Comparative Quantitative Proteomics Reveals the Desiccation Stress Responses of the Intertidal Seaweed NEOPORPHYRA haitanensis

Neoporphyra haitanensis is an economically important red seaweed that inhabits upper intertidal zones. The thallus tolerates extreme fluctuating environmental stresses (e.g., surviving more than 80% water loss during low tides). To elucidate the global molecular responses relevant to this outstanding desiccation tolerance, a quantitative proteomics analysis of N. haitanensis under different desiccation treatments as well as rehydration was performed. According to the clustering of expression patterns and the functional interpretation of the 483 significantly differentially expressed proteins, a three-stage cellular response to desiccation stress and subsequent rehydration was proposed. Stage I: at the beginning of water loss, multiple signal transduction pathways were triggered including lipid signaling, protein phosphorylation cascades, and histone acetylation controlling acetate biosynthesis to further modulate downstream hormone signaling. Protein protection by peptidyl-prolyl isomerase and ROS scavenging systems were also immediately switched on. Stage II: with the aggravation of stress, increases in antioxidant systems, the accumulation of LEA proteins, and the temporary biosynthesis of branched starch were observed. Multiple enzymes involved in redox homeostasis, including peroxiredoxin, thioredoxin, ascorbate peroxidase, superoxide dismutase, glutathione peroxidase, and glutathione reductase, were hypothesized to function in specific cellular compartments. Stage III: when the desiccated thalli had rehydrated for 30 mins, photosynthesis and carbon fixation were recovered, and antioxidant activities and protein structure protection were maintained at a high level. This work increases the understanding of the molecular responses to environmental stresses via a proteomic approach in red seaweeds and paves the way for further functional studies and genetic engineering.     

Effects of desiccation and CO2 concentrations on emersed photosynthesis in Porphyra haitanensis (Bangiales,Rhodophyta), a species farmed in China

The effects on photosynthesis of CO₂ and desiccation in Porphyra haitanensis were investigated to establish the effects of increased atmospheric CO₂ on this alga during emersion at low tides. With enhanced desiccation, net photosynthesis, dark respiration, photosynthetic efficiency, apparent carboxylating efficiency and light saturation point decreased, while the light compensation point and CO₂ compensation point increased. Emersed net photosynthesis was not saturated by the present atmospheric CO₂ level (about 350?ml?m^?3), and doubling the CO₂ concentration (700?ml?m^?3) increased photosynthesis by between 31% and 89% at moderate levels of desiccation. The relative enhancement of emersed net photosynthesis at 700?ml?m^?3 CO₂ was greater at higher temperatures and higher levels of desiccation. The photosynthetic production of Porphyra haitanensis may benefit from increasing atmospheric CO₂ concentration during emersion.     

Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a

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Comparative Analysis of the Complete Plastid Genome Sequence of the Red Alga Gracilaria tenuistipitata var. liui Provides Insights into the Evolution of Rhodoplasts and Their Relationship to Other Plastids

We sequenced to completion the circular plastid genome of the red alga Gracilaria tenuistipitata var. liui. This is the first plastid genome sequence from the subclass Florideophycidae (Rhodophyta). The genome is composed of 183,883 bp and contains 238 predicted genes, including a single copy of the ribosomal RNA operon. Comparisons with the plastid genome of Porphyra pupurea reveal strong conservation of gene content and order, but we found major genomic rearrangements and the presence of coding regions that are specific to Gracilaria. Phylogenetic analysis of a data set of 41 concatenated proteins from 23 plastid and two cyanobacterial genomes support red algal plastid monophyly and a specific evolutionary relationship between the Florideophycidae and the Bangiales. Gracilaria maintains a surprisingly ancient gene content in its plastid genome and, together with other Rhodophyta, contains the most complete repertoire of plastid genes known in photosynthetic eukaryotes.Supplementary material () is available for this article.[Reviewing Editor: Dr. W. Ford Doolittle]     

