BIOLOGIA

Filaments II: the actin superfamily

Actin is a ubiquitous eukaryotic filament-forming protein.
Actin filaments (also called microfilaments or F-actin) consist
of two protofilament polymers wound together in a righthanded
helix (Fig. 1). ATP hydrolysis by actin causes a much
less dramatic change in polymer stability than is seen for GTP
hydrolysis in microtubules. As a result, pure actin shows little
dynamic instability in vitro (Mitchison, 1992), but rather
undergoes “treadmilling” through the polarized addition of ATPbound
subunits. In vivo, actin is much more dynamic than in vitro due to the presence of monomer-binding factors, filamentsevering
agents, and capping/stabilizing agents.
Eukaryotic actin is a member of a large and diverse
superfamily of ATPases that includes Hsp70 chaperones and several classes of sugar/sugar alcohol kinases (Flaherty et al.,
1991; Bork et al., 1992), as well as eukaryotic actin-related proteins
(ARPs; Frankel and Mooseker, 1996; Schafer and Schroer,
1999). Also identified as members of this superfamily were several other bacterial proteins, including MreB, FtsA, and
ParM (Bork et al., 1992). Since initial identification, the
superfamily of actin-like proteins in bacteria has proved to
be very complex, encompassing more than 20 classes of protein
(Derman et al., 2009).
The most common prokaryotic homologue of actin is
MreB. As for tubulin/FtsZ, actin and MreB are very divergent
in primary sequence but have similar structures (Fig. 1), based
on the “actin-fold” that unites the superfamily (Kabsch and
Holmes, 1995). In vitro MreB forms assemblies of two protofilaments
that are similar in structure to F-actin, but lack the
helical twist (van den Ent et al., 2001; Esue et al., 2005). The
conserved function of bacterial MreB (and closely related proteins
such as Mbl and MreBH) appears to be in maintenance of
cell shape (Jones et al., 2001; Graumann, 2007; Margolin,
2009). MreB filaments form a helix below the cell membrane
and influence the position of cell wall synthesis (Fig. 2 A; Jones
et al., 2001; Daniel and Errington, 2003). Consistent with this
function, MreB is generally conserved only among rod-shaped
bacteria, but absent from spherical cocci. Because extant rodshaped
bacterial lineages are probably more ancient, it has been
suggested that the coccal forms have been derived from them
multiple times by the loss of MreB and associated genes
(Margolin, 2009). However, the correlation between prokaryote shape and MreB is not strict: some cocci still possess MreB and
there are rod-shaped bacteria that lack MreB (Margolin, 2009).
ParM (previously StbA) is a plasmid-borne bacterial actin
homologue with a filament-forming role. ParM is only 20%
identical to MreB, which is comparable to the degree of conservation
between actin and either ParM or MreB. Nonetheless,
ParM assembles twisted polymers in vitro that are very reminiscent
of F-actin (van den Ent et al., 2002), but with a left-handed
rather than right-handed twist (Orlova et al., 2007). The energy
of polymerization of ParM is used in the segregation of the R1
plasmid (and others containing the parMRC operon) by pushing
newly synthesized plasmid to the cell poles (Garner et al., 2007;
Salje and Löwe, 2008).
To date, unambiguous ParM homologues are restricted to
a close group of -proteobacteria, the Enterobacteriaceae. It is
likely that the annotated “ParM” genes in the genomes of
Firmicutes, -proteobacteria, and cyanobacteria represent other
classes of bacterial actin-like proteins, rather than true ParM
orthologues. In support of this interpretation, “ParM” encoded
on the Staphylococcus aureus pSK41 plasmid shares only 19%
identity with -proteobacterial ParM sequences and appears to
be more structurally related to archaeal actin-like proteins (Popp
et al., 2010).
Both MreB and FtsA are almost exclusively restricted to
bacteria (Fig. 3). Clear examples of MreB are also found in
euryarchea of the genera Methanopyrus, Methanobrevibacter, and
Methanothermobacter (Yutin et al., 2009). Given their limited
distribution and close similarity to bacterial sequences, these
are most likely the result of horizontal gene transfer from bacteria.
However, it cannot be entirely ruled out that they are rare
but highly conserved genes of linear descent. Several other archaeal
sequences have been identified as possible MreB orthologues
using the “archaeal cluster of orthologous groups” technique (Makarova et al., 2007, 2010). These sequences have a closer
affinity to Hsp70 sequences than to MreB from bacteria or
Methanopyrus and their grouping in arCOG04656 may be an
artifact of the technique. These sequences are not considered as
true MreB members herein (Fig. 3).
Several other actin superfamily members exist in bacteria—
notably: MamK, which is required for magnetosome organization
in Magnetospirillium (Komeili et al., 2006; Pradel et al.,
2006); AlfA, which is involved in plasmid segregation in Bacillus
subtilis in a manner similar to ParM (Becker et al., 2006);
and Ta0583 from the euryarchaeon Thermoplasma acidophilum
(Roeben et al., 2006; Hara et al., 2007). These proteins have
either a limited phylogenetic distribution or their families have
yet to be well delimited (Derman et al., 2009; Yutin et al., 2009).
The possibility that Ta0583 might be the closest prokaryotic
homologue to eukaryotic actin (Hara et al., 2007) has not been
supported by subsequent analyses (Yutin et al., 2009; Ettema
et al., 2011). However, recently an archaeal actin-like family
has been described that is monophyletic with eukaryotic actin
and actin-related proteins (Yutin et al., 2009; Ettema et al.,
2011). This protein family, dubbed “crenactin,” has a localization
in Pyrobaculum cells very similar to MreB in bacteria (Fig. 2 B;
Ettema et al., 2011), but is more closely related to eukaryotic
actin than to MreB or ParM. The possible implications of this
family are discussed further below.



