Functional Partition of a Bacterial Chromosome Through the Interplay of Nucleoid Associated Proteins and Condensin

2018 ◽  
Author(s):  
Virginia S. Lioy ◽  
Axel Cournac ◽  
Martial Marbouty ◽  
Sttphane Duigou ◽  
Julien Mozziconacci ◽  
...  
Keyword(s):  
Bacterial Chromosome ◽  
Associated Proteins

scholarly journals Mutation and Recombination Rates Vary Across Bacterial Chromosome

2019 ◽  
Vol 8 (1) ◽  
pp. 25 ◽  
Author(s):  
Maia Kivisaar
Keyword(s):  
Regional Differences ◽  
Bacterial Chromosome ◽  
Chromosomal Dna ◽  
Recombination Rates ◽  
Recombination Processes ◽  
Growing Body ◽  
Associated Proteins ◽  
Foreign Dna ◽  
Nucleoid Structure

Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure which is established by binding of the nucleoid-associated proteins (NAPs) and other proteins. This review gives an overview of recent findings indicating that the mutagenic and recombination processes in bacteria vary at different chromosomal positions. Involvement of NAPs and other possible mechanisms in these regional differences are discussed. Variations in mutation and recombination rates across the bacterial chromosome may have implications in the evolution of bacteria.

scholarly journals DNA–RNA interactions are critical for chromosome condensation inEscherichia coli

2017 ◽  
Vol 114 (46) ◽  
pp. 12225-12230 ◽  
Author(s):  
Zhong Qian ◽  
Victor B. Zhurkin ◽  
Sankar Adhya
Keyword(s):  
Molecular Mechanism ◽  
Gene Transcription ◽  
Noncoding Rna ◽  
Chromosome Structure ◽  
Chromosome Condensation ◽  
Dna Condensation ◽  
Bacterial Chromosome ◽  
Condensation Process ◽  
Inescherichia Coli ◽  
Associated Proteins

Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding RNA, naRNA4. Here we investigated the molecular mechanism of how naRNA4 and the major NAP, HU, acting together organize the chromosome structure by establishing multiple DNA–DNA contacts (DNA condensation). We demonstrate that naRNA4 uniquely acts by forming complexes that may not involve long stretches of DNA–RNA hybrid. Also, uncommonly, HU, a chromosome-associated protein that is essential in the DNA–RNA interactions, is not present in the final complex. Thus, HU plays a catalytic (chaperone) role in the naRNA4-mediated DNA condensation process.

scholarly journals Nucleoid associated proteins and their effect on E. coli chromosome

2020 ◽  
Author(s):  
Ankit Gupta ◽  
Abdul Wasim ◽  
Jagannath Mondal
Keyword(s):  
Long Range ◽  
Short Range ◽  
Computational Method ◽  
Bacterial Chromosome ◽  
Chromosome Organization ◽  
E Coli ◽  
Complex Interactions ◽  
Long Range Interactions ◽  
Associated Proteins ◽  
Mutant Cells

AbstractA seemingly random and disorganized bacterial chromosome, in reality, is a well organized nucleus-like structure, called the nucleoid, which is maintained by several nucleoid associated proteins(NAPs). Here we present an application of a previously developed Hi-C based computational method to study the effects of some of these proteins on the E. coli chromosome. Simulations with encoded Hi-C data for mutant, hupAB deficient, E. coli cells, revealed a decondensed, axially expanded chromosome with enhanced short range and diminished long range interactions. Simulations for mutant cells deficient in FIS protein revealed that the effects are similar to that of the hupAB mutant, but the absence of FIS led to a greater disruption in chromosome organization. Absence of another NAP, MatP, known to mediate Ter macrodomain isolation, led to enhanced contacts between Ter and its flanking macrodomains but lacked any change in matS sites’ localization. Deficiency of MukBEF, the only SMC complex present in E. coli, led to disorganization of macrodomains. Upon further analysis, it was observed that the above mutations do not significantly impact the local chromosome organization (~ 100 Kb) but only affect the chromosome on a larger scale (>100 Kb). These observations shed more light on the sparsely explored effects of NAPs on the overall chromosome organization and helps us understand the myriad complex interactions NAPs have with the chromosome.

