The role of c-di-GMP signaling in an Aeromonas veronii biovar sobria strain

Aeromonas is a ubiquitous gram-negative bacterium that persists in the environment. It is shown that all isolates of persistent Aeromonas clones show strong biofilm formation ability. C-di-GMP regulates biofilm formation in many bacteria. To investigate the impact of c-di-GMP signaling, we introduced heterologous GGDEF and EAL domain proteins from Salmonella Typhimurium to an Aeromonas veronii biovar sobria strain. Overexpression of the GGDEF domain protein AdrA increased c-di-GMP concentration and biofilm formation and reduced motility. Production of the quorum-sensing signaling molecule C4-homoserine lactone and adhesion to aquatic plant duckweed and amoeba surfaces were enhanced. On the other hand, overexpression of the EAL domain protein YhjH decreased biofilm formation and increased motility.     

Changes in the sugarcane metabolome with stem development. Are they related to sucrose accumulation?

Sucrose content increases with internode development down the stem of sugarcane. In an attempt to determine which other changes in metabolites may be linked to sucrose accumulation gas chromatography-mass spectrometry was used to obtain metabolic profiles from methanol/water extracts of four samples of different age down the stem of cultivar Q117. Extracts were derivatized with either N-methyl-N-(trimethylsilyl) trifluoracetamide (TMS) or N-methyl N-(tert-butyldimethylsilyl) trifluoroacetamide (TBS) separately in order to increase the number of metabolites that could be detected. This resulted in the measurement of 121 and 71 metabolites from the TMS and TBS derivatization, respectively. Fifty-five metabolites were identified using commercial and publicly available libraries. Statistical analysis of the metabolite profiles resulted in clustering of tissue types. Particular metabolites were correlated with the level of sucrose accumulation, which as expected increased down the stem. Metabolites, such as tricarboxylic acid cycle intermediates and amino acids, were more abundant in the M2 sample (meristem to internode 2) that was actively growing and decreased in an apparently coordinated developmentally programmed manner in more mature internodes down the stem. However, other metabolites such as trehalose and raffinose showed positive correlations with sucrose concentration. Here we discuss the technique used to measure metabolites in sugarcane and the changes in metabolite abundance down the sugarcane stem.     

Superior Lithium Storage Capacity of α‐MnS Nanoparticles Embedded in S‐Doped Carbonaceous Mesoporous Frameworks

Herein, a Mn‐based metal–organic framework is used as a precursor to obtain well‐defined α‐MnS/S‐doped C microrod composites. Ultrasmall α‐MnS nanoparticles (3–5 nm) uniformly embedded in S‐doped carbonaceous mesoporous frameworks (α‐MnS/SCMFs) are obtained in a simple sulfidation reaction. As‐obtained α‐MnS/SCMFs shows outstanding lithium storage performance, with a specific capacity of 1383 mAh g^?1 in the 300th cycle or 1500 mAh g^?1 in the 120th cycle (at 200 mA g^?1) using copper or nickel foil as the current collector, respectively. The significant (pseudo)capacitive contribution and the stable composite structure of the electrodes result in impressive rate capabilities and outstanding long‐term cycling stability. Importantly, in situ X‐ray diffraction measurements studies on electrodes employing various metal foils/disks as current collector reveal the occurrence of the conversion reaction of CuS at (de)lithiation process when using copper foil as the current collector. This constitutes the first report of the reaction mechanism for α‐MnS, eventually forming metallic Mn and Li₂S. In situ dilatometry measurements demonstrate that the peculiar structure of α‐MnS/SCMFs effectively restrains the electrode volume variation upon repeated (dis)charge processes. Finally, α‐MnS/SCMFs electrodes present an impressive performance when coupled in a full cell with commercial LiMn_1/3Co_1/3Ni_1/3O₂ cathodes.     

