A rate distortion approach to protein symmetry

A spontaneous symmetry breaking argument is applied to the problem of protein folding, via a rate distortion analysis of the relation between genome coding and the final condensation of the protein molten globule that is, in spirit, analogous to Tlusty’s (2007) exploration of the evolution of the genetic code. In the ‘energy’ picture, the average distortion between codon message and final protein structure, under constraints driven by evolutionary selection, serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding funnel. A dual ‘developmental’ perspective sees the rate distortion function itself as the temperature analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes or affecting the rate of convergence. The rate distortion function appears constrained by the availability of metabolic free energy, with implications for prebiotic evolution, and a nonequilibrium empirical Onsager treatment provides an adaptable statistical model that can be fitted to data, in the same manner as a regression equation. In sum, mechanistic models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a biologically based cognitive paradigm describing folding will be needed for understanding the etiology, prevention, and treatment of these diseases. The developmental formalism introduced here may contribute substantially to such a paradigm.     

Structure and dynamics of the ‘protein folding code’ inferred using Tlusty's topological rate distortion approach

Tlusty's topological rate distortion analysis of the genetic code is applied to protein symmetries and protein folding rates. Unlike the genetic case, numerous thermodynamically accessible ‘protein folding codes’ can be identified from empirical classifications. Folding rates follow from a topologically driven rate distortion argument, a model that can, in principle, be extended to intrinsically disordered proteins. The elaborate cellular regulatory machinery of the endoplasmic reticulum and heat shock proteins is needed to prevent transition between the various thermodynamically ‘natural’ sets of hydrophobic-core protein conformations, and its corrosion by aging would account for the subsequent onset of many protein folding disorders. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the ‘protein folding code’ is really a complicated composite, distributed across protein production and a cellular, or higher, regulatory apparatus acting as a canalizing catalyst that drives the system to converge on particular transitive components within a significantly larger ‘protein folding groupoid’.     

Salt-stress induced changes in the leaf proteome of diploid and tetraploid mandarins with contrasting Na and Cl accumulation behaviour

To understand the genotypic variation of citrus to mild salt stress, a proteomic approach has been carried out in parallel on two citrus genotypes (‘Cleopatra’ and ‘Willow leaf’ mandarins), which differ for Na⁺ and Cl⁻ accumulation, and their cognate autotetraploids (4×). Using two-dimensional electrophoresis approximately 910 protein spots were reproducibly detected in control and salt-stressed leaves of all genotypes. Among them, 44 protein spots showing significant variations at least in one genotype were subjected to mass spectrometry analysis for identification. Salt-responsive proteins were involved in several functions, including photosynthetic processes, ROS scavenging, stress defence, and signalling. Genotype factors affect the salt-responsive pattern, especially that of carbon metabolism. The no ion accumulator ‘Cleopatra’ mandarin genotype showed the highest number of salt-responsive proteins, and up-regulation of Calvin cycle-related proteins. Conversely the ion accumulator ‘Willow leaf’ mandarin showed high levels of several photorespiration-related enzymes. A common set of proteins (twelve spots) displayed higher levels in salt-stressed leaves of 2× and 4× ‘Cleopatra’ and 4× ‘Willow leaf’ mandarin. Interestingly, antioxidant enzymes and heat shock proteins showed higher constitutive levels in 4× ‘Cleopatra’ mandarin and 4× ‘Willow leaf’ mandarin compared with the cognate 2× genotype. This work provides for the first time information on the effect of 8 weeks of salt stress on citrus genotypes contrasting for ion accumulation and their cognate autotetraploids. Results underline that genetic factors have a predominant effect on the salt response, although a common stress response independent from genotype was also found.     

