scholarly journals The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Huahua Jian ◽  
Guanpeng Xu ◽  
Yi Yi ◽  
Yali Hao ◽  
Yinzhao Wang ◽  
...  
Keyword(s):  
Negative Effects ◽  
Metabolic Genes ◽  
Transcriptomic Sequencing ◽  
Prokaryotic Genomes ◽  
Dna Backbone ◽  
Backbone Modification ◽  
Encoding Gene ◽  
Pt Modification ◽  
Restriction Modification ◽  
Competition Assays

AbstractPhosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.

scholarly journals Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications

Biomolecules ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1491
Author(s):  
Sucheng Zhu ◽  
Tao Zheng ◽  
Lingxin Kong ◽  
Jinli Li ◽  
Bo Cao ◽  
...  
Keyword(s):  
Genomic Mapping ◽  
Qualitative And Quantitative Analysis ◽  
Biological Functions ◽  
Time Saving ◽  
Qualitative And Quantitative ◽  
Cleavage Assay ◽  
Dna Backbone ◽  
Pt Modification ◽  
Labor Consuming ◽  
Restriction Modification

DNA phosphorothioate (PT) modification is a novel modification that occurs on the DNA backbone, which refers to a non-bridging phosphate oxygen replaced by sulfur. This exclusive DNA modification widely distributes in bacteria but has not been found in eukaryotes to date. PT modification renders DNA nuclease tolerance and serves as a constitute element of bacterial restriction–modification (R–M) defensive system and more biological functions are awaiting exploration. Identification and quantification of the bacterial PT modifications are thus critical to better understanding their biological functions. This work describes three detailed methods derived from iodine-induced specific cleavage-an iodine-induced cleavage assay (ICA), a deep sequencing of iodine-induced cleavage at PT site (ICDS) and an iodine-induced cleavage PT sequencing (PT-IC-Seq)-for the investigation of PT modifications. Using these approaches, we have identified the presence of PT modifications and quantized the frequency of PT modifications in bacteria. These characterizations contributed to the high-resolution genomic mapping of PT modifications, in which the distribution of PT modification sites on the genome was marked accurately and the frequency of the specific modified sites was reliably obtained. Here, we provide time-saving and less labor-consuming methods for both of qualitative and quantitative analysis of genomic PT modifications. The application of these methodologies will offer great potential for better understanding the biology of the PT modifications and open the door to future further systematical study.

scholarly journals Development of methods derived from iodine-induced specific cleavage for identification and quantitation of DNA phosphorothioate modifications

2019 ◽  
Author(s):  
Sucheng Zhu ◽  
Tao Zheng ◽  
Lingxin Kong ◽  
Jinli Li ◽  
Bo Cao ◽  
...  
Keyword(s):  
Qualitative And Quantitative Analysis ◽  
Time Saving ◽  
Qualitative And Quantitative ◽  
Sequencing Technologies ◽  
Cleavage Assay ◽  
Dna Backbone ◽  
Pt Modification ◽  
Labor Consuming ◽  
Restriction Modification ◽  
Generation Sequencing

Abstract Background DNA phosphorothioate (PT) modifications is a novel modification that occurs on the DNA backbone, which refers to a non-bridging phosphate oxygen replaced by sulfur. This exclusive DNA modification widely distributes in bacteria and archaea but has not been found in eukaryotes to date. PT modification renders DNA nuclease tolerance and servers as a constitute element of bacterial restriction-modification (R-M) defensive system and more biological functions are awaiting exploration. Identification and quantification of the bacterial PT modifications are thus critical to better understanding their biological functions.Results In this report, we describe three detailed methods based on PT-specific iodine-induced cleavage and high-throughput next-generation sequencing technologies: an iodine-induced cleavage assay (ICA), a deep sequencing of iodine-induced cleavage at PT site (ICDS) and an iodine-induced cleavage PT sequencing (PT-IC-Seq), for the investigation of PT modifications. Using these approaches, we have identified the presence of PT modifications and quantized the frequency of PT modifications in bacteria. These characterizations contributed to the high-resolution genomic mapping of PT modifications, in which the distribution of PT modification sites on the genome was marked accurately and the frequency of the specific modified sites was reliably obtained.Conclusion Here, we provide time-saving and less labor consuming methods for both of qualitative and quantitative analysis of genomic PT modifications. The application of these methodologies will provide new opportunities for better understanding the biology of the PT modifications and opens door for future further systematically study.

scholarly journals MEHP interferes with mitochondrial functions and homeostasis in skeletal muscle cells

