Direct Targeting of Proteins from the Cytosol to Organelles: The ER versus Endosymbiotic Organelles

In eukaryotic cells consisting of many different types of organelles, targeting of organellar proteins is one of the most fundamental cellular processes. Proteins belonging to the endoplasmic reticulum (ER), chloroplasts and mitochondria are targeted individually from the cytosol to their cognate organelles. As the targeting to these organelles occurs in the cytosol during or after translation, the most crucial aspect is how specific targeting to these three organelles can be achieved without interfering with other targeting pathways. For these organelles, multiple mechanisms are used for targeting proteins, but the exact mechanism used depends on the type of protein and organelle, the location of targeting signals in the protein and the location of the protein in the organelle. In this review, we discuss the various mechanisms involved in protein targeting to the ER, chloroplasts and mitochondria, and how the targeting specificity is determined for these organelles in plant cells .     

The role of host sex in parasite dynamics: field experiments on the yellow-necked mouse Apodemus flavicollis

We investigated the role of host sex in parasite transmission and questioned: ‘Is host sex important in influencing the dynamics of infection in free living animal populations?’ We experimentally reduced the helminth community of either males or females in a yellow‐necked mice (Apodemus flavicollis) population using an anthelmintic, in replicated trapping areas, and subsequently monitored the prevalence and intensity of macroparasites in the untreated sex. We focussed on the dominant parasite Heligmosomoides polygyrus and found that reducing parasites in males caused a consistent reduction of parasitic intensity in females, estimated through faecal egg counts, but the removal of parasites in females had no significant influence on the parasites in males. This finding suggests that males are responsible for driving the parasite infection in the host population and females may play a relatively trivial role. The possible mechanisms promoting such patterns are discussed.     

Isolation and biochemical characterization of heparin-binding proteins from boar seminal plasma: A dual role for spermadhesins in fertilization

Sperm surface-coated heparin-binding proteins originating from secretions of the male sexual accessory glands, are known to play a pivotal role as extrinsic regulatory factors during sperm capacitation in many mammalian species. They interact with glycosaminoglycans present in the female genital tract and enhance the subsequent zona pellucida-induced acrosome reaction. We have isolated heparin-binding proteins from boar seminal plasma by affinity chromatography on heparin–Sepharose and reverse-phase HPLC. N-Terminal sequence analysis of these proteins identified a boar counterpart of the bovine capacitation factors BSP-A1/2 (also called PDC-109) and BSP-A3. Several carbohydrate- and zona pellucida-binding proteins, which belong to the newly described spermadhesin family, were also identified as heparin-binding proteins. Our results imply that, besides other capacitation factors, members of the spermadhesin family may play a dual role in sperm capacitation and fertilization in the pig. © 1993 Wiley-Liss, Inc.     

The pH-dependent unfolding mechanism of P2 myelin protein: an experimental and computational study

The P2 protein is a small, extrinsic protein of the myelin membrane in the peripheral nervous system that structurally belongs to the fatty acid binding proteins (FABPs) family, sharing with them a 10 strands beta-barrel structure. FABPs appear to be involved in cellular fatty acid transport, but very little is known about the role of P2 in the metabolism of peripheral myelin lipids. Study of protein conformation at different pHs is a useful tool for the characterization of the unfolding mechanisms and the intrinsic conformational properties of the protein, and may give insight into factors that guide protein folding pathways. In particular, low pH conditions have been shown to induce partially folded states in several proteins. In this paper, the acidic unfolding of purified P2 protein was studied with both spectroscopic techniques and molecular dynamics simulation. Both experimental and computational results indicate the presence of a partly folded state at low pH, which shows structural changes mainly involving the lid that is formed by the helix-turn-helix domain. The opening of the lid, together with a barrel relaxation, could regulate the ligand exchanges near the cell membrane, supporting the hypothesis that the P2 protein may transport fatty acids between Schwann cells and peripheral myelin.     

