Plant RNA virus evolution

RNA viruses are the most common viruses of plants, and the evolution of these viruses has been studied both experimentally and phylogenetically. The basic molecular mechanisms for plant virus evolution are similar to those of other viruses, with some notable exceptions. Recent advances include new insights into the origins of plant viruses, analyses of quasispecies and mutation frequencies, population studies on field isolates and practical studies on the importance of virus evolution to agriculture.     

Evidence of influenza a virus RNA in siberian lake ice

Influenza A virus infects a large proportion of the human population annually, sometimes leading to the deaths of millions. The biotic cycles of infection are well characterized in the literature, including in studies of populations of humans, poultry, swine, and migratory waterfowl. However, there are few studies of abiotic reservoirs for this virus. Here, we report the preservation of influenza A virus genes in ice and water from high-latitude lakes that are visited by large numbers of migratory birds. The lakes are along the migratory flight paths of birds flying into Asia, North America, Europe, and Africa. The data suggest that influenza A virus, deposited as the birds begin their autumn migration, can be preserved in lake ice. As birds return in the spring, the ice melts, releasing the viruses. Therefore, temporal gene flow is facilitated between the viruses shed during the previous year and the viruses newly acquired by birds during winter months spent in the south. Above the Arctic Circle, the cycles of entrapment in the ice and release by melting can be variable in length, because some ice persists for several years, decades, or longer. This type of temporal gene flow might be a feature common to viruses that can survive entrapment in environmental ice and snow.     

Bacterial recovery from ancient glacial ice

Ice that forms the bottom 18 m of a 308 m ice core drilled from the Guliya ice cap on the Qinghan-Tibetan plateau in Western China is over 750000 years old and is the oldest glacial ice known to date. Fourteen bacterial isolates have been recovered from samples of this ice from approximately 296 m below the surface (mbs). Based on 16S rDNA sequences, these are members of the alpha- and beta-proteobacterial, actinobacterial and low-G + C Gram-positive bacterial lineages. 16S rDNA molecules have also been amplified directly, cloned and sequenced from the ice-core melt water. These originated from Pseudomonas and Acinetobacter gamma-proteobacterial species. These results demonstrate that bacteria can be recovered from water ice that has frozen for time periods relevant to biological survival through terrestrial ice ages or during interplanetary transport.     

Molecular evidence for an active endogenous microbiome beneath glacial ice

Geologic, chemical and isotopic evidence indicate that Earth has experienced numerous intervals of widespread glaciation throughout its history, with roughly 11% of present day Earth''s land surface covered in ice. Despite the pervasive nature of glacial ice both today and in Earth''s past and the potential contribution of these systems to global biogeochemical cycles, the composition and phylogenetic structure of an active microbial community in subglacial systems has yet to be described. Here, using RNA-based approaches, we demonstrate the presence of active and endogenous archaeal, bacterial and eukaryal assemblages in cold (0–1 °C) subglacial sediments sampled from Robertson Glacier, Alberta, Canada. Patterns in the phylogenetic structure and composition of subglacial sediment small subunit (SSU) ribosomal RNA (rRNA) assemblages indicate greater diversity and evenness than in glacial surface environments, possibly due to facilitative or competitive interactions among populations in the subglacial environment. The combination of phylogenetically more even and more diverse assemblages in the subglacial environment suggests minimal niche overlap and optimization to capture a wider spectrum of the limited nutrients and chemical energy made available from weathering of bedrock minerals. The prevalence of SSU rRNA affiliated with lithoautotrophic bacteria, autotrophic methane producing archaea and heterotrophic eukarya in the subglacial environment is consistent with this hypothesis and suggests an active contribution to the global carbon cycle. Collectively, our findings demonstrate that subglacial environments harbor endogenous active ecosystems that have the potential to impact global biogeochemical cycles over extended periods of time.     

