Phage endolysins are adapted to specific hosts and are evolutionarily dynamic

Endolysins are produced by (bacterio)phages to rapidly degrade the bacterial cell wall and release new viral particles. Despite sharing a common function, endolysins present in phages that infect a specific bacterial species can be highly diverse and vary in types, number, and organization of their catalytic and cell wall binding domains. While much is now known about the biochemistry of phage endolysins, far less is known about the implication of their diversity on phage–host adaptation and evolution. Using CRISPR-Cas9 genome editing, we could genetically exchange a subset of different endolysin genes into distinct lactococcal phage genomes. Regardless of the type and biochemical properties of these endolysins, fitness costs associated to their genetic exchange were marginal if both recipient and donor phages were infecting the same bacterial strain, but gradually increased when taking place between phage that infect different strains or bacterial species. From an evolutionary perspective, we observed that endolysins could be naturally exchanged by homologous recombination between phages coinfecting a same bacterial strain. Furthermore, phage endolysins could adapt to their new phage/host environment by acquiring adaptative mutations. These observations highlight the remarkable ability of phage lytic systems to recombine and adapt and, therefore, explain their large diversity and mosaicism. It also indicates that evolution should be considered to act on functional modules rather than on bacteriophages themselves. Furthermore, the extensive degree of evolvability observed for phage endolysins offers new perspectives for their engineering as antimicrobial agents.

Endolysins are produced by bacteriophages to degrade the host cell wall and release new particles, but the implications of their diversity on phage-host adaptation and evolution is unknown. This study uses CRISPR-Cas9 genome editing to reveal novel insights into bacteriophage endolysin diversity and phage-bacteria interactions as well as into endolysin adaptation towards a new bacterial host.     

Peroxiredoxin-null yeast cells are hypersensitive to oxidative stress and are genomically unstable

Peroxiredoxins are a family of abundant peroxidases found in all organisms. Although these antioxidant enzymes are thought to be critically involved in cellular defense and redox signaling, their exact physiological roles are largely unknown. In this study, we took a genetic approach to address the functions of peroxiredoxins in budding yeast. We generated and characterized a yeast mutant lacking all five peroxiredoxins. The quintuple peroxiredoxin-null mutant was still viable, though the growth rate was lower under normal aerobic conditions. Although peroxiredoxins are not essential for cell viability, peroxiredoxin-null yeast cells were more susceptible to oxidative and nitrosative stress. In the complete absence of peroxiredoxins, the expression of other antioxidant proteins including glutathione peroxidase and glutathione reductase was induced. In addition, the quintuple mutant was hypersensitive to glutathione depletion. Thus, the glutathione system might cooperate with other antioxidant enzymes to compensate for peroxiredoxin deficiency. Interestingly, the peroxiredoxinnull yeast cells displayed an increased rate of spontaneous mutations that conferred resistance to canavanine. This mutator phenotype was rescued by yeast peroxiredoxin Tsa1p, but not by its active-site mutant defective for peroxidase activity. Our findings suggest that the antioxidant function of peroxiredoxins is important for maintaining genome stability in eukaryotic cells.     

Arabidopsis ecotypes and mutants that are recalcitrant to Agrobacterium root transformation are susceptible to germ-line transformation

Germ-line transformation (vacuum infiltration) is frequently used to transform Arabidopsis thaliana using Agrobacterium tumefaciens. We have recently identified several Arabidopsis ecotypes and T-DNA-tagged mutants that are recalcitrant to Agrobacterium-mediated transformation of cut root segments. Some of these ecotypes and mutants are deficient in their ability to bind bacteria. Some are deficient in T-DNA integration. We report here that using a germ-line transformation protocol we transformed these ecotypes and mutants, including attachment- and integration-defective Arabidopsis plants, with a frequency similar to that of highly susceptible wild-type plants. However, we could not transform otherwise highly susceptible Arabidopsis plants by germ-line or root transformation using several vir and attachment-deficient Agrobacterium mutants. These results indicate that certain plant factors important for transformation may exist in germ-line tissue but may be lacking in some somatic cells.     

