Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

Yus, Eva; Maier, Tobias; Michalodimitrakis, Konstantinos; Noort, Vera van; Yamada, Takuji; Chen, Wei‐Hua; Wodke, Judith A. H.; Güell, Marc; Martínez, Sira; Bourgeois, Ronan; Kühner, Sebastian; Raineri, Emanuele; Letunić, Ivica; Kalinina, Olga V.; Rode, Michaela; Herrmann, Richard; Gutiérrez-Gallego, Ricardo; Russell, Robert B.; Gavin, Anne‐Claude; Bork, Peer; Serrano, Luís

doi:10.1126/science.1177263

Cited by 276 publications

(430 citation statements)

References 34 publications

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“…It is notable that the approach to genome streamlining seen here is fundamentally different from that seen in other very small microbes, as exemplified by recent work on the genome reduction in Mycoplasma pneumonia [22][23][24] . Although that genome has been streamlined to a very small size, it has occurred without the loss of regulatory mechanisms needed for the bacterium's interactions with 'high-energy' and highnutrient environments.…”

Section: Research Articlementioning

confidence: 86%

Genomic and functional adaptation in surface ocean planktonic prokaryotes

Yooseph

Nealson

Rusch

et al. 2010

Nature

284

261

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The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0 mm size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass. Molecular taxonomy and phylogeny1 revitalized the field of marine microbiology, allowing for the first time the realization that the 'unseen' and 'unknown' majority of uncultivated microbial taxa could be identified by their 16S ribosomal RNA genes, and identifying widespread clades of marine bacteria and archaea that had no cultivated representatives 2 . More recently, metagenomics has revealed the extent of diversity not fully explained using the available genomes of cultivated marine microbes. When the Sorcerer II Global Ocean Sampling (GOS) expedition metagenomic data were published 3,4 , it was remarkable in its duality of diversity. On the one hand, there seemed to be only a few taxonomic groups that appeared routinely in marine surface water samples. Of these groups, only three (Pelagibacter, Prochlorococcus and Synechococcus) were represented by cultivated marine microbes. On the other hand, despite their apparent ubiquity and abundance in the surface ocean, there was virtually no complete or near-complete genomic assembly of any of the cosmopolitan taxa, implying that these groups, as judged by 16S rRNA sequence, are internally extremely diverse. The GOS data set was also remarkable because of its apparent lack of relatedness to the entire collection of sequenced genomes: using a process called fragment recruitment, which is akin to in silico DNA hybridization, only a few genomes from the entire repertoire of sequenced genomes were found to have a significant number of GOS reads assigned to them.Here we use a large collection of sequenced marine genomes and metagenomic data to show the presence of two major groups in the marine surface picoplankton with striking differences in their met...

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Section: Research Articlementioning

confidence: 86%

Genomic and functional adaptation in surface ocean planktonic prokaryotes

Yooseph

Nealson

Rusch

et al. 2010

Nature

284

261

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“…On the extreme end of the spectrum, some may argue that life resists rational design, emphasizing the unpredictability and variability of living systems by mechanisms such as mutation, natural selection, and emergence. This might be deduced from the detailed and holistic studies on Mycoplasma pneumoniae (one of the bacteria with the smallest genome), which reveal an unexpected transcriptomic and proteomic complexity Yus et al 2009;Güell et al 2009) In this view, when released in natural environments synthetic systems will either be prone to die or evolve in unexpected ways. An in-between position promotes the combination of rational design and directed evolution strategies, including directed evolution (Porcar 2009).…”

Section: Controversies: Engineering and Biological Viewsmentioning

confidence: 99%

Designing de novo: interdisciplinary debates in synthetic biology

Delgado

Porcar

2013

Syst Synth Biol

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Synthetic biology is often presented as a promissory field that ambitions to produce novelty by design. The ultimate promise is the production of living systems that will perform new and desired functions in predictable ways. Nevertheless, realizing promises of novelty has not proven to be a straightforward endeavour. This paper provides an overview of, and explores the existing debates on, the possibility of designing living systems de novo as they appear in interdisciplinary talks between engineering and biological views within the field of synthetic biology. To broaden such interdisciplinary debates, we include the views from the social sciences and the humanities and we point to some fundamental sources of disagreement within the field. Different views co-exist, sometimes as controversial tensions, but sometimes also pointing to integration in the form of intermediate positions. As the field is emerging, multiple choices are possible. They will inform alternative trajectories in synthetic biology and will certainly shape its future. What direction is best is to be decided in reflexive and socially robust ways.

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“…With the aim of better understanding the kinetic properties of processive (or sequentially acting) GT2 enzymes, we here address the recombinant expression and purification of a novel GT from M. genitalium for detailed kinetic characterization of the isolated enzyme. M. genitalium is the smallest free-living organism considered a minimal cell model (39,40) and the subject of intense research in mycoplasma systems biology (41)(42)(43). Due to its reduced genome of only 580 kb and about 480 genes encoding for proteins, it lacks many metabolic pathways like amino acid, nucleotide, fatty acid, and cholesterol biosynthesis and maintains a reduced energy metabolism devoid of Krebs cycle (23,44).…”

mentioning

confidence: 99%

Expression and Characterization of a Mycoplasma genitalium Glycosyltransferase in Membrane Glycolipid Biosynthesis

Andrés¹,

Martínez²,

Planas

2011

Journal of Biological Chemistry

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Background: Glycoglycerolipids, synthesized by glycosyltransferases (glycolipid synthases), are key structural membrane components in mycoplasma. Results: M. genitalium GT MG517 has been recombinantly expressed and kinetically characterized. It is a processive GT transferring glucosyl or galactosyl residues to membrane-bound diacylglycerol, with higher monoglycosyl-than diglycosyltransferase activity. Inhibition of the enzyme results in mycoplasma growth inhibition. Conclusion: The membrane glycoglycerolipids of M. genitalium are synthesized by a single processive glycosyltransferase, GT MG517. It is proposed as a potential therapeutic target against mycoplasma infections. Significance: The essential function of GT MG517 for mycoplasma viability and the absence of glycoglycerolipids in animal host cells of mycoplasma infections make the enzyme a target for drug discovery by designing specific inhibitors.

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Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

Cited by 276 publications

References 34 publications

Genomic and functional adaptation in surface ocean planktonic prokaryotes

Genomic and functional adaptation in surface ocean planktonic prokaryotes

Designing de novo: interdisciplinary debates in synthetic biology

Expression and Characterization of a Mycoplasma genitalium Glycosyltransferase in Membrane Glycolipid Biosynthesis

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