Subcellular fractionation of human liver reveals limits in global proteomic quantification from isolated fractions

The liver plays an important role in metabolism and elimination of xenobiotics, including drugs. Determination of concentrations of proteins involved in uptake, distribution, metabolism, and excretion of xenobiotics is required to understand and predict elimination mechanisms in this tissue. In this work, we have fractionated homogenates of snap-frozen human liver by differential centrifugation and performed quantitative mass spectrometry-based proteomic analysis of each fraction. Concentrations of proteins were calculated by the “total protein approach”. A total of 4586 proteins were identified by at least five peptides and were quantified in all fractions. We found that the xenobiotics transporters of the canalicular and basolateral membranes were differentially enriched in the subcellular fractions and that phase I and II metabolizing enzymes, the cytochrome P450s and the UDP–glucuronyl transferases, have complex subcellular distributions. These findings show that there is no simple way to scale the data from measurements in arbitrarily selected membrane fractions using a single scaling factor for all the proteins of interest. This study also provides the first absolute quantitative subcellular catalog of human liver proteins obtained from frozen tissue specimens. Our data provide quantitative insights into the subcellular distribution of proteins and can be used as a guide for development of fractionation procedures.     

Select what you need: a comparative evaluation of the advantages and limitations of frequently used expression systems for foreign genes

The expression of heterologous proteins in microorganisms using genetic recombination is still the high point in the development and exploitation of modern biotechnology. People can produce bioactive proteins from relatively cheap culture medium instead of expensive extraction. Host cell systems for the expression of heterologous genes are generally prokaryotic or eukaryotic systems, both of which have inherent advantages and drawbacks. An optimal expression system can be selected only if the productivity, bioactivity, purpose, and physicochemical characteristics of the interest protein are taken into consideration, together with the cost, convenience and safety of the system itself. Here, we concisely review the most frequently used prokaryotic, yeast, insect and mammalian expression systems, as well as expression in eukaryote individuals. The merits and demerits of these systems are discussed.     

Dendrochronological analysis of urban trees: climatic response and impact of drought on frequently used tree species

Key message

Distinct species-specific differences were found in the response to temperature, precipitation and the self-calibrated Palmer Drought Severity Index that are confirmed by pointer year analyzes and superposed epoch analyzes.

Abstract

Trees in urban environments are exposed to heat stress, low air humidity and soil drought. The increasing temperatures and the more frequent heat and drought events will intensify the stress level of urban trees. We applied a dendrochronological approach to evaluate the species-specific suitability under increasing risk of drought of five tree species at highly sealed urban sites in the city of Dresden (Germany). Climate-growth correlation analyses show that temperatures and water availability from April to July in the current year and in summer and autumn of the previous year are the main determining factors for radial growth. However, distinct species-specific differences were found in the response to temperature, precipitation and the self-calibrated Palmer Drought Severity Index. During the study period, the influence of temperature and drought on radial growth during summer months increases for Acer platanoides and Acer pseudoplatanus, whereas no changes occurred for Quercus petraea, Quercus rubra, and P. × hispanica. Pointer year analysis and superposed epoch analyses revealed a species-specific response to extreme climatic events. While for A. platanoides and A. pseudoplatanus a higher number of negative pointer years and significant growth declines in drought years were found, Q. petraea and Q. rubra showed more frequent positive pointer years but no significant growth reductions during drought. Based on these response patterns we classified the studied tree species according to their suitability and drought tolerance for urban sites.     

The evolution of cultivated plant species: classical plant breeding versus genetic engineering

Agriculture is the most intensive form of environmental exploitation performed by mankind. It involves replacing the natural ecosystem with an artificial plant community comprising one or more crop species, and weeds can invade the cleared land. Initially, the adoption of agriculture did not necessarily imply an improvement in standard of living (there is, in fact, evidence to the contrary), but as agricultural efficiency improved, surpluses were generated on top of mere subsistence levels. It may take many years of labor in order to obtain a crop that has all of the desired traits. It is not possible to control which genes are transferred from the parents to the offspring, and the results are often uncertain. In comparison, the utilization of genetic engineering to improve crops can be a faster and more precise approach. Unlike traditional breeding, genetic engineering makes it possible to select the specific traits desired and insert the genes that code for them into the plant.     

