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#DNA packaging

9 public questions tagged with this topic.

Microbial Physiology

Which of the following archaeal species does NOT contain histones?

Histones were long considered exclusive to eukaryotes, organizing DNA into nucleosomes with wrapping around octameric cores. Discovery of archaeal histones revealed evolutionary connection, yet distribution is not uniform. Euryarchaeota such as Methanothermus fervidus, Methanothermus sociabilis, and halophiles like Halobacterium salinarum encode HMf and HMt family histones that form tetramers wrapping DNA into nucleosome-like particles and regulating transcription by restricting access. These histones share histone fold motif with eukaryotic H3 and H4. In contrast, most members of Crenarchaeota, particularly hyperthermophilic genera like Sulfolobus acidocaldarius, Thermoproteus, and Pyrolobus, lack sequence homologs of true histones and instead use alternative DNA packaging proteins such as Alba, Sul7d, and Cren7 that coat DNA and introduce supercoiling. This pattern suggests histone-based chromatin is characteristic of Euryarchaeota rather than all archaea, reflecting diverse strategies for genome compaction under extreme conditions and differing sensitivity to thermal denaturation, influencing gene regulation and adaptation. Alba proteins abundant in Sulfolobus bind cooperatively to double-stranded DNA, bridging strands, regulating transcription and protecting against thermal denaturation, illustrating how crenarchaeota employ non-histone architectural proteins functionally analogous to histones yet structurally unrelated, diversifying chromatin strategies across archaeal phylum.

Ref: Sandman & Reeve, Curr Opin Microbiol 2006, Archaeal Histones; White & Bell, Trends Genet 2002, Chromatin in Archaea.

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Cytoskeleton Cilia Flagella Centrosome Nucleus and Chromosomes

A human cell is examined first during interphase and then during cell division. During interphase, its approximately two

Interphase chromatin is loose and indistinct, whereas structured chromosomes become visible during cell division. A centromere slightly away from the middle produces one shorter and one longer arm, identifying a submetacentric chromosome.

Ref: NCERT Class 11 Biology Chapter 8: Cell: The Unit of Life Cytoskeleton Cilia Flagella Centrosome Nucleus and Chromosomes

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Regulation of chromatin structure

How many base pairs of DNA are wrapped around the histone octamer?

Structural biology consensus derived from multiple crystal forms and cryoEM shows nucleosome core particle wraps 146 to 147 base pairs of DNA in 1.65 left-handed superhelical turns around histone octamer disc, creating 14 minor groove contacts. Early nuclease protection assays estimated 146 base pairs resistant to micrococcal digestion. Chromatosome including H1 adds twenty base pairs bringing protection to 167 base pairs. Values 120 base pairs underrepresent wrapped length, 200 equals full repeat with linker, 33 base pairs corresponds roughly to single superhelical turn. This conserved length reflects requirement to bend DNA around octamer while exposing tails for regulation across eukaryotes.

Ref: Luger et al., 1997 2.8 Å Structure; Richmond and Davey 2003: 146-147 bp Wrapped Around Octamer

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Nucleosome Packing

Negative supercoiling in nucleosome is introduced due to:

Topological analysis demonstrates wrapping DNA in left-handed superhelix around histone octamer introduces negative supercoiling, equivalent to underwinding helix and decreasing linking number. When plasmid DNA assembles into nucleosomes in extracts depleted of topoisomerases, agarose gel electrophoresis with intercalators shows more negative writhe, allowing eukaryotes to store negative supercoils without bacterial gyrase. Right-handed wrapping would create positive supercoiling contrary to observations. H1 binding stabilizes fiber but does not generate writhe, methylation adds epigenetic mark without topology change. Negative supercoiling facilitates DNA strand separation during transcription.

Ref: Germond et al., PNAS 1975; Lewin, Genes XII, Negative Supercoiling due to Left-handed Wrap

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Nucleosome Packing

Histone tails emerge from nucleosome core through:

High resolution nucleosome structure at 2.8 angstrom shows histone tails exit core not through gaps at sides but threading between DNA gyres through channels formed where minor grooves face octamer. At specific superhelical locations DNA grooves widen permitting basic tails to protrude without disrupting tight histone-DNA wrapping mediated by arginine anchors. Tail emergence through minor groove allows enzymes like GCN5 acetyltransferase and kinases access for modification while maintaining core stability. Major groove exit would clash with phosphate backbone, linker DNA path distinct from tail path. Thus tails emerge via minor groove regions.

Ref: Luger and Richmond 1998 Crystal; Alberts et al., Molecular Biology of the Cell, Chapter 4: Histone Tail Emergence Minor Groove

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Nucleosome Packing

The 11 nm fiber is also called:

Electron microscopy of chromatin isolated in low ionic strength buffer reveals necklace-like organization: 11 nanometer particles spaced by thin linker DNA resembling beads on string. This configuration corresponds to extended primary chromatin fiber without H1-mediated coiling, exposing nucleosomes individually. Solenoid model describes 30 nanometer helix with six nucleosomes per turn, zig-zag describes two-start helix of 30 nanometer fiber, loop fiber denotes scaffold-anchored 300 nanometer domain. Beads-on-string visualization requires low salt to prevent folding, providing classic illustration of first level packing and histone octamer as repeating bead.

Ref: Olins and Olins 1974 J Cell Biol; Alberts et al., Chapter 4: 11 nm Fiber Called Beads-on-String

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Nucleosome Packing

Number of turns of DNA around histone octamer is:

Quantitation of DNA trajectory around histone octamer shows slightly more than one and half circles. High resolution structures measure 1.65 to 1.67 superhelical turns protecting 147 base pairs, about 83 base pairs per full superhelical turn, creating fourteen histone-DNA contact points via arginine side chains inserted into minor grooves. One turn would protect only 80 base pairs, two full turns would need 166 base pairs which exceeds core length. Value 1.65 explains why linker DNA emerges close together, why H1 can bridge entry exit and sealing two turns, enabling higher order folding into 30 nanometer fiber.

Ref: Luger et al., Nature 1997; Lodish et al., Molecular Cell Biology, 9th ed., 1.65 Turns of DNA

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