DNA catenations that link sister chromatids until the onset of anaphase are maintained by a checkpoint mechanism

Treatment of Allium cepa meristematic cells in metaphase with the topoisomerase II inhibitor ICRF-193, results in bridging of the sister chromatids at anaphase. Separation of the sisters in experimentally generated acentric chromosomal fragments was also inhibited by ICRF-193, indicating that some non-centromeric catenations also persist in metaphase chromosomes. Thus, catenations must be resolved by DNA topoisomerase II at the metaphase-to-anaphase transition to allow segregation of sisters. A passive mechanism could maintain catenations holding sisters until the onset of anaphase. At this point the opposite tension exerted on sister chromatids could render the decatenation reaction physically more favorable than catenation. But this possibility was dismissed as acentric chromosome fragments were able to separate their sister chromatids at anaphase. A timing mechanism (a common trigger for two processes taking different times to be completed) could passively couple the resolution of the last remaining catenations to the moment of anaphase onset. This possibility was also discarded as cells arrested in metaphase with microtubule-destabilising drugs still displayed anaphase bridges when released in the presence of ICRF-193. It is possible that a checkpoint mechanism prevents the release of the last catenations linking sisters until the onset of anaphase. To test whether cells are competent to fully resolve catenations before anaphase onset, we generated multinucleate plant cells. In this system, the nuclei within a single multinucleate cell displayed differences in chromosome condensation at metaphase, but initiated anaphase synchronously. When multinucleates were treated with ICRF-193 at the metaphase-toanaphase transition, tangled and untangled anaphases were observed within the same cell. This can only occur if cells are competent to disentangle sister chromatids before the onset of anaphase, but are prevented from doing so by a checkpoint mechanism.     

A bridging [4Fe-4S] cluster and nucleotide binding are essential for function of the Cfd1-Nbp35 complex as a scaffold in iron-sulfur protein maturation

The essential P-loop NTPases Cfd1 and Nbp35 of the cytosolic iron-sulfur (Fe-S) protein assembly machinery perform a scaffold function for Fe-S cluster synthesis. Both proteins contain a nucleotide binding motif of unknown function and a C-terminal motif with four conserved cysteine residues. The latter motif defines the Mrp/Nbp35 subclass of P-loop NTPases and is suspected to be involved in transient Fe-S cluster binding. To elucidate the function of these two motifs, we first created cysteine mutant proteins of Cfd1 and Nbp35 and investigated the consequences of these mutations by genetic, cell biological, biochemical, and spectroscopic approaches. The two central cysteine residues (CPXC) of the C-terminal motif were found to be crucial for cell viability, protein function, coordination of a labile [4Fe-4S] cluster, and Cfd1-Nbp35 hetero-tetramer formation. Surprisingly, the two proximal cysteine residues were dispensable for all these functions, despite their strict evolutionary conservation. Several lines of evidence suggest that the C-terminal CPXC motifs of Cfd1-Nbp35 coordinate a bridging [4Fe-4S] cluster. Upon mutation of the nucleotide binding motifs Fe-S clusters could no longer be assembled on these proteins unless wild-type copies of Cfd1 and Nbp35 were present in trans. This result indicated that Fe-S cluster loading on these scaffold proteins is a nucleotide-dependent step. We propose that the bridging coordination of the C-terminal Fe-S cluster may be ideal for its facile assembly, labile binding, and efficient transfer to target Fe-S apoproteins, a step facilitated by the cytosolic iron-sulfur (Fe-S) protein assembly proteins Nar1 and Cia1 in vivo.     

