scholarly journals Site-specific methylation in Bacillus subtilis chemotaxis: effect of covalent modifications to the chemotaxis receptor McpB

Microbiology ◽  
2011 ◽  
Vol 157 (1) ◽  
pp. 56-65 ◽  
Author(s):  
George D. Glekas ◽  
Joseph R. Cates ◽  
Theodore M. Cohen ◽  
Christopher V. Rao ◽  
George W. Ordal
Keyword(s):  
Bacillus Subtilis ◽  
Electrostatic Interactions ◽  
Methyl Groups ◽  
Receptor Function ◽  
Site Specific ◽  
Apparent Affinity ◽  
Covalent Modifications ◽  
The One ◽  
A Site ◽  
Homology Models

The Bacillus subtilis chemotaxis pathway employs a receptor methylation system that functions differently from the one in the canonical Escherichia coli pathway. Previously, we hypothesized that B. subtilis employs a site-specific methylation system for adaptation where methyl groups are added and removed at different sites. This study investigated how covalent modifications to the adaptation region of the chemotaxis receptor McpB altered its apparent affinity for its cognate ligand, asparagine, and also its ability to activate the CheA kinase. This receptor has three closely spaced adaptation sites located at residues Gln371, Glu630 and Glu637. We found that amidation, a putative methylation mimic, of site 371 increased the receptor's apparent affinity for asparagine and its ability to activate the CheA kinase. Conversely, amidation of sites 630 and 637 reduced the receptor's ability to activate the kinase but did not affect the apparent affinity for asparagine, suggesting that activity and sensitivity are independently controlled in B. subtilis. We also examined how electrostatic interactions may underlie this behaviour, using homology models. These findings further our understanding of the site-specific methylation system in B. subtilis by demonstrating how the modification of specific sites can have varying effects on receptor function.

Uteroplacental insufficiency induces site-specific changes in histone H3 covalent modifications and affects DNA-histone H3 positioning in day 0 IUGR rat liver

2004 ◽  
Vol 20 (1) ◽  
pp. 108-116 ◽  
Author(s):  
Qi Fu ◽  
Robert A. McKnight ◽  
Xing Yu ◽  
Laiyi Wang ◽  
Christopher W. Callaway ◽  
...  
Keyword(s):  
Histone H3 ◽  
Site Specific ◽  
Promoter Sequences ◽  
Histone Deacetylase 1 ◽  
Protein Levels ◽  
Ppar Γ ◽  
Covalent Modifications ◽  
A Site ◽  
H3 Acetylation ◽  
Carnitine Palmitoyl Transferase I

Uteroplacental insufficiency and subsequent intrauterine growth retardation (IUGR) increase the risk of adult onset insulin resistance and dyslipidemia in humans and rats. IUGR rats are further characterized by postnatal alterations in hepatic PPAR-γ coactivator (PGC-1) and carnitine-palmitoyl-transferase I (CPTI) expression, as well as overall hyperacetylation of histone H3. However, it is unknown whether the histone H3 hyperacetylation is site specific or relates to the changes in gene expression previously described in IUGR rats. We therefore hypothesized that uteroplacental insufficiency causes site-specific modifications in hepatic H3 acetylation and affects the association of acetylated histone H3 with PGC-1 and CPTI promoter sequences. Uteroplacental insufficiency was used to produce asymmetrical IUGR rats. IUGR significantly increased acetylation of H3 lysine-9 (H3/K9), lysine-14 (H3/K14), and lysine-18 (H3/K18) at day 0 of life, and these changes occurred in association with decreased nuclear protein levels of histone deacetylase 1 (HDAC1) and HDAC activity. Chromatin immunoprecipitation using acetyl-H3/K9 antibody and day 0 chromatin revealed that uteroplacental insufficiency affected the association between acetylated H3/K9 and the promoters of PGC-1 and CPTI, respectively, in IUGR liver. At day 21 of life, the neonatal pattern of H3 hyperacetylation persisted only in the IUGR males. We conclude that uteroplacental insufficiency increases H3 acetylation in a site-specific manner in IUGR liver and that these changes persist in male IUGR animals. The altered association of the PGC-1 and CPTI promoters with acetylated H3/K9 correlates with previous reports of IUGR altering the expression of these genes. We speculate that in utero alterations of chromatin structure contribute to fetal programming.

