Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara.

BACKGROUND: Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa. RESULTS: In the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74. In the SSSLs population, 11 genes for 5 domestication traits, including tiller angle, spreading panicle, awn, seed shattering, and red pericarp, were identified and mapped on 5 chromosomes through substitution mapping. Herein, allelic variations of 7 genes were found through sequence alignment with the known genes, that is, TA7-RUF was allelic to PROG1, TA8-RUF was allelic to TIG1, SPR4-NIV was allelic to OsLG1, AN4-RUF was allelic to An-1, SH4-NIV was allelic to SH4, and both RC7-RUF and RC7-NIV were allelic to Rc. Meanwhile, 4 genes, TA11-NIV, SPR3-NIV, AN3-NIV, and AN4-NIV, were considered as the novel genes identified in these SSSLs, because of none known genes for the related domestication traits found in the chromosomal locations of them. CONCLUSION: The results indicated that the SSSLs would be precious germplasm resources for gene mining and utilization from wild rice species, and it laid the foundation for further analyses of the novel domestication genes to better understand the genetic basis in regulating the traits variation during domestication.

Impact of selenium on rhizosphere microbiome of a hyperaccumulation plant Cardamine violifolia.

Cardamine violifolia is the only selenium hyperaccumulation plant found in China. It has been developed as a source of medicinal and edible products that we can consume as selenium supplements. Many planting approaches have been developed to increase the selenium content of C. violifolia for nutrient biofortification. However, the contribution of rhizosphere microbes of C. violifolia to selenium enrichment has not been investigated. In this study, four types of selenium, i.e., selenate, selenite, nanoparticles selenium from Bacillus subtilis (B. subtilis-Se), and organic selenium from yeast (yeast-Se), were added to the soil that C. violifolia was grown in, respectively. Selenate led to the greatest accumulation of selenium in C. violifolia, followed by selenite, B. subtilis-Se, and yeast-Se. Except for yeast-Se, the concentration of selenium in C. violifolia positively correlated with the amount of selenium added to the soil. Furthermore, the different types of exogenous selenium exhibited distinct effects on the rhizosphere microbiome of C. violifolia. Alpha and beta diversity analyses demonstrated that rhizosphere microbiome was more obviously affected by selenium from B. subtilis and yeast than from selenate and selenite. Different microbial species were enriched in the rhizosphere of C. violifolia under various exogenous selenium treatments. B. subtilis-Se application enhanced the abundance of Leucobacter, Sporosarcina, Patulibacter, and Denitrobacter, and yeast-Se application enriched the abundance of Singulishaera, Lactobacillus, Bdellovibrio, and Bosea. Bosea and the taxon belonging to the order Solirubrobacterales were enriched in the samples with selenate and selenite addition, respectively, and the abundances of these were linearly related to the concentrations of selenate and selenite applied in the rhizosphere of C. violifolia. In summary, this study revealed the response of the rhizosphere microbiome of C. violifolia to exogenous selenium. Our findings are useful for developing suitable selenium fertilizers to increase the selenium hyperaccumulation level of this plant.

Multiple fluorescence response behaviors towards antibiotics and bacteria based on a highly stable Cd-MOF.

The abuse of antibiotics has triggered the rise of drug-resistance bacteria, which has seriously threatened public health globally. As a result, carrying out efficient and accurate antibiotic and bacteria identification are quite significant but challenge. Herein, an unprecedented Cd-MOF-based sensor, [CdL]n [1, H2L = 4-(2-methyl-1H-benzo[d]imidazol-1-yl) isophthalic acid] with multiple fluorescence response behaviours towards antibiotics and bacteria was developed. Single-crystal X-ray diffraction revealed that 1 is a mesomeric 2D bilayer, which is comprised of two opposite chiral mono-layers, each assembled by left-handed or right-handed helixes. More interestingly, 1 represented multiplex detection capability towards antibiotics and bacteria through two detection behaviors: toward nitro-antibiotics and chlortetracycline (CTC) via fluorescent quenching, while toward Staphylococcus albus (S. albus) via fluorescent enhancement. Remarkably, 1 showed a low limit of detection (LOD, 47 CFU/mL) accompanied with specificity in the detection of S. albus compared to other bacteria, such as Staphylococcus aureus, Acinetobacter baumannii, Klebsiella pneumonia, Pseudomonas aeruginosa and Escherichia coli. In addition, the LOD could reach to ppm level for nitro-antibiotics and CTC. Moreover, the practical application of 1 was further reinforced through the detection of nitro-antibiotics and CTC, as well as S. albus in fetal calf serum and river water.

