The multicomponent antirestriction system of phage P1 is linked to capsid morphogenesis

Bacterial Type I restriction‐modification (R‐M) systems present a major barrier to foreign DNA entering the bacterial cell. The temperate phage P1 packages several proteins into the virion that protect the phage DNA from host restriction. Isogenic P1 deletion mutants were used to reconstitute the previously described restriction phenotypes associated with darA and darB. While P1ΔdarA and P1ΔdarB produced the expected phenotypes, deletions of adjacent genes hdf and ddrA also produced darA‐like phenotypes and deletion of ulx produced a darB‐like phenotype, implicating several new proteins of previously unknown function in the P1 dar antirestriction system. Interestingly, disruption of ddrB decreased P1's sensitivity to EcoB and EcoK restriction. Proteomic analysis of purified virions suggests that packaging of antirestriction components into P1 virions follows a distinct pathway that begins with the incorporation of DarA and Hdf and concludes with DarB and Ulx. Electron microscopy analysis showed that hdf and darA mutants also produce abnormally high proportions of virions with aberrant small heads, which suggests Hdf and DarA play a role in capsid morphogenesis. The P1 antirestriction system is more complex than previously realized and is comprised of multiple proteins including DdrA, DdrB, Hdf, and Ulx in addition to DarA and DarB.     

Different pathotypes of the sunflower downy mildew pathogen Plasmopara halstedii all contain isometric virions†

Eight pathotypes of Plasmopara halstedii were screened to investigate the occurrence of virions and the potential viral influence on the pathogenicity of the sunflower downy mildew pathogen. In 23 of 26 P. halstedii isolates derived from eight countries in Europe, North America and South America, virions were detected by transmission electron microscopy. By contrast, there were no ultrastructural indications of virus‐like particles in eight other related Oomycetes. The virions of representative P. halstedii isolates were morphologically and biochemically characterized and compared among each other. Regardless of their host's pathotypes, the geographical origin of the isolate and the sensitivity towards the fungicide metalaxyl, the viral characters obtained were uniform. The virions were isometric and measured approximately 37 nm in diameter. One polypeptide of c. 36 kDa and two segments of single‐stranded RNA (3.0 and 1.6 kb) were detected. Both viral RNA segments were detected by capillary electrophoresis in the three remaining P. halstedii isolates where virions were undetectable by transmission electron microscopy. Virus‐specific primers for the 1.6 kb‐segment were synthesized and used to determine and compare a partial sequence of the viral coat protein among virions of different P. halstedii pathotypes. In all tested isolates, fragments of 0.7 kb were amplified which were directly sequenced. Sequence variation was insignificant. As both less aggressive and more aggressive P. halstedii isolates contained virions, the presence or absence of virions could not explain the diverse aggressiveness of the downy mildew pathogen towards sunflower. Moreover, the results indicated that pathogenicity of P. halstedii was not related to variation in morphological or biochemical characters of the virions.     

Characterization of Maize Iranian Mosaic Virus and Comparison with Hawaiian and Other Isolates of Maize Mosaic Virus (Rhabdoviridae)

Maize Iranian mosaic virus (MIMV) was characterized and compared with isolates of Maize mosaic virus (MMV, genus Nucleorhabdovirus, family Rhabdoviridae) in insect transmission, cytopathology and ultrastructure of infected maize cells, virion proteins and serologically. MIMV is naturally transmitted by Ribautodelphax notabilis, a delphacid planthopper, in Iran. In this study, another planthopper, Peregrinus maidis, vector of MMV, transmitted MIMV with an estimated efficiency of 0.4–1.6% following feeding on MIMV‐infected maize plants and 64% following injection of MIMV into the hemolymph, suggesting that P. maidis gut tissues largely blocked MIMV transmission. MIMV and MMV‐HI (Hawaii) induced similar cytopathologies in cells of infected maize leaves, with virions budding through inner nuclear and endoplasmic reticulum membranes. In thin sections, virions of MIMV were significantly shorter than those of MMV‐HI. Sodium dodecyl sulphate polyacrylamide gel electrophoresis analysis of virions of MIMV, MMV‐HI, MMV‐CR (Costa Rica) and MMV‐FL (Florida) yielded six proteins of which four were identified as the putative G, N, P and M proteins of plant rhabdoviruses. The N, P and M proteins of MIMV migrated faster in gels than those of the MMV isolates indicating a lower molecular weight, whereas the bands corresponding to the G proteins migrated similarly for both viruses. Polyclonal antibodies to MMV‐HI failed to react with virions of MIMV in enzyme‐linked immunosorbent assay (ELISA) and with MIMV proteins in Western blots. In contrast, these antibodies reacted strongly with MMV‐HI and MMV‐FL virions in ELISA and with MMV‐HI, MMV‐CR and MMV‐FL proteins in Western blots. Further, in ELISA, polyclonal antibodies to MMV‐MR (Mauritius) reacted weakly with MIMV virions but strongly with MMV‐HI and MMV‐FL virions. Thus, it is concluded that MIMV is a new virus of the Nucleorhabdovirus genus that may be distantly related to MMV.     