Topologies of practice

2011 ◽  
Vol 1 (3) ◽  
pp. 308-311 ◽  
Author(s):  
Mat Coleman
Keyword(s):  
Topological Space ◽  
Human Geography ◽  
The Other ◽  
Site Specific ◽  
Other Hand ◽  
The Difference ◽  
The One ◽  
A Site

Allen’s (2011) provocative argument on the difference between topographic and topologic ontologies in human geography offers human geographers an important opportunity to re-engage with other similarly spirited arguments about the limitations of the topographic. For example, debate over Marston et al.’s (2005) argument for a ‘site ontology’ has tended to sidestep the question of topological space and has instead dwelled on whether or not their representation of human geography research on scale is accurate. However, if Allen’s research gives human geographers another opportunity to take up the question of sociospatial practice as contingent, site-specific, and self-structuring, it also poses at least two problems. On the one hand, Allen characterizes the topographic and topologic according to a too neat calendar of sociospatial relations. On the other hand, Allen overlooks a long-standing appreciation for the topologic in human geography by drawing a strong distinction between past and newer intellectual approaches to power and space.

scholarly journals Identification and Characterization of thedif Site from Bacillus subtilis

2001 ◽  
Vol 183 (3) ◽  
pp. 1058-1068 ◽  
Author(s):  
Stephen A. Sciochetti ◽  
Patrick J. Piggot ◽  
Garry W. Blakely
Keyword(s):  
Bacillus Subtilis ◽  
Site Specific ◽  
In Vivo Recombination ◽  
Chromosome Partitioning ◽  
Septal Localization ◽  
A Site ◽  
Recombination Reactions ◽  
Circular Chromosomes

ABSTRACT Bacteria with circular chromosomes have evolved systems that ensure multimeric chromosomes, formed by homologous recombination between sister chromosomes during DNA replication, are resolved to monomers prior to cell division. The chromosome dimer resolution process inEscherichia coli is mediated by two tyrosine family site-specific recombinases, XerC and XerD, and requires septal localization of the division protein FtsK. The Xer recombinases act near the terminus of chromosome replication at a site known asdif (Ecdif). In Bacillus subtilisthe RipX and CodV site-specific recombinases have been implicated in an analogous reaction. We present here genetic and biochemical evidence that a 28-bp sequence of DNA (Bsdif), lying 6° counterclockwise from the B. subtilis terminus of replication (172°), is the site at which RipX and CodV catalyze site-specific recombination reactions required for normal chromosome partitioning. Bsdif in vivo recombination did not require the B. subtilis FtsK homologues, SpoIIIE and YtpT. We also show that the presence or absence of the B. subtilisSPβ-bacteriophage, and in particular its yopP gene product, appears to strongly modulate the extent of the partitioning defects seen in codV strains and, to a lesser extent, those seen in ripX and dif strains.

scholarly journals UNDERSTANDING THE PHYSICS OF KAPPA (Κ0): INSIGHTS FROM THE EUROSEISTEST NETWORK

2017 ◽  
Vol 50 (3) ◽  
pp. 1515
Author(s):  
O.J. Ktenidou ◽  
N. Abrahamson ◽  
S. Drouet ◽  
F. Cotton
Keyword(s):  
Material Properties ◽  
High Frequency ◽  
Hard Rock ◽  
Small Scale ◽  
Site Conditions ◽  
Site Specific ◽  
The One ◽  
Site Characterisation ◽  
A Site ◽  
Scale Profile

this study we estimate the spectral decay factor κ0 for the EUROSEISTEST array. Site conditions range from soft sediments to hard rock over 14 surface and 6 downhole accelerographs. First, we separate local and regional high frequency attenuation and measure κ0. Second, we use the existing knowledge of the geological profile and material properties to correlate κ0 with different site characterisation parameters (Vs30, resonant frequency, depth-to-bedrock). Third, we use our results to improve our physical understanding of κ0. We propose a conceptual model comprising two new notions. On the one hand, we observe that κ0 stabilises for high Vs values; this may indicate the existence of regional values for hard rock κ0. If so, we propose that borehole measurements may be useful in determining them. On the other hand, we find that material damping may not suffice to account for the total measured attenuation. We propose that, apart from damping, additional site attenuation may be caused by scattering from small-scale profile variability. If this is so, then geotechnical damping measurements may not suffice to infer overall crustal attenuation under a site; but starting with a regional (borehole) value and adding damping, we might define a lower bound for site-specific κ0.

