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.

Nucleoid-associated proteins in Crenarchaea

2011 ◽  
Vol 39 (1) ◽  
pp. 116-121 ◽  
Author(s):  
Rosalie P.C. Driessen ◽  
Remus Th. Dame
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structural Effect ◽  
Chromatin Organization ◽  
Large Set ◽  
Chromosomal Dna ◽  
Amino Acid Sequence Level ◽  
Generic Level ◽  
Architectural Proteins ◽  
Associated Proteins

Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.

scholarly journals Microtubule Retrograde Motors and Their Role in Retroviral Transport

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 483
Author(s):  
Gianfranco Pietrantoni ◽  
Rodrigo Ibarra-Karmy ◽  
Gloria Arriagada
Keyword(s):  
Host Cell ◽  
Reverse Transcription ◽  
Eukaryotic Cell ◽  
Chromosomal Dna ◽  
Viral Dna ◽  
Preintegration Complex ◽  
Retrograde Trafficking ◽  
Microtubule Associated Proteins ◽  
Associated Proteins ◽  
Crowded Environment

Following entry into the host cell, retroviruses generate a dsDNA copy of their genomes via reverse transcription, and this viral DNA is subsequently integrated into the chromosomal DNA of the host cell. Before integration can occur, however, retroviral DNA must be transported to the nucleus as part of a ‘preintegration complex’ (PIC). Transporting the PIC through the crowded environment of the cytoplasm is challenging, and retroviruses have evolved different mechanisms to accomplish this feat. Within a eukaryotic cell, microtubules act as the roads, while the microtubule-associated proteins dynein and kinesin are the vehicles that viruses exploit to achieve retrograde and anterograde trafficking. This review will examine the various mechanisms retroviruses have evolved in order to achieve retrograde trafficking, confirming that each retrovirus has its own strategy to functionally subvert microtubule associated proteins.

scholarly journals HU multimerization shift controls nucleoid compaction

2016 ◽  
Vol 2 (7) ◽  
pp. e1600650 ◽  
Author(s):  
Michal Hammel ◽  
Dhar Amlanjyoti ◽  
Francis E. Reyes ◽  
Jian-Hua Chen ◽  
Rochelle Parpana ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Molecular Mechanisms ◽  
Bacterial Chromosome ◽  
Binding Modes ◽  
Dna Complexes ◽  
X Ray ◽  
X Ray Scattering ◽  
Nucleoid Structure ◽  
Ray Scattering

Molecular mechanisms controlling functional bacterial chromosome (nucleoid) compaction and organization are surprisingly enigmatic but partly depend on conserved, histone-like proteins HUαα and HUαβ and their interactions that span the nanoscale and mesoscale from protein-DNA complexes to the bacterial chromosome and nucleoid structure. We determined the crystal structures of these chromosome-associated proteins in complex with native duplex DNA. Distinct DNA binding modes of HUαα and HUαβ elucidate fundamental features of bacterial chromosome packing that regulate gene transcription. By combining crystal structures with solution x-ray scattering results, we determined architectures of HU-DNA nucleoproteins in solution under near-physiological conditions. These macromolecular conformations and interactions result in contraction at the cellular level based on in vivo imaging of native unlabeled nucleoid by soft x-ray tomography upon HUβ and ectopic HUα38 expression. Structural characterization of charge-altered HUαα-DNA complexes reveals an HU molecular switch that is suitable for condensing nucleoid and reprogramming noninvasiveEscherichia coliinto an invasive form. Collective findings suggest that shifts between networking and cooperative and noncooperative DNA-dependent HU multimerization control DNA compaction and supercoiling independently of cellular topoisomerase activity. By integrating x-ray crystal structures, x-ray scattering, mutational tests, and x-ray imaging that span from protein-DNA complexes to the bacterial chromosome and nucleoid structure, we show that defined dynamic HU interaction networks can promote nucleoid reorganization and transcriptional regulation as efficient general microbial mechanisms to help synchronize genetic responses to cell cycle, changing environments, and pathogenesis.

scholarly journals Replacement of the Bacteriophage Mu Strong Gyrase Site and Effect on Mu DNA Replication