CutC is induced late during copper exposure and can modify intracellular copper content in Enterococcus faecalis

The PreS1 protein is present on the outermost part of the hepatitis B virus (HBV) surface and has been shown to have a pivotal function in viral infectivity and assembly. The development of reagents with high affinity and specificity for PreS1 is of great significance for early diagnosis and treatment of HBV infection. A phage display library of dodecapeptide was screened for interactions with purified PreS1 protein. Alignment of the positive phage clones revealed a putative consensus PreS1 binding motif of HX_nHX_mHP/R. Moreover, a peptide named P7 (KHMHWHPPALNT) was highly enriched and occurred with a surprisingly high frequency of 72%. A thermodynamic study revealed that P7 has a higher binding affinity to PreS1 than the other peptides. Furthermore, P7 was able to abrogate the binding of HBV virions to the PreS1 antibody, suggesting that P7 covers key functional sites on the native PreS1 protein. This newly isolated peptide may, therefore, be a new therapeutic candidate for the treatment of HBV. The consensus motif could be modified to deliver imaging, diagnostic, and therapeutic agents to tissues affected by HBV.     

Cointegrates between bacteriophage P1 DNA and plasmid pBR322 derivatives suggest molecular mechanisms for P1-mediated transduction of small plasmids

Summary We characterized cointegrates formed in an Escherichia coli rec ^– strain between bacteriophage P1 genomes and small plasmids related to pBR322. The partners were, on the one hand, either phage P1 DNA, which carries one copy of IS1, or phage P1-15 DNA, a derivative which lacks the IS1, and, on the other hand, plasmids containing either a split IS1 or no IS1. In the presence of IS1 sequences on both partners, cointegrates were usually formed by reciprocal recombination between IS1 sequences. Cointegrates between P1 and a plasmid carrying no IS1 sequence were formed by transpositional cointegration mediated by IS1 of P1. Cointegrates between P1-15 and small plasmids containing a split IS1 were formed by one of three ways: (a) acquisition of an IS1 by P1-15 followed by reciprocal recombination between IS1 sequences, (b) transpositional cointegration mediated by the split IS1 element, Tn2657, or (c) involvement of the invertible segment carried on P1-15 DNA. Most cointegrates segregated into the small plasmids and phage P1 derivatives. A comparison of the phenomena studied and of their frequencies allowed us to conclude that cointegrate formation is a molecular mechanism involved in the transduction of plasmids smaller than those packageable into P1 virions, although it does not seem to be the only process used.     

Absence of a protein constituent and occurrence of an oversized DNA genome in a high density mutant particle of phage P22

Summary Mutants of P22 phage with abnormal density in CsCl solution (P22ndc phage) were analyzed in detail for this report. Two dimensional polyacrylamide gel electrophoresis revealed that wild-type P22ndc ⁺ phage virions contained a new protein (gpU) in addition to nine already identified proteins, while P22ndc lacked gpU. The molecular weight of gpU was essentially the same as that of gp5 (45 500), and one mature virion of phage P22ndc ¹ contained as many as 30–50 molecules of gpU. As P22ndc is a plaque-forming phage, gpU cannot be essential for the growth and assembly of P22 phage. Both genetical and biochemical analysis of the phage DNA in the virion revealed that P22ndc phage contained 2%–4% longer DNA than wild type P22ndc ⁺. A model is presented to account for the formation of P22ndc phage.     

