ArticlePDF AvailableLiterature Review

The origin and evolution of synapses

October 2009
Nature Reviews Neuroscience 10(10):701-12

October 2009
10(10):701-12

DOI:10.1038/nrn2717

Source
PubMed

Authors:

Tomás J Ryan

Trinity College Dublin

Seth G N Grant

The University of Edinburgh

Understanding the evolutionary origins of behaviour is a central aim in the study of biology and may lead to insights into human disorders. Synaptic transmission is observed in a wide range of invertebrate and vertebrate organisms and underlies their behaviour. Proteomic studies of the molecular components of the highly complex mammalian postsynaptic machinery point to an ancestral molecular machinery in unicellular organisms--the protosynapse--that existed before the evolution of metazoans and neurons, and hence challenges existing views on the origins of the brain. The phylogeny of the molecular components of the synapse provides a new model for studying synapse diversity and complexity, and their implications for brain evolution.

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The synapse is an intensely studied and highly special-

ized cellular site yet surprisingly little is known about its

origins and evolution. A century of electrophysiologi-

cal and pharmacological studies have demonstrated the

importance of synaptic function as a universal property

of neural circuits. During the past two decades, molecu-

lar studies have provided us with an understanding of

the fundamental mechanisms of synaptic transmission

and plasticity, and have shown that these are remarkably

conserved across a range of animal species1.

It remains unknown whether there are central behav-

ioural mechanisms shared by all organisms and whether

these share common ancestry. For example Hebb’s learn-

ing model proposed in the 1940s2 applies only to animals

with neural circuits. Broader concepts of behaviour tra-

versing unicellular organisms to humans were stated in

the nineteenth century. In 1891, C. L. Morgan observed

that “the primary end and object of the receptions of

the influences (stimuli) of the external world or environ-

ment, is to enable the organisms to answer or respond

to these special modes of influence, or stimuli. In other

words, their purpose is to set agoing certain activities.

Now in the unicellular organisms, where both the recep-

tion and the response are effected by one and the same

cell, the activities are for the most part simple, though

even among these protozoa there are some which show

no little complexity of response”3.

Scholarly attempts to investigate or draw theories on

the evolution of the nervous system did not until recently

address the question of the origin and evolution of the

synapse itself. This is not surprising, given the lack of

tools available to explore the synapse in an evolutionar-

ily meaningful way, as the traditional methods to study

synapse structure and function, which rely on micros-

copy and electrophysiology, do not serve this purpose.

To examine the synapse through an evolutionary frame-

work, experimental methods are required that allow the

identification of the specific adaptations that mediated

the diversification and natural selection of synapses

between species. Recent systematic approaches to study

synapse evolution are based on advancements in pro-

teomics and genomics and are coupled with molecular

phylogenetic approaches. Proteomics has provided the

key step in the understanding of this field by identifying

the protein constituents of synapses and their interac-

tions. The postsynaptic proteome of mice has ~1,500 pro-

teins and the presynaptic proteome and synaptic vesicles

also comprise hundreds of proteins4,5, demonstrating the

complexity of mammalian synapses.

The postsynaptic density (PSD) is composed of a set of

multiprotein complexes assembled from diverse protein

classes, such as ion channels, receptors, cell adhesion

and cytoskeletal proteins, kinases and phosphatases,

scaffolding proteins and signalling molecules4,6 (see

Supplementary information S1 (table)). Multiprotein

complexes that are associated with postsynaptic neuro-

transmitter receptors (such as glutamate, serotonin and

acetylcholine receptors) as well as potassium channels

have also been extensively characterised at the PSD

because of their key role in synaptic transmission5.

N-methyl--aspartate (NMDA) receptors, and their

interacting MAGUK (membrane-associated guanylate

kinase) proteins, are particularly well studied and dis-

cussed in detail in this Review. Interestingly, a large

proportion of the MAGUK associated signalling com-

plexes (MASC) proteins has been implicated in synaptic

plasticity and/or learning phenotypes in mutant mice, or

associated with psychiatric disorders in humans5–8. The

general concept of multiprotein signalling complexes

as ‘signalosomes’ has now been widely accepted, and is

*Wellcome Trust Sanger

Institute, Hinxton, Cambridge

CB10 1SA, UK.

‡Wolfson College, University

of Cambridge, Barton Road,

Cambridge, CB3 9BB, UK.

Correspondence to S.G.N.G.

e‑mail: sg3@sanger.ac.uk

doi:10.1038/nrn2717

Published online

9 September 2009

Postsynaptic proteome

The complete set of proteins

currently identified at the

postsynaptic side of the

synapse.

MAGUK

Membrane-associated

guanylate kinase (MAGUK)

proteins act as scaffolds for the

clustering of receptors, ion

channels and associated

signalling proteins at

postsynaptic sites.

The origin and evolution of synapses

Tomás J. Ryan*‡ and Seth G. N. Grant*

Abstract | Understanding the evolutionary origins of behaviour is a central aim in

the study of biology and may lead to insights into human disorders. Synaptic

transmission is observed in a wide range of invertebrate and vertebrate

organisms and underlies their behaviour. Proteomic studies of the molecular

components of the highly complex mammalian postsynaptic machinery point to an ancestral

molecular machinery in unicellular organisms — the protosynapse — that existed before the

evolution of metazoans and neurons, and hence challenges existing views on the origins of

the brain. The phylogeny of the molecular components of the synapse provides a new model

for studying synapse diversity and complexity, and their implications for brain evolution.

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Ursynapse

The last common ancestor

of all synapses. This was the

platform from which diversity

of synaptic proteins

between different organisms

and different synapse types

evolved.

Orthologues

Homologous genes that

separated due to a speciation

event.

Protosynapse

Those synaptic components

that were present before the

emergence of synapses and

most likely contributed to their

evolution.

Bilaterians

Animals belonging to the

phylum Bilateria. These are a

clade of animals with bilateral

symmetry that possess

complex nervous systems.

They are divided into

protostomes and

deuterostomes.

Outgroup

A group of organisms that

serves as a reference group for

determination of the

evolutionary relationship

between monophyletic groups

of organisms.

Choanoflagellates

Organisms belonging to the

phylum Choanoflagellata.

These are unicellular

eukaryotes that can exist in

both free-living and colonial

forms, and are multicellular

metazoans considered to be

the closest unicellular relative

of multicellular metazoans.

Porifera

Phylum of multicellular animals

(poriferans or sponges) that

lack a nervous system.

illustrated by examples in immunology (the mamma-

lian T cell receptor)9 and vision research (the Drosophila

melanogaster InaD complex)10.

Complementary to charting the proteome of syn-

apses, the flood of data from genome sequencing projects

allows the use of comparative genomics to examine how

and when synaptic proteins originated and diversified.

Comparative genomics has revolutionized evolutionary

biology, bolstering our understanding of the relation-

ships between species, and also into the mechanisms

of molecular evolution11. By combining proteomic and

genomic approaches, the postsynaptic proteome pro-

vides unprecedented opportunities for probing and map-

ping the evolution of the synapse across species. Here we

review such attempts and present the evidence accumu-

lated so far as a working model of synapse molecular

evolution, based primarily on the postsynaptic machin-

ery, which has been more extensively studied. We also

make suggestions as to how this topic may be addressed

in the future.

The origin of synapses

The question of origin is central to the study of evo-

lution12. When did synapses first form? What was the

identity of the organism that necessitated this evolution-

ary step? Were the first synapses capable of plasticity?

How are the origins of neurons and synapses related?

Knowing the proteomic composition of synaptic struc-

tures allows the use of comparative genomics to question

what the minimal, ancestral components of the synapse

might have been. If we can deduce the composition of

the last common ancestor of all synapses, the ursynapse,

then we should be in a position to address the question

of how and why the first synapse originated.

We approach the question of the composition of the

ursynapse by taking synaptic proteins identified in ver-

tebrate model organisms and searching for orthologues

in the genomes of two categories of organism. The first

category includes unicellular eukaryotes and multicel-

lular metazoans that lack a nervous system, and pro-

vides a means of identifying synaptic components that

were present before the evolution of the nervous system.

Such proteins, which make up the protosynapse, origi-

nated before the emergence of classical morphological

synapses and have been co-opted for synaptic roles. The

second category is composed of non-bilaterian multi-

cellular metazoans that have a nervous system, which

allows the identification of synaptic components present

in primitive synapses, giving us insight into the com-

position of the synapse at a relatively short time after it

originated (FIG. 1).

Protosynaptic organisms. The most evolutionary ancient

synaptic protein families are conserved in unicellular

eukaryotes such as the yeast Saccharomyces cerevisiae

and the amoeba Dictyostelium discoideum. The calcium

transporter PMCA (plasma membrane calcium ATPase)

and protein kinase C (PKC) are found in both these uni-

cellular species and also have fundamental synaptic

roles in animals13–15. More broadly, when the mamma-

lian MASCs and larger PSD gene sets were compared

against the S. cerevisiae genome, over 21% of the MASC

genes and 25% of the PSD genes were found to have

direct orthologues in protosynaptic organisms, labelling

them as protosynaptic proteins of pre-metazoan ances-

try16. Whether protosynaptic components in yeast form

functional multiprotein complexes in a similar manner

to which they do in neurons is unknown, but loss-of-

function studies in yeast show that many of these genes

are involved in regulating the cell’s response to the envi-

ronment (TABLE 1)16, including vesicular trafficking and

cytoskeletal regulation in response to nutrients, ions

and pheromones from the environment16. A portion

(15%) of yeast PSD orthologues functions in signal trans-

duction pathways that mediate environmental response.

