Root gravitropism: a complex response to a simple stimulus?

Roots avoid depleting their immediate environment of essential nutrients by continuous growth. Root growth is directed by environmental cues, including gravity. Gravity sensing occurs mainly in the columella cells of the root cap. Upon reorientation within the gravity field, the root-cap amyloplasts sediment, generating a physiological signal that promotes the development of a curvature at the root elongation zones. Recent molecular genetic studies in Arabidopsis have allowed the identification of genes that play important roles in root gravitropism. Among them, the ARG1 gene encodes a DnaJ-like protein involved in gravity signal transduction, whereas the AUX1 and AGR1 genes encode proteins involved in polar auxin transport. These studies have important implications for understanding the intra- and inter-cellular signaling processes that underlie root gravitropism.     

Cytochrome c assembly: a tale of ever increasing variation and mystery?

Formation of cytochromes c requires a deceptively simple post-translational modification, the formation of two thioether bonds (or rarely one) between the thiol groups of two cysteine residues found in a CXXCH motif (with some occasional variations) and the vinyl groups of heme. There are three partially characterised systems for facilitating this post-translational modification; within these systems there is also variation. In addition, there are clear indications for two other distinct systems. Here some of the current issues in understanding the systems are analysed.     

Metabolites: a helping hand for pathway evolution?

The evolution of enzymes and pathways is under debate. Recent studies show that recruitment of single enzymes from different pathways could be the driving force for pathway evolution. Other mechanisms of evolution, such as pathway duplication, enzyme specialization, de novo invention of pathways or retro-evolution of pathways, appear to be less abundant. Twenty percent of enzyme superfamilies are quite variable, not only in changing reaction chemistry or metabolite type but in changing both at the same time. These variable superfamilies account for nearly half of all known reactions. The most frequently occurring metabolites provide a helping hand for such changes because they can be accommodated by many enzyme superfamilies. Thus, a picture is emerging in which new pathways are evolving from central metabolites by preference, thereby keeping the overall topology of the metabolic network.     

A simple framework for a complex problem? Predicting wildlife–vehicle collisions

Collisions of vehicles with wildlife kill and injure animals and are also a risk to vehicle occupants, but preventing these collisions is challenging. Surveys to identify problem areas are expensive and logistically difficult. Computer modeling has identified correlates of collisions, yet these can be difficult for managers to interpret in a way that will help them reduce collision risk. We introduce a novel method to predict collision risk by modeling hazard (presence and movement of vehicles) and exposure (animal presence) across geographic space. To estimate the hazard, we predict relative traffic volume and speed along road segments across southeastern Australia using regression models based on human demographic variables. We model exposure by predicting suitable habitat for our case study species (Eastern Grey Kangaroo Macropus giganteus) based on existing fauna survey records and geographic and climatic variables. Records of reported kangaroo–vehicle collisions are used to investigate how these factors collectively contribute to collision risk. The species occurrence (exposure) model generated plausible predictions across the study area, reducing the null deviance by 30.4%. The vehicle (hazard) models explained 54.7% variance in the traffic volume data and 58.7% in the traffic speed data. Using these as predictors of collision risk explained 23.7% of the deviance in incidence of collisions. Discrimination ability of the model was good when predicting to an independent dataset. The research demonstrates that collision risks can be modeled across geographic space with a conceptual analytical framework using existing sources of data, reducing the need for expensive or time‐consuming field data collection. The framework is novel because it disentangles natural and anthropogenic effects on the likelihood of wildlife–vehicle collisions by representing hazard and exposure with separate, tunable submodels.     

The Neurospora circadian clock: simple or complex?

