Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales

6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase; LS) catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. This protein is known to exhibit different quaternary assemblies between species, existing as free pentamers, decamers (dimers of pentamers) and icosahedrally arranged dodecamers of pentamers. A phylogenetic analysis on eubacterial, fungal and plant LSs allowed us to classify them into two categories: Type I LSs (pentameric or icosahedral) and Type II LSs (decameric). The Rhizobiales represent an order of alpha-proteobacteria that includes, among others, the genera Mesorhizobium, Agrobacterium and Brucella. Here, we present structural and kinetic studies on several LSs from Rhizobiales. Interestingly, Mesorhizobium and Brucella encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. We show that Type II LSs appear to be almost inactive, whereas Type I LSs present a highly variable catalytic activity according to the genus. Additionally, we have solved four RibH1/RibH2 crystallographic structures from the genera Mesorhizobium and Brucella. The relationship between the active-site architecture and catalytic properties in these isoenzymes is discussed, and a model that describes the enzymatic behavior is proposed. Furthermore, sequence alignment studies allowed us to extend our results to the genus Agrobacterium. Our results suggest that the selective pressure controlling the riboflavin pathway favored the evolution of catalysts with low reaction rates, since the excess of flavins in the intracellular pool in Rhizobiales could act as a negative factor when these bacteria are exposed to oxidative or nitrosative stress.     

Fatty acids covalently bound to alpha-hemolysin of Escherichia coli are involved in the molten globule conformation: implication of disordered regions in binding promiscuity

Alpha-hemolysin (HlyA) is a pore-forming toxin secreted by pathogenic strains of Escherichia coli. The toxin is synthesized as a protoxin, ProHlyA, which is matured in the cytosol to the active form by acylation at two internal lysines, K563 and K689 (HlyA). It is widely known that the presence of fatty acids is crucial for the hemolytic and cytotoxic effects of the toxin. However, no detailed physicochemical characterization of the structural changes produced by fatty acids in the soluble protein prior to membrane binding has been carried out to date. The effects of chemical denaturants, the ANS binding parameters (Kd and n) and the sensitivity to proteases were compared between the acylated and unacylated protein forms HlyA and ProHlyA. Our results are consistent with a molten globular form of the acylated protein. Moreover, because molten globule proteins are intrinsically disordered proteins, using disorder prediction analyses, we show that HlyA contains 9 regions composed of 10-30 natively disordered amino acids. We propose that this conformation induced by covalently bound fatty acids might provide HlyA with the ability to bind to a variety of molecules during its action mechanism.     

Cyclodextrin glycosyltransferase: a key enzyme in the assimilation of starch by the halophilic archaeon Haloferax mediterranei

A cyclodextrin glycosyltransferase (CGTase, EC 2.4.1.19) was successfully isolated and characterized from the halophilic archaeon Haloferax mediterranei. The enzyme is a monomer with a molecular mass of 77 kDa and optimum activity at 55°C, pH 7.5 and 1.5 M NaCl. The enzyme displayed many activities related to the degradation and transformation of starch. Cyclization was found to be the predominant activity, yielding a mixture of cyclodextrins, mainly α-CD, followed by hydrolysis and to a lesser extent coupling and disproportionation activities. Gene encoding H. mediterranei CGTase was cloned and heterologously overexpressed. Sequence analysis revealed an open reading frame of 2142 bp that encodes a protein of 713 amino acids. The amino acid sequence displayed high homology with those belonging to the α-amylase family. The CGTase is secreted to the extracellular medium by the Tat pathway. Upstream of the CGTase gene, four maltose ABC transporter genes have been sequenced (malE, malF, malG, malK). The expression of the CGTase gene yielded a fully active CGTase with similar kinetic behavior to the wild-type enzyme. The H. mediterranei CGTase is the first halophilic archaeal CGTase characterized, sequenced and expressed.     

A Plains‐wanderer (Pedionomidae) that did not wander plains: a new species from the Oligocene of South Australia