Isolation of a Tetrahymena thermophila strain which induced metaphase I meiotic arrest: new pathway of abortive conjugation

A hypodiploid strain of Tetrahymena thermophila has been obtained that shows arrest at the stage of condensed nuclei, corresponding to metaphase I of normal conjugants and induced arrest at meiotic metaphase I (i.e. at the stage of condensed, bivalent chromosomes) in its wt partner mate. The metaphase I arrested conjugants retained their old macronuclei and most of them underwent cell fusion, instead of separation of exconjugants. The doublets were viable and cortically integrated. When the arrest inducing strain was crossed to the haploid tester strain, the haploid micronuclei were arrested in the meiotic metaphase I as the diploid ones had been; the monovalent, chromosomes were condensed, the arms of sister chromatids were not separated, and they were not segregated. Separation of the arms of sister chromatids and disjunction of bivalent chromosomes were not prerequisite for the formation of microtubular spindles in those cells that were arrested in meiotic metaphase I. After re-feeding, the doublet cells resumed cell divisions, segregating two macronuclei and micronuclei at random. One macronucleus was derived from the arrest inducing strain and the other from the tester strain. Heterokaryon strains with macronuclei derived from the parental arrest inducing strain and with the micronucleus derived from the parental wt tester strain were obtained. Surprisingly, these heterokaryons did not induce meiotic arrest. Thus, the arrest in the melotic metaphase I was induced by the micronucleus and not by the macronucleus of the arrest inducing strain.     

Sororin is a master regulator of sister chromatid cohesion and separation

The maintenance of sister chromatid cohesion from S phase to the onset of anaphase relies on a small but evolutionarily conserved protein called Sororin. Sororin is a phosphoprotein and its dynamic localization and function are regulated by protein kinases, such as Cdk1/cyclin B and Erk2. The association of Sororin with chromatin requires cohesin to be preloaded to chromatin and modification of Smc3 during DNA replication. Sororin antagonizes the function of Wapl in cohesin releasing from S to G₂ phase and promotes cohesin release from sister chromatid arms in prophase via interaction with Plk1. This review focuses on progress of the identification and regulation of Sororin during cell cycle; role of post-translational modification on Sororin function; role of Sororin in the maintenance and resolution of sister chromatid cohesion; and finally discusses Sororin’s emerging role in cancer and the potential issues that need be addressed in the future.     

Sororin is a master regulator of sister chromatid cohesion and separation

The maintenance of sister chromatid cohesion from S phase to the onset of anaphase relies on a small but evolutionarily conserved protein called Sororin. Sororin is a phosphoprotein and its dynamic localization and function are regulated by protein kinases, such as Cdk1/cyclin B and Erk2. The association of Sororin with chromatin requires cohesin to be preloaded to chromatin and modification of Smc3 during DNA replication. Sororin antagonizes the function of Wapl in cohesin releasing from S to G₂ phase and promotes cohesin release from sister chromatid arms in prophase via interaction with Plk1. This review focuses on progress of the identification and regulation of Sororin during cell cycle; role of post-translational modification on Sororin function; role of Sororin in the maintenance and resolution of sister chromatid cohesion; and finally discusses Sororin’s emerging role in cancer and the potential issues that need be addressed in the future.     

C-terminal hydrophobic interactions play a critical role in oligomeric assembly of the P22 tailspike trimer

The tailspike protein from the bacteriophage P22 is a well characterized model system for folding and assembly of multimeric proteins. Folding intermediates from both the in vivo and in vitro pathways have been identified, and both the initial folding steps and the protrimer-to-trimer transition have been well studied. In contrast, there has been little experimental evidence to describe the assembly of the protrimer. Previous results indicated that the C terminus plays a critical role in the overall stability of the P22 tailspike protein. Here, we present evidence that the C terminus is also the critical assembly point for trimer assembly. Three truncations of the full-length tailspike protein, TSPΔN, TSPΔC, and TSPΔNC, were generated and tested for their ability to form mixed trimer species. TSPΔN forms mixed trimers with full-length P22 tailspike, but TSPΔC and TSPΔNC are incapable of forming similar mixed trimer species. In addition, mutations in the hydrophobic core of the C terminus were unable to form trimer in vivo. Finally, the hydrophobic-binding dye ANS inhibits the formation of trimer by inhibiting progression through the folding pathway. Taken together, these results suggest that hydrophobic interactions between C-terminal regions of P22 tailspike monomers play a critical role in the assembly of the P22 tailspike trimer.     