The fungus Neurospora crassa is being used by a number of research groups as a model organism to investigate circadian (daily) rhythmicity. In this review we concentrate on recent work relating to the complexity of the circadian system in this organism. We discuss: the advantages of Neurospora as a model system for clock studies; the frequency (frq), white collar-1 and white collar-2 genes and their roles in rhythmicity; the phenomenon of rhythmicity in null frq mutants and its implications for clock mechanisms; the study of output pathways using clock-controlled genes; other rhythms in fungi; mathematical modelling of the Neurospora circadian system; and the application of new technologies to the study of Neurospora rhythmicity. We conclude that there may be many gene products involved in the clock mechanism, there may be multiple interacting oscillators comprising the clock mechanism, there may be feedback from output pathways onto the oscillator(s) and from the oscillator(s) onto input pathways, and there may be several independent clocks coexisting in one organism. Thus even a relatively simple lower eukaryote can be used to address questions about a complex, networked circadian system.     

Discovering the Brazilian bat fauna: a task for two centuries?

• 1 Brazil is the second most bat species‐rich country in the world, but the available information on the occurrence and distribution of bat species in Brazil is still heterogeneous and fragmented.
• 2 We review the occurrence and distribution of bat species in Brazil, analyse the spatial performance of inventories conducted to date and identify knowledge gaps. We also identify the main factors contributing to the recent increase in the knowledge of the Brazilian bat fauna, and make suggestions for maintaining this momentum into the near future.
• 3 We plotted record coordinates on a map, grouped them in 0.5 degrees of latitude × 0.5 degrees of longitude grid cells, and analysed records for each of the five terrestrial biomes in Brazil, and for the 1439 priority polygons for the conservation of Brazilian biodiversity.
• 4 We identified 5502 formal bat records in Brazil, indicating that less than 10% of the country is minimally surveyed, and that for nearly 60% of Brazil there is not a single record of bat species. Record coverage varies from 79% in the Atlantic Forest to 24% in Amazonia, but none of the Brazilian biomes is well surveyed for bats. Bat species have been recorded in only 15% of the priority areas for Brazilian biodiversity conservation.
• 5 If the current rate of recording bats in empty grid cells (10% every 4 years) was maintained, it would take 33 years for all cells to have a single record. If the current rate of recording ≥20 species in a grid cell (0.8% per year) was maintained, it would take 200 years for the bat fauna of Brazil to be minimally surveyed. Alarmingly, most of the data‐poor areas are at the expansion frontiers of the agro‐business, near the surrounding deforestation fronts.
• 6 We make recommendations for scientific research on bats in Brazil, to ensure the conservation of this ecologically important taxon.

     

Desiccation tolerance: a simple process?

Water is essential for life, and thus the removal of water from a cell is a severe, often lethal stress. This is not a remarkable observation but it is one that is often taken for granted. Desiccation-tolerant cells implement structural, physiological and molecular mechanisms to survive severe water deficit. These mechanisms, and the components and pathways which facilitate them, are poorly understood. Here, recent developments are considered to illustrate the importance of desiccation, longevity and cell stasis in basic microbiology, and the relevance of the topic to the metabolic engineering of sensitive cells, including those of humans.     

The KEOPS complex: a rosetta stone for telomere regulation?

The detailed mechanisms underlying telomere capping and its relationship to telomerase activity are still unclear, although many proteins have been implicated in either or both processes. In this issue of Cell, the surprising identification of a new complex, called KEOPS, which promotes both telomere uncapping and elongation is presented.     

A common export pathway for proteins binding complex redox cofactors?

The precursor polypeptides of periplasmic proteins binding seven types of redox cofactor have unusually long signal sequences bearing a consensus (S/T)-R-R-x-F-L-K motif immediately before the hydrophobic region. Such 'double-arginine' signal sequences are not, in general, found on the precursors of other periplasmic proteins. It is suggested that precursor proteins with double-arginine signal sequences share a common specialization in their export pathway. The nature of this specialization, the structure of the double-arginine signal sequences, and the possible relationship with the double-arginine signal peptide-dependent thylakoid import pathway are discussed.     

Purine salvage in Leishmania: complex or simple by design?

