The origin of a novel gene through overprinting in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>Overlapped genes originate by a) loss of a stop codon among contiguous genes coded in different frames; b) shift to an upstream initiation codon of one of the contiguous genes; or c) by overprinting, whereby a novel open reading frame originates through point mutation inside an existing gene. Although overlapped genes are common in viruses, it is not clear whether overprinting has led to new genes in prokaryotes.</p> <p>Results</p> <p>Here we report the origin of a new gene through overprinting in <it>Escherichia coli </it>K12. The <it>htgA </it>gene coding for a positive regulator of the sigma 32 heat shock promoter arose by point mutation in a 123/213 phase within an open reading frame (<it>yaaW</it>) of unknown function, most likely in the lineage leading to <it>E. coli </it>and <it>Shigella sp</it>. Further, we show that <it>yaaW </it>sequences coding for <it>htgA </it>genes have a slower evolutionary rate than those lacking an overlapped <it>htgA </it>gene.</p> <p>Conclusion</p> <p>While overprinting has been shown to be rather frequent in the evolution of new genes in viruses, our results suggest that this mechanism has also contributed to the origin of a novel gene in a prokaryote. We propose the term <it>janolog </it>(from <it>Jano</it>, the two-faced Roman god) to describe the homology relationship that holds between two genes when one originated through overprinting of the other. One cannot dismiss the possibility that at least a small fraction of the large number of novel ORPhan genes detected in pan-genome and metagenomic studies arose by overprinting.</p

Adaptation to high ethanol reveals complex evolutionary pathways

Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts

Café Scientifique

Alexander DeLuna-Fors es doctor en ciencias biomédicas por la UNAM. Después de desempeñarse como investigador en la UNAM y en la Universidad de Harvard, desde 2009 es investigador del Laboratorio Nacional de Genómica y profesor del Posgrado en Biología Integrativa, ambos del CINVESTAV Irapuato. Su equipo de trabajo combina una serie de estrategias experimentales y computacionales para conocer la forma en que los genes, el ambiente y sus interacciones determinan procesos biológicos complejos como la función metabólica, la respuesta al estrés y el envejecimiento celular. En 2012 fue nombrado miembro afiliado de la World Academy of Sciences (TWAS), reconocimiento que se hace a los científicos jóvenes más destacados del mundo en vías de desarrollo. En esta charla narra su experiencia sobre las estrategias experimentales y computacionales para conocer la forma en que los genes, el ambiente y sus interacciones determinan procesos biológicos para el envejecimiento celular. Las investigaciones recientes han demostrado que el deterioro gradual de las células y los órganos de los seres vivos son factores que controlan el envejecimiento, genéticamente hablando. Comenta que la interacción del ambiente con nuestros genes determina la velocidad a la que envejecemos. Además, algunas intervenciones genéticas o nutrimentales permiten extender o acortar la longevidad de diferentes organismos experimentales. El doctor comparte que en un futuro estos conocimientos podrán incidir en la vejez humana, para que ésta sea más saludable

Need-based up-regulation of protein levels in response to deletion of their duplicate genes.

Many duplicate genes maintain functional overlap despite divergence over long evolutionary time scales. Deleting one member of a paralogous pair often has no phenotypic effect, unless its paralog is also deleted. It has been suggested that this functional compensation might be mediated by active up-regulation of expression of a gene in response to deletion of its paralog. However, it is not clear how prevalent such paralog responsiveness is, nor whether it is hardwired or dependent on feedback from environmental conditions. Here, we address these questions at the genomic scale using high-throughput flow cytometry of single-cell protein levels in differentially labeled cocultures of wild-type and paralog-knockout Saccharomyces cerevisiae strains. We find that only a modest fraction of proteins (22 out of 202) show significant up-regulation to deletion of their duplicate genes. However, these paralog-responsive proteins match almost exclusively duplicate pairs whose overlapping function is required for growth. Moreover, media conditions that add or remove requirements for the function of a duplicate gene pair specifically eliminate or create paralog responsiveness. Together, our results suggest that paralog responsiveness in yeast is need-based: it appears only in conditions in which the gene function is required. Physiologically, such need-based responsiveness could provide an adaptive mechanism for compensation of genetic, environmental, or stochastic perturbations in protein abundance