Yeast orthologues of the mammalian RAS regulator

neuro fibronin 1 (NF1; that is, yeast IRA2), the extracel-

lular signal-regulated kinase 2 (ERK2; also known as

MAPK1; that is, yeast FUS3), and the G-protein guanine

nucleotide binding protein 5 (GNB5; that is, yeast STE4)

regulate cell morphology, stress response and cell pro-

liferation induced by pheromone signalling. Strikingly,

quintessential players that mediate changes dependant on

neuronal activity during synaptic plasticity are also essen-

tial components of the yeast’s response to environmental

changes. The calcium binding protein calmodulin that

activates calcium/calmodulin-dependent protein kinase II

(CaMKII) and the protein phosphatase calcineurin

(which has been associated with Schizophrenia17)

both regulate calcium influx at the cell membrane and

are implicated in postsynaptic signalling pathways in

neurons and in environmental responses in yeast cells18.

Yeast is an excellent organism for the study of genet-

ics and genomics, but is a distant outgroup of metazoans

and is unlikely to hold a quasi-comprehensive set of

proto synaptic proteins. To understand the origin of the

synapse it is desirable to consider a unicellular organ-

ism that is closely related to multicellullar Metazoa.

Choanoflagellates fulfil this role. These unicellular eukary-

otes are the closest unicellular relatives of multicellular

metazoans on account of their cell body structure and

phylogenetic analyses of nuclear and mitochondrial

DNA19,20 (FIG. 1). The genomes of choanoflagellates have

assisted in reconstructing the genome of the last unicel-

lular ancestor of animals, and could also be useful for elu-

cidating the origin of the synapse21. Multicellular Porifera

(sponges), which lack neurons, are further candidates for

the identification of protosynaptic components22.

Bioinformatic analyses of choanoflagellate genomes

using comprehensive PSD gene sets as a starting point

have yet to be reported. However, pioneering studies of

candidate genes have demonstrated the presence of syn-

aptic molecules in choanoflagellates that are absent in

all other non-metazoans, including numerous tyrosine

kinases of the choanoflagellate Monosiga brevicollis23–26.

Rapid phosphorylation of tyrosine kinase substrates was

observed following treatment of starved M. brevicollis

cells with seawater and Enterobacter spp., which demon-

strates that the tyrosine kinase pathway has a role in the

environmental response24. Inhibition of tyrosine kinases

delayed progression of M. brevicollis cultures into log-

arithmic growth, wherease a SRC family tyrosine kinase

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Deuterostomes

Bilaterians

Eumetazoans

Metazoans

Eukaryotes

Ursynapse

Protostomes

Greater signalling complexity,

MASC gene family expansion,

NMDA receptor duplication,

MAGUK duplication

Stargazin

LIMK

Excitatory glutamate receptors (NMDA and AMPA),

kainate receptors,

K+ channels, neuroligin, CASK, erbin

GABA receptors, metabotropic glutamate receptors,

CaMKII, KIR channel, NOS, SynGAP,

S-SCAM, Homer, GKAP, GRIP, CRIPT, agrin, MuSK, ankyrin, neurexin, NCAM

Cadherins, ephrin receptors, receptor and non-receptor tyrosine kinases,

Dlg (MAGUK), shank, calpain, spectrin, PDZ binding proteins

MASC downstream signaling components, PKC, PMCA, NF 1, calmodulin, calcineurin

Vertebrates Lophotrochozans Ecdysozoans Cnidarians Poriferans Choanoflagellates Fungi

Nature Reviews | Neuroscience

With synapses

Without synapses

(protosynaptic)

619–790 mya

Av. 790 mya

581–1,141 mya

Av. 910 mya

766–1,351 mya

Av. 1,036 mya

766–1,351 mya

Av. 1,237 mya

970–1,070 mya

Av. 1,020 mya

1,220–1,513 mya

Av. 1,368 mya

Demosponge

Organism belonging to the

primary class of Porifera.

Demosponges account for

~90% all sponge species.

inhibitor abolished cell proliferation24. Given the central

role of SRC family kinases in plasticity at excitatory syn-

apses, the establishment of this apparatus and mechanism

before the evolution of synapses is of significance27,28.

Molecules that have been implicated in synaptogene-

sis such as cadherins are also present in choanoflagellates,

and co-localize with actin at the cell’s apical collar mem-

brane, surrounding the singular flagellum29. Homophilic

cadherin interactions are essential for excitatory synapse

formation in mammals and in D. melanogaster, in which

cadherin interacts directly with actin at the postsynap-

tic terminal30. Cadherins may therefore be important

for cytoskeletal rearrangement in choanoflagellates and

may represent a precursor to synapse formation. It is

conceivable that the first protein–protein interaction

that led to synaptogenesis would be homophilic, as the

same molecules would be required by both cells, whereas

heterophilic transynaptic protein interactions probably

evolved later.

Comparisons between the PSDs of Bilateria and

sponges have allowed the identification of genes that

were present in a multicellular ancestor of Metazoa

that immediately preceded the emergence of organisms

with synaptic junctions13,31. Additional cell-signalling

and adhesion molecules that have roles in synaptogen-

esis have been identified in the sponge Oscarella carmela,

including ankyrin, neurexin and tyrosine kinase signal-

ling components 32. We postulate that these molecules

originated before the evolution of synapses, in a meta-

zoan/choanoflagellate common ancestor, and there-

fore were instrumental to the development of the first

synaptic junction. Transgenic experiments in unicellu-

lar organisms and sponges may prove useful in testing

this idea.

Many MASC components that have been implicated

in synaptic plasticity in mammals are also present in

the demosponge Amphimedon queenslandica (TABLE 1)13.

Various interaction domains of postsynaptic proteins,

Figure 1 | Phylogenetic tree depicting taxons of current relevance to synapse evolution. An extant model

organism of each clade is displayed at the top of the phylogeny (see Supplementary information S2 (Box) for additional

details on the phylogenetic placing of Porifera relative to Cnidaria). Nodes on the phylogeny represent the divergence

points of various clades and are presented by coloured circles. The red node represents Urbilateria (the last common

ancestor of all bilaterians). The small grey circle represents the ursynapse (last common ancestor of all synapses). Beside

each node the range of published estimations of the given divergence time are given in mya (millions of years ago), as well

as the average (av) estimated divergence time based on published studies (available through the public resource for

knowledge on the timescale and evolutionary history of life, Timetree43,104). Superimposed on the phylogeny are notable

proteins that are involved in synapse formation and/or function, showing at what intervals in evolutionary history various

synaptic components arose. See Supplementary information S3 (Box) for additional details on the possible origins of

GABA and metabotropic glutamate receptors. AMPA, α‑amino‑3‑hydroxy‑5‑methyl‑4‑isoxazolepropionic acid;

CaMKII, calcium/calmodulin‑dependent protein kinase II; CASK, calcium/calmodulin dependent serine protein kinase;

CRIPT, cysteine‑rich PDZ‑binding protein; Dlg, discs, large homolog; GABA, g‑aminobutyric acid; GKAP, guanylate

kinase associated protein; GRIP, glutamate receptor interacting protein; KIR channel, inwardly rectifying potassium

channel; LIMK, LIM domain kinase; MAGUK, membrane‑associated guanylate kinase; MASC, MAGUK associated

signalling complex; MuSK, muscle specific kinase; NCAM, neural cell adhesion molecule; NF1, neurofibromin 1;

NMDA, N‑methylase‑d‑aspartate; NOS, nitric oxide synthase; PKC, protein kinase C; PMCA, plasma membrane calcium

transporting ATPase; Shank, SH3 and multiple ankyrin repeat domains; S‑SCAM, membrane associated guanylate kinase,

WW and PDZ domain containing 2; SynGAP, synaptic Ras GTPase activating protein.

