scholarly journals In the Bacillus stearothermophilus DnaB-DnaG Complex, the Activities of the Two Proteins Are Modulated by Distinct but Overlapping Networks of Residues

2006 ◽  
Vol 188 (4) ◽  
pp. 1534-1539 ◽  
Author(s):  
Jenny Thirlway ◽  
Panos Soultanas
Keyword(s):  
Size Distribution ◽  
Bacillus Stearothermophilus ◽  
The Other ◽  
Linker Region ◽  
Terminal Domain ◽  
Structural Importance ◽  
Helicase Dnab ◽  
Terminal Domains

ABSTRACTWe demonstrate the primase activity ofBacillus stearothermophilusDnaG and show that it initiates at 3′-ATC-5′ and 3′-ATT-5′ sites synthesizing primers that are 22 or 23 nucleotides long. In the presence of the helicase DnaB the size distribution of primers is different, and a range of additional smaller primers are also synthesized. Nine residues from the N- and C-terminal domains of DnaB, as well as its linker region, have been reported previously to affect this interaction. InBacillus stearothermophilusonly three residues from the linker region (I119 and I125) and the N-terminal domain (Y88) of DnaB have been shown previously to have direct structural importance, and I119 and I125 mediate DnaG-induced effects on DnaB activity. The functions of the other residues (L138, T191, E192, R195, and M196) are still a mystery. Here we show that the E15A, Y88A, and E15A Y88A mutants bind DnaG but are not able to modulate primer size, whereas the R195A M196A mutant inhibited the primase activity. Therefore, four of these residues, E15 and Y88 (N-terminal domain) and R195 and M196 (C-terminal domain), mediate DnaB-induced effects on DnaG activity. Overall, the data suggest that the effects of DnaB on DnaG activity and vice versa are mediated by distinct but overlapping networks of residues.

OBSERVATIONS ON AMYLOLYTIC BACTERIA: III. CULTURAL CONDITIONS INFLUENCING THE BREAKDOWN OF STARCH BY STENOTHERMOPHILIC BACTERIA BELONGING TO BACILLUS STEAROTHERMOPHILUS

1952 ◽  
Vol 30 (4) ◽  
pp. 360-370 ◽  
Author(s):  
Egon Stark ◽  
P. A. Tetrault
Keyword(s):  
Yeast Extract ◽  
Bacillus Stearothermophilus ◽  
Soluble Starch ◽  
The Other ◽  
Ph Changes ◽  
Proteose Peptone ◽  
Cultural Conditions ◽  
Initial Ph ◽  
Commercial Medium ◽  
Agar Media

Thirty-five cultures of Bacillus stearothermophilus hydrolyzed five starches under various cultural conditions. Hydrolysis occurred regardless of the type, brand, or batch of starch; regardless of the initial pH or of the subsequent pH changes of the medium. Starch in broth was better attacked than in agar media. Some cultures hydrolyzed 0.5%, but not 1% starch; others hydrolyzed easily 10% soluble starch. Length of incubation was important. Certain cultures never formed acid or sugar from starch. Dextrinization was a more reliable indication of starch hydrolysis than was the formation of acid or sugar. Soluble starch gave more consistent results in repeated experiments than did nonsoluble starches. The type of protein medium determines strongly the formation of amylase. Trypticase was the best commercial medium, yeast extract came second. The other 10 media yielded fewer amylolytic cultures. Yeast extract added to media enhanced amylase formation, except with trypticase. Tryptose, proteose-peptone, and neopeptone inhibited the growth of most cultures.

scholarly journals Structural insights into the interaction of helicase and primase in Mycobacterium tuberculosis

2018 ◽  
Vol 475 (21) ◽  
pp. 3493-3509 ◽  
Author(s):  
Dhakaram Pangeni Sharma ◽  
Ramachandran Vijayan ◽  
Syed Arif Abdul Rehman ◽  
Samudrala Gourinath
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Replication Initiation ◽  
Binding Studies ◽  
Functional Conservation ◽  
Terminal Domain ◽  
Binding Domains ◽  
Initiation System ◽  
Helical Hairpin ◽  
Helicase Dnab ◽  
Species Specific