Genome Structure of the Heavy Metal Hyperaccumulator Noccaea caerulescens and Its Stability on Metalliferous and Nonmetalliferous Soils

Noccaea caerulescens (formerly known as Thlaspi caerulescens), an extremophile heavy metal hyperaccumulator model plant in the Brassicaceae family, is a morphologically and phenotypically diverse species exhibiting metal tolerance and leaf accumulation of zinc, cadmium, and nickel. Here, we provide a detailed genome structure of the approximately 267-Mb N. caerulescens genome, which has descended from seven chromosomes of the ancestral proto-Calepineae Karyotype (n = 7) through an unusually high number of pericentric inversions. Genome analysis in two other related species, Noccaea jankae and Raparia bulbosa, showed that all three species, and thus probably the entire Coluteocarpeae tribe, have descended from the proto-Calepineae Karyotype. All three analyzed species share the chromosome structure of six out of seven chromosomes and an unusually high metal accumulation in leaves, which remains moderate in N. jankae and R. bulbosa and is extreme in N. caerulescens. Among these species, N. caerulescens has the most derived karyotype, with species-specific inversions on chromosome NC6, which grouped onto its bottom arm functionally related genes of zinc and iron metal homeostasis comprising the major candidate genes NICOTIANAMINE SYNTHASE2 and ZINC-INDUCED FACILITATOR-LIKE1. Concurrently, copper and organellar metal homeostasis genes, which are functionally unrelated to the extreme traits characteristic of N. caerulescens, were grouped onto the top arm of NC6. Compared with Arabidopsis thaliana, more distal chromosomal positions in N. caerulescens were enriched among more highly expressed metal homeostasis genes but not among other groups of genes. Thus, chromosome rearrangements could have facilitated the evolution of enhanced metal homeostasis gene expression, a known hallmark of metal hyperaccumulation.Noccaea caerulescens (formerly known as Thlaspi caerulescens) is a diploid (2n = 14) biennial or short-living perennial plant from the family Brassicaceae. N. caerulescens is native to Europe, with a patchy distribution from the United Kingdom and France to Slovakia and from Germany and Poland southward to northern Spain and Italy. The widespread occurrence in Scandinavia is thought to represent naturalized populations over the past few hundred years (Koch et al., 1998, and refs. therein). N. caerulescens is one of the 120 Noccaea spp., which, together with two other genera, constitute the tribe Coluteocarpeae (approximately 127 species; Al-Shehbaz, 2012). However, the generic treatment of the tribe is far from settled, and up to 12 genera are recognized in Coluteocarpeae by F.K. Meyer (Meyer, 2001, 2006a, 2006b; Koch and German, 2013).Together with the metal hyperaccumulator species Arabidopsis halleri, N. caerulescens is among the most prominent plant model systems for the study of heavy metal hyperaccumulation and associated hypertolerance (Krämer, 2010; Hanikenne and Nouet, 2011; Pollard et al., 2014). N. caerulescens is a hyperaccumulator of zinc (Zn) on metalliferous as well as nonmetalliferous soils and of cadmium (Cd) on metalliferous soils (Reeves et al., 2001; Krämer, 2010), and its populations on serpentine soils are known to hyperaccumulate nickel (Ni; Reeves and Brooks, 1983; Reeves, 1988; Visioli et al., 2012; Maestri et al., 2013). N. caerulescens is a morphologically highly diverse species comprising at least two, but up to eight (http://www.gbif.org), recognized subspecies with partly overlapping distribution ranges (the simplest treatment includes ssp. caerulescens and sylvestris, the latter including populations formerly described as Thlaspi calaminare or N. caerulescens ssp. calaminare). As the morphological variation often has a clinal character, the taxonomic and biological value of various intraspecific taxa is questionable, and detailed studies will be needed to resolve this issue (for discussion, see Koch and German, 2013). In addition to pervasive morphological variation (Koch and German, 2013) apparently reinforced by geographical constraints (Besnard et al., 2009), there is also pronounced phenotypic variation in metal tolerance and accumulation (Escarré et al., 2000; Reeves et al., 2001; Assunção et al., 2006; Xing et al., 2008; Krämer, 2010; Tuomainen et al., 2010).Although N. caerulescens is the most commonly studied metal hyperaccumulator model species, with more than 210 studies published on the subject (Pollard et al., 2014), the detailed genome structure of N. caerulescens remains unresolved. Assunção et al. (2006) published the first amplified fragment-length polymorphism-based genetic linkage map and identified quantitative trait loci for Zn accumulation in roots. Another amplified fragment-length polymorphism-based genetic map based on a cross between two accessions with differential Cd accumulation and tolerance was used to identify quantitative trait loci associated with the accumulation of Cd and Zn (Deniau et al., 2006). Both maps comprised the expected seven linkage groups with dense clusters of linked markers located on each linkage group, most likely corresponding to centromeric regions with suppressed recombination rates. Apart from the tentative identification of centromeres, small numbers of orthologous markers shared with Arabidopsis thaliana and A. halleri did not allow the establishment of chromosome collinearity between these genomes for inference of the genome structure of N. caerulescens.More recently, Mandáková and Lysak (2008) reconstructed karyotype evolution in eight Brassicaceae species of tribes in extended lineage II (Franzke et al., 2011) by comparative chromosome painting (CCP) using chromosome-specific bacterial artificial chromosome (BAC) contigs of A. thaliana. They concluded that genomes of all the analyzed species with seven or 14 chromosome pairs (n = 7/14) were derived from the eight chromosomes of the Ancestral Crucifer Karyotype (ACK; n = 8) via an ancestral n = 7 genome named the proto-Calepineae Karyotype (PCK). The genome of N. caerulescens (accession Korenec), analyzed as a representative of the tribe Coluteocarpeae (formerly Noccaeeae) by Mandáková and Lysak (2008), has descended from a PCK-like ancestor but showed a remarkably high number of secondary chromosome rearrangements. By comparison with the ancestral PCK, in N. caerulescens six of the seven ancestral chromosomes were reshuffled by inversions encompassing pericentromeric regions. However, that study did not establish the detailed structure of the N. caerulescens genome, including precise positions of chromosome break points. Consequently, evolutionary steps leading to the origin of the inversion chromosomes were reconstructed only approximately, and gene content could not be estimated.Our study here provides a detailed comparative genome structure of N. caerulescens and relates the genome structure to the evolution of heavy metal-related extreme traits. Based on a more precise definition of ancestral genomic blocks within the ACK (Cheng et al., 2013) and using PCK as the most probable ancestral genome of N. caerulescens, we carried out a detailed analysis of the entire karyotype, including inversions, by means of CCP. Furthermore, considering the unusually high incidence of inversions, we were intrigued to find out whether this variation is unique to the reference accession (Mandáková and Lysak, 2008) or fixed in populations on both nonmetalliferous and metalliferous soils enriched for different heavy metal elements. Toward this aim, we constructed detailed comparative karyotypes for 13 populations of N. caerulescens from metalliferous and nonmetalliferous soils throughout the European species distribution range, including, in particular, populations from southern France known for the extraordinarily high concentrations of Zn and Cd in their leaves (St. Félix de Pallières and Viviez; Reeves et al., 2001). Next, we asked whether the inversions are specific to N. caerulescens or shared by other Coluteocarpeae species by deducing the chromosome structure and evolution of the N. caerulescens genome in comparison with two other species from the tribe Coluteocarpeae, Noccaea jankae and Raparia bulbosa. Finally, we addressed the question of whether chromosome inversions and rearrangements might have affected the physical positions of metal homeostasis candidate genes that were proposed to act in naturally selected metal hyperaccumulation and associated hypertolerance of N. caerulescens. We tested for the clustering of functionally related metal homeostasis genes in closer proximity on the chromosome toward supergene formation as well as for the relation between changes in chromosomal position and gene expression among metal homeostasis genes.     

Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

Polyhalogenated aromatic compounds are harmful environmental contaminants and tend to persist in anoxic soils and sediments. Dehalococcoides mccartyi strain DCMB5, a strain originating from dioxin-polluted river sediment, was examined for its capacity to dehalogenate diverse chloroaromatic compounds. Strain DCMB5 used hexachlorobenzenes, pentachlorobenzenes, all three tetrachlorobenzenes, and 1,2,3-trichlorobenzene as well as 1,2,3,4-tetra- and 1,2,4-trichlorodibenzo-p-dioxin as electron acceptors for organohalide respiration. In addition, 1,2,3-trichlorodibenzo-p-dioxin and 1,3-, 1,2-, and 1,4-dichlorodibenzo-p-dioxin were dechlorinated, the latter to the nonchlorinated congener with a remarkably short lag phase of 1 to 4 days following transfer. Strain DCMB5 also dechlorinated pentachlorophenol and almost all tetra- and trichlorophenols. Tetrachloroethene was dechlorinated to trichloroethene and served as an electron acceptor for growth. To relate selected dechlorination activities to the expression of specific reductive dehalogenase genes, the proteomes of 1,2,3-trichlorobenzene-, pentachlorobenzene-, and tetrachloroethene-dechlorinating cultures were analyzed. Dcmb_86, an ortholog of the chlorobenzene reductive dehalogenase CbrA, was the most abundant reductive dehalogenase during growth with each electron acceptor, suggesting its pivotal role in organohalide respiration of strain DCMB5. Dcmb_1041 was specifically induced, however, by both chlorobenzenes, whereas 3 putative reductive dehalogenases, Dcmb_1434, Dcmb_1339, and Dcmb_1383, were detected only in tetrachloroethene-grown cells. The proteomes also harbored a type IV pilus protein and the components for its assembly, disassembly, and secretion. In addition, transmission electron microscopy of DCMB5 revealed an irregular mode of cell division as well as the presence of pili, indicating that pilus formation is a feature of D. mccartyi during organohalide respiration.     