The separation of RNA polymerases I and II achieved by fractionation of plant chromatin

Chromatin-bound RNA polymerase I and II from soybean hypocotyl can be separated by differential centrifugation. While all detectable RNA polymerase I is pelleted in association with chromatin, nearly all of the RNA polymerase II activity is not pelleted even at high speeds. Substitution of pH 6 for pH 8 isolation medium results in several-fold greater recovery of chromatin-bound RNA polymerase II.     

Widespread plant species: natives versus aliens in our changing world

Estimates of the level of invasion for a region are traditionally based on relative numbers of native and alien species. However, alien species differ dramatically in the size of their invasive ranges. Here we present the first study to quantify the level of invasion for several regions of the world in terms of the most widely distributed plant species (natives vs. aliens). Aliens accounted for 51.3% of the 120 most widely distributed plant species in North America, 43.3% in New South Wales (Australia), 34.2% in Chile, 29.7% in Argentina, and 22.5% in the Republic of South Africa. However, Europe had only 1% of alien species among the most widespread species of the flora. Across regions, alien species relative to native species were either as well-distributed (10 comparisons) or more widely distributed (5 comparisons). These striking patterns highlight the profound contribution that widespread invasive alien plants make to floristic dominance patterns across different regions. Many of the most widespread species are alien plants, and, in particular, Europe and Asia appear as major contributors to the homogenization of the floras in the Americas. We recommend that spatial extent of invasion should be explicitly incorporated in assessments of invasibility, globalization, and risk assessments.     

A method for separation and determination of cytokinin nucleotides from plant tissues

Recent progress in the study of cytokinin metabolism in plants indicates that quantitative analysis of cytokinin nucleotides is essential for elucidation of early steps of the biosynthetic pathway. However, traditional procedures for purification and quantification of cytokinin cannot discriminate the various nucleotides. We describe here a method for separation and determination of cytokinin nucleotides through a series of anion-exchange column chromatography steps followed by liquid chromatography-mass spectrometry. This method enabled us to analyze the amount of each species of cytokinin nucleotide in plant tissues.     

Trace elements distribution and species fractionation in the wheat (Triticum aestivum) plant

Abstract

The status of 13 trace elements’ (both essential and toxic) was investigated in individual parts of the winter wheat plant(Triticum aestivum) taken during its whole cultivation period. The study includes the determination of total concentrations, portions soluble in 0.02 mol L^?1 Tris-HCI buffer solution (pH = 7.5), and the fractionation of soluble species of elements by SEC and ICP/MS. Ligands of trace elements from a low-molecular weight SEC fraction were isolated by affinity chromatography and characterised by MALDI/MS analyses and by amino acids composition. Inhomogeneous accumulation of trace elements was found in the analysed plant tissues. The concentrations of elements are also affected by the maturity of the plants. The distribution of the soluble species of the elements between chromatographic fractions exhibited some regularity in all the samples. Substantial amounts of trace elements are located in a low-molecular weight fraction (< 2 kDa). Only chromatograms of Zn (grain) and Cu (all samples) contain significant medium-molecular and high-molecular weight fractions. Compounds isolated from the low-molecular weight fractions are rich in cystein and dicarboxylic amino acids or their amides. MALDI/MS spectra of these compounds isolated from shoots, straw and grain confirmed the presence of the phytochelatin PC₅.     

Macromolecular distribution near the limits of density-gradient columns. Some applications to the separation and fractionation of glycoproteins.

