Nucleic Acids Research, Vol 27, Issue 5 1243-1250, Copyright © 1999 by Oxford University Press
DM Prescott
Genes in the germline (micronuclear) genome of hypotrichous ciliates are
interrupted by multiple, short, non-coding, AT-rich sequences called
internal eliminated segments, or IESs. During conversion of a micronucleus
to a somatic nucleus (macronucleus) after cell mating, all IESs are excised
from the germline genes and the gene segments, called macronuclear-destined
segments, or MDSs, are spliced. Excision of the approximately 150 000 IESs
from a haploid germline genome in Oxytricha nova requires approximately 150
000 recombinant events. In three of 10 genes the MDSs are scrambled. During
macronuclear development the MDSs are unscrambled, possibly by folding of
the DNA to allow MDSs to ligate in the correct order. The nine MDSs in the
actin I gene of O.nova are scrambled in the random order,
3-4-6-5-7-9-2-1-8, and MDS 2 is inverted. The 14 MDSs in the alphaTP gene
of O.nova and Stylonychia mytilus are scrambled in the non-random order,
1-3-5-7-9-11-2-4-6-8-10- 12-13-14. The 45 MDSs in the DNA pol alpha gene
are non-randomly scrambled into an odd/even series, with an inversion of
one-third of the gene. Additional IESs have been inserted into these three
genes during evolution of Oxytricha trifallax, slightly modifying
scrambling patterns. The non-random scrambled patterns in the alphaTP and
DNA pol alpha genes are explained by multiple, simultaneous IES insertions.
The randomly scrambled pattern in the actin I gene may arise from an
initially non-randomly scrambled pattern by recombination among multiple
IESs. Alternatively, IESs inserted sporadically (individually) in a
non-scrambled configuration might subsequently recombine, converting a
non-scrambled gene into a randomly scrambled one. IESs shift along a DNA
molecule, most likely as a result of mutations at MDS/IES junctions.
Shifting of IESs has the effect of 'transferring' nucleotides from one MDS
to another, but does not change the overall sequence of nucleotides in the
combined MDSs. In addition to shifting in position, IESs accumulate
mutations at a high rate and increase and decrease in length within a
species and during speciation. The phenomena of IESs and of MDS scrambling
represent remarkable flexibility of the hypotrich genome, possibly
reflecting a process of MDS shuffling that facilitates the evolution of
genes.
REVIEWS
The evolutionary scrambling and developmental unscrambling of germline genes in hypotrichous ciliates
Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA. prescotd@spot.colorado.edu
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