Plant and animal transglutaminases: do similar functions imply similar structures?

In plants the post-translational modification of proteins by polyamines catalysed by transglutaminases has been studied since 1987; it was identified by the production of glutamyl-polyamine derivatives, biochemical features, recognition by animal antibodies and modification of typical animal substrates. Transglutaminases are widespread in all plant organs and cell compartments studied until now, chloroplast being the most studied. Substrates are: photosynthetic complexes and Rubisco in chloroplasts, cytoskeleton and cell wall proteins. Roles either specific of plants or in common with animals are related to photosynthesis, fertilisation, stresses, senescence and programmed cell death, showing that the catalytic function is conserved across the kingdoms. AtPng1p, the first plant transglutaminase sequenced shows undetectable sequence homology to the animal enzymes, except for the catalytic triad. It is, however, endowed with a calcium-dependent activity that allowed us to build a three-dimensional model adopting as a template the animal tranglutaminase 2.     

Do variables that affect similar bistable apparent-movement displays result in similar changes in perception?

Two bistable apparent-movement displays (i.e. ones that generate two qualitatively different kinds of movement percepts under different conditions) were compared. They were designed to be as similar as possible spatially, and were studied with identical stimulus manipulations to see whether changes in balance between their bistable percepts would be similar. Results show that the two displays had different response characteristics to the same stimulus manipulations. Two models of motion perception that have previously predicted at least one kind of bistable apparent motion were considered in terms of how well they address the current data. As yet, neither model has been shown to predict the motion states and bistable behavior of the two displays studied here. It is concluded that results of the type described here (specifically, differences in the psychophysical functions yielded by two structurally similar but qualitatively different bistable displays) present a challenge for theories of motion perception.     

Do proteins with similar folds have similar transition state structures? A diffuse transition state of the 169 residue apoflavodoxin

Apoflavodoxin from Anabaena PCC 7119 is a 169 residue globular protein of known structure and energetics. Here, we present a comprehensive Phi-value analysis to characterize the structure of its transition state. A total of 34 non-disruptive mutations are made throughout the structure and a range of Phi-values from zero to one are observed. In addition, a small set of eight aliphatic small-to-large mutations have been introduced in the hydrophobic core of the protein and they have been analyzed to investigate the feasibility of stabilizing the unfolding transition state by creating new non-native interactions. We find that the transition state of apoflavodoxin (so far the largest protein subjected to Phi-analysis) is diffuse and that it can be stabilized by unspecific hydrophobic interactions that can speed up the folding reaction. The data gathered on the apoflavodoxin transition state are compared with results from experimental studies in other proteins to revisit the relationship between the native state topology and transition state structure.     

Comparison of inhibitory activity of isomeric triazolopyridine derivatives towards adenosine receptor subtypes or do similar structures reveal similar bioactivities?

The synthesis of an array of 8-amino-2-aryl-[1,2,4]triazolo[1,5-a]pyridine-6-carboxyl amide derivatives is described for the first time. A subset of 20 derivatives were compared to their isomeric 5-amino-2-aryl-[1,2,4]triazolo[1,5-a]pyridine-7-carboxyl amide counterparts with regard to their potential to inhibit the human adenosine 2a (hA2a) receptor and their selectivity against the human adenosine 1 (hA1) receptor. Based on the analysis of H-bond donor/acceptor capabilities of the isomeric triazolopyridine pairs it can be concluded that the H-bond donor strength of the free amino functionality is the main determinant for hA2a inhibitory activity and hA1 selectivity.     

Nuclear and mitochondrial DNA repair: similar pathways?

Mitochondrial DNA (mtDNA) alterations are implicated in a broad range of human diseases and alterations of the mitochondrial genome are assumed to be a result of its high susceptibility to oxidative damage and its limited DNA repair compared to nuclear DNA (nDNA). Characterization of DNA repair mechanisms has generally focused on these processes in nDNA but increasing interest and research effort have contributed to our knowledge of the mechanisms underlying DNA repair in mitochondria. In this review, we make comparisons between nDNA and mtDNA repair pathways and propose a model for how these pathways interact in mitochondria.     

How similar are daily and seasonal biological clocks?

