A FERM-adjacent (FA) region defines a subset of the 4.1 superfamily and is a potential regulator of FERM domain function

Abstract

Background: Proteins containing FERM domains comprise a diverse group of eukaryotic proteins that bind membrane proteins and lipids. In doing so, they organise membrane microstructure, and coordinate the disposition of signalling and cell adhesion complexes. In protein 4.1R, phosphorylation adjacent to the FERM domain regulates its activity, and membrane mechanical properties.

Results: A novel sequence domain has been detected in a subset of proteins that contain FERM domains. This subset includes the true 4.1 proteins, some tyrosine phosphatases, rho-GEF proteins and type II transmembrane proteins, as well as some uncharacterised FERM proteins. This FERM-adjacent region is always closely proximate to the C-terminal of the FERM domain. This sequence is likely to be folded with elements of alpha and beta structure. The FERM-adjacent region of 4.1R contains serine residues phosphorylated by PKC and PKA; these appear conserved in about half of all other FERM-adjacent regions. Phylogenetic analyses indicate that all proteins containing a FERM-adjacent region arose from a single ancestor after FERM domains had started to proliferate in genomes of animals, plants and mycetozoa.

Conclusion: The FERM-adjacent region defines a subset of the FERM proteins in animals. The conservation of motifs in this region that are potential substrates for kinases together with the known regulatory phosphorylation of 4.1R in this region raises the possibility that the FERM-adjacent region is a regulatory adaptation in this subset of the FERM proteins.

Figure 1

The FERM-adjacent (FA) region. An HMM for the FA region was used to search the Uniprot non-redundant database. The alignment shown here represents sequences detected with the HMM in human, D. melanogaster and C. elegans. The alignment was generated by aligning the sequences to the HMM using HMMALIGN. The sequences shown are all adjacent to the C-terminal end of FERM domains, but not all FERM domains are adjacent to this sequence. Note the presence of a protein kinase A consensus sequence [KR][KR][X][ST] (boxed) in human protein 4.1R (41_HUMAN): the serine (asterisked) in this motif is a physiological PKA substrate. A PKC substrate site is also marked. In 4.1G (E41L2_HUMAN) another serine is phosphorylated in vivo (white asterisk). Secondary structure predictions generated are shown below the alignment. Jpred: E beta-strand; H alpha-helix. Disopred: * disorder. Jnet: B inaccessible to water. The proteins are grouped according to the classes shown in Fig. 2.

Figure 2

Examples of classes of proteins containing the FA region. The figure shows the modular organisation of FA region proteins in schematic outline. The proteins all contain FERM domains in their N-terminal region (although splice variation at certain N-termini can add extra sequence upstream of the FERM domain). On the C-terminal side of the FERM and FA regions are diverse sequences. Examples shown are as follows. (a) The true 4.1 proteins have a C-terminal domain (CTD) that binds receptors; and in mammals a spectrin-actin binding domain (SAB) promotes the binding of spectrin to actin. There are four such in vertebrate genomes, and one such in invertebrate genomes. (b) A group of poorly characterised proteins (two in vertebrate genomes, one in invertebrates) have FERM and FA regions, plus transmembrane segments in their C-terminal regions. They have no N-terminal signal sequences, and appear to be Type II membrane proteins. (c) The non-receptor tyrosine phosphatase protein PTP-MEG1 in mammals, PTP-MEG (split central complex) in fly and protein-tyrosine phosphatase 1 in worm are non-receptor tyrosine phosphatases localised at membranes; they have roles in control of cellular proliferation and control of interaction with extracellular matrix. Notably, the FA region was not found in the other FERM domain phosphatases PTPH1, PTP-E1 and PTP36. (d) CDEP is a GEF for Rho family GTPases. The FA region is also found in the related FARP2 gene product. (e) A variety of other proteins lack further domains recognised by SMART or Pfam. These include Band 4.1-like protein 5 and NBL-4.

Figure 3

Phylogenetic tree of lobe B of FERM domains. This tree was produced by Maximum Likelihood (Phylip proml) analysis of a non-redundant selection of FERM domain lobe B sequences. The grey shading lies over proteins that contain both FERM and FA regions: proteins outside the shading contain FERM domains, but not the FA. FERM/FA region proteins are colour coded to indicate their class of sequence as given in Fig 2: (a) red (b) orange (c) green (d) blue (e) purple.