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Transcription, translation, and the evolution of specialists and generalists.

ABSTRACT: We used DNA microarrays to measure transcription and iTRAQ 2D liquid chromatography-mass spectrometry/mass spectrometry (a mass-tag labeling proteomic technique) to measure protein expression in 14 strains of Escherichia coli adapted for hundreds of generations to growth-limiting concentrations of either lactulose, methylgalactoside, or a 72:28 mixture of the two. The two ancestors, TD2 and TD10, differ only in their lac operons and have similar transcription and protein expression profiles. Changes in transcription and protein expression are observed at 30-250 genes depending on the evolved strain. Lactulose specialists carry duplications of the lac operon and show increased transcription and translation at lac. Methylgalactoside specialists are galS(-) and so constitutively transcribe and translate mgl, which encodes a transporter of methylgalactoside. However, there are two strains that carry lac duplications, are galS(-), and show increased transcription and translation at both operons. One is a generalist, the other a lactulose specialist. The generalist fails to sweep to fixation because its lac(+), galS(+) competitor expresses the csg adhesin and sticks to the chemostat wall, thereby preventing complete washout. Transcription and translation are sometimes decoupled. Lactulose-adapted strains show increased protein expression at fru, a fructose transporter, without evidence of increased transcription. This suggests that fructose, produced by the action of beta-galactosidase on lactulose, may leach from cells before being recouped. Reduced expression, at "late" flagella genes and the constitutive gat operon, is an adaptation to starvation. A comparison with two other long-term evolution experiments suggests that certain aspects of adaptation are predictable, some are characteristic of an experimental system, whereas others seem erratic.

SUBMITTER: Zhong S

PROVIDER: S-EPMC2782325 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Transcription, translation, and the evolution of specialists and generalists.

Zhong Shaobin S Miller Stephen P SP Dykhuizen Daniel E DE Dean Antony M AM

Molecular biology and evolution 20090825 12

We used DNA microarrays to measure transcription and iTRAQ 2D liquid chromatography-mass spectrometry/mass spectrometry (a mass-tag labeling proteomic technique) to measure protein expression in 14 strains of Escherichia coli adapted for hundreds of generations to growth-limiting concentrations of either lactulose, methylgalactoside, or a 72:28 mixture of the two. The two ancestors, TD2 and TD10, differ only in their lac operons and have similar transcription and protein expression profiles. Cha ...[more]

PMID: 19706726

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Project description:Abstract Specialization is a widespread but highly ambiguous and context‐dependent ecological concept. This quality makes comparisons across related studies difficult and makes associated terms such as “specialist” and “generalist” scientifically obscure. Here, we present a metric‐based framework to quantify specialization in 141 Quercus species using functional traits, biogeography, and species interactions. Rankings of specialization based on five metrics were used to answer questions about how specialization is used colloquially (i.e., individual species assessment by experts) and influenced by phylogenetics (Ancestral Character State Reconstruction, Automatic Shift Detection), biogeography (patterns of clustering by region and with climate), and species threat level (IUCN Red List). Metric‐based ranking can be representative of specialization in a consistent and practical manner, correlating with IUCN Red List data, and the mean scores of individual expert assessments. Specialization is shown to be highly correlated with precipitation seasonality and only moderately influenced by evolutionary history. Data‐deficient species were more likely to be highly specialized, and higher specialization was positively correlated with greater IUCN threat level. Frameworks for characterizing specialization and generalization can be done using metric ranking and can turn concepts that are often unclear into a definitive system. Metric‐based rankings of specialization can also be used to reveal interesting insights about a clade's evolutionary history and geographic distribution when paired with the related phylogenetic and geographic data. Metric‐based rankings can be applied to other systems and be a valuable tool for identifying species at risk and in need of conservation. A variety of metrics related to specialization are used to quantify and rank the concept in 141 species of Quercus (oaks). These rankings are used to explore evolutionary and biogeographic patterns, as well as specialization as a concept's usage by scientists.

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Transcription, translation, and the evolution of specialists and generalists.

Publications

Transcription, translation, and the evolution of specialists and generalists.

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