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LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022; 4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.
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Affiliation(s)
- Nicole LeBlanc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Nicole LeBlanc,
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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Construction of a minimal genome as a chassis for synthetic biology. Essays Biochem 2016; 60:337-346. [DOI: 10.1042/ebc20160024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.
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Genome variations associated with viral susceptibility and calcification in Emiliania huxleyi. PLoS One 2013; 8:e80684. [PMID: 24260453 PMCID: PMC3834299 DOI: 10.1371/journal.pone.0080684] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 10/10/2013] [Indexed: 11/19/2022] Open
Abstract
Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies.
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Two rep genes in small cryptic plasmid pKST21 of Escherichia coli. Curr Microbiol 2013; 67:437-41. [PMID: 23680975 DOI: 10.1007/s00284-013-0386-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/17/2013] [Indexed: 10/26/2022]
Abstract
The complete nucleotide sequence of a small cryptic plasmid pKST21 from Escherichia coli was determined. This plasmid is 1,460 bp long with an overall GC content of 51 %. Based on sequence analysis, the presence of two segments with different average GC density was observed. The segment with higher GC content revealed 98-90 % similarity to several small plasmids of E. coli and to pCR1 from Gram-positive Corynebacterium renale. Plasmid pKST21 possesses two conversely oriented open reading frames encoding proteins with a high degree of amino acid identity to Rep proteins involved in replication. ORF1 encodes replication protein similar to RepA protein of Bartonella tribocorum or Bacillus cereus plasmids or to the putative plasmid Rep protein from ecologically close Selenomonas ruminantium. ORF2 similarly encodes a replication protein, which shares 97 % homology with Rep protein from C. renale. Genetic diversity observed in plasmid pKST21 indicates a mosaic structure of the plasmid with different segments acquired from different sources. Deletion analysis showed that both fragments carrying the repA and repB genes are necessary for the replication of pKST21 in E. coli. The presence of plasmid with the same gene composition was revealed in 14 % of tested E. coli isolates from the rumen of sheep. All these strains produced identical ERIC-PCR profiles indicating isogenic origin of the strain and lack of horizontal gene transfer of pKST21 plasmid.
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Kaderbhai NN, Broadhurst DI, Ellis DI, Goodacre R, Kell DB. Functional genomics via metabolic footprinting: monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry. Comp Funct Genomics 2010; 4:376-91. [PMID: 18629082 PMCID: PMC2447367 DOI: 10.1002/cfg.302] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2003] [Revised: 04/23/2003] [Accepted: 05/22/2003] [Indexed: 12/14/2022] Open
Abstract
We sought to test the hypothesis that mutant bacterial strains could be discriminated from each other on the basis of the metabolites they secrete into the medium (their
‘metabolic footprint’), using two methods of ‘global’ metabolite analysis (FT–IR and
direct injection electrospray mass spectrometry). The biological system used was
based on a published study of Escherichia coli tryptophan mutants that had been
analysed and discriminated by Yanofsky and colleagues using transcriptome analysis.
Wild-type strains supplemented with tryptophan or analogues could be discriminated
from controls using FT–IR of 24 h broths, as could each of the mutant strains in both
minimal and supplemented media. Direct injection electrospray mass spectrometry
with unit mass resolution could also be used to discriminate the strains from each
other, and had the advantage that the discrimination required the use of just two
or three masses in each case. These were determined via a genetic algorithm. Both
methods are rapid, reagentless, reproducible and cheap, and might beneficially be
extended to the analysis of gene knockout libraries.
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Affiliation(s)
- Naheed N Kaderbhai
- Institute of Biological Sciences, University of Wales, Aberystwyth, Wales Ceredigion SY23 3DD, UK
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Cygler M, Hung MN, Wagner J, Matte A. Bacterial structural genomics initiative: overview of methods and technologies applied to the process of structure determination. Methods Mol Biol 2008; 426:537-559. [PMID: 18542889 DOI: 10.1007/978-1-60327-058-8_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The focus over the last several years on increasing the number of three-dimensional structures of macromolecules by implementation of high throughput methodology has led to the establishment of dedicated structural genomics programs around the world. These worldwide efforts have in turn led to development of novel, parallelized approaches to cloning, expression, purification, and crystallization of proteins. This chapter describes in some detail the approaches and protocols that have been implemented in the Bacterial Structural Genomics Initiative.
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Affiliation(s)
- Miroslaw Cygler
- Biotechnology Research Institute, National Research Council Canada, Montreal, Canada
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Abstract
Classically, metabolism was investigated by studying molecular characteristics of enzymes and their regulators in isolation. This reductionistic approach successfully established mechanistic relationships with the immediate interacting neighbors and allowed reconstruction of network structures. Severely underdeveloped was the ability to make precise predictions about the integrated operation of pathways and networks that emerged from the typically nonlinear and complex interactions of proteins and metabolites. The burden of metabolic engineering is a consequence of this fact-one cannot yet predict with any certainty precisely what needs to be engineered to produce more complex phenotypes. What was and still is missing are concepts, methods, and algorithms to integrate data and information into a quantitatively coherent whole, as well as theoretical concepts to reliably predict the consequence of environmental stimuli or genetic interventions. This introduction and perspective to Domain 3, Metabolism and Metabolic Fluxes, starts with a brief overview of the panoply of global measurement technologies that herald the dawning of systems biology and whose impact on metabolic research is apparent throughout the Domain 3. In the middle section, applications to Escherichia coli are used to illustrate general concepts and successes of computational methods that approach metabolism as a network of interacting elements, and thus have potential to fill the gap in quantitative data and information integration. The final section highlights prospective focus areas for future metabolic research, including functional genomics, eludication of evolutionary principles, and the integration of metabolism with regulatory networks.
