冠状病毒特征与进化优势

冠状病毒是近年来新发突发传染病的重要来源,因家族成员庞大、宿主谱广、突变株多样,在进化中展示了其优越性。本文通过回顾冠状病毒基因组特征、感染宿主动物与受体分布及基因突变等方面的研究进展,对其在进化和传播中存在的优势进行总结和讨论,以期引起对相关病毒防控的重视。     

Darwinian selection for sites of Asn-linked glycosylation in phylogenetically disparate eukaryotes and viruses

Numerous protists and rare fungi have truncated Asn-linked glycan precursors and lack N-glycan-dependent quality control (QC) systems for glycoprotein folding in the endoplasmic reticulum. Here, we show that the abundance of sequons (NXT or NXS), which are sites for N-glycosylation of secreted and membrane proteins, varies by more than a factor of 4 among phylogenetically diverse eukaryotes, based on a few variables. There is positive correlation between the density of sequons and the AT content of coding regions, although no causality can be inferred. In contrast, there appears to be Darwinian selection for sequons containing Thr, but not Ser, in eukaryotes that have N-glycan-dependent QC systems. Selection for sequons with Thr, which nearly doubles the sequon density in human secreted and membrane proteins, occurs by an increased conditional probability that Asn and Thr are present in sequons rather than elsewhere. Increasing sequon densities of the hemagglutinin (HA) of influenza viruses A/H3N2 and A/H1N1 during the past few decades of human infection also result from an increased conditional probability that Asn, Thr, and Ser are present in sequons rather than elsewhere. In contrast, there is no selection on sequons by this mechanism in HA of A/H5N1 or 2009 A/H1N1 (Swine flu). Very strong selection for sequons with both Thr and Ser in glycoprotein of M_r 120,000 (gp120) of HIV and related retroviruses results from this same mechanism, as well as amino acid composition bias and increases in AT content. We conclude that there is Darwinian selection for sequons in phylogenetically disparate eukaryotes and viruses.     

BMPs and Chordin regulate patterning of the directive axis in a sea anemone

The TGF-β molecules Dpp/BMP2/4/7 and their antagonist Sog/Chd play a conserved role in establishing the dorso-ventral (DV) axis in bilaterians. Homologues of BMPs and the antagonist, Chordin, have been isolated from Cnidaria and show a striking asymmetric expression pattern with respect to the primary oral-aboral (OA) axis. We used Morpholino knockdowns of Nematostella dpp (bmp2/4), bmp5-8, chordin, and tolloid to investigate their function during early development of the sea anemone Nematostella vectensis. Molecular analysis of the BMP Morpholino phenotypes revealed an upregulated and radialized expression of bmps and chordin in ectoderm and endoderm indicating a negative feedback loop. Our data further suggest that BMP signaling is required for symmetry breaking of bmp and chordin expression during gastrulation. While bmps and chordin marker genes of the ectodermal OA axis extended aborally, other ectodermal markers of the OA axis were not significantly affected. By contrast, expression of other endodermal marker genes marking both the OA and the directive axis were abolished. Our data suggest that the logic of BMP2/4 signaling and the BMP antagonist, Chordin, differs significantly between Cnidaria and Bilateria, yet the double negative feedback loop detected in Nematostella bears systemic similarities with part of the regulatory network of the DV axis patterning system in amphibians.     

Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold

Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes.Flagellated bacteria have tailored their motility to diverse habitats. For example, the enteric model organisms Salmonella enterica serovar Typhimurium and Escherichia coli colonize animal digestive tracts and can reside outside a host, assembling flagella over their cell body to swim. However, a diverse spectrum of flagellar swimming ability is seen across the bacterial kingdom. Caulobacter crescentus inhabits low-nutrient freshwater environments where it swims using a high-efficiency flagellar motor (1, 2), whereas Vibrio species produce high-speed, sodium-driven polar flagella to capitalize on the high sodium gradient of their marine habitat (3). On the other hand, the ε-proteobacteria and spirochetes, many of which thrive exclusively in association with a host, have evolved characteristically rapid and powerful swimming capabilities that enable them to bore through mucous layers coating epithelial cells or between tissues. Indeed, the ε-proteobacteria Campylobacter jejuni and Helicobacter pylori are capable of continued swimming in high-viscosity media that immobilize E. coli or Vibrio cells (4–6), and similar behavior is observed for spirochetes (7, 8).Despite differences in the organisms’ swimming ability, the flagellar motor is composed of a conserved core of ∼20 structural proteins (9). The mechanism of flagellar motility is conserved (10), with torque generated by rotor and stator components (9). Stator complexes, heterooligomers of four motility A (MotA) and two motility B (MotB) proteins, are thought to form a ring that surrounds the axial driveshaft. Transmembrane helices of MotA and MotB form an ion channel, and MotB features a large periplasmic domain that binds peptidoglycan (11, 12) and the flagellar structural component, the P-ring (13). The stator complex couples ion flux to exertion of force on the cytoplasmic rotor ring (the C-ring), which transmits torque to the axial driveshaft (the rod), universal joint (the hook), and helical propeller (the filament), culminating in propulsion of the bacterium. Biophysical (14) and freeze-fracture (15) studies together with modeling (16) have proposed that a tight ring of ∼11 stator complexes dynamically assembles around the rod above the outer lobe of the C-ring in closely related Salmonella and E. coli motors (which we collectively refer to as the “enteric motor”). However, despite these conclusions, and although the structures observed in subtomogram averages have been proposed to be the stator complexes (17–19), the locations and stoichiometries of the stator complexes remain to be confirmed.How can we explain the wide diversity in flagellar swimming abilities in the context of a conserved core flagellar motor? Biophysical studies suggest that the source of the difference lies, at least in part, in variations in the mechanical output of the motors themselves. Torques of motors from different bacteria have been shown to range over an order of magnitude, and torque correlates with swimming speed and the ability of bacteria to propel themselves through different viscosities, indicating that adaptations are likely to be at the level of the motor itself. [Torque also varies within a single species, up to a maximum value, as a function of the number of stator complexes incorporated into the motor (14)]. For example, C. crescentus motors have been measured to produce torques of 350 pN⋅nm (2). Estimates for the torque of the enteric motor ranges from ∼1,300 to ∼2,000 pN⋅nm (20, 21). The ε-proteobacterium H. pylori has been estimated to swim with torque of 3,600 pN⋅nm (22), and spirochetes are capable of swimming with 4,000 pN⋅nm of torque (21, 23). Sodium-driven motor torques in Vibrio spp. have been measured between ∼2,000 and 4,000 pN⋅nm (24), depending on the magnitude of the sodium gradient. It is noteworthy, however, that an estimated sodium motive force in Vibrio spp. that is lower than the standard E. coli proton motive force nevertheless drives the Vibrio motor with higher torque than the E. coli motor (24, 25), further suggesting that torque differences likely exist at the level of the motor. However, the molecular mechanism by which different motors might produce different torques has not been investigated.The simplest scenario for tuning motor torque would be evolved adaptation of motor architecture. In support of this scenario, we recently showed that many motors have evolved additional structures not found in the well-studied enteric motors (18), and we observed that the C-ring radius varies among species (17, 18). One of the most widespread novel structures is a periplasmic basal disk directly beneath the outer membrane, often co-occurring with varied uncharacterized additional structures, which we collectively term “disk complexes.” Consistently, disk complexes have been seen only in motors that produce torque higher than that in E. coli or Salmonella. For example, the sodium-driven ∼2,000+ pN⋅nm torque motors of Vibrio species assemble a disk complex featuring a basal disk beneath the outer membrane (18) in addition to smaller H- and T-rings composed of FlgOT (flagella O, T) and MotXY (motility X, Y), respectively (26, 27). It has been shown that the T-ring interacts with stator complexes in Vibrio spp. (28), although the exact location and number of stator complexes in Vibrio spp. remains unclear. ε-Proteobacteria such as Helicobacter species, C. jejuni, and Wolinella succinogenes also assemble disk complexes composed of large basal disks beneath the outer membrane together with additional smaller disks (18, 29). Although these and other cases of additional disks have been reported (18, 30), their relation to flagellar function remains enigmatic, and it is unclear if these widespread disk complexes are homologous or analogous.In this study, we hypothesized that bacteria have tuned their swimming abilities by evolving structural adaptations to their flagellar motors that would result in altered torque generation. Using electron cryo-tomography and subtomogram averaging, we found that Vibrio polar γ-proteobacterial and Campylobacter ε-proteobacterial flagellar motors incorporate 13 and 17 stator complexes, respectively, compared with the ∼11 in enteric bacteria. In both cases, these stator complexes are scaffolded into wider stator rings relative to the enteric motor by components of their respective disk complexes. The wider C. jejuni stator ring is further reflected in a considerably wider rotor C-ring. Further analysis of the components of the Vibrio and C. jejuni disk complexes reveals that they share a core protein, FlgP, but each has acquired diverse additional components to form divergent disk-complex architectures. We conclude by showing that our structural data of wider stator rings featuring additional stator complexes can quantitatively account for the differences in torque between different flagellar motors.     