Agrobacterium tumefaciens Growth Pole Ring Protein: C Terminus and Internal Apolipoprotein Homologous Domains Are Essential for Function and Subcellular Localization.

The Agrobacterium growth pole ring (GPR) protein forms a hexameric ring at the growth pole (GP) that is essential for polar growth. GPR is large (2,115 amino acids) and contains 1,700 amino acids of continuous α-helices. To dissect potential GPR functional domains, we created deletions of regions with similarity to human apolipoprotein A-IV (396 amino acids), itself composed of α-helical domains. We also tested deletions of the GPR C terminus. Deletions were inducibly expressed as green fluorescent protein (GFP) fusion proteins and tested for merodiploid interference with wild-type (WT) GPR function, for partial function in cells lacking GPR, and for formation of paired fluorescent foci (indicative of hexameric rings) at the GP. Deletion of domains similar to human apolipoprotein A-IV in GPR caused defects in cell morphology when expressed in trans to WT GPR and provided only partial complementation to cells lacking GPR. Agrobacterium-specific domains A-IV-1 and A-IV-4 contain predicted coiled coil (CC) regions of 21 amino acids; deletion of CC regions produced severe defects in cell morphology in the interference assay. Mutants that produced the most severe effects on cell shape also failed to form paired polar foci. Modeling of A-IV-1 and A-IV-4 reveals significant similarity to the solved structure of human apolipoprotein A-IV. GPR C-terminal deletions profoundly blocked complementation. Finally, peptidoglycan (PG) synthesis is abnormally localized circumferentially in cells lacking GPR. The results support the hypothesis that GPR plays essential roles as an organizing center for membrane and PG synthesis during polar growth.IMPORTANCE Bacterial growth and division are extensively studied in model systems (Escherichia coli, Bacillus subtilis, and Caulobacter crescentus) that grow by dispersed insertion of new cell wall material along the length of the cell. An alternative growth mode-polar growth-is used by some Actinomycetales and Proteobacteria species. The latter phylum includes the family Rhizobiaceae, in which many species, including Agrobacterium tumefaciens, exhibit polar growth. Current research aims to identify growth pole (GP) factors. The Agrobacterium growth pole ring (GPR) protein is essential for polar growth and forms a striking hexameric ring structure at the GP. GPR is long (2,115 amino acids), and little is known about regions essential for structure or function. Genetic analyses demonstrate that the C terminus of GPR, and two internal regions with homology to human apolipoproteins (that sequester lipids), are essential for GPR function and localization to the GP. We hypothesize that GPR is an organizing center for membrane and cell wall synthesis during polar growth.

Baicalin Represses Type Three Secretion System of Pseudomonas aeruginosa through PQS System.

Therapeutics that target the virulence of pathogens rather than their viability offer a promising alternative for treating infectious diseases and circumventing antibiotic resistance. In this study, we searched for anti-virulence compounds against Pseudomonas aeruginosa from Chinese herbs and investigated baicalin from Scutellariae radix as such an active anti-virulence compound. The effect of baicalin on a range of important virulence factors in P. aeruginosa was assessed using luxCDABE-based reporters and by phenotypical assays. The molecular mechanism of the virulence inhibition by baicalin was investigated using genetic approaches. The impact of baicalin on P. aeruginosa pathogenicity was evaluated by both in vitro assays and in vivo animal models. The results show that baicalin diminished a plenty of important virulence factors in P. aeruginosa, including the Type III secretion system (T3SS). Baicalin treatment reduced the cellular toxicity of P. aeruginosa on the mammalian cells and attenuated in vivo pathogenicity in a Drosophila melanogaster infection model. In a rat pulmonary infection model, baicalin significantly reduced the severity of lung pathology and accelerated lung bacterial clearance. The PqsR of the Pseudomonas quinolone signal (PQS) system was found to be required for baicalin's impact on T3SS. These findings indicate that baicalin is a promising therapeutic candidate for treating P. aeruginosa infections.

Heat Shock Protein DnaJ in Pseudomonas aeruginosa Affects Biofilm Formation via Pyocyanin Production.