Rapid loss of glacial ice reveals stream community assembly processes

Glacial retreat creates new habitat which is colonized and developed by plants and animals during the process of primary succession. While there has been much debate about the relative role of deterministic and stochastic processes during terrestrial succession, evidence from freshwater ecosystems remains minimal and a general consensus is lacking. Using a unique 27 years record of community assembly following glacial recession in southeast Alaska, we demonstrate significant change in the trait composition of stream invertebrate communities as catchment glacial cover decreased from ～70% to zero. Functional diversity increased significantly as glacier cover decreased and taxonomic richness increased. Null modelling approaches led to a key finding that niche filtering processes were dominant when glacial cover was extensive, reflecting water temperature and dispersal constraints. Thereafter the community shifted towards co‐occurrence of stochastic and deterministic assembly processes. A further novel discovery was that intrinsic functional redundancy developed throughout the study, particularly because new colonizers possessed similar traits to taxa already present. Rapid glacial retreat is occurring in Arctic and alpine environments worldwide and the assembly processes observed in this study provide new fundamental insights into how glacially influenced stream ecosystems will respond. The findings support tolerance as a key primary successional mechanism in this system, and have broader value for developing our understanding of how biological communities in river ecosystems assemble or restructure in response to environmental change.     

Microbial life in glacial ice and implications for a cold origin of life

Application of physical and chemical concepts, complemented by studies of prokaryotes in ice cores and permafrost, has led to the present understanding of how microorganisms can metabolize at subfreezing temperatures on Earth and possibly on Mars and other cold planetary bodies. The habitats for life at subfreezing temperatures benefit from two unusual properties of ice. First, almost all ionic impurities are insoluble in the crystal structure of ice, which leads to a network of micron-diameter veins in which microorganisms may utilize ions for metabolism. Second, ice in contact with mineral surfaces develops a nanometre-thick film of unfrozen water that provides a second habitat that may allow microorganisms to extract energy from redox reactions with ions in the water film or ions in the mineral structure. On the early Earth and on icy planets, prebiotic molecules in veins in ice may have polymerized to RNA and polypeptides by virtue of the low water activity and high rate of encounter with each other in nearly one-dimensional trajectories in the veins. Prebiotic molecules may also have utilized grain surfaces to increase the rate of encounter and to exploit other physicochemical features of the surfaces.     

Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp

Background  

South America's western coastline, extending in a near-straight line across some 35 latitudinal degrees, presents an elegant setting for assessing both contemporary and historic influences on cladogenesis in the marine environment. Southern bull-kelp (Durvillaea antarctica) has a broad distribution along much of the Chilean coast. This species represents an ideal model taxon for studies of coastal marine connectivity and of palaeoclimatic effects, as it grows only on exposed rocky coasts and is absent from beaches and ice-affected shores. We expected that, along the central Chilean coast, D. antarctica would show considerable phylogeographic structure as a consequence of the isolating effects of distance and habitat discontinuities. In contrast, we hypothesised that further south - throughout the region affected by the Patagonian Ice Sheet at the Last Glacial Maximum (LGM) - D. antarctica would show relatively little genetic structure, reflecting postglacial recolonisation.     

Isolation and characterization of coliforms from glacial ice and water in Canada's High Arctic

Ellesmere Island is the northern most member of the Canadian Arctic Archipelago with over one-third of the land mass covered by ice. A joint services expedition to the island's Blue Mountains offered a unique opportunity for microbiological studies of resident bacteria in an environment uninhabited by man. Over 100 samples of water and ice were collected from stream, lake and glacier and the filtrate cultured under canvas. Bacterial growth was harvested onto swabs for transport back to the UK and 50 coliforms chosen at random for identification and antibiotic susceptibility testing. Most of the glacial strains were capsulated, pigmented and some over 2000 years old. Genera such as Serratia, Enterobacter, Klebsiella and Yersinia were found; speciation was inconclusive and some organisms remain unidentified. Ampicillin resistance was evident in 80% of water isolates as opposed to 30% of the glacial organisms, but the isolates were generally exquisitely susceptible to antibiotics. The facility for ampicillin resistance did not appear to be transferable. Plasmid DNA was found in 33% of the glacial organisms and over 50% of the water isolates. Similar profiles were identified within and apparently between species and required plasmid restriction analysis to help establish identity. Plasmid-free Serratia spp. were subjected to genomic fingerprinting. Indistinguishable patterns were found within sets of isolates both widely spaced by distance and collection date and it was postulated that coliforms able to survive an Arctic environment had spread extensively throughout the expedition area. In conclusion, this study contributes towards knowledge of naturally occurring antibiotic resistance, confirms the presence of plasmids and genotypic data provided evidence that potentially ancient organisms from glaciers can be cultured from water samples significantly distant.     

