Defining cosQ, the Site Required for Termination of Bacteriophage λ DNA Packaging

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 495-506 ◽  
Author(s):  
Douglas J Wieczorek ◽  
Michael Feiss
Keyword(s):  
Insertional Mutagenesis ◽  
Dna Looping ◽  
Saturation Mutagenesis ◽  
Bacteriophage Λ ◽  
Recognition Sequence ◽  
Optimal Sequence ◽  
Bottom Strand ◽  
Double Stranded Dna ◽  
The Right ◽  
Half Site

Abstract Bacteriophage λ is a double-stranded DNA virus that processes concatemeric DNA into virion chromosomes by cutting at specific recognition sites termed cos. A cos is composed of three subsites: cosN, the nicking site; cosB, required for packaging initiation; and cosQ, required for termination of chromosome packaging. During packaging termination, nicking of the bottom strand of cosN depends on cosQ, suggesting that cosQ is needed to deliver terminase to the bottom strand of cosN to carry out nicking. In the present work, saturation mutagenesis showed that a 7-bp segment comprises cosQ. A proposal that cosQ function requires an optimal sequence match between cosQ and cosNR, the right cosN half-site, was tested by constructing double cosQ mutants; the behavior of the double mutants was inconsistent with the proposal. Substitutions in the 17-bp region between cosQ and cosN resulted in no major defects in chromosome packaging. Insertional mutagenesis indicated that proper spacing between cosQ and cosN is required. The lethality of integral helical insertions eliminated a model in which DNA looping enables cosQ to deliver a gpA protomer for nicking at cosN. The 7 bp of cosQ coincide exactly with the recognition sequence for the Escherichia coli restriction endonuclease, EcoO109I.

scholarly journals Expanding the chemical space of synthetic cyclic peptides using a promiscuous macrocyclase from prenylagaramide biosynthesis

2020 ◽  
Author(s):  
Snigdha Sarkar ◽  
Wenjia Gu ◽  
Eric W. Schmidt
Keyword(s):  
Enzymatic Synthesis ◽  
Cyclic Peptides ◽  
Chemical Space ◽  
Saturation Mutagenesis ◽  
Recognition Sequence ◽  
Drug Candidates ◽  
New Class ◽  
Dual Action ◽  
The Right

ABSTRACTCyclic peptides are excellent drug candidates, placing macrocyclization reactions at the apex of drug development. PatG and related dual-action proteases from cyanobactin biosynthesis are responsible for cleaving off the C-terminal recognition sequence and macrocyclizing the substrate to provide cyclic peptides. This reaction has found use in the enzymatic synthesis of diverse macrocycles. However, these enzymes function best on substrates that terminate with the non-proteinogenic thiazole/thiazoline residue, complicating synthetic strategies. Here, we biochemically characterize a new class of PatG-like macrocyclases that natively use proline, obviating the necessity of additional chemical or biochemical steps. We experimentally define the biochemical steps involved in synthesizing the widespread prenylagaramide-like natural products, including macrocyclization and prenylation. Using saturation mutagenesis, we show that macrocyclase PagG and prenyltransferase PagF are highly promiscuous, producing a library of more than 100 cyclic peptides and their prenylated derivatives in vitro. By comparing our results to known cyanobactin macrocyclase enzymes, we catalog a series of enzymes that collectively should synthesize most small macrocycles. Collectively, these data reveal that, by selecting the right cyanobactin macrocyclase, a large array of enzymatically synthesized macrocycles are accessible.

scholarly journals Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism

2016 ◽  
Vol 80 (1) ◽  
pp. 161-186 ◽  
Author(s):  
Peixuan Guo ◽  
Hiroyuki Noji ◽  
Christopher M. Yengo ◽  
Zhengyi Zhao ◽  
Ian Grainge
Keyword(s):  
Close Contact ◽  
Motion Mechanism ◽  
Channel Size ◽  
Left Handed ◽  
Double Stranded Dna ◽  
Directional Movement ◽  
Two Factors ◽  
Rotation Motion ◽  
The Right ◽  
Small Channels

SUMMARYThe ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including FoF1ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.

scholarly journals IMPROVEMENT OF THE OPERATING PROCEDURE OF WOOD HARVESTING AND TRANSPORTATION USING INFORMATION TECHNOLOGY

2020 ◽  
Vol 9 (4) ◽  
pp. 90-98
Author(s):  
Aleksandr Mokhirev ◽  
Marina Gerasimova ◽  
Mihail Krasil'nikov
Keyword(s):  
Operating Procedure ◽  
Minimum Cost ◽  
Maximum Flow ◽  
Dynamic Structure ◽  
Computer Application ◽  
Optimal Sequence ◽  
Wood Harvesting ◽  
Logging Industry ◽  
Different Seasons ◽  
The Right

Making the right management decisions in the logging industry is a complex multi-factorial task. The multivariance of solutions consists of various options for the application of technological chains of logging operations and timber transportation. Indeed, today the market offers a lot of options for systems of forestry machines, with or without forest storage with timber transportation at different seasons. Previous studies propose mathematical dependencies, an algorithm, and methods to solve all these problems. It makes it possible to search for the maximum flow of minimum cost in the dynamic structure of the technological process of performing work at the enterprise. They determine the conditions for solving the problem by the graph method. However, the proposed calculations for graphs with a large number of vertices and arcs connecting them are very laborious and require a lot of time. To solve this problem, the article presents the development of a computer application that performs basic calculations and calculates the optimal technological sequence of operations. The algorithms of the application, its description and principle of operation have been presented. The developed program enables to automate the process of finding the optimal sequence of technological operations in the logging enterprise operating procedure. Upon receipt of the results, it is possible to compare and analyze various process options for decision making.

