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European Journal of Protistology 61 (2017) 399–408
REVIEW
Unusual features of non-dividing somatic macronuclei in the ciliate class Karyorelictea
a,b b a b,c,∗
Ying Yan , Anna J. Rogers , Feng Gao , Laura A. Katz
a
Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
b
Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
c
Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
Available online 22 May 2017
Abstract
Genome structure and nuclear organization have been intensely studied in model ciliates such as Tetrahymena and Paramecium,
yet few studies have focused on nuclear features of other ciliate clades including the class Karyorelictea. In most ciliates, both
the somatic macronuclei and germline micronuclei divide during cell division and macronuclear development only occurs after
conjugation. However, the macronuclei of Karyorelictea are non-dividing (i.e. division minus (Div−)) and develop anew from
micronuclei during each asexual division. As macronuclei age within Karyorelictea, they undergo changes in morphology and
DNA content until they are eventually degraded and replaced by newly developed macronuclei. No less than two macronuclei
and one micronucleus are present in karyorelictid species, which suggests that a mature macronucleus 1) might be needed
to sustain the cell while a new macronucleus is developing and 2) likely plays a role in guiding the development of the new
macronucleus. Here we use a phylogenetic framework to compile information on the morphology and development of nuclei in
Karyorelictea, largely relying on the work of Dr. Igor Raikov (1932–1998). We synthesize data to speculate on the functional
implications of key features of Karyorelictea including the presence of at least two macronuclei in each cell and the inability
for macronuclei to divide.
© 2017 The Authors. Published by Elsevier GmbH. This is an open access article under the CC BY-NC-ND license (http://
creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Karyorelictea; Non-dividing macronuclei; Nuclear architecture
Introduction and Blackburn 1985). Yet the bulk of the work on ciliates
has predominately focused on only a few lineages, such as
Ciliates are a clade of single-celled eukaryotes defined by Paramecium and Tetrahymena (Class Oligohymenophorea;
the presence of cilia and dimorphic nuclei (Kovaleva and Aury et al. 2006; Chalker 2008; Eisen et al. 2006; Mochizuki
Raikov 1992; Prescott 1994; Raikov 1982, 1985). Numerous and Gorovsky 2004; Yao 2008) and Oxytricha and Stylony-
key discoveries have been made through studies of cili- chia (Class Spirotrichea; Chen et al. 2014; Nowacki et al.
ates, including the discovery of self-splicing RNA (Cech 2008).
1986; Kruger et al. 1982) and telomeres/telomerases (Greider As described in detail below, the monophyletic class
Karyorelictea, the focus of this manuscript, appears unique
∗ among ciliates in that their somatic macronuclei cannot divide
Corresponding author at: Department of Biological Sciences, Smith Col-
(Table 1; Raikov 1982). Instead, Karyorelictea differentiate
lege, 44 College Lane, Northampton, MA 01063, USA. Fax: +1 413 585
3786. new macronuclei from micronuclei with each cell division
E-mail address: [email protected] (L.A. Katz).
http://dx.doi.org/10.1016/j.ejop.2017.05.002
0932-4739/© 2017 The Authors. Published by Elsevier GmbH. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/ licenses/by-nc-nd/4.0/).
400 Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408
Table 1. Unusual nuclear features in karyorelictids in comparisons with other major ciliates classes.
a c
Subphylum Class Mac Div Mac Mac differentation Mac aging b
differentation during asexual
post conjugation division
Postciliodesmatophora Karyorelictea Div− + + +
Heterotrichea Div+ + − −
Intramacronucleata Litostomatea Div+ + − −
− −
Armophorea Div+ +
Spirotrichea Div+ + − −
Colpodea Div+ + − −
Nassophorea Div+ + − −
Phyllopharyngea Div+ + − −
Prostomatea Div+ + − −
Plagiopylea Div+ + − −
Oligohymenophorea Div+ + − −
a
Ability of macronuclear division. b Macronuclear differentiation.
c
Macronuclei age as they persist through several generations without dividing (see text for more detail).
and an individual macronucleus only persists for a few gen- tivable, the genus Loxodes has been cultivated successfully
erations before degrading (Table 1; Raikov 1985). In all other in a few labs (e.g. Bobyleva 1981; Buonanno et al. 2005;
ciliates, the macronuclei divide by amitosis (i.e. dividing Finlay et al. 1986), likely accounting for the limited data on
without centromeres and metaphase plates) during vegetative this clade.
growth and only differentiate from zygotic nuclei following Here we describe some unusual features within the class
conjugation (e.g. Gao et al. 2016; Raikov 1982). Through- Karyorelictea, focusing on their somatic macronuclei. We
out the remainder of this manuscript, we use the abbreviation divide the manuscript into three parts: 1) a description of the
−
Div to describe the absence of macronuclear division in contributions from Dr. Igor Raikov, who generated the bulk
Karyorelictea; all remaining classes of ciliates are Div+ of data on members of the class Karyorelictea; 2) insights into
as they contain macronuclei that divide through amitosis the cell biology of the Karyorelictea based on microscopic
(Table 1). analyses; and 3) knowledge of life cycles, and particularly
The class Karyorelictea is composed of ∼170 ciliate macronuclear development, in diverse lineages within the
morphospecies divided into six families (Loxodidae, Trach- class Karyorelictea. Finally, we end with hypotheses on the
elocercidae, Kentrophoridae, Geleiidae, Cryptopharyngidae evolutionary significance of Div− macronuclei.
and Wilbertomorphidae; Fig. 1; Lynn 2008). However,
limited molecular data are available in karyorelictids; for
Raikov and Karyorelictea
example, as we write this manuscript, only eight protein-
coding genes have been released on GenBank for the
Dr. Igor B. Raikov (1932–1998) was the leading researcher
class Karyorelictea. The current phylogeny of Karyorelictea
in the study of Karyorelictea, and most information about
has largely relied on small subunit rDNA sequences (e.g.
these ciliates stems from his work and the work of his col-
Andreoli et al. 2009; Campello-Nunes et al. 2015; Gao et al.