Filaments III: intermediate filaments

Eukaryotic intermediate filaments (IFs) are unlike microtubules
and microfilaments in structure, biochemistry, and phylogenetic
distribution. Unlike actin and tubulin, which are globular proteins
that form polarized protofilaments, IF proteins are extended
dimers that overlap to form unpolarized cables. There are many
types of IF protein in vertebrates, most of which can be grouped
into five classes: (1) type I (acidic) keratins; (2) type II (basic)
keratins; (3) vimentin and desmin; (4) -internexin and neurofilament
proteins; and (5) lamins (Fuchs and Weber, 1994). Lamins
are also present in protosomes, suggesting that all IF protein
families are derived from a single lamin-like sequence in the
common metazoan ancestor (Weber et al., 1989; Dodemont
et al., 1994; Bovenschulte et al., 1995). Significantly, however,
eukaryotic IF proteins have only been found unambiguously in
animals and their relatives (Erber et al., 1998), suggesting that
they are an innovation specific to this lineage and not present in
the last eukaryotic common ancestor (LECA; see Fig. 3).
The bacterium Caulobacter crescentus encodes a protein
with a predicted arrangement of coiled-coils similar to that in
animal lamin A (Ausmees et al., 2003). This protein, CreS or
crescentin, forms helical filaments that are necessary for the
vibrioid or helical cell shapes adopted by Caulobacter. Although
crescentin was originally described only as “IF-like”, the
function and predicted secondary structure of the protein have
often been interpreted as evidence that bacteria possess ancient
homologues of eukaryotic IFs. However, there are several arguments
against such an interpretation. First, CreS has a very
restricted distribution (Fig. 3); to date, it has only been found in
Caulobacter. Given this restricted range, if lamin A and
crescentin are truly homologous, then CreS would most likely represent a lateral transfer of a eukaryotic gene to Caulobacter
rather than a true bacterial homologue. Second, identifiable
homologues of eukaryotic IF proteins are restricted to metazoa
(or possibly holozoa; Fig. 3) and may not have been present in
the LECA—precluding vertical inheritance from prokaryotes.
Third, similarities in predicted protein architecture (in this instance,
coiled-coil positions) are not equivalent to fold homology.
At present, it is not possible to compare eukaryotic IF
proteins and crescentin for evidence of fold homology, as there
are no representatives of either family for which full structures
have been determined. Moreover, although orthologues of crescentin
have not been identified outside of Caulobacter, there is
evidence that CreS is a member of a larger family of bacterial
proteins (Bagchi et al., 2008). All of these proteins are predicted
to contain long stretches of coiled-coils, but the vast majority
have no striking architectural similarity to lamin A (or other
vertebrate IF proteins). Hence, the distribution of coiled-coil
regions in crescentin and lamin A is more likely an example of
convergence than a reflection of shared ancestry.