Activation-Tagged Tobacco Mutants that are Tolerant to Antimicrotubular Herbicides are Cross-Resistant to Chilling Stress

T-DNA activation tagging was used to generate tobacco mutants with increased tolerance to antimicrotubular herbicides and chilling stress. After transformation, protoplast-derived calli were screened for tolerance to treatments that affect microtubule assembly. In one screen mutants with tolerance to aryl carbamates (a blocker of microtubule assembly) were selected, the second screen was targeted to chilling-tolerant mutants that could survive for several months at 3°C, a third screen combined both factors. The resistance of these mutants to aryl carbamates or chilling was accompanied by resistance of microtubules to these factors. The carbamate tolerant mutants were cross-resistant to chilling stress. This was mirrored by an adaptive reorganization of microtubules and a reduction of microtubule dynamics in response to chilling. The analysis of these mutants suggests (1) that microtubule dynamics limit the tolerance to chilling and EPC, and (2) that the cold sensitivity of microtubules limits chilling tolerance in tobacco.     

Microfilament bundles and cell shape are related to adhesiveness to substratum and are dissociable from growth control in cultured fibroblasts

The distribution of microfilament bundles in cells was examined using antibodies to fibroblast myosin and indirect immunofluorescence microscopy. There is no correlation between the presence of bundles of microfilaments and normal growth control. A normal cell line (Balb/c 3T3) cultured on a poorly adhesive substratum showed no microfilament bundles. Similarly, a mutant cell line (AD6) with normal growth, but a rounded shape due to defective adhesiveness to substratum, showed no bundle formation. On the other hand, two transformed cell lines with a flat morphology (Swiss SV3T3 and Balb MSV-85) showed extensive bundle formation. When a transformed cell line with poor adhesiveness (MC5-5) was treated with CSP (a major surface glycoprotein of normal cells) which increases adhesiveness to substratum, the cells formed extensive microfilament bundles without any decrease in growth. We conclude that the distribution of microfilament bundles is related to adhesiveness to substratum and cell shape but not to growth properties.     

Blur and disparity are complementary cues to depth

Estimating depth from binocular disparity is extremely precise, and the cue does not depend on statistical regularities in the environment. Thus, disparity is commonly regarded as the best visual cue for determining 3D layout. But depth from disparity is only precise near where one is looking; it is quite imprecise elsewhere. Away from fixation, vision resorts to using other depth cues-e.g., linear perspective, familiar size, aerial perspective. But those cues depend on statistical regularities in the environment and are therefore not always reliable. Depth from defocus blur relies on fewer assumptions and has the same geometric constraints as disparity but different physiological constraints. Blur could in principle fill in the parts of visual space where disparity is imprecise. We tested this possibility with a depth-discrimination experiment. Disparity was more precise near fixation and blur was indeed more precise away from fixation. When both cues were available, observers relied on the more informative one. Blur appears to play an important, previously unrecognized role in depth perception. Our findings lead to a new hypothesis about the evolution of slit-shaped pupils and have implications for the design and implementation of stereo 3D displays.     

NudE and NudEL are required for mitotic progression and are involved in dynein recruitment to kinetochores

NudE and NudEL are related proteins that interact with cytoplasmic dynein and LIS1. Their functional relationship and involvement in LIS1 and dynein regulation are not completely understood. We find that NudE and NudEL each localize to mitotic kinetochores before dynein, dynactin, ZW10, and LIS1 and exhibit additional temporal and spatial differences in distribution from the motor protein. Inhibition of NudE and NudEL caused metaphase arrest with misoriented chromosomes and defective microtubule attachment. Dynein and dynactin were both displaced from kinetochores by the injection of an anti-NudE/NudEL antibody. Dynein but not dynactin interacted with NudE surprisingly through the dynein intermediate and light chains but not the motor domain. Together, these results identify a common function for NudE and NudEL in mitotic progression and identify an alternative mechanism for dynein recruitment to and regulation at kinetochores.     

Reactions to children's faces: Males are more affected by resemblance than females are, and so are their brains

The detection of genetic relatedness (i.e., kinship) affects the social, parental, and sexual behavior of many species. In humans, self-referent phenotype matching based on facial resemblance may indicate kinship, and it has been demonstrated that facial resemblance increases perceptions of trustworthiness and attractiveness [Proc. R. Soc. Lond., B Biol. Sci. 269 (2002) 1307–1312; Proc. R. Soc. Lond., B Biol. Sci. (in press)]. However, investigations of sex differences in reaction to facial resemblance have produced mixed results [Evol. Hum. Behav. 25 (2004) 142–154; Evol. Hum. Behav. 23 (2002) 159–166; Evol. Hum. Behav. 24 (2003) 81–87]. Here, we replicate the effects of Platek et al. [Evol. Hum. Behav. 23 (2002) 159–166] using high-resolution color morphing. We also extend these findings using functional magnetic resonance imaging (fMRI) to demonstrate a possible neural mechanism that may account for the observed sex difference. These data support the hypothesis that human males may use and favor facial resemblance as a paternity cue.     