The helicase–primase interaction is an essential event in DNA replication and is mediated by the highly variable C-terminal domain of primase (DnaG) and N-terminal domain of helicase (DnaB). To understand the functional conservation despite the low sequence homology of the DnaB-binding domains of DnaGs of eubacteria, we determined the crystal structure of the helicase-binding domain of DnaG from Mycobacterium tuberculosis (MtDnaG-CTD) and did so to a resolution of 1.58 Å. We observed the overall structure of MtDnaG-CTD to consist of two subdomains, the N-terminal globular region (GR) and the C-terminal helical hairpin region (HHR), connected by a small loop. Despite differences in some of its helices, the globular region was found to have broadly similar arrangements across the species, whereas the helical hairpins showed different orientations. To gain insights into the crucial helicase–primase interaction in M. tuberculosis, a complex was modeled using the MtDnaG-CTD and MtDnaB-NTD crystal structures. Two nonconserved hydrophobic residues (Ile605 and Phe615) of MtDnaG were identified as potential key residues interacting with MtDnaB. Biosensor-binding studies showed a significant decrease in the binding affinity of MtDnaB-NTD with the Ile605Ala mutant of MtDnaG-CTD compared with native MtDnaG-CTD. The loop, connecting the two helices of the HHR, was concluded to be largely responsible for the stability of the DnaB–DnaG complex. Also, MtDnaB-NTD showed micromolar affinity with DnaG-CTDs from Escherichia coli and Helicobacter pylori and unstable binding with DnaG-CTD from Vibrio cholerae. The interacting domains of both DnaG and DnaB demonstrate the species-specific evolution of the replication initiation system.

Multidetectors for Analysis of the Composition of Copolymers as a Function of Molecular Size Distribution by Steric Exclusion Chromatography

1973 ◽  
Vol 46 (2) ◽  
pp. 449-463 ◽  
Author(s):  
D. J. Harmon ◽  
V. L. Folt
Keyword(s):  
Liquid Chromatography ◽  
Size Distribution ◽  
Oil Content ◽  
Molecular Size ◽  
The Other ◽  
Additional Information ◽  
Steric Exclusion ◽  
Gel Permeation ◽  
Exclusion Chromatography ◽  
Molecular Size Distribution

Abstract Analysis of molecular size distribution of polymers by steric exclusion liquid chromatography (GPC) is well known. Problems exist, however. These problems involve copolymers and polymer blends. The objectives of the research were to develop methods of analyzing comonomer distribution in copolymers, to study the breakdown of one polymer independent of another in a polymer blend, and to obtain any additional information as might be available. The separations were performed on a Waters Model 200 Gel Permeation Chromatograph. Detectors employed were a Waters R-4 differential refractometer, a Wilks Miran-1 infrared analyzer, and a Beckman Model 144 UV photometer. Examples are given of analysis of average styrene, styrene distribution, and oil content of oil extended SBR. The data is compared with that obtained by other methods. In general the agreement is good. The ability to examine one polymer of a blend independent of the other is also demonstrated. Since elastomers are frequently used as blends, this becomes very important to such studies as milling and extrusion behavior.

Singer and the Pareto distribution: A note

2021 ◽  
pp. 239980832110423
Author(s):  
John B Parr
Keyword(s):  
Income Inequality ◽  
Size Distribution ◽  
Pareto Distribution ◽  
The Other

Singer was the first to draw attention to the fact that the Pareto Law (originally employed to describe income inequality) could also be applied to the size distribution of urban centres. His argument was illustrated with evidence from seven nations at various points in time. As part of his study, Singer attempted to demonstrate two propositions relating to the Pareto distribution of centre size. One was that the populations of larger centres could be described by the Pareto distribution, while the other was that the populations of the smaller (non-urban) centres would also conform to this distribution. It is argued that neither proposition can be regarded as valid.

Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding

2019 ◽  
Vol 167 (1) ◽  
pp. 1-14
Author(s):  
Koji Nagata ◽  
Akitoshi Okada ◽  
Jun Ohtsuka ◽  
Takatoshi Ohkuri ◽  
Yusuke Akama ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Molecular Model ◽  
Structural Basis ◽  
Terminal Domain ◽  
Helicase Dnab ◽  
Accumulation Mechanism ◽  
Interaction Domains ◽  
Α Helix ◽  
Available Information

Abstract Loading the bacterial replicative helicase DnaB onto DNA requires a specific loader protein, DnaC/DnaI, which creates the loading-competent state by opening the DnaB hexameric ring. To understand the molecular mechanism by which DnaC/DnaI opens the DnaB ring, we solved 3.1-Å co-crystal structure of the interaction domains of Escherichia coli DnaB–DnaC. The structure reveals that one N-terminal domain (NTD) of DnaC interacts with both the linker helix of a DnaB molecule and the C-terminal domain (CTD) of the adjacent DnaB molecule by forming a three α-helix bundle, which fixes the relative orientation of the two adjacent DnaB CTDs. The importance of the intermolecular interface in the crystal structure was supported by the mutational data of DnaB and DnaC. Based on the crystal structure and other available information on DnaB–DnaC structures, we constructed a molecular model of the hexameric DnaB CTDs bound by six DnaC NTDs. This model suggested that the binding of a DnaC would cause a distortion in the hexameric ring of DnaB. This distortion of the DnaB ring might accumulate by the binding of up to six DnaC molecules, resulting in the DnaB ring to open.

scholarly journals Functions of the N- and C-Terminal Domains of Human RAP74 in Transcriptional Initiation, Elongation, and Recycling of RNA Polymerase II

