The Blueprint of a Minimal Cell: MiniBacillus

Reuß, Daniel R.; Commichau, Fabian M.; Gundlach, Jan; Zhu, Bingyao; Stülke, Jörg

doi:10.1128/mmbr.00029-16

Cited by 64 publications

(74 citation statements)

References 177 publications

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“…1; Table 1). The deletions were designed following the outline of a minimal cell based on B. subtilis (Reuß et al 2016a). First priority was given to large dispensable regions and cellular functions, which are not necessary for the survival of the cell (e.g., sporulation, antibiotic production, motility, metabolism of secondary carbon sources, and genes of unknown functions).…”

Section: Construction Of Genome-reduced Strainsmentioning

confidence: 99%

“…Genes can also be essential because of their role in the protection of the cell against harmful molecules (Commichau et al 2013). Large-scale studies identified 253 and 295 genes as being individually essential for growth of B. subtilis and E. coli, respectively, on rich medium at 37°C (Gerdes et al 2003;Kobayashi et al 2003;Reuß et al 2016a). Although the E. coli genome contains 13 essential genes of unknown function, B. subtilis possesses only one essential gene whose function remains to be discovered (Juhas et al 2014).…”

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confidence: 99%

“…For both E. coli and B. subtilis, it remains to be evaluated how far the genome reduction can go. However, given the different cellular organization and biology of E. coli, M. mycoides, and B. subtilis, genome reduction approaches with these and other bacteria are required to get a final glimpse of the very essence of life (Reuß et al 2016a;Martínez-Garcia and de Lorenzo 2016).…”

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confidence: 99%

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Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

et al. 2016

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Understanding cellular life requires a comprehensive knowledge of the essential cellular functions, the components involved, and their interactions. Minimized genomes are an important tool to gain this knowledge. We have constructed strains of the model bacterium, Bacillus subtilis, whose genomes have been reduced by ∼36%. These strains are fully viable, and their growth rates in complex medium are comparable to those of wild type strains. An in-depth multi-omics analysis of the genome reduced strains revealed how the deletions affect the transcription regulatory network of the cell, translation resource allocation, and metabolism. A comparison of gene counts and resource allocation demonstrates drastic differences in the two parameters, with 50% of the genes using as little as 10% of translation capacity, whereas the 6% essential genes require 57% of the translation resources. Taken together, the results are a valuable resource on gene dispensability in B. subtilis, and they suggest the roads to further genome reduction to approach the final aim of a minimal cell in which all functions are understood.

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Section: Construction Of Genome-reduced Strainsmentioning

confidence: 99%

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confidence: 99%

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Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

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“…We are interested in the identification of the essential cellular components that are required for the viability of B. subtilis cells with the aim to construct strains that harbor only the minimal set of genes to fulfill the essential cellular functions (25,26,27). For B. subtilis, RNase Y and RNase J1 were originally described as being essential (18,19,28,29,30).…”

Section: Introductionmentioning

confidence: 99%

Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis

Benda

Woelfel

Gunka

et al. 2020

Preprint

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RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase -α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β' subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed massive decreases in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.If the continued activity of a protein may become harmful to the bacteria, it is important not only to prevent expression of the corresponding gene but also to take two important measures: (i) switch off the protein's activity and (ii) degrade the mRNA to exclude further production of the protein. The inactivation or even degradation of proteins is well documented in the model bacteria. For example, in both E. coli and B. subtilis the uptake of toxic ammonium is limited by a regulatory interaction of the ammonium transporter with GlnK, a regulatory protein of the PII family (1,2). Similarly, the uptake of potentially toxic potassium can be prevented by inhibition of potassium transporters at high environmental potassium concentrations, either by the second messenger cyclic di-AMP or by interaction with a dedicated modified signal transduction protein, PtsN (3,4,5). To prevent the accumulation of potentially harmful mRNAs, bacteria rely on a very fast mRNA turnover. Indeed, in E. coli and B. subtilis more than 80% of all transcripts have average half-lives of less than 8 minutes, as compared to about 30 minutes and 10 hours in yeast or human cells, respectively (6,7,8,9). Thus, the mRNA turnover is much faster than the generation time. The high mRNA turnover rate in bacteria contributes to the fast adaptation even in rapidly growing cells. The rapid mRNA turnover is therefore a major factor to resolve the apparent growth speed-adaptation trade-off. 4RNases are the key elements to achieve the rapid mRNA turnover in bacteria. Theses enzymes can degrade bulk mRNA in a rather unspecific manner, just depending on the accessibility of the RNA molecules as well as perform highly specific cleavages that serve to process an RNA molecule to its mature form. In all organisms, RNA degradation involves an interplay ...

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“…Describing the minimal number of genes that are non-dispensable for life is one of the main challenges in biology, specifically in regard to the rational engineering of a living system. In recent years, theoretical and experimental studies have addressed the question of what constitutes a minimal genome, mainly using prokaryotes as model organisms (1)(2)(3)(4)(5). While there are many fundamental processes common to all un-cellular life (6)(7)(8)(9), bacteria inhabit almost all known niches on the planet, from intracellular parasites to the Atacama desert (10)(11)(12).…”

Section: Introductionmentioning

confidence: 99%

Comparative Gene Essentiality across the Bacterial Domain

Shaw

Hermoso

Lluch‐Senar

et al. 2020

Preprint

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Comparative genomics among bacteria has been used to gain insight into the minimal number of conserved genes in biological pathways. Essentiality studies have provided information regarding which genes are non-dispensable (essential, E) for cell growth. Here, we integrated studies of gene conservation, essentiality and function, performed in 47 diverse bacterial species. We showed there is a modest positive correlation between genome size and number of essential genes. Interestingly, we observed a clear shift in the functions assigned to these essential genes as genome size increases. For instance, essential genes related to transcription and translation dominate small genomes. In contrast, in large genomes functions of essential genes are related with cellular processing and metabolism. Finally, and most intriguing, we found a group of genes that while being highly conserved are also typically non-essential. This suggests that some housekeeping genes confer a significant survival benefit in nature while being non-essential in vitro.

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The Blueprint of a Minimal Cell: MiniBacillus

Cited by 64 publications

References 177 publications

Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis

Comparative Gene Essentiality across the Bacterial Domain

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