dna organization
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2022 ◽  
Vol 2022 ◽  
pp. 1-13
Author(s):  
Mehrdad Rafati Rahimzadeh ◽  
Mehravar Rafati Rahimzadeh ◽  
Sohrab Kazemi ◽  
Roghayeh Jafarian Amiri ◽  
Marzieh Pirzadeh ◽  
...  

Aluminum poisoning has been reported in some parts of the world. It is one of the global health problems that affect many organs. Aluminum is widely used daily by humans and industries. Residues of aluminum compounds can be found in drinking water, food, air, medicine, deodorants, cosmetics, packaging, many appliances and equipment, buildings, transportation industries, and aerospace engineering. Exposure to high levels of aluminum compounds leads to aluminum poisoning. Aluminum poisoning has complex and multidimensional effects, such as disruption or inhibition of enzymes activities, changing protein synthesis, nucleic acid function, and cell membrane permeability, preventing DNA repair, altering the stability of DNA organization, inhibition of the protein phosphatase 2A (PP2A) activity, increasing reactive oxygen species (ROS) production, inducing oxidative stress, decreasing activity of antioxidant enzymes, altering cellular iron homeostasis, and changing NF-kB, p53, and JNK pathway leading to apoptosis. Aluminum poisoning can affect blood content, musculoskeletal system, kidney, liver, and respiratory and nervous system, and the extent of poisoning can be diagnosed by assaying aluminum compounds in blood, urine, hair, nails, and sweat. Chelator agents such as deferoxamine (DFO) are used in the case of aluminum poisoning. Besides, combination therapies are recommended.


2021 ◽  
Author(s):  
Elizabeth T. Ogunbunmi ◽  
Aaron P. Roznowski ◽  
Bentley A. Fane

Most icosahedral viruses condense their genomes into volumetrically constrained capsids. However, concurrent genome biosynthesis and packaging is specific to single-stranded (ss) DNA viruses. ssDNA genome packaging combines elements found in both double-stranded (ds) DNA and ssRNA systems. Similar to dsDNA viruses, the genome is packaged into a preformed capsid. Like ssRNA viruses, there are numerous capsid-genome associations. In ssDNA microviruses, the DNA binding protein J guides the genome between 60 icosahedrally ordered DNA binding pockets. It also partially neutralizes the DNA’s negative phosphate backbone. øX174-related microviruses, such as G4 and α3, have J proteins that differ in length and charge organization. This suggests that interchanging J proteins could alter the path used to guide DNA in the capsid. Previously, a øXG4J chimera, in which the øX174 J gene was replaced with the G4 gene, was characterized. It displayed lethal packaging defects, which resulted in procapsids being removed from productive assembly. Here, we report the characterization of another inviable chimera, øXα3J. Unlike øXG4J, øXα3J efficiently packaged DNA but produced non-infectious particles. These particles displayed a reduced ability to attach to host cells, suggesting internal DNA organization could distort the capsid’s outer surface. Mutations that restored viability altered J-coat protein contact sites. These results provide evidence that the organization of ssDNA can affect both packaging and post-packaging phenomena. Importance ssDNA viruses utilize icosahedrally ordered protein-nucleic acids interactions to guide and organize their genomes into preformed shells. As previously demonstrated, chaotic genome-capsid associations can inhibit øX174 packaging by destabilizing packaging complexes. However, the consequences of poorly organized genomes may extend beyond the packaging reaction. As demonstrated herein, it can lead to uninfectious packaged particles. Thus, ssDNA genomes should be considered an integral and structural virion component, affecting the properties of the entire particle, which includes the capsid’s outer surface.


2021 ◽  
Author(s):  
Luiza Sisdelli ◽  
Maria I. Cordioli ◽  
Fernanda Vaisman ◽  
Osmar Monte ◽  
Carlos Longui ◽  
...  

2021 ◽  
Vol 22 (13) ◽  
pp. 6798
Author(s):  
Monika Tunjić-Cvitanić ◽  
Juan J. Pasantes ◽  
Daniel García-Souto ◽  
Tonči Cvitanić ◽  
Miroslav Plohl ◽  
...  

Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we have identified 52 satDNAs composing the satellitome of C. gigas and constituting about 6.33% of the genome. Satellitome analysis reveals unusual, highly scattered organization of relatively short satDNA arrays across the whole genome. However, peculiar chromosomal distribution and densities are specific for each satDNA. The inspection of the organizational forms of the 11 most abundant satDNAs shows association with constitutive parts of Helitron mobile elements. Nine of the inspected satDNAs are dominantly found in mobile element-associated form, two mostly appear standalone, and only one is present exclusively as Helitron-associated sequence. The Helitron-related satDNAs appear in more chromosomes than other satDNAs, indicating that these mobile elements could be leading satDNA propagation in C. gigas. No significant accumulation of satDNAs on certain chromosomal positions was detected in C. gigas, thus establishing a novel pattern of satDNA organization on the genome level.


Author(s):  
Esther Miriklis ◽  
Ashley Rozario ◽  
Eli Rothenberg ◽  
Toby D.M. Bell ◽  
Donna Rose Whelan

2021 ◽  
Vol 22 (5) ◽  
pp. 2414
Author(s):  
Lucía del Priore ◽  
María Inés Pigozzi

During meiosis, the number of crossovers vary in correlation to the length of prophase chromosome axes at the synaptonemal complex stage. It has been proposed that the regular spacing of the DNA loops, along with the close relationship of the recombination complexes and the meiotic axes are at the basis of this covariation. Here, we use a cytogenomic approach to investigate the relationship between the synaptonemal complex length and the DNA content in chicken oocytes during the pachytene stage of the first meiotic prophase. The synaptonemal complex to DNA ratios of specific chromosomes and chromosome segments were compared against the recombination rates obtained by MLH1 focus mapping. The present results show variations in the DNA packing ratios of macro- and microbivalents and also between regions within the same bivalent. Chromosome or chromosome regions with higher crossover rates form comparatively longer synaptonemal complexes than expected based on their DNA content. These observations are compatible with the formation of higher number of shorter DNA loops along meiotic axes in regions with higher recombination levels.


