Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery

EF-hand Ca²⁺-binding proteins (CBPs), such as S100 proteins (S100s) and calmodulin (CaM), are signaling proteins that undergo conformational changes upon increasing intracellular Ca²⁺. Upon binding Ca²⁺, S100 proteins and CaM interact with protein targets and induce important biological responses. The Ca²⁺-binding affinity of CaM and most S100s in the absence of target is weak (^CaK_D > 1 μM). However, upon effector protein binding, the Ca²⁺ affinity of these proteins increases via heterotropic allostery (^CaK_D < 1 μM). Because of the high number and micromolar concentrations of EF-hand CBPs in a cell, at any given time, allostery is required physiologically, allowing for (i) proper Ca²⁺ homeostasis and (ii) strict maintenance of Ca²⁺-signaling within a narrow dynamic range of free Ca²⁺ ion concentrations, [Ca²⁺]^free. In this review, mechanisms of allostery are coalesced into an empirical “binding and functional folding (BFF)” physiological framework. At the molecular level, folding (F), binding and folding (BF), and BFF events include all atoms in the biomolecular complex under study. The BFF framework is introduced with two straightforward BFF types for proteins (type 1, concerted; type 2, stepwise) and considers how homologous and nonhomologous amino acid residues of CBPs and their effector protein(s) evolved to provide allosteric tightening of Ca²⁺ and simultaneously determine how specific and relatively promiscuous CBP-target complexes form as both are needed for proper cellular function.     

Amyloid by Design: Intrinsic Regulation of Microbial Amyloid Assembly

The term amyloid has historically been used to describe fibrillar aggregates formed as the result of protein misfolding and that are associated with a range of diseases broadly termed amyloidoses. The discovery of “functional amyloids” expanded the amyloid umbrella to encompass aggregates structurally similar to disease-associated amyloids but that engage in a variety of biologically useful tasks without incurring toxicity. The mechanisms by which functional amyloid systems ensure nontoxic assembly has provided insights into potential therapeutic strategies for treating amyloidoses. Some of the most-studied functional amyloids are ones produced by bacteria. Curli amyloids are extracellular fibers made by enteric bacteria that function to encase and protect bacterial communities during biofilm formation. Here we review recent studies highlighting microbial functional amyloid assembly systems that are tailored to enable the assembly of non-toxic amyloid aggregates.     

A hybrid behavioural rule of adaptation and drift explains the emergent architecture of antagonistic networks

Ecological processes that can realistically account for network architectures are central to our understanding of how species assemble and function in ecosystems. Consumer species are constantly selecting and adjusting which resource species are to be exploited in an antagonistic network. Here we incorporate a hybrid behavioural rule of adaptive interaction switching and random drift into a bipartite network model. Predictions are insensitive to the model parameters and the initial network structures, and agree extremely well with the observed levels of modularity, nestedness and node-degree distributions for 61 real networks. Evolutionary and community assemblage histories only indirectly affect network structure by defining the size and complexity of ecological networks, whereas adaptive interaction switching and random drift carve out the details of network architecture at the faster ecological time scale. The hybrid behavioural rule of both adaptation and drift could well be the key processes for structure emergence in real ecological networks.     

Eunotia amazonica sp. nov. (Bacillariophyta), a common stalk-forming species from the Rio Negro basin (Brazilian Amazon)

A new stalk-forming diatom was observed at high relative abundances on periphytic samples collected in the Rio Negro hydrographic basin (Brazilian Amazon) and is here described using light and scanning electron microscopy. We also present ecological preferences of the new species. Eunotia amazonica sp. nov. co-dominated periphytic samples collected during the rainy seasons of 2013 and 2014 near the city of Manaus (Amazonas, Brazil). The main diagnostic feature of the new species is the stalk-forming growth form (‘Cymbella-like’) illustrated here for the first time in the genus Eunotia Ehrenberg. Previous reports on growth forms in common European databases for this genus included colonial (‘ribbon-like’) but also ‘mobile’, ‘fixed by pads’ or ‘without structures of fixation’. We demonstrated that the three dominant Eunotia species in periphytic samples from the Rio Negro all exhibited distinct ‘growth forms’ or habits: Eunotia amazonica sp. nov. (stalked), Eunotia intricans Metzeltin & Lange-Bertalot (ribbon-like) and Eunotia rabenhorstiana (Grunow) Hustedt (branched-arborescent). The high diversity of species, many of which are unknown to science, as well as the poorly known life-forms and habits of the Eunotiaceae in the region, partially prevent the use of metrics based on life-form to assess ecological changes. Generic assumptions based on robust statistical methods may obscure reality and lead to biased conclusions of diatom community changes in poorly explored regions such as Neotropical freshwater rivers, where the Eunotiaceae are largely dominant, particularly in the Amazon basin.     

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre‐existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution – historical continuity of a deterministic network that links past and present functional associations of its components.     

Root exudates and their ecological consequences in forest ecosystems: Problems and perspective北大核心CSCD

Researches on rhizosphere ecological processes and the underlying mechanisms have become one of the most active and sensitive hotspots in soil science. Root exudates have specialized roles in mediating the nutrient cycling and signal transduction within root-soil-microbe interactions. They are the key driving factors in regulating the functions of rhizosphere micro-ecosystem, and serve as a major premise for the concept and ecological processes in rhizosphere. However, due to the instinctive advantages of crops, such as short life cycles and convenient operation, most previous studies on root exudation mainly focused on agricultural ecosystems and were primarily targeted at providing practical guidelines. In contrast, there have been relatively few investigations on root exudates of trees, which highly limited the comprehensive knowledge of the potential mechanisms of root exudates in mediating soil biogeochemical processes in forest ecosystems. Hence, in this review, based on the main findings in our previous studies and the emerging frontiers in rhizosphere ecology, we specifically reviewed the ecological consequences and key remaining challenges in researches on root exudation in forests. Finally, we identify several topics and research outlooks for guiding future work to facilitate studies on root exudation and its ecological consequences in forest ecosystems. © Chinese Journal of Plant Ecology     

微生物对水环境污染物的趋化性研究进展

随着人类活动的干扰以及社会工业化进程的加剧,水环境污染现象日益严峻。微生物是水环境污染治理和修复的主要驱动者。越来越多的研究发现,水环境中污染物的去除速率与微生物的趋化功能密切相关。综述了近几年有关微生物对水环境中无机盐、溶解性有机物和重金属等的趋化特性研究进展,讨论并展望了基于趋化功能微生物精准调控的水环境污染强化治理技术的应用前景及主要问题。     

外来物种刺槐对黄土丘陵区植物群落功能结构的影响

在黄土丘陵区草原带、森林草原带和森林带3个植被带选取成对的刺槐群落和乡土植物群落功能性状值,研究不同植被带刺槐群落、乡土植物群落功能结构的变化,以及同一植被带下刺槐的引入对群落功能结构的影响.结果表明: 刺槐群落和乡土植物群落的叶碳、叶氮、叶磷、比叶面积、叶组织密度等功能性状随植被带的变化规律一致.刺槐群落叶碳、叶氮、比叶面积显著高于乡土植物群落,且2种群落功能多样性指数(FR_ic、FE_ve、FD_iv、FD_is、Rao)随植被带的变化趋势并不完全一致,在森林带刺槐的引入提高了植物群落功能多样性,在草原带降低了植物群落功能多样性.