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Rollins DK, Zhai D, Joe AL, Guidarelli JW, Murarka A, Gonzalez R. A novel data mining method to identify assay-specific signatures in functional genomic studies. BMC Bioinformatics 2006; 7:377. [PMID: 16907975 PMCID: PMC1599756 DOI: 10.1186/1471-2105-7-377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Accepted: 08/14/2006] [Indexed: 11/25/2022] Open
Abstract
Background: The highly dimensional data produced by functional genomic (FG) studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays). Although dimensionality reduction methods such as principal component analysis (PCA) have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. Results: The proposed method (PM) is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data – a study of classification of human tissue samples and a study of E. coli cultures with different medium formulations. Conclusion We have developed a PCA-based method that effectively identifies assay-specific signatures in ranked groups of genes from the full data set in a more efficient and simplistic procedure than current approaches. Although this work demonstrates the ability of the PM to identify assay-specific signatures in DNA microarray experiments, this approach could be useful in areas such as proteomics and metabolomics.
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Affiliation(s)
- Derrick K Rollins
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Dongmei Zhai
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Alrica L Joe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jack W Guidarelli
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Abhishek Murarka
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77251-1892, USA
| | - Ramon Gonzalez
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77251-1892, USA
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Suzuki N, Nonaka H, Tsuge Y, Inui M, Yukawa H. New multiple-deletion method for the Corynebacterium glutamicum genome, using a mutant lox sequence. Appl Environ Microbiol 2006; 71:8472-80. [PMID: 16332837 PMCID: PMC1317446 DOI: 10.1128/aem.71.12.8472-8480.2005] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to the difficulty of multiple deletions using the Cre/loxP system, a simple, markerless multiple-deletion method based on a Cre/mutant lox system combining a right-element (RE) mutant lox site with a left-element (LE) mutant lox site was employed for large-scale genome rearrangements in Corynebacterium glutamicum. Eight distinct genomic regions that had been identified previously by comparative analysis of C. glutamicum R and C. glutamicum 13032 genomes were targeted for deletion. By homologous recombination, LE and RE mutant lox sites were integrated at each end of a target region. Highly efficient and accurate deletions between the two chromosomal mutant lox sites in the presence of Cre recombinase were realized. A deletion mutant lacking 190 kb of chromosomal regions, encoding a total of 188 open reading frames (ORFs), was obtained. These deletions represent the largest genomic excisions in C. glutamicum reported to date. Despite the loss of numerous predicted ORFs, the mutant exhibited normal growth under standard laboratory conditions. The Cre/loxP system using a pair of mutant lox sites provides a new, efficient genome rearrangement technique for C. glutamicum. It should facilitate the understanding of genome functions of microorganisms.
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Affiliation(s)
- Nobuaki Suzuki
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), 9-2, Kizugawadai, Kizu-Cho, Soraku-Gun, Kyoto 619-0292, Japan
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Suzuki N, Nonaka H, Tsuge Y, Okayama S, Inui M, Yukawa H. Multiple large segment deletion method for Corynebacterium glutamicum. Appl Microbiol Biotechnol 2005; 69:151-61. [PMID: 15843930 DOI: 10.1007/s00253-005-1976-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 03/18/2005] [Accepted: 03/22/2005] [Indexed: 10/25/2022]
Abstract
A precise and scarless genome excision method, employing the Cre/loxP system in concert with double-strand break (DSB)-stimulated intramolecular recombination was developed. The DSBs were mediated by the restriction endonuclease, I-SceI. It permitted multiple deletions of independent 14-, 43-, and 10-kb-long genomic regions on the Corynebacterium glutamicum genome. Accuracy of deletion was confirmed by the loss of marker genes, PCR, and sequencing of new genome joints. Eleven, 58, and 4 genes were predicted on the 14-, 43-, and 10-kb deleted regions, respectively. Although the resultant mutant lost a total of 67 kb encoding 73 genes, it still exhibited normal growth under standard laboratory conditions. Such a large segment deletion method in which multiple, successive deletions are possible is useful for genome engineering.
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Affiliation(s)
- Nobuaki Suzuki
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawadai, Kizu-Cho, Soraku-Gun, Kyoto, Japan
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Suzuki N, Okayama S, Nonaka H, Tsuge Y, Inui M, Yukawa H. Large-scale engineering of the Corynebacterium glutamicum genome. Appl Environ Microbiol 2005; 71:3369-72. [PMID: 15933044 PMCID: PMC1151864 DOI: 10.1128/aem.71.6.3369-3372.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The engineering of Corynebacterium glutamicum is important for enhanced production of biochemicals. To construct an improved C. glutamicum genome, we developed a precise genome excision method based on the Cre/loxP recombination system and successfully deleted 11 distinct genomic regions identified by comparative analysis of C. glutamicum genomes. Despite the loss of several predicted open reading frames, the mutant cells exhibited normal growth under standard laboratory conditions. With a total of 250 kb (7.5% of the genome), the 11 genomic regions were loaded with cryptic prophages, transposons, and genes of unknown function which were dispensable for cell growth, indicating recent horizontal acquisitions to the genome. This provides an interesting background for functional genomic studies and can be used in the improvement of cell traits.