城市住宅建筑系统流量-存量动态模拟——以北京市为例

地面建筑物的累积与更新是城市化过程的结果与显性特征之一。城市建筑系统在不同层面上与外部环境系统进行着物质能量交换,对这种交互产生的资源压力与环境胁迫的关注,使其成为城市代谢研究领域中的热点问题。系统分析与模拟城市建筑物流量-存量的动态变化过程及其资源环境响应,对于揭示城市建筑系统代谢机理,提高城市总体规划精准性、强化资源系统韧性管理、提升废弃物处置效率等宏观战略具有重要意义。以北京市为例,基于Stella建模平台,构建了城市居民住宅建筑系统流量-存量的动态模拟模型,定量模拟了不同管理情景下钢材需求量与建筑拆除垃圾产生量的变化区间。结果表明:(1)基准情景下,北京住宅建筑新建流量前期增速较快,2005年达到峰值3024.1万m~2,而拆除流量约于2057年达到峰值,拆除面积为2073.14万m~2;城市住宅建筑存量最高值出现在2075年左右,面积为7.51亿m~2;(2)与基准情景相比,如果人均住宅建筑面积提高到45 m~2,从现在到模拟期结束(2019—2100)将增加钢铁需求量3251.65万t;而如果延长住宅建筑寿命至设计值,同期可减少钢铁需求量3022.9万t;(3)基准情景、大面积情景以及长寿命情景下,北京市城镇住宅建筑拆除垃圾峰值产生量分别为0.29亿t、0.39亿t、0.20亿t,政府管理部门应采取有针对性的应对措施,提前做出综合利用和处理处置方案。     

The evolution of nocturnal behaviour in sweat bees,Megalopta genalis and M. ecuadoria (Hymenoptera: Halictidae): an escape from competitors and enemies?

Evolutionary transitions to dim-light foraging (predawn matinal, crepuscular, nocturnal) have occurred repeatedly in bees, and may be associated with an escape from enemies or competitors. To date, however, little information has been available to test these hypotheses. Here we provide the first detailed information on the nesting behaviour of two species of Neotropical, nocturnal sweat bees, Megalopta genalis and M. ecuadoria (Hymenoptera: Halictidae). Females are facultatively social or solitary, and construct nests in dead wood. Nocturnal foraging behaviour is bimodal. Bees began foraging after sunset (∼18:30 h) and ceased foraging approximately 1 h later even though nocturnal flowers with pollen were still abundant; a second foraging bout occurred in the predawn morning, which began at ∼04:45 h and ended around sunrise (∼06:15 h) when diurnal-blooming flowers were abundant. Bees are capable of controlled flight in full light. They utilized pollen from both canopy and understory plant species, which have diurnal or nocturnal pollen anthesis. Megalopta nests are attacked by generalist predators such as ants, as well as the endoparasitic fly Melaloncha sp. nov. (Phoridae), the beetle Macrosaigon gracilis (Rhipophoridae), the parasitic wasp Lophostigma cincta (Mutillidae), and the brood parasite Megalopta byroni (Halictidae). Overall nest survivorship rates were comparable to those for diurnal relatives, but rates of cell parasitism for Megalopta (< < 5%) were substantially lower than they are for day-flying relatives, offering some support for the hypothesis that the evolution of nocturnal behaviour enables escape from natural enemies.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 377–387.     

The Rop GTPase: an emerging signaling switch in plants

G proteins are ubiquitous molecular switches in eukaryotic signal transduction, but their roles in plant signal transduction had not been clearly established until recent studies of the plant-specific Rop subfamily of RHO GTPases. Rop participates in signaling to an array of physiological processes including cell polarity establishment, cell growth, morphogenesis, actin dynamics, H₂O₂ generation, hormone responses, and probably many other cellular processes in plants. Evidence suggests that plants have developed unique molecular mechanisms to control this universal molecular switch through novel GTPase-activating proteins and potentially through a predominant class of plant receptor-like serine/threonine kinases. Furthermore, the mechanism by which Rop regulates specific processes may also be distinct from that for other GTPases. These advances have raised the exciting possibility that the elucidation of Rop GTPase signaling may lead to the establishment of a new paradigm for G protein-dependent signal transduction in plants.     

