The Frustrated Gene:
Origins of Eukaryotic Gene Expression
Hiten D. Madhani1,*
1Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
Eukarytotic gene expression is frustrated by a series of steps that are generally not observed in
prokaryotes and are therefore not essential for the basic chemistry of transcription and translation.
Their evolution may have been driven by the need to defend against parasitic nucleic acids.
The goal of this piece is to consider why
gene expression in eukaryotes is the
way that it is. Students of molecular
biology learn that many key elements of
eukaryotic gene expression are generally
absent from eubacteria. Because eukary-
otic features such as chromatin, pre-
mRNA processing, and small RNAs offer
many opportunities for regulatory control,
it might be tempting to think that these
attributes evolved to drive the evolution of
complex, multicellular organisms. How-
ever, the ubiquity of these gene expres-
sion elements and available phylogenetic
data argue that the core elements of
eukaryotic gene expression were estab-
lished within the ancient unicellular pro-
genitor of modern eukaryotes. In addition,
the widespread abundance of prokary-
otes throughout the biosphere means
that none of the eukaryotic ‘‘embellish-
ments’’ are required for the operation of
the central dogma of molecular biology
per se. What, then, drove their initial
The Frustrated Gene: A Metaphor
As a frame for thinking about this ques-
tion, consider how one might view the
eukaryotic gene expression apparatus
as a human organization. It would seem
to be a highly bureaucratic one, replete
with unnecessary impediments that re-
duce its ostensible output. It would be
as if overeager managers implemented
bureaucratic roadblocks to each phase:
chromatin obstructs transcription; introns
and therequirement foracapstructure on
pre-mRNA stymie translation; and contin-
polyadenylate (polyA) tails diminishes
overall output. For the individual gene
(as for many an office worker), this would
be a frustrating environment in which to
work. As detailed below, the hoops
through which a gene is forced to jump
between transcription and translation
may have evolved as part of a cellular
defensive strategy rather than a desire
for efficiency. Through this metaphorical
lens, eukaryotic evolution can be seen
as the consequences of what bureau-
crats term ‘‘enterprise risk manage-
ment,’’ wherein a focus on potential
hazards drives the management of the
The Existential Threat of Parasitic
To understand the origins of complex
eukaryotic gene expression mechanisms,
it is helpful to consider that the evolution
of the earliest life forms likely coincided
with or was quickly followed by the evolu-
tion of the first selfish nucleic acid para-
sites (Dawkins, 1976). Whatever their
form, these could have extinguished early
of cellular resources) were it not for the
rapid evolution of host mechanisms
limiting their negative impacts.
Here, parasitic nucleic acids will be
defined as those that, at the very least,
utilize host ribosomes in order to synthe-
size proteins required for their own repli-
cation, thereby resulting in fitness costs
for the host. An understanding of the
impact of parasitic nucleic acids on host
genomes, as well as features of specific
parasites, will be important for the argu-
ment developed below. I will focus on
the most ubiquitous parasitic DNAs:
transposable elements and viruses.
Eukaryotes are targeted by three types
of transposable elements: cut-and-paste
DNA transposons, non-LTR (long terminal
repeat) retrotransposons, and LTR retro-
transposons (Craig et al., 2002). Each
has a distinct replicative program, but
they share the common goal of increasing
their copy number relative to the re-
mainder of the genome. Integration into
new sites in chromatin is a requirement
for success, as is the ability to use host
RNA polymerase II (RNA pol II) and host
ribosomes. Because of sexual reproduc-
tion, transposable elements can prolifer-
ate within populations despite a negative
impact on host fitness (Hickey, 1982).
Sex facilitates population spread beyond
a single maternal or paternal lineage.
The ability of mobile genetic elements to
spread through a population via sex partly
accounts for the widespread evolution of
antitransposon defense mechanisms, as
well as for the focused action of these
systems in the germline. Eukaryotes are
also infected by three broad classes of
exogenous parasitic nucleic acids: DNA
viruses, RNA viruses, and retroviruses.
Viruses use diverse strategies for replica-
tion and spread, among which the retro-
viruses notably require entry into the
stranded DNA into chromatin. Like trans-
posable elements, retroviruses use host
RNA Pol II to express their genes. Viruses
that use their own RNA polymerase face
many challenges to gene expression, as
Thus, a conflict is set up in which the
host, which can be from any of the three
domains of life, needs to develop strate-
gies to sense and silence parasitic nucleic
acids, whereas the latter need to replicate
744 Cell 155, November 7, 2013 ª2013 Elsevier Inc.
Galej, W.P., Oubridge, C., Newman, A.J., and
Nagai, K. (2013). Crystal structure of Prp8 reveals
active site cavity of the spliceosome. Nature 493,
Gornik, S.G., Ford, K.L., Mulhern, T.D., Bacic, A.,
McFadden, G.I., and Waller, R.F. (2012). Loss of
nucleosomal DNA condensation coincides with
appearance of a novel nuclear protein in dinofla-
gellates. Curr. Biol. 22, 2303–2312.
Greber, U.F., Willetts, M., Webster, P., and Helen-
ius, A. (1993). Stepwise dismantling of adenovirus
2 during entry into cells. Cell 75, 477–486.
Hickey, D.A. (1982). Selfish DNA: a sexually-trans-
mitted nuclear parasite. Genetics 101, 519–531.
