Der p 5 Crystal Structure Provides Insight into the Group 5 Dust Mite Allergens

Group 5 allergens from house dust mites elicit strong IgE antibody binding in mite-allergic patients. The structure of Der p 5 was determined by x-ray crystallography to better understand the IgE epitopes, to investigate the biologic function in mites, and to compare with the conflicting published Blo t 5 structures, designated 2JMH and 2JRK in the Protein Data Bank. Der p 5 is a three-helical bundle similar to Blo t 5, but the interactions of the helices are more similar to 2JMH than 2JRK. The crystallographic asymmetric unit contains three dimers of Der p 5 that are not exactly alike. Solution scattering techniques were used to assess the multimeric state of Der p 5 in vitro and showed that the predominant state was monomeric, similar to Blo t 5, but larger multimeric species are also present. In the crystal, the formation of the Der p 5 dimer creates a large hydrophobic cavity of ∼3000 ų that could be a ligand-binding site. Many allergens are known to bind hydrophobic ligands, which are thought to stimulate the innate immune system and have adjuvant-like effects on IgE-mediated inflammatory responses.     

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.     

[FeFe] Hydrogenase Genetic Diversity Provides Insight into Molecular Adaptation in a Saline Microbial Mat Community

Degenerate primers for the [FeFe] hydrogenase (hydA) were developed and used in PCRs to examine hydA in microbial mats that inhabit saltern evaporative ponds in Guerrero Negro (GN), Mexico. A diversity of deduced HydA was discovered that revealed unique variants, which may reflect adaptation to the environmental conditions present in GN.Hydrogen (H₂) is an important intermediate in the decomposition of organic matter in anaerobic environments and is the basis for many syntrophic interactions that occur in the food chain such as those between acetogens and methanogens and/or sulfate reducers. Little is known concerning the potential role of fermentative bacteria and/or H₂ cycling in phototrophic microbial mat systems, such as the 6-cm-thick and extremely diverse microbial mats inhabiting the saline ponds at the Exportadora de Sal SA saltern in Guerrero Negro (GN), Baja California Sur, Mexico. Recent 16S rRNA gene surveys in GN revealed an abundance of bacteria in the upper 2 mm of the mat that, based on their phylogenetic affiliation, are thought to harbor fermentative metabolisms (6, 8, 13, 16, 20, 28). Similarly, previous studies have shown that the flux of H₂ from the surface of the phototrophic mats present in GN is ∼150-fold higher during the night than during the day (9). Together, these results suggest the potential for fermentative metabolisms in H₂ and carbon cycling in the GN saline mat environment.The [FeFe] hydrogenase has a central role in primary and secondary substrate fermentations, catalyzing the oxidation of excess reducing equivalents coupled to the reduction of protons, yielding H₂ (2, 17, 29, 30). The [FeFe] hydrogenase is only known to occur in anaerobic bacteria and a small number of green algae (23, 29, 30), making this a useful biomarker for examining the diversity and distribution of this functional class of organism. Eighty-two putative [FeFe] hydrogenase large-subunit protein sequences (HydA) present in the GenBank database that represent the known diversity of putative HydA were screened for the L1 ([FLI]TSC[C/S]P[GAS]W[VIQH]) and L2 ([IVLF]MPCx[ASRD]K[KQ]xE) (conserved residues are in bold and underlined, and bracketed positions indicate “semiconserved” residues at that position) signature sequence motifs (17, 30). Degenerate PCR primers, corresponding to positions 272 to 279 (AD[M/L]TIMEE) and positions 420 to 427 (TGGVMEAA) in the Clostridium pasteurianum protein sequence, were designed for use in specific gene amplifications.Mat core samples (1 by 6 cm) were collected at 2:00 pm from pond 4 (35°C, pH 8.0, and 80 ppt salt) near pond 5 at the Exportadora de Sal saltworks, GN, on 13 February 2005. Mat cores were sectioned in 1-mm increments on site and immediately flash frozen in liquid nitrogen as previously described (16). Genomic DNA was extracted by bead beating in the presence of phenol-chloroform-isoamyl alcohol and sodium dodecyl sulfate as previously described (7) and was quantified by using the High DNA Mass Ladder (Invitrogen, Carlsbad, CA). Approximately 500-bp fragments of hydA were amplified in triplicate using primers FeFe-272F (5′-GCHGAYMTBACHATWATGGARGA-3′, where H = A, C, T; Y = C, T; M = A, C; B = C, G, T; W = A, T; R = A, G; 432-fold degeneracy) and FeFe-427R (5′-GCNGCYTCCATDACDCCDCCNGT-3′, where N = A, C, T, G; Y = C, T; D = A, G, T; 864-fold degeneracy) and 35 cycles of PCR as previously described (4). An empirically determined annealing temperature of 56.5°C, a MgCl₂ concentration of 1.5 mM, and a primer concentration of 1 μM for each forward and reverse primer were utilized in 50-μl PCR mixtures containing 10 ng of genomic DNA as the template. Equal 40-μl volumes of three replicate PCR products were pooled, purified using the Promega Wizard purification kit (Madison, WI), quantified using the Low Mass DNA Ladder (Invitrogen), cloned using the pGEM Easy Vector System (Promega), and sequenced by using the M13F-M13R primer pair as previously described (5).Deduced amino acid sequences were screened for the presence of the L1 and L2 HydA sequence motifs as described above. ClustalX (version 2.0.8) (15) was employed to align inferred amino acid sequences and to create distance matrices for use in identifying and clustering operational taxonomic units (OTUs) with DOTUR (26). Calculations of Shannon diversity and Chao1 and Ace1 deduced amino acid sequence richness were completed with DOTUR by using the furthest-neighbor algorithm and a precision of 0.01. The phylogenetic position of putative HydA was assessed with MRBAYES (10, 25). Tree topologies were sampled every 500 generations for 2,000,000 generations (burnin = 1,000,000) by using the WAG evolutionary model with fixed amino acid frequencies and gamma-shaped rate variation with a proportion of invariable sites as recommended by ProtTest (1). The Saccharomyces cerevisiae Narf protein, a homolog of HydA, was used as the outgroup. The phylogenetic tree was projected using TreeView (version 1.6.6) (21).An unexpectedly diverse assemblage of putative HydA variants was present in the top 1 mm of the GN microbial mat, corresponding to the photic zone. At a sequence identity threshold (SIT) of 100%, the predicted Shannon diversity index was 3.84 and the mean Chao1 HydA richness was 187 unique OTUs (see Fig. S1a in the supplemental material). When a 99% SIT was applied, the predicted Chao1 richness estimate decreased 56% to 82 unique OTUs and the Shannon diversity index decreased slightly to 3.55 (data not shown). A further decrease in the SIT from 99 to 85% resulted in a slight decrease (23%) in the Chao1 predicted richness and a modest decrease in the Shannon diversity index from 3.55 to 3.28, suggesting that the majority of the putative HydA OTUs present in the top 1 mm of the mat is a result of recent evolution or speciation.The putative HydA variants from GN resolved into 42 OTUs which clustered into one of seven distinct phylogenetic clusters (Fig. ​(Fig.1A),1A), although clusters 5 and 7 could not be adequately resolved. Intriguingly, the mean identity scores determined from sequence alignment matrices for members of each of the seven sequence clusters recovered from GN, when compared to sequences in the GenBank database, were very low (47.5 to 73.2%) (Table ​(Table1),1), suggesting that the putative HydA sequences recovered from GN represent novel sequence space.Open in a separate windowFIG. 1.(A) Phylogenetic tree based on deduced putative HydA amino acid sequences from GN and reference HydA sequences. Nodes with posterior probabilities of <50% were collapsed in this analysis (posterior probabilities of 100 are denoted by asterisks). Bar, one substitution per 10 sites. (B) Partial-length deduced amino acid sequences of environmental and reference deduced HydA sequences illustrating the phylogenetic coherence of novel substitutions and insertions in and upstream of L1 sequence motif. Cluster designations (C1 to C7) correspond to those presented in Table ​Table11.

