes, metabolites, etc., into a dynamic understanding of symbiosis function. We review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial symbionts, and symbiotic protection of animal hosts from pathogens. As omic datasets become increasingly complex, computationally sophisticated downstream analyses are essential to reveal interactions not evident from visual inspection of the data. We discuss two approaches, phylogenomics and transcriptional clustering, that can divide the primary output of omics studies-long lists of factors-into manageable subsets, and we describe how they have been applied to analyze large datasets and generate testable hypotheses.
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Affiliation(s)
- J Chaston
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York 14853, USA
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5
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Olds BP, Coates BS, Steele LD, Sun W, Agunbiade TA, Yoon KS, Strycharz JP, Lee SH, Paige KN, Clark JM, Pittendrigh BR. Comparison of the transcriptional profiles of head and body lice. INSECT MOLECULAR BIOLOGY 2012; 21:257-268. [PMID: 22404397 DOI: 10.1111/j.1365-2583.2012.01132.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Head and body lice are both blood-feeding parasites of humans although only the body louse is a potent disease vector. In spite of numerous morphological and life history differences, head and body lice have recently been hypothesized to be ecotypes of the same species. We took a comparative genomics approach to measure nucleotide diversity by comparing expressed sequence tag data sets from head and body lice. A total of 10 771 body louse and 10 770 head louse transcripts were predicted from a combined assembly of Roche 454 and Illumina sequenced cDNAs from whole body tissues collected at all life stages and during pesticide exposure and bacterial infection treatments. Illumina reads mapped to the 10 775 draft body louse gene models from the whole genome assembly predicted nine presence/absence differences, but PCR confirmation resulted in a single gene difference. Read per million base pair estimates indicated that 14 genes showed significant differential expression between head and body lice under our treatment conditions. One novel microRNA was predicted in both lice species and 99% of the 544 transcripts from Candidatus riesia indicate that they share the same endosymbiont. Overall, few differences exist, which supports the hypothesis that these two organisms are ecotypes of the same species.
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Affiliation(s)
- Brett P Olds
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Léon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Médigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H. The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PLoS One 2011; 6:e27909. [PMID: 22125637 PMCID: PMC3220699 DOI: 10.1371/journal.pone.0027909] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 10/27/2011] [Indexed: 12/15/2022] Open
Abstract
Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.
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Affiliation(s)
- John M. Chaston
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sarah L. Tucker
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Aaron W. Andersen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Archna Bhasin
- Department of Biology, Valdosta State University, Valdosta, Georgia, United States of America
| | - Edna Bode
- Institut für Molekulare Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Institut für Molekulare Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Alexander O. Brachmann
- Institut für Molekulare Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Charles E. Cowles
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kimberly N. Cowles
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Creg Darby
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America
| | - Limaris de Léon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin Drace
- Department of Biology, Mercer University, Macon, Georgia, United States of America
| | - Zijin Du
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Alain Givaudan
- Institut National de la Recherche Agronomique-Université de Montpellier II, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Erin E. Herbert Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kelsea A. Jewell
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jennifer J. Knack
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | | | - Ryan Kukor
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anne Lanois
- Institut National de la Recherche Agronomique-Université de Montpellier II, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Phil Latreille
- Monsanto Company, St. Louis, Missouri, United States of America
| | | | - Carolyn M. Lipke
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Renyi Liu
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Xiaojun Lu
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Pradeep R. Marri
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Claudine Médigue
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Genoscope and CNRS-UMR 8030, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Evry, France
| | - Megan L. Menard
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nancy M. Miller
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Nydia Morales-Soto
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Stacie Norton
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Jean-Claude Ogier
- Institut National de la Recherche Agronomique-Université de Montpellier II, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Samantha S. Orchard
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dongjin Park
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Youngjin Park