The remarkable fauna of Australia evolved in isolation from other landmasses for millions of years, yet understanding the evolutionary history of endemic avian lineages on the continent is confounded by the ability of birds to disperse over geographical barriers even after vicariance events. The Plains‐wanderer Pedionomus torquatus (Charadriiformes) is an enigmatic, predominantly sedentary, quail‐like bird that occurs exclusively in sparse native grasslands of southeastern Australia. It is the only known species of its family (Pedionomidae), and its closest relatives are the South American seedsnipes (Thinocoridae). Here we describe a further representative of this lineage, Oligonomus milleri gen. et sp. nov., from the Late Oligocene of South Australia (26–24 Ma), which pre‐dates the earliest record of P. torquatus by c. 22 Ma and attests to the presence of this lineage during Australia's period of isolation (50–15 Ma). Based on the morphology of the coracoid and the palynological record, we propose that O. milleri and P. torquatus were ecologically disparate taxa and that, similar to coeval marsupials, O. milleri inhabited well‐wooded habitats, suggesting that the preference for grassland in the extant P. torquatus and thinocorids is likely to be convergent and not ancestral. The speciation event leading to the evolution of the extant Plains‐wanderer was probably triggered by the spread of grasslands across Australia in the Late Miocene–Pliocene, which this record pre‐dates. The presence of a pedionomid in the Late Oligocene of Australia strengthens the hypothesis of a Gondwanan divergence of the lineages giving rise to Thinocoridae and Pedionomidae.     

Modelling the amount of materials to improve inventory datasets of greenhouse infrastructures

Purpose

Previous studies have shown the importance of including agricultural capital goods in environmental assessments. In particular for protected crops, greenhouse structural components may account for nearly 30 % of the total in environmental impact categories such as resource depletion and global warming. The lack of appropriate datasets can make it difficult to include these structural components. The present paper provides a modelling approach for the greenhouse inventory stage to provide better assessments of greenhouse production systems.

Methods

In this study, four main greenhouse structures were assessed: a glass greenhouse, a multi-tunnel greenhouse, a local Mediterranean type known as the parral greenhouse and a low-tunnel greenhouse. After selecting the main materials of the structure, we generated equations to calculate the amount of the main structural materials as a function of the main greenhouse dimensions. We performed a quality assessment of the data used for different greenhouse structures. We also calculated a simplified environmental assessment made by the different structures to the climate change category in order to test the effects of the different amounts of material in the four greenhouse types.

Results and discussion

Equations to calculate the amount of the main greenhouse materials as a function of greenhouse size are provided. For the four greenhouse types under consideration, statistical correlations showed a good fit between the amounts of greenhouse materials and the parameters related to the main greenhouse dimensions, such as greenhouse perimeter, surface and volume. The results from the complementary impact assessment study show that glass greenhouses contributed the most in the climate change category, with an average value of 2.9 kg CO₂ eq m^?2. After variability was taken into account, multi-tunnel and parral greenhouses showed similar values of between 0.5 and 1.3 kg CO₂ eq m^?2, while low-tunnel greenhouses had the lowest ranges, between 0.4 and 0.6 kg CO₂ eq m^?2. The environmental assessment was done using the square metre as a reference flow, so the actual impact depends on the functional unit selected, which is usually the yield.

Conclusions

Application of the equations developed in this study provides an easy way to calculate the quantity of materials used to make greenhouses of different dimensions, thus resulting in more accurate calculation of greenhouse production system impacts. This analysis also highlights the importance of the different amounts of materials used to build these structures and, therefore, the need to include ranges of uncertainty in environmental analyses.     

A monoclonal antibody against p53 cross-reacts with processing bodies

The p53 tumor suppressor protein is an important regulator of cell proliferation and apoptosis. p53 can be found in the nucleus and in the cytosol, and the subcellular location is key to control p53 function. In this work, we found that a widely used monoclonal antibody against p53, termed Pab 1801 (Pan antibody 1801) yields a remarkable punctate signal in the cytoplasm of several cell lines of human origin. Surprisingly, these puncta were also observed in two independent p53-null cell lines. Moreover, the foci stained with the Pab 1801 were present in rat cells, although Pab 1801 recognizes an epitope that is not conserved in rodent p53. In contrast, the Pab 1801 nuclear staining corresponded to genuine p53, as it was upregulated by p53-stimulating drugs and absent in p53-null cells. We identified the Pab 1801 cytoplasmic puncta as P Bodies (PBs), which are involved in mRNA regulation. We found that, in several cell lines, including U2OS, WI38, SK-N-SH and HCT116, the Pab 1801 puncta strictly colocalize with PBs identified with specific antibodies against the PB components Hedls, Dcp1a, Xrn1 or Rck/p54. PBs are highly dynamic and accordingly, the Pab 1801 puncta vanished when PBs dissolved upon treatment with cycloheximide, a drug that causes polysome stabilization and PB disruption. In addition, the knockdown of specific PB components that affect PB integrity simultaneously caused PB dissolution and the disappearance of the Pab 1801 puncta. Our results reveal a strong cross-reactivity of the Pab 1801 with unknown PB component(s). This was observed upon distinct immunostaining protocols, thus meaning a major limitation on the use of this antibody for p53 imaging in the cytoplasm of most cell types of human or rodent origin.     