2020 ◽  
Vol 40 (4) ◽  
Author(s):  
Yi-Huan Chen ◽  
Yi-Ju Wu ◽  
Wei-Cheng Chen ◽  
Tzong-Shyuan Lee ◽  
Tsui-Chun Tsou ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Acid Oxidation ◽  
Oxygen Species ◽  
Negative Effects ◽  
Oxidative Phosphorylation System ◽  
Metabolic Genes ◽  
Mitochondrial Functions ◽  
High Efficient ◽  
The Stability ◽  
Ethylhexyl Phthalate

Abstract Di (2-ethylhexyl) phthalate (DEHP) is a plasticizer frequently leached out from polyvinyl chloride (PVC) products and is quickly metabolized to its monoester equivalent mono(2-ethylhexyl) phthalate (MEHP) once enters organisms. Exposure to DEHP/MEHP through food chain intake has been shown to modified metabolism but its effect on the development of metabolic myopathy of skeletal muscle (SKM) has not been revealed so far. Here, we found that MEHP repressed myogenic terminal differentiation of proliferating myoblasts (PMB) and confluent myoblasts (CMB) but had weak effect on this process once it had been initiated. The transition of mitochondria (MITO) morphology from high efficient filamentary network to low efficient vesicles was triggered by MEHP, implying its negative effects on MITO functions. The impaired MITO functions was further demonstrated by reduced MITO DNA (mtDNA) level and SDH enzyme activity as well as highly increased reactive oxygen species (ROS) in cells after MEHP treatment. The expression of metabolic genes, including PDK4, CPT1b, UCP2, and HO1, was highly increased by MEHP and the promoters of PDK4 and CPT1b were also activated by MEHP. Additionally, the stability of some subunits in the oxidative phosphorylation system (OXPHOS) complexes was found to be reduced by MEHP, implying defective oxidative metabolism in MITO and which was confirmed by repressed palmitic acid oxidation in MEHP-treated cells. Besides, MEHP also blocked insulin-induced glucose uptake. Taken together, our results suggest that MEHP is inhibitory to myogenesis and is harmful to MITO functions in SKM, so its exposure should be avoided or limited.

scholarly journals Comparative transcriptomic analyses of glucosinolate metabolic genes during the formation of Chinese kale seeds

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yijiao Zhao ◽  
Zeyuan Chen ◽  
Jiaxuan Chen ◽  
Bingxing Chen ◽  
Weiling Tang ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Sequencing Analysis ◽  
Biosynthetic Genes ◽  
Seed Formation ◽  
Catabolic Enzymes ◽  
Metabolic Genes ◽  
Chinese Kale ◽  
Transcriptomic Sequencing ◽  
Embryo Stage ◽  
Two Stages

Abstract Background To understand the mechanism of glucosinolates (GSs) accumulation in the specific organs, combined analysis of physiological change and transcriptome sequencing were applied in the current study. Taking Chinese kale as material, seeds and silique walls were divided into different stages based on the development of the embryo in seeds and then subjected to GS analysis and transcriptome sequencing. Results The main GS in seeds of Chinese kale were glucoiberin and gluconapin and their content changed with the development of the seed. During the transition of the embryo from torpedo- to the early cotyledonary-embryo stage, the accumulation of GS in the seed was accompanied by the salient decline of GS in the corresponding silique wall. Thus, the seed and corresponding silique wall at these two stages were subjected to transcriptomic sequencing analysis. 135 genes related to GS metabolism were identified, of which 24 genes were transcription factors, 81 genes were related to biosynthetic pathway, 25 genes encoded catabolic enzymes, and 5 genes matched with transporters. The expression of GS biosynthetic genes was detected both in seeds and silique walls. The high expression of FMOGS-OX and AOP2, which is related to the production of gluconapin by side modification, was noted in seeds at both stages. Interestingly, the expression of GS biosynthetic genes was higher in the silique wall compared with that in the seed albeit lower content of GS existed in the silique wall than in the seed. Combined with the higher expression of transporter genes GTRs in silique walls than in seeds, it was proposed that the transportation of GS from the silique wall to the seed is an important source for seed GS accumulation. In addition, genes related to GS degradation expressed abundantly in the seed at the early cotyledonary-embryo stage indicating its potential role in balancing seed GS content. Conclusions Two stages including the torpedo-embryo and the early cotyledonary-embryo stage were identified as crucial in GS accumulation during seed development. Moreover, we confirmed the transportation of GS from the silique wall to the seed and proposed possible sidechain modification of GS biosynthesis may exist during seed formation.