Filaments IV: WACA proteins

Prokaryotes have a fourth class of filament-forming proteins
known as Walker A cytoskeletal ATPases (WACAs; Michie and
Löwe, 2006). WACA proteins are a diverse family of ATPases
(Koonin, 1993), which are themselves part of the extremely
large superclass of P-loop proteins including signal recognition
particle proteins, Rho/Ras GTPases and cytoskeletal motors
(Leipe et al., 2002). The WACA MinD is an active ATPase
(de Boer et al., 1991) that forms dynamic filaments around the
cell periphery in E. coli and inhibits Z ring formation (Pichoff
and Lutkenhaus, 2001; Shih et al., 2003). In Bacillus subtilis,
MinD is statically associated with the cell poles (Marston et al.,
1998; Marston and Errington, 1999), making it unclear if dynamic
polymerization is an evolutionarily conserved feature of
MinD biology. MinD sequences are found in many groups of
bacteria (Fig. 3) and there are putative orthologues identified in
Euryarchaeota (Leipe et al., 2002). However, the distinctions between
the prokaryotic WACA families are yet to be fully resolved,
so it is presently unclear if these archaeal sequences are monophyletic
with bacterial MinD. Even if not strict MinD orthologues,
examples of WACA proteins do appear to be present in
both Euryarcheaota and Crenarchaeota (Makarova et al., 2010).
Several other bacterial WACA proteins have been described.
ParA, ParF, and Soj all play roles in DNA segregation
by different mechanisms (Pogliano, 2008; Löwe and Amos,
2009), demonstrating an apparent versatility of this system for
segregation. It is perhaps surprising, therefore, that there are no
eukaryotic WACA filaments. The fold of MinD and Soj is distantly
related to that of eukaryotic septins (Cordell and Löwe,
2001; Leonard et al., 2005; Löwe and Amos, 2009), but this
most likely reflects the distant relationship shared by all P-loop
GTPases (Leipe et al., 2002). There are, however, MinD genes
of bacterial ancestry in Viridiplantae (green algae and land plants)
and some stramenopiles (Fig. 3), which play a role in plastid
division (Marrison et al., 1999; Colletti et al., 2000; Kanamaru
et al., 2000). It is noteworthy that all eukaryotes that possess
MinD genes also encode endosymbiont-derived FtsZ.




Prokaryotic division: a common problem with many solutions

If there is an overarching theme running through the evolution
of the prokaryotic cytoskeleton, it appears to be this: plasticity.
Each of the major families of cytomotive filament-forming
proteins consists of several paralogues, which are often as divergent
from each other as they are from eukaryotic homologues.
Some of the classes—such as FtsA (from the MreB/actin
superfamily) or the newly identified FtsZ-like families—may
not form filaments in vivo at all. However, among those
families that do polymerize, lateral interactions in the core
filament appear to be quite malleable over evolutionary timescales
without disrupting polymerization (for example, straight
MreB filaments, against left-handed twisting ParM and righthanded
actin).
There is also plasticity in the biological function for
which filaments are used—FtsZ and MreB are involved in cell
division and morphology, while their homologues TubZ and
ParM play roles in plasmid segregation. The result is that prokaryotes
use different systems to solve common problems. In
bacteria, active DNA segregation can be achieved by at least
three types of segregation machinery (Ebersbach and Gerdes,
2005; Hayes and Barillà, 2006). Type I systems use WACA
proteins, such as ParA and Soj. Type II systems are based on
the actin homologue ParM. Type III systems are those from
Bacillus that use tubulin-like homologues, such as TubZ and
RepX. In a striking example of apparent convergence, both
ParM (type II) and TubZ (type III) form similar helical filaments
that probably act to push apart plasmids (van den Ent
et al., 2002; Aylett et al., 2010). However, it is type I systems
that are by far the most wide spread in bacteria. It is interesting,
then, that filaments based on WACA proteins are not
conserved in eukaryotes, and may not be widely used in chromosome
segregation in archaea (Bernander, 2000; Makarova
et al., 2010). Significantly, none of the cytoskeletal protein
families is ubiquitous to all prokaryotes, or even one of the
two prokaryotic domains of life. The role for FtsZ in cytokinesis
appears to be the function under most selective pressure
for retention (Erickson, 2007), but even this protein has been
lost from several lineages of bacteria and the entire crenarchaeal
clade.

