Erratum: “Conformational state switching and pathways of chromosome dynamics in cell cycle” [Appl. Phys. Rev. 7, 031403 (2020)]

AbstractHerein we report that the 18-base telomeric oligodeoxynucleotides (ODNs) designed from the Lactobacillus rhamnosus GG genome promote differentiation of skeletal muscle myoblasts which are myogenic precursor cells. We termed these myogenetic ODNs (myoDNs). The activity of one of the myoDNs, iSN04, was independent of Toll-like receptors, but dependent on its conformational state. Molecular simulation and iSN04 mutants revealed stacking of the 13-15th guanines as a core structure for iSN04. The alkaloid berberine bound to the guanine stack and enhanced iSN04 activity, probably by stabilizing and optimizing iSN04 conformation. We further identified nucleolin as an iSN04-binding protein. Results showed that iSN04 antagonizes nucleolin, increases the levels of p53 protein translationally suppressed by nucleolin, and eventually induces myotube formation by modulating the expression of genes involved in myogenic differentiation and cell cycle arrest. This study shows that bacterial-derived myoDNs serve as aptamers and are potential nucleic acid drugs directly targeting myoblasts.

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Choreography of the Mycobacterium Replication Machinery during the Cell Cycle

mBio ◽

10.1128/mbio.02125-14 ◽

2015 ◽

Vol 6 (1) ◽

Cited By ~ 39

Author(s):

Damian Trojanowski ◽

Katarzyna Ginda ◽

Monika Pióro ◽

Joanna Hołówka ◽

Partycja Skut ◽

...

Keyword(s):

Cell Cycle ◽

Chromosome Segregation ◽

Mycobacterium Smegmatis ◽

Chromosome Replication ◽

Specific Cell ◽

Replication Machinery ◽

Content Type ◽

Chromosome Dynamics ◽

Mycobacterial Cell ◽

Slow Growing

ABSTRACT It has recently been demonstrated that bacterial chromosomes are highly organized, with specific positioning of the replication initiation region. Moreover, the positioning of the replication machinery (replisome) has been shown to be variable and dependent on species-specific cell cycle features. Here, we analyzed replisome positions in Mycobacterium smegmatis, a slow-growing bacterium that exhibits characteristic asymmetric polar cell extension. Time-lapse fluorescence microscopy analyses revealed that the replisome is slightly off-center in mycobacterial cells, a feature that is likely correlated with the asymmetric growth of Mycobacterium cell poles. Estimates of the timing of chromosome replication in relation to the cell cycle, as well as cell division and chromosome segregation events, revealed that chromosomal origin-of-replication (oriC) regions segregate soon after the start of replication. Moreover, our data demonstrate that organization of the chromosome by ParB determines the replisome choreography. IMPORTANCE Despite significant progress in elucidating the basic processes of bacterial chromosome replication and segregation, understanding of chromosome dynamics during the mycobacterial cell cycle remains incomplete. Here, we provide in vivo experimental evidence that replisomes in Mycobacterium smegmatis are highly dynamic, frequently splitting into two distinct replication forks. However, unlike in Escherichia coli, the forks do not segregate toward opposite cell poles but remain in relatively close proximity. In addition, we show that replication cycles do not overlap. Finally, our data suggest that ParB participates in the positioning of newly born replisomes in M. smegmatis cells. The present results broaden our understanding of chromosome segregation in slow-growing bacteria. In view of the complexity of the mycobacterial cell cycle, especially for pathogenic representatives of the genus, understanding the mechanisms and factors that affect chromosome dynamics will facilitate the identification of novel antimicrobial factors.

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CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics

10.1101/195966 ◽

2017 ◽

Author(s):

Hanhui Ma ◽

Li-Chun Tu ◽

Ardalan Naseri ◽

Yu-Chieh Chung ◽

David Grunwald ◽

...

Keyword(s):