scholarly journals DNA sequence-directed cooperation between nucleoid-associated proteins

2020 ◽  
Author(s):  
Aleksandre Japaridze ◽  
Wayne Yang ◽  
Cees Dekker ◽  
William Nasser ◽  
Georgi Muskhelishvili
Keyword(s):  
Dna Sequence ◽  
Binding Sites ◽  
Growth Cycle ◽  
Higher Order ◽  
Bacterial Chromosome ◽  
Protein Binding Sites ◽  
Force Microscopy ◽  
Atomic Force ◽  
Associated Proteins ◽  
Nucleoprotein Complexes

AbstractNucleoid associated proteins (NAPs) are a class of highly abundant DNA binding proteins in bacteria and archaea. While the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding to the bacterial chromosome and stabilising higher-order nucleoprotein complexes. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding-site arrangements. We find that spatial organisation of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction, as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiations within the bacterial chromosome.

Photoreceptor disk membrane substructures by means of the complementary freeze-fracture-replica methods

1978 ◽  
Vol 36 (2) ◽  
pp. 156-157
Author(s):  
A. Tonosaki ◽  
M. Yamasaki ◽  
H. Washioka ◽  
J. Mizoguchi
Keyword(s):  
Cell Membranes ◽  
Freeze Fracture ◽  
Purple Membrane ◽  
Remarkable Case ◽  
Single Face ◽  
Disk Membrane ◽  
Associated Proteins ◽  
Photoreceptor Membranes

A vertebrate disk membrane is composed of 40 % lipids and 60 % proteins. Its fracture faces have been classed into the plasmic (PF) and exoplasmic faces (EF), complementary with each other, like those of most other types of cell membranes. The hypothesis assuming the PF particles as representing membrane-associated proteins has been challenged by serious questions if they in fact emerge from the crystalline formation or decoration effects during freezing and shadowing processes. This problem seems to be yet unanswered, despite the remarkable case of the purple membrane of Halobacterium, partly because most observations have been made on the replicas from a single face of specimen, and partly because, in the case of photoreceptor membranes, the conformation of a rhodopsin and its relatives remains yet uncertain. The former defect seems to be partially fulfilled with complementary replica methods.

Characterization of microtubules by dark-field STEM and replication

1991 ◽  
Vol 49 ◽  
pp. 152-153
Author(s):  
S.B. Andrews ◽  
R.D. Leapman ◽  
P.E. Gallant ◽  
T.S. Reese
Keyword(s):  
Protein Interactions ◽  
Low Dose ◽  
Unit Length ◽  
Dark Field ◽  
Carbon Films ◽  
Microtubule Associated Proteins ◽  
Molecular Weights ◽  
Freeze Dried ◽  
Protein Motors ◽  
Associated Proteins

As part of a study on protein interactions involved in microtubule (MT)-based transport, we used the VG HB501 field-emission STEM to obtain low-dose dark-field mass maps of isolated, taxol-stabilized MTs and correlated these micrographs with detailed stereo images from replicas of the same MTs. This approach promises to be useful for determining how protein motors interact with MTs. MTs prepared from bovine and squid brain tubulin were purified and free from microtubule-associated proteins (MAPs). These MTs (0.1-1 mg/ml tubulin) were adsorbed to 3-nm evaporated carbon films supported over Formvar nets on 600-m copper grids. Following adsorption, the grids were washed twice in buffer and then in either distilled water or in isotonic or hypotonic ammonium acetate, blotted, and plunge-frozen in ethane/propane cryogen (ca. -185 C). After cryotransfer into the STEM, specimens were freeze-dried and recooled to ca.-160 C for low-dose (<3000 e/nm2) dark-field mapping. The molecular weights per unit length of MT were determined relative to tobacco mosaic virus standards from elastic scattering intensities. Parallel grids were freeze-dried and rotary shadowed with Pt/C at 14°.