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including PDZ binding domains, are almost completely

conserved between the sponge and the Bilateria, argu-

ing strongly in favour of the existence of an assembled

multiprotein structure. Five of the postsynaptic proteins

are present and co-expressed in epithelial flask cells of

A. queenslandica (discs large homologue (Dlg), guanylate

kinase-associated protein (GKAP), glutamate receptor

interacting protein (GRIP), Homer and cysteine-rich

PDZ-binding protein (CRIPT)), implying that they

may form a protosynaptic complex involved in sensing

environmental stimuli and that they could represent an

evolutionary precursor to synaptic sites33. Importantly, a

number of channels and receptors that have crucial roles

at synapses are also expressed in the sponge, including

inhibitory GABA receptors, the K+ channel KIR, and

metabotropic (G-protein coupled) glutamate receptors

Table 1 | The origin and ancestral functions of protosynaptic proteins

Molecule Clade of origin Organism reported Ancestral function

PKA Fungi S. cerevisiae16 Nutrient induced cell proliferation106

NF1 Fungi S. cerevisiae16 Stress response107

Calmodulin Fungi S. cerevisiae16 Ca2+ dependant stress response18

Calcineurin Fungi S. cerevisiae16 Ca2+ dependant stress response108

ERK2 Fungi S. cerevisiae16 Pheromone induced cell proliferation109

GNB5 Fungi S. cerevisiae16 Pheromone induced signalling110

SNAP‑25 Fungi S. cerevisiae111 Vacuolar morphogenesis and trafficking111

Syntaxin Fungi S. cerevisiae16 Vacuolar morphogenesis and trafficking111

TRP channels Fungi S. cerevisiae112 Osmolarity stress response112

Cadherin Choanoflagellata M. brevicollis24 Unknown, co‑localizes with actin filaments

at the apical collar29

SRC kinase Choanoflagellata M. brevicollis113 Regulation of cell proliferation24

RAF kinase Choanoflagellata M. brevicollis24 Unknown

Ephrin receptors Choanoflagellata M. brevicollis26 Unknown

Calpain Choanoflagellata M. brevicollis114 Unknown

Spectrin Choanoflagellata M. brevicollis115 Unknown

Dlg (MAGUK) Choanoflagellata M. brevicollis13,116 Unknown

Shank Choanoflagellata M. brevicollis13,116 Unknown

Agrin Porifera O. carmela31 Unknown

MuSK Porifera O. carmela31 Unknown

Ankyrin Porifera O. carmela31 Unknown

Neurexin Porifera O. carmela31 Unknown

NCAM Porifera O. carmela31 Unknown

GABA receptors Porifera A. queenslandica13 Unknown

mGluR receptors Porifera A. queenslandica13 Unknown, activity modulates Ca2+ influx35

KIR channels Porifera A. queenslandica13 Unknown

CaMKII Porifera A. queenslandica13 Unknown

NOS Porifera A. queenslandica13 Unknown

SynGAP Porifera A. queenslandica13 Unknown

S‑SCAM Porifera A. queenslandica13 Unknown, located in epithelial cells117

Homer Porifera A. queenslandica13 Unknown, located in epithelial cells13

GKAP Porifera A. queenslandica13 Unknown, located in epithelial cells13

GRIP Porifera A. queenslandica13 Unknown, located in epithelial cells13

CRIPT Porifera A. queenslandica13 Unknown, located in epithelial cells13

A. queenslandica, Amphimedon queenslandica; CaMKII, calcium/calmodulin‑dependent protein kinase II; CRIPT, cysteine‑rich

PDZ‑binding protein; Dlg, discs large homolog; ERK2, extracellular signal‑regulated kinase 2; GKAP, guanylate kinase associated

protein; GNB5, guanine nucleotide binding protein β5; GRIP, glutamate receptor interacting protein; KIR channel, inwardly rectifying

potassium channel; M. brevicollis, Monosiga brevicollis; MuSK, muscle specific kinase; NCAM, neural cell adhesion molecule; NF1,

neurofibromin 1; NOS, nitric oxide synthase; O. carmela, Oscarella carmela; PKA, protein kinase A; S. cerevisiae, Saccharomyces

cerevisiae; Shank, SH3 and multiple ankyrin repeat domains; SNAP‑25, synaptosome‑associated protein of 25,000 daltons; S‑SCAM,

membrane associated guanylate kinase, WW and PDZ domain containing 2; SynGAP, synaptic Ras GTPase activating protein; TRP

channel, transient receptor potential channel.

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Cnidarian

Animal belonging to the

phylum Cnidaria. Cnidarians

are animals with radial

symmetry including jellyfish,

coral, hyrda and anemones.

Cnidarian nervous systems

consist of diffuse neuronal

net-like structures.

Clade

An evolutionary group

consisting of a given single

common ancestor and all of its

descendants.

Protostomes

Animals belonging to the

phylum Protostomia, an animal

clade that includes the

superphyla Ecdysozoa

(arthropods and nematodes)

and Lophotrochozoa.

Deuterostomes

Animals belonging to the

superphylum Deuterostomia

that includes the subphylum

Vertebrata.

(mGluRs)13,34. mGluR activity has been demonstrated in

cells cultured from the sponge Geodia cydonium, which

responds to the presence of glutamate by rising its intra-

cellular calcium concentration35. Indeed, application of

electrical or tactile stimuli to the sponge Rhabdocalyptus

dawsoni, causes it to propagate an electrical impulse that

controls water flow through the organism36. As no exci-

tatory, ionotropic glutamate receptors have been identi-

fied in sponges it seems that inhibitory GABA receptors

evolved in the common ancestor of Porifera and Bilateria,

and importantly, preceded the origin of excitatory

ionotropic glutamate receptors.

The above evidence not only demonstrates the exist-

ence of MASC components and electrically active ion

channels in sponges, but implies that there is a co-localized

protosynaptic complex expressed in an anatomical region

that has a role in environmental adaptation, and this

complex emerged around the same time, in evolution-

ary terms, as the first synaptic channels and receptors.

Of course, many of these proteins have also evolved non-

neuronal functions in animals and indeed their presence

in unicellular organisms and sponges demonstrates their

fundamental roles in intracellular signalling. For exam-

ple PI3K (phosphoinositide 3-kinase) is a protooncogene

that regulates cell division, and MAGUK family mem-

bers are known regulators of mammalian T cell activa-

tion9,37,38. Nevertheless, these pleiotropic proteins have

evolved discrete synaptic functions and it is compelling

to see that a substantial number of synaptic proteins

regulate environmental adaptations in unicellular organ-

isms such as yeast and choanoflagellates, and co-localize

in the sensory cells of sponges13,37,39. Protosynaptic pro-

teins represent therefore a pre-adaptation that later co-

opted for synaptic function and may have contributed to

the development of the first synapse.

Primitive metazoans with synapses. The complimen-

tary approach to investigate the origins of the synapse

is to search the genomes of primitive metazoans with

visible synapses, such as the cnidarian Nematostella vect-

ensis, which phylogenetically branched off ~200 million

years before the bilaterians (FIG. 1) and has a rudimentary

nervous system13. Common features of cnidarians and

bilaterians are representative of a common ancestor that

would have existed following the origin of the synapse

in early metazoans (TABLE 2). The most notable feature

of cnidarians is the emergence of postsynaptic iono-

tropic glutamate receptors including NMDA receptors

and AMPA receptors (α-amino-3-hydroxy-5-methyl-

4-isoxazolepropionic acid receptors), which mediate

synaptic plasticity in the vertebrate CNS40,41.

Additionally, the postsynaptic transmembrane

protein neuroligin originated in a common ances-

tor of N. vectensis and bilaterians, and interacts tran-

synaptically with the presynaptic and protosynaptic

protein neurexin during synaptogenesis42. The neurexin–

neuroligin interaction has an essential and general role in

the formation of both excitatory and inhibitory synapses.

It is noteworthy that ectopic expression of neurexin

or neuroligin in non-neuronal cells co-cultured with

neurons is sufficient to induce synaptic differentiation

of the non-neuronal cells42. All of the ion channels that

emerged after the cnidarian–poriferan split interact

with protosynaptic intracellular scaffold proteins that

are expressed in sponges and which therefore evolved

earlier. In effect, upstream transmembrane receptors

plug into a pre-existing intracellular machinery and

this provides a framework for the emergence of a higher

complexity of signalling pathways (FIG. 2).

Comparing vertebrates and invertebrates

Owing to the pioneering studies of the molecular

mechanisms of synaptic plasticity in the lophotro-

chozoan Aplysia californica (sea slug) and the parallel

mechanisms subsequently discovered in mice1, one

might assume that an invertebrate synapse is essentially

identical to a vertebrate synapse. Recent evidence chal-

lenges this paradigm, highlighting the degree of diver-

gence that has occurred between the synaptic proteomes

of vertebrates and invertebrates16. Bilaterians comprise

two major clades: the protostomes and the deuterostomes.

Protostomes include among other phyla the invertebrate

Arthropoda (arthropods) and Nematoda (nematodes)

(FIG. 1), whereas deuterostomes include the subphylum

Vertebrata (vertebrates). The time of divergence of pro-

tostomes and deuterostomes is estimated at ~910 mil-

lion years ago43. The hypothetical last common ancestor

of all protostomes and deuterostomes is referred to as

Urbilateria, which gave rise to the vast majority of ani-

mal diversity that exists in nature today44. On the one

Table 2 | Synaptic proteins present in early organisms with a nervous system

Molecule Clade idenified Organism Synaptic function

NMDA receptors Cnidaria N. vectensis13 Induction of synaptic plasticity118

AMPA receptors Cnidaria N. vectensis13 Fast synaptic transmission and plasticity119

Kainate receptors Cnidaria N. vectensis13 Modulation of synaptic transmission and

plasticity120

Shaker channel Cnidaria N. vectensis13 Synaptic homeostasis121

Neuroligin Cnidaria N. vectensis13 Synapse formation42

Erbin Cnidaria N. vectensis13 Modulation of voltage dependant calcium

channels122

CASK Cnidaria N. vectensis13 Regulation of neurotransmitter release123

AMPA, α‑amino‑3‑hydroxy‑5‑methyl‑4‑isoxazolepropionic acid; CASK, calcium/calmodulin‑dependent serine protein kinase;

NMDA, N‑methyl‑d‑aspartate; N. vectensis, Nematostella vectenis.