Hollien, J. (2013). Evolution of the unfolded protein
response. Biochim. Biophys. Acta 1833, 2458–
James, E.R., and Green, D.R. (2002). Infection
and the origins of apoptosis. Cell Death Differ. 9,
Joshua-Tor, L., and Hannon, G.J. (2011). Ancestral
roles of small RNAs: an Ago-centric perspective.
Cold Spring Harb. Perspect. Biol. 3, a003772.
Koonin, E.V. (2006). The origin of introns and their
role in eukaryogenesis: a compromise solution to
the introns-early versus introns-late debate? Biol.
Direct 1, 22.
Law, J.A., Du, J., Hale, C.J., Feng, S., Krajewski,
K., Palanca, A.M., Strahl, B.D., Patel, D.J., and
Jacobsen, S.E. (2013). Polymerase IV occupancy
at RNA-directed DNA methylation sites requires
SHH1. Nature 498, 385–389.
Le Hir, H., and Se ´raphin, B. (2008). EJCs at the
heart of translational control. Cell 133, 213–216.
Li, V.C., Davis, J.C., Lenkov, K., Bolival, B., Fuller,
M.T., and Petrov, D.A. (2009). Molecular evolution
of the testis TAFs of Drosophila. Mol. Biol. Evol.
Loo, Y.M., and Gale, M., Jr. (2011). Immune
signaling by RIG-I-like receptors. Immunity 34,
Lynch, M., and Conery, J.S. (2003). The origins of
genome complexity. Science 302, 1401–1404.
Madhani, H.D., and Guthrie, C. (1992). A novel
base-pairing interaction between U2 and U6
snRNAs suggests a mechanism for the catalytic
activation of the spliceosome. Cell 71, 803–817.
Makarova, K.S., Wolf, Y.I., and Koonin, E.V. (2013).
Comparative genomics of defense systems in
archaea and bacteria. Nucleic Acids Res. 41,
Nakano, K., Ando, T., Yamagishi, M., Yokoyama,
K., Ishida, T., Ohsugi, T., Tanaka, Y., Brighty,
D.W., and Watanabe, T. (2013). Viral interference
with host mRNA surveillance, the nonsense-medi-
ated mRNA decay (NMD) pathway, through a new
function of HTLV-1 Rex: implications for retroviral
replication. Microbes Infect. 15, 491–505.
Parker, R. (2012). RNA degradation in Saccharo-
myces cerevisae. Genetics 191, 671–702.
Peng, J.C., and Lin, H. (2013). Beyond transpo-
sons: the epigenetic and somatic functions of the
Piwi-piRNA mechanism. Curr. Opin. Cell Biol. 25,
Pikaard, C.S., Haag, J.R., Pontes, O.M., Blevins,
T., and Cocklin, R. (2013). A transcription fork
model for Pol IV and Pol V-dependent RNA-
directed DNA methylation. Cold Spring Harb.
Symp. Quant. Biol. 77, 205–212.
Rogozin, I.B., Carmel, L., Csuros, M., and Koonin,
E.V. (2012). Origin and evolution of spliceosomal
introns. Biol. Direct 7, 11.
Roth, S.L., Malani, N., and Bushman, F.D. (2011).
target DNA in vivo. J. Virol. 85, 7393–7401.
Shabalina, S.A., and Koonin, E.V. (2008). Origins
and evolution of eukaryotic RNA interference.
Trends Ecol. Evol. 23, 578–587.
Shuman, S. (2002). What messenger RNA capping
tells us about eukaryotic evolution. Nat. Rev. Mol.
Cell Biol. 3, 619–625.
Smolle, M., Workman, J.L., and Venkatesh, S.
(2013). reSETting chromatin during transcription
elongation. Epigenetics 8, 10–15.
van der Veen, R., Arnberg, A.C., van der Horst, G.,
Bonen, L., Tabak, H.F., and Grivell, L.A. (1986).
Excised group II introns in yeast mitochondria are
lariats and can be formed by self-splicing in vitro.
Cell 44, 225–234.
Walsh, D., Mathews, M.B., and Mohr, I. (2013).
Tinkering with translation: protein synthesis in
virus-infected cells. Cold Spring Harb. Perspect.
Biol. 5, a012351.
Werner, M., Purta, E., Kaminska, K.H., Cymerman,
I.A., Campbell, D.A., Mittra, B., Zamudio, J.R.,
Sturm, N.R., Jaworski, J., and Bujnicki, J.M.
(2011). 20-O-ribose methylation of cap2 in human:
function and evolution in a horizontally mobile
family. Nucleic Acids Res. 39, 4756–4768.
Yu, Y.T., Maroney, P.A., Darzynkiwicz, E., and
Nilsen, T.W. (1995). U6 snRNA function in nuclear
pre-mRNA splicing: a phosphorothioate interfer-
ence analysis of the U6 phosphate backbone.
RNA 1, 46–54.
Zhang, F., Wang, J., Xu, J., Zhang, Z., Koppetsch,
B.S., Schultz, N., Vreven, T., Meignin, C., Davis, I.,
Zamore, P.D., et al. (2012). UAP56 couples piRNA
clusters to the perinuclear transposon silencing
machinery. Cell 151, 871–884.
Zilberman, D., Gehring, M., Tran, R.K., Ballinger,
T., and Henikoff, S. (2007). Genome-wide analysis
of Arabidopsis thaliana DNA methylation uncovers
an interdependence between methylation and
transcription. Nat. Genet. 39, 61–69.
Cell 155, November 7, 2013 ª2013 Elsevier Inc. 749