1999 ◽  
Vol 181 (18) ◽  
pp. 5783-5789 ◽  
Author(s):  
M. L. Pato ◽  
M. Banerjee
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Bacteriophage Mu ◽  
Chromosomal Dna ◽  
E Coli ◽  
Repeat Sequences ◽  
Central Fragment ◽  
Entire Chromosome ◽  
Nucleoid Structure ◽  
Replicative Transposition

ABSTRACT The bacteriophage Mu strong gyrase site (SGS) is required for efficient replicative transposition and functions by promoting the synapsis of prophage termini. To look for other sites which could substitute for the SGS in promoting Mu replication, we have replaced the SGS in the middle of the Mu genome with fragments of DNA from various sources. A central fragment from the transposing virus D108 allowed efficient Mu replication and was shown to contain a strong gyrase site. However, neither the strong gyrase site from the plasmid pSC101 nor the major gyrase site from pBR322 could promote efficient Mu replication, even though the pSC101 site is a stronger gyrase site than the Mu SGS as assayed by cleavage in the presence of gyrase and the quinolone enoxacin. To look for SGS-like sites in the Escherichia coli chromosome which might be involved in organizing nucleoid structure, fragments of E. coli chromosomal DNA were substituted for the SGS: first, repeat sequences associated with gyrase binding (bacterial interspersed mosaic elements), and, second, random fragments of the entire chromosome. No fragments were found that could replace the SGS in promoting efficient Mu replication. These results demonstrate that the gyrase sites from the transposing phages possess unusual properties and emphasize the need to determine the basis of these properties.

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 Biochemical and immunological analyses of cytoskeletal domains of neurons.

1986 ◽  
Vol 102 (1) ◽  
pp. 252-262 ◽  
Author(s):  
I Peng ◽  
L I Binder ◽  
M M Black
Keyword(s):  
Regional Differences ◽  
Sympathetic Neurons ◽  
Distribution Patterns ◽  
Sympathetic Ganglia ◽  
Microtubule Associated Proteins ◽  
Explant Cultures ◽  
Associated Proteins ◽  
Morphological Differences ◽  
Cultured Sympathetic Neurons

We have used cultured sympathetic neurons to identify microtubule proteins (tubulin and microtubule-associated proteins [MAPs]) and neurofilament (NF) proteins in pure preparations of axons and also to examine the distribution of these proteins between axons and cell bodies + dendrites. Pieces of sympathetic ganglia containing thousands of neurons were plated onto culture dishes and allowed to extend neurites. Dendrites remained confined to the ganglionic explant or cell body mass (CBM), while axons extended away from the CBM for several millimeters. Axons were separated from cell bodies and dendrites by dissecting the CBM away from cultures, and the resulting axonal and CBM preparations were analyzed using biochemical, immunoblotting, and immunoprecipitation methods. Cultures were used after 17 d in vitro, when 40-60% of total protein was in the axons. The 68,000-mol-wt NF subunit is present in both axons and CBM in roughly equal amounts. The 145,000- and 200,000-mol-wt NF subunits each consist of several variants which differ in phosphorylation state; poorly and nonphosphorylated species are present only in the CBM, whereas more heavily phosphorylated forms are present in axons and, to a lesser extent, the CBM. One 145,000-mol-wt NF variant was axon specific. Tubulin is roughly equally distributed between CBM and axon-like neurites of explant cultures. MAP-1a, MAP-1b, MAP-3, and the 60,000-mol-wt MAP are also present in the CBM and axon-like neurites and show distribution patterns similar to that of tubulin. In contrast, MAP-2 was detected only in the CBM, while tau and the 210,000-mol-wt MAP were greatly enriched in axons compared to the CBM. In immunostaining analyses, MAP-2 localized to cell bodies and dendrite-like neurites, but not to axon-like neurites, whereas antibodies to tubulin and MAP-1b localized to all regions of the neurons. The regional differences in composition of the neuronal cytoskeleton presumably generate corresponding differences in its structure, which may, in turn, contribute to the morphological differences between axons and dendrites.

scholarly journals The R1162 Mob Proteins Can Promote Conjugative Transfer from Cryptic Origins in the Bacterial Chromosome