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Homologues

Set of genes or proteins that

are related by descent, that is,

they share a common ancestor.

Genome duplication

Duplication of an entire

genome that results in an

abundance of duplicated

genes, most of which are lost.

Two rounds of genome

duplication are believed to

have occurred at the base of

the chordate lineage.

Gene duplication

Duplication of a given gene

owing to replication errors and

resulting in two redundant

copies of the original gene.

Paralogues

Homologous genes that

separated because of a gene

duplication event.

hand, comparisons between protostomes and deuteros-

tomes allow inferences as to the features of the urbilat-

erian, because whatever is common to protostomes and

deuterostomes was present in the common ancestor. On

the other hand, comparisons between protostomes and

deuterostomes can identify features that have evolved

specifically within each clade16.

Few direct comparisons have been made for synapses

at the morphological level. One anecdotal difference is

that D. melanogaster dendrites can develop from the pri-

mary neurite (that normally give rise to axons) as well as

from the neuronal body, whereas in deuterostomes den-

drites have only been reported to arise independently

from axons45. At the molecular level, the urbilaterian

would have possessed many of the canonical neuro-

transmitter receptors, including acetylcholine, GABA,

glycine, dopamine and serotonin receptors, as these are

found in both protostomes and deuterostomes (FIG. 1)46,47.

The voltage-dependant calcium channel subunit star-

gazin (FIG. 2) is a canonical urbilaterian synaptic protein,

as it is present in all bilaterians and is absent in cnidar-

ians. When protostome genomes including D. mela-

nogaster, Caenorhabditis elegans and Apis mellifera

were searched using the mouse PSD and MASC gene

sets, 44.8% and 46.2%, respectively, had orthologues in

D. melanogaster16. This shows that the PSDs of proto-

stomes and deuterostomes share a core set of homologous

proteins that has expanded divergently since the urbilate-

rian ancestor, and that in vertebrates the PSD and MASC

complexes have more components. Genomic compari-

sons can identify which mouse PSD proteins are absent

from protostome genomes and are therefore specific

to vertebrate synapses. However, such analyses cannot

identify the actual components of the protostome PSD or

MASC complexes. Indeed, the D. melanogaster PSD

could include numerous protostome specific proteins.

Comparative proteomics can address this problem. Mass

spectrometric analysis of the D. melanogaster MASC

detected 220 proteins, showing that D. melanogaster

possesses a MASC similar in size to that of mouse (186

proteins). However, it is the content of the MASC that

differs between the two organisms, and this feature can-

not be observed at the level of genomic sequence com-

parison. When the isolated D. melanogaster MASC was

compared across species in the same manner as for the

mouse, 71% of the D. melanogaster MASC components

were found to have orthologues in yeast, whereas mice

MASC components only had 21.2% yeast orthologues,

showing that the majority of D. melanogaster MASC pro-

teins are ancestral, being common to all eukaryotes and

not of invertebrate or metazoan origin16. Therefore, the

mouse MASC is enriched for recently evolved proteins,

relative to that of invertebrates. Additionally, when the

components of the mouse MASC were classified accord-

ing to gene ontology categories, over 60% were found to

be ‘upstream’ signalling components, such as receptors,

scaffolding proteins and signal transduction molecules

(FIG. 3). Conversely, only 25% of the D. melanogaster

MASC falls into this category, with the majority pertain-

ing to the category of ‘downstream’ components, such

as metabolic enzymes, chaperones and mitochondrial

proteins. These numbers suggest that the deuterostome

MASC has evolved a significantly greater degree of

signalling complexity.

The paradigm of the NMDA receptor carboxy‑terminus

and its interactions. Besides the evolution of synaptic

complexity, there is evidence that the organization of

these proteins, mediated by their interaction domains,

has also differentially evolved. For example, GKAP

(guanylate kinase associated protein) and shank (SH3

and multiple ankyrin repeats domain) are both post-

synaptic scaffolding proteins that regulate synapse

assembly in animals and are present in sponges13,48,49.

However, the GKAP PDZ domain necessary for its

interaction with shank is deuterostome specific, and

is likely to influence synaptogenesis13,50. The signifi-

cance of domain evolution at the synapse is exempli-

fied by the intracellular carboxy-terminal domains of

the NMDA receptor, which interacts with proteins of the

MASC51,52. Comparison of the amino acid sequence of

various excitatory and metabotropic glutamate recep-

tors across species revealed a significant vertebrate–

invertebrate dichotomy in the protein size of NMDA

receptors51. Specifically, the vertebrate NMDA receptor

NR2 (NMDA receptor 2) subunits possess intracellu-

lar carboxy-terminal domains five times larger than all

known invertebrate, protostome NR2 protein sequences

(FIG. 4). This evolutionary dichotomy is unique to the

NR2 subunit as no differences of this magnitude were

observed for any other neurotransmitter receptor sub-

unit. Within the protostome and deuterostome clades

the NR2 carboxy-terminal domains retain a relatively

conserved size of ~100 amino acids in protostomes and

~600 amino acids in deuterostomes. The larger, deutero-

stome NR2 carboxy-terminus contains many protein

interaction sites and phosphorylation sites that are not

present in protostomes, arguing strongly in favour of a

higher complexity of NMDA receptor interactions in

vertebrates (FIG. 4). A high degree of sequence conserva-

tion of the carboxy-terminal domain is seen in the deu-

terostome clade, demonstrating functional significance

of this domain, which has been elegantly demonstrated

with respect to hippocampal synaptic plasticity and

memory formation by in vivo genetic studies53.

NR2 duplication and carboxy‑terminal divergence.

Two rounds of whole genome duplication have occurred

in a common ancestor of chordates in the deutero-

stome clade54. As a result many D. melanogaster genes

have up to four orthologues in mouse. Synaptic gene

families that have undergone chordate specific expan-

sion include sodium and potassium channels, calcium

channels, transient receptor potential (TRP) channels,

glutamate and GABA receptors, ephrin receptors, pro-

tein kinase C (PKC), plasma membrane calcium ATPase

(PMCA), cadherin, neuroligin, Dlg, nitric oxide syn-

thase (NOS), calcium/calmodulin-dependent protein

kinase II (CaMKII) and GKAP13,55. NMDA recep-

tors have evolved further in vertebrates due to gene

duplications of the NR2 subunit that have resulted in

four distinct paralogues (NR2A–NR2D), which have

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Ionotropic glutamate receptors

Metabotropic glutamate receptors

Calcium ion binding proteins

Protein kinase activity

Small GTPase signal transduction

Translational elongation

Protein biosynthesis

Fungi Protostomes Deuterostomes

NR2/MAGUK gene

family expansion

Stargazin

NMDA receptors

AMPA receptors

Neuroligins

mGluRs

SynGAP

CaMKII

Dlg (MAGUKS)

Calcineurin

Calmodulin

Fungi

Emergence of titular MASC components

Evolution of PSD and MASC components

Choanoflagellates Poriferans Cnidarians Protosomes Deuterostomes

Upstream

Downstream

Upstream

Downstream

Bilaterians

diverged a great extent with respect to their spatio-

temporal expression patterns56. The four NR2 subunits

have also diverged at the level of protein sequence, but

pri marily in their intracellular domains — with no

motif being conserved between the four paralogues

except the terminal PDZ binding domain that inter-

acts with the MAGUKs51. Therefore although the NR2

amino-terminal domains that contain the extracellular

Figure 2 | Evolution of postsynaptic components. a | Various protein types (left column) that constitute the

postsynaptic density (PSD) and membrane‑associated guanylate kinase (MAGUK) associated signalling complexes

(MASCs) in unicellular eukaryotes (fungi), protostomes and deuterostomes are ordered based on whether they have

‘upstream’ or ‘downstream’ signalling roles. Non‑coloured fields represent the absence of a given protein. Dark grey

rectangles represent presence of protein. Grey rectangles represent enrichment of a protein type in protostomes, or

protostomes and deuterostomes when compared with unicellular eukaryotes. Light grey rectangles represent enrichment

of a protein type in deuterostomes when compared with protostomes. The diagrams above each column represent the

molecular assembly of MASC, in which upstream proteins (blue circles) are connected to downstream proteins (yellow

triangles) through intermediate signalling proteins (red rectangle). The relative proportions of these proteins in

eukaryotes, protostomes and deuterostomes is therefore illustrated. b | The emergence of titular MASC components

across clades is illustrated. Proteins are ordered based on whether they are located ‘upstream’ or ‘downstream’ in synaptic

signal transduction pathways16. Non‑coloured fields represent the absence of a given protein, whereas dark grey

rectangles denote its presence. Diagrams of MASC structure are placed above each clade, along with an illustration of a

representative model organism. AMPA, α‑amino‑3‑hydroxy‑5‑methyl‑4‑isoxazolepropionic acid; CaMKII, calcium/cal‑

modulin‑dependent protein kinase II; Dlg, discs large homologue; mGluRs, metabotropic glutamate receptors; NMDA,

N‑methyl‑d‑aspartate; NR2, NMDA receptor 2; SynGAP, synaptic Ras GTPase activating protein. Diagrams in part a are

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Signalling and/or structural

components

Channels and

receptors

Cytoskeletal and

cell adhesion

G proteins and

modulators

Kinases

MAGUKs; adaptors;

scaffolders

Protein phosphatases

Signaling molecule

and enzymes

Synaptic vesicles;

protein transport

Transcription and

translation

Uncharacterized

dMASC

mMASC

Immunological synapse

A region that can form

between two cells of the

immune system in close

contact. The immunolgical

synapse originally reffered to

the interaction between a T cell

and an antigen-presenting cell.