Multiple Forms of Multifunctional Proteins in Health and Disease

Protein science has moved from a focus on individual molecules to an integrated perspective in which proteins emerge as dynamic players with multiple functions, rather than monofunctional specialists. Annotation of the full functional repertoire of proteins has impacted the fields of biochemistry and genetics, and will continue to influence basic and applied science questions - from the genotype-to-phenotype problem, to our understanding of human pathologies and drug design. In this review, we address the phenomena of pleiotropy, multidomain proteins, promiscuity, and protein moonlighting, providing examples of multitasking biomolecules that underlie specific mechanisms of human disease. In doing so, we place in context different types of multifunctional proteins, highlighting useful attributes for their systematic definition and classification in future research directions

Additional file 3: Table S1. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts

YGOB data set analysis, including dN/dS data, likelihood-ratio tests' results, and S. cerevisiae protein properties and functions for 535 orthogroups. (XLSX 242 kb

Additional file 4: Table S2. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts

FOR data set analysis, including dN/dS data, likelihood-ratio tests' results for 462 orthogroups. (XLSX 57 kb

Additional file 1: Figure S1. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts

Analysis of evolution rates in fungal WGD orthogroups. The S. cerevisiae PSK1/PSK2 orthogroup is shown as an example of significantly relaxed purifying selection after duplication. Gray branches indicate the orthologs of PSK1/PSK2 in ascomycetes species that diverged before the WGD (yellow star), while black branches indicate post-WGD species with two paralogous clades. Average dN/dS ratios are shown for both non-WGD (ω0) and post-WGD genes (ωwgd); the p-value is from the likelihood ratio test of the alternative hypothesis of different rates of protein evolution between ω0 and ωwgd. (EPS 1264 kb

Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora

Abstract Background Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. We asked whether genome reduction is driven by metabolic engineering strategies resulted from the interaction with the host. As its widely known, the loss of enzyme coding genes leads to metabolic network restructuring sometimes improving the production rates. In this case, the production rate of reduced-carbon in the metabolism of the chromatophore. Results We reconstructed the metabolic networks of the chromatophore of P. chromatophora CCAC 0185 and a close free-living relative, the cyanobacterium Synechococcus sp. WH 5701. We found that the evolution of free-living to host-restricted lifestyle rendered a fragile metabolic network where >80% of genes in the chromatophore are essential for metabolic functionality. Despite the lack of experimental information, the metabolic reconstruction of the chromatophore suggests that the host provides several metabolites to the endosymbiont. By using these metabolites as intracellular conditions, in silico simulations of genome evolution by gene lose recover with 77% accuracy the actual metabolic gene content of the chromatophore. Also, the metabolic model of the chromatophore allowed us to predict by flux balance analysis a maximum rate of reduced-carbon released by the endosymbiont to the host. By inspecting the central metabolism of the chromatophore and the free-living cyanobacteria we found that by improvements in the gluconeogenic pathway the metabolism of the endosymbiont uses more efficiently the carbon source for reduced-carbon production. In addition, our in silico simulations of the evolutionary process leading to the reduced metabolic network of the chromatophore showed that the predicted rate of released reduced-carbon is obtained in less than 5% of the times under a process guided by random gene deletion and genetic drift. We interpret previous findings as evidence that natural selection at holobiont level shaped the rate at which reduced-carbon is exported to the host. Finally, our model also predicts that the ABC phosphate transporter (pstSACB) which is conserved in the genome of the chromatophore of P. chromatophora strain CCAC 0185 is a necessary component to release reduced-carbon molecules to the host. Conclusion Our evolutionary analysis suggests that in the case of Paulinella chromatophora natural selection at the holobiont level played a prominent role in shaping the metabolic specialization of the chromatophore. We propose that natural selection acted as a “metabolic engineer” by favoring metabolic restructurings that led to an increased release of reduced-carbon to the host

Additional file 2: Figure S2. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts

Results are consistent for most orthogroups when using two alternative data sets. (A) Comparison of Likelihood-Ratio Test (LRT) values for the hypothesis test comparing the two evolutionary models (null: ω0 = ωwgd; alternative: ω0 ≠ ωwgd) using sequences from two different datasets: the Yeast Genome Order Browser (YGOB) [14] and the Fungal Orthogroups Repository (FOR) [35]. (B) Venn diagram of orthogroups in which the alternative hypothesis (ω0 ≠ ωwgd) is accepted in the YGOB and the FOR data sets, (C) Comparison of non-WGD (gray dots) and post-WGD dN/dS ratios of 426 orthogroups calculated for sequences for the YGOB and the FOR data sets. (EPS 2241 kb