Filaments and membranes in the mitotic apparatus

1983 ◽  
Vol 41 ◽  
pp. 544-547
Author(s):  
Kent McDonald
Keyword(s):  
Intermediate Filaments ◽  
Mitotic Spindle ◽  
Mitotic Apparatus ◽  
Light Microscope Level ◽  
Microtubule Associated Proteins ◽  
Recent Developments ◽  
Associated Proteins ◽  
Force Generator ◽  
Spindle Function ◽  
Antibody Technology

At the light microscope level the recent developments and interest in antibody technology have permitted the localization of certain non-microtubule proteins within the mitotic spindle, e.g., calmodulin, actin, intermediate filaments, protein kinases and various microtubule associated proteins. Also, the use of fluorescent probes like chlorotetracycline suggest the presence of membranes in the spindle. Localization of non-microtubule structures in the spindle at the EM level has been less rewarding. Some mitosis researchers, e.g., Rarer, have maintained that actin is involved in mitosis movements though the bulk of evidence argues against this interpretation. Others suggest that a microtrabecular network such as found in chromatophore granule movement might be a possible force generator but there is little evidence for or against this view. At the level of regulation of spindle function, Harris and more recently Hepler have argued for the importance of studying spindle membranes. Hepler also believes that membranes might play a structural or mechanical role in moving chromosomes.

Analysis of the Mechanism of Microtubule Dynamic Instability Using a UV Microbeam to Sever Elongating Microtubules

1988 ◽  
Vol 46 ◽  
pp. 122-123
Author(s):  
R.A Walker ◽  
S. Inoue ◽  
E.D. Salmon
Keyword(s):  
Dynamic Instability ◽  
Microtubule Dynamic ◽  
Gtp Hydrolysis ◽  
Abrupt Transition ◽  
Microtubule Associated Proteins ◽  
Asymmetrical Structure ◽  
Associated Proteins

Microtubules polymerized in vitro from tubulin purified free of microtubule-associated proteins exhibit dynamic instability (1,2,3). Free microtubule ends exist in persistent phases of elongation or rapid shortening with infrequent, but, abrupt transitions between these phases. The abrupt transition from elongation to rapid shortening is termed catastrophe and the abrupt transition from rapid shortening to elongation is termed rescue. A microtubule is an asymmetrical structure. The plus end grows faster than the minus end. The frequency of catastrophe of the plus end is somewhat greater than the minus end, while the frequency of rescue of the plus end in much lower than for the minus end (4).The mechanism of catastrophe is controversial, but for both the plus and minus microtubule ends, catastrophe is thought to be dependent on GTP hydrolysis. Microtubule elongation occurs by the association of tubulin-GTP subunits to the growing end. Sometime after incorporation into an elongating microtubule end, the GTP is hydrolyzed to GDP, yielding a core of tubulin-GDP capped by tubulin-GTP (“GTP-cap”).

Alzheimer's Paired Helical Filaments Contain Insoluble Cytoskeletal Elements

1985 ◽  
Vol 43 ◽  
pp. 748-751
Author(s):  
P. Gambetti ◽  
G. Perry ◽  
L. Autillo-Gambetti
Keyword(s):  
Paired Helical Filaments ◽  
Microscope Level ◽  
Antigenic Determinants ◽  
Light Microscope Level ◽  
Neuronal Cytoskeleton ◽  
Ionic Detergent ◽  
Associated Proteins ◽  
Pathologic Lesions ◽  
10 Nm Filaments ◽  
Cytoskeletal Elements

Neurofibrillary tangles (NFT) are one of the major pathologic lesions of Alzheimer's disease. These neuronal inclusions are predominantly composed of paired helical filaments (PHF), which consist of two 10 nm filaments winding around each other with an approximately 80 nm periodicity. Besides PHF, NFT comprise also 15 nm filaments, 10 nm filaments which are probably neurofilaments, microtubules and granular material. At variance with the neuronal cytoskeleton, PHF are insoluble in ionic detergent.Studies at the light microscope level have shown that NFT have unique antigenic determinants as well as determinants in common with elements of the normal neuronal cytoskeleton such as neurofilaments and microtubule-associated proteins. The present study uses immunocytochemistry and cytochemistry at the electron microscope level to assess which NFT component contains these determinants and whether these antigenic determinants are soluble in an ionic detergent.

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