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Affiliation(s)
- Nobuaki Suzuki
- Microbiology Research Group, Research Institute of Innovative Technology for Earth (RITE), 9-2, Kizugawadai, Kizu-Cho, Soraku-Gun, Kyoto 619-0292, Japan
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Metfies K, Medlin L. Ribosomal RNA probes and microarrays: their potential use in assessing microbial biodiversity. Methods Enzymol 2005; 395:258-78. [PMID: 15865972 DOI: 10.1016/s0076-6879(05)95016-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The awareness that global biological diversity is affected by numerous, mostly human-made threats has made biodiversity assessment an important scientific issue for decades. Biodiversity includes different levels of complexity, such as community diversity, habitat diversity, genetic diversity, and species diversity. The application of molecular methods to answer ecological questions permits issues of biodiversity to be addressed at all levels. Microorganisms dominate global biological diversity in terms of their species numbers. However, their small size and limited morphological features make it challenging to obtain a comprehensive view of their biodiversity. The application of ribosomal RNA (rRNA) probes contributes significantly to the assessment of biodiversity at the molecular level. DNA microarrays offer a great potential to facilitate the application of molecular probes and other DNA analytical methods to answer ecological and biodiversity questions. We provide an introduction into the application of rRNA probes and DNA microarrays for the assessment of microbial biodiversity, as well as protocols for the implementation of DNA microarrays.
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Affiliation(s)
- Katja Metfies
- Alfred Wegener Institute, D-27570 Bremerhaven, Germany
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Misra RV, Horler RSP, Reindl W, Goryanin II, Thomas GH. EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res 2005; 33:D329-33. [PMID: 15608209 PMCID: PMC539982 DOI: 10.1093/nar/gki028] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
EchoBASE (http://www.ecoli-york.org) is a relational database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. Its aim is to collate information from a wide range of sources to provide clues to the functions of the approximately 1500 gene products that have no confirmed cellular function. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. Experiments that can be held within EchoBASE include proteomics studies, microarray data, protein–protein interaction data, structural data and bioinformatics studies. EchoBASE also contains annotated information on ‘orphan’ enzyme activities from this microbe to aid characterization of the proteins that catalyse these elusive biochemical reactions.
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Affiliation(s)
- Raju V Misra
- Department of Biology (Area 10), University of York, PO Box 373,York, YO10 5YW, UK
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Fang G, Ho C, Qiu Y, Cubas V, Yu Z, Cabau C, Cheung F, Moszer I, Danchin A. Specialized microbial databases for inductive exploration of microbial genome sequences. BMC Genomics 2005; 6:14. [PMID: 15698474 PMCID: PMC549560 DOI: 10.1186/1471-2164-6-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 02/07/2005] [Indexed: 11/10/2022] Open
Abstract
Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore , a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya) has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis) associated to related organisms for comparison.
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Affiliation(s)
- Gang Fang
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
- Unité de Génétique des Génomes Bactériens, CNRS URA2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Christine Ho
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
| | - Yaowu Qiu
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
| | - Virginie Cubas
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
| | - Zhou Yu
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
| | - Cédric Cabau
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
| | - Frankie Cheung
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
| | - Ivan Moszer
- Plate-forme Intégration et Analyse Génomiques, Genopole, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Unité de Génétique des Génomes Bactériens, CNRS URA2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Antoine Danchin
- HKU-Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
- Unité de Génétique des Génomes Bactériens, CNRS URA2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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15
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Schaechter M. Escherichia coli and Salmonella 2000: the View From Here. EcoSal Plus 2004; 1. [PMID: 26443369 DOI: 10.1128/ecosalplus.1.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Indexed: 06/05/2023]
Abstract
In 1995, an editorial in Science (267:1575) commented that predictions made some 25 years previously regarding "Biology and the Future of Man" were largely fulfilled but that "the most revolutionary and unexpected findings were not predicted." We would be glad to do as well! As we stated at the beginning, our work as editors of the Escherichia coli and Salmonella book did not endow us with special powers of prophecy but it does permit us to express our excitement for the future. In our opinion, E. coli and S. enterica will continue to play a central role in biological research. This is not because they are intrinsically more interesting than any other bacteria, as we believe that all bacteria are equally interesting. However, knowledge builds on knowledge, and it is here that these two species continue to have a large edge not only over other microorganisms but also, for some time to come, over all other forms of life. It is interesting in this connection that biotechnology, having made detours through other microorganisms, always seems to return to E. coli.
