Neurophilosophy

Synapse proteomics & brain evolution

When it comes to human brain evolution, it is often said that size matters. The human cerebral cortex is much larger than that of other primates, and therefore its expansion must have been a vital feature of human evolution. Researchers have therefore emphasized the importance of encephalization, the process by which brain mass increased dramatically in relation to total body mass that occurred in the human lineage.

However, a new study which used bioinformatics to compare the synapses of distantly related species suggests that size may not be the most important factor in human brain evolution after all. Instead, the new findings, which were published online in Nature Neuroscience on Sunday, suggest that it is an increase in the complexity and number of synapses that was crucial for the emergence of complex behaviours and cognition.

The term synapse refers to the tiny gap found at the junction between two nerve cells. It is across this gap – which measures just 40 nanometers, or billionths of a meter – that chemicals released from one neuron diffuse to the other, so that a signal is transmitted between the two.

On the receiving end of the synapses of mammals, immediately beneath the membrane, there is a dense network of proteins called the postsynaptic density (PSD). The PSD contains more than 1,000 proteins, which can broadly be divided into 3 different classes: the components of around 12 parallel but converging signaling pathways, with the components of each one clustered to form an enormous macromolecular complex; the cytoskeletal and scaffolding proteins which tether the complexes to precise locations at the membrane, in close proximity to the receptors which activate them; and the enzymes which regulate the movements and functions of the complexes and their individual components within the membrane.

The regulatory enzymes act by making minor modifications in the structure of the signaling pathway components. One apparently ubiquitous form of modification involves the addition of a small molecule called a phosphate group to a specific site on the target protein. This process, phosphorylation, is catalyzed by enzymes called a kinases. It is reversible, and acts like a switch – the phosphate groups can be removed by another group of enzymes called phosphatases, and the addition or removal of a phosphate group activates or inhibits a target protein.

These signaling pathways are incredibly complex – the enzymes all act on multiple targets, and differ in their effects on each. Furthermore, they are subject to the same regulatory mechanisms as the proteins they regulate. They too can have phosphate groups or other small molecules added or removed, and in some cases, activate or inhibit themselves by catalyzing modifications of their own structure.

The interactions between these signaling pathways are very poorly understood,  largely because researchers were until recently only able to investigate one or two of the components at any one time. This is where proteomics comes into its own, because it allows for simultaneous analysis of hundreds or thousands of molecules, enabling researchers to begin teasing apart the pathways and networks instead of plucking individual components out one at a time.

One recent proteomics study of the mouse PSD identified about 300 proteins which could be modified by phosphorylation. As well as the kinases and phosphatases, these included scaffolding proteins, neurotransmitter receptors and voltage-gated ion channels. In all, more than 700 different phosphorylation sites were identified, with some molecules having just one or two, and others having a dozen or more.

The new study, led by Seth Grant, director of the Genes to Cognition Program at the Wellcome Trust Sanger Centre in Cambridge, takes this type of large-scale analysis a step further. It compared more than 600 postsynaptic proteins in 19 different species, but focused on the synaptic phosphoproteome (the number and identity of the synaptic proteins capable of undergoing phosphorylation) in one invertebrate and one mammalian species (the fruit fly and mouse, respectively). In particular, two of the macromolecular complexes found at the synapse were compared.

This analysis showed that the synapses in mice are far more complex and have many more signaling pathways than the synapses in fruit flies. For example, the fruit fly has only one subtype of NMDA receptor, because it only has one type of receptor subunit. Mice have four different subunits, which can combine differentially form 16 receptor subtypes. In all, mice were found to have approximately twice as many phosphoproteins as fruit flies; the differences between mice and humans were not so large.

Yeast were also included in the comparison, and were found to have approximately 25% of the postsynaptic proteins present in human synapses, despite being single-celled eukaryotes (i.e. they have DNA packaged into nucleus) which lack a nervous system. 

Thus there is a strong correlation between complexity of the synaptic proteome corresponds to the computational capacity of the brain, with an organism’s repertoire of behaviours increasing along with the complexity and number of synapses in its nervous system. A single-celled organism such as yeast is capable of responding only by stereotyped movements towards a source of food or away from a noxious stimulus, while small invertebrates such as the fruit fly which have are capable of simple learning.

In mammals, however, the much larger number of signaling pathways, coupled with a larger number of neurons, allows for more complex behaviours. One particular species of mammal – humans – has a brain containing hundreds of billions of neurons, and perhaps a quadrillion or more extremely complex, highly modifiable synapses, which gives it cognitive capabilities that are unparalleled in the animal kingdom. 

The new study also points towards an evolutionary history of the synapse, in which a simple prototypical synapse emerged in a single-celled eukaryote, and subsequently underwent repeated step-wise expansion and diversification  components as multicellular organisms branched from single-celled organisms, and again as vertebrates branched from the invertebrates. This is supported by a study published a year ago which showed that sea sponges have proto-synapses, despite lacking a nervous system.


Emes, R.D., et al. (2008). Evolutionary expansion and anatomical specialization of synapse proteome complexity. Nat. Neurosci. DOI: 10.1038/nn.2135