An ecocultural model predicts Neanderthal extinction through competition with modern humans

Archaeologists argue that the replacement of Neanderthals by modern humans was driven by interspecific competition due to a difference in culture level. To assess the cogency of this argument, we construct and analyze an interspecific cultural competition model based on the Lotka−Volterra model, which is widely used in ecology, but which incorporates the culture level of a species as a variable interacting with population size. We investigate the conditions under which a difference in culture level between cognitively equivalent species, or alternatively a difference in underlying learning ability, may produce competitive exclusion of a comparatively (although not absolutely) large local Neanderthal population by an initially smaller modern human population. We find, in particular, that this competitive exclusion is more likely to occur when population growth occurs on a shorter timescale than cultural change, or when the competition coefficients of the Lotka−Volterra model depend on the difference in the culture levels of the interacting species.Neanderthals are a human species (or subspecies) that went extinct, after making a small contribution to the modern human genome (1, 2). Hypotheses for the Neanderthal extinction and their replacement by modern humans, in particular as recorded in Europe, can be classified into those emphasizing competition with modern humans and those arguing that interspecific competition was of minor relevance. Among the latter are the climate change (3) and epidemic/endemic (4) hypotheses. However, an ecocultural niche modeling study has shown that Neanderthals and modern humans exploited similar niches in Europe (5), which, together with a recent reassessment of European Paleolithic chronology showing significant spatiotemporal overlap of the two species (6), suggests a major role for interspecific competition in the demise of the Neanderthals.Replacement of one species (or population) by another is ultimately a matter of numbers. One competing species survives while the other is reduced to, or approaches, zero in size. In the classical Lotka−Volterra model of interspecific competition, this process is called competitive exclusion (7). If Neanderthals were indeed outcompeted by modern humans, the question arises: Wherein lay the advantage to the latter species? Many suggestions have been made, including better tools (8), better clothing (9, 10), and better economic organization (11). These hypotheses share the premise that modern humans were culturally more advanced than the coeval Neanderthals.The purpose of our paper is threefold. First, we extend the Lotka−Volterra-type model of interspecific competition by incorporating the “culture level” of a species as a variable that interacts with population size (12, 13). Here, culture level may be interpreted as the number of cultural traits, toolkit size, toolkit sophistication, etc. Although, as noted above, many anthropological and archaeological discussions invoke interspecific cultural competition, there is, to the best of our knowledge, no mathematical theory of this ecocultural process. A mechanistic resource competition model is difficult to justify at present, because there is a limited understanding of “what the species are competing for… [or] how they compete” (14). Second, we use our interspecific cultural competition model to explore, analytically and numerically, the possibility that a difference in culture level, or in underlying learning ability, may produce competitive exclusion of a comparatively (although not absolutely) large regional (Neanderthal) population by an initially smaller (modern human) one. Third, we assume the competition coefficients of the Lotka−Volterra model to depend explicitly on the difference in the culture levels of the interacting species (rather than to be constants) and ask how this modification affects the invasion and subsequent dynamics.Dependence of the culture/technology level of a human population on its size has been the focus of many theoretical (15–21) as well as psychological (22–24), archaeological (25, 26), and ethnological (27–30) studies. However, the coupled dynamics of population size and culture level, where both quantities are treated as variables, has received less theoretical attention (12, 13, 31, 32).Taking refs. 12 and 13 as the point of departure, we extend previous treatments by introducing two such populations in direct competition with each other in the Lotka−Volterra framework. The two populations are described in terms of their size, N_i (≥0), their culture level z_i (≥0), i (=1, 2), and parameters to be defined below. We ask whether a population can be replaced by an initially smaller one, which has an advantage in culture level or in learning ability. This ecological perspective on the competition between “size−culture profiles” may inform ongoing debate on the replacement of Neanderthals by modern humans.     

Every heart beat is under neural command: an hypothesis relating to the cardiac rhythm

In the human heart there is a sequential contraction of the systemic veins, systemic venous sinus and the pectinated right atrium, 'the systemic waltz', and sequential contraction of the pulmonary veins, pulmonary venous sinus and pectinated left atrium, 'the pulmonary waltz'. The systemic veins contract earlier than the pulmonary veins creating a 'duet. We hypothesise that this waltz and duet point to a complex extracardiac control of the cardiac rhythm on a beat-to-beat neural basis.     

Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses

Essential amino acids (EAA) consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS) and betaine-homocysteine S-methyltransferase (BHMT) diverged from the expected Tree of Life (ToL) relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.     

Reemergence and Autochthonous Transmission of Dengue Virus,Eastern China, 2014

In 2014, 20 dengue cases were reported in the cities of Wenzhou (5 cases) and Wuhan (15 cases), China, where dengue has rarely been reported. Dengue virus 1 was detected in 4 patients. Although most of these cases were likely imported, epidemiologic analysis provided evidence for autochthonous transmission.