Positive selection

Positive selection is said to

occur when a given genetic

variant rises to prevalence in a

population by increasing the

reproductive fitness of the

organism in a given

environment. Positive selection

at the level of amino acid

sequence is identified by the

dN/dS ratio.

Non-synonymous nucleotide

substitution

A nucleotide substitution in the

coding sequence of a gene that

alters the amino acid sequence

of the protein.

Synonymous nucleotide

substitution

A nucleotide substitution in the

coding sequence of a gene that

does not alter the amino acid

sequence of the protein.

ligand-binding and transmembrane domains, are largely

conserved throughout vertebrate evolution, selection

has acted primarily on the intracellular domains of the

NR2 proteins. The evolutionary divergence of the NR2

carboxy-terminal domains has resulted in different

MASC sets being recruited by different NMDA recep-

tors depending on the particular NR2 subunit present.

Experimental evidence has shown that a number of

NMDA receptor interacting proteins, such as SynGAP

(synaptic Ras GTPase activating protein)57, adaptor pro-

tein 2 (AP2)58, calcineurin59, cyclin dependant kinase 5

(CDK5)60, PSD95 and SAP102 (REF. 61) interact specifically

or preferentially with particular NR2 subunits.

NMDA‑receptor–MAGUK interactions. MAGUKs are

intracellular scaffolds that anchor and traffic NMDA

receptors and AMPA receptors to the synapse39,62. They

are composed of PDZ domains, a SRC homology 3 (SH3)

domain and a guanylate kinase domain. The MAGUK

family has 22 members classified into 7 subfamilies

(MAG1, CASK, MPP, ZO, DLG, CCNB and CARMA)52,

all of which originated in metazoans: 4 subfamilies are of

ancient origin and are present in Porifera (MAGI, MPP,

DLG, DLG5); 2 subfamilies (ZO, CACNB) emerged

later in cnidarians and bilaterians; and the CARMA

(CARD–MAGUK) subfamily, which functions in signal

transduction at immunological synapses63, is deuterostome

specific. Although most MAGUK subfamilies are com-

mon to both protostomes and deuterostomes, five show

deuterostome specific gene expansion thereby bolster-

ing the number of MAGUKs available. For example, Dlg

has only been duplicated in vertebrates, giving rise to

four paralogues: DLG1–DLG4 (also known as SAP97,

PSD93, SAP102, and PSD95, respectively), and muta-

tions in DLG1–DLG4 in mice result in distinct behav-

ioural phenotypes64–66. Deuterostomes have single NR2

and Dlg genes whereas chordates have four paralogues

of each, thus the number of potential chordate NR2–

Dlg interactions has expanded to be 12-fold greater67

(FIG. 4b). This particular interaction serves as an exam-

ple for the combinatorial complexity at the level of

protein interactions that has evolved for chordate

synaptic proteins.

GABA and metabotropic glutamate receptor evolution.

Inhibitory GABA receptors also display deuterostome

specific expansion, with two primary clades of genomi-

cally clustered subunits. The first contains α, γ and ε

subunits, the second includes ρ, β, σ, θ and π subunits68.

The two groups diverged within the deuterostome clade,

in a common ancestor of chordates and urochordates68.

Protostomes by contrast possess a small compliment of

GABA-receptor-like subunits69. GABA receptor subunits

have also undergone mammalian specific gene dupli-

cation and loss. The GABA receptor ε and τ subunits

evolved by duplication of the γ and β subunits, respec-

tively, and the β4 and γ4 subunits were eliminated dur-

ing evolution68,70. Positive selection has since acted on the

protein coding region of the θ subunit, whereas the ε has

displayed evidence of relaxation of constraint (neutral

evolution)68. The functional significance of these evolu-

tionary events is unknown, but may lie in ligand binding

affinity or receptor sensitivity.

Metabotropic glutamate receptors, also have an

ancient origin at the base of Metazoans, and show

substantial expansion in vertebrates13,71. mGluRs are

classified into three groups (I–III) based on sequence

homology. Whereas vertebrates have two to three

members in each group, invertebrates have one71,72.

Presynaptic proteins. Comparative genomics has made

progress in examining the evolution of presynaptic pro-

teins across bilaterians. One study addressed the conser-

vation of 120 presynaptic proteins between vertebrates

and insects73. This protein set showed strong but variable

conservation, and interestingly the degree of conserva-

tion for exocytotic proteins (such as synaptobrevin 2

(VAMP2)) was found to correlate with the number of

interacting partners. This is consistent with reports dem-

onstrating that protein connectivity generally correlates

with protein conservation, that is, the more interactions a

given protein has, the more likely it is to have its sequence

conserved throughout evolution74. However, for endocytic

proteins (such as synaptojanin) the degree of conservation

did not correlate with the number of protein interactions.

The reason for this dichotomy is unknown but may lie in

group specific protein size and domain structure.

Another study selected 150 primarily presynaptic

genes and studied them with respect to conservation of

their coding sequences and adjacent non-coding genomic

elements across 8 vertebrate species including human and

mouse75. The vast majority of the gene set was found to

be under strong purifying selection, with non-synonymous

nucleotide substitution to synonymous nucleotide substitution

ratios (dN/dS ratios) over fivefold lower than the genomic

average. This outcome is consistent with reports of genes

expressed in the brain being under more conservative

selective pressure than genes expressed in other tissues76.

Figure 3 | Comparative proteomics of mouse and Drosophila melanogaster MASC.

Pie charts showing the proportion of various functional classes of proteins in the isolated

Drosophila melanogaster membrane‑associated guanylate kinase (MAGUK) associated

signalling complex (dMASC) and mouse MASC (mMASC). The mMASC is enriched for

‘upstream’ signalling components (blue circles in right panels). Figure is modified, with

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NR2ANR2 NR2B NR2C NR2D

PSD95 PSD93 SAP102

Dlg

b Mouse NMDA receptor

a Drosophila NMDA

receptor

Membrane

PSD95

CaMKII

NMDA receptor

complex/MASC

Synapse diversity

Variability of synaptic protein composition is visible not

only between different organisms. There is also a paral-

lel between the evolutionary origin of synaptic genes

and their expression pattern in the mammalian brain.

In general terms, the evolution of synaptic genes at the

eukaryote–metazoan and metazoan–chordate bounda-

ries preceded their expression in different populations

of neurons and synapses and thereby allowed diversity of

function in nervous systems that have emerged later, in

evolutionary terms, and that are generally larger16. For

example, MASC mRNA expression has been compared

between 22 regions of the mouse brain, and this has shown

that the genes of most variable expression originated since

the deuterostome common ancestor, whereas genes of low

expression variability are of ancient, pre-metazoan origin

(FIG. 5). It is likely that the relative expression of MASC

components results in different combinatorial versions of

MASC components in separate brain regions, contributing

to synaptic and neuronal diversity.

Innovative transgenic methods have contributed to our

knowledge of synapse diversity, showing that expression

pattern of synaptic proteins is an identifier of neuronal

subsets. One study conducted whole genome expression

analysis on mRNA isolated from 12 discrete green fluo-

rescent protein (GFP)-tagged GABAergic or glutamater-

gic neuronal populations of the mouse brain, to produce

a phylogeny of neuronal subtypes77. Using this method

it was shown that among genes that exhibited variable

expression between brain regions, synaptic and axonal

components were significantly over-represented and

that there was more expression diversity in GABAergic

neuronal subpopulations than in glutamatergic ones.

Importantly, genes expressed in the brain with hetero-

geneous expression patterns are enriched for paralogues,

which lends credence to the hypothesis that gene dupli-

cation leads to the subfunctionalisation of duplicates by

divergence of expression patterns77,78. Indeed, the excita-

tory glutamate receptors and MAGUKs fall into the highly

variable region and have undergone chordate specific gene

duplication16. The resolution of such profiling studies will

increase in the future as larger sets of genes are studied in

more discrete anatomical regions79. The development of

sophisticated transgenic technologies, such as those using

tagged ribosomal proteins expressed in discrete neuronal

populations, will facilitate such studies80,81.

Human synapse evolution

What makes us human is one of the oldest and most

tantalising questions in biology82–84. The most striking

feature of humans is our increased cognitive capacity.