A melting pot of multicontinental mtDNA lineages in admixed Venezuelans

The arrival of Europeans in Colonial and post-Colonial times coupled with the forced introduction of sub-Saharan Africans have dramatically changed the genetic background of Venezuela. The main aim of the present study was to evaluate, through the study of mitochondrial DNA (mtDNA) variation, the extent of admixture and the characterization of the most likely continental ancestral sources of present-day urban Venezuelans. We analyzed two admixed populations that have experienced different demographic histories, namely, Caracas (n = 131) and Pueblo Llano (n = 219). The native American component of admixed Venezuelans accounted for 80% (46% haplogroup [hg] A2, 7% hg B2, 21% hg C1, and 6% hg D1) of all mtDNAs; while the sub-Saharan and European contributions made up ～10% each, indicating that Trans-Atlantic immigrants have only partially erased the native American nature of Venezuelans. A Bayesian-based model allowed the different contributions of European countries to admixed Venezuelans to be disentangled (Spain: ～38.4%, Portugal: ～35.5%, Italy: ～27.0%), in good agreement with the documented history. Seventeen entire mtDNA genomes were sequenced, which allowed five new native American branches to be discovered. B2j and B2k, are supported by two different haplotypes and control region data, and their coalescence ages are 3.9 k.y. (95% C.I. 0-7.8) and 2.6 k.y. (95% C.I. 0.1-5.2), respectively. The other clades were exclusively observed in Pueblo Llano and they show the fingerprint of strong recent genetic drift coupled with severe historical consanguinity episodes that might explain the high prevalence of certain Mendelian and complex multi-factorial diseases in this region.     

Viroporins: structure and biological functions

Viroporins are small, hydrophobic proteins that are encoded by a wide range of clinically relevant animal viruses. When these proteins oligomerize in host cell membranes, they form hydrophilic pores that disrupt a number of physiological properties of the cell. Viroporins are crucial for viral pathogenicity owing to their involvement in several diverse steps of the viral life cycle. Thus, these viral proteins, which include influenza A virus matrix protein 2 (M2), HIV-1 viral protein U (Vpu) and hepatitis C virus p7, represent ideal targets for therapeutic intervention, and several compounds that block their pore-forming activity have been identified. Here, we review recent studies in the field that have advanced our knowledge of the structure and function of this expanding family of viral proteins.     

Structural basis for the regulation mechanism of the tyrosine kinase CapB from Staphylococcus aureus

Bacteria were thought to be devoid of tyrosine-phosphorylating enzymes. However, several tyrosine kinases without similarity to their eukaryotic counterparts have recently been identified in bacteria. They are involved in many physiological processes, but their accurate functions remain poorly understood due to slow progress in their structural characterization. They have been best characterized as copolymerases involved in the synthesis and export of extracellular polysaccharides. These compounds play critical roles in the virulence of pathogenic bacteria, and bacterial tyrosine kinases can thus be considered as potential therapeutic targets. Here, we present the crystal structures of the phosphorylated and unphosphorylated states of the tyrosine kinase CapB from the human pathogen Staphylococcus aureus together with the activator domain of its cognate transmembrane modulator CapA. This first high-resolution structure of a bacterial tyrosine kinase reveals a 230-kDa ring-shaped octamer that dissociates upon intermolecular autophosphorylation. These observations provide a molecular basis for the regulation mechanism of the bacterial tyrosine kinases and give insights into their copolymerase function.     

Acute pre-learning stress and declarative memory: impact of sex,cortisol response and menstrual cycle phase

This study explores the influence of pre-learning stress on performance on declarative memory tasks in healthy young adults in relation to sex and menstrual cycle phase. The sample was composed of 119 students (32 men and 87 women) from 18 to 25 years of age. The women were tested in different hormonal stages (30 in follicular phase, 34 in luteal phase, and 23 using oral contraceptives). The participants were exposed to the Trier Social Stress Test (TSST) or a control condition. Afterwards, their memory performance was measured using a standardized memory test (Rey's Auditory Verbal Learning Test). In the control condition, all groups of women recalled more words than men, but these differences disappeared in the group exposed to TSST because men's performance on the memory test improved, but only to the level of women. In addition, our data suggest that in women the relationship between cortisol and memory can be modulated by sex hormone levels, since in luteal women a negative relationship was found between memory performance and peak cortisol level. These results confirm that sex differences need to be considered in the relationship between pre-learning stress and memory performance.