Cloning and expression of the NaeI restriction endonuclease-encoding gene and sequence analysis of the NaeI restriction-modification system

Gene ◽  
1995 ◽  
Vol 155 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Christopher H. Taron ◽  
Elizabeth M. Van Cott ◽  
Geoffrey G. Wilson ◽  
Laurie S. Moran ◽  
Barton E. Slatko ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Restriction Endonuclease ◽  
Cloning And Expression ◽  
Modification System ◽  
Restriction Modification System ◽  
Encoding Gene ◽  
Restriction Modification

Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes

2016 ◽  
Vol 14 (02) ◽  
pp. 1641003 ◽  
Author(s):  
Anna Ershova ◽  
Ivan Rusinov ◽  
Mikhail Vasiliev ◽  
Sergey Spirin ◽  
Anna Karyagina
Keyword(s):  
Natural Transformation ◽  
Methylation Status ◽  
Classical Type ◽  
Type Ii ◽  
Cellular Processes ◽  
Prokaryotic Genomes ◽  
Different Strains ◽  
Restriction Modification ◽  
Gatc Site ◽  
Site Avoidance

Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see text]-GATC-3[Formula: see text] site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes.In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population.

scholarly journals A DNA Methyltransferase Can Protect the Genome from Postdisturbance Attack by a Restriction-Modification Gene Complex

2002 ◽  
Vol 184 (22) ◽  
pp. 6100-6108 ◽  
Author(s):  
Noriko Takahashi ◽  
Yasuhiro Naito ◽  
Naofumi Handa ◽  
Ichizo Kobayashi
Keyword(s):  
Dna Methyltransferase ◽  
Dna Methyltransferases ◽  
Cell Killing ◽  
Gene Complex ◽  
Prokaryotic Genomes ◽  
A Cell ◽  
Gene Complexes ◽  
Potential Mobility ◽  
Restriction Modification

ABSTRACT In prokaryotic genomes, some DNA methyltransferases form a restriction-modification gene complex, but some others are present by themselves. Dcm gene product, one of these orphan methyltransferases found in Escherichia coli and related bacteria, methylates DNA to generate 5′-CmCWGG just as some of its eukaryotic homologues do. Vsr mismatch repair function of an adjacent gene prevents C-to-T mutagenesis enhanced by this methylation but promotes other types of mutation and likely has affected genome evolution. The reason for the existence of the dcm-vsr gene pair has been unclear. Earlier we found that several restriction-modification gene complexes behave selfishly in that their loss from a cell leads to cell killing through restriction attack on the genome. There is also increasing evidence for their potential mobility. EcoRII restriction-modification gene complex recognizes the same sequence as Dcm, and its methyltransferase is phylogenetically related to Dcm. In the present work, we found that stabilization of maintenance of a plasmid by linkage of EcoRII gene complex, likely through postsegregational cell killing, is diminished by dcm function. Disturbance of EcoRII restriction-modification gene complex led to extensive chromosome degradation and severe loss of cell viability. This cell killing was partially suppressed by chromosomal dcm and completely abolished by dcm expressed from a plasmid. Dcm, therefore, can play the role of a “molecular vaccine” by defending the genome against parasitism by a restriction-modification gene complex.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

Expression of the melanoma antigen-encoding gene in pancreatic cancer

2001 ◽  
Vol 120 (5) ◽  
pp. A162-A162
Author(s):  
A KUTUP ◽  
S HOSCH ◽  
S PAPE ◽  
P SCHEUNEMANN ◽  
W KNOEFEL ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Melanoma Antigen ◽  
Encoding Gene

Undesirable Effects of Goal Setting on Perceived Fairness, Commitment, and Unethical Behavior

2018 ◽  
Vol 62 (2) ◽  
pp. 97-107 ◽  
Author(s):  
Nina Keith
Keyword(s):  
Goal Setting ◽  
Unethical Behavior ◽  
The United States ◽  
Goal Commitment ◽  
Management Technique ◽  
Long Term Effects ◽  
Perceived Fairness ◽  
Negative Effects ◽  
Positive Effects ◽  
And Performance

Abstract. The positive effects of goal setting on motivation and performance are among the most established findings of industrial–organizational psychology. Accordingly, goal setting is a common management technique. Lately, however, potential negative effects of goal-setting, for example, on unethical behavior, are increasingly being discussed. This research replicates and extends a laboratory experiment conducted in the United States. In one of three goal conditions (do-your-best goals, consistently high goals, increasingly high goals), 101 participants worked on a search task in five rounds. Half of them (transparency yes/no) were informed at the outset about goal development. We did not find the expected effects on unethical behavior but medium-to-large effects on subjective variables: Perceived fairness of goals and goal commitment were least favorable in the increasing-goal condition, particularly in later goal rounds. Results indicate that when designing goal-setting interventions, organizations may consider potential undesirable long-term effects.

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