1998 ◽  
Vol 18 (4) ◽  
pp. 2130-2142 ◽  
Author(s):  
Lei Lei ◽  
Delin Ren ◽  
Ann Finkelstein ◽  
Zachary F. Burton
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Initiation ◽  
Pol Ii ◽  
Terminal Domain ◽  
Multiple Round ◽  
Major Late Promoter ◽  
Central Loop ◽  
Transcription Cycle ◽  
Terminal Domains

ABSTRACT Transcription factor IIF (TFIIF) cooperates with RNA polymerase II (pol II) during multiple stages of the transcription cycle including preinitiation complex assembly, initiation, elongation, and possibly termination and recycling. Human TFIIF appears to be an α2β2 heterotetramer of RNA polymerase II-associating protein 74- and 30-kDa subunits (RAP74 and RAP30). From inspection of its 517-amino-acid (aa) sequence, the RAP74 subunit appears to comprise separate N- and C-terminal domains connected by a flexible loop. In this study, we present functional data that strongly support this model for RAP74 architecture and further show that the N- and C-terminal domains and the central loop of RAP74 have distinct roles during separate phases of the transcription cycle. The N-terminal domain of RAP74 (minimally aa 1 to 172) is sufficient to deliver pol II into a complex formed on the adenovirus major late promoter with the TATA-binding protein, TFIIB, and RAP30. A more complete N-terminal domain fragment (aa 1 to 217) strongly stimulates both accurate initiation and elongation by pol II. The region of RAP74 between aa 172 and 205 and a subregion between aa 170 and 178 are critical for both accurate initiation and elongation, and mutations in these regions have similar effects on initiation and elongation. Based on these observations, RAP74 appears to have similar functions in initiation and elongation. The central region and the C-terminal domain of RAP74 do not contribute strongly to single-round accurate initiation or elongation stimulation but do stimulate multiple-round transcription in an extract system.

scholarly journals Developmentally regulated cytokeratin gene in Xenopus laevis.

1985 ◽  
Vol 5 (10) ◽  
pp. 2575-2581 ◽  
Author(s):  
J A Winkles ◽  
T D Sargent ◽  
D A Parry ◽  
E Jonas ◽  
I B Dawid
Keyword(s):  
Amino Acid ◽  
Xenopus Laevis ◽  
Intermediate Filament ◽  
Type I ◽  
Developmentally Regulated ◽  
Amino Acid Homology ◽  
Intermediate Filament Proteins ◽  
Functional Roles ◽  
Terminal Domain ◽  
Terminal Domains

We have determined the sequence of cloned cDNAs derived from a 1,665-nucleotide mRNA which transiently accumulates during Xenopus laevis embryogenesis. Computer analysis of the deduced amino acid sequence revealed that this mRNA encodes a 47-kilodalton type I intermediate filament subunit, i.e., a cytokeratin. As is common to all intermediate filament subunits so far examined, the predicted polypeptide, named XK70, contains N- and C-terminal domains flanking a central alpha-helical rod domain. The overall amino acid homology between XK70 and a human 50-kilodalton type I keratin is 47%; homology within the alpha-helical domain is 57%. The N-terminal domain, which is not completely contained in our cDNAs, is basic, contains 42% serine plus alanine, and includes five copies of a six-amino-acid repeating unit. The C-terminal domain has a high alpha-helical content and contains a region with sequence homology to the C-terminal domains of other type I and type III intermediate filament proteins. We suggest that different keratin filament subtypes may have different functional roles during amphibian oogenesis and embryogenesis.

scholarly journals Population traits of the burrowing toad Rhinella fernandezae (Gallardo, 1957) (Anura, Bufonidae)

2008 ◽  
Vol 68 (1) ◽  
pp. 137-140 ◽  
Author(s):  
LC. Sanchez ◽  
M. Busch
Keyword(s):  
Sex Ratio ◽  
Size Distribution ◽  
Total Population ◽  
Buenos Aires ◽  
The Other ◽  
Differential Mortality ◽  
Buenos Aires Province ◽  
Country House

Size distribution, sex ratio and use of burrows of the burrowing toad Rhinella fernandezae were studied in Buenos Aires province, Argentina. Two sites separated by approximately 300 m were studied: one was a road next to a swamp, and the other a garden of a country house located further from the swamp. We identified toad burrows, and individuals were sexed, measured and given an individual mark. Burrows were examined in subsequent months after the first sampling to assess the presence of toads. We found significant differences in the size distribution between areas, being the proportion of juveniles greater at the site next to the swamp where the reproduction of the species was observed. This result may suggest that the site located near to the swamp functions as a source habitat of individuals that migrate to the other site, where recruitment would be very scarce. Sex proportion of adults did not differ from 1:1 in neither the total population nor in each site, suggesting that there was not differential mortality by sex. Some toads changed burrows throughout the study period, but there were not differences in the frequency of change between adults and juveniles.

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