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | | | - Darby Renneckar Sugar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gregory R. Richards
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zoé Rouy
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Genoscope and CNRS-UMR 8030, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Evry, France
| | - Brad Slominski
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kathryn Slominski
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Holly Snyder
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Brian C. Tjaden
- Department of Computer Science, Wellesley College, Wellesley, Massachusetts, United States of America
| | - Ransome van der Hoeven
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Roy D. Welch
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Cathy Wheeler
- Department of Biology, Hiram College, Hiram, Ohio, United States of America
| | - Bosong Xiang
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Sophie Gaudriault
- Institut National de la Recherche Agronomique-Université de Montpellier II, Montpellier, France
- Université Montpellier, Montpellier, France
| | - Brad Goodner
- Department of Biology, Hiram College, Hiram, Ohio, United States of America
| | - Steven C. Slater
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
| | - Steven Forst
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Barry S. Goldman
- Monsanto Company, St. Louis, Missouri, United States of America
- * E-mail: (B.Goldman); (HG-B)
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (B.Goldman); (HG-B)
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Scott JJ, Budsberg KJ, Suen G, Wixon DL, Balser TC, Currie CR. Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps. PLoS One 2010; 5:e9922. [PMID: 20360970 PMCID: PMC2847949 DOI: 10.1371/journal.pone.0009922] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 03/01/2010] [Indexed: 11/18/2022] Open
Abstract
Background Leaf-cutter ants use fresh plant material to grow a mutualistic fungus that serves as the ants' primary food source. Within fungus gardens, various plant compounds are metabolized and transformed into nutrients suitable for ant consumption. This symbiotic association produces a large amount of refuse consisting primarily of partly degraded plant material. A leaf-cutter ant colony is thus divided into two spatially and chemically distinct environments that together represent a plant biomass degradation gradient. Little is known about the microbial community structure in gardens and dumps or variation between lab and field colonies. Methodology/Principal Findings Using microbial membrane lipid analysis and a variety of community metrics, we assessed and compared the microbiota of fungus gardens and refuse dumps from both laboratory-maintained and field-collected colonies. We found that gardens contained a diverse and consistent community of microbes, dominated by Gram-negative bacteria, particularly γ-Proteobacteria and Bacteroidetes. These findings were consistent across lab and field gardens, as well as host ant taxa. In contrast, dumps were enriched for Gram-positive and anaerobic bacteria. Broad-scale clustering analyses revealed that community relatedness between samples reflected system component (gardens/dumps) rather than colony source (lab/field). At finer scales samples clustered according to colony source. Conclusions/Significance Here we report the first comparative analysis of the microbiota from leaf-cutter ant colonies. Our work reveals the presence of two distinct communities: one in the fungus garden and the other in the refuse dump. Though we find some effect of colony source on community structure, our data indicate the presence of consistently associated microbes within gardens and dumps. Substrate composition and system component appear to be the most important factor in structuring the microbial communities. These results thus suggest that resident communities are shaped by the plant degradation gradient created by ant behavior, specifically their fungiculture and waste management.
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Affiliation(s)
- Jarrod J. Scott
- United States Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Smithsonian Tropical Research Institute (STRI), Balboa, Ancon, Republic of Panamá
| | - Kevin J. Budsberg
- United States Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Soil Science, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Garret Suen
- United States Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Devin L. Wixon
- Department of Botany, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Teri C. Balser
- United States Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Soil Science, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Cameron R. Currie
- United States Department of Energy (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Smithsonian Tropical Research Institute (STRI), Balboa, Ancon, Republic of Panamá
- * E-mail:
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Daigle BJ, Srinivasan BS, Flannick JA, Novak AF, Batzoglou S. Current Progress in Static and Dynamic Modeling of Biological Networks. SYSTEMS BIOLOGY FOR SIGNALING NETWORKS 2010. [DOI: 10.1007/978-1-4419-5797-9_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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9
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Isolation and characterization of Xenorhabdus nematophila transposon insertion mutants defective in lipase activity against Tween. J Bacteriol 2009; 191:5325-31. [PMID: 19542289 DOI: 10.1128/jb.00173-09] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified Xenorhabdus nematophila transposon mutants with defects in lipase activity. One of the mutations, in yigL, a conserved gene of unknown function, resulted in attenuated virulence against Manduca sexta insects. We discuss possible connections between lipase production, YigL, and specific metabolic pathways.
