Synthesis of a trans-Acting Inhibitor of DNA Maturation by Prohead Mutants of Phage λ

Bacteriophage lambda with mutations in genes that control prohead assembly and other head precursors cannot mature their DNA. In this paper we present evidence that the failure of these phage mutants to mature DNA is a reflection of a mechanism that modulates terminase nicking activity during normal phage development. We have constructed plasmids that contain the lambda-cohesive end site (cos) and the genes that code for DNA terminase, the enzyme that matures DNA by cutting at cos. The DNA terminase genes are under control of a thermosensitive cI repressor. These plasmids lack most of the genes involved in prohead morphogenesis and other head precursors. However, when repression is lifted by destruction of the thermosensitive repressor, the terminase synthesized is able to cut almost 100% of the plasmids. Therefore, these plasmids can mature in the absence of proheads and other head gene products. The plasmids are also able to complement mutants of lambda deficient in terminase and DNA maturation. However, in these complementation experiments, if the phage carry mutations in prohead genes E or B, not only is phage DNA maturation blocked, but the plasmid also fails to mature. These experiments show that, in the absence of proheads, phage lambda produces a trans-acting inhibitor of maturation. The genetic determinant of this inhibitor maps in a region extending from the middle of gene B to the end of gene C. A model is proposed in which the nicking activity of DNA-bound terminase is inhibited by the trans-acting inhibitor. Prohead (and other factors) binding to this complex would release the block to allow DNA cleavage and packaging.     

Fibronectin Assembly in the Crypts of?Cytokinesis-Blocked?Multilobular Cells Promotes Anchorage-Independent Growth

Anchorage-independent growth is a characteristic feature of cancer cells. However, it is unclear whether it represents a cause or a consequence of tumorigenesis. For normal cells, integrin-mediated adhesion is required for completion of the G1 and cytokinesis stages of the cell cycle. This study identified a mechanism that can drive anchorage-independent growth if the G1 checkpoint is suppressed. Cells with defective G1 checkpoint progressed through several rounds of the cell cycle in suspension in spite of uncompleted cytokinesis, thereby forming bi- and multilobular cells. Aurora B and CEP55 were localized to midbodies between the lobes, suggesting that the cytokinesis process reached close to abscission. Integrin-mediated re-attachment of such cells induced cytokinesis completion uncoupled from karyokinesis in most cells. However, a portion of the cells instead lost the constriction and became binucleated. Also, long-term suspension culture in soft agar produced colonies where the cytokinesis block was overcome. This process was fibronectin-dependent since fibronectin-deficient cells did not form colonies unless fibronectin was expressed or exogenously added. While fibronectin normally is not deposited on non-adherent single cells, bi/multilobular cells accumulated fibronectin in the intussusceptions. Based on our data we conclude: 1) Suppression of the G1 checkpoint allows multiple rounds of the cell cycle in detached cells and thereby enables matrix formation on their surface. 2) Uncompleted cytokinesis due to cell detachment resumes if integrin interactions are re-formed, allowing colony formation in soft agar 3) Such delayed cell division can generate binucleated cells, a feature known to cause chromosomal instability.     

Can Nanotechnology Improve the Sustainability of Biobased Products?

Recent developments in nanotechnology, especially in the area of nanoclay composites, are improving the technical performance of biobased polymers and moving them toward technical and economic competitiveness with petroleum‐based polymers and conventional composites. We assess whether these developments also improve the environmental sustainability of biopolymers, by using a life cycle approach. We estimate energy use and emissions from the nanoclay production process and compare these with prior life cycle data for biopolymers as well as other fibers, and we find that nanoclay production results in lower energy use and greenhouse gas emissions than production of many common biopolymers and glass fibers. Nanoclay composites hence can improve the life cycle environmental performance of several common biopolymers. However, for some biopolymers the relative performance depends on the functional unit.     

Plate Tectonics of Virus Shell Assembly and Reorganization in Phage Φ8, a Distant Relative of Mammalian Reoviruses

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DNA Synthesis at the Site of a Red-Mediated Exchange in Phage λ

In phage lambda, progeny particles bearing unreplicated chromosomes are recombinant by action of lambda's Red system only near the right end of the chromosome. These recombinants are frequently heterozygous (heteroduplex) for markers located there. In replication-blocked crosses involving two heavy-labeled parents we find that particles in the solitary peak, containing progeny with fully conserved DNA, vary in density. Those on the heavy side of this peak are more apt to be heterozygous than are those on the light side. The data fit a model in which a double chain cut at cos, lambda's packaging origin, is followed by partial exonucleolytic degradation of lambda's r chain from the right end leftward. The exposed l chain, which thereby constitutes a 3' overhang, invades an intact, circular homologue after itself suffering some degradation. Completion of the recombinant chromosome sometimes involves DNA synthesis primed by the invading chain.     

