Genes that move the window of viability of life: Lessons from bacteria thriving at the cold extreme

de Lorenzo, Víctor

doi:10.1002/bies.201000101

Cited by 11 publications

(7 citation statements)

References 28 publications

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“…Stabilized MetA proteins partially suppressed the temperature-sensitive phenotype of both dnaK and triple protease deficient mutants. Because improving the growth of E. coli at higher temperatures has an immediate application in realizing the bacterial cell factory, this improvement might also facilitate the identification of target genes and proteins, enabling thermotolerance or improved growth at higher operating temperatures [28-30]. …”

Section: Discussionmentioning

confidence: 99%

Stabilized homoserine o-succinyltransferases (MetA) or L-methionine partially recovers the growth defect in Escherichia coli lacking ATP-dependent proteases or the DnaK chaperone

2013

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BackgroundThe growth of Escherichia coli at elevated temperatures is limited due to the inherent instability of homoserine o-succinyltransferase, MetA, which is the first enzyme in the methionine biosynthesis pathway. MetA is also unstable under other stressful conditions, such as weak organic acids and oxidative stress. The MetA protein unfolds, even at 25°C, forms considerable aggregates at 37°C and completely aggregates at 44°C.ResultsWe extended the MetA mutation studies using a consensus concept based on statistics and sequence database analysis to predict the point mutations resulting in increased MetA stability. In this study, four single amino acid substitutions (Q96K, I124L, I229Y and F247Y) in MetA designed according to the consensus concept and using the I-mutant2.0 modeling tool conferred accelerated growth on the E. coli strain WE at 44°C. MetA mutants that enabled E. coli growth at higher temperatures did not display increased melting temperatures (Tm) or enhanced catalytic activity but did show improved in vivo stability at mild (37°C) and elevated (44°C) temperatures. Notably, we observed that the stabilized MetA mutants partially recovered the growth defects of E. coli mutants in which ATP-dependent proteases or the DnaK chaperone was deleted. These results suggest that the impaired growth of these E. coli mutants primarily reflect the inherent instability of MetA and, thus, the methionine supply. As further evidence, the addition of methionine recovered most of the growth defects in mutants lacking either ATP-dependent proteases or the DnaK chaperone.ConclusionsA collection of stable single-residue mutated MetA enzymes were constructed and investigated as background for engineering the stabilized mutants. In summary, the mutations in a single gene, metA, reframe the window of growth temperature in both normal and mutant E. coli strains.

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Section: Discussionmentioning

confidence: 99%

Stabilized homoserine o-succinyltransferases (MetA) or L-methionine partially recovers the growth defect in Escherichia coli lacking ATP-dependent proteases or the DnaK chaperone

2013

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“…Information on the metabolic capabilities of microorganisms at very low temperatures has provided a new perspective on microbial survival strategies in the Earth's cryosphere (12,15,16); however, specific knowledge about their physiology under frozen conditions is still very limited. More precisely, while it is clear that DNA damage and repair are highly relevant to microbial survival, it is not known if microorganisms have the capacity to repair DNA damage under the conditions existing in an ice matrix (i.e., high ionic strength and low water activity and temperature).…”