Daily and seasonal timing systems in insects have usually been supposed to share similar mechanisms, because both rely in large measure on information from the daily light-dark cycle: daily clocks can ensure that activity coincides with the appropriate time of day, and seasonal time is indicated most reliably by daylength. However, several lines of evidence suggest that the systems are different. For example, receptor features, photosensitive pigments, clocks, and the effectors that mediate responses to information derived from the clock may have different daily, seasonal and general functions and properties, and several different systems are known. There are many different additional elements in the seasonal response. Therefore, these responses may not rely on similar timing mechanisms, despite the long-standing belief that the seasonal clock has circadian components. Such a difference would be consistent with the fact that temporal responses serve a very wide range of purposes, meeting many different ecological needs on different time frames. Consequently, understanding the seasonal relevance of the photoperiodic responses is more important than revealing any possible involvement with circadian systems.     

How do biological systems discriminate among physically similar ions?

This paper reviews the history of understanding how biological systems can discriminate so strikingly among physically similar ions, especially alkali cations. Appreciation of qualitative regularities ("permitted sequences") and quantitative regularities ("selectivity isotherms") in ion selectivity grew first from studies of ion exchangers and glass electrodes, then of biological systems such as enzymes and cell membranes, and most recently of lipid bilayers doped with model pores and carriers. Discrimination of ions depends on both electrostatic and steric forces. "Black-box" studies on intact biological membranes have in some cases yielded molecular clues to the structure of the actual biological pores and carriers. Major current problems involve the extraction of these molecules; how to do it, what to do when it is achieved, and how (and if) it is relevant to the central problems of membrane function. Further advances are expected soon from studies of rate barriers within membranes, of voltage-dependent ("excitable") conducting channels, and of increasingly complex model systems and biological membranes.     

Are in vivo and in situ brain tissues mechanically similar?

Brain tissue mechanical properties have been well-characterized in vitro, and were found to be inhomogeneous, nonlinear anisotropic and influenced by neurological development and postmortem time interval prior to testing. However, brain in vivo is a vascularized tissue, and there is a paucity of information regarding the effect of perfusion on brain mechanical properties. Furthermore, mechanical properties are often extracted from preconditioned tissue, and it remains unclear if these properties are representative of non-preconditioned tissue. We present non-preconditioned (NPC) and preconditioned (PC) relaxation responses of porcine brain (N = 10) obtained in vivo, in situ and in vitro, at anterior, mid and posterior regions of the cerebral cortex during 4mm indentations at either 3 or 1 mm/s. Material property characteristics showed no dependency on the site tested, thus revealing that cortical gray matter on the parietal and frontal lobes can be considered homogenous. In most cases, preconditioning decreased the shear moduli, with a more pronounced effect in the dead (in situ and in vitro) brain. For most conditions, it was found that only the long-term time constant of relaxation (tau > 20 s) significantly decreased from in vivo to in situ modes (p < 0.02), and perfusion had no effect on any other property. These findings support the concept that perfusion does not affect the stiffness of living cortical tissue.     

Baclofen and γ-hydroxybutyrate: similar effects on cerebral dopamine neurones

Baclofen (20 mg/kg) caused an increase in the content of homovanillic acid (HVA) and dopamine (DA) in rat brain 2–3 h after drug injection without appreciable changes in the level of other monoamines and their main metabolites. Six and eight hours after baclofen, the content of HVA but not that of DA was reduced. Moreover, baclofen initially (20 min after injection) reduced, but later (105 min post drug) enhanced the accumulation of HVA induced by probenecid. The shortlasting (20 min) initial reduction of HVA elevation in probenecid-pretreated animals as well as the longlasting (6–8 h) decrease of HVA levels in rats injected with baclofen alone are interpreted to be due to a decreased release and metabolism of DA, probably as a consequence of the blockade of impulse flow in mesolimbic and nigro-striatal DA neurones. The increase in HVA and DA seen during the first few hours is thought to result from enhanced DA synthesis similar to that known for γ-hydroxybutyrate (GHB). This initial rise in HVA due to synthesis stimulation probably masked a reduction of HVA to be expected immediately after baclofen injection. The similarity between baclofen and GHB is stressed by the finding that baclofen counteracted the increase of HVA occuring after chlorpromazine and D-amphetamine but not that induced by the benzoquinolizine derivative, Ro 4-1284.     

Comparative molecular dynamics—Similar folds and similar motions?

