Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, Avenida Dr. Aiguader 88, 08003 Barcelona, Spain.
Science (Impact Factor: 33.61). 11/2009; 326(5957):1263-8. DOI: 10.1126/science.1177263
Source: PubMed


To understand basic principles of bacterial metabolism organization and regulation, but also the impact of genome size, we systematically studied one of the smallest bacteria, Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients. More than 1300 growth curves were recorded in the presence of various nutrient concentrations. Measurements of biomass indicators, metabolites, and 13C-glucose experiments provided information on directionality, fluxes, and energetics; integration with transcription profiling enabled the global analysis of metabolic regulation. Compared with more complex bacteria, the M. pneumoniae metabolic network has a more linear topology and contains a higher fraction of multifunctional enzymes; general features such as metabolite concentrations, cellular energetics, adaptability, and global gene expression responses are similar, however.

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Available from: Vera van Noort,
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    • "However, an accurate essentiality study is limited by the completeness of the genome annotation. Therefore, M. pneumoniae is an ideal organism due to its reduced genome size (816 kb) (Guell et al, 2009; Kuhner et al, 2009; Yus et al, 2009, 2012; Schmidl et al, 2010; Maier et al, 2011; van Noort et al, 2012; Lluch-Senar et al, 2013) and its detailed genome annotation based on experimental data. The current annotation of the M. pneumoniae genome contains 694 ORFs (32 of which are smORFs), 311 ncRNAs and 43 conventional RNAs (tRNAs, rRNAs, etc.) (Supplementary Table S2); all genes are well supported by transcriptome data, or in combination with proteome data [Supplementary Materials and Methods or for details (Wodke et al, 2014)]. "
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    ABSTRACT: Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for 10% of all ORFs, are the most frequently essential genomic components (53%), followed by conventional ORFs (49%). Essentiality of smORFs may be explained by their function as members of protein and/or DNA/RNA complexes. In larger proteins, essentiality applied to individual domains and not entire proteins, a notion we could confirm by expression of truncated domains. The fraction of essential non-coding RNAs (ncRNAs) non-overlapping with essential genes is 5% higher than of non-transcribed regions (0.9%), pointing to the important functions of the former. We found that the minimal essential genome is comprised of 33% (269,410 bp) of the M. pneumoniae genome. Our data highlight an unexpected hidden layer of smORFs with essential functions, as well as non-coding regions, thus changing the focus when aiming to define the minimal essential genome. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.
    Molecular Systems Biology 01/2015; 11(1):780. DOI:10.15252/msb.20145558 · 10.87 Impact Factor
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    • "Furthermore, bacteria engineered with an artificial network of mutually inhibitory gene coding sequences that permit adaptation to two different nutrient environments are able to adapt to a changed nutrient environment in less than an hour, in spite of the absence of pre-existing pathways (Kashiwagi et al. 2006). Finally, sequencing showed that the bacterium, M. pneumoniae, with a 'reduced genome' , which has adapted to living in nutrient rich lungs, had lost many of its transcription factors that regulate metabolism, but in spite of this both environmental stresses and metabolic insults induced complex and specific transcriptional responses similar to more complex bacteria (Yus et al. 2009). These examples indicate empirically that the adaptation to environmental stress in bacteria is only at best very loosely coupled to the genome and involves features that are not resolvable in terms of the inheritance of DNA sequence alone. "
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    ABSTRACT: We regard the basic unit of the organism, the cell, as a complex dissipative natural process functioning under the second law of thermodynamics and the principle of least action. Organisms are conglomerates of information bearing cells that optimise the efficiency of energy (nutrient) extraction from its ecosystem. Dissipative processes, such as peptide folding and protein interaction, yield phenotypic information from which form and function emerge from cell to cell interactions within the organism. Organisms, in Darwin's ‘proportional numbers’, in turn interact to minimise the free energy of their ecosystems. Genetic variation plays no role in this holistic conceptualisation of the life process.
    The Journal of Physiology 06/2014; 592(11). DOI:10.1113/jphysiol.2014.271775 · 5.04 Impact Factor
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    • "Fragmentation spectra results for the detected metabolites of S. melliferum, M. gallisepticum and A. laidlawii, and fragmentation spectra of the analyzed ion standards from the Metlin database [23] in the same experimental conditions (fixed collision energy of 20 eV). "
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    ABSTRACT: We present a systematic study of three bacterial species that belong to the class Mollicutes, the smallest and simplest bacteria, Spiroplasma melliferum, Mycoplasma gallisepticum, and Acholeplasma laidlawii. To understand the difference in the basic principles of metabolism regulation and adaptation to environmental conditions in the three species, we analyzed the metabolome of these bacteria. Metabolic pathways were reconstructed using the proteogenomic annotation data provided by our lab. The results of metabolome, proteome and genome profiling suggest a fundamental difference in the adaptation of the three closely related Mollicute species to stress conditions. As the transaldolase is not annotated in Mollicutes, we propose variants of the pentose phosphate pathway catalyzed by annotated enzymes for three species. For metabolite detection we employed high performance liquid chromatography coupled with mass spectrometry. We used liquid chromatography method - hydrophilic interaction chromatography with silica column - as it effectively separates highly polar cellular metabolites prior to their detection by mass spectrometer.
    PLoS ONE 03/2014; 9(3):e89312. DOI:10.1371/journal.pone.0089312 · 3.23 Impact Factor
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