Disentangling genetic and epigenetic determinants of ultrafast adaptation

A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical–experimental framework for disclosing the presence of such adaptation‐speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation–accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic‐adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data‐driven individual‐based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation‐speeding mechanisms in general.publishedVersio

Physiological function of the CDF proteins in eukaryotic organisms

Metale ciężkie, to naturalnie występujące metale, półmetale i metaloidy, wśród których znajdują się mikroelementy niezbędne dla prawidłowego funkcjonowania organizmów oraz pierwiastki balastowe, które nie pełnią żadnych funkcji biologicznych. W toku ewolucji organizmy żywe wykształciły szereg mechanizmów komórkowych odpowiedzialnych za pobieranie i usuwanie nadmiaru tych pierwiastków ze swoich komórek. Istotną rolę w tych procesach pełnią białka z rodziny CDF (z ang. Cation Diffusion Facilitator). Odpowiadają one zarówno za dostarczanie kluczowych mikroelementów Zn i Fe do wnętrza komórek i organelli takich jak aparat Golgiego i endosomy, jak i za aktywne wydzielanie nadmiaru różnych metali ciężkich z cytoplazmy do wakuoli lub do przestrzeni zewnątrzkomórkowej. W ostatnich latach biologiczna rola białek CDF w komórkach eukariotycznych została znacznie przybliżona dzięki intensywnym badaniom prowadzonym na drożdżach Saccharomyces cerevisiae, ssakach i roślinach. Niniejsza praca prezentuje najbardziej aktualną wiedzę o lokalizacji komórkowej i funkcji eukariotycznych transporterów CDF.Heavy metals are naturally occurring metals, semi-metals and metalloids, including the microelements essential for the proper function of living cells, as well as the non-essential elements having no established biological functions. Organisms have evolved multiple mechanisms to maintain heavy metal homeostasis within their cells. The family of CDF (Cation Diffusion Facilitator) proteins has been shown to play a crucial role in these processes. Members of CDF contribute to the delivery of micronutrients, such as Fe or Zn, into the cells and cellular organelles, such as Golgi compartment and endosomes, as well as to the efflux of a variety of heavy metals into the vacuole or extracellular space. Recently, the biological role of CDF proteins in eukaryotic cells has been greatly clarified by extensive research on the yeast Saccharomyces cerevisiae, mammals and plants. This work presents the current knowledge about the cellular localization and function of eukaryotic CDF transporters

Muscle Glycogen Phosphorylase and Its Functional Partners in Health and Disease

Glycogen phosphorylase (PG) is a key enzyme taking part in the first step of glycogenolysis. Muscle glycogen phosphorylase (PYGM) differs from other PG isoforms in expression pattern and biochemical properties. The main role of PYGM is providing sufficient energy for muscle contraction. However, it is expressed in tissues other than muscle, such as the brain, lymphoid tissues, and blood. PYGM is important not only in glycogen metabolism, but also in such diverse processes as the insulin and glucagon signaling pathway, insulin resistance, necroptosis, immune response, and phototransduction. PYGM is implicated in several pathological states, such as muscle glycogen phosphorylase deficiency (McArdle disease), schizophrenia, and cancer. Here we attempt to analyze the available data regarding the protein partners of PYGM to shed light on its possible interactions and functions. We also underline the potential for zebrafish to become a convenient and applicable model to study PYGM functions, especially because of its unique features that can complement data obtained from other approaches

BestKeeper based evaluation of reference genes stability in cucumber plants grown in varying NO₃⁻ supply.

<p>The stability values were calculated based on the pairwise correlation between genes and BI (BestKeeper Index). The highest Person coefficient values representing the most stable genes are marked in bold. Genes ranked at the lowest positions by geNorm and NormFinder for each set of analyzed samples were not included (-) in BestKeeper evaluation.</p

Reliable Reference Genes for Normalization of Gene Expression in Cucumber Grown under Different Nitrogen Nutrition

