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microtubule-deficient macronuclei 
can divide as the somatic cortex appears to play 
a crucial role in positioning and even elongating 
the macronucleus (Jaeckel-Williams, 1978; Tucker 
et al., 1980). Microtubules and microfilaments are 
also implicated in micronuclear division , although 
the relative importance of each to chromosomal 
movement has not been resolved (LaFountain & 
Davidson, 1980; Lewis, Witkus, & Vernon, 1976). 
 Spindle microtubules in the dividing micronucleus 
of Paramecium typically have 15 protofilaments 
compared to the “normal” 13 for other organelles 
(Eichenlaub-Ritter & Tucker, 1984). 
 The macronucleus in oligohymenophoreans , as 
for ciliates in general, varies in size, and therefore 
DNA amount, with cell size (e.g., Kazubski, 1963; 
Lynn & Berger, 1972, 1973; Morat, 1982). Division 
of the macronucleus is often slightly unequal 
(Berger, 2001; Morat, 1982). Yet, ciliates maintain 
a roughly proportional nuclear:cytoplasmic ratio 
over the course of many cell cycles. The mecha-
nisms responsible for this regulation have been 
extensively explored, especially in Paramecium
(Berger, 2001). Nilsson (2000) has argued that the 
minimal units of segregation during macronuclear 
division in Tetrahymena represent full genomes, 
although how this is accomplished remains to be 
 The macronucleus in oligohymenophoreans 
develops from a product of the zygotic nucleus , 
which typically divides two or three times to pro-
vide nuclei for differentiation (Raikov, 1972). The 
 macronuclear anlage undergoes a series of changes 
in its fine structure until it has developed nucleoli 
and begins transcription (Weiske-Benner & Eckert, 
1985). As in the spirotrichs ( see Chapter 7 ), the 
development of the oligohymenophorean anlage 
involves DNA amplification , chromosome frag-
mentation , sequence elimination , addition of telom-
eres , and amplification of some genes, particularly 
ribosomal genes (Prescott, 1994; Schmidt, 1996). 
Moreover, this development may be epigenetically 
regulated by the parental or maternal macronu-
cleus, even to the level of the precise excision of 
eliminated sequences (Meyer & Duharcourt, 1996; 
Preer, 2000). 
 Much of the research on oligohymenophoreans 
has focused on Paramecium and Tetrahymena in 
which chromosome fragmentation and sequence 
elimination occur by different mechanisms. In 
Paramecium , a terminal inverted repeat unit flanks 
the internally eliminated sequences (IESs) and 
bears some similarity to the transposable elements 
found in spirotrichs (Klobutcher & Herrick, 1995, 
1997). The quality of this flanking sequence is 
critical as single base pair changes in it can prevent 
IES elimination (Mayer, Mikami, & Forney, 1998; 
Matsuda, Mayer, & Forney, 2004). In Tetrahymena , 
a consensus sequence has not been identified, appar-
ently leading to less precision in the elimination of 
sequences (Austerberry, Snyder, & Yao, 1989; 
Yao, Duharcourt, & Chalker, 2002). However, 
there is an internal 10-bp core to the chromosome 
breakage sequence – AAACCAACC?C – that is 
completely conserved and possibly represents a 
regulatory protein binding site (Hamilton et al., 
2006). Sequence−specific information may also be 
provided by molecules, for example by small RNAs, 
that derive from the parental macronucleus and that 
can control DNA rearrangements and processing in 
the developing macronucleus through homology-
dependent mechanisms (Kowalczyk, Anderson, 
Arce-Larreta, & Chalker, 2006; Le Mouel, Butler, 
Caron, & Meyer, 2003; Meyer, Butler, Dubrana, 
Duharcourt, & Caron, 1997). 
 In both cases, the processes of fragmentation of 
and excision from micronuclear chromosomes result 
in macronuclear “chromosomes” that are shorter than 
the micronuclear chromosomes, although not as short 
as the gene-sized pieces of spirotrichs ( see Chapter 7 ). 