Differential requirements of a mitotic acetyltransferase in somatic and germ line cells

During mitosis different types of cells can have differential requirements for chromosome segregation. We isolated two new alleles of the separation anxiety gene (san). san was previously described in both Drosophila and in humans to be required for centromeric sister chromatid cohesion (Hou et al., 2007; Williams et al., 2003). Our work confirms and expands the observation that san is required in vivo for normal mitosis of different types of somatic cells. In addition, we suggest that san is also important for the correct resolution of chromosomes, implying a more general function of this acetyltransferase. Surprisingly, during oogenesis we cannot detect mitotic defects in germ line cells mutant for san. We hypothesize the female germ line stem cells have differential requirements for mitotic sister chromatid cohesion.     

On the use of spleen mass as a measure of avian immune system strength

The avian spleen has been frequently used in studies of avian ecology, parasitology, and evolution to infer immune system strength in birds. Traditionally, it has been assumed that a large spleen is representative of a strong immune system and conclusions based on this assumption have led to interesting interpretations of the role of disease and parasitism, for example in predator-prey interactions. This assumption of a positive relationship between spleen size and immune system strength has been made despite an incomplete understanding of the physiology of the avian spleen and little evidence of the validity of such an assumption. In this response, we demonstrate that the assumption of a predictable, positive relationship between spleen size and immunocompetence may be unjustified based on what is known of avian splenology. We also review recent research that may indicate that the inverse of the above assumption is true and we discuss general limitations of the use of the spleen as an indicator of immune system strength in birds. Finally, we make recommendations for future research topics in this field of study.     

Structure-based analysis of GPCR function: evidence for a novel pentameric assembly between the dimeric leukotriene B4 receptor BLT1 and the G-protein

We produced human leukotriene B(4) (LTB(4)) receptor BLT1 as a recombinant protein in Escherichia coli. This detergent-solubilized receptor displays two states with regard to its affinity for LTB(4): (i) a low-affinity state (K(a)=7.8x10(8)M(-1)) that involves a receptor homodimer (BLT1.LTB(4))(2); we report evidence for a central role of the sixth transmembrane helix in regulating the stability of this homodimer; (ii) a high-affinity state (K(a)=1.3x10(10)M(-1)) upon interaction of the receptor with the heterotrimeric GDP-loaded G-protein, Galpha(i2)beta(1)gamma(2). Association of the G-protein with recombinant BLT1 induces GDP-GTP exchange by the Galpha subunit. These results indicate that isolated BLT1 is fully representative of the in vivo receptor with regard to high-affinity recognition of LTB(4), association with a G-protein and activation of Galpha. Using a combination of mass spectrometry after chemical cross-linking and neutron-scattering in solution with the native complex, we establish unambiguously that only one G-protein trimer binds to a receptor dimer to form the stoichiometrically defined (BLT1.LTB(4))(2):Galpha(i2)beta(1)gamma(2) pentameric assembly. This suggests that receptor dimerization could be crucial to transduction of the LTB(4)-induced signal.     

Identification of a segment in the precursor of pulmonary surfactant protein SP-B, potentially involved in pH-dependent membrane assembly of the protein