Molecular characterization and expression analysis of ubiquitin-activating enzyme E1 gene in Citrus reticulata

Ubiquitin-activating enzyme E1 (UBE1) catalyzes the first step in the ubiquitination reaction, which targets a protein for degradation via a proteasome pathway. UBE1 plays an important role in metabolic processes. In this study, full-length cDNA and DNA sequences of UBE1 gene, designated CrUBE1, were obtained from ‘Wuzishatangju’ (self-incompatible, SI) and ‘Shatangju’ (self-compatible, SC) mandarins. 5 amino acids and 8 bases were different in cDNA and DNA sequences of CrUBE1 between ‘Wuzishatangju’ and ‘Shatangju’, respectively. Southern blot analysis showed that there existed only one copy of the CrUBE1 gene in genome of ‘Wuzishatangju’ and ‘Shatangju’. The temporal and spatial expression characteristics of the CrUBE1 gene were investigated using semi-quantitative RT-PCR (SqPCR) and quantitative real-time PCR (qPCR). The expression level of the CrUBE1 gene in anthers of ‘Shatangju’ was approximately 10-fold higher than in anthers of ‘Wuzishatangju’. The highest expression level of CrUBE1 was detected in pistils at 7 days after self-pollination of ‘Wuzishatangju’, which was approximately 5-fold higher than at 0 h. To obtain CrUBE1 protein, the full-length cDNA of CrUBE1 genes from ‘Wuzishatangju’ and ‘Shatangju’ were successfully expressed in Pichia pastoris. Pollen germination frequency of ‘Wuzishatangju’ was significantly inhibited with increasing of CrUBE1 protein concentrations from ‘Wuzishatangju’.     

Conspicuous males suffer higher predation risk: visual modelling and experimental evidence from lizards

Colour pattern variation is a striking and widespread phenomenon. Differential predation risk between individuals is often invoked to explain colour variation, but empirical support for this hypothesis is equivocal. We investigated differential conspicuousness and predation risk in two species of Australian rock dragons, Ctenophorus decresii andC. vadnappa . To humans, the coloration of males of these species varies between ‘bright’ and ‘dull’. Visual modelling based on objective colour measurements and the spectral sensitivities of avian visual pigments showed that dragon colour variants are differentially conspicuous to the visual system of avian predators when viewed against the natural background. We conducted field experiments to test for differential predation risk, using plaster models of ‘bright’ and ‘dull’ males. ‘Bright’ models were attacked significantly more often than ‘dull’ models suggesting that differential conspicuousness translates to differential predation risk in the wild. We also examined the influence of natural geographical range on predation risk. Results from 22 localities suggest that predation rates vary according to whether predators are familiar with the prey species. This study is among the first to demonstrate both differential conspicuousness and differential predation risk in the wild using an experimental protocol. Copyright 2003 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.      

The evolution of senescence in multi-component systems

Actuarial senescence is characterized by an increase in mortality rate with increasing chronological age. The reliability theory of senescence proposes that organisms’ vital functions can be modelled as a suite of damageable, irreplaceable elements (typically genes or their products) that protect their bearer from condition-dependent death so long as at least one of the elements remains intact. Current incarnations of the reliability theory of senescence are continuous-time models with no explicit evolutionary component. Here, we use elementary probability theory and evolutionary dynamics analysis to derive a discrete-time version of the reliability theory of senescence. We include three variations on this theme: the ‘Series’ model in which damage to any of n elements results in death, the ‘Parallel’ model, in which damage accumulates in random order and damage to all n elements results in death, and the ‘Cascade’ (multi-stage) model, which is like the Parallel model, except the irreparable damage necessarily follows a strict sequence. For simplicity, we refer to the state of having multiple elements as ‘redundancy’, but this does not imply that the elements are necessarily identical. We show that redundancy leads to actuarial senescence in the Parallel and Cascade models but not in the Series model. We further demonstrate that in the Parallel and Cascade models, lifetime reproductive output (a potential proxy for fitness in populations with discrete generations) is a positive but decelerating function of redundancy. The positive nature of the fitness function leads to the prediction that redundancy and senescence should evolve from non-redundant, non-senescing ancestral populations; however, the deceleration of the fitness function leads to the prediction that this evolution towards increased redundancy will eventually be limited by mutation-selection balance. Using evolutionary dynamics analysis involving the discrete-generation quasispecies equation, we confirm these two predictions. Finally, we show that a population's equilibrium redundancy is sensitive to the environmental conditions that prevailed during its evolution, such as the rate of extrinsic mortality.     

