Partial protein domains: evolutionary insights and bioinformatics challenges

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.With the rapid expansion in the number of determined protein sequences - over 92 million in UniProt in March 2015 - an ever-increasing number of biologists are using bioinformatics tools for annotation of these sequences. One widely used strategy is to identify occurrences of Pfam families within the sequence of interest [1]. A Pfam family is a multiple sequence alignment of the occurrences of a particular domain both in different species and in different regions of the same protein. The concept underpinning Pfam is that proteins typically comprise one or more domains (regions), each of which is an evolutionary unit that generally has a well-defined biological function. A significant sequence similarity between a query protein and a Pfam family provides the basis for annotations. Two recent articles [2,3] in Genome Biology evaluate the implications of having the query sequence only matching part of a Pfam family, which is an intriguing finding, given that a Pfam family is considered to be an evolutionary unit.     

Base Excision Repair of Chemotherapeutically-Induced Alkylated DNA Damage Predominantly Causes Contractions of Expanded GAA Repeats Associated with Friedreich's Ataxia

Expansion of GAA·TTC repeats within the first intron of the frataxin gene is the cause of Friedreich''s ataxia (FRDA), an autosomal recessive neurodegenerative disorder. However, no effective treatment for the disease has been developed as yet. In this study, we explored a possibility of shortening expanded GAA repeats associated with FRDA through chemotherapeutically-induced DNA base lesions and subsequent base excision repair (BER). We provide the first evidence that alkylated DNA damage induced by temozolomide, a chemotherapeutic DNA damaging agent can induce massive GAA repeat contractions/deletions, but only limited expansions in FRDA patient lymphoblasts. We showed that temozolomide-induced GAA repeat instability was mediated by BER. Further characterization of BER of an abasic site in the context of (GAA)₂₀ repeats indicates that the lesion mainly resulted in a large deletion of 8 repeats along with small expansions. This was because temozolomide-induced single-stranded breaks initially led to DNA slippage and the formation of a small GAA repeat loop in the upstream region of the damaged strand and a small TTC loop on the template strand. This allowed limited pol β DNA synthesis and the formation of a short 5''-GAA repeat flap that was cleaved by FEN1, thereby leading to small repeat expansions. At a later stage of BER, the small template loop expanded into a large template loop that resulted in the formation of a long 5''-GAA repeat flap. Pol β then performed limited DNA synthesis to bypass the loop, and FEN1 removed the long repeat flap ultimately causing a large repeat deletion. Our study indicates that chemotherapeutically-induced alkylated DNA damage can induce large contractions/deletions of expanded GAA repeats through BER in FRDA patient cells. This further suggests the potential of developing chemotherapeutic alkylating agents to shorten expanded GAA repeats for treatment of FRDA.     

The evolutionary emergence of stochastic phenotype switching in bacteria

Stochastic phenotype switching - or bet hedging - is a pervasive feature of living systems and common in bacteria that experience fluctuating (unpredictable) environmental conditions. Under such conditions, the capacity to generate variable offspring spreads the risk of being maladapted in the present environment, against offspring likely to have some chance of survival in the future. While a rich subject for theoretical studies, little is known about the selective causes responsible for the evolutionary emergence of stochastic phenotype switching. Here we review recent work - both theoretical and experimental - that sheds light on ecological factors that favour switching types over non-switching types. Of particular relevance is an experiment that provided evidence for an adaptive origin of stochastic phenotype switching by subjecting bacterial populations to a selective regime that mimicked essential features of the host immune response. Central to the emergence of switching types was frequent imposition of 'exclusion rules' and 'population bottlenecks' - two complementary faces of frequency dependent selection. While features of the immune response, exclusion rules and bottlenecks are likely to operate in many natural environments. Together these factors define a set of selective conditions relevant to the evolution of stochastic switching, including antigenic variation and bacterial persistence.     