植物中的非编码RNA及其作用机制

非编码RNA(non-codingRNA,ncRNA)是近年来发现的一类能够转录但不能编码蛋白质、具有特定功能的RNA分子。ncRNA参与了生命过程中的许多重要环节。该文主要介绍植物中的非编码RNA的类型、研究方法以及功能。     

Plant Mitochondrial RNA Editing

RNA editing affects messenger RNAs and transfer RNAs in plant mitochondria by site-specific exchange of cytidine and uridine bases in both seed and nonseed plants. Distribution of the phenomenon among bryophytes has been unclear since RNA editing has been detected in some but not all liverworts and mosses. A more detailed understanding of RNA editing in plants required extended data sets for taxa and sequences investigated. Toward this aim an internal region of the mitochondrial nad5 gene (1104 nt) was analyzed in a large collection of bryophytes and green algae (Charales). The genomic nad5 sequences predict editing in 30 mosses, 2 hornworts, and 7 simple thalloid and leafy liverworts (Jungermanniidae). No editing is, however, required in seven species of the complex thalloid liverworts (Marchantiidae) and the algae. RNA editing among the Jungermanniidae, on the other hand, reaches frequencies of up to 6% of codons being modified. Predictability of RNA editing from the genomic sequences was confirmed by cDNA analysis in the mosses Schistostega pennata and Rhodobryum roseum, the hornworts Anthoceros husnotii and A. punctatus, and the liverworts Metzgeria conjugata and Moerckia flotoviana. All C-to-U nucleotide exchanges predicted to reestablish conserved codons were confirmed. Editing in the hornworts includes the removal of genomic stop codons by frequent reverse U-to-C edits. Expectedly, no RNA editing events were identified by cDNA analysis in the marchantiid liverworts Ricciocarpos natans, Corsinia coriandra, and Lunularia cruciata. The findings are discussed in relation to models on the phylogeny of land plants. Received: 2 April 1998 / Accepted: 4 August 1998     

RNA Interference in Plant Defense Systems

Russian Journal of Plant Physiology - Plant pests and pathogens, including viruses, reduce the biological potential of crops and undermine food safety. The methods of crop protection based on...     

RNA recombination in brome mosaic virus, a model plus strand RNA virus.

Studies on the molecular mechanism of genetic recombination in RNA viruses have progressed at the time when experimental systems of efficient recombination crossovers were established. The system of brome mosaic virus (BMV) represents one of the most useful and most advanced tools for investigation of the molecular aspects of the mechanism of RNA-RNA recombination events. By using engineered BMV RNA components, the occurrence of both homologous and nonhomologous crosses were demonstrated among the segments of the BMV RNA genome. Studies show that the two types of crossovers require different RNA signal sequences and that both types depend upon the participation of BMV replicase proteins. Mutations in the two BMV-encoded replicase polypeptides (proteins 1a and 2a) reveal that their different regions participate in homologous and in nonhomologous crossovers. Based on all these data, it is most likely that homologous and nonhomologous recombinant crosses do occur via two different types of template switching events (copy-choice mechanism) where viral replicase complex changes RNA templates during viral RNA replication at distinct signal sequences. In this review we discuss various aspects of the mechanism of RNA recombination in BMV and we emphasize future projections of this research.     

RNA干扰与植物抗病毒

RNA干扰是多种生物体内由双链RNA介导的同源mRNA降解现象,是植物体内天然的抗病毒机制。然而病毒在长期进化过程中也获得了通过编码沉默抑制蛋白来对抗植物体RNAi系统的能力。本文对RNA干扰过程、病毒编码的沉默抑制蛋白及利用干扰技术进行抗病毒基因工程研究进行简要综述。     

Diversity of bacterial forms in ice wedge of the Mamontova Gora glacial complex (Central Yakutiya)

Electron microscopic investigation of four samples of ancient ice wedge from the Pleistocene glacial complex of Mamontova Gora (Yakutiya, Russia) revealed high diversity of bacteriomorphic particles. Their structural features included the presence of electron-transparent zones, presumably inclusions containing storage compounds, and microenvironments (capsules or external sheaths). These features may be a result of adaptive strategies providing for microbial survival under permafrost conditions. Predominance of rod-shaped forms morphologically resembling coryneform actinobacteria was found. X-ray microanalysis revealed organic origin of bacteriomorphic particles. Some particles were characterized by incomplete spectra of the major biogenic elements, resulting probably from low-temperature damage to the cellular structures. Total numbers of aerobic heterotrophic bacteria determined by plating on nutrient media were comparable to the values obtained for permafrost soils and Arctic ice. Predominance of coryneform actinobacteria was observed. Abundance of these evolutionarily early groups of actinobacteria may indicate the ancient origin of the microflora of the relic frozen rocks.