TABLE 1.

Phylogeny of partial-length putative HydA sequence clusters

Surface Location of Individual Residues of SlpA Provides Insight into the Lactobacillus brevis S-Layer

Bacterial surface layer (S-layer) proteins are excellent candidates for in vivo and in vitro nanobiotechnological applications because of their ability to self-assemble into two-dimensional lattices that form the outermost layer of many Eubacteria and most Archaea species. Despite this potential, knowledge about their molecular architecture is limited. In this study, we investigated SlpA, the S-layer protein of the potentially probiotic bacterium Lactobacillus brevis ATCC 8287 by cysteine-scanning mutagenesis and chemical modification. We generated a series of 46 mutant proteins by replacing single amino acids with cysteine, which is not present in the wild-type protein. Most of the replaced amino acids were located in the self-assembly domain (residues 179 to 435) that likely faces the outer surface of the lattice. As revealed by electron microscopy, all the mutant proteins were able to form self-assembly products identical to that of the wild type, proving that this replacement does not dramatically alter the protein conformation. The surface accessibility of the sulfhydryl groups introduced was studied with two maleimide-containing marker molecules, TMM(PEG)₁₂ (molecular weight [MW], 2,360) and AlexaFluor488-maleimide (MW = 720), using both monomeric proteins in solution and proteins allowed to self-assemble on cell wall fragments. Using the acquired data and available domain information, we assigned the mutated residues into four groups according to their location in the protein monomer and lattice structure: outer surface of the lattice (9 residues), inner surface of the lattice (9), protein interior (12), and protein-protein interface/pore regions (16). This information is essential, e.g., in the development of therapeutic and other health-related applications of Lactobacillus S-layers.Bacterial surface layers (S-layers) are cell envelope structures ubiquitously found in gram-positive and gram-negative bacteria as well as in Archaea. S-layers are composed of identical (glyco)protein subunits with a molecular mass in the range of 40 to 200 kDa. The proteins self-assemble into two-dimensional crystalline structures with oblique (p1, p2), square (p4), or hexagonal (p3, p6) symmetry, covering the entire cell surface. The subunits are held together and attached to the underlying cell wall by noncovalent interactions and they have an intrinsic ability to spontaneously form regular layers in solution and on solid supports (24). S-layers have been shown to have roles in the determination and maintenance of cell shape as virulence factors, as mediators of cell adhesion, and as regulators of immature dendritic and T cells. Moreover, they can also function as a protective coat, molecular sieve, murein hydrolase, and ion trap (4, 8, 13, 17, 19, 25, 29).S-layer proteins have several properties that make them an attractive target for the development of nanobiotechnological applications both in vivo and in vitro. In particular, a high number of protein subunits are displayed at the bacterial cell surface. Moreover, the protein subunits are able to spontaneously self-assemble into a regularly arranged lattice structure both in solution and on solid supports (1, 27, 30, 31). However, despite the high prevalence of S-layers in nature, their molecular structure remains poorly elucidated. In particular, knowledge about the spatial organization of amino acid residues in S-layer proteins or the interactions between these residues and other subunits is limited. The poor solubility of protein assemblies and the absence of stoichiometrically defined oligomers have hindered attempts to apply nuclear magnetic resonance or hydrogen/deuterium exchange mass spectroscopy. In addition, the intrinsic property of S-layer proteins to form two-dimensional lattices has hampered efforts to obtain three-dimensional crystals required for X-ray crystallography (12, 31). To our knowledge, only part of the structure of one S-layer protein, SbsC of Geobacillus stearothermophilus, has been determined by X-ray crystallography (18). Since high-resolution, three-dimensional structural data are mostly lacking, traditional mutation-based techniques are presently the methods of choice. In cysteine-scanning mutagenesis (CSM), a series of mutant proteins is generated by replacing single residues with cysteine, which contains a sulfhydryl group amenable to further chemical modification. The spatial locations of amino acid residues within the S-layer protein SbsB of gram-positive thermophile G. stearothermophilus PV72/p2 have been analyzed by CSM. A total of 75 residues out of 920 were studied, identifying 23 residues located at the surface of protein monomers, five of those located on the outer surface of the protein lattice (10). These mutant proteins were subsequently analyzed by a cross-linking screen to assess residues accessible in monomeric form to the protein/protein interface and the inner surface of the lattice (12).In the genus Lactobacillus, S-layers have been found in several species. S-layer protein genes have been sequenced from L. brevis, L. helveticus, and L. acidophilus group organisms. Sequence similarity between Lactobacillus S-layer protein genes can be found only between closely related Lactobacillus species. Therefore, the primary sequences of Lactobacillus S-layer proteins show extensive variability, with the number of identical amino acids varying from 7 to 100% between different proteins. As a group, Lactobacillus S-layer proteins differ from those of most other bacteria in their smaller sizes (25 to 71 kDa) and higher calculated isoelectric point (pI) values (9.4 to 10.4) (1). The presence of two or more S-layer protein genes in the same strain is common in lactobacilli (5, 6, 11, 28, 35); however, only one S-layer protein gene, slpA, has so far been described to be present in the genome of L. brevis ATCC 8287. SlpA is a 435-amino-acid, 46-kDa S-layer protein that assembles into a lattice of oblique symmetry on the bacterial surface (2, 36). L. brevis ATCC 8287 has GRAS (generally recognized as safe) status and has been shown to possess probiotic properties (21), which make SlpA a very attractive subject, e.g., in the development of live oral vaccines. Moreover, a recent report using differential scanning calorimetry suggests that in comparison with other S-layer proteins, SlpA is resistant to high temperatures (21). This thermal stability could prove potentially useful in a variety of in vitro S-layer applications currently being planned or under development (27, 30, 31). Recently, SlpA was characterized to consist of an N-terminal cell wall binding domain (residues 1 to 178) and a C-terminal self-assembly domain (179 to 435) (3). For the development of applications that take advantage of these characteristics, further investigation of SlpA at the molecular level is essential.Herein, we use CSM and targeted chemical modification to assign 46 amino acid residues of SlpA to spatial locations in the protein monomer and in the lattice according to their surface accessibility. We focused mainly on the self-assembly domain, the region facing the outer surface of the protein lattice and thus most amenable to insertions and chemical modification. Two different marker molecules were used to modify cysteine-containing mutant proteins that were either in solution or attached to the cell wall. The results were subsequently evaluated taking advantage of the recent new information on SlpA domain boundaries (3). We were able to distinguish residues located in the outer and inner surfaces of the lattice, protein interior, and interface/pore regions. The information gathered here can be used in the development of further biotechnological and nanobiological applications, both in vitro and in vivo, that benefit from a thermostable S-layer protein from a GRAS bacterium with health-beneficial properties.     