Heat shock proteins (HSPs) play important biological roles, and they are implicated in bacterial response to environmental stresses and in pathogenesis of infection. The role of HSPs in P. aeruginosa, however, remains to be fully elucidated. Here, we report the unique role of HSP DnaJ in biofilm formation and pathogenicity in P. aeruginosa. A dnaJ mutant produced hardly any pyocyanin and formed significantly less biofilms, which contributed to decreased pathogenicity as demonstrated by reduced mortality rate in a Drosophila melanogaster infection model. The reduced pyocyanin production in the dnaJ mutant was a result of the decreased transcription of phenazine synthesis operons including phzA1, phzA2, phzS, and phzM. The reduction of biofilm formation and initial adhesion in the dnaJ mutant could be reversed by exogenously added pyocyanin or extracellular DNA (eDNA). Consistent with such observations, absence of dnaJ significantly reduced the release of eDNA in P. aeruginosa and addition of exogenous pyocyanin could restore eDNA release. These results indicate dnaJ mutation caused reduced pyocyanin production, which in turn caused the decreased eDNA, resulting in decreased biofilm formation. DnaJ is required for pyocyanin production and full virulence in P. aeruginosa; it affects biofilm formation and initial adhesion via pyocyanin, inducing eDNA release.

The Two-Operon-Coded ABC Transporter Complex FpvWXYZCDEF is Required for Pseudomonas aeruginosa Growth and Virulence Under Iron-Limiting Conditions.

Iron is essential for all organisms. Bacteria have devolved sophisticated systems to maintain intracellular iron homeostasis. FpvCDEF(PA2407-2410) has been reported as an ABC transporter involved in pyoverdine-Fe uptake which does not affect growth under iron-limiting condition, when it is deleted in PAO1. In this study, we proved that fpvCDEF and fpvWXYZ(PA2403-2406) constituted an ABC transporter complex containing two operons: fpvWXYZCDE and fpvF. The operon fpvWXYZCDE was regulated by iron negatively and the single gene operon fpvF was constitutively expressed. Inactivation of any one of the components, fpvW, fpvC, fpvD, fpvE, and fpvF, led to increased expression of fpvWXYZCDE suggesting that each component of fpvWXYZCDEF could be involved in iron uptake. The ABC transporter complex encoded by fpvWXYZCDEF plays important roles in growth, oxidative stress resistance, and virulence, since the deletion of fpvWXYZCDEF resulted in defective growth, increased sensitivity to H2O2, and decreased virulence compared with PAO1(ΔfpvCDEF) and the wild type PAO1 under iron-limiting condition.

The role of the temperature-regulated acyltransferase (PA3242) on growth, antibiotic resistance and virulence in Pseudomonas aeruginosa.

Pseudomonas aeruginosa (PAO1) is an important opportunistic pathogen that thrives in various environments. It is known that the structural variations of the lipopolysaccharide (LPS), including lipid A moiety play an important role in encountering environmental changes. Genes PA3242 and PA0011 have recently been reported to be responsible for secondary-acylation of lipid A in P. aeruginosa. In this study, we confirmed that the PA3242-dependant secondary acylation affects the growth, antibiotic resistance and virulence of PAO1 and functions as a more predominant acyltransferase than PA0011. PA3242 mutant showed inhibited growth at 37 °C and inviability at 28 °C in rich medium LB. The inactivation of PA3242 leads to more sensitivity to a wide range of antibiotics than PAO1(ΔPA0011). Moreover, the virulence of PAO1(ΔPA3242) was attenuated more significantly than that of PAO1 and PAO1(ΔPA0011). The outer membrane integrity and stability of PAO1(ΔPA3242) were seriously compromised. Furthermore, PAO1(ΔPA3242) lost most of pilus and exhibited severely damaged cell envelope, which is probably responsible for the deficiency of swimming, swarming and twitching. These results partially explained the decreased antibiotic resistance and attenuated virulence of PAO1(ΔPA3242) compared to PAO1(ΔPA0011) and PAO1. Our study demonstrated that PA3242-dependent secondary acylation of lipid A plays a predominant role in growth, antibiotic resistance and virulence of PAO1 than PA0011.

Genotypes and transmitted drug resistance among treatment-naive HIV-1-infected patients in a northwestern province, China: trends from 2003 to 2013.