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Assairi L, Bertrand T, Ferdinand J, Slavova-Azmanova N, Christensen M, Briozzo P, Schaeffer F, Craescu CT, Neuhard J, Bârzu O, Gilles AM. Deciphering the function of an ORF: Salmonella enterica DeoM protein is a new mutarotase specific for deoxyribose. Protein Sci 2004; 13:1295-303. [PMID: 15075407 PMCID: PMC2286760 DOI: 10.1110/ps.03566004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We identified in Salmonella enterica serovar Typhi a cluster of four genes encoding a deoxyribokinase (DeoK), a putative permease (DeoP), a repressor (DeoQ), and an open reading frame encoding a 337 amino acid residues protein of unknown function. We show that the latter protein, called DeoM, is a hexamer whose synthesis is increased by a factor over 5 after induction with deoxyribose. The CD spectrum of the purified recombinant protein indicated a dominant contribution of betatype secondary structure and a small content of alpha-helix. Temperature and guanidinium hydrochloride induced denaturation of DeoM indicated that the hexamer dissociation and monomer unfolding are coupled processes. DeoM exhibits 12.5% and 15% sequence identity with galactose mutarotase from Lactococcus lactis and respectively Escherichia coli, which suggested that these three proteins share similar functions. Polarimetric experiments demonstrated that DeoM is a mutarotase with high specificity for deoxyribose. Site-directed mutagenesis of His183 in DeoM, corresponding to a catalytically active residue in GalM, yielded an almost inactive deoxyribose mutarotase. DeoM was crystallized and diffraction data collected for two crystal systems, confirmed its hexameric state. The possible role of the protein and of the entire gene cluster is discussed in connection with the energy metabolism of S. enterica under particular growth conditions.
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Affiliation(s)
- Liliane Assairi
- Laboratoire de Chimie Structurale des Macromolécules, Unité de Recherche Associeé 2185 du Cantre National de la Recherche Scientifique, Institut Pasteur, 75724 Paris 15, France
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Carroll PM, Dougherty B, Ross-Macdonald P, Browman K, FitzGerald K. Model systems in drug discovery: chemical genetics meets genomics. Pharmacol Ther 2003; 99:183-220. [PMID: 12888112 DOI: 10.1016/s0163-7258(03)00059-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Animal model systems are an intricate part of the discovery and development of new medicines. The sequencing of not only the human genome but also those of the various pathogenic bacteria, the nematode Caenorhabditis elegans, the fruitfly Drosophila, and the mouse has enabled the discovery of new drug targets to push forward at an unprecedented pace. The knowledge and tools in these "model" systems are allowing researchers to carry out experiments more efficiently and are uncovering previously hidden biological connections. While the history of bacteria, yeast, and mice in drug discovery are long, their roles are ever evolving. In contrast, the history of Drosophila and C. elegans at pharmaceutical companies is short. We will briefly review the historic role of each model organism in drug discovery and then update the readers as to the abilities and liabilities of each model within the context of drug development.
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Affiliation(s)
- Pamela M Carroll
- Department of Applied Genomics, Bristol-Myers Squibb, Pennington NJ 08534, USA
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18
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Abstract
Most proteins have been formed by gene duplication, recombination, and divergence. Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes.
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Affiliation(s)
- Cyrus Chothia
- Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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19
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Zhang H, Javor GT. Regulation of the isofunctional genes ubiD and ubiX of the ubiquinone biosynthetic pathway of Escherichia coli. FEMS Microbiol Lett 2003; 223:67-72. [PMID: 12799002 DOI: 10.1016/s0378-1097(03)00343-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The expressions of the isofunctional genes ubiD and ubiX of the ubiquinone biosynthetic pathway of Escherichia coli were compared under a variety of growth conditions and in several genetic backgrounds. LacZ operon fusions were constructed and were inserted in single copies into strain MC4100 and into its fnr, arcA or hemA carrying derivatives. During aerobic growth the expressions of both ubiD and ubiX depended on the carbon source: succinate>glycerol>glucose. Mutations in fnr, arcA or hemA increased the expressions of both genes. During anaerobic growth in LB medium glucose strongly inhibited the expression of ubiD but not of ubiX.
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Affiliation(s)
- Haitao Zhang
- Department of Biochemistry, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA
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20
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Cheung KJ, Badarinarayana V, Selinger DW, Janse D, Church GM. A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res 2003; 13:206-15. [PMID: 12566398 PMCID: PMC420364 DOI: 10.1101/gr.401003] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Changes in DNA supercoiling are induced by a wide range of environmental stresses in Escherichia coli, but the physiological significance of these responses remains unclear. We now demonstrate that an increase in negative supercoiling is necessary for transcriptional activation of a large subset of osmotic stress-response genes. Using a microarray-based approach, we have characterized supercoiling-dependent gene transcription by expression profiling under conditions of high salt, in conjunction with the microbial antibiotics novobiocin, pefloxacin, and chloramphenicol. Algorithmic clustering and statistical measures for gauging cellular function show that this subset is enriched for genes critical in osmoprotectant transport/synthesis and rpoS-driven stationary phase adaptation. Transcription factor binding site analysis also supports regulation by the global stress sigma factor rpoS. In addition, these studies implicate 60 uncharacterized genes in the osmotic stress regulon, and offer evidence for a broader role for supercoiling in the control of stress-induced transcription.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Cytoprotection/drug effects
- Cytoprotection/genetics
- DNA Gyrase/drug effects
- DNA Gyrase/genetics
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- DNA, Bacterial/genetics
- DNA, Superhelical/genetics
- DNA, Superhelical/physiology
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/physiology
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Gene Expression Profiling/methods
- Gene Expression Regulation, Bacterial/drug effects
- Gene Expression Regulation, Bacterial/genetics
- Gene Expression Regulation, Bacterial/physiology
- Genome, Bacterial
- Multigene Family/drug effects
- Multigene Family/genetics