laborators. Raikov characterized in detail the fine structure
2016; Xu et al. 2015; Yan et al. 2016), with the excep-
of nuclei for more than 20 karyorelictid species, including
tion of the family Cryptopharyngidae for which there are
representatives from four of the six families in Karyorelictea
currently no molecular data. Phylogenetic analyses indicate
(e.g. Kovaleva and Raikov 1992; Raikov 1982, 1985; Raikov
that both the class Karyorelictea and its five families with
and Karadzhan 1985; Raikov and Kovaleva 1990). Using an
molecular data are monophyletic and fall sister to the class
impulse cytofluorimeter, Raikov isolated individual nuclei
Heterotrichea, the other member of the subphylum Postcil-
and measured their DNA content. From these data on the
iodesmatophora (Campello-Nunes et al. 2015; Gao and Katz
morphology and DNA content of karyorelictid nuclei, Raikov
2014; Gao et al. 2016; Xu et al. 2015; Yan et al. 2016). Most
and his collaborator, Dr. Valentine G. Kovaleva, described the
karyorelictids are specialized to interstitial marine environ- −
Div macronuclei as “paradiploid”, implying that mature
ments such as sand, and recently they were also found to be
macronuclear are nearly diploid and similar to micronuclei
epibionts of benthic harpacticoid copepods in the deep sea
in DNA content (Kovaleva and Raikov 1978; Ovchinnikova
(Sedlacek et al. 2013); the one exception is the genus Lox-
et al. 1965), which is unusual as the macronuclei in other
odes, which is found in low oxygen freshwater environments
ciliate species can be highly polyploid (for example 45 in
(Fenchel 1967, 1968; Finlay and Fenchel 1986). Additionally,
Tetrahymena, 800 in Paramecium and ∼13150 in Spirosto-
while none of the rest of Karyorelictea are reported as cul-
mum; Duret et al. 2008; Ovchinnikova et al. 1965; Woodard
Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408 401
Fig. 1. A cartoon tree of Karyorelictea showing main diversity of nuclear clustering within and among families based on small subunit rDNA
(SSU-rDNA) maximum likelihood tree. Cell sizes are drawn roughly to scale. There are currently no molecular data on Cryptopharyngidae
(*); thus it is displayed as an orphan family. Scale bar: 100 m.
et al. 1972). Raikov’s many other contributions are high- be nuclei enclosed by a fused membrane or nuclei that
lighted in some of the work we review below. are closely associated with one another. A unit of two
macronuclei and one micronucleus is the smallest and most
frequent grouping, though groups of four macronuclei and
two micronuclei are also commonly described in karyore-
Part I: nuclear structure
lictid species (Raikov 1994). Many karyorelictids possess
multiple groups of either 2 + 1 or 4 + 2 units (e.g. Trachelo-
Insights from light microscopy
raphis oligostriata and T. colubis; Fig. 1; Al-Rasheid 2001;
As in all other ciliates, karyorelictids have both somatic
Xu et al. 2011b). Free nuclei, which are common in other
macronuclei and germline micronuclei in every individ-
multinucleate ciliates, are also often found in multinucle-
ual cell. The majority of macronuclei and micronuclei in
ate karyorelictids (e.g. Kentrophoros flavus and K. gracilis;
Karyorelictea are spherical or elliptical, and are usually
Fig. 1), and in many cases, these free nuclei form a longitu-
5–10 m (macronuclei) and 2–4 m (micronuclei) in diam-
dinal line along the cell meridian (Fig. 1; Xu et al. 2011a).
eter or length (Raikov 1985). Karyorelictean ciliates with
In karyorelictids, nuclear grouping and number of nuclei
only one macronucleus have not yet been found, while this
may relate to body shape and size in some, but not all lineages
arrangement of nuclei is common in all other ciliate classes
(Table 2). In Loxodes and Remanella (Loxodidae), larger
(Lynn 2008; Raikov 1982). This suggests that each karyore-
cells tend to have more macronuclei and micronuclei, but
lictean cell requires a minimum of two macronuclei and one
the same pattern is not found in Trachelocercidae (Table 2).
micronucleus to survive (Andreoli et al. 2009; Lynn 2008;
For example, both Trachelocerca sagitta and Trachelocerca
Raikov 1982).
stephani have single nuclear groups with 4 macronuclei and
Nuclei in karyorelictids can be distributed throughout
2 micronuclei; however, the size of T. sagitta is ∼5 fold that
the cell body or clustered together as “nuclear groups” or
of T. stephani (Table 2). There is also considerable variation
“nuclear complexes” (Fig. 1). Nuclear groups can either
402 Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408 (1996) (1996) (1996) (1996) (1989)
(1983) (1983)
Dragesco Dragesco Dragesco Dragesco Rieder Rieder
Volkonitin (2001)
(2002) (2002) (2002) (2016) (2016) (2013)
(2011b) (2013) (1995) and and and and (1996c) (1996c) and and (1996b) (1996a)
(1994) and
(1973)
al. al. al.
al. al.
et et et
et et
Foissner Foissner Epstein Foissner Raikov Yan Yan Borror Al-Rasheid Dragesco Foissner Foissner Dragesco Dragesco Xu Yan Foissner Foissner Xu Foissner Foissner Foissner Foissner References
mic
group mic
11–54 6–12 5–37
mic mic
× × ×
mic
mic mic mic
3–9 5–12 3–7 10–16
mic mic mic mic 2 2 2
+ + + + mic mic
mic) mic) mic) 1 2
1 1–3
+ + + mic mic mic mic mic mic
3 6
2 1 2 + + + +
2–3 2 2 2 2 1 2 micronucleus.
+ +
+ + + mac mac mac mac
+ + + + + + +
mac mac mac
nuclei/nuclear mac mac mac mac
mac mac Mic, mac mac mac
mac mac mac mac mac of mac mac
6–12 (4 3 7–14 2–3 4 4 4 4 10 2–3 17–39 (4 10–24 3–5 2 2 18–26 16 # m
a macronucleus.
3 2 5 4.5
× × × ×
a 2 6 3.6 3 6 2.2 4 2.6–2.9 2.8–3.6 5 2 3–5 1.5–2 Mic diameter/ Mac,
m species.