Investigation of the molecular similarity in closely related protein systems: The PrP case study

The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mutants, structurally similar to their native isoform but inherently prone to amyloid conversion, may be a viable strategy to elucidate the structural features connected with amyloidogenesis. In this article, we present a computational protocol based on the combination of molecular dynamics (MD) and grid‐based approaches suited for the pairwise comparison of closely related protein structures. This method was applied on the cellular prion protein (PrP^C) as a case study and, in particular, addressed to the quali/quantification of the structural features conferred by either E200K mutations and treatment with CaCl₂, both able to induce the scrapie conversion of PrP. Several schemes of comparison were developed and applied to this case study, and made up suitable of application to other protein systems. At this purpose an in‐house python codes has been implemented that, together with the parallelization of the GRID force fields program, will spread the applicability of the proposed computational procedure. Proteins 2015; 83:1751–1765. © 2015 Wiley Periodicals, Inc.     

Collapse transitions in protein-like lattice polymers: The effect of sequence patterns

The collapse transition of lattice protein-like heteropolymers has been studied by means of the Monte Carlo method. The protein model has been reduced to the α-carbon trace restricted to a high coordination lattice. The sequences of model heteropolymers contain two types of mers: hydrophobic/nonpolar (H) and hydrophilic/polar (P). Interactions of HH and PP pairs were assumed to be negative (weaker attractions of PP pairs) while the contact energy for HP pairs was equal to zero. All sequence-specific short-range interactions have been neglected in the present studies. It has been found that homopolymeric chains undergo a smooth collapse transition to a dense globular state. The globule lacks any signatures of local ordering that could be interpreted as a model of protein secondary structure. Hetero-polymers with the sequences of hydrophilic and hydrophobic residues characteristic for α- and β-type proteins undergo a somewhat sharper (though continuous) collapse transition to a dense globular state with elements of local ordering controlled by the sequence. The helical pattern induces more secondary structure than the β-type pattern. For all examined sequences the level of local ordering was lower than the average secondary structure content of globular proteins. The results are compared with other theoretical work and with known experimental facts. The implications for the reduced modeling of protein systems are briefly discussed. © 1997 John Wiley & Sons, Inc. Biopoly 42: 537–548, 1997     

The role of protein sequence and amino acid composition in amyloid formation: scrambling and backward reading of IAPP amyloid fibrils

The specific functional structure of natural proteins is determined by the way in which amino acids are sequentially connected in the polypeptide. The tight sequence/structure relationship governing protein folding does not seem to apply to amyloid fibril formation because many proteins without any sequence relationship have been shown to assemble into very similar β-sheet-enriched structures. Here, we have characterized the aggregation kinetics, seeding ability, morphology, conformation, stability, and toxicity of amyloid fibrils formed by a 20-residue domain of the islet amyloid polypeptide (IAPP), as well as of a backward and scrambled version of this peptide. The three IAPP peptides readily aggregate into ordered, β-sheet-enriched, amyloid-like fibrils. However, the mechanism of formation and the structural and functional properties of aggregates formed from these three peptides are different in such a way that they do not cross-seed each other despite sharing a common amino acid composition. The results confirm that, as for globular proteins, highly specific polypeptide sequential traits govern the assembly pathway, final fine structure, and cytotoxic properties of amyloid conformations.     