基于线粒体基因组的藏马高原适应及系统发育分析

研究测定了西藏那曲（4,500m）、云南中甸（3,300m）、云南德钦（3,300m）地区3匹藏马线粒体全基因组序列。3个地区的藏马线粒体基因组全长以及结构均与韩国济州岛的马类似,但比瑞典马线粒体基因组短。藏马基因组在DNA序列上的两两相似性达993％。通过对线粒体蛋白编码区的分析发现,NADH6基因的蛋白序列在三匹藏马中均表现快速进化的现象。这表明NADH6基因在藏马高原适应进化过程中扮演着重要角色。此外,利用7匹藏马的D—loop区域序列以及与其亲缘关系较近的马的序列首次构建的藏马的系统发育树显示,那曲藏马与中甸、德钦藏马属于不同的分支,且存在较大的遗传多样性,表明藏马可能为多地区起源。     

Insights into the binding of agonist and antagonist to TAS2R16 receptor: a molecular simulation study

The human bitter taste receptors (TAS2Rs) belong to the GPCR family, while the activation mechanism and how TAS2Rs recognise bitter ligands are poorly understood. In this study, 3D structure of TAS2R16 was constructed using homology modelling complemented with molecular dynamics method. Salicin and probenecid were docked to TAS2R16 receptor to investigate the possible activation mechanism of TAS2R16. The results show that salicin and probenecid locate at the binding pocket made up of transmembrane helices TM3, TM5 and TM7, and the second and third extracellular loops ECL2 and ECL3. Structural analysis reveals that the network interactions at the third intracellular loop ICL3 may play a crucial role in stabilising the inactive state of TAS2R16, and structural change in the intracellular region is correlated with the activation of TAS2R16. The binding energies of salicin and probenecid to TAS2R16 are ?152.81 ± 15.09 and ?271.90 ± 26.97 kJ/mol, respectively, indicating that a potential antagonist should have obviously stronger binding affinity.     

New Insights into Plagiogrammaceae (Bacillariophyta) Based on Multigene Phylogenies and Morphological Characteristics with the Description of a New Genus and Three New Species

Plagiogrammaceae, a poorly described family of diatoms, are common inhabitants of the shallow marine littoral zone, occurring either in the sediments or as epiphytes. Previous molecular phylogenies of the Plagiogrammaceae were inferred but included only up to six genera: Plagiogramma, Dimeregramma, Neofragilaria, Talaroneis, Psammogramma and Psammoneis. In this paper, we describe a new plagiogrammoid genus, Orizaformis, obtained from Bohai Sea (China) and present molecular phylogenies of the family based on three and four genes (nuclear-encoded large and small subunit ribosomal RNAs and chloroplast-encoded rbcL and psbC). Also included in the new phylogenies is Glyphodesmis. The phylogenies suggest that the Plagiogrammaceae is composed of two major clades: one consisting of Talaroneis, Orizaformis and Psammoneis, and the second of Glyphodesmis, Psammogramma, Neofragilaria, Dimeregramma and Plagiogramma. In addition, we describe three new species within established genera: Psammoneis obaidii, which was collected from the Red Sea, Saudi Arabia; and Neofragilaria stilus and Talaroneis biacutifrons from the Mozambique Channel, Indian Ocean, and illustrate two new combination taxa: Neofragilaria anomala and Neofragilaria lineata. Our observations suggest that the biodiversity of the family is strongly needed to be researched, and the phylogenetic analyses provide a useful framework for future studies of Plagiogrammaceae.     

Insights into the regenerative property of plant cells and their receptivity to transgenesis: Wheat as a research case study