9
5.5 6.3 2.2
44
8
×
3.5 52 52 4 6
× ×
× ×
10 2–2.6 5–12 × × × × ×
4 7–105–8 2–4 2–3 3–4 (2 ∼ 7–10 3–6 7.9 8 6 12.5 8 7.3 10 3–5 5–12 2-3 5–6 6.6–9.3 7–8 Mac diameter/
karyorelictid
m
diverse
width/
in
20–30 30 35 62.7 87 90 30 – 50 41–50 80–84 40–80 10–20 25 15 30–40 Cell
group
m
length/
nuclei/nuclear 500–2000 1100–2300 50–60 400–9001000–1500 40–60 30–50 8 6–8 4 285–500 62–75 5–6 2–3 15–43 1300 400–500 15 340 700 1500–2000 75–100 10 437 800–10001000 40–50 10 500–1000 800–1250 300–600 800–1500 1000–3000 180 Cell 209–250 340–440 45 50–90
of
number
aragoi haloetes
obscura incaudata ditis ditis sagitta stephani and
fistulosus
sulcata multinucleata
size
striatus magnus
cell name
of
figure.
Tracheloraphis Kentrophoros Tracheloraphis primitarum Tracheloraphis phoenicopterus Wilbertomorpha Trachelolophos quadrinucleatus Tracheloraphis Tracheloraphis oligostriata Trachelocerca Trachelocerca Trachelolophos binucleatus Trachelocerca Trachelocerca Trachelocerca Trachelocerca Apotrachelocerca arenicola Kovalevaia Prototrachelocerca caudata Prototrachelocerca fasciolata Loxodes Loxodes Remanella Taxa Apocryptopharynx hippocampoides table from
estimated
Summary is
2. available.
not
, Number Kentrophoridae Trachelocercidae Family Wilbertomorphidae Cryptopharyngidae Loxodidae − a Table
Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408 403
Fig. 2. Examples of karyorelictid macronuclei showing different composition of nucleoli (1), crystalloid bodies (2), chromocenters (3) and
unknown spheres (4): A. macronucleus with a single nucleolus and crystalloid plus numerous chromatin bodies (arrowheads) from Trache-
loraphis caudatus (modified from Raikov 1994). B. macronucleus with a large chromocenter, nucleolus and sphere found in Trachelocerca
multinucleata (modified from Raikov 1989). C. macronucleus with a large number of small nucleoli in Geleia orbis (modified from Raikov
1984). D. simple macronucleus with multiple nucleoli Remanella granulosa (modified from SEM in Raikov and Kovaleva 1990).
within species. For example, the length of Prototrachelocerca and are also typically less electron dense than the fibrillar
fasciolata varies between 1000 and 3000 m with 10–24 core of nucleoli (Raikov 1990). No consistent association
macronuclei and 3–7 micronuclei, and Loxodes magnus can between nuclear bodies (spheres or crystalloids) and other
have 8–31 macronuclei and 5–32 micronuclei (Bobyleva et al. nuclear structures has been found in karyorelictean macronu-
1980). clei (Table 3; Raikov 1985, 1990).
Like in other ciliates, no nucleoli nor evidence of RNA syn-
thesis has been found in karyorelictean micronuclei during
Insights from electron microscopy
vegetative stages (Raikov 1982). Compared to macronu-
Fine structure analyses of karyorelictid nuclei reveal vari-
clei, micronuclei stain intensely and homogeneously with
ability in compositions of macronuclei while micronuclei
Feulgen indicating that they are packed with condensed chro-
have more canonical eukaryotic features (Raikov 1985,
matin (Raikov 1985). In Remanella multinucleata and Geleia
1994). In contrast to other ciliates, the somatic macronuclei of
orbis, small nuclear bodies that appear to be crystalloids
Karyorelictea are relatively small, ranging from 5 to 10 m in
are sometimes found in the micronuclear periphery (i.e. the
diameter (Raikov 1982, 1985). Karyorelictean macronuclei
space between the chromatin mass and the nuclear envelope;
are also described as the “vesicular type” due to their shape,
Kovaleva and Raikov 1978; Raikov 1979, 1984).
and they often include nucleoli, chromocenters (i.e. areas of
condensed chromatin), and “nuclear bodies” (Raikov 1985,
1989). Nucleoli in karyorelictids have a similar ultrastructure Part II: development of macronuclei
to other eukaryotes and are described as having a classical fib-
rillar core and granular cortex (Raikov 1985). Nucleoli serve Nuclear reorganization
as the location for the generation of rRNAs (Raikov 1982). The common ancestor of Karyorelictea evolved a
The number of nucleoli varies among karyorelictid species mechanism to segregate nuclei between generations by differ-
from one to over 100 (Fig. 2A–D; Raikov 1985). entiating at least one new macronucleus from a micronucleus
Chromocenters and chromatin bodies are two types of with each division (Orias 1991a). This contrasts with all other
densely staining regions of chromatin varying by size and ciliates in which macronuclei divide through amitosis either
number (Fig. 2A). Chromatin bodies are usually smaller and with microtubules placed inside or outside the macronuclear
more numerous than chromocenters, and chromocenters may envelope (subphylum Intramacronucleata and the class Het-
be formed by the fusion of chromatin bodies (Fig. 2A; Raikov erotrichea, respectively; Lynn 2008).