Eukaryogenesis: families and specialization

Despite being based on homologous filaments, the eukaryotic
cytoskeleton is not simply a more extensive version of the prokaryotic
one (Fig. 2 C). The complex eukaryotic cytoskeleton is
actually based on a smaller set of ancestral cytomotive filaments
than that of prokaryotes. With the notable exception of the prokaryote-
like division machineries associated with some plastids,
only one paralogue of an MreB/crenactin family protein
and one FtsZ/TubZ protein seems to have founded the eukaryotic
cytoskeleton. However, this small selection has undergone
several rounds of gene duplication and specialization from this
ancestral set.
Heterodimers of - and -tubulin make up the vast majority
of tubulin in eukaryotic cells. They are sufficient for the production
of microtubules in vitro, and it is very likely that they were the first types to evolve from the single proto-tubulin
ancestor. However, they are not the only ancestral tubulins.
Analyses suggest that the tubulin family encompasses at least six
classes, named , , , , , and , with a further two divergent
types ( and ) being found in some organisms (Vaughan et al.,
2000; Dutcher, 2003). -Tubulin plays an essential role in microtubule
nucleation (through the action of the conserved -tubulin
ring complex) and is, like - and -, ubiquitous to all eukaryotes.
In contrast, - and -tubulin have centriolar roles (Dutcher
and Trabuco, 1998; Chang and Stearns, 2000; Ruiz et al., 2000)
and are conserved in nearly all organisms that build centrioles/
basal bodies and absent from organisms that have lost cilia/
flagella (Hodges et al., 2010). At least five of the classes of tubulin
(, , , , and ) can be traced back to the last common
eukaryotic common ancestor (Fig. 3). All of the tubulin types
are more closely related to one another than to FtsZ/TubZ
(Vaughan et al., 2000; Dutcher, 2003), implying that they all
descended from a common proto-tubulin by gene duplication.
Both duplication and specialization into functionally distinct
classes must have occurred before the LECA.
There are striking parallels between the proto-eukaryotic
evolution of tubulins and that of actin. The proteins most similar
in sequence to conventional actin are the ARPs. The ARPs cover
at least eight major families (Sehring et al., 2007) that are found
only in eukaryotes. Four ARP families (ARP4, 5, 6/7, and 8/9)
are not associated with cytoplasmic actin, but are nuclear proteins
involved in chromatin remodeling (Chen and Shen, 2007;
Dion et al., 2010). The remaining families—ARP1, 2, 3, and
10/11—have important roles in modification or extension of cytoplasmic
actin function. ARP1 is an integral part of the dynactin
complex, which links the actin- and tubulin-based cytoskeleton
(Schroer, 2004). Yeast Arp10p and metazoan Arp11 (ARP10/11
family members) are also part of the dynactin complex (Eckley
and Schroer, 2003; Clark and Rose, 2006). In contrast, a complex
of seven subunits formed around a heterodimer of ARP2 and
ARP3 is a major F-actin nucleator in most eukaryotes (Pollard
and Beltzner, 2002; Goley and Welch, 2006). The only ARP that
appears to form filaments is Arp1p (Schafer et al., 1994; Bingham
and Schroer, 1999). These filaments are much shorter than those
seen for actin, but have similar morphology.