1. Expressions are derived for the distribution at density-gradient equilibrium of macromolecules whose densities are (a) close to the values characterizing the solution limits or (b) outside the span of the gradient. 2. Density-distribution predicted by the expressions agree with those obtained by rigorous methods. 3. The distribution equations are applied to hypothetical mixtures of proteins and glycoproteins in commonly used density-gradient media to simulate separation and fractionation conditions. 4. It is shown that CsBr, although less efficient than CsCl for fractionation, is nevertheless adequate for most purposes; in analytical experiments it may often have advantages over CsCl. Limitations on the use of LiBr are explored. 5. An expression is derived which allows the variance of the partial specific volume of the macromolecular component to be determined from the variance of the buoyant density. It is shown that the relative resolving powers of different salts is expressed by their values of the quantity (formula: see text). 6. The equations are applied to a well-characterized glycoprotein preparation at equilibrium in CsCl and in Cs2SO4:it is shown that the much wider distribution in CsCl than in Cs2SO4 is explicable in terms of the variance in buoyant density and the solvation properties of the salts. 7. Limitations of the expressions arise when dispersity in density is represented by a low apparent molecular weight; realistic simulations can then only be obtained when the component is fully banded.     

Control of plant species diversity and community invasibility by species immigration: seed richness versus seed density

Immigration rates of species into communities are widely understood to influence community diversity, which in turn is widely expected to influence the susceptibility of ecosystems to species invasion. For a given community, however, immigration processes may impact diversity by means of two separable components: the number of species represented in seed inputs and the density of seed per species. The independent effects of these components on plant species diversity and consequent rates of invasion are poorly understood. We constructed experimental plant communities through repeated seed additions to independently measure the effects of seed richness and seed density on the trajectory of species diversity during the development of annual plant communities. Because we sowed species not found in the immediate study area, we were able to assess the invasibility of the resulting communities by recording the rate of establishment of species from adjacent vegetation. Early in community development when species only weakly interacted, seed richness had a strong effect on community diversity whereas seed density had little effect. After the plants became established, the effect of seed richness on measured diversity strongly depended on seed density, and disappeared at the highest level of seed density. The ability of surrounding vegetation to invade the experimental communities was decreased by seed density but not by seed richness, primarily because the individual effects of a few sown species could explain the observed invasion rates. These results suggest that seed density is just as important as seed richness in the control of species diversity, and perhaps a more important determinant of community invasibility than seed richness in dynamic plant assemblages.     

Biomarker discovery: proteome fractionation and separation in biological samples.

Proteomics, analogous with genomics, is the analysis of the protein complement present in a cell, organ, or organism at any given time. While the genome provides information about the theoretical status of the cellular proteins, the proteome describes the actual content, which ultimately determines the phenotype. The broad application of proteomic technologies in basic science and clinical medicine has the potential to accelerate our understanding of the molecular mechanisms underlying disease and may facilitate the discovery of new drug targets and diagnostic disease markers. Proteomics is a rapidly developing and changing scientific discipline, and the last 5 yr have seen major advances in the underlying techniques as well as expansion into new applications. Core technologies for the separation of proteins and/or peptides are one- and two-dimensional gel electrophoresis and one- and two-dimensional liquid chromatography, and these are coupled almost exclusively with mass spectrometry. Proteomic studies have shown that the most effective analysis of even simple biological samples requires subfractionation and/or enrichment before protein identification by mass spectrometry. Selection of the appropriate technology or combination of technologies to match the biological questions is essential for maximum coverage of the selected subproteome and to ensure both the full interpretation and the downstream utility of the data. In this review, we describe the current technologies for proteome fractionation and separation of biological samples, based on our lab workflow for biomarker discovery and validation.     