Nonnative Gracilaria vermiculophylla tetrasporophytes are more difficult to debranch and are less nutritious than gametophytes

Theory predicts that the maintenance of haplodiplontic life cycles requires ecological differences between the haploid gametophytes and diploid sporophytes, yet evidence of such differences remain scarce. The haplodiplontic red seaweed Gracilaria vermiculophylla has invaded the temperate estuaries of the Northern Hemisphere, where it commonly modifies detrital and trophic pathways. In native populations, abundant hard substratum enables spore settlement, and gametophyte:tetrasporophyte ratios are ~40:60. In contrast, many non‐native populations persist in soft‐sediment habitats without abundant hard substratum, and can be 90%–100% tetrasporophytic. To test for ecologically relevant phenotypic differences, we measured thallus morphology, protein content, organic content, “debranching resistance” (i.e., tensile force required to remove a branch from its main axis node), and material properties between male gametophytes, female gametophytes, and tetrasporophytes from a single, nonnative site in Charleston Harbor, South Carolina, USA in 2015 and 2016. Thallus length and surface area to volume ratio differed between years, but were not significantly different between ploidies. Tetrasporophytes had lower protein content than gametophytes, suggesting the latter may be more attractive to consumers. More force was required to pull a branch from the main axis of tetrasporophytes relative to gametophytes. A difference in debranching resistance may help to maintain tetrasporophyte thallus durability relative to gametophytes, providing a potential advantage in free‐floating populations. These data may shed light on the invasion ecology of an important ecosystem engineer, and may advance our understanding of life cycle evolution and the maintenance of life cycle diversity.     

Correlated pay-offs are key to cooperation

The general belief that cooperation and altruism in social groups result primarily from kin selection has recently been challenged, not least because results from cooperatively breeding insects and vertebrates have shown that groups may be composed mainly of non-relatives. This allows testing predictions of reciprocity theory without the confounding effect of relatedness. Here, we review complementary and alternative evolutionary mechanisms to kin selection theory and provide empirical examples of cooperative behaviour among unrelated individuals in a wide range of taxa. In particular, we focus on the different forms of reciprocity and on their underlying decision rules, asking about evolutionary stability, the conditions selecting for reciprocity and the factors constraining reciprocal cooperation. We find that neither the cognitive requirements of reciprocal cooperation nor the often sequential nature of interactions are insuperable stumbling blocks for the evolution of reciprocity. We argue that simple decision rules such as ‘help anyone if helped by someone’ should get more attention in future research, because empirical studies show that animals apply such rules, and theoretical models find that they can create stable levels of cooperation under a wide range of conditions. Owing to its simplicity, behaviour based on such a heuristic may in fact be ubiquitous. Finally, we argue that the evolution of exchange and trading of service and commodities among social partners needs greater scientific focus.     

Metabolic networks are NP-hard to reconstruct

High-throughput data from various omics and sequencing techniques have rendered the automated metabolic network reconstruction a highly relevant problem. Our approach reflects the inherent probabilistic nature of the steps involved in metabolic network reconstruction. Here, the goal is to arrive at networks which combine probabilistic information with the possibility to obtain a small number of disconnected network constituents by reduction of a given preliminary probabilistic metabolic network. We define automated metabolic network reconstruction as an optimization problem on four-partite graph (nodes representing genes, enzymes, reactions, and metabolites) which integrates: (1) probabilistic information obtained from the existing process for metabolic reconstruction from a given genome, (2) connectedness of the raw metabolic network, and (3) clustering of components in the reconstructed metabolic network. The practical implications of our theoretical analysis refer to the quality of reconstructed metabolic networks and shed light on the problem of finding more efficient and effective methods for automated reconstruction. Our main contributions include: a completeness result for the defined problem, polynomial-time approximation algorithm, and an optimal polynomial-time algorithm for trees. Moreover, we exemplify our approach by the reconstruction of the sucrose biosynthesis pathway in Chlamydomonas reinhardtii.