Little is known about the genetic events that led to the

emergence of human specific behaviour but it is widely

assumed that the enlarged and convoluted neocortex is

the basis for our increased mental abilities (see article by

Pasko Rakic in this issue)85. Here, we posit that the evolu-

tion of the synapse complement might have enabled the

increase of neuronal cell types and, in turn, the neuronal

network complexity of the human brain. Due to difficul-

ties in obtaining appropriate tissue samples for proteomic

work the investigation of human synaptic complexes is

Figure 4 | NMDA receptor carboxy-terminal evolution. Schematic comparing the

Drosophila melanogaster NR2 containing NMDA receptor (a) and the mouse NR2

containing NMDA (N‑methyl‑d‑aspartate) receptors (b). The PDZ binding domains at the

carboxy‑terminus of both D. melanogaster NMDA receptor 2 (NR2; SVL) and mouse NR2

(ESDV) are indicated. Note that the mouse NR2 intracellular domain is five times larger

than that of D. melanogaster. The diagrams compare the evolution of NMDA receptor

signalling complexity in D. melanogaster and mouse showing protein–protein

interactions at the NR2 carboxy‑termini. The only established protein interaction site on

the D. melanogaster NR2 carboxy‑terminus is the interaction of Dlg (discs large

homologue; SAP97 orthologue) (Bayes A. and S.G.N.G., unpublished data) through the

PDZ binding domain. The vertebrate NR2B carboxy‑terminus has numerous established

primary and secondary interacting proteins (zoom out) and therefore a greater degree of

NMDA receptor signalling complexity. Furthermore, the number of potential interactions

of the NMDA receptor with MAGUK (membrane‑associated guanylate kinase)

components differ between protostome and deuterostome synapses. In the case of

protostomes only one such interaction can occur, between NR2 and the protostome

MAGUK, Dlg. Because of gene family expansion in chordates there are four available NR2

subunits (NR2A–NR2D) and four MAGUKs (PSD95, SAP102, PSD93 and SAP97). Three of

the MAGUK paralogues can interact with any of the four NR2 subunits, making twelve

potential deuterostome NR2–MAGUK interactions. As NMDA receptors are considered

to be tetramers that contain two NR2 subunits, the existence of tri‑heteromeric NMDA

receptor channel further increases this combinatorial complexity105.

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Yeast

Protostome

Deuterostome

Percentage of (high/low)

variability genes

High variability

Low variability

dN/dS ratio

The ratio of non-synonymous

nucleotide substitutions to

synonymous nucleotide

substitution for a given

protein-coding gene. A dN/dS

ratio of <1 implies purifying

selection or conservative

evolution, ~0 implies

relaxation of constraint or

neutral evolution, >1 implies

positive selection or adaptive

evolution. This measure is

based on Kimura’s theory of

molecular evolution, which

argues that the vast majority of

nucleotide sequence changes

are functionally neutral.

not straightforward. In the mean time, there are examples

of positive selection (accelerated evolution) of particular

synaptic, primate and human proteins, including recep-

tors for acetylcholine, oxytocin, kainate, dopamine and

glutamate receptor subunits86. Of particular interest is the

NR2A subunit, which shows evidence of positive selec-

tion in primates and happens to be the NR2A paralogue

that is expressed postnatally in mammals.

The human genes of GABA(A) receptor subunits

display a disproportionate number of mutations in

microRNA target recognition sites, indicating alterations

in human GABA receptor gene expression87. MAOA

(monoamine oxidase A), an enzyme that catabolises

neurotransmitters, has been shown to be under posi-

tive selection in humans88. Within populations, genetic

variations of MAOA have also been implicated in anti-

social behaviour in humans89,90. Additionally, dopamine

receptor subunit D4 (DRD4) and GABA(A) receptor β2

subunit (GABRB2) variants are under positive selection

in human populations, and are associated with attention

deficit hyperactivity disorder, and schizophrenia, respec-

tively91–96 . It is possible that positive selection on synaptic

proteins has contributed to the evolution of human behav-

iour at the cost of increased vulnerability to psychiatric

conditions97–99.

Comparison of protein expression levels in the

brains of human and non-human primates has led to

the identification of numerous proteins, including syn-

aptic proteins such as CaMKII, that are upregulated

specifically in the human brain100,101. Currently, we can

only speculate about the function of the human specific

variants of synaptic proteins and the reasons why their

selection sometimes correlates with ‘disease’ phenotypes.

Cell culture studies allied with transgenic ‘humaniza-

tion’ of genes in model organisms may help to elucidate

the role of these genes in primate and/or human brain

evolution.

Conclusions

In this Review we discuss how the synapse, a fundamental

structural and functional unit of the nervous system, is

a fertile platform with which to explore the evolution of

the brain. Many mammalian synaptic components existed

before the appearance of synapses, and some of these may

have been pivotal to the origin of the ursynapse. It is con-

ceivable that synapses would have evolved before axons

and dendrites, as an organism with a small number of

closely associated neurons would not need axonal pro-

jections for neuron to neuron communication. By the

same logic, without the synaptic specifications, axons or

dendrites would have no relevance. Similarly, synapse for-

mation would have evolved before other stages in neural

development including neuronal migration. Therefore we

posit that synapse formation is one of the exceptions to the

trend that ontogeny recapitulates phylogeny as, although

it is the final stage of neural development, it necessarily

evolved before the earlier developmental stages. We con-

sider the emergence of the synapse to be a crucial step

in the origin of the nervous system. Indeed, one could

argue that the evolution of synapses led to the evolution

of neurons, as a neuron is defined by synaptic connec-

tions. We refer to this model of the origins of the brain

as the ‘synapse first’ model. It may prove useful to profile

the expression of PSD and MASC genes during synaptic

development with respect to phylogenetic origin, in order

to test the ‘ontogeny recapitulates phylogeny’ evo–devo

paradigm in the context of synaptogenesis102,103.

Studies focusing on synapse evolution are at early stages,

but it is now an intellectually and technologically oppor-

tune time to launch into this topic. The focus has been on

excitatory glutamate receptor associated postsynaptic pro-

teins, as this family of proteins is well known and of cen-

tral importance to synaptic function. These studies should

be expanded to include all presynaptic and post synaptic

proteins. Most of our knowledge on the topic of synapse

evolution is based on data derived from comparative

genomics and proteomics. It will be necessary to expand

on these studies with thoughtful functional experiments.

Comparing the physiological and behavioural importance

of ancient and mammalian specific synaptic genes through

loss-of-function experiments in mice may aid in identi-

fying the functional roles for which they were selected.

Transgenic gain-of-function studies in organisms without

synapses might establish what combinations of synaptic

proteins resulted in the origin of the synapse. Finally, meth-

ods already applied to mice should be applied to humans

to see to what extent the evolution of the synapse has

contributed to the evolution of the human brain.

Figure 5 | MASC signalling diversity within the brain. a | Model depicting expression

variation of MASC (membrane‑associated guanylate kinase (MAGUK) associated

signalling complex) components throughout the deuterostome brain where different

combinations of MASC proteins are found in different synapses. Four different MASC

complexes comprised of various combinations of discrete upstream (coloured circles),

intermediate (red rectangles) and downstream (yellow triangles) proteins are expressed

in different regions of the brain (arrows). b | MASC components of ancient pre‑metazoan

origin (present in yeast), protostome origin and deuterostome origin are displayed in a

histogram that shows their percentage composition of genes of high expression

variability and low expression variability. MASC genes of deuterostome origin are

enriched for genes of high expression variability in the mouse brain: ancient genes are

uniformly expressed and recent genes are most variable. Figure is modified, with

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Acknowledgements

We thank members of the Genes to Cognition Programme for

useful discussions. T.J.R. was supported by a Wellcome Trust

Ph.D. Studentship at time of writing.

DATABASES

UniProtKB: http://www.uniprot.org

CRIPT | Dlg | ERK2 | GKAP | GNB5 | GRIP | Homer | NF1 | PKC |

PMCA

FURTHER INFORMATION

Seth G. N. Grant’s homepage:http://www.sanger.ac.uk/

Teams/faculty/grant/

Timetree: http://www.timetree.org/

SUPPLEMENTARY INFORMATION

See online article: S1 (table) | S2 (box) | S3 (box)

ALL LINKS ARE ACTIVE IN THE ONLINE PDF

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Biographies

Tomás Ryan received a B.A. in human genetics from the University of

Dublin, Trinity College (Ireland). He was awarded a Wellcome Trust

Ph.D. Studentship to study in the research group of Seth Grant at the

Wellcome Trust Sanger Institute and Darwin College, University of

Cambridge (UK), where he was a final year graduate student at time

of writing. His thesis research focused on the generation and analysis

of transgenic mouse models of NMDA (N-methyl--aspartate) recep-

tor molecular evolution. He is currently a Junior Research Fellow at

Wolfson College, University of Cambridge.

Seth Grant is a neuroscientist best known for his work using mouse

genetics and synapse proteomics to study plasticity and learning.

This work has uncovered unexpectedly high molecular complexity

in synapse protein complexes and the postsynaptic density providing

avenues to study synapse evolution and brain disease. He received

degrees in physiology, medicine and surgery from the University of

Sydney, Australia, and postdoctoral training at Cold Spring Harbor

Laboratory, USA, and with Eric Kandel at Columbia University,

USA. He currently heads the Genes to Cognition Programme

at the Wellcome Trust Sanger Institute in Cambridge UK and is

Professor of Molecular Neuroscience at Edinburgh and Cambridge

Universities, UK.

