Does Prokaryotes Undergo Chromatin Remodeling?

Chromatin remodeling is a dynamic modification of chromatin architecture that allows access to condensed genomic DNA to the regulatory transcription machinery proteins, controlling gene expression. This process is primarily carried out by covalent histone modifications by specific enzymes. The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. Chromatin remodelers are ATP-driven enzymes that dynamically alter their positions and composition. Histones can be displaced by chromatin remodeling complexes, exposing underlying DNA sequences to polymerases and other enzymes.

Chromatin remodeling is primarily through posttranslational modifications of histone proteins, which allow transcription signals to reach their destinations on the DNA strand. To counterbalance the repressive nature of chromatin, various chromatin remodeling factors use the energy of ATP hydrolysis to facilitate the interaction of chromatin. Chromatin remodeling is critical in this process, as the organization of eukaryotic DNA into compact chromatin presents a natural barrier to all DNA-related events. Chromosome remodeling or chromatin opening is essential for gene expression.

In eukaryotes, DNA is tightly wound into a complex called chromatin, which can be “opened” through chromatin remodeling. Chromatin remodeling can be considered a consequence of nucleosome disruption, as chromatin-remodeling complexes interact and disrupt nucleosome conformation. Bacteria provoke histone modifications and chromatin remodeling in infected cells, thereby altering the host’s transcriptional program.

In summary, chromatin remodeling is a crucial process for gene expression, repair of DNA double-strand breaks (DSBs), and regulation of aging.

Is there chromatin in prokaryotes?

DNA compaction and chromosome condensation are crucial processes in the cell cycle. In prokaryotic cells, chromosomal DNA is compacted by a factor of 1, 000, while in eukaryotic interphase nuclei, it is about 100. The “chromatin architecture” proteins from eukaryotes and prokaryotes have three similar modes of action, suggesting that principles of DNA compaction are preserved across kingdoms. E. coli cells have tens of thousands of copies of small nucleoid-associated proteins that act to compact bacterial DNA by bending it at angles sometimes approaching 180°. This compacting process collapses DNA like a long strip of continuous-feed printer paper, neatly packed in a box 1, 000 times shorter than paper’s length.

Eukaryotic chromosomes undergo additional condensation in prophase to prepare for alignment in metaphase and segregation in anaphase before cell division. This additional mitotic condensation is only ~2X for the diminutive chromosomes of S. cerevisiae but is an order of magnitude higher in human chromosomes and reaches an astonishing 1, 000X in mitotic chromosomes of barley. The varying degree of mitotic condensation reflects the length of the DNA in the chromosome vis-à-vis the size of the mitotic spindle in that particular organism.

In prokaryotes, no additional chromosome condensation is observed prior to cell division, leading up to chromosome segregation proper. This lack of apparent “process of condensation” or the period of obvious tightening of the entire nucleoid in prokaryotes may lead to the argument that the prokaryotic chromosome does not have to be condensed in any organized way due to the “mandatory condensation” in prokaryotic cells due to molecular crowding. One reason prokaryotic nucleoids do not globally change their compaction state is because the prokaryotic genome is transcribed continuously.

Why do bacteria not have chromatin?

Bacteria are unicellular organisms that lack a well-defined nucleus and membrane-bound organelles. Examples of bacteria include Escherichia coli, Pseudomonas, Staphylococcus, and Lactobacillus. They possess chromatin suspended in the cytoplasm as a discrete nucleoid, and their double-stranded circular DNA is coated with proteins. Furthermore, some bacteria possess linear double-stranded DNA, as observed in Streptomyces.

Do prokaryotes have euchromatin or heterochromatin?

Euchromatin is the most active part of the genome in eukaryotes, and in prokaryotes, it is the only form of chromatin present. Euchromatin consists of repeating subunits called nucleosomes, which are approximately 11 nm in diameter and contain four histone protein pairs. Each core histone protein has a ‘tail’ structure, which can vary in several ways, acting as “master control switches” through different methylation and acetylation states.

Approximately 147 base pairs of DNA are wound around the histone octamers, or a little less than 2 turns of the helix. Nucleosomes along the strand are linked together via the histone and a short space of open linker DNA.

The key distinction between euchromatin and heterochromatin is that the nucleosomes in euchromatin are much more widely spaced, allowing for easier access of different protein complexes to the DNA strand and increased gene transcription. Euchromatin resembles a set of beads on a string at large magnifications and can appear lighter in color than heterochromatin due to its less compact structure. Cytogenetic banding, also known as Giemsa staining, is used to visualize chromosomes, allowing us to differentiate chromosomal subsections, irregularities, or rearrangements.

Does chromatin remodeling occur in eukaryotes?

Eukaryotic chromatin is a flexible and dynamic system that responds to environmental, metabolic, and developmental cues through the action of a family of “nucleosome remodeling” ATPases. These enzymes experience conformation changes as they bind and hydrolyze ATP, interacting with DNA and histones, and altering histone-DNA interactions in target nucleosomes. Their action can lead to complete or partial disassembly of nucleosomes, the exchange of histones for variants, the assembly of nucleosomes, or the movement of histone octamers on DNA.

Remodeling processes are essential for every aspect of genome function, including replication and transcription. They are often integrated with other mechanisms like histone modifications or RNA metabolism to assemble stable, epigenetic states. However, the organization of eukaryotic genomes into chromatin can lead to the occlusion of DNA sequence by histones and nonhistone chromatin components. This necessitates regulatory factors and complex machineries to gain access to DNA sequence.