- Novobiocin/pharmacology
- Oligonucleotide Array Sequence Analysis/methods
- Osmotic Pressure
- Pefloxacin/pharmacology
- Potassium/metabolism
- Sigma Factor/genetics
- Sodium Chloride/pharmacology
- Stress, Mechanical
- Temperature
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
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Affiliation(s)
- Kevin J Cheung
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Salmelin C, Vilpo J. Induction of SOS response, cellular efflux and oxidative stress response genes by chlorambucil in DNA repair-deficient Escherichia coli cells (ada, ogt and mutS). Mutat Res 2003; 522:33-44. [PMID: 12517410 DOI: 10.1016/s0027-5107(02)00231-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chlorambucil (CLB) is a bifunctional alkylating drug widely used as an anticancer agent and as an immunosuppressant. It is known to be mutagenic, teratogenic and carcinogenic. The cellular actions of CLB have remained poorly investigated. It is very likely that DNA damage and its repair are the key elements determining the destiny of CLB-exposed cells. We investigated the role of two specific DNA repair pathways involved in CLB-induced mutagenicity and gene expression changes by using Escherichia coli strains lacking either (i) two DNA methyltransferase functions (O(6)-methylguanine-DNA methyltransferase I (ada) and II (ogt)), or (ii) mismatch repair (MutS (mutS)). Mutagenicity was determined as the development of ciproxin and rifampicin resistance and the gene expression changes were assessed using expression profiling of all E. coli 4290 open reading frames (ORFs) by cDNA array. Chlorambucil-induced mutants in mutS cells, implying the importance of mismatch repair in preventing CLB-induced mutations. It also induced mutants in the ada, ogt strain, but to a lesser extent than in the wild-type strain. The simultaneous upregulation of several genes of the SOS response, cellular efflux and oxidative stress response, was demonstrated in both of the DNA repair-deficient strains but not in the wild-type cells. These and our previous results show that single-gene knock-out cells use specific gene regulation strategies to avoid mutations and cell death induced by agents such as chlorambucil.
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Affiliation(s)
- Camilla Salmelin
- Department of Clinical Chemistry, Tampere University Hospital and Tampere University Medical School, PO Box 2000, FIN-33521 Tampere, Finland.
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22
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Glasner JD, Liss P, Plunkett G, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 2003; 31:147-51. [PMID: 12519969 PMCID: PMC165572 DOI: 10.1093/nar/gkg125] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2002] [Revised: 10/23/2002] [Accepted: 10/23/2002] [Indexed: 11/12/2022] Open
Abstract
ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing community annotation of genomes and tracking of information as genome projects move from preliminary data collection through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ASAP supports three levels of users: public viewers, annotators and curators. Public viewers can currently browse updated annotation information for Escherichia coli K-12 strain MG1655, genome-wide transcript profiles from more than 50 microarray experiments and an extensive collection of mutant strains and associated phenotypic data. Annotators worldwide are currently using ASAP to participate in a community annotation project for the Erwinia chrysanthemi strain 3937 genome. Curation of the E. chrysanthemi genome annotation as well as those of additional published enterobacterial genomes is underway and will be publicly accessible in the near future.
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Affiliation(s)
- Jeremy D Glasner
- Animal Health and Biomedical Sciences, University of Wisconsin-Madison, 656 Linden Dr Madison, WI 53706-1581, USA
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23
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Saveanu C, Miron S, Borza T, Craescu CT, Labesse G, Gagyi C, Popescu A, Schaeffer F, Namane A, Laurent-Winter C, Bârzu O, Gilles AM. Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function. Protein Sci 2002; 11:2551-60. [PMID: 12381839 PMCID: PMC2373726 DOI: 10.1110/ps.0217502] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Structural genomics is a new approach in functional assignment of proteins identified via whole-genome sequencing programs. Its rationale is that nonhomologous proteins performing similar or related biological functions might have similar tertiary structure. We used dye pseudoaffinity chromatography, two-dimensional gel electrophoresis, and mass spectrometry to identify two novel Escherichia coli nucleotide-binding proteins, YnaF and YajQ. YnaF exhibited significant sequence identity with MJ0577, an ATP-binding protein from a hyperthermophile (Methanococcus jannaschii), and with UspA, a protein from Haemophilus influenzae that belongs to the Universal Stress Protein family. YnaF conserves the ATP-binding site and the dimeric structure observed in the crystal of MJ0577. The protein YajQ, present in many bacterial genomes, is missing in eukaryotes. In the absence of significant similarities of YajQ to any solved structure, we determined its structural and ligand-binding properties by NMR and isothermal titration calorimetry. We demonstrate that YajQ is composed of two domains, each centered on a beta-sheet, that are connected by two helical segments. NMR studies, corroborated with local sequence conservation among YajQ homologs in various bacteria, indicate that one of the beta-sheets is mostly involved in biological activity.
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Affiliation(s)
- Cosmin Saveanu
- Laboratoire de Chimie Structurale des Macromolécules, (CNRS URA 2185) Institut Pasteur, 75724 Paris Cédex 15, France
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24
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Dirk LMA, Williams MA, Houtz RL. Specificity of chloroplast-localized peptide deformylases as determined with peptide analogs of chloroplast-translated proteins. Arch Biochem Biophys 2002; 406:135-41. [PMID: 12234499 DOI: 10.1016/s0003-9861(02)00426-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Peptide deformylase (DEF; EC 3.5.1.88) removes the N-formyl group from nascent polypeptides. Two nuclear-encoded DEFs in Arabidopsis thaliana (At) are localized to chloroplasts, and thus, the N-termini of chloroplast-translated proteins may be a consequence of AtDEFs' substrate specificity. Using peptide analogs of select chloroplast-translated proteins, AtDEF1 activity was as much as 100-fold lower than AtDEF2 activity and showed little variance with peptide sequence. However, AtDEF2 activity was significantly influenced by peptide sequence, with the most efficiently processed substrate mimicking the N-terminus of the nascent D1 polypeptide, a core protein of photosystem II. Though AtDEF2's specificity was predictive of N-formyl retention for some chloroplast proteins, exceptions suggests that additional factors in vivo aid in determining the retention of an N-formyl group.