The costs and benefits in an unusual symbiosis: experimental evidence that bitterling fish (Rhodeus sericeus) are parasites of unionid mussels in Europe

Interspecific symbiotic relationships involve a complex network of interactions, and understanding their outcome requires quantification of the costs and benefits to both partners. We experimentally investigated the costs and benefits in the relationship between European bitterling fish (Rhodeus sericeus) and freshwater mussels that are used by R. sericeus for oviposition. This relationship has hitherto been thought mutualistic, on the premise that R. sericeus use mussels as foster parents of their embryos while mussels use R. sericeus as hosts for their larvae. We demonstrate that R. sericeus is a parasite of European mussels, because it (i) avoids the cost of infection by mussel larvae and (ii) imposes a direct cost on mussels. Our experiments also indicate a potential coevolutionary arms race between bitterling fishes and their mussel hosts; the outcome of this relationship may differ between Asia, the centre of distribution of bitterling fishes, and Europe where they have recently invaded.     

The search for stability on narrow supports: an experimental study in cats and dogs

Kinematic and coordination variables were studied in two carnivorans, one with known locomotor capabilities in arboreal substrates (cat), and the other a completely terrestrial species (dog). Two horizontal substrates were used: a flat trackway on the ground (overground locomotion) and an elevated and narrow runway (narrow-support locomotion). Despite their different degree of familiarity with the ‘arboreal’ situation, both species developed a strategy to adapt to narrow supports. The strategy of cats was based on using slower speeds, coupled with modifications to swing phase duration, to keep balance on narrow supports. The strategy of dogs relied on high speeds to gain in dynamic stability, and they increased cycle frequency by reducing swing phase duration. Furthermore, dogs showed a high variability in limb coordination, although a tendency to canter-like coordination was observed, and also avoided whole-body aerial phases. In different ways, both strategies suggested a reduction of peak vertical forces, and hence a reduction of the vertical oscillations of the centre of mass. Finally, lateral oscillation was reduced by the use of a crouched posture.     

The nucleotide sequence of a regulatory gene present on a plasmid in an enterotoxigenic Escherichia coli strain of serotype O167:H5

A DNA fragment that can functionally substitute for cfaD, the positive regulatory gene involved in expression of CFA/I fimbriae, has recently been cloned from an Escherichia coli strain of serotype O167:H5 that produces CS5 fimbriae. Nucleotide sequence determination showed that the fragment contained a gene, csvR (Coli Surface Virulence factor Regulator) homologous to the cfaD gene, which encoded for a protein of 301 amino acid residues. The csvR gene was found to be located between two different insertion sequences. Comparison of the amino acid sequence of the CsvR and CfaD proteins showed that CsvR is 34 amino acid residues longer at the C-terminus and, in the sequence, it also contains an insertion of two amino acid residues. The similarity between CfaD and Rns, the positive regulator of CS1 and CS2 expression, is much higher (97%) than between CsvR and CfaD (87%). This is reflected by the fact that the level of expression of CFA/I fimbriae induced by CsvR is not as high as when expression is induced by CfaD or Rns.     

The aerobactin iron uptake system in enteropathogenic Escherichia coli: evidence for an extinct transposon

Abstract It has previously been demonstrated that the precursor form of the phosphate-binding protein (pre-PhoS) is accumulated in both the cytoplasmic membrane and the cytoplasm under conditions of phosphate-binding protein (PhoS) hyperproduction in Escherichia coli [11]. In this study, the trypsin accessibility of these 2 pre-PhoS pools has been investigated in spheroplasts. The results demonstrate that the membrane-associated pre-PhoS is not accessible to trypsin, and thus has not been translocated. The sensitivity to trypsin of mature PhoS, membrane-associated pre-PhoS and cytoplasmic pre-PhoS was compared. The results suggest a difference in conformation between membrane-associated and cytoplasmic pre-PhoS since the former is more trypsin-sensitive than the latter. Mature PhoS is resistant to trypsin. The significance of these results with regard to the export mechanism for periplasmic proteins is discussed.     