Acceleration of oxidative protein folding by curcumin through novel non-redox chemistry

Curcumin, the major constituent of turmeric is a known antioxidant. We have examined the oxidative folding of the model four-disulfide-bond-containing protein bovine pancreatic ribonuclease A (RNase A) in its presence; results indicate that RNase A regeneration rate increases in a curcumin-dependent manner. Examination of the native tendency of the fully-reduced polypeptide and the stability of key folding intermediates suggests that the increased oxidative folding rate can be attributed to native-like elements induced within the fully-reduced polypeptide and the stabilization of native-like species by this non-redox-active natural product. Our results provide a template for the design of curcuminoid-based synthetic small-molecule fold catalysts that accelerate the folding of ER-processed proteins; this assumes significance given that nitrosative stress and dysfunction of the ER-resident oxidoreductase protein disulfide isomerise due to S-nitrosylation are factors associated with the pathogenesis of Alzheimer’s and Parkinson’s diseases.     

Structural analysis of protein folding by the long-chain archaeal chaperone FKBP26

In the cell, protein folding is mediated by folding catalysts and chaperones. The two functions are often linked, especially when the catalytic module forms part of a multidomain protein, as in Methanococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. Here, we show that FKBP26 chaperone activity requires both a 50-residue insertion in the catalytic FKBP domain, also called ‘Insert-in-Flap’ or IF domain, and an 80-residue C-terminal domain. We determined FKBP26 structures from four crystal forms and analyzed chaperone domains in light of their ability to mediate protein-protein interactions. FKBP26 is a crescent-shaped homodimer. We reason that folding proteins are bound inside the large crescent cleft, thus enabling their access to inward-facing peptidyl-prolyl cis/trans isomerase catalytic sites and ipsilateral chaperone domain surfaces. As these chaperone surfaces participate extensively in crystal lattice contacts, we speculate that the observed lattice contacts reflect a proclivity for protein associations and represent substrate interactions by FKBP26 chaperone domains. Finally, we find that FKBP26 is an exceptionally flexible molecule, suggesting a mechanism for nonspecific substrate recognition.     

Mode of action of the antiprion drugs 6AP and GA on ribosome assisted protein folding

The ribosome, the protein synthesis machinery of the cell, has also been implicated in protein folding. This activity resides within the domain V of the main RNA component of the large subunit of the ribosome. It has been shown that two antiprion drugs 6-aminophenanthridine (6AP) and Guanabenz (GA) bind to the ribosomal RNA and inhibit specifically the protein folding activity of the ribosome. Here, we have characterized with biochemical experiments, the mode of inhibition of these two drugs using ribosomes or ribosomal components active in protein folding (referred to as ’ribosomal folding modulators’ or RFMs) from both bacteria Escherichia coli and yeast Saccharomyces cerevisiae, and human carbonic anhydrase (HCA) as a sample protein. Our results indicate that 6AP and GA inhibit the protein folding activity of the ribosome by competition with the unfolded protein for binding to the ribosome. As a result, the yield of the refolded protein decreases, but the rate of its refolding remains unaffected. Further, 6AP- and GA mediated inhibition of RFM mediated refolding can be reversed by the addition of RFMs in excess. We also demonstrate with delayed addition of the ribosome and the antiprion drugs that there is a short time-span in the range of seconds within which the ribosome interacts with the unfolded protein. Thus we conclude that the protein folding activity of the ribosome is conserved from bacteria to eukaryotes and most likely the substrate for RFMs is an early refolding state of the target protein.     