Proteins possessing the same fold may undergo similar motions, particularly if these motions involve large conformational transitions. The increasing amounts of structural data provide a useful starting point with which to test this hypothesis. We have performed a total of 0.29 micros of molecular dynamics across a series of proteins within the same fold family (periplasmic binding proteinlike) in order to address to what extent similarity of motion exists. Analysis of the local conformational space on these timescales (10-20 ns) revealed that the behavior of the proteins could be readily distinguished between an apo-state and a ligand-bound state. Moreover, analysis of the root-mean-square fluctuations reveals that the presence of the ligand exerts a stabilizing effect on the protein, with similar motions occurring, but with reduced magnitude. Furthermore, the conformational space in the presence of the ligand appears to be dictated by sequence but not by the type of ligand present. In contrast, apo-simulations showed considerable overlap of conformational space across the fold as a result of their ability to undergo larger fluctuations. Indeed, we observed several transitions from different simulations between states corresponding to the closed-cleft and open-cleft forms of the fold, with the predominant motions being conserved across the different proteins. Thus, large-scale conformational changes do indeed appear to be conserved across this fold architecture, but smaller conformational motions appear to reflect the differences in sequence and local fold.     

Mexical plant phenology: is it similar to Mediterranean communities?

The sclerophyllous, evergreen vegetation found in Mexico under tropical climate is named 'Mexical' (MEX) and presents many traits that have been thought to converge under a Mediterranean climate. Flowering phenology is strongly similar across Mediterranean-type ecosystems (MTEs) and this paper investigates MEX plant phenology in this context. The common history of the vegetation and the differences in the climatic conditions experienced by MEX and MTE taxa provide an ideal scenario to infer the relative importance of natural selection and historical constraints in the phenological response of plants to climatic conditions. This study has involved collecting field and bibliographic data on flowering phenology of MEX communities to detect (1) similarities at the community level between MTEs and MEX, (2) similarities between Tertiary and Quaternary taxa in MTEs and MEX, and (3) similarities between congeneric taxa from MEX and MTEs (taxa sharing a common ancestor but having evolved under different climates). Flowering in MEX does not occur mainly in spring, as in MTEs, but in summer, suggesting a response that maximizes water use in the rainy season. Flowering phenology of MEX species differed from their MTE congeneric species, suggesting that even though a common ancestor is shared, environmental pressures have led to different phenological responses in MEX and MTE plants. The flowering season for species that originated in the Tertiary and Quaternary did not differ in MEX, as expected, because of climatic uniformity along the whole time line. In MTEs, flowering differences between Tertiary and Quaternary species were not congruent, suggesting that the balance between the historical constraints and the selective force of the Mediterranean climate is different among the three MTEs, and a particular explanation is needed for each. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 297–303.     

Do nematode and macrofauna assemblages provide similar ecological assessment information?

Do nematode and macrofauna assemblages provide similar ecological assessment information? To answer this question, in the summer of 2006, subtidal soft-bottom assemblages were sampled and environmental parameters were measured at seven stations covering the entire salinity gradient of the Mondego estuary. Principal components analysis (PCA) was performed on the environmental parameters, thus establishing different estuarine stretches. The ecological status of each community was determined by applying the Maturity Index and the Index of Trophic Diversity to the nematode data and the Benthic Assessment Tool to the macrofaunal data. Overall, the results indicated that the answer to the initial question is not straightforward. The fact that nematode and macrofauna have provided different responses regarding environmental status may be partially explained by local differentiation in microhabitat conditions, given by distinct sampling locations within each estuarine stretch and by different response-to-stress times of each benthic community. Therefore, our study suggests that both assemblages should be used in marine pollution monitoring programs.     

Canopy and litter ant assemblages share similar climate–species density relationships

Tropical forest canopies house most of the globe''s diversity, yet little is known about global patterns and drivers of canopy diversity. Here, we present models of ant species density, using climate, abundance and habitat (i.e. canopy versus litter) as predictors. Ant species density is positively associated with temperature and precipitation, and negatively (or non-significantly) associated with two metrics of seasonality, precipitation seasonality and temperature range. Ant species density was significantly higher in canopy samples, but this difference disappeared once abundance was considered. Thus, apparent differences in species density between canopy and litter samples are probably owing to differences in abundance–diversity relationships, and not differences in climate–diversity relationships. Thus, it appears that canopy and litter ant assemblages share a common abundance–diversity relationship influenced by similar but not identical climatic drivers.     

Do disparate mechanisms of duplication add similar genes to the genome?

Gene duplication is the fundamental source of new genes. Biases in duplication have profound implications for the dynamics of gene content during evolution. In this article, we compare genes arising from whole gene duplication (WGD), smaller scale duplication (SSD) and singletons in Saccharomyces cerevisiae. Our results demonstrate that genes duplicated by WGD and SSD are similarly biased with respect to codon bias and evolutionary rate, although differing significantly in their functional constituency.