BACKGROUND: Transmitted drug resistance (TDR) reduces the efficacy of initial antiretroviral treatment and has become a public health concern. Little information is available regarding the genetic diversity of HIV-1 and the prevalence of TDR among treatment-naïve patients in a northwestern province of China since the implementation of national free antiretroviral therapy (ART). METHODS: Blood samples from 372 HIV-1 treatment-naive patients were collected between 2003 and 2013 in Shaanxi province. Viral RNA was extracted for nested PCR, and phylogenetic reconstruction and recombination analyses were performed to characterize patterns of the HIV-1 subtypes. Genotypic drug resistance testing was performed using an in-house assay to determine trends in the prevalence of HIV-1 transmitted drug resistance. RESULTS: Multiple genotypes were identified among the patients in Shaanxi, including B (25.0%), C (0.3%), G (0.3%), and CRF01_AE (39.2%), CRF07_BC (32.7%), CRF08_BC (0.8%), CRF55_01B (1.1%), and URFs (0.6%). The subtypes were associated with the transmission routes (χ2 = 77.113, p < 0.01). In this study, a low baseline CD4+ T cell count and a high viral load were found among CRF01_AE-infected patients compared with patients who were infected with non-CRF01_AE (p<0.01) through sexual transmission; however, the CRF01_AE subtype was not associated with a low baseline CD4+ T cell count or a high viral load in Chinese patients infected through blood transmission (p = 0.249). The overall TDR rate in this population was 4.4% between 2003 and 2013. A univariate logistic regression model revealed that a low CD4 T cell count (≤ 100 cells/µL) was associated with the development of drug-resistant strains. CONCLUSION: Our work revealed diverse HIV-1 subtype distributions in Shaanxi province. We identified a low and stable TDR time trend among ART-naive patients. These findings enhance our understanding of HIV-1 genetic diversity and provide some guidelines for the improvement and implementation of a comprehensive public health strategy of HIV-1 TDR prevention.

Genome Sequence of Mycoplasma columbinum Strain SF7.

Mycoplasma columbinum is a member of nonglycolytic Mycoplasma species which can hydrolyze arginine. Increasingly research has revealed that M. columbinum is associated with respiratory disease of pigeons and that the respiratory disease symptoms could be eliminated via the use of mycoplasma treatment medicine. Here we report the genome sequence of M. columbinum strain SF7, which is the first genome report for M. columbinum.

Genome sequence of Mycoplasma iowae strain 695, an unusual pathogen causing deaths in turkeys.

Mycoplasma iowae is associated mainly with reduced hatchability in turkeys and is well known for the unusual ability of phenotypic variation in the Mycoplasma surface components as well as a relative resistance to heat, bile salts, and many antimicrobials. A subset of unique genes and a gene cluster responsible for these characteristics could be identified from the genome. Here, we report the first genome sequence of this species.

Multiple amino acid substitutions involved in enhanced pathogenicity of LPAI H9N2 in mice.

Human infection of avian influenza H9N2 virus highlighted the need to better understand the mechanism of interspecies transmission. In this study, we generated mouse-adapted influenza virus (ma01) through serial lung-to-lung passages of a wild-type H9N2 (A/chicken/Hubei/01/1999). Ma01 caused highly lethal infection in mice with severe lung pathology and extended tissue tropism. Nine amino acid substitutions of ma01 were observed in five viral genes (those for PB2, PA, NA, M1, and NS1). Of these mutations, substitutes of PB2(627), PA(349), PA(605), NA(88), and NA(356) were absent in influenza H9N2. Furthermore, the targets of wild-type virus responding to mouse microRNA mmu-mir-1940 and mmu-mir-1904 were eliminated in ma01. The mutation PB2(627) of ma01 confirmed as a key virulence determinant of influenza H5N1 was responsible for the altered recognition of mmu-mir-1904. In addition, induction of IL-1ß, IL-6, TNF-α, and IFN-ß was found in significantly higher levels in ma01 infected mouse peripheral blood than parental strain. These results demonstrate that multiple amino acid substitutions and avoidance of microRNA recognitions may be essential for lethal infection and high speed of virus growth can outcompete the antiviral response of infected host.

Genome sequence of duck pathogen Mycoplasma anatis strain 1340.

Mycoplasma anatis, a member of the class Mollicutes, is the causative agent of a contagious infectious disease of domestic ducklings, wild birds, and eggs. Increasing reports show that coinfection of M. anatis with Escherichia coli results in substantial economic impacts on the duck farms in China. Here, we announce the first genome sequence of M. anatis.

Genome sequence of poultry pathogen Riemerella anatipestifer strain RA-YM.

Riemerella anatipestifer is a Gram-negative, rod-shaped bacterium associated with epizootic infections in poultry. R. anatipestifer strain RA-YM, belonging to the serotype 1 prevalent in China, is a clinically isolated strain with high-level virulence. Here, we report the first genome sequence of this species.