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Affiliation(s)
- Lynnette M A Dirk
- Department of Horticulture, Plant Physiology/Biochemistry/Molecular Biology Program, N-32-D Agricultural Science Center North, University of Kentucky, Lexington, KY 40546-0091, USA
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25
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Liang P, Riley M. A comparative genomics approach for studying ancestral proteins and evolution. ADVANCES IN APPLIED MICROBIOLOGY 2002; 50:39-72. [PMID: 11677689 DOI: 10.1016/s0065-2164(01)50003-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- P Liang
- Josephine Bay Paul Center for Molecular Evolution and Comparative Biology, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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26
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Abstract
The well-researched Escherichia coli genome offers the opportunity to explore the value of using protein families within a single organism to enrich functional annotation procedures and to study mechanisms of protein evolution. Having identified multimodular proteins resulting from gene fusion, and treated each module as a separate protein, nonoverlapping sequence-similar families in E. coli could be assembled. Of 3,902 proteins of length 100 residues or more, 2,415 clustered into 609 protein families. The relatedness of function among members of each family was dissected in detail. Data on paralogous protein families provides valuable information in attributing putative function to unknown genes, supplementing existing function annotation. Enzymes, transporters, and regulators represent the three major types of proteins in E. coli. They are shown to have distinctive patterns in gene duplication and divergence and gene fusion, suggesting that details of protein evolution have been different for genes in these categories. Data for the complete list of paralogous protein families and updated functional annotation for E. coli K-12 are accessible in GenProtEC (http://genprotec.mbl.edu).
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Affiliation(s)
- Ping Liang
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA.
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27
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Kolisnychenko V, Plunkett G, Herring CD, Fehér T, Pósfai J, Blattner FR, Pósfai G. Engineering a reduced Escherichia coli genome. Genome Res 2002; 12:640-7. [PMID: 11932248 PMCID: PMC187512 DOI: 10.1101/gr.217202] [Citation(s) in RCA: 202] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Our goal is to construct an improved Escherichia coli to serve both as a better model organism and as a more useful technological tool for genome science. We developed techniques for precise genomic surgery and applied them to deleting the largest K-islands of E. coli, identified by comparative genomics as recent horizontal acquisitions to the genome. They are loaded with cryptic prophages, transposons, damaged genes, and genes of unknown function. Our method leaves no scars or markers behind and can be applied sequentially. Twelve K-islands were successfully deleted, resulting in an 8.1% reduced genome size, a 9.3% reduction of gene count, and elimination of 24 of the 44 transposable elements of E. coli. These are particularly detrimental because they can mutagenize the genome or transpose into clones being propagated for sequencing, as happened in 18 places of the draft human genome sequence. We found no change in the growth rate on minimal medium, confirming the nonessential nature of these islands. This demonstration of feasibility opens the way for constructing a maximally reduced strain, which will provide a clean background for functional genomics studies, a more efficient background for use in biotechnology applications, and a unique tool for studies of genome stability and evolution.
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28
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Salmelin C, Vilpo J. Chlorambucil-induced high mutation rate and suicidal gene downregulation in a base excision repair-deficient Escherichia coli strain. Mutat Res 2002; 500:125-34. [PMID: 11890942 DOI: 10.1016/s0027-5107(02)00004-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Chlorambucil (CLB; N,N-bis(2-chloroethyl)-p-aminophenylbutyric acid) is a bifunctional alkylating agent widely used as an anticancer drug and also as an immunosuppressant. Its chemical structure and clinical experience indicate that CLB is mutagenic and carcinogenic. We have investigated the ability of CLB to induce mutations and gene expression changes in the wild-type (WT) Escherichia coli strain AB1157 and in the base excision repair-deficient (alkA1, tag-1) E. coli strain MV1932 using a rifampicin (rif) forward mutation system and a cDNA array method. The results showed that CLB is a potent mutagen in MV1932 cells compared with the E. coli WT strain AB1157, emphasizing the role of 3-methyladenine DNA glycosylases I and II in protecting the cells from CLB-induced DNA damage and subsequent mutations. Global gene expression profiling revealed that nine genes in WT E. coli and 100 genes in MV1932, of a total of 4290 genes, responded at least 2.5-fold to CLB. Interestingly, all of these MV1932 genes were downregulated, while 22% were upregulated in WT cells. The downregulated genes in MV1932 represented most (19/23) functional categories, and unexpectedly, many of them code for proteins responsible for genomic integrity. These include: (i) RecF (SOS-response, adaptive mutation), (ii) RecC (resistance to cross-linking agents), (iii) HepA (DNA repair, a possible substitute of RecBCD), (iv) Ssb (DNA recombination repair, controls RecBCD), and (v) SbcC (genetic recombination). Our results strongly suggest that in addition to the DNA damage itself, the downregulation of central protecting genes is responsible for the decreased cell survival (demonstrated in a previous work) and the increased mutation rate (this work) of DNA repair-deficient cells, when exposed to CLB.