The Solution Structure of the Lantibiotic Immunity Protein NisI and Its Interactions with Nisin

Many Gram-positive bacteria produce lantibiotics, genetically encoded and posttranslationally modified peptide antibiotics, which inhibit the growth of other Gram-positive bacteria. To protect themselves against their own lantibiotics these bacteria express a variety of immunity proteins including the LanI lipoproteins. The structural and mechanistic basis for LanI-mediated lantibiotic immunity is not yet understood. Lactococcus lactis produces the lantibiotic nisin, which is widely used as a food preservative. Its LanI protein NisI provides immunity against nisin but not against structurally very similar lantibiotics from other species such as subtilin from Bacillus subtilis. To understand the structural basis for LanI-mediated immunity and their specificity we investigated the structure of NisI. We found that NisI is a two-domain protein. Surprisingly, each of the two NisI domains has the same structure as the LanI protein from B. subtilis, SpaI, despite the lack of significant sequence homology. The two NisI domains and SpaI differ strongly in their surface properties and function. Additionally, SpaI-mediated lantibiotic immunity depends on the presence of a basic unstructured N-terminal region that tethers SpaI to the membrane. Such a region is absent from NisI. Instead, the N-terminal domain of NisI interacts with membranes but not with nisin. In contrast, the C-terminal domain specifically binds nisin and modulates the membrane affinity of the N-terminal domain. Thus, our results reveal an unexpected structural relationship between NisI and SpaI and shed light on the structural basis for LanI mediated lantibiotic immunity.     

Association between the BsmI Polymorphism in the Vitamin D Receptor Gene and Breast Cancer Risk: Results from a Pakistani Case-Control Study

Background

Vitamin D is postulated to decrease the risk of breast cancer by inhibiting cell proliferation via the vitamin D receptor (VDR). Two common single nucleotide polymorphisms (SNPs) in the VDR gene, rs1544410 (BsmI) and rs2228570 (FokI), are inconsistently associated with breast cancer risk in Caucasian populations, while data for Asians are scarce. Here, we investigated the possible contribution of these SNPs to breast cancer risk in Pakistani breast cancer patients and in controls participating in a hospital-based breast cancer case-control study (PAK-BCCC).

Methods

Genotyping of the BsmI and FokI SNPs was performed by PCR-based restriction fragment length polymorphism (RFLP) analysis of 463 genetically enriched female breast cancer cases with known BRCA1/2 status and in 1,012 controls from Pakistan. The association between SNP genotypes and breast cancer risk was investigated by logistic regression adjusted for potential breast cancer risk factors and stratified by BRCA1/2 status and family history. Odds ratios (ORs) and 95% confidence intervals (CIs) were reported.

Results

The b allele of the BsmI was associated with an increased breast cancer risk (per b allele OR 1.28, 95% CI 1.09–1.49, P = 0.003). Subgroup analysis revealed that this effect was restricted to BRCA1/2 non-carriers (per b allele OR 1.33, 95% CI 1.11–1.59, P = 0.002) and was stronger in those who reported a positive family history of breast and/or ovarian cancer (per b allele OR 1.64, 95% CI 1.20–2.22, P = 0.002). No association with breast cancer risk was detected for the FokI SNP.

Conclusions

The BsmI polymorphism in the VDR gene may be associated with an increased breast cancer risk in Pakistani women negative for BRCA1/2 germline mutations.