Entropy Perspectives of Molecular and Evolutionary Biology.

Attempts to find and quantify the supposed low entropy of organisms and its preservation are revised. The absolute entropy of the mixed components of non-living biomass (approximately -1.6 × 10 J K L) is the reference to which other entropy decreases would be ascribed to life.

On the Edge of Dispensability, the Chloroplast Genes.

The polypeptides encoded by the chloroplast genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I. Except for Charophyceae (algae related to higher plants) and a few Prasinophyceae, all eukaryotic algae lack genes. Among vascular plants, the genes are absent in epiphytic and in some species scattered among different genera, families, and orders.

Evolution and Function of the Chloroplast. Current Investigations and Perspectives.

Chloroplasts are the place for the major conversion of the sun's radiation energy to chemical energythat is usable by organisms[…].

Reply to Comment on 'The cancer Warburg effect may be a testable example of the minimum entropy production rate principle'.

The minimum rate principle is applied to the chemical reaction in a steady-state open cell system where, under constant supply of the glucose precursor, reference to time or to glucose consumption does not affect the conclusions.

The cancer Warburg effect may be a testable example of the minimum entropy production rate principle.

Cancer cells consume more glucose by glycolytic fermentation to lactate than by respiration, a characteristic known as the Warburg effect. In contrast with the 36 moles of ATP produced by respiration, fermentation produces two moles of ATP per mole of glucose consumed, which poses a puzzle with regard to the function of the Warburg effect. The production of free energy (ΔG), enthalpy (ΔH), and entropy (ΔS) per mole linearly varies with the fraction (x) of glucose consumed by fermentation that is frequently estimated around 0.

The rise of the photosynthetic rate when light intensity increases is delayed in ndh gene-defective tobacco at high but not at low CO2 concentrations.

The 11 plastid ndh genes have hovered frequently on the edge of dispensability, being absent in the plastid DNA of many algae and certain higher plants. We have compared the photosynthetic activity of tobacco (Nicotiana tabacum, cv. Petit Havana) with five transgenic lines (ΔndhF, pr-ΔndhF, T181D, T181A, and ndhF FC) and found that photosynthetic performance is impaired in transgenic ndhF-defective tobacco plants at rapidly fluctuating light intensities and higher than ambient CO2 concentrations.

Thermodynamic balance of photosynthesis and transpiration at increasing CO2 concentrations and rapid light fluctuations.

Experimental and theoretical flux models have been developed to reveal the influence of sun flecks and increasing CO2 concentrations on the energy and entropy balances of the leaf. The rapid and wide range of fluctuations in light intensity under field conditions were simulated in a climatic gas exchange chamber and we determined the energy and entropy balance of the leaf based on radiation and gas exchange measurements. It was estimated that the energy of photosynthetic active radiation (PAR) accounts for half of transpiration, which is the main factor responsible for the exportation of the entropy generated in photosynthesis (Sg) out of the leaf in order to maintain functional the photosynthetic machinery.

Hypothesis: increase of the ratio singlet oxygen plus superoxide radical to hydrogen peroxide changes stress defense response to programmed leaf death.

The level of reactive oxygen species (ROS) increases under different stresses and, by destroying cellular components, may cause cell death. In addition, ROS are part of the complex network of transduction signals that induce defense reactions against stress or, alternatively, trigger programmed cell death, and key questions are the levels of each ROS that, respectively determine defense and death responses of the cell. The answer to those questions is difficult because there are several patterns of cell death that frequently appear mixed and are hardly distinguishable.

Proteomic identification of a basic peroxidase stabilized within acetylated polymannan polysaccharide of Aloe barbadensis.

Acetylated polymannan polysaccharide (ApmP) isolated from Aloe barbadensis Miller contains a stable peroxidase that was solubilized to investigate its biochemical, electrophoretic, immunological, and proteomic properties. In the electrophoretic band corresponding to the solubilized peroxidase, proteomic analysis detected seven tryptic peptides that matched homologous peptides covering one third of the ATP22a peroxidase of Arabidopsis thaliana. All the characteristics tested indicated that the activity stabilized within the ApmP pertains to the basic secretory peroxidase family, which includes members that have several biotechnological uses.