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Affiliation(s)
- Camilla Salmelin
- Leukemia Research Laboratory, Department of Clinical Chemistry, Tampere University Hospital and Tampere University Medical School, P.O. Box 2000, FIN-33521 Tampere, Finland
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29
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Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wüthrich K, Bailey JE, Sauer U. Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol 2002; 184:152-64. [PMID: 11741855 PMCID: PMC134756 DOI: 10.1128/jb.184.1.152-164.2002] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular carbon flux distribution in wild-type and pyruvate kinase-deficient Escherichia coli was estimated using biosynthetically directed fractional 13C labeling experiments with [U-13C6]glucose in glucose- or ammonia-limited chemostats, two-dimensional nuclear magnetic resonance (NMR) spectroscopy of cellular amino acids, and a comprehensive isotopomer model. The general response to disruption of both pyruvate kinase isoenzymes in E. coli was a local flux rerouting via the combined reactions of phosphoenolpyruvate (PEP) carboxylase and malic enzyme. Responses in the pentose phosphate pathway and the tricarboxylic acid cycle were strongly dependent on the environmental conditions. In addition, high futile cycling activity via the gluconeogenic PEP carboxykinase was identified at a low dilution rate in glucose-limited chemostat culture of pyruvate kinase-deficient E. coli, with a turnover that is comparable to the specific glucose uptake rate. Furthermore, flux analysis in mutant cultures indicates that glucose uptake in E. coli is not catalyzed exclusively by the phosphotransferase system in glucose-limited cultures at a low dilution rate. Reliability of the flux estimates thus obtained was verified by statistical error analysis and by comparison to intracellular carbon flux ratios that were independently calculated from the same NMR data by metabolic flux ratio analysis.
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Affiliation(s)
- Marcel Emmerling
- Institute of Biotechnology, ETH Zürich, CH-8093 Zürich, Switzerland
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30
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Zheng Y, Roberts RJ, Kasif S. Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol 2002; 3:RESEARCH0060. [PMID: 12429059 PMCID: PMC133444 DOI: 10.1186/gb-2002-3-11-research0060] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2002] [Revised: 07/08/2002] [Accepted: 08/22/2002] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The current speed of sequencing already exceeds the capability of annotation, creating a potential bottleneck. A large proportion of the genes in microbial genomes remains uncharacterized. Here we propose a new method for functional annotation using the conservation patterns of gene clusters. If several gene clusters show the same coevolution pattern across different genomes it is reasonable to infer they are functionally related. The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome. RESULTS As a proof of concept, we applied our method to the genome of Escherichia coli K12 strain. Our method establishes functional relationships among 176 gene clusters, comprising 738 E. coli genes. The accuracy of pair phylogenetic profiles was compared with the single-gene phylogenetic profile and was shown to be higher. As a result, we are able to suggest functional roles for several previously unknown genes or unknown genomic regions in E. coli. We also examined the robustness of coevolution signals across a larger set of genomes and suggest a possible upper limit of accuracy for the phylogenetic profile methods. CONCLUSIONS The higher-order phylogenetic profiles, such as the gene-pair phylogenetic profiles, can detect functional dependences that are missed by using conventional single-gene phylogenetic profile or the chromosomal proximity method only. We show that the gene-pair phylogenetic profile is more accurate than the single-gene phylogenetic profiles.
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Affiliation(s)
- Yu Zheng
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
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31
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Abstract
Microarray technology provides a new tool with which molecular ecologists and evolutionary biologists can survey genome-wide patterns of gene expression within and among species. New analytical approaches based on analysis of variance will allow quantification of the contributions of among individual variation, genotype, sex, microenvironment, population structure, and geography to variation in gene expression. Applications of this methodology are reviewed in relation to studies of mechanisms of adaptation and divergence; delineation of developmental and physiological pathways and networks; characterization of quantitative genetic parameters at the level of transcription ('quantitative genomics'); molecular dissection of parasitism and symbiosis; and studies of the diversification of gene content. Establishment of microarray resources is neither prohibitively expensive nor technologically demanding, and a commitment to development of gene expression profiling methods for nonmodel organisms could have a tremendous impact on molecular and genetic research at the interface of organismal and population biology.
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Affiliation(s)
- Greg Gibson
- Department of Genetics, North Carolina State University, Gardner Hall, Raleigh, NC 27695-7614, USA.
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32
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Díaz E, Ferrández A, Prieto MA, García JL. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev 2001; 65:523-69, table of contents. [PMID: 11729263 PMCID: PMC99040 DOI: 10.1128/mmbr.65.4.523-569.2001] [Citation(s) in RCA: 288] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications.