In the present work, the hydrophobic properties of proSP-B, the precursor of pulmonary surfactant protein SP-B, have been analyzed under different pH conditions, and the sequence segment at position 111-135 of the N-terminal domain of the precursor has been detected as potentially possessing pH-dependent hydrophobic properties. We have studied the structure and lipid-protein interactions of the synthetic peptides BpH, with sequence corresponding to the segment 111-135 of proSP-B, and BpH-W, bearing the conservative substitution F127W to use the tryptophan as an intrinsic fluorescent probe. Peptide BpH-W interacts with both zwitterionic and anionic phospholipid vesicles at neutral pH, as monitored by the blue-shifted maximum emission of its tryptophan reporter. Insertion of tryptophan into the membranes is further improved at pH 5.0, especially in negatively-charged membranes. Peptides BpH and BpH-W also showed pH-dependent properties to insert into phospholipid monolayers. We have also found that the single sequence variation F120K decreases substantially the interaction of this segment with phospholipid surfaces as well as its pH-dependent insertion into deeper regions of the membranes. We hypothesize that this region could be involved in pH-triggered conformational changes occurring in proSP-B along the exocytic pathway of surfactant in type II cells, leading to the exposure of the appropriate segments for processing and assembly of SP-B within surfactant lipids.     

Cooperative dimerization of a stably folded protein directed by a flexible RNA in the assembly of the HIV Rev dimer–RRE stem II complex

The binding of the HIV‐1 Rev protein as an oligomer to a viral RNA element, the Rev‐response element (RRE), mediates nuclear export of genomic RNA. Assembly of the Rev–RRE ribonucleoprotein (RNP) complex is nucleated by the binding of the first Rev molecule to stem IIB of the RRE. This is followed by stepwise addition of a total of ~six Rev molecules along the RRE through a combination of RNA–protein and protein–protein interactions. RRE stem II, which forms a three‐way junction consisting of stems IIA, IIB and IIC, has been shown to bind to two Rev molecules in a cooperative manner, with the second Rev molecule binding to the junction region of stem II. The results of base substitutions at the stem II junction, and characterization of stem II junction variants selected from a randomized library showed that an “open” flexible structure is preferred for binding of the second Rev molecule, and that binding of the second Rev molecule to the junction region is not sequence‐specific. Alanine substitutions of a number of Rev amino acid residues implicated to be important for Rev folding in previous structural studies were found to result in a dramatic decrease in the binding of the second Rev molecule. These results support the model that proper folding of Rev is critical in ensuring that the flexible RRE is able to correctly position Rev molecules for specific RNP assembly, and suggests that targeting Rev folding may be effective in the inhibition of Rev function. Copyright © 2015 John Wiley & Sons, Ltd.     

Boreal predator co‐occurrences reveal shared use of seismic lines in a working landscape

Interspecific interactions are an integral aspect of ecosystem functioning that may be disrupted in an increasingly anthropocentric world. Industrial landscape change creates a novel playing field on which these interactions take place, and a key question for wildlife managers is whether and how species are able to coexist in such working landscapes. Using camera traps deployed in northern Alberta, we surveyed boreal predators to determine whether interspecific interactions affected occurrences of black bears (Ursus americanus), coyotes (Canis latrans), and lynx (Lynx canadensis) within a landscape disturbed by networks of seismic lines (corridors cut for seismic exploration of oil and gas reserves). We tested hypotheses of species interactions across one spatial‐only and two spatiotemporal (daily and weekly) scales. Specifically, we hypothesized that (1) predators avoid competition with the apex predator, gray wolf (Canis lupus), (2) they avoid competition with each other as intraguild competitors, and (3) they overlap with their prey. All three predators overlapped with wolves on at least one scale, although models at the daily and weekly scale had substantial unexplained variance. None of the predators showed avoidance of intraguild competitors or overlap with prey. These results show patterns in predator space use that are consistent with both facilitative interactions or shared responses to unmeasured ecological cues. Our study provides insight into how predator species use the working boreal landscape in relation to each other, and highlights that predator management may indirectly influence multiple species through their interactions.     

Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly

Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3'-5' directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3' end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a 'splayed' conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the α-proteobacteria.     

Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly

Ecology Letters (2010) 13: 1503-1514 ABSTRACT: The phylogenetic structure and distribution of functional traits in a community can provide insights into community assembly processes. However, these insights are sensitive to the spatial scale of analysis. Here, we use spatially explicit, neighbourhood models of tree growth and survival for 19 tree species, a highly resolved molecular phylogeny and information on eight functional traits to quantify the relative efficacy of functional similarity and shared ancestry in describing the effects of spatial interactions between tree species on demographic rates. We also assess the congruence of these results with observed phylogenetic and functional structure in the neighbourhoods of live and dead trees. We found strong support for models in which the effects of spatial neighbourhood interactions on tree growth and survival were scaled to species-specific mean functional trait values (e.g., wood specific gravity, leaf succulence and maximum height) but not to phylogenetic distance. The weak phylogenetic signal in functional trait data allowed us to independently interpret the static neighbourhood functional and phylogenetic patterns. We observed greater functional trait similarity in the neighbourhoods of live trees relative to those of dead trees suggesting that environmental filtering is the major force structuring this tree community at this scale while competitive interactions play a lesser role.     

Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants

Determining how pollinators visit plants vs. how they carry and transfer pollen is an ongoing project in pollination ecology. The current tools for identifying the pollens that bees carry have different strengths and weaknesses when used for ecological inference. In this study we use three methods to better understand a system of congeneric, coflowering plants in the genus Clarkia and their bee pollinators: observations of plant–pollinator contact in the field, and two different molecular methods to estimate the relative abundance of each Clarkia pollen in samples collected from pollinators. We use these methods to investigate if observations of plant–pollinator contact in the field correspond to the pollen bees carry; if individual bees carry Clarkia pollens in predictable ways, based on previous knowledge of their foraging behaviors; and how the three approaches differ for understanding plant–pollinator interactions. We find that observations of plant–pollinator contact are generally predictive of the pollens that bees carry while foraging, and network topologies using the three different methods are statistically indistinguishable from each other. Results from molecular pollen analysis also show that while bees can carry multiple species of Clarkia at the same time, they often carry one species of pollen. Our work contributes to the growing body of literature aimed at resolving how pollinators use floral resources. We suggest our novel relative amplicon quantification method as another tool in the developing molecular ecology and pollination biology toolbox.     

Influences of microhabitat use and foraging mode similarities on intra- and interspecific aggressive interactions in a size-structured stream fish assemblage

Aggressive interactions, foraging behaviour and microhabitat use were observed among four sympatric stream fishes inhabiting the water column: ayu (Plecoglossus altivelis), white-spotted charr (Salvelinus leucomaenis), masu salmon (Oncorhynchus masou) and Japanese dace (Tribolodon hakonensis), each species being categorised into five body-size classes (species-size groups; SSG's). Aggressive interactions were observed between most pairs of SSG's, an almost linear dominance order being apparent throughout the three-month study period. Ayu were relatively subordinate in June, but became the second most dominant in July and the most dominant in August, as a consequence of a reversal in dominance order with salmon. In contrast, smaller-sized dace, which continually suffered from intra- and interspecific aggression, occupied the most subordinate ranks throughout the study period. Intensive aggression was observed among various SSG's, exhibiting same microhabitat propensity throughout the three months. The direction and frequency of aggressive interactions varied month by month due to a reversal in dominance order between ayu and masu salmon, and/or changes in density, body size and resource use of the component members. Opponent selectivity was higher within SSG's, where resource use was assumed to be highly overlapping, rather than among SSG's throughout the study period. Correlation analysis indicated that opponent selectivity in aggressive interactions among SSG's was positively correlated with similarity in microhabitat selectivity in June, but not in other months or with that in foraging habits, suggesting that intensive aggressive behaviour reflected overlapping habitat use among assemblage members during a certain period.     