Overexpression and incorporation of GagPol precursor does not impede packaging of HIV-1 tRNA<Superscript><Emphasis Type="Italic">Lys3</Emphasis></Superscript> but promotes intracellular budding of virus-like particles

We have recently demonstrated that alteration of the human immunodeficiency virus type 1 (HIV-1) Gag/Gag-Pol ratio in virus-producing cells reduces the infectivity of progeny viruses and hinders the formation of stable virion RNA dimers without impairing virion packaging of the viral genomic RNA. In addition, we have previously shown that the expression of GagPol mediates the selective packaging of tRNA ^Lys3 . In this study we report that overexpression of uncleaved GagPol in the virus-producing cell did not alter the packaging levels of tRNA ^Lys3 . Similarly, altering the virion-associated Gag/GagPol ratio did not affect the virion packaging of the HIV-1 envelope protein nor cyclophilin A. Thin section electron microscopy analysis of the cells overexpressing protease-defective [PR(-)] GagPol revealed immature virions but no mature virions. These immature virions were seen both extracellularly and in membrane-bound cytoplasmic vacuoles. Furthermore, an accumulation of electron-dense material was occasionally found at the plasma membrane and associated with intracytoplasmic membranous vacuoles in cells expressing excess PR(–) GagPol. No intracellular HIV was seen in the wild-type control. Density gradient analysis showed that the overall density of these mutant virions with excess PR(–) GagPol was identical to that of the wild-type HIV-1. The findings indicate that overexpression of PR(–) GagPol, in the presence of Gag synthesis, promotes intracellular budding of the mutant virions and inhibits virus maturation.     

Differences in peptide-binding specificity of two ankylosing spondylitis-associated HLA-B27 subtypes

Two HLA-B27 subtypes, B*2702 and B*2705, both associated with ankylosing spondylitis, were tested for binding affinity with a panel of polyalanine model nonapeptides carrying Arg at position 2 (P2) and a series of different amino acids at position 9 (P9). The alpha chains were isolated from BTB(B*2705), C1R/B*2702 (a B*2702 transfectant cell line) and from the NW(B*2702) cell line that has a peculiar peptide presentation behavior. Peptide binding was measured by the HLA alpha chain refolding assay. The results obtained show that: 1) Peptides with basic residues (Arg and Lys) and also aliphatic (Leu) and aromatic (Phe and Tyr) peptides at P9 have a similar high affinity in the binding to B*2705; 2) B*2702 binds well to P9 aliphatic and aromatic peptides but only very weakly to P9 basic peptides. Since both B*2702 and B*2705 are associated with AS the presumed arthritogenic peptide is hypothesized to have an aromatic or aliphatic residue at position 9. Peptides with basic residues in this position would be excluded as candidates because of their low binding affinity with B*2702.     

Endophytic microorganisms as potential growth promoters of banana

The potential of endophytic microorganisms in promoting the growth of their host plant was determined by artificially introducing five isolates (bacterial and fungal strains: UPM31F4, UPM31P1, UPM14B1, UPM13B8, UPM39B3) isolated from the roots of wild bananas into both healthy and diseased banana plantlets (Berangan cv. Intan). The response of the host plants to endophytic infection was assessed by measuring the change in four growth parameters: plant height, pseudostem diameter, root mass and total number of leaves. The endophytes tested as growth promoters were found to have a significant effect in both healthy and Fusarium-infected (diseased) plantlets. In both experimental systems, the bacterial isolate UPM39B3 (Serratia) and fungal isolate UPM31P1 (Fusarium oxysporum) showed promising growth-promoting properties. Isolate UPM39B3 (Serratia) induced the largest increases in all four growth parameters in healthy plantlets – 3.14 cm (height), 1.12 cm (pseudostem diameter), 2.12 g (root mass) and 1.12 (total number of leaves plant⁻¹) – followed by isolate UPM31P1 (Fusarium oxysporum). The beneficial effect of UPM39B3 (Serratia) and UPM31P1 (Fusarium oxysporum) was also reflected in the diseased plantlets, where pre-treatments with the isolates either singly (T6: UPM31P1; T8: UPM39B3) or in a mixture (T7: UPM31P1 + UPM39B3; T9: UPM14B1 + UPM13B8 + UPM39B3) were able to sustain the growth of plantlets, with significantly higher growth values than those in diseased plantlets that were not infected with endophytes (T10: FocR4). These results demonstrate the economic significance of these endophytic isolates, particularly UPM39B3 (Serratia) and UPM31P1 (Fusarium oxysporum), both as potential growth promoters of banana and as agents rendering tolerance towards Fusarium wilt as a strategy in the management of Fusarium wilt of banana via improved vegetative growth.     