The fundamental issue of chromatin biology is ensuring access to DNA despite the compact and protective chromatin organization, which generates a default state of inaccessibility and inactivity of the DNA subject to it. This is due to several reasons, such as proteins not easily associateing with DNA sequences touching the nucleosomal histone surface, nucleosomal DNA being strongly bent during its path around the histone octamer, and nonhistone chromatin components interacting with nucleosomes bearing chemical modifications.

Do bacteria have chromatin remodeling?

Bacteria, similar to viruses, cause histone modifications and chromatin remodeling in infected cells, altering the host’s transcriptional program and often dampening the innate immune response. This is similar to viruses. ScienceDirect uses cookies and all rights are reserved, including those for text and data mining, AI training, and similar technologies. Open access content is licensed under Creative Commons terms.

Is chromatin absent in bacteria?

The interplay between chromatin and transcription by RNA polymerase (RNAP) has been studied extensively in all domains of life. In bacteria, chromatin is compacted into a membrane-free region called the nucleoid, which changes shape and composition depending on the bacterial state. Transcription plays a crucial role in shaping the nucleoid and organizing it into domains. Several mechanisms impact transcription, including occlusion of RNAP binding, roadblocking RNAP progression, constraining DNA topology, RNA-mediated interactions, and macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and mediate gene regulation.

The current understanding of these mechanisms focuses on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. Methodological advances have enabled a paradigm shift in the field of bacterial transcription to focus on gene regulation in their native state. This will help coordinate and dynamically regulate gene expression in changing environments.

In eukaryotes and archaea, DNA compaction is achieved by histones that assemble into regular, repeating structures. The role of these structures in mediating gene expression is best understood in eukaryotes, where extensive post-translational modifications by chromatin regulators alter the properties of discrete, octa-histone nucleosomes to repress transcription when tightly packed or allow transcription initiation in nucleosome-free promoter regions and elongation though modified nucleosomes. However, the comparable structuring, preserving, and expression-mediating functions of DNA compaction in bacteria remain poorly understood.

What is the remodeling of chromatin?

Chromatin remodeling is the process of rearranging chromatin from a condensed state to a transcriptionally accessible state, enabling transcription factors or DNA binding proteins to access DNA and control gene expression. This process is crucial for various applications, including text and data mining, AI training, and similar technologies. Copyright © 2024 Elsevier B. V., its licensors, and contributors.

What is the key difference between prokaryotic and eukaryotic chromosomes?

Eukaryotic cells have a membrane-bound nucleus and organelles, while prokaryotic cells lack a nucleus. All chromosomes are within the nucleus, while prokaryotic cells are located in the nucleoid, which lacks a membrane. This difference allows for simultaneous transcription and translation in prokaryotes, as they lack a nuclear membrane. In contrast, transcription occurs first within the nucleus, followed by translation by a ribosome in the cytoplasm.

Eukaryotic cells contain more genetic material than prokaryotic cells, with each human cell having around 2m base pairs of DNA. This is due to the need for editing the RNA molecule before it leaves the nucleus. In summary, eukaryotic cells have a more complex structure and contain more genetic material than prokaryotic cells.

Is there heterochromatin in bacteria?

Heterochromatin, a protein found in eukaryotic organisms, is often associated with eukaryotic organisms. However, bacteria also contain areas with densely protein-occupied chromatin that silence gene expression. One such protein is the conserved protein Hfq, which is strongly enriched at AT-rich DNA regions. Polyphosphate (polyP), an ancient and highly conserved polyanion, is essential for the site-specific DNA binding properties of Hfq in bacteria.

The absence of polyP alters the DNA binding profile of Hfq, causes unsolicited prophage and transposon mobilization, and increases mutagenesis rates and DNA damage-induced cell death. In vitro reconstitution of the system revealed that Hfq and polyP interact with AT-rich DNA sequences and form phase-separated condensates, mediated by the intrinsically disordered C-terminal extensions of Hfq. The researchers propose that polyP serves as a newly identified driver of heterochromatin formation in bacteria. PolyP, an ancient biomolecule, has various functions, including stress resistance, virulence, blood clotting, and modulating amyloidogenic processes in eukaryotes.

Is chromatin only in eukaryotes?

The DNA within nuclear genes is organized into a coil with histone proteins at its center, which compacts the DNA and forms the dense chromosomal package called chromatin. Chromatin is found only in eukaryotic cells, while prokaryotic cells have a different arrangement called a genophore. Chromatin structure varies depending on the cell cycle stage, such as when the cell is not dividing or in interphase.

It can be present in two forms: euchromatin, the active part of the genome, and heterochromatin, which contains mainly inactive DNA but provides structural support to the chromosomes. Heterochromatin is further divided into constitutive heterochromatin, which contains repetitive sequences, and facultative heterochromatin, which may sometimes be expressed as proteins.

What are the two types of chromatin remodeling?

Chromatin remodeling is a dynamic process that allows access to condensed genomic DNA to regulatory transcription machinery proteins, controlling gene expression. This process is primarily carried out by covalent histone modifications by specific enzymes, such as histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and ATP-dependent chromatin remodeling complexes that move, eject, or restructure nucleosomes.

Chromatin remodeling also plays an epigenetic regulatory role in various biological processes, including egg cell DNA replication, apoptosis, chromosome segregation, development, and pluripotency. Aberrations in chromatin remodeling proteins are associated with human diseases, including cancer.

The transcriptional regulation of the genome is primarily controlled at the preinitiation stage by binding core transcriptional machinery proteins to the core promoter sequence on the coding region of the DNA. However, DNA is tightly packaged in the nucleus with the help of packaging proteins, primarily histone proteins, which form repeating units of nucleosomes that occlude many DNA regulatory regions. Chromatin remodeling alters nucleosome architecture to expose or hide regions of DNA for transcriptional regulation.