Isolation and characterisation of EfeM, a periplasmic component of the putative EfeUOBM iron transporter of Pseudomonas syringae pv. syringae

The EfeM protein is a component of the putative EfeUOBM iron-transporter of Pseudomonas syringae pathovar syringae and is thought to act as a periplasmic, ferrous-iron binding protein. It contains a signal peptide of 34 amino acid residues and a C-terminal ‘Peptidase_M75’ domain of 251 residues. The C-terminal domain contains a highly conserved ‘HXXE’ motif thought to act as part of a divalent cation-binding site. In this work, the gene (efeM or ‘Psyr_3370’) encoding EfeM was cloned and over-expressed in Escherichia coli, and the mature protein was purified from the periplasm. Mass spectrometry confirmed the identity of the protein (M_W 27,772 Da). Circular dichroism spectroscopy of EfeM indicated a mainly α-helical structure, consistent with bioinformatic predictions. Purified EfeM was crystallised by hanging-drop vapor diffusion to give needle-shaped crystals that diffracted to a resolution of 1.6 Å. This is the first molecular study of a peptidase M75 domain with a presumed iron transport role.     

The kinetics of a weakly electron-coupled proton transfer in azurin

The thermodynamics and kinetics of the weakly electron-coupled proton transfer of Pseudomonas aeruginosa azurin have been studied and quantitatively determined using fast scan cyclic voltammetry (CV), in which the protein is adsorbed on two types of electrode (pyrolytic graphite ‘edge’ (PGE) or 1-decanethiol modified gold). Electron transfer is coupled to a slow protonation of His35, which is not a ligand to the copper ion but is located approximately 8 Å away. Protonation of His35 produces small changes in the reduction potential of the copper site, which are time-resolved within the scan rate range 0.01-100 V s⁻¹.     

A mathematical model for cell size control in fission yeast

Experimental investigations of cell size control in fission yeast Schizosaccharomyces pombe have illustrated that the cell cycle features ‘sizer’ and ‘timer’ phases which are distinguished by a growth rate changing point. Based on current biological knowledge of fission yeast size control, we propose here a model of ordinary differential equations (ODEs) for a possible explanation of the facts and control mechanism which is coupled with the cell cycle. Simulation results of the ODE model are demonstrated to agree with experimental data for the wild type and the cdc2-33 mutant. We show that the coupling of cell growth to cell division by translational control may account for observed properties of size control in fission yeast. As the translational control in the expression of cycle proteins Cdc13 and Cdc25 constructs positive feedback loops, the dynamical activities of the key components undergoes a rapid rising after a preliminary stage of slow increase. The coupling of this dynamical behavior to the elongation of the cell naturally gives rise to a rate change point and to ‘sizer’ and ‘timer’ phases, which characterize the cell cycle of fission yeast.     

Assimilate translocation and expression of sucrose transporter,OsSUT1, contribute to high-performance ripening under heat stress in the heat-tolerant rice cultivar Genkitsukushi

High temperature reduces the grain quality of rice, a situation likely to become more frequent because of global warming. We studied the effects of high-temperature stress on grain quality of heat-tolerant cultivar ‘Genkitsukushi’ and heat-sensitive cultivar ‘Tsukushiroman’. When day/night temperatures were 31/26 °C from heading until maturity, the grain quality of ‘Genkitsukushi’ was rated at the first inspection grade (high quality), whereas ‘Tsukushiroman’ showed a remarkable increase in the percentage of white immature kernels (low quality). Nonstructural carbohydrate content in the stem of ‘Genkitsukushi’ the early maturation was significantly higher than in ‘Tsukushiroman’ and greatly decreased under high temperature. From 14 to 21 days after heading, the expression of the sucrose transporter gene, OsSUT1, was higher in the stem of ‘Genkitsukushi’ grown under high temperature than in ‘Tsukushiroman’. In addition, the expression of OsSUT1 in the grains of ‘Genkitsukushi’ was significantly higher than in ‘Tsukushiroman’ during the ripening period. These results indicate that sugar transport functions more effectively in ‘Genkitsukushi’ than in ‘Tsukushiroman’, and that the effectiveness of sugar transport contributes to maintaining high grain quality in ‘Genkitsukushi’ under high-temperature conditions.     

