PLANT GENOMIC

Eukaryotic genome
● Eukaryotic cells must fit approximately up
to 2 m of unpacked DNA into the spherical
nucleus, which is a less than 10-micron
diameter space (1 μm = 10-6 m) (Fig. 3.1).

● This represents a packaging ratio of

approximately 1000- to 10,000-fold. This
wondrous feat is accomplished by the
packing of linear DNA molecules into
chromatin (DNA with its associated
proteins).
● In eukaryotes, the term genome is
often used interchangeably with
the terms genomic DNA,
chromosomal DNA, or nuclear
DNA (to distinguish it from
organelle or plasmid DNA).

● The compaction (Fig. 3.2.) of the

genome into chromatin forms the
substrate relevant to the vital
processes of DNA replication,
recombination, transcription,
repair, and chromosome
segregration.
Chromatin structure:
● The first clear insights into
chromatin structure came
about by serendipity.
● Nuclease experiments
performed for other reasons
revealed that the DNA in
chromatin degrades into a
series of discrete fragment sizes
separated by 180 bp (Fig. 3.3).
● This fragment size is now known
to represent the DNA associated
with a single nucleosome
(mononucleosome).
 Histones
Two types of histones exist,
the highly conserved core
histones (molecular weight
11,000–16,000 daltons or Da)
and the much more variable
linker histones (slightly larger,
> 20,000 Da) (Fig. 3.4).
● The core histones are present in the
nucleosome as an octamer composed of
a dimer of histones H2A and H2B at
each end and a tetramer of histones H3
and H4 in the center, around which 146
bp of genomic DNA is wound (Fig.
3.5).
● The linker histone H1 (or alternative
forms such as histone H5 and H1°)
occurs between core octamers, where
the DNA enters and exits the
nucleosome.
 Nucleosomes
● The term “nucleosome” specifically refers to the core octamer of
histones plus the linker histone and approximately 180 bp of DNA.
● The core particle is comprised of 146 bp DNA plus the core histone
octamer.
● The core histone octamer acts like a spool; the negatively charged DNA
wraps nearly twice around the positively charged histones in 1.67 left-
handed superhelical turns (Fig. 3.5).
● Histones can be removed from DNA by high salt concentration, so the
major interactions between DNA and the core histones appear to be
electrostatic in nature.
 Beads-on-a-string: the 10 nm fiber
● The beads-on-a-string appearance of chromatin can be visualized by
electron microscopy as a 10–11 nm fiber after low salt extraction (Fig.
3.2).
● The beads represent DNA wrapped around the histone core octamer and
the string represents the DNA double helix.
● The linker histone is not required for this level of packing.
● Since isolation occurs under nonphysiological conditions, the question
remains as to whether the 10–11 nm fiber is present in vivo or is a
consequence of the extraction procedure.
 The 30 nm fiber

● Chromatin released from nuclei by nuclease digestion has the canonical beads-on-
a-string structure in lower salt concentrations (≤ 10 mm).

● On the addition of salt (i.e. increasing the ionic strength), or when observed in situ,
nucleosomal arrays form a compact fiber of approximately 30 nm in diameter.

● Because of the difficulty in maintaining the integrity of this fragile chromatin

structure during isolation, the structure remains poorly understood.
 Loop domains
● The 30 nm fiber is, in turn, further compacted into structures not yet
fully understood. Looped domains form that contain 50–100 kb of DNA
(the length of loops is approximately 0.25 μm) (see Fig. 3.2).

● These loops may be created by attaching DNA to proteins associated

with an underlying nuclear scaffold.

● In the interphase of the cell cycle, the packing ratio is 1000-fold.

Organelle Genomes: Chloroplasts And
Mitochondria
● Both mitochondria and chloroplasts contain
their own genetic information (Fig. 3.9).

● The genomes are usually, but not always,

circular. In circular form, the mitochondrial and
chloroplast genomes look remarkably similar to
bacterial genomes.

● This similarity, along with other observations,

led to the “endosymbiont hypothesis” – the idea
that both mitochondria and chloroplasts are
derived from primitive organisms that were
free-living and much like bacterial organisms.
● Organelle genomes are inherited independently of the nuclear genome
and they exhibit a uniparental mode of inheritance, with traits being
passed to offspring only from their mother.

● The organelles are only contributed from the maternal gamete (e.g. egg
cell), and not from the paternal gamete (e.g. sperm cell or pollen grain).
 Chloroplast DNA (cpDNA)
● Chloroplasts are found in higher plants, some protozoans, and algae.
The cpDNA encodes enzymes involved in photosynthesis.

● The most standard depiction of cpDNA is as a circular, double-stranded

DNA molecule, ranging in size from 120 to 160 kb, with 20–40 copies per
organelle.

● However, this is a subject of debate. Recent studies suggest that, in fact,

most cpDNA is linear and only a minor amount is in a circular form.

● Whatever the form, cpDNA is free of the associated proteins

characteristic of eukaryotic DNA. Compared with nuclear DNA of the
same organism, it has a different buoyant density and base composition.
 Mitochondrial DNA (mtDNA)
● Mitochondria are found in plants, animals, fungi, and aerobic protists.
The mtDNA encodes essential enzymes involved in ATP production
(Disease box 3.1).
● mtDNA is usually a circular, double-stranded DNA molecule that is not
packaged with histones.
● There are a few exceptions where mtDNA is linear, generally in lower
eukaryotes such as yeast and some other fungi.
● mtDNA differs greatly in size among organisms. In animals, it is typically
16–18 kb, while in plants it ranges in size from 100 kb to 2.5 Mb.
● There are multiple copies of mtDNA per organelle, with anywhere from
several to as many as 30 copies in Euglena protozoans.