Activity, polypeptide and gene identification of thylakoid Ndh complex in trees: potential physiological relevance of fluorescence assays.

Three evergreen (Laurus nobilis, Viburnum tinus and Thuja plicata) and two autumnal abscission deciduous trees (Cydonia oblonga and Prunus domestica) have been investigated for the presence (zymogram and immunodetection) and functionality (post-illumination chlorophyll fluorescence) of the thylakoid Ndh complex. The presence of encoding ndh genes has also been investigated in T. plicata.

Plastid ndh genes in plant evolution.

The plastid ndh genes encode components of the thylakoid Ndh complex which purportedly acts as an electron feeding valve to adjust the redox level of the cyclic photosynthetic electron transporters. During the process of evolution from endosymbiosis to modern chloroplast, most cyanobacterial genes were lost or transferred to nucleus. Eleven ndh genes are among the 150-200 genes remaining in higher plant chloroplast DNA, out of some 3000 genes in the original prokaryotic Cyanobacteria in which homologues to ndh genes encode components of the respiratory Complex I and probably other complexes.

Entropy decrease associated to solute compartmentalization in the cell.

We have deduced equations to quantify the entropy associated to the compartmentalization of components in eukaryotic cells as a function of cell and compartment volumes, and of the concentration of solutes. On the basis of known and plausible values of volume and solute concentrations and the deduced equations, we estimate that the contribution of compartmentalization to the decrease of entropy is approximately -14.4 x 10(-14)JK(-1)cell(-1) (-0.

Functional characterization of the thylakoid Ndh complex phosphorylation by site-directed mutations in the ndhF gene.

To investigate the phosphorylation of the NDH-F subunit of the thylakoid Ndh complex, we constructed three site-directed mutant transgenic tobaccos (Nicotiana tabacum) (T181A, T181S and T181D) in which the (541)ACT(543) triplet encoding the Thr-181 has been substituted by GCT, TCT or GAT encoding alanine, serine and aspartic acid, respectively. Western blots with phospho-threonine antibody detected the 73 kD NDH-F phosphorylated polypeptide in control but not in mutant tobaccos. Differences in Ndh activity, chlorophyll fluorescence and photosynthesis among mutants and control plant demonstrate the key role of the phosphorylation of conserved Thr-181 in the activity and function of the Ndh complex.

Multiple phosphorylation sites in the beta subunit of thylakoid ATP synthase.

Proteomic analyses of the beta subunit of the plastid ATP synthase of barley (Hordeum vulgare L.) revealed that mature protein was not carboxy terminus processed and suggested the correction of the 274 codon (GAT to AAT) in the data bank that was confirmed by DNA sequencing. Six isoforms of the ATP synthase beta subunit with pI ranging from 4.

Are organisms committed to lower their rates of entropy production? Possible relevance to evolution of the Prigogine theorem and the ergodic hypothesis.

The physiology at limiting and stress conditions challenges the current view that the overall reaction of metabolic processes is always far from equilibrium and, therefore, that organisms are not committed to lower their rates of entropy production. Plausibly, critical steps of natural selection takes place at limiting conditions, near equilibrium, in the linear range response of entropy production, and consequently the trend to lower the rate of entropy production could be the fitness arrow of biological evolution. The evolutionary relevance of the Prigogine theorem is discussed in connection with the ergodic hypothesis of Boltzmann.

Characterization of the 5'- and 3'-ends of mRNAs of ndhH, ndhA and ndhI genes of the plastid ndhH-D operon.

The monocistronic mRNAs of ndhH and ndhA genes of the plastid ndhH-D operon accumulate during senescence. In a step forward to discover the mechanisms involved in the production of mature transcripts of the ndhH-D operon, we determined the 5 - and 3 -ends of low-molecular-weight ndhH, ndhA and ndhI transcripts of barley. The 3'-end of the only ndhH mRNA detected (1622 b) extends 421 b into exon1 of ndhA.

