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Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

ABSTRACT: Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of 'A' versus 'T' and 'G' versus 'C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides 'U' and 'C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides 'A' and 'G' at non-synonymous coding sites.

SUBMITTER: Chen WH

PROVIDER: S-EPMC4844684 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Chen Wei-Hua WH Chen Wei-Hua WH Lu Guanting G Bork Peer P Hu Songnian S Lercher Martin J MJ

Nature communications 20160421

Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of 'A' versus 'T' and 'G' versus 'C'), which explains nucleotide skews acro ...[more]

PMID: 27098217

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Project description:BACKGROUND:Speciation is driven by many different factors. Among those are trade-offs between different ways an organism utilizes resources, and these trade-offs can constrain the manner in which selection can optimize traits. Limited migration among allopatric populations and species interactions can also drive speciation, but here we ask if trade-offs alone are sufficient to drive speciation in the absence of other factors. RESULTS:We present a model to study the effects of trade-offs on specialization and adaptive radiation in asexual organisms based solely on competition for limiting resources, where trade-offs are stronger the greater an organism's ability to utilize resources. In this model resources are perfectly substitutable, and fitness is derived from the consumption of these resources. The model contains no spatial parameters, and is therefore strictly sympatric. We quantify the degree of specialization by the number of ecotypes evolved and the niche breadth of the population, and observe that these are sensitive to resource influx and trade-offs. Resource influx has a strong effect on the degree of specialization, with a clear transition between minimal diversification at high influx and multiple species evolving at low resource influx. At low resource influx the degree of specialization further depends on the strength of the trade-offs, with more ecotypes evolving the stronger trade-offs are. The specialized organisms persist through negative frequency-dependent selection. In addition, by analyzing one of the evolutionary radiations in greater detail we demonstrate that a single mutation alone is not enough to establish a new ecotype, even though phylogenetic reconstruction identifies that mutation as the branching point. Instead, it takes a series of additional mutations to ensure the stable coexistence of the new ecotype in the background of the existing ones. CONCLUSIONS:Trade-offs are sufficient to drive the evolution of specialization in sympatric asexual populations. Without trade-offs to restrain traits, generalists evolve and diversity decreases. The observation that several mutations are required to complete speciation, even when a single mutation creates the new species, highlights the gradual nature of speciation and the importance of phyletic evolution.

Project description:Ambient assisted living (AAL) technologies present one approach to counter the challenges of demographic change in terms of an aging population, rising care needs, and lacking care personnel by supporting (older) people in need of care and enabling a longer and more independent staying at own home. Although the number of studies focusing on AAL users' acceptance and perception has increased in the last years, trade-off decisions-the weighing of perceived benefits and barriers of technology usage-have not been studied so far. Nevertheless, this is of high relevance: A realistic evaluation of adoption behaviors in different stakeholders (patients, care personnel) requires an understanding of exactly the weighing process of benefits against the barriers in line with the decision of the final willingness to use AAL technology. The current study applied a conjoint analysis approach and investigates people's decision behavior to use an AAL system for a family member in need of care. Study participants (n = 140) had to decide between realistic care scenarios consisting of different options of two benefits (increase in safety, relief of caring burden of relatives) and two barriers (access to personal data and data handling) of technology usage. Results revealed data access and privacy to be most relevant for the decision to use AAL technology at home. However, care experience essentially influenced the decision patterns. For the care experienced group, data access should be limited to most trusted persons and close relatives, rather than to medical professionals. The most important reasons to use AAL are the emotional relief and the felt safety for the person in care. For care novices, in contrast, data access should be in the exclusive responsibility of medical professionals. The reasons that militate in favor of using AAL technology are the increase in process efficiency and medical safety. The results are useful to develop user-tailored technology concepts and derive user-specific communication guidelines within and across clinical and home care contexts.

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Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Publications

Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

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