The potential role of phoresy in the evolution of parasitism: radiolabelling (tritium) evidence from an astigmatid mite

Using tritium as a radiolabel marker of interspecific fluid transfer, we present experimental evidence that the heteromorphic deutonymph of an astigmatid mite (Hemisarcoptes cooremani) acquires materials (at least water) directly from the haemolymph of its beetle host (Chilocorus cacti). This acquisition is above that obtained from atmospheric vapour. The material acquired from the host is necessary for the completion of the ontogeny of H. cooremani and is likely procured through the action of the caudal ventral suckers of the heteromorphic deutonymph (hypopus). On gross morphological criteria, this mite-beetle relationship was previously defined as phoretic (for dispersal). Scanning electron photomicrographs of the physical relationship between the hypopodes and the heetles shed light on the parasitic nature of the hypopus of H. cooremani. Our findings are discussed in terms of the evolution of parasitism from a free-living astigmatid form. This transition into parasitism is facilitated by the heteromorphic hypopus and represents a classic wolf-insheep's-clothing strategy. The heteromorph retains the characteristic phoretic morphology while exploiting the host in transit.     

The role of CAM in high rainfall cloud forests: an in situ comparison of photosynthetic pathways in Bromeliaceae

Crassulacean acid metabolism (CAM), an advanced photosynthetic pathway conferring water conservation to plants in arid habitats, has enigmatically been reported in some species restricted to extremely wet tropical forests. Of these, epiphytic Bromeliaceae may possess absorbent foliar trichomes that hinder gas‐exchange when wetted, imposing further limitations on carbon dioxide (CO₂) uptake. The hypothesis that the metabolic plasticity inherent to CAM confers an ecological advantage over conventional C₃ plants, when constant rainfall and mist might inhibit gas‐exchange was investigated. Gas‐exchange, fluorometry and organic acid and mineral nutrient contents were compared for the bromeliads Aechmea dactylina (CAM) and Werauhia capitata (C₃) in situ at the Cerro Jefe cloud forest, Panama (annual rainfall > 4 m). Daily carbon gain and photosynthetic nutrient use efficiencies were consistently higher for A. dactylina, due to a greater CO₂ uptake period, recycling of CO₂ from respiration and a dynamic response of CO₂ uptake to wetting of leaf surfaces. During the dry season CAM also had water conserving and photoprotective roles. A paucity of CAM species at Cerro Jefe suggests a recent radiation of this photosynthetic pathway into the wet cloud forest, with CAM extending diversity in form and function for epiphytes.     

The disappearance of an hsc70 species in mung bean seed during germination: purification and characterization of the protein

We have purified a 73 kDa protein from the cytosolic fraction of mung bean seeds. It comprises 0.5–1% of the total protein in seeds. This purified protein is a bona fide hsc70 on the basis of several lines of evidence. First, antibodies against bovine brain hsc70 cross-react with the purified 73 kDa protein. Second, the purified protein comigrates on two-dimensional gels with one of the heat-inducible hsc70s in mung bean seedlings. Third, similar to other hsc70 species, the purified 73 kDa protein has a high affinity for ATP. Finally, the hydrolysis of ATP by the purified protein can be stimulated by peptides; ATPase activity increases from 40 nmol/h to 165 nmol/h per mg of protein. The purified mung bean hsc70 autophosphorylates at a substoichiometric level. Moreover, the amount of this hsc70 species diminishes while new species of hsc70s appear after germination, suggesting that the expressionof hsc70 in mung bean is subject to developmental regulation.     

The distribution and localization of an UDP-glucose: Flavonol 3-O-glucosyl transferase activity in pollen

Summary The occurrence of UDP-glucose: flavonol 3-O-glucosyltransferase activity in pollen extracts of various plant species was tested. In case ofAlnus, Quercus, Narcissus andTulipa pollen high enzyme activity could be detected. The high level of enzyme activity inTulipa pollen made short time extraction experiments possible, which showed that the O-glucosyltransferase activity might be located in the pollen wall, possibly in the exine.Abbreviations UDP-glucose uridine diphospho-D-glucose - UDP-rhamnose uridine diphospho-L-rhamnose - DTE dithioerythritol