From a holistic perspective, the discovery of cellular plasticity, a very interesting property of totipotency, underlies many topical issues in biology with important medical applications, while transgenesis is a core research tool in biology. Partially known, some basic mechanisms involved in the regenerative property of cells and in their receptivity to transgenesis are common to plant and animal cells and highlight the principle of the unity of life. Transgenesis provides an important investigative instrument in plant physiology and is regarded as a valuable tool for crop improvement. The economic, social, cultural and scientific importance of cereals has led to a rich stream of research into their genetics, biology and evolution. Sustained efforts to achieve the results obtained in the fields of genetic engineering and applied biotechnology reflect this deep interest. Difficulties encountered in creating genetically modified cereals, especially wheat, highlighted the central notions of tissue culture regeneration and transformation competencies. From the perspective of combining or encountering these competencies in the same cell lineage, this reputedly recalcitrant species provides a stimulating biological system in which to explore the physiological and genetic complexity of both competencies. The former involves two phases, dedifferentiation and redifferentiation. Cells undergo development switches regulated by extrinsic and intrinsic factors. The re-entry into the cell division cycle progressively culminates in the development of organized structures. This is achieved by global chromatin reorganization associated with the reprogramming of the gene expression pattern. The latter is linked with surveillance mechanisms and DNA repair, aimed at maintaining genome integrity before cells move into mitosis, and with those mechanisms aimed at genome expression control and regulation. In order to clarify the biological basis of these two physiological properties and their interconnectedness, we look at both competencies at the core of defense/adaptive mechanisms and survival, between undifferentiated cell proliferation and organization, constituting a transition phase between two different dynamic regimes, a typical feature of critical dynamic systems. Opting for a candidate-gene strategy, several gene families could be proposed as relevant targets for investigating this hypothesis at the molecular level.     

Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

Non-coding RNAs (crRNAs) produced from clustered regularly interspaced short palindromic repeats (CRISPR) loci and CRISPR-associated (Cas) proteins of the prokaryotic CRISPR-Cas systems form complexes that interfere with the spread of transmissible genetic elements through Cas-catalysed cleavage of foreign genetic material matching the guide crRNA sequences. The easily programmable targeting of nucleic acids enabled by these ribonucleoproteins has facilitated the implementation of CRISPR-based molecular biology tools for in vivo and in vitro modification of DNA and RNA targets. Despite the diversity of DNA-targeting Cas nucleases so far identified, native and engineered derivatives of the Streptococcus pyogenes SpCas9 are the most widely used for genome engineering, at least in part due to their catalytic robustness and the requirement of an exceptionally short motif (5′-NGG-3′ PAM) flanking the target sequence. However, the large size of the SpCas9 variants impairs the delivery of the tool to eukaryotic cells and smaller alternatives are desirable. Here, we identify in a metagenome a new CRISPR-Cas9 system associated with a smaller Cas9 protein (EHCas9) that targets DNA sequences flanked by 5′-NGG-3′ PAMs. We develop a simplified EHCas9 tool that specifically cleaves DNA targets and is functional for genome editing applications in prokaryotes and eukaryotic cells.     

Insights into the evolution of heliozoa (Protozoa, Sarcodina) as provided by ultrastructural studies on a new species of flagellate from the genus Pteridomonas

The fine structure of Pteridomonas danica , a new species of helioflagellate (protozoa), is described. The organism has a single apical flagellum which bears two rows of tripartite tubular hairs. There are two kinetosomes which are bound to each other and to the surface of the single nucleus by amorphous electron-dense material. The flagellum is surrounded by a wreath of fine arms, which are supported internally by triads of microtubules. The triads terminate on the nucleus. The mitochondria have tubular cristae which contain wisps of intracristal material. The dictyosomes are located in the posterior part of the cell, being clustered around the internal element of the contractile stalk. Extrusomes are present. Pteridomonas has substantial similarities with the colourless flagellate Ciliophrys and with the pedinellid algal flagellates. As Ciliophrys resembles the actinophryid heliozoa in several important respects, the evidence supports the contention that these heliozoa have a common ancestry with the heterokont algae and have evolved along a line involving the pedinellids and some colourless helioflagellates. If the perceived relationships are to be reflected in their taxonomy, then a substantial reclassification of these organisms is required.     

Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia,a persistent threat to global agriculture

The fungal genus Puccinia, comprising of several menacing pathogens, has been a persistent peril to global agriculture. Genome sequencing of various members of Puccinia offers a scope to excavate their genomic riddles. The present study has been addressed at exploring the complex niceties of codon and amino acid usage patterns and subsequent elucidation of the determinants that drive such behavior. Multivariate statistical analysis revealed a complex interplay of natural selection for translation and compositional bias to be operational on the codon usage patterns. Gene expression level was observed to be the most competent factor governing codon usage behavior of the genus. In spite of subtle AT richness of the genus, potential highly expressed gene sets were found to preferentially employ GC rich optimal codons. Estimation of relative dinucleotide abundance revealed preference toward the employment of GpA, CpA, TpC, and TpG dinucleotides and restraint from using TpA dinucleotide among the members of the genus. Extensive codon context analysis revealed that codon pairs with GpA, CpA, TpC, and TpG dinucleotides were over-represented and codon pairs with TpA dinucleotide were extensively avoided at the codon–codon (cP3–cA1) junctions. Amino acid usage signatures of the genus were found to be influenced considerably by several imperative factors like aromatic and hydrophobic character of the encoded gene products, genomic compositional constraint, and gene expressivity. Detailed know-how of the potential highly expressed gene sets and associated optimal codons in the genus promise to be informative for the scientific community engaged in combating Puccinia pathogenesis.     

Predominant east to west colonizations across major oceanic barriers: Insights into the phylogeographic history of the hydroid superfamily Plumularioidea,suggested by a mitochondrial DNA barcoding marker

We provide preliminary insights into the global phylogeographic and evolutionary patterns across species of the hydrozoan superfamily Plumularioidea (Cnidaria: Hydrozoa). We analyzed 1,114 16S sequences of 198 putative species of Plumularioidea collected worldwide. We investigated genetic connections and divergence in relation to present‐day and ancient biogeographic barriers, climate changes and oceanic circulation. Geographical distributions of most species are generally more constrained than previously assumed. Some species able to raft are dispersed widely. Human‐mediated dispersal explains some wide geographical ranges. Trans‐Atlantic genetic connections are presently unlikely for most of the tropical‐temperate species, but were probably more frequent until the Miocene–Pliocene transition, before restriction of the Tethys Sea and the Central American Seaway. Trans‐Atlantic colonizations were predominantly directed westwards through (sub)tropical waters. The Azores were colonized multiple times and through different routes, mainly from the east Atlantic, at least since the Pliocene. Extant geminate clades separated by the Isthmus of Panama have predominantly Atlantic origin. Various ancient colonizations mainly directed from the Indian Ocean to the Atlantic occurred through the Tethys Sea and around South Africa in periods of lower intensity of the Benguela upwelling. Thermal tolerance, population sizes, dispersal strategies, oceanic currents, substrate preference, and land barriers are important factors for dispersal and speciation of marine hydroids.     

Climatic Factors Drive Population Divergence and Demography: Insights Based on the Phylogeography of a Riparian Plant Species Endemic to the Hengduan Mountains and Adjacent Regions

Quaternary climatic factors have played a significant role in population divergence and demography. Here we investigated the phylogeography of Osteomeles schwerinae, a dominant riparian plant species of the hot/warm-dry river valleys of the Hengduan Mountains (HDM), Qinling Mountains (QLM) and Yunnan-Guizhou Plateau (YGP). Three chloroplast DNA (cpDNA) regions (trnD-trnT, psbD-trnT, petL-psbE), one single copy nuclear gene (glyceraldehyde 3-phosphate dehydrogenase; G3pdh), and climatic data during the Last Interglacial (LIG; c. 120–140 ka), Last Glacial Maximum (LGM; c. 21 ka), and Current (c. 1950–2000) periods were used in this study. Six cpDNA haplotypes and 15 nuclear DNA (nDNA) haplotypes were identified in the 40 populations of O. schwerinae. Spatial Analysis of Molecular Variance, median-joining networks, and Bayesian phylogenetic trees based on the cpDNA and nDNA datasets, all suggested population divergence between the QLM and HDM-YGP regions. Our climatic analysis identified significant heterogeneity of the climatic factors in the QLM and HDM-YGP regions during the aforementioned three periods. The divergence times based on cpDNA and nDNA haplotypes were estimated to be 466.4–159.4 ka and 315.8–160.3 ka, respectively, which coincide with the time of the weakening of the Asian monsoons in these regions. In addition, unimodal pairwise mismatch distribution curves, expansion times, and Ecological Niche Modeling suggested a history of population expansion (rather than contraction) during the last glaciation. Interestingly, the expansion times were found being well consistent with the intensification of the Asian monsoons during this period. We inferred that the divergence between the two main lineages is probably caused by disruption of more continuous distribution because of weakening of monsoons/less precipitation, whilst subsequent intensification of the Asian monsoons during the last glaciation facilitated the expansion of O. schwerinae populations.     