scholarly journals REC-MEDIATED RECOMBINATIONAL HOT SPOT ACTIVITY IN BACTERIOPHAGE LAMBDA. I. HOT SPOT ACTIVITY ASSOCIATED WITH SPI-DELETIONS AND bio SUBSTITUTIONS

Genetics ◽  
1974 ◽  
Vol 77 (3) ◽  
pp. 409-423
Author(s):  
Kenneth D McMilin ◽  
Mary M Stahl ◽  
Franklin W Stahl
Keyword(s):  
Dna Synthesis ◽  
Genetic Marker ◽  
Density Gradient ◽  
Hot Spot ◽  
The Other ◽  
Bacteriophage Λ ◽  
Chromosomal Distribution ◽  
Recombinant Phage ◽  
Spot Activity ◽  
The Right

ABSTRACT In order to survey the distribution along the bacteriophage λ chromosome of Rec-mediated recombination events, crosses are performed using conditions which block essentially all DNA synthesis. One parent is density-labeled and carries a genetic marker in the left terminal λ gene (A), while the other parent is unlabeled and carries a genetic marker in the right terminal λ gene (R). Both parents are deleted for the λ recombination genes int and red, together with other recombination-associated genes, by virtue of either (1) a pure deletion or (2) a bio insertion-deletion. The distribution in a cesium density gradient of the resulting A+R+ recombinant phage reflects the chromosomal distribution of the recombination events which gave rise to those phage.

Gene regulation at the right operator (OR) of bacteriophage λ

1980 ◽  
Vol 139 (2) ◽  
pp. 147-161 ◽  
Author(s):  
Russell Maurer ◽  
Barbara J. Meyer ◽  
Mark Ptashne
Keyword(s):  
Gene Regulation ◽  
Bacteriophage Λ ◽  
The Right

Basis for the Right-Handed Helical Sense of Double-Stranded DNA:  Formation of the Right-Handed Helix byl-Oligonucleotides Fixed in Low-antiGlycosyl Conformation

2001 ◽  
Vol 123 (20) ◽  
pp. 4845-4846 ◽  
Author(s):  
Hidehito Urata ◽  
Hidetaka Miyagoshi ◽  
Tetsuya Kumashiro ◽  
Keiji Mori ◽  
Keiko Shoji ◽  
...  
Keyword(s):  
Double Stranded Dna ◽  
The Right

scholarly journals piggyBac-Based Insertional Mutagenesis and Enhancer Detection as a Tool for Functional Insect Genomics

Genetics ◽  
2003 ◽  
Vol 163 (2) ◽  
pp. 647-661 ◽  
Author(s):  
Carsten Horn ◽  
Nils Offen ◽  
Sverker Nystedt ◽  
Udo Häcker ◽  
Ernst A Wimmer
Keyword(s):  
Drosophila Melanogaster ◽  
Functional Genomics ◽  
Transposable Element ◽  
X Chromosome ◽  
Insertional Mutagenesis ◽  
Expression System ◽  
Saturation Mutagenesis ◽  
Noncoding Regions ◽  
Enhancer Detection ◽  
Species Specific

Abstract Transposon mutagenesis provides a fundamental tool for functional genomics. Here we present a non-species-specific, combined enhancer detection and binary expression system based on the transposable element piggyBac: For the different components of this insertional mutagenesis system, we used widely applicable transposons and distinguishable broad-range transformation markers, which should enable this system to be operational in nonmodel arthropods. In a pilot screen in Drosophila melanogaster, piggyBac mutator elements on the X chromosome were mobilized in males by a Hermes-based jumpstarter element providing piggyBac transposase activity under control of the α1-tubulin promoter. As primary reporters in the piggyBac mutator elements, we employed the heterologous transactivators GAL4Δ or tTA. To identify larval and adult enhancer detectors, strains carrying UASp-EYFP or TRE-EYFP as secondary reporter elements were used. Tissue-specific enhancer activities were readily observed in the GAL4Δ/UASp-based systems, but only rarely in the tTA/TRE system. Novel autosomal insertions were recovered with an average jumping rate of 80%. Of these novel insertions, 3.8% showed homozygous lethality, which was reversible by piggyBac excision. Insertions were found in both coding and noncoding regions of characterized genes and also in noncharacterized and non-P-targeted CG-number genes. This indicates that piggyBac will greatly facilitate the intended saturation mutagenesis in Drosophila.

Roles for λ Orf and Escherichia coli RecO, RecR and RecF in λ Recombination

Genetics ◽  
1997 ◽  
Vol 147 (2) ◽  
pp. 357-369
Author(s):  
James A Sawitzke ◽  
Franklin W Stahl
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Gene Product ◽  
Strand Break ◽  
Bacteriophage Λ ◽  
Recf Pathway ◽  
The Right ◽  
Mutant Cells ◽  
Λ Red ◽  
Red Recombination

Bacteriophage λ lacking its Red recombination functions requires either its own gene product, Orf, or the product of Escherichia coli's recO, recR and recF genes (RecORF) for efficient recombination in recBC sbcB sbcC mutant cells (the RecF pathway). Phage crosses under conditions of a partial block to DNA replication have revealed the following: (1) In the presence of Orf, RecF pathway recombination is similar to λ Red recombination; (2) Orf is necessary for focusing recombination toward the right end of the chromosome as λ is conventionally drawn; (3) RecORF-mediated RecF pathway recombination is not focused toward the right end of the chromosome, which may indicate that RecORF travels along the DNA; (4) both Orf- and RecORF-mediated RecF pathway recombination are stimulated by DNA replication; and (5) low level recombination in the simultaneous absence of Orf and RecORF may occur by a break-copy mechanism that is not initiated by a double strand break. Models for the roles of Orf and RecO, RecR and RecF in recombination are presented.

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