2008 ◽  
Vol 191 (5) ◽  
pp. 1574-1580 ◽  
Author(s):  
Richard Meyer
Keyword(s):  
Escherichia Coli ◽  
Host Range ◽  
Active Site ◽  
Bacterial Chromosome ◽  
Broad Host Range ◽  
Conjugative Transfer ◽  
Chromosomal Dna ◽  
Bacterial Dna ◽  
Pectobacterium Atrosepticum ◽  
Broad Host Range Plasmid

ABSTRACT The mobilization proteins of the broad-host-range plasmid R1162 can initiate conjugative transfer of a plasmid from a 19-bp locus that is partially degenerate in sequence. Such loci are likely to appear by chance in the bacterial chromosome and could act as cryptic sites for transfer of chromosomal DNA when R1162 is present. The R1162-dependent transfer of chromosomal DNA, initiated from one such potential site in Pectobacterium atrosepticum, is shown here. A second active site was identified in Escherichia coli, where it is also shown that large amounts of DNA are transferred. This transfer probably reflects the combined activity of the multiple cryptic origins in the chromosome. Transfer of chromosomal DNA due to the presence of a plasmid in the cytoplasm describes a previously unrecognized potential for the exchange of bacterial DNA.

scholarly journals Suppression of telomere capping defects of Saccharomyces cerevisiae yku70 and yku80 mutants by telomerase

2021 ◽  
Author(s):  
Cory L Holland ◽  
Brian A Sanderson ◽  
James K Titus ◽  
Monica F Weis ◽  
Angelica M Riojas ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Double Strand Breaks ◽  
Temperature Sensitive ◽  
Chromosomal Dna ◽  
Strand Breaks ◽  
Growth Defects ◽  
Structural Reinforcement ◽  
Associated Proteins ◽  
Telomere Capping ◽  
Dna Ends

Abstract The Ku complex performs multiple functions inside eukaryotic cells, including protection of chromosomal DNA ends from degradation and fusion events, recruitment of telomerase, and repair of double-strand breaks (DSBs). Inactivation of Ku complex genes YKU70 or YKU80 in cells of the yeast S. cerevisiae gives rise to mutants that exhibit shortened telomeres and temperature-sensitive growth. In this study we have investigated the mechanism by which overexpression of telomerase suppresses the temperature sensitivity of yku mutants. Viability of yku cells was restored by overexpression of the Est2 reverse transcriptase and TLC1 RNA template subunits of telomerase, but not the Est1 or Est3 proteins. Overexpression of other telomerase- and telomere-associated proteins (Cdc13, Stn1, Ten1, Rif1, Rif2, Sir3, Sir4) did not suppress the growth defects of yku70 cells. Mechanistic features of suppression were assessed using several TLC1 RNA deletion derivatives and Est2 enzyme mutants. Supraphysiological levels of three catalytically inactive reverse transcriptase mutants (Est2-D530A, Est2-D670A and Est2-D671A) suppressed the loss of viability as efficiently as the wildtype Est2 protein, without inducing cell senescence. Roles of proteins regulating telomere length were also determined. The results support a model in which chromosomes in yku mutants are stabilized via a replication-independent mechanism involving structural reinforcement of protective telomere cap structures.

scholarly journals CRISPR-Cas Systems in Prokaryotes

2015 ◽  
Vol 64 (3) ◽  
pp. 193-202 ◽  
Author(s):  
Michał Burmistrz ◽  
Krzysztof Pyrc
Keyword(s):  
Molecular Biology ◽  
Nucleic Acids ◽  
Protein Complexes ◽  
Mechanisms Of Action ◽  
Current Status ◽  
Different Types ◽  
Associated Proteins ◽  
Foreign Dna

Prokaryotic organisms possess numerous strategies that enable survival in hostile conditions. Among others, these conditions include the invasion of foreign nucleic acids such as bacteriophages and plasmids. The clustered regularly interspaced palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) system provides the majority of bacteria and archaea with adaptive and hereditary immunity against this threat. This mechanism of immunity is based on short fragments of foreign DNA incorporated within the hosts genome. After transcription, these fragments guide protein complexes that target foreign nucleic acids and promote their degradation. The aim of this review is to summarize the current status of CRISPR-Cas research, including the mechanisms of action, the classification of different types and subtypes of these systems, and the development of new CRISPR-Cas-based molecular biology tools.

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