Regioselectivity in β-Galactosidase-catalyzed Transglycosylation for the Enzymatic Assembly of D-Galactosyl-D-mannose

The regioselectivity of β-galactosidase derived from Bacillus circulans ATCC 31382 (β-1,3-galactosidase) in transgalactosylation reactions using D-mannose as an acceptor was investigated. This D-mannose associated regioselectivity was found to be different from reactions using either GlcNAc or GalNAc as acceptors, not only for β-1,3-galactosidase but also for β-galactosidases of different origins. The relative hydrolysis rate of Galβ-pNP and D-galactosyl-D-mannoses, of various linkages, was also measured in the presence of β-1,3-galactosidase and was found to correlate well with the ratio of disaccharides formed by transglycosylation. The unexpected regioselectivity using D-mannose can therefore be explained by an anomalous specificity in the hydrolysis reaction. By utilizing the identified characteristics of both regioselectivity and hydrolysis specificity using D-mannose, an efficient method for enzymatic synthesis of β-1,3-, β-1,4- and β-1,6-linked D-galactosyl-D-mannose was subsequently established.     

On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch?

Expression of a retroviral protein, Gag, in mammalian cells is sufficient for assembly of immature virus-like particles (VLPs). VLP assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We have investigated the role of SP1, a spacer between CA and NC in HIV-1 Gag, in VLP assembly. Mutational analysis showed that even subtle changes in the first 4 residues of SP1 destroy the ability of Gag to assemble correctly, frequently leading to formation of tubes or other misassembled structures rather than proper VLPs. We also studied the conformation of the CA-SP1 junction region in solution, using both molecular dynamics simulations and circular dichroism. Consonant with nuclear magnetic resonance (NMR) studies from other laboratories, we found that SP1 is nearly unstructured in aqueous solution but undergoes a concerted change to an α-helical conformation when the polarity of the environment is reduced by addition of dimethyl sulfoxide (DMSO), trifluoroethanol, or ethanol. Remarkably, such a coil-to-helix transition is also recapitulated in an aqueous medium at high peptide concentrations. The exquisite sensitivity of SP1 to mutational changes and its ability to undergo a concentration-dependent structural transition raise the possibility that SP1 could act as a molecular switch to prime HIV-1 Gag for VLP assembly. We suggest that changes in the local environment of SP1 when Gag oligomerizes on nucleic acid might trigger this switch.     

Role of cis-Acting Sites in Stimulation of the Phage λ PRM Promoter by CI-Mediated Looping

The lysogenic state of phage λ is maintained by the CI repressor. CI binds to three operators each in the right operator (O_R) and left operator (O_L) regions, which lie 2.4 kb apart. At moderate CI levels, the predominant binding pattern is two dimers of CI bound cooperatively at each regulatory region. The resulting tetramers can then interact, forming an octamer and a loop of the intervening DNA. CI is expressed from the P_RM promoter, which lies in the O_R region and is subjected to multiple regulatory controls. Of these, the most recently discovered is stimulation by loop formation. In this work, we have investigated the mechanism by which looping stimulates P_RM. We find that two cis-acting sites lying in the O_L region are involved. One site, an UP element, is required for stimulation. Based on the behavior of other promoters with UP elements located upstream of the −35 region, we suggest that a subunit of RNA polymerase (RNAP) bound at P_RM binds to the UP element located in the O_L region. In addition, adjacent to the UP element lies a binding site for integration host factor (IHF); this site plays a less critical role but is required for stimulation of the weak prm240 allele. A loop with CI at the O_L2 and O_L3 operators does not stimulate P_RM, while one with CI only at O_L2 provides some stimulation. We discuss possible mechanisms for stimulation.     

What can Dictyostelium bring to the study of Pseudomonas infections?

Bacterial infections are complex events. They are studied in a variety of simple model systems, using mammalian or non-mammalian hosts, all of which fail to reproduce fully the situation in infected patients. Each model presents a combination of conceptual, practical, and ethical advantages and disadvantages. In this review, we detail the use of Dictyostelium discoideum amoebae as a model to study Pseudomonas aeruginosa. More specifically, our aim is to explore what this additional model system can bring to our understanding of Pseudomonas infections. The study of interactions between Dictyostelium amoebae and Pseudomonas provides a view of the selection pressures exerted by environmental predators on Pseudomonas. It also represents a unique system to assess the virulence of very large numbers of Pseudomonas strains.     