Bioactivation of diesel exhaust particle extracts and their major nitrated polycyclic aromatic hydrocarbon components, 1-nitropyrene and dinitropyrenes, by human cytochromes P450 1A1, 1A2, and 1B1

The genotoxicities of four samples of diesel exhaust particle (DEP) extracts (DEPE) and nine nitroarenes found in DEPE were investigated after activation catalyzed by human cytochrome P450 (P450) family 1 enzymes co-expressed with NADPH-cytochrome P450 reductase (NPR) in Escherichia coli membranes. The DEPE samples induced umu gene expression in Salmonella typhimurium TA1535/pSK1002 without any P450 system and were further activated by human P450 1B1/NPR membranes. Moderate activation of the DEPE sample by P450 1A2/NPR membranes was also observed, but not by either P450 1A1/NPR or NPR membranes. 1-Nitropyrene (1-NP) was strongly activated by human P450 1B1/NPR membranes. 1,8-Dinitropyrene (1,8-DNP) was most highly activated by P450 1A1 and 1B1 systems for the three DNPs tested. In contrast, 1,3-DNP was inactivated by P450 1A1/NPR, 1A2/NPR, and 1B1/NPR systems and slightly activated by NPR membranes. 2-Nitrofluoranthene (2-NF) and 3-nitrofluoranthene (3-NF) showed activities similar to 1-NP after bioactivation by P450 1B1/NPR membranes. However, the genotoxicities of 6-nitrochrysene, 7-nitrobenz[a]anthracene, and 6-nitrobenzo[a]pyrene were all weak in the present assay system. Apparent genotoxic activities of DEPE were very low compared with standard nitroarenes in the presence of P450s, possibly because unknown component(s) of DEPE had inhibitory effects on the bioactivation of 1-NP and 1,8-DNP catalyzed by human P450 1B1. These results suggest that environmental chemicals existing in airborne DEP, in addition to 1-NP, 1,6-DNP, 1,8-DNP, 2-NF, and 3-NF, can be activated by human P450 1B1. Biological actions of air pollutants such as nitroarenes to human extrahepatic tissues may be of concern in tissues in which P450 1B1 is expressed.     

Thirteen new chromosome-7 congenic lines

Thirteen new congenic lines have been produced which have chromosome-7 segments introduced from different strains onto the C57BL/10Sn background. Sublines B10.P(61NX)C,D, and E received chromosome-7 segments from P/J, B10.CE(62NX) from CE/J, B10.SEC(64NX)A,C,E, and F from SEC/1Re, B10.SM(65NX) from SM/J, B10.WB(66NX) from WB/Re, B10.A(67NX) from A/SnGrf, B10.AKR(68NX) from AKR/SnGrf, and B10.K(69NX) from C3H.K. Isograft testing indicated that three sublines, B10.P(61NX)D, B10.CE(62NX)B, and B10.WB(66NX)B are histoisogenic, i.e., histocompatible within each line. With the exception of B10.A(67NX), B10.AK(68NX), and B10.K(69NX), which have not been isografted, the remaining sublines showed residual heterozygosity on isografting. The three histoisogenic lines have undergone F₁ testing and have been found to possess theH-4 ^a allele and new and distinct alleles at theH-1 locus. They have been designated B10.P(61NX)-H-4^a H-1 ^d , B10.WB(66NX)-H-4^a H-1 ^e , and B10.CE(62NX)-H-4^a H-1 ^f . Direct exchange of grafts has indicated the following genotypes: B10.A(67NX)-H-4^a H-1 ^b , B10.AK(68NX)-H-4^a H-1 ^b , and B10.K(69NX)-F-4^a H-1 ^b . The B10.SEC(64NX) and B10.SM(65NX) sublines have not been typed completely forH-4 andH-1. F ₁ testing or direct exchange of skin grafts indicated that B10.P(61NX)-H-4^a H-1 ^d , B10.WB(66NX)-H-4^a H-1 ^e , B10.A(67NX)-H-4^a H-1 ^b B10.AK(68NX)-H-4^a H-1 ^b and B10.K(69NX)-H-4^a H1 ^b possess nonon-H-1 histocompatibility differences from the G57BL/10 background.     