1979, 1990, 1994). Chromatin bodies may represent lowly Division patterns of Loxodes and lineages with two other
expressed heterochromatin regions, but the functional impli- common nuclear group types in karyorelictids exemplify the
cations of chromocenters are as yet unknown. diversity of processes within this class. In the simplest case
Another unusual aspect of the fine structure of some kary- of two macronuclei and one micronucleus in each cell (e.g.
orelictean macronuclei is the presence of nuclear bodies, Loxodes rostrum; Fig. 3A–D), the two parental macronuclei
which are either classified as spheres or crystalloids (Fig. 2A, are separated into the daughter cells while the micronucleus
B; Table 3; Raikov 1979, 1984, 1985, 1990). These nuclear undergoes mitosis twice (Fig. 3A–C) and two micronuclei
bodies are of unknown function and are not present in all from the second mitosis differentiate into new macronu-
Karyorelictea: for example, they have not been described in clei (Fig. 3C, D; Raikov 1957). In species with two nuclear
the genus Loxodes (Table 3; Raikov 1979, 1990). Crystalloids groups, each with one macronucleus and one micronu-
are typically composed of some type of proteinaceous fila- cleus (e.g. Loxodes striatus), each micronucleus divides once
ments, packed tightly together and parallel, and are usually (Fig. 3E, F), with one of the daughter micronuclei develop-
less electron dense than the fibrillar core of nucleoli (Raikov ing into the new macronucleus while the other divides again
1979, 1985, 1990, 1994). In spheres, filaments are tangled to reset micronuclear number of the daughter cells (Fig. 3G,
404 Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408
H; Raikov 1957). In species with four macronuclei and two
micronuclei in a nuclear group (e.g. Tracheloraphis colu- (1985)
(1978) (1980) (1996)
ber), each nuclear group is divided in half and then each half
(two macronuclei and one micronucleus) undergoes similar (1981)
developmental processes to form a complete nuclear group (1989)
al. Kovaleva Kovaleva Karadzhan Kovaleva
(four macronuclei and two micronuclei) after micronuclei al. et
(1985) (1979) and and and et and (1984) divide twice (Fig. 3I–L; Raikov 1969). Instead of generating
a completely new nuclear group in one of the daughter cells,
karyorelictean species that divide by the third method effec- References
Raikov Raikov Raikov Raikov Raikov Raikov Bobyleva Raikov Raikov
tively decrease the age difference of nuclei between daughter
cells, i.e. if a completely new nuclear group is generated and
passed on to one of the daughter cells while the other one
receives the parental nuclear group, there is a one-generation with
chromatin age difference between the offspring and this age difference
with aging/other
macronuclei,
matrix
would increase each division.
and
with chromocenters
chromocenters nucleoli, nucleoli with
aging contact with
Development of macronuclei continuous
in in
Given the inability of karyorelictean macronuclei to divide
−
(i.e they are Div ), nearly half of the macronuclei in each contact
occasionally bodies chromocenters structures nucleoli, N/A None continuous
matrix cell are newly differentiated from micronuclei following cell
division. As described below, the general pattern of macronu-
clear development in karyorelictean species appears similar
to other ciliates except that no evidence for genomic amplifi-
nmnm Sometimes – nm Always cation during development has been recorded (Raikov 1957,
width Associations
observable
nmnm In nm Sometimes Sometimes
1959, 1982). Macronuclear development begins with cre- nm Always
Fiber N/A Not
7–8 7–8 10–12 10–12 7–8 ation of vacuoles in the developing macronucleus (Fig. 4A),
which is followed by the formation of chromatin granules
(Fig. 4B). In some species the size and number of chromatin m 10–12
granules decrease during development (e.g. Tracheloraphis 8
to margaritatus; Fig. 4C; Raikov 1957), suggesting that DNA
up
elimination may be occurring (Raikov 1994). DNA elimi-
m,
nation is a common aspect of macronuclear development in
m7
species.
other ciliates where regions of germline DNA are selectively
Diameter
N/A – –
– – 2
excised or deleted (Prescott 1994). Later, the emergence of
nucleoli indicates the maturation of macronuclei (Fig. 4D;
Raikov 1985). The few studies focusing on conjugation in
RNA RNA – RNA – RNA 2–3
karyorelictid
Karyorelictea show differences compared to dividing cells;
for instance, macronuclear development is blocked during
Material N/A Protein Protein Protein Protein Protein Protein – Protein conjugation and resumes only after cells separate (Raikov diverse
in 1990).
Aging of macronuclei
Since karyorelictean macronuclei cannot divide, they age, inclusions
and the macronuclei within a cell are always at different ages
Crystal/sphere Sphere Sphere Sphere Sphere Sphere Sphere
None Sphere (Raikov 1982). As macronuclei age, changes occur in their
size, shape, staining properties, and fine structure (Raikov
1985). The size of young macronuclei is often between that macronuclear
of micronuclei and mature macronuclei; for example, in of
Trachelocerca multinucleata, micronuclei are measured at
table
5–6 m in diameter, and young macronuclei are 5–7 m,
while mature macronuclei are 8–10 m in diameter (Raikov phoenicopterus dogieli crassus
obscura geopetiti
tubiformis
1989). Young macronuclei also stain less strongly with Feul- multinucleata
Summary gen than mature or old macronuclei, and possess smaller
applicable.
orbis
3.
available. and more scattered chromatin bodies (Bobyleva et al. 1980;
not
not Kovaleva and Raikov 1978; Raikov and Kovaleva 1996). In
, − Table TaxonLoxodes Inclusion
Remanella Tracheloraphis Tracheloraphis N/A,
Tracheloraphis Trachelocerca Trachelocerca Kentrophoros Geleia
contrast, mature macronuclei stain darker and have larger
Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408 405
Fig. 3. Nuclear reorganization during cell division in karyorelictids. A–D. Pattern of nuclear group with two macronuclei and one micronucleus
(modified from Loxodes rostrum, Raikov 1957): two parental macronuclei are segregated into daughter cells and each daughter cell receives
a newly differentiated macronucleus. E–H. Pattern for a nuclear group with two macronuclei and two micronuclei (modified from L. striatus,
Raikov 1957): similar to the first pattern with an additional micronuclear division. I–L. Pattern for nuclear group with four macronuclei and
two micronuclei (modified from Trachelocerca coluber, Raikov 1969): the parental nuclear group is separated into two halves, and the full
complement of nuclei is restored by nuclear division and differentiation.
Fig. 4. Macronuclear development in Tracheloraphis margaritatus (Feulgen staining, modified from Raikov 1957). A. vacuolization stage
from a macronuclear anlagen. B. macronuclear anlagen forming numerous chromatin granules. C. dechromatinization stage. D. appearance
of nucleoli.
chromocenters (Bobyleva et al. 1980; Kovaleva and Raikov et al. 1980; Kovaleva and Raikov 1978; Raikov et al. 1963).