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confidence: 99%

DNA Double-Strand Break Repair at −15°C

Dieser

Battista

Christner

2013

Appl Environ Microbiol

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The survival of microorganisms in ancient glacial ice and permafrost has been ascribed to their ability to persist in a dormant, metabolically inert state. An alternative possibility, supported by experimental data, is that microorganisms in frozen matrices are able to sustain a level of metabolic function that is sufficient for cellular repair and maintenance. To examine this experimentally, frozen populations of Psychrobacter arcticus 273-4 were exposed to ionizing radiation (IR) to simulate the damage incurred from natural background IR sources in the permafrost environment from over ϳ225 kiloyears (ky). High-molecularweight DNA was fragmented by exposure to 450 Gy of IR, which introduced an average of 16 double-strand breaks (DSBs) per chromosome. During incubation at ؊15°C for 505 days, P. arcticus repaired DNA DSBs in the absence of net growth. Based on the time frame for the assembly of genomic fragments by P. arcticus, the rate of DNA DSB repair was estimated at 7 to 10 DSBs year ؊1 under the conditions tested. Our results provide direct evidence for the repair of DNA lesions, extending the range of complex biochemical reactions known to occur in bacteria at frozen temperatures. Provided that sufficient energy and nutrient sources are available, a functional DNA repair mechanism would allow cells to maintain genome integrity and augment microbial survival in icy terrestrial or extraterrestrial environments. The results from decades of studying the stability of DNA in bacteria may be summarized in two uncomplicated axioms. First, genomic DNA is not inert; the genetic material will degrade with time, and damage will accumulate unless that degradation is repaired. And second, if this degradation is not reversed, the cell will die. The repair processes that cope with DNA damage are integral to life, and it is assumed that all species express means of maintaining genetic integrity.The importance of DNA repair to cell viability motivated extensive study of the biochemistry and molecular biology of these repair processes in model organisms such as Escherichia coli (1). Although the advantages of using this species for such studies are well documented, there is a question as to whether detailed knowledge of DNA repair in E. coli as observed under standard laboratory conditions adequately represents the full spectrum of bacterial responses to DNA damage. For instance, DNA repair is an energy-intensive activity (2, 3), but microbial species in nature rarely experience optimal conditions for growth or have access to nutrient excess. Without a generous supply of energy, cells may need to generate a more measured response, rationing available resources in a manner that prioritizes the most important tasks for survival. Moreover, viability in the absence of cellular reproduction is sustained only by cells that do not accumulate a level of damage (e.g., to DNA) that exceeds a threshold beyond which effective repair is no longer possible.Genomic DNA and viable bacteria are preserved in ancient ice and permafrost for hun...

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“…An interesting proof of principle that such a shift is possible was provided by a study that reported the reduction of the minimal growth temperature of an E. coli strain from 8°C to below 4°C upon the transfer of two chaperonin genes from a psychrophilic bacterium (33). If the genes responsible for this shift of growth range can be transferred to other hosts by horizontal gene transfer, the corresponding traits can move among bacterial species and change their niche specificities (34). Several genes encoding new metabolic functions have been found previously to be horizontally acquired by pathogens, providing a selective advantage in host tissues and access to new niches (35).…”

Section: Discussionmentioning

confidence: 99%

Acetoin Synthesis Acquisition Favors Escherichia coli Growth at Low pH

Vivijs

Moons

Aertsen

et al. 2014

Appl Environ Microbiol

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Some members of the family Enterobacteriaceae ferment sugars via the mixed-acid fermentation pathway. This yields large amounts of acids, causing strong and sometimes even lethal acidification of the environment. Other family members employ the 2,3-butanediol fermentation pathway, which generates comparatively less acidic and more neutral end products, such as acetoin and 2,3-butanediol. In this work, we equipped Escherichia coli MG1655 with the budAB operon, encoding the acetoin pathway, from Serratia plymuthica RVH1 and investigated how this affected the ability of E. coli to cope with acid stress during growth. Acetoin fermentation prevented lethal medium acidification by E. coli in lysogeny broth (LB) supplemented with glucose. It also supported growth and higher stationary-phase cell densities in acidified LB broth with glucose (pH 4.10 to 4.50) and in tomato juice (pH 4.40 to 5.00) and reduced the minimal pH at which growth could be initiated. On the other hand, the acetoin-producing strain was outcompeted by the nonproducer in a mixed-culture experiment at low pH, suggesting a fitness cost associated with acetoin production. Finally, we showed that acetoin production profoundly changes the appearance of E. coli on several diagnostic culture media. Natural E. coli strains that have laterally acquired budAB genes may therefore have escaped detection thus far. This study demonstrates the potential importance of acetoin fermentation in the ecology of E. coli in the food chain and contributes to a better understanding of the microbiological stability and safety of acidic foods.

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Genes that move the window of viability of life: Lessons from bacteria thriving at the cold extreme

Cited by 11 publications

References 28 publications

Stabilized homoserine o-succinyltransferases (MetA) or L-methionine partially recovers the growth defect in Escherichia coli lacking ATP-dependent proteases or the DnaK chaperone

Stabilized homoserine o-succinyltransferases (MetA) or L-methionine partially recovers the growth defect in Escherichia coli lacking ATP-dependent proteases or the DnaK chaperone

DNA Double-Strand Break Repair at −15°C

Acetoin Synthesis Acquisition Favors Escherichia coli Growth at Low pH

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