Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids

Previous work has shown that molecular phylogenies of plastids, cyanobacteria, and proteobacteria based on the rubisco (ribulose-1,5- bisphosphate carboxylase/oxygenase) genes rbcL and rbcS are incongruent with molecular phylogenies based on other genes and are also incompatible with structural and biochemical information. Although it has been much speculated that this is the consequence of a single horizontal gene transfer (of a proteobacterial or mitochondrial rubisco operon into plastids of rhodophytic and chromophytic algae), neither this hypothesis nor the alternative hypothesis of ancient gene duplication have been examined in detail. We have conducted phylogenetic analyses of all available bacterial rbcL sequences, and representative plastid sequences, in order to explore these alternative hypothesis and fully examine the complexity of rubisco gene evolution. The rbcL phylogeny reveals a surprising number of gene relationships that are fundamentally incongruent with organismal relationships as inferred from multiple lines of other molecular evidence. On the order of six horizontal gene transfers are implied by the form I (L8S8) rbcL phylogeny, two between cyanobacteria and proteobacteria, one between proteobacteria and plastids, and three within proteobacteria. Alternatively, a single ancient duplication of the form I rubisco operon, followed by repeated and pervasive differential loss of one operon or the other, would account for much of this incongruity. In all probability, the rubisco operon has undergone multiple events of both horizontal gene transfer and gene duplication in different lineages.      

Plasticity of Noddy Parents and Offspring to Sea-Surface Temperature Anomalies

Behavioral and/or developmental plasticity is crucial for resisting the impacts of environmental stressors. We investigated the plasticity of adult foraging behavior and chick development in an offshore foraging seabird, the black noddy (Anous minutus), during two breeding seasons. The first season had anomalously high sea-surface temperatures and ‘low’ prey availability, while the second was a season of below average sea-surface temperatures and ‘normal’ food availability. During the second season, supplementary feeding of chicks was used to manipulate offspring nutritional status in order to mimic conditions of high prey availability. When sea-surface temperatures were hotter than average, provisioning rates were significantly and negatively impacted at the day-to-day scale. Adults fed chicks during this low-food season smaller meals but at the same rate as chicks in the unfed treatment the following season. Supplementary feeding of chicks during the second season also resulted in delivery of smaller meals by adults, but did not influence feeding rate. Chick begging and parental responses to cessation of food supplementation suggested smaller meals fed to artificially supplemented chicks resulted from a decrease in chick demands associated with satiation, rather than adult behavioral responses to chick condition. During periods of low prey abundance, chicks maintained structural growth while sacrificing body condition and were unable to take advantage of periods of high prey abundance by increasing growth rates. These results suggest that this species expresses limited plasticity in provisioning behavior and offspring development. Consequently, responses to future changes in sea-surface temperature and other environmental variation may be limited.     

Sex-specific chick provisioning and diving behaviour in the wedge-tailed shearwater Puffinus pacificus

Mechanisms that drive sex-specific foraging behaviour in seabirds are not fully understood. In some cases, sexual-size dimorphism has been implicated. However, recent empirical work indicates that foraging behaviour may also differ between sexes of monomorphic seabird taxa. We simultaneously examined sex-specific differences in adult foraging behaviour, chick provisioning rates and maximum dive-depths in a monomorphic seabird, the wedge-tailed shearwater Puffinus pacificus . We found significant divergence between sexes. Mean foraging trip length was longer, provisioning rate lower and mean maximum dive-depth shallower in females. We found no evidence of divergence in foraging behaviour due to condition-dependant increases in self-provisioning by females, or differences in the nest attendance patterns of each sex. In addition, chick body condition did not influence meal mass or trip length differently in one or other sex. Consistent with results obtained for dimorphic species we suggest that inter-sexual competition at the foraging grounds provides the most parsimonious explanation for the sex-specific differences observed in this monomorphic species. Based on our findings we believe this possibility warrants further critical investigation.     

Structural characterization of monoclonal antibodies targeting C-terminal Ser404 region of phosphorylated tau protein

Targeting tau with immunotherapies is currently the most common approach taken in clinical trials of patients with Alzheimer’s disease. The most prominent pathological feature of tau is its hyperphosphorylation, which may cause the protein to aggregate into toxic assemblies that collectively lead to neurodegeneration. Of the phospho-epitopes, the region around Ser³⁹⁶/Ser⁴⁰⁴ has received particular attention for therapeutic targeting because of its prominence and stability in diseased tissue. Herein, we present the antigen-binding fragment (Fab)/epitope complex structures of three different monoclonal antibodies (mAbs) that target the pSer⁴⁰⁴ tau epitope region. Most notably, these structures reveal an antigen conformation similar to a previously described pathogenic tau epitope, pSer⁴²², which was shown to have a β-strand structure that may be linked to the seeding core in tau oligomers. In addition, we have previously reported on the similarly ordered conformation observed in a pSer³⁹⁶ epitope, which is in tandem with pSer⁴⁰⁴. Our data are the first Fab structures of mAbs bound to this epitope region of the tau protein and support the existence of proteopathic tau conformations stabilized by specific phosphorylation events that are viable targets for immune modulation.     