Arctic and boreal plant species decline at their southern range limits in the Rocky Mountains

Climate change is predicted to cause a decline in warm‐margin plant populations, but this hypothesis has rarely been tested. Understanding which species and habitats are most likely to be affected is critical for adaptive management and conservation. We monitored the density of 46 populations representing 28 species of arctic‐alpine or boreal plants at the southern margin of their ranges in the Rocky Mountains of Montana, USA, between 1988 and 2014 and analysed population trends and relationships to phylogeny and habitat. Marginal populations declined overall during the past two decades; however, the mean trend for 18 dicot populations was ?5.8% per year, but only ?0.4% per year for the 28 populations of monocots and pteridophytes. Declines in the size of peripheral populations did not differ significantly among tundra, fen and forest habitats. Results of our study support predicted effects of climate change and suggest that vulnerability may depend on phylogeny or associated anatomical/physiological attributes.     

Palmitate activation and esterification in microsomal fractions of rat liver.

Palmitoyl-CoA synthetase activity in the microsomal fraction of rat liver was measured directly by palmitoyl-CoA production, and indirectly by converting the palmitoyl-CoA into palmitoylcarnitine under optimum conditions. Even in the latter system, palmitoyl-CoA accumulated. The rate of palmitoyl-CoA hydrolysis and the inhibition of palmitoyl-CoA synthetase by palmitoyl-CoA were each estimated to be less than 10% of the maximum rate of palmitoyl-CoA production. The concentration of palmitoyl-CoA present in the assay systems used for measuring palmitate esterification to glycerol phosphate and the activity of palmitoyl-CoA synthetase by using the carnitine-linked determination were measured. These concentrations were not altered by the addition of glycerol phosphate, or of carnitine plus carnitine palmitoyltransferase. The relationship between the activity of palmitoyl-CoA synthetase and the rate of glycerolipid synthesis was investigated. The latter activity was measured by using palmitoyl-CoA generated from palmitate, palmitoyl--AMP or palmitoylcarnitine. It is concluded that, at optimum substrate concentrations, the activity of glycerol phosphate acyltransferase is rate-limiting in the synthesis of phosphatidate by rat liver microsomal fractions. The implications of these results in the measurement of palmitoyl-CoA synthetase and in the control of glycerolipid synthesis are discussed.     

T-system membranes in microsomal fractions of crayfish muscles: identification and differences in protein composition

Specific binding of 3H-ouabain and ruthenium red (RR) to membranes of T-tubules in crayfish muscles was used to identify the subfraction containing vesicles originating from the T-system. The microsomal fraction was prepared by differential centrifugation, and subfractions were separated in continuous or discontinuous sucrose density gradients. 3H-ouabain binding was estimated by scintillation counting; RR binding was examined by electron microscopy. The light subfraction was identified using both methods as that containing vesicles of T-tubules. Protein separation by SDS-electrophoresis revealed marked differences between the subfraction containing vesicles of T-tubules and other subfractions, the most distinctive feature being the presence of a protein of Mr 46,000 predominantly in the light subfraction.     

Tissue culture evaluation of NaCl tolerance in Medicago species: Cellular versus whole plant response

Tissue culture responses to three levels of NaCl (0, 85mM and 170 mM) were evaluated in several Medicago species including: M. dzhawakhetica, M. marina, M. rhodopea, M. rupestris, M. sativa (alfalfa) and M. suffruticosa. The whole plant responses of the same genotypes were evaluated in half-strength Hoagland's solution containing 0, 51.5, and 103 mM NaCl. One or more genotypes of M. dzhawakhetica, M. rhodopea, M. rupestris, and M. sativa exhibited in vitro NaCl tolerance at 85 mM. In addition, one genotype each of M. dzhawakhetica, M. rhodopea, and M. sativa was tolerant of 170 mM NaCl. However, all of the genotypes that demonstrated NaCl tolerance in vitro were NaCl sensitive at the whole plant level. Conversely, M. marina the only species exhibiting whole plant NaCl tolerance, had the most NaCl sensitive genotypes at the in vitro level. Although an in vitro NaCl tolerance mechanism which confers whole plant NaCl tolerance was not observed, a potential NaCl tolerance germplasm source, M. marina, was identified.