The strange genome of Oxytricha

Joel Duff (
Mon, 28 Sep 1998 12:11:19 -0700


Following up on an example presented by Shapiro in a recent seminar I
looked up some articles on the genome of Oxytricha. First I must correct
one error in my recent post. I believe I indicated that this organisms
splices itself up into many small pieces which it then reassembles at a
later point but this is not quite accurate as will be explained below.

To give you some idea of the wild reorganizations that this organism puts
its genome through I will quite several paragraphs from Prescott 1992
Trends in Genetics 8(12):439-445.

"Hypotrichs contain both a germ-line nucleus (micronucleus) and a somatic
nucleus (macronucleus). Following cell mating a copy of the micronucleus
gives rise to a new macronucleus, and the old macronucleus is destroyed.
The micronuclear genome has evolved remarkable features in its DNA
organization that are altered during the development of a micronucleus into
a macronucleus. For example, all genes in the micronuclear genome are
interrupted by "nonfunctional" sequences that are spliced out of the DNA to
make functional macronuclear genes during development. Functional segments
within some micronuclear genes are scrambled, and these segments are
spliced into a different order during development of the macronuclear
genes. Also, massive elimination of micronuclear DNA sequences yields a
macronucleus with a much lower sequence complexity. Finally, during
processing every macronuclear gene comes to reside in a physically
separate, small DNA molecule. Each different DNA molecule is amplified to
bout 1000 copies in the DNA-rich macronucleus" pg 439

The micronucleus:
"The DNA in micronuclear chromosomes has the very high molecular weight
(more than 1000 kbs) typical of eukaryotic chromosomes. Genes occur in
groups along the DNA molecule, with short sequences between genes within a
group, and much longer repetitive and unique sequences between groups of
genes. The genes in micronuclear DNA are silent in vegetatively growing
cells; for example, no RNA synthesis is detectable by autoradiography. The
micronucleus undergoes meiosis when cells mate. ... Cells in a mated pair
exchange haploid micronuclei. An exchanged micronucleus fuses with a
stationary micronucleus to make a new diploid micronucleus in each cell.
The cells separate, and the new micronucleus divides by mitosis without
cell division. One daughter micronucleus remains as the germ-line nucleus,
and the other develops into a new somatic macronucleus over several days.
While the new macronucleus is forming, the old macronuclei are degraded,
along with left over diploid and haploid micronuclei.


"The organization of DNA is dramatically changed during development of a
micronucleus into a macronucleus. In the macronucleus all the DNA occurs
as short molecules ranging in size from a few hundred base pairs to about
15,000 bp with an average size of around 2200 bp, varying slightly from one
hypotrich species to another. Each DNA molecule contains a single
transcription unit, or gene. ..........
The gene-sized molecules are crated by excision of genes from the
micronuclear chromosomes. In the process, all repetitious sequences and
all nongenic unique sequences, accounting for about 95% of the germ-line
DNA complexity in Oxytricha, are eliminated. Thus, the gene-sized
macronuclear DNA molecualres represent only about 5% of the germ-line DNA
sequences. These sequences encode all the nuclear RNA needed for
vegetative growth. The macronucleus contains roughly 24,000 different
molecules, each with an average of about 1000 copies, although some, such
as the molecules encoding rRNA, are differentially amplified further to
about 100,000 copies. Altogether, a macronucleus in O. nova contains about
2.5 x 107 gene-sized molecules. "

One of the most amazing things is the presence of internal eliminated
sequences (IESs) which are sequences found in every micronuclear gene yet
examined. Further the Macronuclear destined sequences (MDSs) may actually
be scrambled in order such that more than simple splicing and attachment of
an ordered set of exons is required to reproduce a functional gene. One
of the most dramatic examples of this is the DNA polymerase alpha gene
which consists of 45 MDSs and 36 IESs. Not only that but the MDSs are
quite scrambled and half of them are transcribed on the opposite strand.

That the genome can be rearranged within the micronucleus can be clearly
demonstrated by looking at closely related species and genera. Let us take
the example of Beta-TP gene for two species of oxytricha and one of

O. nova MDS1/IES1/MDS2+intron/IES2/MDS3/IES3/MDS4
S. mytilus MSD1/IES1/MDS2+intron/IES2/MDS3
O. trifallax

So far the majority of genes examined show interspecific and intraspecific
organizations of MDS and IES elements. It is the recombination between
IESs that quite possible results in the scrambled MDSs (genes) and likely
creates many novel open reading frames as a result of mixing and matching
of different MDSs. What is even more surprising is that this isn't just
losses and gains and particular sites but can involve significant changes
in nucleotide sequence at the interchange points. See DuBois and Prescott
(1995) PNAS 92:3888-3892 for more details. This is from the abstract of
that paper:

"... Here we report that the micronuclear actin I gene in Oxytricha
trifallax WR consists of 10 MDSs and 9 IESs compared to the previously
reported 9 MDSs and 8 IESs in the micronuclear actin I gene of Oxytricha
nova. The MDSs in the actin I gene are scrambled in a similar pattern in
the two species, but the positions of MDS-IES junctions are shifted by up
to 14 base bp for scrambled and 138 bp for the nonscrambled MDSs. The
shifts in MDS-IES junctions created differences in the repeat sequences
that are believed to guide MDS splicing. "

The strange genome of Oxytricha is not the only example but rather the
whole order Hypotrichida shows a propensity for this type of genome
rearrangement. Truly fascinated and awe-inspiring stuff. May we praise
the Lord for his truly awesome creation!

Joel Duff
Southern Illinois University

Additional refs:
Prescott D. M. and M. L. DuBois (1996) Internal eliminated segments (IESs)
of Oxytrichidae. Journal Eukaryotic Microbiology 43(6):432-441

Dubois, M. L. and D. M. Prescott (1995) Scrambling of the actin I gene in
two Oxytricha species. Proceedings National Academy Sciences USA 92:3888-3892

Jacobs M. E. and L. Klobutcher, L (1996) The long and short of
development DNA deletion in Euplotes crassus. Journal Eukaryotic
Microbiology 43(6):442-452