Editing of plastid RNA in Arabidopsis thaliana ecotypes.

Post-transcriptional maturation of plastid-encoded mRNAs from land plants includes editing by making cytidine to uridine alterations at highly specific positions; this usually restores codon identities for conserved amino acids that are important for the proper function of the affected proteins. In contrast to the rather constant number of editing sites their location varies greatly, even between closely related taxa. Here, we experimentally determined the specific pattern of editing sites (the editotype) of the plastid genome of Arabidopsis thaliana ecotype Columbia (Col-0).

Involvement of the thylakoidal NADH-plastoquinone-oxidoreductase complex in the early responses to ozone exposure of barley (Hordeum vulgare L.) seedlings.

A possible implication of the plastid NADH-plastoquinone-oxidoreductase (Ndh) complex in the response against ozone-mediated oxidative stress in barley (Hordeum vulgare L.) leaves was investigated. After a 4 h treatment, exposure of barley seedlings to moderate ozone concentrations produced leaf-age-dependent increases in lipid peroxidation, peroxidase, and Ndh complex activities in the thylakoid membranes.

Topology of the plastid Ndh complex and its NDH-F subunit in thylakoid membranes.

We have investigated the topologies of Ndh (a plastid complex with NADH dehydrogenase activity) and its NDH-F subunit in thylakoids by trypsin and proteinase V8 digestion of both intact and Triton X-100-permeabilized barley thylakoids and identification of the products with antibodies against specific sequences of the NDH-A, NDH-K and NDH-F subunits. Antibody binding and protection against proteinases were also assayed. The analysis of the digestion products of NDH-F by immunodetection and matrix-assisted laser-desorption ionization-time-of-flight allowed us to propose its membrane topology and to compare it with bioinformatic predictions and with that of the homologous subunit (ND5/NuoL/NQO12) of the respiratory complex I.

The activity of the chloroplastic Ndh complex is regulated by phosphorylation of the NDH-F subunit.

Hydrogen peroxide (H(2)O(2)) induces increases, to different degrees, in transcripts, protein levels, and activity of the Ndh complex (EC 1.6.5.

Post-transcriptional control of chloroplast gene expression. Accumulation of stable psaC mRNA is due to downstream RNA cleavages in the ndhD gene.

Intergenic cleavages, intron splicing, and editing of primary transcripts of the plastid ndhH-D operon produce multiple overlapping RNAs, of which the most abundant by far is the monocistronic 400-nucleotide mRNA of psaC (encoding the PsaC protein of photosystem I), in contrast with the low level of transcripts of the six ndh genes. Like other plastid operons containing genes for functionally unrelated proteins, the contrasting accumulation of ndh and psaC transcripts provides a model to investigate the mechanisms of the post-transcriptional control of gene expression, a feature of chloroplast genetic machinery, with a minimum of interference by transcriptional control. In leek (Allium porrum L), the ndhD transcript (which follows the psaC gene and ends the ndhH-D operon) requires C --> U editing to restore its start codon and may be used as a marker for the processing of psaC and ndhD transcripts.

Differential leaf stress responses in young and senescent plants.

Responses to low temperature, mechanical wounding and salicylic acid (SA) treatments were studied in 3-week-old (young) and 6-week-old (senescent) Arabidopsis thaliana (L.) Heynh. plants by analyzing increases in Pal1 and Pr1 expression and superoxide dismutase (SOD; EC 1.

Age-related loss of rooting capability in Arabidopsis thaliana and its reversal by peptides containing the Arg-Gly-Asp (RGD) motif.

We describe here an experimental system to study the age-related decline of adventitious root formation in Arabidopsis thaliana L. (Heynh), ecotype Landsberg erecta (Ler). The system is based on the different rooting capacity of hypocotyls from de-rooted juvenile (12-day-old) and adult (26-day-old) plants.