Disassembly of Tobacco Mosaic Virus by Membrane Lipid Isolated from Tobacco Leaves and Polyornithine

In vitro disassembly of tobacco mosaic virus (TMV) virions occurred in the presence of both polyornithine and a lipid fraction isolated from tobacco leaf membrane. The latter could be replaced by lecithine. Disassembly of 10 μg of TMV virions was attained in the presence of a 500-mg leaf equivalent of membrane lipid and 20 μg of polyornithine in 1 ml of 0.01 M Tris-HCl buffer, pH 7.4 at 30 C. Similarity and dissimilarity between the in vitro disassembly and the in vivo uncoating mechanisms are discussed.     

Phosphate-assisted phytoremediation of arsenic by Brassica napus and Brassica juncea: Morphological and physiological response

In this study, we examined the potential role of phosphate (P; 0, 50, 100 mg kg^?1) on growth, gas exchange attributes, and photosynthetic pigments of Brassica napus and Brassica juncea under arsenic (As) stress (0, 25, 50, 75 mg kg^?1) in a pot experiment. Results revealed that phosphate supplementation (P100) to As-stressed plants significantly increased shoot As concentration, dry biomass yield, and As uptake, in addition to the improved morphological and gas exchange attributes and photosynthetic pigments over P0. However, phosphate-assisted increase in As uptake was substantially (up to two times) greater for B. napus, notably due to higher shoot As concentration and dry biomass yield, compared to B. juncea at the P100 level. While phosphate addition in soil (P100) led to enhanced shoot As concentration in B. juncea, it reduced shoot dry biomass, primarily after 50 and 75 mg kg^?1 As treatments. The translocation factor and bioconcentration factor values of B. napus were higher than B. juncea for all As levels in the presence of phosphate. This study demonstrates that phosphate supplementation has a potential to improve As phytoextraction efficiency, predominantly for B. napus, by minimizing As-induced damage to plant growth, as well as by improving the physiological and photosynthetic attributes.     

Inhibition of gene expression of T7-related phages by prophage P1

Summary The gene expression of nine phages of the T7 group was compared after infection of Escherichia coli B(P1). With the exception of phage 13a which grew normally, all of them infected E. coli B(P1) abortively. Differences were found in the efficiency of host killing which ranged from 100% for phage 13a to 37% for phage A1122. Infection by T7 prevented colony formation by about 70% of the cells but they showed filamentous growth until about 2h after infection. It was shown by SDS-polyacrylamide gel electrophoresis and autoradiography of [³⁵S]methionine-labelled phage-coded proteins that all phages except for 13a showed measurable expression only of the early genes. No correlation was observed between killing capacity and the pattern of gene expression, and the ability to hydrolyse S-adenosyl-methionine (SAM, a cofactor for the P1 restriction endonuclease) by means of a phage-coded SAMase. Mixed infection of E. coli B(P1) with 13a and T7 yielded mixed progeny indistinguishable from that observed after mixed infection of the normal host E. coli B. Genetic crosses with amber mutants of 13a and T7 showed that the 13a marker opo ⁺ (overcomes P one), required for growth on B(P1), is located in the early region, to the left of gene 1 (RNA polymerase gene).     