Cell Cycle ◽

Cell Cycle Progression ◽

Living Cells ◽

Genomic Region ◽

List Type ◽

Relaxation Dynamic ◽

Cycle Progression ◽

Chromosome Dynamics ◽

Chromosomal Loci ◽

Dna Imaging

SUMMARYIn contrast to the well-studied condensation and folding of chromosomes during mitosis, their dynamics in interphase are less understood. We developed a sensitive, multicolor system, CRISPR-Sirius, allowing the real-time tracking of the dynamics of chromosomal loci. We tracked loci kilobases to megabases apart and found significant variation in the inter-locus distances of each pair, indicating differing degrees of DNA contortion. We resolved two distinct modes of dynamics of loci: saltatory local movements as well as translational movements of the domain. The magnitude of both of these modes of movements increased from early to late G1, whereas the translational movements were reduced in early S. The local fluctuations decreased slightly in early S and more markedly in mid-late S. These newly observed movements and their cell cycle-dependence are indicative of a hitherto unrecognized compaction-relaxation dynamic of the chromosomal fiber operating concurrently with changes in the extent of observed genomic domain movements.IN BRIEFDistinct chromosome folding and dynamics during cell cycle progression were dissected by CRISPR-Sirius DNA imaging in living cells.HIGHLIGHTSCRISPR-Sirius allows tracking of pairs of chromosomal loci having kilobase to megabase inter-locus distancesPair-wise tracking of loci allows measurement of both local and domain dynamicsChromosomal fiber relaxation is positively correlated with local dynamicsGenomic region size contributes to local and domain movementsDistinct chromosome dynamics were uncovered during cell cycle progression in interphase

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Moment-Based Estimation of State-Switching Rates in Cell Populations

10.1101/2022.01.06.475260 ◽

2022 ◽

Author(s):

Michael M Saint-Antoine ◽

Abhyudai Singh

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Tumor Cell ◽

Simulated Data ◽

Computational Method ◽

Cell Populations ◽

Biologically Relevant ◽

Fluctuation Test ◽

State Switching

In isogenic cell populations, cells can switch back and forth between different gene expression states. These expression states can be biologically relevant. For example, a certain expression state may cause a tumor cell to be resistant to treatment, while another state may leave it vulnerable to treatment. However, estimating the rates of state-switching can be difficult, because experimentally measuring a cell's transcriptome often involves destroying the cell, so it can only be measured once. In this paper, we propose a computational method to estimate the rate of switching between expression states, given data from a Luria-Delbrück style fluctuation test that is experimentally simple and feasible. We then benchmark this method using simulated data to test its efficacy, with varying assumptions made about cell cycle timing distribution in the simulations.

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Identification of the Myogenetic Oligodeoxynucleotides (myoDNs) That Promote Differentiation of Skeletal Muscle Myoblasts by Targeting Nucleolin

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2020.616706 ◽

2021 ◽

Vol 8 ◽

Author(s):

Sayaka Shinji ◽

Koji Umezawa ◽

Yuma Nihashi ◽

Shunichi Nakamura ◽

Takeshi Shimosato ◽

...

Keyword(s):

Cell Cycle ◽

Skeletal Muscle ◽

Myogenic Differentiation ◽

P53 Protein ◽

Lactobacillus Rhamnosus ◽

Conformational State ◽

Myotube Formation ◽

Cycle Arrest ◽

Expression Of Genes ◽

Myogenic Precursor

Herein we report that the 18-base telomeric oligodeoxynucleotides (ODNs) designed from the Lactobacillus rhamnosus GG genome promote differentiation of skeletal muscle myoblasts which are myogenic precursor cells. We termed these myogenetic ODNs (myoDNs). The activity of one of the myoDNs, iSN04, was independent of Toll-like receptors, but dependent on its conformational state. Molecular simulation and iSN04 mutants revealed stacking of the 13–15th guanines as a core structure for iSN04. The alkaloid berberine bound to the guanine stack and enhanced iSN04 activity, probably by stabilizing and optimizing iSN04 conformation. We further identified nucleolin as an iSN04-binding protein. Results showed that iSN04 antagonizes nucleolin, increases the levels of p53 protein translationally suppressed by nucleolin, and eventually induces myotube formation by modulating the expression of genes involved in myogenic differentiation and cell cycle arrest. This study shows that bacterial-derived myoDNs serve as aptamers and are potential nucleic acid drugs directly targeting myoblasts.

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Inhibition of DNA topoisomerase II by ICRF-193 induces polyploidization by uncoupling chromosome dynamics from other cell cycle events.

The Journal of Cell Biology ◽

10.1083/jcb.126.6.1341 ◽

1994 ◽

Vol 126 (6) ◽

pp. 1341-1351 ◽

Cited By ~ 108

Author(s):

R Ishida ◽

M Sato ◽

T Narita ◽

K R Utsumi ◽

T Nishimoto ◽

...