Whole Genome Analysis of Leptospira licerasiae Provides Insight into Leptospiral Evolution and Pathogenicity

The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010^T and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.     

Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax

Background

An estimated 2.85 billion people live at risk of Plasmodium vivax transmission. In endemic countries vivax malaria causes significant morbidity and its mortality is becoming more widely appreciated, drug-resistant strains are increasing in prevalence, and an increasing number of reports indicate that P. vivax is capable of breaking through the Duffy-negative barrier long considered to confer resistance to blood stage infection. Absence of robust in vitro propagation limits our understanding of fundamental aspects of the parasite''s biology, including the determinants of its dormant hypnozoite phase, its virulence and drug susceptibility, and the molecular mechanisms underlying red blood cell invasion.

Methodology/Principal Findings

Here, we report results from whole genome sequencing of five P. vivax isolates obtained from Malagasy and Cambodian patients, and of the monkey-adapted Belem strain. We obtained an average 70–400 X coverage of each genome, resulting in more than 93% of the Sal I reference sequence covered by 20 reads or more. Our study identifies more than 80,000 SNPs distributed throughout the genome which will allow designing association studies and population surveys. Analysis of the genome-wide genetic diversity in P. vivax also reveals considerable allele sharing among isolates from different continents. This observation could be consistent with a high level of gene flow among parasite strains distributed throughout the world.