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Affiliation(s)
- E Díaz
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
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33
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Van Dyk TK, DeRose EJ, Gonye GE. LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains. J Bacteriol 2001; 183:5496-505. [PMID: 11544210 PMCID: PMC95439 DOI: 10.1128/jb.183.19.5496-5505.2001] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A sequenced collection of plasmid-borne random fusions of Escherichia coli DNA to a Photorhabdus luminescens luxCDABE reporter was used as a starting point to select a set of 689 nonredundant functional gene fusions. This group, called LuxArray 1.0, represented 27% of the predicted transcriptional units in E. coli. High-density printing of the LuxArray 1.0 reporter strains to membranes on agar plates was used for simultaneous reporter gene assays of gene expression. The cellular response to nalidixic acid perturbation was analyzed using this format. As expected, fusions to promoters of LexA-controlled SOS-responsive genes dinG, dinB, uvrA, and ydjM were found to be upregulated in the presence of nalidixic acid. In addition, six fusions to genes not previously known to be induced by nalidixic acid were also reproducibly upregulated. The responses of two of these, fusions to oraA and yigN, were induced in a LexA-dependent manner by both nalidixic acid and mitomycin C, identifying these as members of the LexA regulon. The responses of the other four were neither induced by mitomycin C nor dependent on lexA function. Thus, the promoters of ycgH, intG, rihC, and a putative operon consisting of lpxA, lpxB, rnhB, and dnaE were not generally DNA damage responsive and represent a more specific response to nalidixic acid. These results demonstrate that cellular arrays of reporter gene fusions are an important alternative to DNA arrays for genomewide transcriptional analyses.
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Affiliation(s)
- T K Van Dyk
- Central Research and Development Department, DuPont Company, Wilmington, Delaware 19880-0173, USA.
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34
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Serres MH, Riley M. MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. MICROBIAL & COMPARATIVE GENOMICS 2001; 5:205-22. [PMID: 11471834 DOI: 10.1089/omi.1.2000.5.205] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An enriched classification system for cellular functions of gene products of Escherichia coli K-12 was developed based on the initial classification by Riley. In the new classification scheme, MultiFun, cellular functions are divided into 10 major categories: Metabolism, Information Transfer, Regulation, Transport, Cell Processes, Cell Structure, Location, Extra-chromosomal Origin, DNA Site, and Cryptic Gene. These major categories are further sub-divided into a hierarchical scheme. Two thousand nine hundred twenty-two gene products of E. coli K-12 were assigned to one or more functions depending on the role they play in the cell. Functional assignments were made to 66% of E. coli gene products, ranging from 1 to 16 assignments per gene product. The expansion of cellular function categories and the assignment to more than one category (multifunction) provides a more complete description of the gene products and their roles and hence better reflects the functional complexity of organisms. We believe this classification system will be useful in the field of genome analysis, both for annotation purposes and for comparative studies. The functional classification scheme and the cellular function assignments made to E. coli gene products can be accessed from the web at the databases GenProtEC (http://genprotec.mbl.edu) and EcoCyc (http://www.ecocyc.org).
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Affiliation(s)
- M H Serres
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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Nahum LA, Riley M. Divergence of function in sequence-related groups of Escherichia coli proteins. Genome Res 2001; 11:1375-81. [PMID: 11483578 PMCID: PMC311106 DOI: 10.1101/gr.180901] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2001] [Accepted: 05/14/2001] [Indexed: 11/24/2022]
Abstract
The most prominent mechanism of molecular evolution is believed to have been duplication and divergence of genes. Proteins that belong to sequence-related groups in any one organism are candidates to have emerged from such a process and to share a common ancestor. Groups of proteins in Escherichia coli having sequence similarity are mostly composed of proteins with closely related function, but some groups comprise proteins with unrelated functions. In order to understand how function can change while sequences remain similar, we have examined some of these groups in detail. The enzymes analyzed in this work include representatives of amidotransferases, phosphotransferases, decarboxylases, and others. Most sequence-related groups contain enzymes that are in the same classes of Enzyme Commission (EC) numbers. We have concentrated on groups that are heterogeneous in that respect, and also on groups containing more than one enzyme of any pathway. We find that although the EC number may differ, the reaction chemistry of these sequence-related proteins is the same or very similar. Some of these families illustrate how diversification has taken place in evolution, using common features of either reaction chemistry or ligand specificity, or both, to create catalysts for different kinds of biochemical reactions. This information has relevance to the area of functional genomics in which the activities of gene products of unknown reading frames are attributed by analogy to the functions of sequence-related proteins of known function.
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Affiliation(s)
- L A Nahum
- The Josephine Bay Paul Center-Marine Biological Laboratory, Woods Hole, Massachusetts 02543-1015, USA
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Abstract
Five years after the publication of the second edition of the reference book Escherichia coli and Salmonella: Cellular and Molecular Biology, and on the eve of launching a successor venture, the editors and colleagues examine where we stand in our quest for an understanding of these organisms. The main areas selected for this brief inquiry are genomics, evolution, molecular multifunctionality, functional backups, regulation of gene expression, cell biology, sensing of the environment, and ecology.
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Affiliation(s)
- M Schaechter
- San Diego State University, San Diego, California, USA.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2447210 DOI: 10.1002/cfg.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M. A functional update of the Escherichia coli K-12 genome. Genome Biol 2001; 2:RESEARCH0035. [PMID: 11574054 PMCID: PMC56896 DOI: 10.1186/gb-2001-2-9-research0035] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Revised: 06/08/2001] [Accepted: 07/10/2001] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. RESULTS The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. CONCLUSIONS Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.
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Affiliation(s)
- M H Serres
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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MultiFun, a Multifunctional Classification Scheme forEscherichia coliK-12 Gene Products. ACTA ACUST UNITED AC 2000. [DOI: 10.1089/mcg.2000.5.205] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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