2020 ◽  
Vol 8 ◽  
Author(s):  
Maria-Cecilia D. Costa ◽  
Frank Johannes

The DNA of a human cell has all the information necessary to produce more than 20,400 different proteins. This information is written in an amount of DNA that, if stretched end-to-end, would measure about one meter. You can imagine how challenging it is to keep all this information in an organized way. Other animals, bacteria, and plants face the very same challenge. The solutions to the problem of DNA organization found by cells include tightly packing the DNA and switching genes “on” and “off” as needed. The study of these switches is called epigenetics. Epigenetics is a fast-growing field of research that is changing our understanding of genetic information.


2020 ◽  
Vol 202 (21) ◽  
Author(s):  
Juan A. Subirana ◽  
Xavier Messeguer

ABSTRACT DNA tandem repeats, or satellites, are well described in eukaryotic species, but little is known about their prevalence across prokaryotes. Here, we performed the most complete characterization to date of satellites in bacteria. We identified 121,638 satellites from 12,233 fully sequenced and assembled bacterial genomes with a very uneven distribution. We also determined the families of satellites which have a related sequence. There are 85 genomes that are particularly satellite rich and contain several families of satellites of yet unknown function. Interestingly, we only found two main types of noncoding satellites, depending on their repeat sizes, 22/44 or 52 nucleotides (nt). An intriguing feature is the constant size of the repeats in the genomes of different species, whereas their sequences show no conservation. Individual species also have several families of satellites with the same repeat length and different sequences. This result is in marked contrast with previous findings in eukaryotes, where noncoding satellites of many sizes are found in any species investigated. We describe in greater detail these noncoding satellites in the spirochete Leptospira interrogans and in several bacilli. These satellites undoubtedly play a specific role in the species which have acquired them. We discuss the possibility that they represent binding sites for transcription factors not previously described or that they are involved in the stabilization of the nucleoid through interaction with proteins. IMPORTANCE We found an enigmatic group of noncoding satellites in 85 bacterial genomes with a constant repeat size but variable sequence. This pattern of DNA organization is unique and had not been previously described in bacteria. These findings strongly suggest that satellite size in some bacteria is under strong selective constraints and thus that satellites are very likely to play a fundamental role. We also provide a list and properties of all satellites in 12,233 genomes, which may be used for further genomic analysis.


mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Zhenfeng Zhang ◽  
Zhengyan Zhan ◽  
Bing Wang ◽  
Yuanyuan Chen ◽  
Xiuqiang Chen ◽  
...  

ABSTRACT Archaeal chromatin proteins Cren7 and Sul7d from Sulfolobus are DNA benders. To better understand their architectural roles in chromosomal DNA organization, we analyzed DNA compaction by Cren7 and Sis7d, a Sul7d family member, from Sulfolobus islandicus at the single-molecule (SM) level by total single-molecule internal reflection fluorescence microscopy (SM-TIRFM) and atomic force microscopy (AFM). We show that both Cren7 and Sis7d were able to compact singly tethered λ DNA into a highly condensed structure in a three-step process and that Cren7 was over an order of magnitude more efficient than Sis7d in DNA compaction. The two proteins were similar in DNA bending kinetics but different in DNA condensation patterns. At saturating concentrations, Sis7d formed randomly distributed clusters whereas Cren7 generated a single and highly condensed core on plasmid DNA. This observation is consistent with the greater ability of Cren7 than of Sis7d to bridge DNA. Our results offer significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaea. IMPORTANCE A long-standing question is how chromosomal DNA is packaged in Crenarchaeota, a major group of archaea, which synthesize large amounts of unique small DNA-binding proteins but in general contain no archaeal histones. In the present work, we tested our hypothesis that the two well-studied crenarchaeal chromatin proteins Cren7 and Sul7d compact DNA by both DNA bending and bridging. We show that the two proteins are capable of compacting DNA, albeit with different efficiencies and in different manners, at the single molecule level. We demonstrate for the first time that the two proteins, which have long been regarded as DNA binders and benders, are able to mediate DNA bridging, and this previously unknown property of the proteins allows DNA to be packaged into highly condensed structures. Therefore, our results provide significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaeota.


eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Stefan Golfier ◽  
Thomas Quail ◽  
Hiroshi Kimura ◽  
Jan Brugués

Loop extrusion by structural maintenance of chromosomes (SMC) complexes has been proposed as a mechanism to organize chromatin in interphase and metaphase. However, the requirements for chromatin organization in these cell cycle phases are different, and it is unknown whether loop extrusion dynamics and the complexes that extrude DNA also differ. Here, we used Xenopus egg extracts to reconstitute and image loop extrusion of single DNA molecules during the cell cycle. We show that loops form in both metaphase and interphase, but with distinct dynamic properties. Condensin extrudes DNA loops non-symmetrically in metaphase, whereas cohesin extrudes loops symmetrically in interphase. Our data show that loop extrusion is a general mechanism underlying DNA organization, with dynamic and structural properties that are biochemically regulated during the cell cycle.


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