1978; Raikov and Kovaleva 1996). Mature macronuclei tend The functional implications of changing DNA content are
to be relatively more abundant in multinuclear cells (Raikov unknown.
1985). Old macronuclei stain darker still and have more The Div− macronuclei in karyorelictids also have a
irregular shapes with a higher presence of spheres in some relatively short life span. They persist only through 3–7
species (e.g. Kentrophoros tubiformis and Kovalevaia (Trach- cell divisions as estimated from the percentage of degen-
elonema) sulcata; Bobyleva et al. 1980; Kovaleva and Raikov erating macronuclei per cell in Loxodes magnus, while
1978; Raikov and Kovaleva 1996). macronuclei appear to exist longer in Kentrophoros fistulo-
DNA accumulation in macronuclei accompanies the mor- sum (Raikov 1985, 1994; Raikov and Kovaleva 1996). In
phological changes of aging. For example, the increasing contrast, macronuclei in other ciliates divide by amitosis for
staining darkness of macronuclei indicates DNA synthe- many generations until conjugation occurs. Macronuclear
sis (i.e. likely replication of certain genes; Bobyleva et al. amitosis is estimated to occur for 40–60 cell divisions in
1980; Kovaleva and Raikov 1978; Raikov 1994; Raikov et al. Tetrahymena thermophila (Class Oligomenophorea), and for
1963). DNA accumulation also generates macronuclei with more than 100 in Dileptus anser (Class Litostomatea; Lynn
a wide distribution of DNA content even within the same and Doerder 2012; Yudin and Uspenskaya 2007). The short
cell (Raikov 1994). For example, in Loxodes magnus, DNA life span of Div− macronuclei in Karyorelictea might func-
content of young macronuclei is ∼4C while aging macronu- tion as a mechanism to avoid the accumulation of deleterious
clei reach an average of 5–6C; in Kovalevaia sulcata, old mutations in Div− nuclei.
macronuclei vary in DNA content from 2C to 12C (Bobyleva
406 Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408
Implications of unusual nuclear features in award 1R15GM113177 and NSF award 1541511to Dr. Laura
Karyorelictea A. Katz.
Since the 1950’s, karyorelictean nuclei have been investi-
gated primarily using cytochemical and microscopy methods, References
including Feulgen staining. Here we speculate on the impli-
cations of the patterns described above. We propose two
Al-Rasheid, K.A.S., 2001. New records of interstitial ciliates (Pro-
possible explanations for the maintenance of a minimum
tozoa Ciliophora) from the Saudi coasts of the Red Sea. Trop.
of two macronuclei within each cell. One possibility is Zool. 14, 133–156.
that a mature macronucleus is necessary to sustain the cell Andreoli, I., Mangini, L., Ferrantini, F., Santangelo, G., Verni, F.,
while the new macronucleus is developing, so every kary- Petroni, G., 2009. Molecular phylogeny of unculturable Kary-
orelictid cell has at least one old and one newly-developed orelictea (Alveolata, Ciliophora). Zool. Scr. 38, 651–662.
Aury, J.M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B.M.,
macronucleus. In Paramecium tetraurelia (Class Oligohy-
Segurens, B., Daubin, V., Anthouard, V., Aiach, N., Arnaiz, O.,
menophorea), parental macronuclei generate 80% of the total
Billaut, A., Beisson, J., Blanc, I., Bouhouche, K., Camara, F.,
RNA during the first two cell divisions following conjuga-
Duharcourt, S., Guigo, R., Gogendeau, D., Katinka, M., Keller,
tion and as the new macronucleus develops (Berger 1973;
A.M., Kissmehl, R., Klotz, C., Koll, F., Le Mouel, A., Lep-
Lepere et al. 2008). Another possible explanation is that the
ere, G., Malinsky, S., Nowacki, M., Nowak, J.K., Plattner, H.,
old macronucleus plays an important role in the develop-
Poulain, J., Ruiz, F., Serrano, V., Zagulski, M., Dessen, P., Beter-
ment of the new macronucleus through epigenetic processes,
mier, M., Weissenbach, J., Scarpelli, C., Schachter, V., Sperling,
perhaps by enabling RNA-mediated rearrangements. Such L., Meyer, E., Cohen, J., Wincker, P., 2006. Global trends of
phenomena have been documented in several model ciliates whole-genome duplications revealed by the ciliate Paramecium
including Tetrahymena (e.g. Mochizuki 2010), Paramecium tetraurelia. Nature 444, 171–178.
(e.g. Garnier et al. 2004) and Oxytricha (e.g. Yerlici and Berger, J.D., 1973. Nuclear differentiation and nucleic-acid
synthesis in well-fed exconjugants of Paramecium aurelia. Chro-
Landweber 2014). These two possible scenarios are not mutu-
mosoma 42, 247–268.
ally exclusive.
Bobyleva, N.N., 1981. Cultivation and cloning of the primitive cil-
The Div− macronuclei are unique to Karyorelictea. Sev-
iates of the genus Loxodes and some aspects of their biology.
eral explanations have been proposed for the evolution of
Tsitologiya 23, 1073–1077.
this feature. One hypothesis is that Div− macronuclei are the
Bobyleva, N.N., Kovaleva, V.G., Raikov, I.B., 1981. Some charac-
ancestral state in ciliates and Div+ macronuclei have evolved
teristics of deoxyribonucleic-acid replication in unable to fission
twice in the Heterotrichea and Intramacronucleata (i.e. all
macro-nuclei of lower infusorians. Tsitologiya 23, 1195.
remaining ciliate classes; Katz 2001; Orias 1991a,b). Alter- Bobyleva, N.N., Kudrjavtsev, B.N., Raikov, I.B., 1980. Changes
natively, Karyorelictea may have lost the ability to divide of the DNA content of differentiating and adult macronuclei
their macronuclei, either stochastically or due to selection. In of the ciliate Loxodes magnus (Karyorelictida). J. Cell Sci. 44,
the latter case, macronuclear division may have been lost to 375–394.