Extreme weather events influence the phytoplankton community structure in a large lowland subtropical lake (Lake Okeechobee, Florida, USA)

We demonstrate a major ecological change in a large lake ecosystem in response to a series of extreme weather events. Phytoplankton community dynamics in subtropical Lake Okeechobee are described from 2000 through early 2008 with emphasis on inter-relationships among phytoplankton populations and associated environmental variables in this large, shallow eutrophic lake. The lake experienced the physical effects of three hurricanes in 2004–2005, which caused massive sediment resuspension, near total elimination of submerged aquatic vegetation, elevated biologically available nutrients and total suspended solids, and lower water transparency. Patterns of long-term co-dominance by nitrogen (N)-fixing cyanobacteria and meroplanktonic diatoms abruptly changed to dominance by only meroplanktonic diatoms. The planktonic cyanobacteria genera Anabaena and Planktolyngbya both decreased approximately an order of magnitude in the post-hurricane period despite large surpluses of bioavailable nutrients. Meroplanktonic diatoms (mostly Aulacoseira spp.) declined approximately 20%, perhaps because of superior competitive ability for light in a polymictic, turbid water column. Canonical Correspondence Analysis (CCA) suggested that reduction in planktonic cyanobacteria after compression of the photic zone and the persistence of meroplanktonic diatoms were related to light utilization traits for the key algal taxa and indicated that pre-existing light limitation and crustacean grazing pressure were intensified in the post-hurricane period.     

Scats and den contents as indicators of the diet of stoats (Mustela erminea) in the Tasman Valley,South Canterbury,New Zealand

Stoats are significant predators of native fauna in New Zealand. They occur in many habitat types and consume a wide range of prey. The diet of stoats in the Tasman River, South Canterbury, was studied by analysis of scats and den contents. Analysis of 206 scats showed that stoats ate mainly lagomorphs, birds and invertebrates. Minor components included mice, lizards, fish and hedgehogs. Stoats ate more birds in spring than in autumn, and female stoats ate more invertebrates than did males. The contents of 219 dens collected in the same area at the same time provided further information. Birds and lagomorphs occurred at high frequency in dens, and other components were minor. Remains in dens were larger than in scats and allowed identification of many more prey items to species level. Den contents revealed a potentially substantial impact of stoats on threatened shorebirds locally; this impact was not detected by analysis of scats.     

Composition,size, and biomass of zooplankton in large productive Florida lakes

Crustacean zooplankton data were compiled from long-term observational studies at seven large shallow Florida lakes, to determine whether there are general characteristics in regard to species composition, body size, and biomass. In particular, we examined whether patterns in body size and species richness fit empirical models developed by Stanley Dodson. The lakes included range in size from 125 to 1730 km² and encompass mesotrophic to hyper-eutrophic conditions. We found that zooplankton biomass was strongly dominated by one species of calanoid copepod—Arctodiaptomus dorsalis. Large daphnids were absent, and Cladocera assemblages were dominated by small taxa such as Ceriodaphnia, Chydorus, and Eubosmina. The total number of species of pelagic cladocerans (8–12) was consistent with Dodson’s predictions based on lake area. The average size of crustacean zooplankton in Florida lakes is small in comparison with temperate communities. A. dorsalis is the smallest calanoid copepod in North America, and the mean length of Cladocera (0.6 mm) is consistent with Dodson’s results that size decreases from temperate to tropical zones. Total biomass of crustacean zooplankton was very low, ratios of zooplankton to phytoplankton biomass (0.01–0.1) are among the lowest reported in the literature, and the zooplankton displayed short-lasting early spring peaks in biomass. Cladocera were almost entirely absent in spring and summer. Factors known to occur in Florida lakes, which appear to explain these characteristics of biomass, include intense fish predation and high summer water temperature.     