scholarly journals Site-specific analysis of N-glycans from different sheep prion strains

2021 ◽  
Vol 17 (2) ◽  
pp. e1009232
Author(s):  
Natali Nakić ◽  
Thanh Hoa Tran ◽  
Mislav Novokmet ◽  
Olivier Andreoletti ◽  
Gordan Lauc ◽  
...  
Keyword(s):  
Prion Protein ◽  
Prion Diseases ◽  
Mammalian Species ◽  
Site Specific ◽  
Prion Strains ◽  
Glycosylation Sites ◽  
Specific Analysis ◽  
Wide Range ◽  
The One ◽  
A Site

Prion diseases are a group of neurodegenerative diseases affecting a wide range of mammalian species, including humans. During the course of the disease, the abnormally folded scrapie prion protein (PrPSc) accumulates in the central nervous system where it causes neurodegeneration. In prion disorders, the diverse spectrum of illnesses exists because of the presence of different isoforms of PrPSc where they occupy distinct conformational states called strains. Strains are biochemically distinguished by a characteristic three-band immunoblot pattern, defined by differences in the occupancy of two glycosylation sites on the prion protein (PrP). Characterization of the exact N-glycan structures attached on either PrPC or PrPSc is lacking. Here we report the characterization and comparison of N-glycans from two different sheep prion strains. PrPSc from both strains was isolated from brain tissue and enzymatically digested with trypsin. By using liquid chromatography coupled to electrospray mass spectrometry, a site-specific analysis was performed. A total of 100 structures were detected on both glycosylation sites. The N-glycan profile was shown to be similar to the one on mouse PrP, however, with additional 40 structures reported. The results presented here show no major differences in glycan composition, suggesting that glycans may not be responsible for the differences in the two analyzed prion strains.

scholarly journals The ripX Locus of Bacillus subtilis Encodes a Site-Specific Recombinase Involved in Proper Chromosome Partitioning

1999 ◽  
Vol 181 (19) ◽  
pp. 6053-6062 ◽  
Author(s):  
Stephen A. Sciochetti ◽  
Patrick J. Piggot ◽  
David J. Sherratt ◽  
Garry Blakely
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Holliday Junction ◽  
Independent Manner ◽  
Site Specific ◽  
E Coli ◽  
Chromosome Partitioning ◽  
A Site

ABSTRACT The Bacillus subtilis ripX gene encodes a protein that has 37 and 44% identity with the XerC and XerD site-specific recombinases of Escherichia coli. XerC and XerD are hypothesized to act in concert at the dif site to resolve dimeric chromosomes formed by recombination during replication. Cultures of ripX mutants contained a subpopulation of unequal-size cells held together in long chains. The chains included anucleate cells and cells with aberrantly dense or diffuse nucleoids, indicating a chromosome partitioning failure. This result is consistent with RipX having a role in the resolution of chromosome dimers inB. subtilis. Spores contain a single uninitiated chromosome, and analysis of germinated, outgrowing spores showed that the placement of FtsZ rings and septa is affected in ripXstrains by the first division after the initiation of germination. The introduction of a recA mutation into ripXstrains resulted in only slight modifications of the ripXphenotype, suggesting that chromosome dimers can form in a RecA-independent manner in B. subtilis. In addition to RipX, the CodV protein of B. subtilis shows extensive similarity to XerC and XerD. The RipX and CodV proteins were shown to bind in vitro to DNA containing the E. coli dif site. Together they functioned efficiently in vitro to catalyze site-specific cleavage of an artificial Holliday junction containing adif site. Inactivation of codV alone did not cause a discernible change in phenotype, and it is speculated that RipX can substitute for CodV in vivo.

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