Conclusions

Our study shows that it is feasible to perform whole genome sequencing of P. vivax field isolates and rigorously characterize the genetic diversity of this parasite. The catalogue of polymorphisms generated here will enable large-scale genotyping studies and contribute to a better understanding of P. vivax traits such as drug resistance or erythrocyte invasion, partially circumventing the lack of laboratory culture that has hampered vivax research for years.     

Insight into Date Palm Diversity: Genetic and Morphological Investigations

Date palm (Phoenix dactylifera) is an important crop plant both from nutritional and economic points of view. The assessment of genetic diversity and population differentiation of date palms are evaluative for its dynamic conservation and sustainable utilization of its genetic diversity. Estimates of genetic diversity based on molecular markers and fruit characteristics were performed in samples of 23 date palms growing in Ahvaz city (Khuzestan province of Iran). Clustering based on fruit morphological features separated the cultivars in different groups. These cultivars differed significantly in morphological features (P =?0.001). Start codon targeted (SCoT) polymorphism markers revealed a good level of genetic variability (10.17 to 45.76%) in these cultivars. Moreover, STRUCTURE analysis revealed the presence of within-population genetic variability. Analysis of molecular variance revealed a significant genetic difference among date palms, while it showed a higher degree of within-cultivar genetic variability compared with that of among-population diversity. Some degree of common shared alleles occurred between date palm cultivars. Gst versus Nm analysis showed that some of the SCoT markers have a high discrimination power and may have a potential local adaptive value. The Mantel test showed a significant association (r =?0.40, P =?0.001) between morphological and genetic distances. Therefore, both morphological and SCoT molecular data can be used in genetic screening of date palms in the available germplasm.

     

Complete Mitochondrial Genome Sequence Data Provides Genetic Evidence That the Brown Dog Tick Rhipicephalus sanguineus (Acari: Ixodidae) Represents a Species Complex

Ticks are blood-sucking ectoparasites of great medical and veterinary significance that can transmit bacteria, protozoa, fungi and viruses, and cause a variety of human and animal diseases worldwide. In the present study, we sequenced the complete mitochondrial (mt) genome of Rhipicephalus sanguineus from China (RSC) and compared with that of R. sanguineus from USA (RSU). Nucleotide sequence difference in the full mt genome was 11.23% between RSC and RSU. For the 13 protein-coding genes, comparison revealed sequence divergences at both the nucleotide (9.34-15.65%) and amino acid (2.54-19.23%) levels between RSC and RSU. In addition, sequence comparison of the conserved mt cox1 and cytb genes among multiple individual R. sanguineus revealed substantial nucleotide differences between RSC and RSU but limited sequence variation within RSC. Phylogenetic analysis of ticks based on the amino acid sequence data of 13 protein-coding genes revealed that R. sanguineus from China and R. sanguineus from USA represent sister taxa (likely separate species). Taken together, the findings support the recently proposal that R. sanguineus tick may represents a species complex of at least two closely related species.     

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.     

High Genetic Connectivity Inferred from Whole-Genome Resequencing Provides Insight into the Phylogeographic Pattern of Larimichthys polyactis

Marine Biotechnology - Compared with terrestrial biota, marine fishes usually present lower genetic differentiation among different geographical populations because of high-level gene flow and lack...     