Geography is more important than host plant use for the population genetic structure of a generalist insect herbivore

Population divergence can occur due to mechanisms associated with geographic isolation and/or due to selection associated with different ecological niches. Much of the evidence for selection‐driven speciation has come from studies of specialist insect herbivores that use different host plant species; however, the influence of host plant use on population divergence of generalist herbivores remains poorly understood. We tested how diet breadth, host plant species and geographic distance influence population divergence of the fall webworm (Hyphantria cunea; FW). FW is a broadly distributed, extreme generalist herbivore consisting of two morphotypes that have been argued to represent two different species: black‐headed and red‐headed. We characterized the differentiation of FW populations at two geographic scales. We first analysed the influence of host plant and geographic distance on genetic divergence across a broad continental scale for both colour types. We further analysed the influence of host plant, diet breadth and geographic distance on divergence at a finer geographic scale focusing on red‐headed FW in Colorado. We found clear genetic and morphological distinction between red‐ and black‐headed FW, and Colorado FW formed a genetic cluster distinct from other locations. Although both geographic distance and host plant use were correlated with genetic distance, geographic distance accounted for up to 3× more variation in genetic distance than did host plant use. As a rare study investigating the genetic structure of a widespread generalist herbivore over a broad geographic range (up to 3,000 km), our study supports a strong role for geographic isolation in divergence in this system.     

Modelling the interactions between Pseudomonas putida and Escherichia coli O157:H7 in fish‐burgers: use of the lag‐exponential model and of a combined interaction index

Aims: The objective of the current study was to examine the interactions between Pseudomonas putida and Escherichia coli O157:H7 in coculture studies on fish‐burgers packed in air and under different modified atmospheres (30 : 40 : 30 O₂ : CO₂ : N₂, 5 : 95 O₂ : CO₂ and 50 : 50 O₂ : CO₂), throughout the storage at 8°C. Methods and Results: The lag‐exponential model was applied to describe the microbial growth. To give a quantitative measure of the occurring microbial interactions, two simple parameters were developed: the combined interaction index (CII) and the partial interaction index (PII). Under air, the interaction was significant (P < 0·05) only within the exponential growth phase (CII, 1·72), whereas under the modified atmospheres, the interactions were highly significant (P < 0·001) and occurred both in the exponential and in the stationary phase (CII ranged from 0·33 to 1·18). PII values for E.  coli O157:H7 were lower than those calculated for Ps. putida. Conclusions: The interactions occurring into the system affected both E. coli O157:H7 and pseudomonads subpopulations. The packaging atmosphere resulted in a key element. Significance and Impact of the Study: The article provides some useful information on the interactions occurring between E. coli O157:H7 and Ps. putida on fish‐burgers. The proposed index describes successfully the competitive growth of both micro‐organisms, giving also a quantitative measure of a qualitative phenomenon.     

Design of enhanced agonists through the use of a new virtual screening method: application to peptides that bind class I major histocompatibility complex (MHC) molecules

A new screening procedure is described that uses docking calculations to design enhanced agonist peptides that bind to major histocompatibility complex (MHC) class I receptors. The screening process proceeds via single mutations of one amino acid at the positions that directly interact with the MHC receptor. The energetic and structural effects of these mutations have been studied using fragments of the original ligand that vary in length. The results of these docking studies indicate that the mutant affinity ranking of long peptides can be practically reproduced with a screening approach performed using fragments of six residues. Fragments of four and five residues could mimic, in some cases, the structural arrangement of the side chains of the full-length peptide. We have compared the structural and energetic results of the docking calculations with experimental data using three unrelated ligand peptides that differ greatly in their affinity for the MHC complex. Analysis of the affinity of the fragments led to the identification of three important parameters in the construction of fragments that mimic the structural and energetic properties of the full-length ligand: the length of the fragment; its intermolecular energy; and the number and localization, internal or terminal, of the anchor residues. The results of this new peptide-design methodology have been applied to suggest new peptides derived from the MUC1-8 peptide that could be used as murine vaccines that trigger the immune response through the MHC class I protein H-2K(b).