Purine nucleotides function in a variety of vital cellular and metabolic processes including energy production, cell signaling, synthesis of vitamin-derived cofactors and nucleic acids, and as determinants of cell fate. Unlike their mammalian and insect hosts, Leishmania cannot synthesize the purine ring de novo and are absolutely dependent upon them to meet their purine requirements. The obligatory nature of purine salvage in these parasites, therefore, offers an attractive paradigm for drug targeting and, consequently, the delineation of the pathway has been under scientific investigation for over 30 years. Here, we review recent developments that reveal how purines flux in Leishmania and offer a potential 'Achilles' heel' for future validation.     

Devising a pathway for hyaluronan catabolism: are we there yet?

Hyaluronan is a negatively charged, high molecular weight glycosaminoglycan found predominantly in the extracellular matrix. Intracellular locations for hyaluronan have also been documented in cytoplasm, nucleus, and nucleolus. The polymer has an extraordinarily high rate of turnover in vertebrate tissues. The focus here is to formulate a metabolic pathway for hyaluronan degradation using all available data, including the recently acquired information on the hyaluronidase gene family. Such a catabolic scheme has defied explication up to now. In somatic tissues, stepwise processing occurs, from the extracellular high molecular weight space filling, antiangiogenic approximately 107-kDa polymer, to intermediate sized highly angiogenic, inflammatory, and immune-stimulating fragments, and ultimately to tetrasaccharides that are antiapoptotic and potent inducers of heat-shock proteins. It is proposed that the high molecular weight extracellular polymer is tethered to the cell surface by the combined efforts of hyaluronan receptors and hyaluronidase-2 (Hyal-2). The hyaluronan is cleaved to a 20-kDa intermediate-sized fragment, the limit product of Hyal-2 digestion. These fragments are delivered to endosomal- and ultimately lysosomal-like structures. Further catabolism occurs there by Hyal-1, coordinated with the activity of two lysosomal beta-exoglycosidases, beta-glucuronidase and beta-N-acetyl-glucosaminidase. A membrane-associated mini-organelle is postulated, the hyaluronasome, in which coordinated synthetic and catabolic enzyme reactions occur. The hyaluronasome can respond to the physiological states of the cell by a series of membrane-bound and soluble hyaluronan-associated receptors, binding proteins, and cofactors that trigger enzymatic events and signal transduction pathways. These in turn can be modulated by the amounts and sizes of the hyaluronan polysaccharides generated in the catabolic cascade. Most of these highly dynamic interactions remain to be determined. It is also proposed that malignant cells can commandeer some of these interactions for facilitating tumor growth and spread.     

In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase – Cytochrome c

The fast development of software and hardware is notably helping in closing the gap between macroscopic and microscopic data. Using a novel theoretical strategy combining molecular dynamics simulations, conformational clustering, ab-initio quantum mechanics and electronic coupling calculations, we show how computational methodologies are mature enough to provide accurate atomistic details into the mechanism of electron transfer (ET) processes in complex protein systems, known to be a significant challenge. We performed a quantitative study of the ET between Cytochrome c Peroxidase and its redox partner Cytochrome c. Our results confirm the ET mechanism as hole transfer (HT) through residues Ala194, Ala193, Gly192 and Trp191 of CcP. Furthermore, our findings indicate the fine evolution of the enzyme to approach an elevated turnover rate of 5.47×10⁶ s⁻¹ for the ET between Cytc and CcP through establishment of a localized bridge state in Trp191.     

Overproduction of CcmABCDEFGH restores cytochrome c maturation in a DsbD deletion strain of E. coli: another route for reductant?

The multidomain transmembrane protein DsbD is essential for cytochrome c maturation (Ccm) in Escherichia coli and transports reductant to the otherwise oxidising environment of the bacterial periplasm. The Ccm proteins ABCDEFGH are also essential and we show that the overproduction of these proteins can unexpectedly complement for the absence of DsbD in a deletion strain by partially restoring the production of an exogenous c-type cytochrome under aerobic and anaerobic conditions. This suggests that one or more of the Ccm proteins can provide reductant to the periplasm. The Ccm proteins do not, however, restore the normal disulfide mis-isomerisation phenotype of the deletion strain, as shown by assay of the multidisulfide-bonded enzyme urokinase.