Whole Genome Sequence of a Turkish Individual

Although whole human genome sequencing can be done with readily available technical and financial resources, the need for detailed analyses of genomes of certain populations still exists. Here we present, for the first time, sequencing and analysis of a Turkish human genome. We have performed 35x coverage using paired-end sequencing, where over 95% of sequencing reads are mapped to the reference genome covering more than 99% of the bases. The assembly of unmapped reads rendered 11,654 contigs, 2,168 of which did not reveal any homology to known sequences, resulting in ∼1 Mbp of unmapped sequence. Single nucleotide polymorphism (SNP) discovery resulted in 3,537,794 SNP calls with 29,184 SNPs identified in coding regions, where 106 were nonsense and 259 were categorized as having a high-impact effect. The homo/hetero zygosity (1,415,123∶2,122,671 or 1∶1.5) and transition/transversion ratios (2,383,204∶1,154,590 or 2.06∶1) were within expected limits. Of the identified SNPs, 480,396 were potentially novel with 2,925 in coding regions, including 48 nonsense and 95 high-impact SNPs. Functional analysis of novel high-impact SNPs revealed various interaction networks, notably involving hereditary and neurological disorders or diseases. Assembly results indicated 713,640 indels (1∶1.09 insertion/deletion ratio), ranging from −52 bp to 34 bp in length and causing about 180 codon insertion/deletions and 246 frame shifts. Using paired-end- and read-depth-based methods, we discovered 9,109 structural variants and compared our variant findings with other populations. Our results suggest that whole genome sequencing is a valuable tool for understanding variations in the human genome across different populations. Detailed analyses of genomes of diverse origins greatly benefits research in genetics and medicine and should be conducted on a larger scale.     

The Glove-like Structure of the Conserved Membrane Protein TatC Provides Insight into Signal Sequence Recognition in Twin-Arginine Translocation

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Highlights? Crystal structures of TatC from the thermophile Aquifex aeolicus are presented ? The architecture of TatC generates a glove-shaped pocket buried in the bilayer ? Molecular dynamics reveal destabilization of the membrane around the pocket ? Correlation to biochemical results suggest the signal sequence binds in this pocket     

142 Insight Into the Mitochondrial Genome of Emiliania Huxleyi (Haptophyta)

Emiliania huxleyi (Lohmann) Hay et Mohler 1967 (CCMP373) is the most abundant representative of the Haptophyta, and can be found in oceanic and neritic waters from subpolar to tropical latitudes. Blooms of this coccolithophorid may reach cell densities of 2.106 ml⁻¹ and emit vast amounts of DMS (dimethyl sulfide), with the potential to affect the global climate. We report here the DNA sequence of more than 21 kb of the mitochondrial genome of this species, out of an approximate total of 30 kb. Preliminary annotation of the genome using database searches identified at least 16 genes. The data were also compared to the unpublished mitochondrial genome of Pavlova lutheri , another member of the haptophytes, and some important differences were identified. Although the gene content of E. huxleyi mtDNA seems to closely resemble that of P. lutheri mtDNA, the gene order differs substantially. Access to the P. lutheri and E. huxleyi mitochondrial genomes will permit the comparative analysis of two deeply diverging members of an ancient and ecologically significant lineage. Among other potential applications, the data will help to clarify phylogeny within the haptophytes as well as to determine the phylogenetic position of this division in relation to other groups of algae, such as heterokonts, dinoflagellates and cryptophytes.     

社鼠（Niviventer confucianus）线粒体基因组全序列分析

社鼠（Niviventer confucianus）属于啮齿目（Rodentia）、鼠科（Muridae）、白腹鼠属（Niviventer）,关于该物种的分子系统学研究极少。为获取社鼠线粒体基因组全序列,提取其基因组总DNA,参照近缘物种线粒体基因组全序列设计34对特异性引物,利用PCR扩增全部片段后进行测序,之后对其基因组组成及结构特点进行了初步分析。结果表明,社鼠线粒体基因组全序列长16 281 bp（GenBank收录号：KJ152220）,包含22个tRNA基因、13个蛋白质编码基因、2个rRNA基因和1个非编码控制区;基因组核苷酸组成为34.0%A、28.6%T、24.9%C、12.5%G。将所得序列与社鼠近缘物种（川西白腹鼠、小家鼠、褐家鼠）的线粒体全基因组进行比较,结果显示,四个物种的线粒体基因组虽然在基因组大小、部分tRNA二级结构、部分蛋白质编码基因的起始或终止密码子及控制区长度和碱基组成上有差异,但基因组结构和序列特征方面都具有较高的相似性。四个物种线粒体全基因组间的遗传距离显示,社鼠与川西白腹鼠距离最近,而与小家鼠距离最远。该研究为利用线粒体全基因组信息进行啮齿类分子系统学研究提供了有价值的资料。