Online summary

• The molecular composition of the synapse has recently been

proved to be useful for studying the evolution of the brain.

• Synapse proteomics data sets, such as those of the postsynaptic

density (PSD) and associated protein complexes when combined

with comparative genomics have provided unprecedented insights

into the evolution of synapses.

• The PSD that is found in organisms with nervous systems has

evolved from an ancient protosynaptic core that exists in uni-

cellular organisms and multicellular organisms without nervous

systems.

• Comparisons of vertebrate PSD and synaptogenesis genes with

orthologues from sponges and cnidarians open an avenue for

speculating as to what may have contributed to the origin of the

first synapse.

• Comparative proteomics has shown that vertebrate excitatory

synapses have evolved to be significantly more complex than

invertebrates.

TOC

000 The origin and evolution of synapses

Tomás J. Ryan and Seth G. N. Grant

Tracing the phylogeny of the molecular components

of synapses, Ryan and Grant speculate on the core

components of the last common ancestor of all

synapses and posit that the diversification of upstream

signalling components contributed to increased

signalling complexity later in evolution.

ONLINE ONLY

Glial Physiology and Pathophysiology

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Feb 2013

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Scott Andersen

In simple terms, consciousness is constituted by multiple goals for action and the continuous adjudication of such goals to implement action, which is referred to as the maps of meaning (MoM) consciousness theory. The MoM theory triangulates through three parallel corollaries: action (behavior), mechanism (morphology/pathophysiology), and goals (teleology). (1) An organism’s consciousness contains fluid, nested goals. These goals are not intentionality, but intersectionality, via the Darwinian byproduct of embodiment meeting the world, i.e., Darwinian inclusive fitness or randomization and then survival of the fittest. (2) These goals are formed via a gradual descent under inclusive fitness and are the abstraction of a “match” between the evolutionary environment and the organism. (3) Human consciousness implements the brain efficiency hypothesis, genetics, epigenetics, and experience-crystallized efficiencies, not necessitating best or objective but fitness, i.e., perceived efficiency based on one’s adaptive environment. These efficiencies are objectively arbitrary but determine the operation and level of one’s consciousness, termed as extreme thrownness. (4) Since inclusive fitness drives efficiencies in the physiologic mechanism, morphology, and behavior (action) and originates one’s goals, embodiment is necessarily entangled to human consciousness as it is at the intersection of mechanism or action (both necessitating embodiment) occurring in the world that determines fitness. (5) Perception is the operant process of consciousness and is the de facto goal adjudication process of consciousness. Goal operationalization is fundamentally efficiency-based via one’s unique neuronal mapping as a byproduct of genetics, epigenetics, and experience. (6) Perception involves information intake and information discrimination, equally underpinned by efficiencies of inclusive fitness via extreme thrownness. Perception is not a ‘frame rate’ but Bayesian priors of efficiency based on one’s extreme thrownness. (7) Consciousness and human consciousness are modular (i.e., a scalar level of richness, which builds up like building blocks) and dimensionalized (i.e., cognitive abilities become possibilities as the emergent phenomena at various modularities such as the stratified factors in factor analysis). (8) The meta dimensions of human consciousness seemingly include intelligence quotient, personality (five-factor model), richness of perception intake, and richness of perception discrimination, among other potentialities. (9) Future consciousness research should utilize factor analysis to parse modularities and dimensions of human consciousness and animal models.

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Electrical synapses are neuronal gap junction (GJ) channels associated with a macromolecular complex called the electrical synapse density (ESD), which regulates development and dynamically modifies electrical transmission. However, the proteomic makeup and molecular mechanisms utilized by the ESD that direct electrical synapse formation are not well understood. Using the Mauthner cell of zebrafish as a model, we previously found that the intracellular scaffolding protein ZO1b is a member of the ESD, localizing postsynaptically, where it is required for GJ channel localization, electrical communication, neural network function, and behavior. Here, we show that the complexity of the ESD is further diversified by the genomic structure of the ZO1b gene locus. The ZO1b gene is alternatively initiated at three transcriptional start sites resulting in isoforms with unique N-termini that we call ZO1b-Alpha, -Beta, and -Gamma. We demonstrate that ZO1b-Beta and ZO1b-Gamma are broadly expressed throughout the nervous system and localize to electrical synapses. By contrast, ZO1b-Alpha is expressed mainly non-neuronally and is not found at synapses. We generate mutants in all individual isoforms, as well as double mutant combinations in cis on individual chromosomes, and find that ZO1b-Beta is necessary and sufficient for robust GJ channel localization. ZO1b-Gamma, despite its localization to the synapse, plays an auxiliary role in channel localization. This study expands the notion of molecular complexity at the ESD, revealing that an individual genomic locus can contribute distinct isoforms to the macromolecular complex at electrical synapses. Further, independent scaffold isoforms have differential contributions to developmental assembly of the interneuronal GJ channels. We propose that ESD molecular complexity arises both from the diversity of unique genes and from distinct isoforms encoded by single genes. Overall, ESD proteomic diversity is expected to have critical impacts on the development, structure, function, and plasticity of electrical transmission.

Incorporating evolution into neuroscience teaching

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Full-text available

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Neuroscience courses can be enriched by including an evolutionary perspective. To that end, this essay identifies several concepts critical to understanding nervous system evolution and offers numerous examples that can be used to illustrate those concepts. One critical concept is that the distribution of features among today’s species can be used to reconstruct a feature’s evolutionary history, which then makes it possible to distinguish cases of homology from convergent evolution. Another key insight is that evolution did not simply add new features to old nervous systems, leaving the old features unchanged. Instead, both new and old features have changed, and they generally did so along divergent trajectories in different lineages, not in a linear sequence. Some changes in nervous system organization can be linked to selective pressures (i.e, adaptation), especially if they occurred convergently in different lineages. However, nervous system evolution has also been subject to various constraints, which is why many neural features are, in a sense, suboptimal. An overarching theme is that evolution has brought forth tremendous diversity across all levels of the nervous system and at all levels of organization, from molecules to neural circuits and behavior. This diversity provides excellent research opportunities, but it can also complicate the extrapolation of research findings across species.

Evolution of Dynamic Coordination

Chapter

Jul 2010

An examination of how widely distributed and specialized activities of the brain are flexibly and effectively coordinated. A fundamental shift is occurring in neuroscience and related disciplines. In the past, researchers focused on functional specialization of the brain, discovering complex processing strategies based on convergence and divergence in slowly adapting anatomical architectures. Yet for the brain to cope with ever-changing and unpredictable circumstances, it needs strategies with richer interactive short-term dynamics. Recent research has revealed ways in which the brain effectively coordinates widely distributed and specialized activities to meet the needs of the moment. This book explores these findings, examining the functions, mechanisms, and manifestations of distributed dynamical coordination in the brain and mind across different species and levels of organization. The book identifies three basic functions of dynamic coordination: contextual disambiguation, dynamic grouping, and dynamic routing. It considers the role of dynamic coordination in temporally structured activity and explores these issues at different levels, from synaptic and local circuit mechanisms to macroscopic system dynamics, emphasizing their importance for cognition, behavior, and psychopathology. ContributorsEvan Balaban, György Buzsáki, Nicola S. Clayton, Maurizio Corbetta, Robert Desimone, Kamran Diba, Shimon Edelman, Andreas K. Engel, Yves Fregnac, Pascal Fries, Karl Friston, Ann Graybiel, Sten Grillner, Uri Grodzinski, John-Dylan Haynes, Laurent Itti, Erich D. Jarvis, Jon H. Kaas, J.A. Scott Kelso, Peter König, Nancy J. Kopell, Ilona Kovács, Andreas Kreiter, Anders Lansner, Gilles Laurent, Jörg Lücke, Mikael Lundqvist, Angus MacDonald, Kevan Martin, Mayank Mehta, Lucia Melloni, Earl K. Miller, Bita Moghaddam, Hannah Monyer, Edvard I. Moser, May-Britt Moser, Danko Nikolic, William A. Phillips, Gordon Pipa, Constantin Rothkopf, Terrence J. Sejnowski, Steven M. Silverstein, Wolf Singer, Catherine Tallon-Baudry, Roger D. Traub, Jochen Triesch, Peter Uhlhaas, Christoph von der Malsburg, Thomas Weisswange, Miles Whittington, Matthew Wilson

Mimicking bacterial learning and memory in tungsten based two-sided single layers of WSeO, WSeS, WSeSe, and WSeTe

Article

May 2023

We mimic bacterial learning and memory abilities in tungsten based two-sided single layers of WSeO, WSeS, WSeSe, and WSeTe, where the thickness of the material represents the growth in time. We aim to create a quantum memristor like system to show learning and memory abilities of bacteria with time while it grows. Its governing equation is derived, and it was found to be similar to the gene regulatory response model of the bacteria. Polarization is calculated from the Berry phase theory to plot its relation with the degauss parameter in time, which leads to bow-tie like memory switches similar to phase-change memories. We attribute this behavior to a specific bacteria, that is, Geobacter metallireducens. Mimicking bacteria’s learning and memory abilities will open a way to merge physical intelligence with quantum computing computationally.

