Low complexity regions (LCRs) in protein sequences, also defined in some contexts as compositionally biased regions (CBRs), are regions in protein sequences that differ from the composition and complexity of most proteins that is normally associated with globular structure. LCRs have different properties from normal regions regarding structure, function and evolution.
Structure LCRs were originally thought to be unstructured and flexible linkers that served to separate the structured (and functional) domains of complex proteins, but they are also capable of forming secondary structures, like helices (more often) and even sheets. They may play a structural role in proteins such as collagens, myosin, keratins, silk, cell wall proteins. Tandem repeats of short oligopeptides that are rich in glycine, proline, serine or threonine are capable of forming flexible structures that bind ligands under certain pH and temperature conditions. Proline is a well-known alpha-helix breaker, however, amino acid repeats composed of proline may form poly-proline helices.
Functions LCRs were originally thought as 'junk' regions or as neutral linkers between domains; however, experimental and computational evidence increasingly indicates that they may play important adaptive and conserved roles, relevant to biotechnology, heterologous protein expression, medicine, as well as to our understanding of protein evolution. LCRs of eukaryotic proteins have been involved in human diseases, especially neurodegenerative ones, where they tend to form amyloids in humans and other eukaryotes. They have been reported to have adhesive roles, function in excreted sticky proteins used for prey capture, or have roles as transducers of molecular movement, e.g. in the prokaryotic TonB/TolA systems. LCRs may form surfaces for interaction with phospholipid bilayers, or as positive charge clusters for DNA binding, or as negative or even histidine-acidic charge clusters for coordinating calcium, magnesium or zinc ions. They may also play important roles in protein translation, as tRNA 'sponges', slowing down translation in order to allow time for the correct folding of the nascent polypeptide chain. They may even function as frame-shift checkpoints, by shifting to an unusual amino acid content that makes the protein highly unstable or insoluble, which in turn triggers fast recycling, before any further cellular damage. Analyses on model and non-model eukaryotic proteomes have revealed that LCRs are frequently found in proteins involved in binding of nucleic acids (DNA or RNA), in transcription, receptor activity, development, reproduction and immunity whereas metabolic proteins are depleted of LCRs. A bioinformatics study of the UniProt annotation of LCR containing proteins observed that 44% (9751/22259) of Bacterial and 44% (662/1521) of Archaeal LCRs are detected in proteins of unknown function, however, a significant number of proteins of known function (from many different species), especially those involved in translation and the ribosome, nucleic acid binding, metal-ion binding, and protein folding were also found to contain LCRs.
Properties LCRs are more abundant in eukaryotes, but they also have a significant presence in many prokaryotes. On average, 0.05 and 0.07% of the bacterial and archaeal proteomes (total amino acids of LCRs in a given proteome/total amino acids of that proteome) form LCRs whereas for five model eukaryotic proteomes (human, fruitfly, yeast, fission yeast, Arabidopsis) this coverage was significantly higher (on average, 0.4%; between 2 and 23 times higher than prokaryotes). Eukaryotic LCRs tend to be longer than prokaryotic LCRs. The average size of a eukaryotic LCR is 42 amino acids long, whereas bacterial, archaeal and phage LCRs are 38, 36 and 33 amino acids long, respectively. In the Archaea, the halobacterium Natrialba magadii has the highest number of LCRs and the highest enrichment for LCRs. In Bacteria, Enhygromyxa salina, a delta proteobacterium that belongs to myxobacteria has the highest number of LCRs and the highest enrichment for LCRs. Intriguingly, four of the top five bacteria with the highest enrichment for LCRs are also myxobacteria. The three most enriched amino acids within LCRs of Bacteria are proline, glycine and alanine, whereas in Archaea they are threonine, aspartate and proline. In Phages, they are alanine, glycine and proline. Glycine and proline emerge as very enriched amino acids in all three evolutionary lineages, whereas alanine is highly enriched in Bacteria and Phages but not enriched in Archaea. On the other hand, hydrophobic (M, I, L, V) and aromatic amino acids (F, Y, W) as well as cysteine, arginine and asparagine are heavily under-represented in LCRs. Very similar trends for amino acids with a high (G, A, P, S, Q) and low (M, V, L, I, W, F, R, C) occurrence within LCRs have been observed in eukaryotes as well. This observed pattern of certain amino acids being over-represented (enriched for) or under-represented in LCRs could be partially explained by the energy cost for synthesis or metabolism of each of the amino acids. Another possible explanation, which does not exclude the previous explanation of energy cost could be the reactivity of certain amino acids. For example, Cysteine is a very reactive amino acid that would not be tolerated in high numbers within a small region of a protein. Similarly, extremely hydrophobic regions can form non-specific protein–protein interactions among themselves and with other moderately hydrophobic regions in mammalian cells. Thus, their presence may disturb the balance of protein-protein interaction networks within the cell, especially if the carrier proteins are highly expressed. A third explanation may be based on micro-evolutionary forces and, more specifically, on the bias of DNA polymerase slippage for certain di- tri- or tetra-nucleotides .
Amino acid enrichment for certain functional categories of LCRs A bioinformatics analysis of prokaryotic LCRs identified 5 types of amino acid enrichment, for certain functional categories of LCRs:
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