Proteins with a BPI/LBP/PLUNC-Like Domain: Revisiting the Old and Characterizing the New 1033 Bioinformatics of the TULIP domain superfamily Klaus O. Kopec, Vikram Alva and Andrei N. Lupas 1 Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076 T ¨ ubingen, Germany Abstract Proteins of the BPI (bactericidal/permeability-increasing protein)-like family contain either one or two tandem copies of a fold that usually provides a tubular cavity for the binding of lipids. Bioinformatic analyses show that, in addition to its known members, which include BPI, LBP [LPS (lipopolysaccharide)- binding protein)], CETP (cholesteryl ester-transfer protein), PLTP (phospholipid-transfer protein) and PLUNC (palate, lung and nasal epithelium clone) protein, this family also includes other, more divergent groups containing hypothetical proteins from fungi, nematodes and deep-branching unicellular eukaryotes. More distantly, BPI-like proteins are related to a family of arthropod proteins that includes hormone-binding proteins (Takeout-like; previously described to adopt a BPI-like fold), allergens and several groups of uncharacterized proteins. At even greater evolutionary distance, BPI-like proteins are homologous with the SMP (synaptotagmin-like, mitochondrial and lipid-binding protein) domains, which are found in proteins associated with eukaryotic membrane processes. In particular, SMP domain-containing proteins of yeast form the ERMES [ER (endoplasmic reticulum)-mitochondria encounter structure], required for efficient phospholipid exchange between these organelles. This suggests that SMP domains themselves bind lipids and mediate their exchange between heterologous membranes. The most distant group of homologues we detected consists of uncharacterized animal proteins annotated as TM (transmembrane) 24. We propose to group these families together into one superfamily that we term as the TULIP (tubular lipid-binding) domain superfamily. Introduction LPS (lipopolysaccharides) are major contributors to the pathogenicity of Gram-negative bacteria. On infection, animals recognize LPS using LBP (LPS-binding protein) and initiate an immune response to boost inflammation [1,2]. When the primary structure of LBP was determined 20 years ago, sequence comparisons showed its homology with BPI (bactericidal/permeability-increasing protein) and CETP (cholesteryl ester-transfer protein) [3]. BPI is also a part of the innate immune response; however, it antagonizes LBP by neutralizing LPS and therefore dampening the inflammatory reaction [4,5]. The tertiary structure of BPI was solved in 1997 [1] and comprises two tandem domains, connected by a seven-stranded anti-parallel β -sheet. Despite statistically insignificant sequence similarity, the two domains have the same fold, consisting of a long α-helix wrapped in a highly curved anti-parallel β -sheet. The extent of the structural similarity and the unusual nature of the fold led Kleiger et al. [6] to propose that the two domains arose Key words: BPI-like family protein, cholesteryl ester-transfer protein (CETP), palate, lung and nasal epithelium clone (PLUNC), tubular lipid-binding (TULIP), synaptotagmin-like, mitochondrial and lipid-binding protein domain (SMP domain). Abbreviations used: BPI, bactericidal/permeability-increasing protein; CETP, cholesteryl ester- transfer protein; ER, endoplasmic reticulum; ERMES, ER-mitochondria encounter structure; ESAG5, expression site-associated gene 5; HMM, hidden Markov model; JHBP, juvenile hormone-binding protein; LPS, lipopolysaccharide; LBP, LPS-binding protein; Mdm, mitochondrial distribution and morphology; Mmm1, maintenance of mitochondrial morphology 1; PLUNC, palate, lung and nasal epithelium clone; LPLUNC, long PLUNC; SMP, synaptotagmin-like, mitochondrial and lipid-binding protein; SPLUNC, short PLUNC; TM, transmembrane; TULIP, tubular lipid-binding. 1 To whom correspondence should be addressed (email andrei.lupas@tuebingen.mpg.de). from a common ancestor. BPI binds phosphatidylcholine in a tubular cavity, and this hydrophobic tunnel is potentially also the binding site for LPS in LBP. The second aforementioned LBP homologue, CETP, is involved in the transfer of lipids between HDL (high-density lipoprotein) and LDL (low- density lipoprotein) in blood [7]. CETP adopts the same tandem domain architecture as BPI; its crystal structure was solved with cholesteryl ester bound inside the hydrophobic cavity and a phospholipid at the entrance to the cavity in each of the domains. LBP, CETP and BPI are the founding members of a protein superfamily, which has been progressively extended over the years due to improvements in the sensitivity of sequence comparison methods and the growth of sequence databases. We refer to the domain defining this superfamily, corresponding to the N-terminal domain of BPI, as TULIP (tubular lipid-binding) domain [8]. Since the homology of the C-terminal domain of BPI to TULIP seems likely, but cannot be established by statistical measures of sequence similarity, we refer to it as TULIP-like. The increase in sensitivity from sequence–sequence comparisons (BLAST), [9] to sequence–profile comparisons (PSI–BLAST), [10] allowed for the inclusion of the PLUNC (palate, lung and nasal epithelium clone) proteins into the TULIP superfamily [11]. PLUNC proteins are speculated to be involved in host defence because of their homology with LBP and BPI, and because of their localization in tissues often exposed to pathogens, e.g. the oral cavity, but their biological functions are poorly characterized [12]. PLUNC proteins have two subgroups: LPLUNC (long PLUNC), Biochem. Soc. Trans. (2011) 39, 1033–1038; doi:10.1042/BST0391033 C  The Authors Journal compilation C  2011 Biochemical Society Biochemical Society Transactions www.biochemsoctrans.org