Parallel gene size and isoform expansion of ancient neuronal genes

Article

Mar 2024
CURR BIOL

How nervous systems evolved is a central question in biology. A diversity of synaptic proteins is thought to play a central role in the formation of specific synapses leading to nervous system complexity. The largest animal genes, often spanning hundreds of thousands of base pairs, are known to be enriched for expression in neurons at synapses and are frequently mutated or misregulated in neurological disorders and diseases. Although many of these genes have been studied independently in the context of nervous system evolution and disease, general principles underlying their parallel evolution remain unknown. To investigate this, we directly compared orthologous gene sizes across eukaryotes. By comparing relative gene sizes within organisms, we identified a distinct class of large genes with origins predating the diversification of animals and, in many cases, the emergence of neurons as dedicated cell types. We traced this class of ancient large genes through evolution and found orthologs of the large synaptic genes potentially driving the immense complexity of metazoan nervous systems, including in humans and cephalopods. Moreover, we found that while these genes are evolving under strong purifying selection, as demonstrated by low dN/dS ratios, they have simultaneously grown larger and gained the most isoforms in animals. This work provides a new lens through which to view this distinctive class of large and multi-isoform genes and demonstrates how intrinsic genomic properties, such as gene length, can provide flexibility in molecular evolution and allow groups of genes and their host organisms to evolve toward complexity.

Physics of smart active matter: integrating active matter and control to gain insights into living systems

Article

Jun 2023
SOFT MATTER

We offer our opinion on the benefits of integration of insights from active matter physics with principles of regulatory interactions and control to develop a field we term "smart active matter". This field can provide insight into important principles in living systems as well as aid engineering of responsive, robust and functional collectives.

The concept of neuroglia

Chapter

May 2023

N -Methyl-D-Aspartate Receptors

Chapter

Oct 2019

Neurons are excitable cells. They use ions and electrical signaling to talk to each to other, and when they talk to each other, neurons control behavior. The Oxford Handbook of Neuronal Ion Channels is an accessible reference describing the nature and properties of ion channels in neurons. The book explains how ion channels open and close, how they can be selective for specific ions, and how they give rise to action potentials. There are in-depth chapters discussing specific classes of ion channels: potassium channels, sodium channels, neurotransmitter-gated ion channels, and other specialized channels. Throughout the handbook, important insight is provided on the contribution ion channels make to neuronal excitability and to synaptic transmission. The handbook goes further to discuss a group of human diseases such as epilepsy, pain, and migraines that can be caused by ion channel dysfunction called channelopathies. For neuroscientists, biophysicists, and neuropharmacologists, this handbook is a valuable reference of ion channel biology and function.

A Developmental Change in NMDA Receptor-Associated Proteins at Hippocampal Synapses

Article

Full-text available

Feb 2000

The membrane-associated guanylate kinases [Chapsyn-110/postsynaptic density-93 (PSD-93), synapse-associated protein-90 (SAP-90)/PSD-95, and SAP-102] are believed to cluster and anchor NMDA receptors at the synapse and to play a role in signal transduction. We have investigated the developmental changes in expression of these proteins in rat hippocampus using biochemical analyses and quantitative immunogold electron microscopy. At postnatal day 2 (P2), SAP-102 was highly expressed, whereas PSD-93 and PSD-95 were low. SAP-102 expression increased during the first week, stayed stable through P35, and showed a reduced expression at 6 months. From P2 through 6 months, PSD-93 and PSD-95 increased. For PSD-95, the percent of labeled synapses increased almost threefold with age, whereas the number of gold particles per labeled synapse did not change significantly, suggesting that the increase in PSD-95 is attributable primarily to an increase in the number of synapses containing PSD-95. In contrast, for SAP-102, both percent labeled synapses and the number of gold particles per labeled synapse decreased during this time. From Western blots of hippocampus and immunogold analysis of CA1 synapses, the high expression of NR2B at P2 coincides with the high level of SAP-102 at synapses, whereas the later expression of NR2A coincides with that of PSD-93 and PSD-95. To determine whether the changes in PSD-93/95 and SAP-102 reflect preferred associations with NR2A and NR2B, respectively, we measured co-immunoprecipitation in the adult hippocampus. These studies suggest that there is a preference for complexes of NR2A/PSD-93/95 and NR2B/SAP-102. These results indicate that individual receptor-associated proteins may have specific functions that are critical to synapse development.

The Timetree of Life

Article

Apr 2009

The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrial impacts, and other features. The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routine estimation and utilization of these so-called ‘time-trees’ could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). They could help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology. This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects of the evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included.

Evolution by Gene Duplication

Book

Susumu Ohno

Dopamine

Article

Dec 2003

Dopamine is expressed in restricted brain areas involved in numerous integrative functions contributing to automated behaviours that are highly adaptive. During ontogenesis, dopamine can have a trophic action, which influences cortical specification directly, especially in prefrontal areas. Such a role is attested by the close relationships existing between the development of dopamine cortical innervation and cognitive abilities. Interestingly, such a proposal is reinforced by phylogenetic data. During the last stages of evolution in mammals, the characteristic extension of dopamine cortical innervation is also correlated with the development of cognitive capacities. More generally, the contribution of dopamine will be to increase the processing of cortical information through basal ganglia, either during the course of evolution or development. In this respect, dysmaturation suspected in schizophrenia and attention deficit-hyperactivity disorder in children can emphasize such a defect in basal ganglia processing. Remarkably, these diseases are improved by dopamine antagonists and agonists, respectively. In this line of evidence, experimental studies showed that selective lesions of the dopamine neurones in rats or primates can actually provide motor, limbic and cognitive deficits, in later cases especially when the mesocorticolimbic dopamine pathways are altered. Data resulting from lesion studies also showed significant alteration in attentional processes, thus raising the question of the direct involvement of dopamine in regulating attention. Dopamine can act as a powerful regulator and integrator of different aspects of brain functions. For example, in Parkinson's disease, besides motor impairment, dopamine degeneration is also expressed by alterations of both limbic, executive and cognitive functions, both improved by dopamine receptor agonists and dopa therapy. Dopamine has thus to be considered as a key regulator that contributes to behavioural adaptation and to the anticipatory processes necessary for preparing voluntary action consequent upon intention. In this respect, the alteration of dopamine transmission with age could contribute to cognitive impairment. Therefore, to normalize dopamine transmission pharmacologically could actually improve the cognitive and limbic deficits during normal aging, as it does in psychiatric and neurological disorders.

Plasma membrane calcium ATPases as critical regulators of calcium homeostasis during neuronal cell function

Article

Jan 1999

L. Garcia Michael

Evolution by Gene Duplication

Article

Nov 1971

Susumu Ohno

Enhanced long-term potentiation and impaired learning in mice with mutant postsynaptic density-95 protein

Article

Dec 1998

Specific patterns of neuronal firing induce changes in synaptic strength that may contribute to learning and memory. If the postsynaptic NMDA (N-methyl-D-aspartate) receptors are blocked, long-term potentiation (LTP) and long-term depression (LTD) of synaptic transmission and the learning of spatial information are prevented. The NMDA receptor can bind a protein known as postsynaptic density-95 (PSD-95), which may regulate the localization of and/or signalling by the receptor. In mutant mice lacking PSD-95, the frequency function of NMDA-dependent LTP and LTD is shifted to produce strikingly enhanced LTP at different frequencies of synaptic stimulation. In keeping with neural-network models that incorporate bidirectional learning rules, this frequency shift is accompanied by severely impaired spatial learning. Synaptic NMDA-receptor currents, subunit expression, localization and synaptic morphology are all unaffected in the mutant mice. PSD-95 thus appears to be important in coupling the NMDA receptor to pathways that control bidirectional synaptic plasticity and learning.

The Origin of Species By Means of Natural Selection

Article

May 1951
ACAD MED

Charles Darwin

Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome

Article

Oct 2005
J NEUROCHEM

Characterization of the composition of the postsynaptic proteome (PSP) provides a framework for understanding the overall organization and function of the synapse in normal and pathological conditions. We have identified 698 proteins from the postsynaptic terminal of mouse CNS synapses using a series of purification strategies and analysis by liquid chromatography tandem mass spectrometry and large-scale immunoblotting. Some 620 proteins were found in purified postsynaptic densities (PSDs), nine in AMPA-receptor immuno-purifications, 100 in isolates using an antibody against the NMDA receptor subunit NR1, and 170 by peptide-affinity purification of complexes with the C-terminus of NR2B. Together, the NR1 and NR2B complexes contain 186 proteins, collectively referred to as membrane-associated guanylate kinase-associated signalling complexes. We extracted data from six other synapse proteome experiments and combined these with our data to provide a consensus on the composition of the PSP. In total, 1124 proteins are present in the PSP, of which 466 were validated by their detection in two or more studies, forming what we have designated the Consensus PSD. These synapse proteome data sets offer a basis for future research in synaptic biology and will provide useful information in brain disease and mental disorder studies.

The Organization of Behavior: A Neuropsychological Theory

Chapter

Jan 1949

D.O. Hebb

The origin and evolution of synapses

Abstract

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