 Oligohymenophorean macronuclear chromosomes 
range in size from from 20–2,500 kb for Paramecium
species (Rautian & Potekhin, 2002; Steele, Barkovy-
Gallagher, Preer, & Preer, 1994), from 21–1,500 kb 
in Tetrahymena (Altschuler & Yao, 1985; Conover 
& Brunk, 1986), and from 2–300 kb in Glaucoma
(Katzen, Cann, & Blackburn, 1981). Breakage of 
 micronuclear chromosomes forms many new chro-
mosome “ends”, and this has provided ciliate molecu-
lar biologists with a useful model to investigate the 
structure, formation, and maintenance of telomeres 
(Blackburn, 1986). The CCCCAA oligonucleotide 
repeat characterizes the telomeres of the macronu-
clear chromosomes of Tetrahymena (Blackburn & 
Gall, 1978; Yao & Yao, 1981), Glaucoma (Katzen 
et al., 1981), and Paramecium (Yao & Yao, 1981). The 
abundance of ends and the need for their re-construc-
tion and maintenance lead to the discovery of the 
ribonucleoprotein enzyme complex responsible for 
these processes, now called telomerase (Blackburn, 
1992; Greider & Blackburn, 1987). 
 Some years prior to these discoveries, it had 
been possible to separate micronuclei and macro-
nuclei, so that at least pure macronuclear prepara-
tions could be analyzed for sequence complexity 
(Gorovsky, Yao, Keevert, & Pleger, 1975; Soldo & 
Godoy, 1972). With renaturation kinetic analyses, 
15.6 Nuclei, Sexuality and Life Cycle 321
most macronuclear DNA sequences behaved as 
unique sequences, with very little highly repeated 
sequences and up to 20% moderately repetitive 
(McTavish & Sommerville, 1980; Soldo & Godoy; 
Yao & Gorovsky, 1974). The highly and moder-
ately repetitive fraction are apparently eliminated 
during development of the macronuclear anlage 
(Yao & Gall, 1979). 
 As for other classes of ciliates, examples are now 
accumulating of genetic code deviations among 
 oligohymenophoreans . Of the three universal stop 
codons – UAA, UGA, and UAG, oligohymeno-
phoreans , such as the hymenostome Tetrahymena
(Horowitz & Gorovsky, 1985), the peniculine 
Paramecium (Caron & Meyer, 1985; Preer, Preer, 
Rudman, & Barnett, 1985), and the peritrichs 
Vorticella and Opisthonecta (Sánchez-Silva et al., 
2003) use only UGA. The codons UAA and UAG 
are now used by Paramecium and Tetrahymena
as sense codons for glutamine and glutamic acid 
(Caron & Meyer; Preer et al., 1985), while UAA 
has been confirmed as the “glut” codon in peri-
trichs (Sánchez-Silva et al., 2003). There are two 
explanations for these deviations. First, tRNAs have 
been described that decode for these novel amino 
acid assignments (Hanyu, Kuchino, & Nishimura, 
1986; Sánchez-Silva et al., 2003). As with genetic 
code deviations in other ciliates, another explana-
tion is the evolution of translational release factors 
with a higher specificity for one or other of the 
universal stop codons (Caron, 1990). This predic-
tion was confirmed by analyses of the spirotrich 
eukaryotic release factor 1, which is the protein 
that recognizes stop codons and terminates transla-
tion (Inagaki & Doolittle, 2001; Lozupone, Knight, 
& Landweber, 2001). This higher specificity then 
allowed the evolution of tRNA anticodons to use 
the now-available and unused stop codons. 
 Conjugation of oligohymenophoreans , typed 
as temporary and equal or isogamontic in most 
groups, was first described by Hertwig (1889) in 
Paramecium (Raikov, 1972). However, the peri-
trichs conjugate by total cell fusion, typically of 
unequal-sized conjugants ; they are therefore ani-
sogamontic (Raikov, 1972). The macroconjugant is 
large and sessile while the microconjugant is small 
and free-swimming. Microconjugants may arise by 
unequal cell division, rapid successive divisions 
without intervening growth or direct transforma-
tion of microzooids in Zoothamnium species that 
show colonial polymorphism (Raikov, 1972). The 
endosymbiotic apostome Collinia , described by 
Collin (1909a) as an Anoplophrya species, appears 
to undertake