Borror, A.C., 1973. Tracheloraphis haloetes sp. n. (Ciliophora,
avoid the cost of high mutational loads in polyploid macronu-
Gymnostomatida)—description and a key to species of genus
clei (Katz 2001). A similar argument has been made for the
Tracheloraphis. J. Protozool. 20, 554–558.
evolution of sex in eukaryotes as a means for resetting ploidy
Buonanno, F., Saltalamacchia, P., Miyake, A., 2005. Defence
and removing deleterious mutations (Katz and Kovner 2010;
function of pigmentocysts in the karyorelictid ciliate Loxodes
Kondrashov 1997; Normark et al. 2003). With the emerging
striatus. Eur. J. Protistol. 41, 151–158.
tools of single-cell ‘omics’, we will be able to further explore
Campello-Nunes, P.H., Fernandes, N., Schlegel, M., Silva-Neto,
both the nature and implication of nuclear architecture within
I.D., 2015. Description and phylogenetic position of Corlissina
Karyorelictea, and gain more insights into the evolution of maricaensis gen. nov., sp. nov. (Karyorelictea, Geleiidae), a
genome features in ciliates. novel interstitial ciliate from Brazil, with redefinition of the
family Geleiidae. Int. J. Syst. Evol. Microbiol. 65, 4297–4308.
Cech, T.R., 1986. The generality of self-splicing RNA: relationship
to nuclear mRNA splicing. Cell 44, 207–210.
Acknowledgements Chalker, D.L., 2008. Dynamic nuclear reorganization during
genome remodeling of Tetrahymena. Biochim. Biophys. Acta:
Mol. Cell Res. 1783, 2130–2136.
We are grateful to Mr. Xyrus Maurer-Alcalá, Dr. Jean-
Chen, X., Bracht, J.R., Goldman, A.D., Dolzhenko, E., Clay, D.M.,
David Grattepanche and the rest of the Katz lab for their
Swart, E.C., Perlman, D.H., Doak, T.G., Stuart, A., Amemiya,
conversations and reading of drafts of this manuscript.
C.T., Sebra, R.P., Landweber, L.F., 2014. The architecture of a
Thanks also to Dr. Weibo Song and Dr. John Clamp for their
scrambled genome reveals massive levels of genomic rearrange-
support of 5th IRCN-BC Ciliate Biodiversity Worskshop in
ment during development. Cell 158, 1187–1198.
Guam where some of these ideas were developed. Ms. Ying Dragesco, J., 2002. Infraciliature de quinze especes de cilies mesop-
Yan is supported by China Scholarship Council Scholarship sammiques marins comprenant Trachelocerca stephani comb,
for joint PhD students. This work is supported by an NIH nova, T. bodiani comb. nova, Tracheloraphis filiformis spec,
Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408 407
nova, T. exilis spec, nova, et Sathrophilus arenicolus spec. nova. (Engelmann, 1862) and Loxodes magnus Stokes, 1887 (Proto-
Linzer Biologische Beiträge 34, 1545–1626. zoa, Ciliophora). Zool. Anz. 210, 3–13.
Duret, L., Cohen, J., Jubin, C., Dessen, P., Gout, J.F., Mousset, Gao, F., Katz, L.A., 2014. Phylogenomic analyses support the bifur-
S., Aury, J.M., Jaillon, O., Noel, B., Arnaiz, O., Betermier, M., cation of ciliates into two major clades that differ in properties
Wincker, P., Meyer, E., Sperling, L., 2008. Analysis of sequence of nuclear division. Mol. Phylogenet. Evol. 70, 240–243.
variability in the macronuclear DNA of Paramecium tetraurelia: Gao, F., Warren, A., Zhang, Q., Gong, J., Miao, M., Sun, P., Xu, D.,
a somatic view of the germline. Genome Res. 18, 585–596. Huang, J., Yi, Z., Song, W., 2016. The all-data-based evolution-
Eisen, J.A., Coyne, R.S., Wu, M., Wu, D., Thiagarajan, M., Wort- ary hypothesis of ciliated protists with a revised classification
man, J.R., Badger, J.H., Ren, Q., Amedeo, P., Jones, K.M., of the Phylum Ciliophora (Eukaryota, Alveolata). Sci. Rep. 6,
Tallon, L.J., Delcher, A.L., Salzberg, S.L., Silva, J.C., Haas, B.J., 24874.
Majoros, W.H., Farzad, M., Carlton, J.M., Smith, R.K., Garg, J., Garnier, O., Serrano, V., Duharcourt, S., Meyer, E., 2004.
Pearlman, R.E., Karrer, K.M., Sun, L., Manning, G., Elde, N.C., RNA-mediated programming of developmental genome rear-
Turkewitz, A.P., Asai, D.J., Wilkes, D.E., Wang, Y., Cai, H., rangements in Paramecium tetraurelia. Mol. Cell. Biol. 24,
Collins, K., Stewart, B.A., Lee, S.R., Wilamowska, K., Wein- 7370–7379.
berg, Z., Ruzzo, W.L., Wloga, D., Gaertig, J., Frankel, J., Tsao, Greider, C.W., Blackburn, E.H., 1985. Identification of a specific
C.C., Gorovsky, M.A., Keeling, P.J., Waller, R.F., Patron, N.J., telomere terminal transferase activity in Tetrahymena extracts.
Cherry, J.M., Stover, N.A., Krieger, C.J., Del Toro, C., Ryder, Cell 43, 405–413.
H.F., Williamson, S.C., Barbeau, R.A., Hamilton, E.P., Orias, E., Katz, L.A., 2001. Evolution of nuclear dualism in ciliates: a reanaly-
2006. Macronuclear genome sequence of the ciliate Tetrahymena sis in light of recent molecular data. Int. J. Syst. Evol. Microbiol.
thermophila, a model eukaryote. PLoS Biol. 4, e286. 51, 1587–1592.