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10
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Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D. Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 2009; 19:1084-92. [PMID: 19237465 DOI: 10.1101/gr.089714.108] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Identification and characterization of functional elements in the noncoding regions of genomes is an elusive and time-consuming activity whose output does not keep up with the pace of genome sequencing. Hundreds of bacterial genomes lay unexploited in terms of noncoding sequence analysis, although they may conceal a wide diversity of novel RNA genes, riboswitches, or other regulatory elements. We describe a strategy that exploits the entirety of available bacterial genomes to classify all noncoding elements of a selected reference species in a single pass. This method clusters noncoding elements based on their profile of presence among species. Most noncoding RNAs (ncRNAs) display specific signatures that enable their grouping in distinct clusters, away from sequence conservation noise and other elements such as promoters. We submitted 24 ncRNA candidates from Staphylococcus aureus to experimental validation and confirmed the presence of seven novel small RNAs or riboswitches. Besides offering a powerful method for de novo ncRNA identification, the analysis of phylogenetic profiles opens a new path toward the identification of functional relationships between co-evolving coding and noncoding elements.
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Affiliation(s)
- Antonin Marchais
- Université Paris-Sud 11, CNRS, UMR8621, Institut de Génétique et Microbiologie, F-91405 Orsay Cedex, France
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11
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Jiang Z. Protein Function Predictions Based on the Phylogenetic Profile Method. Crit Rev Biotechnol 2008; 28:233-8. [PMID: 19051102 DOI: 10.1080/07388550802512633] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol 2007; 25:1281-9. [PMID: 17965706 DOI: 10.1038/nbt1354] [Citation(s) in RCA: 267] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 10/04/2007] [Indexed: 12/11/2022]
Abstract
The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.
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Affiliation(s)
- Susanne Schneiker
- Department of Genetics, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
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Suen G, Arshinoff BI, Taylor RG, Welch RD. Practical Applications of Bacterial Functional Genomics. Biotechnol Genet Eng Rev 2007; 24:213-42. [DOI: 10.1080/02648725.2007.10648101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Suen G, Jakobsen JS, Goldman BS, Singer M, Garza AG, Welch RD. Bacterial postgenomics: the promise and peril of systems biology. J Bacteriol 2006; 188:7999-8004. [PMID: 16997947 PMCID: PMC1698175 DOI: 10.1128/jb.01195-06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Garret Suen
- Department of Biology, Syracuse University, Syracuse, New York 13244, USA
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Joshi SM, Pandey AK, Capite N, Fortune SM, Rubin EJ, Sassetti CM. Characterization of mycobacterial virulence genes through genetic interaction mapping. Proc Natl Acad Sci U S A 2006; 103:11760-5. [PMID: 16868085 PMCID: PMC1544243 DOI: 10.1073/pnas.0603179103] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We have previously shown that approximately 5% of the genes encoded by the genome of Mycobacterium tuberculosis are specifically required for the growth or survival of this bacterium during infection. This corresponds to hundreds of genes, most of which have no identifiable function. As a unique approach to characterize these genes, we developed a method to rapidly delineate functional pathways by identifying mutations that modify each other's phenotype, i.e., "genetic interactions". Using this method, we have defined a complex set of interactions between virulence genes in this pathogen, and find that the products of unlinked genes associate to form multisubunit transporters that are required for bacterial survival in the host. These findings implicate a previously undescribed family of transport systems in the pathogenesis of tuberculosis, and identify genes that are likely to function in the metabolism of their substrates. This method can be readily applied to other organisms at either the single pathway level, as described here, or at the system level to define quantitative genetic interaction networks.
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Affiliation(s)
- Swati M. Joshi
- *Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Amit K. Pandey
- *Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Nicole Capite
- *Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Christopher M. Sassetti
- *Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655; and
- To whom correspondence should be addressed. E-mail:
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Integrated Protein Interaction Networks for 11 Microbes. LECTURE NOTES IN COMPUTER SCIENCE 2006. [DOI: 10.1007/11732990_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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