Lactate uptake contributes to the NAD(P)H biphasic response and tissue oxygen response during synaptic stimulation in area CA1 of rat hippocampal slices

Synaptic train stimulation (10 Hz × 25 s) in hippocampal slices results in a biphasic response of NAD(P)H fluorescence indicating a transient oxidation followed by a prolonged reduction. The response is accompanied by a transient tissue PO₂ decrease indicating enhanced oxygen utilization. The activation of mitochondrial metabolism and/or glycolysis may contribute to the secondary NAD(P)H peak. We investigated whether extracellular lactate uptake via monocarboxylate transporters (MCTs) contributes to the generation of the NAD(P)H response during neuronal activation. We measured the effect of lactate uptake inhibition [using the MCT inhibitor α-cyano-4-hydroxycinnamate (4-CIN)] on the NAD(P)H biphasic response, tissue PO₂ response, and field excitatory post-synaptic potential in hippocampal slices during synaptic stimulation in area CA1 (stratum radiatum). The application of 4-CIN (150–250 μmol/L) significantly decreased the reduction phase of the NAD(P)H response. When slices were supplemented with 20 mmol/L lactate in 150–250 μmol/L 4-CIN, the secondary NAD(P)H peak was restored; whereas 20 mmol/L pyruvate supplementation did not produce a recovery. Similarly, the tissue PO₂ response was decreased by MCT inhibition; 20 mmol/L lactate restored this response to control levels at all 4-CIN concentrations. These results indicate that lactate uptake via MCTs contributes significantly to energy metabolism in brain tissue and to the generation of the delayed NAD(P)H peak after synaptic stimulation.     

Ectomycorrhizal fungi of the Seychelles: diversity patterns and host shifts from the native Vateriopsis seychellarum (Dipterocarpaceae) and Intsia bijuga (Caesalpiniaceae) to the introduced Eucalyptus robusta (Myrtaceae), but not Pinus caribea (Pinaceae)

Ectomycorrhizal (ECM) fungi form highly diverse communities in temperate forests, but little is known about their community ecology in tropical ecosystems. Using anatomotyping and rDNA sequencing, ECM fungi were identified on root tips of the introduced Eucalyptus robusta and Pinus caribea as well as the endemic Vateriopsis seychellarum and indigenous Intsia bijuga in the Seychelles. Sequencing revealed 30 species of ECM fungi on root tips of V. seychellarum and I. bijuga, with three species overlapping. Eucalyptus robusta shared five of these taxa, whereas P. caribea hosted three unique species of ECM fungi that were likely cointroduced with containerized seedlings. The thelephoroid (including the anamorphic genus Riessiella), euagaric, boletoid and hymenochaetoid clades of basidiomycetes dominated the ECM fungal community of native trees. Two species of Annulatascaceae (Sordariales, Ascomycota) were identified and described as ECM symbionts of V. seychellarum. The low diversity of native ECM fungi is attributed to deforestation and long-term isolation of the Seychelles. Native ECM fungi associate with exotic eucalypts, whereas cointroduced ECM fungi persist in pine plantations for decades.     

Lamellipodial actin mechanically links myosin activity with adhesion-site formation

Cell motility proceeds by cycles of edge protrusion, adhesion, and retraction. Whether these functions are coordinated by biochemical or biomechanical processes is unknown. We find that myosin II pulls the rear of the lamellipodial actin network, causing upward bending, edge retraction, and initiation of new adhesion sites. The network then separates from the edge and condenses over the myosin. Protrusion resumes as lamellipodial actin regenerates from the front and extends rearward until it reaches newly assembled myosin, initiating the next cycle. Upward bending, observed by evanescence and electron microscopy, results in ruffle formation when adhesion strength is low. Correlative fluorescence and electron microscopy shows that the regenerating lamellipodium forms a cohesive, separable layer of actin above the lamellum. Thus, actin polymerization periodically builds a mechanical link, the lamellipodium, connecting myosin motors with the initiation of adhesion sites, suggesting that the major functions driving motility are coordinated by a biomechanical process.