Epstein, S.S., 1994. A new marine interstitial ciliate from the Katz, L.A., Kovner, A.M., 2010. Alternative processing of scram-
Northwest Atlantic Coast Tracheloraphis primitarum sp. n. bled genes generates protein diversity in the ciliate Chilodonella
(Ciliophora, Kinetofragminophora, Karyorelictida, Trachelocer- uncinata. J. Exp. Zool. B 314, 480–488.
cidae). J. Eukaryot. Microbiol. 41, 500–503. Kondrashov, A.S., 1997. Evolutionary genetics of life cycles. Annu.
Fenchel, T., 1967. The ecology of marine microbenthos I. The quan- Rev. Ecol. Syst. 28, 391–435.
titative importance of ciliates as compared with metazoans in Kovaleva, V.G., Raikov, I.B., 1978. Diminution and re-
various types of sediments. Ophelia 4, 121–137. synthesis of DNA during development and senescence
Fenchel, T., 1968. The ecology of marine microbenthos II. The food of diploid macronuclei of ciliate Trachelonema sulcata
of marine benthic ciliates. Ophelia 5, 73–121. (Gymnostomata–Karyorelictida). Chromosoma 67, 177–192.
Finlay, B.J., Fenchel, T., 1986. Photosensitivity in the ciliated Proto- Kovaleva, V.G., Raikov, I.B., 1992. Ultrastructural peculiarities
zoan Loxodes—pigment granules, absorption and action spectra, of the meiotic prophase in the ciliate Tracheloraphis totevi
blue-light perception, and ecological significance. J. Protozool. (Karyorelictida)—synaptonemal complexes and sheaths around
33, 534–542. bivalents. Acta Protozool. 31, 133–141.
Finlay, B.J., Fenchel, T., Gardener, S., 1986. Oxygen perception Kruger, K., Grabowski, P.J., Zaug, A.J., Sands, J., Gottschling,
and O-2 toxicity in the fresh-water ciliated Protozoan Loxodes. D.E., Cech, T.R., 1982. Self-splicing RNA: autoexcision and
J. Protozool. 33, 157–165. autocyclization of the ribosomal RNA intervening sequence of
Foissner, W., 1995. Kentrophoros (Ciliophora, Karyorelictea) has Tetrahymena. Cell 31, 147–157.
oral vestiges: a reinvestigation of K. fistulosus (Faure-Fremiet, Lepere, G., Betermier, M., Meyer, E., Duharcourt, S., 2008. Mater-
1950) using protargol impregnation. Arch. Protistenkd. 146, nal noncoding transcripts antagonize the targeting of DNA
165–179. elimination by scanRNAs in Paramecium tetraurelia. Gene Dev.
Foissner, W., 1996a. The infraciliature of Cryptopharynx setigerus 22, 1501–1512.
Kahl, 1928 and Apocryptophalynx hippocampoides nov. gen., Lynn, D.H., 2008. The Ciliated Protozoa: Characterization, Classi-
nov. spec. (Ciliophora, karyorelictea), with an account on evo- fication, and Guide to the Literature. Springer, New York.
lution in loxodid ciliates. Arch. Protistenkd. 146, 309–327. Lynn, D.H., Doerder, F.P., 2012. The life and times of Tetrahymena.
Foissner, W., 1996b. A redescription of Remanella multinucleata Method Cell Biol. 109, 11–27.
(Kahl, 1933) nov. gen., nov. comb. (Ciliophora, Karyorelictea), Mochizuki, K., 2010. RNA-directed epigenetic regulation of DNA
emphasizing the infraciliature and extrusomes. Eur. J. Protistol. rearrangements. Essays Biochem. 48, 89–100.
32, 234–250. Mochizuki, K., Gorovsky, M.A., 2004. Small RNAs in genome
Foissner, W., 1996c. Updating the trachelocercids (Ciliophora, rearrangement in Tetrahymena. Curr. Opin. Genet. Dev. 14, 181.
Karyorelictea). 2. Prototrachelocerca nov. gen. (Prototrache- Normark, B.B., Judson, O.P., Moran, N.A., 2003. Genomic signa-
locercidae nov. fam.), with a redescription of P. fasciolata tures of ancient asexual lineages. Biol. J. Linn. Soc. 79, 69–84.
(Sauerbrey, 1928) nov. comb. and P. caudata (Dragesco & Nowacki, M., Vijayan, V., Zhou, Y., Schotanus, K., Doak, T.G.,
Raikov, 1966) nov. comb. Eur. J. Protistol. 32, 336–355. Landweber, L.F., 2008. RNA-mediated epigenetic programming
Foissner, W., Dragesco, J., 1996. Updateing the Trachelocercids of a genome-rearrangement pathway. Nature 451, 153–154.
(Ciliophora, Karyorelictea). III. Redefinition of the Gnera Trach- Orias, E., 1991a. On the evolution of the karyorelict ciliate life
elocerca Ehrenberg and Tracheloraphis Dragesco, and evolution cycle: heterophasic ciliates and the origin of ciliate binary fission.
in trachelocercid ciliates. Arch. Protistenkd. 147, 43–91. Biosystems 25, 67–73.
Foissner, W., Rieder, N., 1983. Light and scanning electron- Orias, E., 1991b. Evolution of amitosis of the ciliate macronucleus:
microscopical studies about the infraciliature of Loxodes striatus gain of the capacity to divide. J. Protozool. 38, 217–221.
408 Y. Yan et al. / European Journal of Protistology 61 (2017) 399–408
Ovchinnikova, L., Cheissin, E., Selivanova, G., 1965. Photomet- Raikov, I.B., Cheissin, E.M., Buze, E.G., 1963. A photometric study
ric study of the DNA content in the nuclei of Spirostomum of DNA content of macro and micronucleus in Paramecium cau-
ambiguum (Ciliata, Heterotricha). Acta Protozool. 3, 69–78. datum, Nassula ornata and Loxodes magnus. Acta Protozool. 1,
Prescott, D.M., 1994. The DNA of ciliated Protozoa. Microbiol. 285–300.