Indeterminate growth in long-lived freshwater turtles as a component of individual fitness

Although evidence that reptiles exhibit indeterminate growth remains equivocal and based on inadequate data, the assumption that they do is still widely accepted as a general trait of reptiles. We examined patterns of variation in adult growth using long-term mark-recapture data on 13 populations of 9 species representing 3 families of freshwater turtles located in South Carolina, Michigan, and Arizona in the USA and in Ontario, Canada. Across 13 study populations, growth rates of all adults and only those that grew averaged 1.5 and 1.9 mm/yr respectively. Sources of variation in growth rates included species, population, sex, age, and latitude. Most adults of both sexes with recapture intervals greater than 10 years grew, but across all populations an average of 19 % of individuals did not grow (some with recapture intervals up to 30 years). For known-age adults of three species, the highest growth rates occurred during the 10 years following sexual maturity, and the proportions of non-growing individuals increased with age. Growth rates of adults were on average 92 % lower than those of juveniles. Based on linear relationships of clutch size and body size of females at average juvenile and adult growth rates it would take 0.7 (0.2–1.2) years and 8.6 (min–max = 2.3–18.5) years, respectively, to grow enough to increase clutch size by one egg. The majority of within population variation in adult body size in 3 species appeared to be a combination of differences in ages at maturity and juvenile and early adult growth, rather than indeterminate growth. The results from our study populations indicate that increases in body size (and associated reproductive output) that results from indeterminate growth are not substantial enough to represent a major factor in the evolution of life histories in general or the evolution of longevity and aging specifically.     

The expression analysis of Sfrs10 and Celf4 during mouse retinal development

Processing of mRNAs including, alternative splicing (AS), mRNA transport and translation regulation are crucial to eukaryotic gene expression. For example, >90% of the genes in the human genome are known to undergo alternative splicing thereby expanding the proteome production capacity of a limited number of genes. Similarly, mRNA export and translation regulation plays a vital role in regulating protein production. Thus, it is important to understand how these RNA binding proteins including alternative splicing factors (ASFs) and mRNA transport and translation factors regulate these processes. Here we report the expression of an ASF, serine-arginine rich splicing factor 10 (Sfrs10) and a mRNA translation regulation factor, CUGBP, elav like family member 4 (Celf4) in the developing mouse retina. Sfrs10 was expressed throughout postnatal (P) retinal development and was observed progressively in newly differentiating neurons. Immunofluorescence (IF) showed Sfrs10 in retinal ganglion cells (RGCs) at P0, followed by amacrine and bipolar cells, and at P8 it was enriched in red/green cone photoreceptor cells. By P22, Sfrs10 was observed in rod photoreceptors in a peri-nuclear pattern. Like Sfrs10, Celf4 expression was also observed in the developing retina, but with two distinct retinal isoforms. In situ hybridization (ISH) showed progressive expression of Celf4 in differentiating neurons, which was confirmed by IF that showed a dynamic shift in Celf4 localization. Early in development Celf4 expression was restricted to the nuclei of newly differentiating RGCs and later (E16 onwards) it was observed in the initial segments of RGC axons. Later, during postnatal development, Celf4 was observed in amacrine and bipolar cells, but here it was predominantly cytoplasmic and enriched in the two synaptic layers. Specifically, at P14, Celf4 was observed in the synaptic boutons of rod bipolar cells marked by Pkc-α. Thus, Celf4 might be regulating AS early in development besides its known role of regulating mRNA localization/translation. In all, our data suggests an important role for AS and mRNA localization/translation in retinal neuron differentiation.     

The PR-Set7 binding domain of Riz1 is required for the H4K20me1-H3K9me1 trans-tail ‘histone code’ and Riz1 tumor suppressor function

PR-Set7/Set8/KMT5a is the sole histone H4 lysine 20 monomethyltransferase (H4K20me1) in metazoans and is essential for proper cell division and genomic stability. We unexpectedly discovered that normal cellular levels of monomethylated histone H3 lysine 9 (H3K9me1) were also dependent on PR-Set7, but independent of its catalytic activity. This observation suggested that PR-Set7 interacts with an H3K9 monomethyltransferase to establish the previously reported H4K20me1-H3K9me1 trans-tail ‘histone code’. Here we show that PR-Set7 specifically and directly binds the C-terminus of the Riz1/PRDM2/KMT8 tumor suppressor and demonstrate that the N-terminal PR/SET domain of Riz1 preferentially monomethylates H3K9. The PR-Set7 binding domain was required for Riz1 nuclear localization and maintenance of the H4K20me1-H3K9me1 trans-tail ‘histone code’. Although Riz1 can function as a repressor, Riz1/H3K9me1 was dispensable for the repression of genes regulated by PR-Set7/H4K20me1. Frameshift mutations resulting in a truncated Riz1 incapable of binding PR-Set7 occur frequently in various aggressive cancers. In these cancer cells, expression of wild-type Riz1 restored tumor suppression by decreasing proliferation and increasing apoptosis. These phenotypes were not observed in cells expressing either the Riz1 PR/SET domain or PR-Set7 binding domain indicating that Riz1 methyltransferase activity and PR-Set7 binding domain are both essential for Riz1 tumor suppressor function.