Physiological approach to explain the ecological success of ‘superclones’ in aphids: Interplay between detoxification enzymes, metabolism and fitness

‘Superclones’ are predominant and time-persistent genotypes, exhibiting constant fitness across different environments. However, causes of this ecological success are still unknown. Therefore, we studied the physiological mechanisms that could explain this success, evaluating the effects of wheat chemical defences on detoxification enzymes [cytochrome P450 monooxygenases (P450), glutathione S-transferases (GST), esterases (EST)], standard metabolic rate (SMR), and fitness-related traits [adult body mass and intrinsic rate of increase (r_m)] of two ‘superclones’ (Sa1 and Sa2) of the grain aphid, Sitobion avenae. Additionally, we compared ‘superclones’ with a less-frequent genotype (Sa46). Genotypes were reared on three wheat cultivars with different levels of hydroxamic acids (Hx; wheat chemical defences). Detoxification enzymes and SMR did not differ between wheat hosts. However, GST and EST were different between ‘superclones’ and Sa46, while Sa1 showed a higher SMR than Sa2 or Sa46 (p = 0.03). Differences between genotypes were found for r_m, which was higher for Sa1 than for Sa2 or Sa46. For all cases, genotype-host interactions were non-significant, except for aphid body mass. In conclusion, ‘superclones’ exhibit a broad host range, flat energetic costs for non-induced detoxification enzymes, and low variation in their reproductive performance on different defended hosts. However, physiological specialization of ‘superclones’ that could explain their ecological success was not evident in this study.     

Predator-induced changes in fluted giant clam (Tridacna squamosa) shell morphology

Predator-induced defences have been demonstrated in numerous marine molluscs, but never in giant clams (Bivalvia: Tridacnidae). Water-borne cues from the predatory crab Myomenippe hardwickii were tested for their ability to induce changes in the shell morphology, strength and growth of juvenile fluted giant clams, Tridacna squamosa. Specimens were maintained in effluent from tanks holding ‘fed crabs’, ‘starved crabs’ and ‘no crabs’. To ensure changes were due to predator cues only, food for the crabs was provided ex situ and measures were taken to minimise the prey signal. After 182 days, MANOVA identified differences in various shell parameters relating to shape and strength. CDA showed a clear change in overall morphology, with strong separation among the three treatments. Effluent from ‘fed crabs’ had a greater influence than effluent from ‘starved crabs’, possibly because the starved crabs were perceived as weaker, and thus less risk. Significantly more clams died in ‘fed crabs’ treatments (25%) and ‘starved crabs’ treatments (30%) compared to the ‘no crabs’ control (0%). This degree of mortality has not been observed in similar experiments elsewhere and represents a new challenge to interpret. We suggest that the cause is unlikely to be related to the plastic responses, but rather a result of some form of crab-associated contaminant.     

The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): great difference in the A+T-rich region compared to Liriomyza trifolii

The complete mitochondrial genome sequence of Liriomyza sativae Blanchard (15,551 bp) was determined and analyzed in this study. The circular genome contained 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and an A + T-rich region. The initiation codons of COI and ND1 were ‘ATCA’ and ‘GTG’, respectively. ND2 gene used the truncated termination codon ‘T’. All the tRNA genes had the typical cloverleaf secondary structures except for tRNA^Ser(AGN) gene, which was found with the absence of a DHU arm. In addition, a tRNA-like secondary structure (tRNA^Met) was found in the A + T-rich region. The great difference was that the length of L. sativae A + T-rich region was 597 bp shorter than that of Liriomyza trifolii (Burgess). Meanwhile, some minor differences such as ‘TATA’ block were also observed in L. sativae in contrast to ‘TACA’ block in L. trifolii. There were also some essential structure elements such as ‘TATA’ block, ‘G(A)_nT’ block, poly-T stretch and stem-and-loop structure in the A + T-rich region of L. sativae mitochondrial genome.