Keyword(s):

Cell Cycle ◽

Mammalian Cells ◽

Topoisomerase Ii ◽

Chromosome Condensation ◽

S Phase ◽

Cdc2 Kinase ◽

Torsional Strain ◽

Chromosome Dynamics ◽

M Phase ◽

Topo Ii

ICRF-193, a novel noncleavable, complex-stabilizing type topoisomerase (topo) II inhibitor, has been shown to target topo II in mammalian cells (Ishida, R., T. Miki, T. Narita, R. Yui, S. Sato, K. R. Utsumi, K. Tanabe, and T. Andoh. 1991. Cancer Res. 51:4909-4916). With the aim of elucidating the roles of topo II in mammalian cells, we examined the effects of ICRF-193 on the transition through the S phase, when the genome is replicated, and through the M phase, when the replicated genome is condensed and segregated. Replication of the genome did not appear to be affected by the drug because the scheduled synthesis of DNA and activation of cdc2 kinase followed by increase in mitotic index occurred normally, while VP-16, a cleavable, complex-stabilizing type topo II inhibitor, inhibited all these processes. In the M phase, however, late stages of chromosome condensation and segregation were clearly blocked by ICRF-193. Inhibition at the stage of compaction of 300-nm diameter chromatin fibers to 600-nm diameter chromatids was demonstrated using the drug during premature chromosome condensation (PCC) induced in tsBN2 baby hamster kidney cells in early S and G2 phases. In spite of interference with M phase chromosome dynamics, other mitotic events such as activation of cdc2 kinase, spindle apparatus reorganization and disassembly and reassembly of nuclear envelopes occurred, and the cells traversed an unusual M phase termed "absence of chromosome segregation" (ACS)-M phase. Cells then continued through further cell cycle rounds, becoming polyploid and losing viability. This effect of ICRF-193 on the cell cycle was shown to parallel that of inactivation of topo II on the cell cycle of the ts top2 mutant yeast. The results strongly suggest that the essential roles of topo II are confined to the M phase, when the enzyme decatenates intertwined replicated chromosomes. In other phases of the cycle, including the S phase, topo II may thus play a complementary role with topo I in controlling the torsional strain accumulated in various genetic processes.

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Chromosome dynamics and spatial organization during the non-binary cell cycle of a predatory bacterium

10.1101/2020.12.21.419010 ◽

2020 ◽

Author(s):

Jovana Kaljević ◽

Terrens N. V. Saaki ◽

Sander K. Govers ◽

Ophélie Remy ◽

Renske van Raaphorst ◽

...

Keyword(s):

Cell Cycle ◽

Cell Division ◽

Cell Cycle Progression ◽

Spatial Organization ◽

Chromosome Replication ◽

Circular Chromosome ◽

Cycle Progression ◽

Bdellovibrio Bacteriovorus ◽

Chromosome Dynamics ◽

Complex Chromosome

AbstractIn bacteria, the dynamics of chromosome replication and segregation are tightly coordinated with cell cycle progression, and largely rely on specific spatiotemporal arrangement of the chromosome. Whereas these key processes are mostly investigated in species that divide by binary fission, they remain mysterious in bacteria producing larger number of descendants. Here, we establish the predatory bacterium Bdellovibrio bacteriovorus as a model to investigate the non-binary processing of a circular chromosome. Our data reveal its extreme compaction in a dense polarized nucleoid. We also show that a first binary-like cycle of replication and asymmetric segregation is followed by multiple asynchronous rounds of replication and progressive ParABS-dependent partitioning, uncoupled from cell division. Surprisingly, ParB localization at the centromere is cell-cycle regulated. Altogether, our findings support a model of complex chromosome choreography, leading to the generation of variable numbers of offspring, highlighting the adaptation of conserved mechanisms to achieve non-binary reproduction in bacteria.

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Maytansine-Induced Mitotic Arrest in Human Lymphoblasts

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100079747 ◽

1977 ◽

Vol 35 ◽

pp. 460-461

Author(s):

Tai-Te Chao ◽

John Sullivan ◽

Awtar Krishan

Keyword(s):

Electron Microscopy ◽

Cell Cycle ◽

Transmission Electron Microscopy ◽

Tubulin Polymerization ◽

Vinca Alkaloids ◽

Antimitotic Activity ◽

Transmission Electron ◽

Flow Microfluorometry ◽

Brain Tubulin

Maytansine, a novel ansa macrolide (1), has potent anti-tumor and antimitotic activity (2, 3). It blocks cell cycle traverse in mitosis with resultant accumulation of metaphase cells (4). Inhibition of brain tubulin polymerization in vitro by maytansine has also been reported (3). The C-mitotic effect of this drug is similar to that of the well known Vinca- alkaloids, vinblastine and vincristine. This study was carried out to examine the effects of maytansine on the cell cycle traverse and the fine struc- I ture of human lymphoblasts.Log-phase cultures of CCRF-CEM human lymphoblasts were exposed to maytansine concentrations from 10-6 M to 10-10 M for 18 hrs. Aliquots of cells were removed for cell cycle analysis by flow microfluorometry (FMF) (5) and also processed for transmission electron microscopy (TEM). FMF analysis of cells treated with 10-8 M maytansine showed a reduction in the number of G1 cells and a corresponding build-up of cells with G2/M DNA content.

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