Rev. 58, 233–267. Raikov, I.B., Karadzhan, B.P., Kaur, R., 1989. Fine-structure of
Raikov, I.B., 1957. Reorganization of the Nuclear Apparatus in Cil- macronuclei and micronuclei of the lower marine ciliate Tra-
iate and the Problem of the Origin of the Binuclearity, vol. 15. chelocerca obscura (Karyorelictida). Arch. Protistenkd. 137,
Vestnik Leningrad University, pp. 21–37. 25–44.
Raikov, I.B., 1959. Der Formwechsel des Kernapparates einiger Woodard, J., Gorovsky, M.A., Kaneshiro, E., 1972. Cytochemical
niederer Ciliaten. II. Die Gattung Loxodes. Arch. Protistenkd. studies on problem of macronuclear subnuclei in Tetrahymena.
104, 1–42. Genetics 70, 251–260.
Raikov, I.B., 1969. The macronucleus of ciliates. In: Research in Xu, Y., Huang, J., Warren, A., Al-Rasheid, K.A.S., Al-Farraj, S.A.,
Protozoology. Pergamon Press, New York. Song, W.B., 2011a. Morphological and molecular information
Raikov, I.B., 1979. Fine-structure of the nuclear apparatus of of a new species of Geleia (Ciliophora, Karyorelictea), with
Remanella multinucleata Kahl (Ciliophora, Gymnostomata). redescriptions of two Kentrophoros species from China. Eur. J.
Arch. Protistenkd. 121, 1–19. Protistol. 47, 172–185.
Raikov, I.B., 1982. The Protozoan Nucleus: Morphology and Evo- Xu, Y., Li, J., Gao, F., Hu, X., Al-Rasheid, K.A., 2011b. Apotra-
lution. Springer-Verlag, Wien. chelocerca arenicola (Kahl, 1933) n. g., comb. n. (Protozoa,
Raikov, I.B., 1984. Fine-structure of the nuclear-apparatus of the Ciliophora, Trachelocercidae): morphology and phylogeny. J.
marine psammobiotic ciliate Geleia orbis Faure-Fremiet (Kary- Eukaryot. Microbiol. 58, 504–510.
orelictida). Arch. Protistenkd. 128, 231–252. Xu, Y., Li, J.M., Song, W.B., Warren, A., 2013. Phylogeny and
Raikov, I.B., 1985. Primitive never-dividing macronuclei of some establishment of a new ciliate family, Wilbertomorphidae fam.
lower ciliates. Int. Rev. Cytol. 95, 267–325. nov (Ciliophora, Karyorelictea), a highly specialized taxon rep-
Raikov, I.B., 1989. Ultrastructure of the nuclear-apparatus of resented by Wilbertomorpha colpoda gen. nov., spec. nov. J.
the marine psammobiotic ciliate Trachelocerca multinucleata Eukaryot. Microbiol. 60, 480–489.
Dragesco (Karyorelictida). Arch. Protistenkd. 137, 199–209. Xu, Y., Pan, H.B., Miao, M., Hu, X.Z., Al-Farraj, S.A., Al-Rasheid,
Raikov, I.B., 1990. The karyorelictid nuclear-apparatus—a model K.A.S., Song, W.B., 2015. Morphology and phylogeny of two
of nuclear differentiation. Zool. Sci. 7, 5–12. species of Loxodes (Ciliophora, Karyorelictea), with descrip-
Raikov, I.B., 1994. The nuclear-apparatus of some primitive ciliates, tion of a new subspecies, Loxodes striatus orientalis subsp. n. J.
the karyorelictids—structure and divisional reorganization. Ital. Eukaryot. Microbiol. 62, 206–216.
J. Zool. 61, 19–28. Yan, Y., Xu, Y., Yi, Z., Warren, A., 2013. Redescriptions of three
Raikov, I.B., Karadzhan, B.P., 1985. Fine-structure and cyto- trachelocercid ciliates (Protista, Ciliophora, Karyorelictea), with
chemistry of the nuclei of the primitive ciliate Tracheloraphis notes on their phylogeny based on small subunit rRNA gene
crassus (Karyorelictida). Protoplasma 126, 114–129. sequences. Int. J. Syst. Evol. Microbiol. 63, 3506–3514.
Raikov, I.B., Kovaleva, V.G., 1978. Fine-structure of the nuclear Yan, Y., Xu, Y., Al-Farraj, S.A., Al-Rasheid, K.A.S., Song, W.B.,
complex of the psammophilic gymnostome ciliate Trachelo- 2016. Morphology and phylogeny of three trachelocercids (Pro-
raphis phoenicopterus (Cohn). Protistologica 14, 269–282. tozoa, Ciliophora, Karyorelictea), with description of two new
Raikov, I.B., Kovaleva, V.G., 1980. Electron-microscopic cyto- species and insight into the evolution of the family Trachelocer-
chemistry of the macronuclei and micronuclei of the lower cidae. Zool. J. Linn. Soc. Lond. 177, 306–319.
ciliate Tracheloraphis dogieli (Karyorelictida). Tsitologiya 22, Yao, M.C., 2008. Molecular biology. RNA rules. Nature 451,
1139–1145. 131–132.
Raikov, I.B., Kovaleva, V.G., 1990. Ultrastructure of the nuclear- Yerlici, V.T., Landweber, L.F., 2014. Programmed genome rear-
apparatus of the lower ciliate Remanella granulosa Kahl rangements in the ciliate Oxytricha. Microbiol. Spectr. 2.
(Karyorelictida). Protoplasma 155, 106–115. Yudin, A.L., Uspenskaya, Z.I., 2007. Nuclear differentiation for
Raikov, I.B., Kovaleva, V.G., 1996. Nuclear groups and diversity of mating types in the ciliate Dileptus anser: a hypothesis. Cell
macronuclei of Kentrophoros tubiformis (Ciliophora, Karyore- Biol. Int. 31, 428–432.
lictida) from the Japan sea. Eur. J. Protistol. 32, 327–335.
Raikov, I.B., Volkonitin, A.F., 1989. A new marine psammobiotic
ciliate from the Japan Sea, Trachelocerca obscura sp. n. (Cil-
iophora, Karyorelictida, Trachelocercidae). Acta Protozool. 28, 61–67.