Involvement of a Tryptophan Residue in the Assembly of Bacteriophages φ80 and Lambda

The assembly of infective particles of bacteriophages lambda and phi80 from heads and tails was found to be inhibited by l-tryptophan and some of its analogues, most notably tryptamine. Both the rate of assembly and the final yield of phage were inhibited. The amino acid l-phenylalanine had a slight inhibitory effect, whereas all other amino acids found in proteins were ineffective. Evidence was presented to show that the binding of heads to tails was the affected process in the assay for assembly of infective units. The plaque-forming ability of preassembled phage was not affected by these inhibitors. Results of three different types of experiments suggest that inhibition is due to interaction of inhibitors with the head substructure. The assembly reaction is highly dependent on pH, ionic strength, and the presence of detergents.     

Mutations in the N Terminus of the ?X174 DNA Pilot Protein H Confer Defects in both Assembly and Host Cell Attachment

The øX174 DNA pilot protein H forms an oligomeric DNA-translocating tube during penetration. However, monomers are incorporated into 12 pentameric assembly intermediates, which become the capsid''s icosahedral vertices. The protein''s N terminus, a predicted transmembrane helix, is not represented in the crystal structure. To investigate its functions, a series of absolute and conditional lethal mutations were generated. The absolute lethal proteins, a deletion and a triple substitution, were efficiently incorporated into virus-like particles lacking infectivity. The conditional lethal mutants, bearing cold-sensitive (cs) and temperature-sensitive (ts) point mutations, were more amenable to further analyses. Viable particles containing the mutant protein can be generated at the permissive temperature and subsequently analyzed at the restrictive temperature. The characterized cs defect directly affected host cell attachment. In contrast, ts defects were manifested during morphogenesis. Particles synthesized at permissive temperature were indistinguishable from wild-type particles in their ability to recognize host cells and deliver DNA. One mutation conferred an atypical ts synthesis phenotype. Although the mutant protein was efficiently incorporated into virus-like particles at elevated temperature, the progeny appeared to be kinetically trapped in a temperature-independent, uninfectious state. Thus, substitutions in the N terminus can lead to H protein misincorporation, albeit at wild-type levels, and subsequently affect particle function. All mutants exhibited recessive phenotypes, i.e., rescued by the presence of the wild-type H protein. Thus, mixed H protein oligomers are functional during DNA delivery. Recessive and dominant phenotypes may temporally approximate H protein functions, occurring before or after oligomerization has gone to completion.     

Directionality and Nonreciprocality of Chi-Stimulated Recombination in Phage λ

Chi's are genetic elements that stimulate generalized recombination in their locale in phage λ. All Chi's, wherever located on λ's chromosome, act asymmetrically in crosses blocked in DNA replication: (1) They stimulate exchange primarily to their left on the conventional λ map, and (2) the stimulated exchange is frequently nonreciprocal, the recombinant carrying the Chi element being produced less often than the complementary product.     

Structures of the Laccase-catalyzed Oxidation Products of Hydroxy-benzoic Acids in the Presence of ABTS [2,2′-Azino-di-(3-ethylbenzothiazoline-6-sulfonic Acid)]

Esters selected from the combination of tricycloalkanecarboxylic acids and some representative pyrethroidal alcohols were prepared, and their insecticidal activities were measured by topical application on housefly, mosquito and German cockroach. Both the exo- and endo-isomers of 2,3-trimethylenenorbornane-2-carboxylic acid exhibited a high level of activity when esterified with m-phenoxymandelonitrile. Piperonyl butoxide showed a strong synergistic effect on some of the esters. Several structural resemblances were found among these active tricyclic acids and the chrysanthemummonocarboxylic acids, which were suggested to be related to insecticidal activity.     

Maturation characteristics of Rubus pennsylvanicus fruit: are black and red the same?

Summary Fruit of the blackberry, Rubus pennsylvanicus Poir. (Rosaceae), were examined to determine variation in maturation characteristics. Maturation timing and rate varied greatly among individual fruits, resulting in a bi-colored fruiting display comprised largely of two maturation stages, pre-ripe (salmon and scarlet) and ripe (dark brown and black). While ripe fruit were generally larger and heavier than pre-ripe fruit, exhibiting greater fresh and dry fruit weight, diameter, water content, and total seed weight, no significant differences were found in energy content, i.e. numbers of calories per gram pulp, or in pulp:seed ratio. The differences between ripe and pre-ripe fruit appear to be due largely to an increase in water content and seed weight with maturity. The fact that little energetic benefit accrues to the preferential selection of ripe fruit suggests that bi-colored Rubus displays may be considered to be unicolored.