Insights into the effects of alpha-synuclein expression and proteasome inhibition on glutathione metabolism through a dynamic in silico model of Parkinson's disease: validation by cell culture data

Dopaminergic neurodegeneration during Parkinson disease (PD) involves several pathways including proteasome inhibition, alpha-synuclein (alpha-syn) aggregation, mitochondrial dysfunction, and glutathione (GSH) depletion. We have utilized a systems biology approach and built a dynamic model to understand and link the various events related to PD pathophysiology. We have corroborated the modeling data by examining the effects of alpha-syn expression in the absence and presence of proteasome inhibition on GSH metabolism in dopaminergic neuronal cultures. We report here that the expression of the mutant A53T form of alpha-syn is neurotoxic and causes GSH depletion in cells after proteasome inhibition, compared to wild-type alpha-syn-expressing cells and vector control. Modeling data predicted that GSH depletion in these cells was due to ATP loss associated with mitochondrial dysfunction. ATP depletion elicited by combined A53T expression and proteasome inhibition results in decreased de novo synthesis of GSH via the rate-limiting enzyme gamma-glutamyl cysteine ligase. Based on these data and other recent reports, we propose a novel dynamic model to explain how the presence of mutated alpha-syn protein or proteasome inhibition may individually impact on mitochondrial function and in combination result in alterations in GSH metabolism via enhanced mitochondrial dysfunction.     

Biochemical and Structural Insights into RNA Binding by Ssh10b,a Member of the Highly Conserved Sac10b Protein Family in Archaea

Proteins of the Sac10b family are highly conserved in Archaea. Ssh10b, a member of the Sac10b family from the hyperthermophilic crenarchaeon Sulfolobus shibatae, binds to RNA in vivo. Here we show that binding by Ssh10b destabilizes RNA secondary structure. Structural analysis of Ssh10b in complex with a 25-bp RNA duplex containing local distortions reveals that Ssh10b binds the two RNA strands symmetrically as a tetramer with each dimer bound asymmetrically to a single RNA strand. Amino acid residues involved in double-stranded RNA binding are similar, but non-identical, to those in dsDNA binding. The dimer-dimer interaction mediated by the intermolecular β-sheet appears to facilitate the destabilization of base pairing in the secondary structure of RNA. Our results suggest that proteins of the Sac10b family may play important roles in RNA transactions requiring destabilization of RNA secondary structure in Sulfolobus.     

An Investigation into the Effect of Soil and Vegetation on the Successful Creation of a Hay Meadow on a Clay‐Capped Landfill

This paper investigates the effect that manipulation of soil and vegetation conditions has on plant community development during attempts to create neutral hay meadow communities on a clay‐capped landfill in Somerset, United Kingdom. The objectives are (1) to determine the effect of manipulation of soil and vegetation on the development of the target plant community, (2) to identify whether these treatments had an effect on edaphic factors (physical and chemical properties, earthworm populations), and (3) to establish which, if any, of these edaphic parameters are underlying factors in determining the vascular plant community composition. In 2001 a commercial hay meadow seed mix was sown on three substrate treatments: (i) bare clay, (ii) a mixture of topsoil and compost ameliorant in equal proportions, and (iii) over naturally colonized vegetation. Plant community development and edaphic factors were monitored between 2001 and 2007. Although initially the presence of ameliorant promoted germination and growth of seeded species, after 2004 nonseeded competitive grasses dominated the sward. Where ameliorant was removed the target community continued to develop proving this to be the most successful treatment. This was found to be a due to suppression of competition from Elytrigia repens (Common couch), which grew most abundantly on soils with high organic matter and high soil water levels within the soil. Contrary to previous research, Trifolium repens (white clover) was not found to reduce forb diversity in this study. No evidence was found of earthworm abundance affecting plant community development.