<div><p>In plants, nitrogen is the most important nutritional factor limiting the yield of cultivated crops. Since nitrogen is essential for synthesis of nucleotides, amino acids and proteins, studies on gene expression in plants cultivated under different nitrogen availability require particularly careful selection of suitable reference genes which are not affected by nitrogen limitation. Therefore, the objective of this study was to select the most reliable reference genes for qPCR analysis of target cucumber genes under varying nitrogen source and availability. Among twelve candidate cucumber genes used in this study, five are highly homologous to the commonly used internal controls, whereas seven novel candidates were previously identified through the query of the cucumber genome. The expression of putative reference genes and the target <i>CsNRT1.1</i> gene was analyzed in roots, stems and leaves of cucumbers grown under nitrogen deprivation, varying nitrate availability or different sources of nitrogen (glutamate, glutamine or NH₃). The stability of candidate genes expression significantly varied depending on the tissue type and nitrogen supply. However, in most of the outputs genes encoding CACS, TIP41, F-box protein and EFα proved to be the most suitable for normalization of <i>CsNRT1.1</i> expression. In addition, our results suggest the inclusion of 3 or 4 references to obtain highly reliable results of target genes expression in all cucumber organs under nitrogen-related stress.</p></div

Candidate cucumber genes ranked according to their expression stability as determined by NormFinder.

<p>Stability values are listed from the most stable to the least stable gene.</p>*<p>Samples from two-week-old plants grown under nitrate, ammonia, glutamine or glutamate for 4 or 12 hours.</p>**<p>Samples from 4-week-old plants grown under nitrogen deficiency, 0.5 mM nitrate, 10 mM nitrate, temporary nitrate provision, temporary nitrate starvation or temporary nitrate re-supply.</p

GeNorm based evaluation of candidate gene expression in samples from plants grown in different nitrogen compounds.

<p>Average expression stability values (<i>M</i>) of the remaining candidate cucumber reference genes during stepwise exclusion of the least stable reference gene in roots (a), stems (c), leaves (e) and all cucumbers organs taken together (g). The lowest the M values indicate the most stable expression of candidate cucumber genes. Determination of optimal number of reference genes based on pairwise variation (V) analysis of normalization factors of the candidate reference genes in roots (b), stems (d), leaves (f) and all cucumber organs taken together (h). The V_n/n+1 value was calculated for every comparison between two of the twelve consecutive candidate reference genes. According to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072887#pone.0072887-Vandesompele1" target="_blank">[14]</a>, additional (n+1)^th reference gene should be included into analysis whenever the V_n/n+1 value drops below the 0.15 threshold.</p

BestKeeper based evaluation of reference genes stability in cucumber plants grown in different nitrogen compounds.

<p>The stability values were calculated based on the pairwise correlation between genes and BI (BestKeeper Index). The highest Person coefficient values representing the most stable genes are marked in bold. Genes ranked at the lowest positions by geNorm and NormFinder for each set of analyzed samples were not included (-) in BestKeeper evaluation.</p

GeNorm based evaluation of candidate gene expression in samples from plants grown in different nitrate supply.

<p>Average expression stability values (<i>M</i>) of the remaining candidate cucumber reference genes during stepwise exclusion of the least stable reference gene in roots (a), stems (c), leaves (e) and all cucumbers organs taken together (g). The lowest the M values indicate the most stable expression of candidate cucumber genes. Determination of optimal number of reference genes based on pairwise variation (V) analysis of normalization factors of the candidate reference genes in roots (b), stems (d), leaves (f) and all cucumber organs taken together (h). The V_n/n+1 value was calculated for every comparison between two of the twelve consecutive candidate reference genes. According to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072887#pone.0072887-Vandesompele1" target="_blank">[14]</a>, additional (n+1)^th reference gene should be included into analysis whenever the V_n/n+1 value drops below the 0.15 threshold.</p

Description of cucumber candidate reference genes based on the comparison with their Arabidopsis orthologs.

<p>Seven of the twelve candidate cucumber reference genes (<i>CACS</i>, <i>TIP41</i>, <i>PDF2</i>, <i>GW881873</i>, <i>YSL8</i>, <i>HEL</i>) have been recently retrieved from the whole cucumber genome sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072887#pone.0072887-Migocka1" target="_blank">[36]</a> using the novel reference genes identified in <i>Arabidopsis</i> as the query sequences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072887#pone.0072887-Czechowski1" target="_blank">[3]</a>. The commonly used remaining five genes (<i>ACT</i>, <i>TUA</i>, <i>UBI-1</i>, <i>EFα</i>, <i>CYP</i>) were previously available in the Genbank database as partial cDNAs. The full cDNAs and exon/intron organization of all 12 candidate genes were established using BlastN, and FGENESH or FGENESH+.</p