Regiospecificity of Human Cytochrome P450 1A1-Mediated Oxidations: The Role of Steric Effects

Abstract

Cytochrome P450 1A1 oxidizes a diverse range of substrates, including the procarcinogenic xenobiotic benzo[a]pyrene (B[a]P) and endogenous fatty acid precursors of prostaglandins, such as arachidonic acid (AA) and eicosapentaenoic acid (EA). We have investigated the extent to which enzyme-substrate interactions govern regio- and stereoselectivity of oxidation of these compounds by using docking and molecular dynamics (MD) simulations to examine the likelihood of substrate oxidation at various sites. Due to structural differences between the substrates analyzed, B[a]P and its diols (planar, rigid), and the fatty acids AA and EA (long, flexible), different docking strategies were required. B[a]P, B[a]P-7,8-diols, (+) 7S,85- and (-) 7R,8R-diols, were docked into the active site of a homology model of P450 1A1 using an automated routine. Affinity (Accelrys, San Diego, CA). AA and EA, on the other hand, required a series of restrained MD simulations to obtain a variety of productive binding modes. All complexes were evaluated by MD-based in silico site scoring to predict product profiles based on certain geometric criteria, such as angle and distance of a given substrate atom from the ferryl oxygen. For all substrates studied, the in vitro profiles were generally reflected by the in silico scores, which suggests that steric factors play a key role in determining regiospecificity in P450 1A1-mediated oxidations. We have also shown that molecular dynamics simulations may be very useful in determination of product profiles for structurally diverse substrates of P450 enzymes.     

Comparative studies on the metabolism of linoleic acid by rumen bacteria,protozoa, and their mixture in vitro

Linoleic acid was differentially catabolized by the various rumen microbial fractions, such as rumen bacteria (B), protozoa (P), and their mixture (BP). The predominant isomer of conjugated linoleic acids (CLA) synthesized by B, P, and BP from linoleic acid was 9c11t-CLA. The formation of 9c11t-CLA was higher (P < 0.05) in P suspension (53.6 μg/mg microbial nitrogen) compared with B (38.3 μg/mg microbial nitrogen) and BP (28.8 μg/mg microbial nitrogen) suspensions by 12 h of incubation. The second most abundant CLA isomer was 10t12c. The accumulation of 10t12c-CLA in BP suspension was 2.3 times lower (P < 0.05) than that in B suspension (84.8 μg/mg microbial nitrogen) by 12 h of incubation. The accumulation of 10t-18:1 in BP suspension during 6- and 12-h incubation periods were not different (P > 0.05) than that in B suspension (6.8 and 14.0 μg/mg microbial nitrogen, respectively). However, the accumulation of 11t-18:1 in BP suspension at 6- and 12-h incubations were 2.7 and 3.3 times higher (P < 0.05), respectively, than that in B suspension. There were no significant accumulations of 11t-18:1, 10t-18:1, and 18:0 in P suspension throughout the incubation period. It was concluded that B, P, and BP metabolized linoleic acid to different isomers of CLA, whereas B, including BP, was only capable of biohydrogenating the CLA isomers to 18:0 by the reduction of 18:1 isomers. P was incapable of biohydrogenating LA, but its association with B in the BP suspension altered the biohydrogenation of LA significantly compared with B alone.     

光质和光周期对山白兰苗木生长、生理的影响

为筛选出山白兰(Michelia baillonii)苗木培育过程中适宜的光环境，该研究以一年生山白兰幼苗为试验材料，设置12、16 h·d^-1两个光周期，配合使用红蓝复合光(8R1B、6R1B)、红蓝紫绿复合光(8R1B1P1G、6R1B1P1G)4种光质和白光(W)对照，采用双因素随机区组试验设计和隶属函数法，探讨了山白兰苗木生长、光合色素、内源激素含量对不同光质和光周期处理的响应规律。结果表明：(1)光质、光周期及其交互作用对山白兰苗高增长量、叶面积、叶绿素a、玉米素(ZR)、脱落酸(ABA)的含量、内源激素比值[IAA/ABA、(IAA+GA₃+ZR)/ABA]等均有显著影响(P<0.05)。(2)16 h·d^-1光周期有利于苗高增长量、叶面积、苗木质量指数、生物量、叶绿素a、生长素(IAA)、ZR的含量、内源激素比值的提高。(3)当光周期为16 h·d^-1时，8R1B处理下的苗高增长量、叶面积和苗木质量指数均最大，分别为21.84 cm、158.39 cm²和2...