CORE Metadata, citation and similar papers at core.ac.uk Provided by Universidade do Minho: RepositoriUM Biotechnology Advances 33 (2015) 358–369 Contents lists available at ScienceDirect Biotechnology Advances journal homepage: www.elsevier.com/locate/biotechadv Research review paper Recombinant CBM-fusion technology — Applications overview Carla Oliveira, Vera Carvalho, Lucília Domingues, Francisco M. Gama ⁎ CEB — Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal article info abstract Article history: Carbohydrate-binding modules (CBMs) are small components of several enzymes, which present an indepen- Received 12 September 2014 dent fold and function, and specific carbohydrate-binding activity. Their major function is to bind the enzyme Received in revised form 6 February 2015 to the substrate enhancing its catalytic activity, especially in the case of insoluble substrates. The immense diver- Accepted 9 February 2015 sity of CBMs, together with their unique properties, has long raised their attention for many biotechnological ap- Available online 14 February 2015 plications. Recombinant DNA technology has been used for cloning and characterizing new CBMs. In addition, it Keywords: has been employed to improve the purity and availability of many CBMs, but mainly, to construct bi-functional fi Carbohydrate-binding modules CBM-fused proteins for speci c applications. This review presents a comprehensive summary of the uses of Heterologous expression systems CBMs recombinantly produced from heterologous organisms, or by the original host, along with the latest ad- Recombinant CBM-fusions vances. Emphasis is given particularly to the applications of recombinant CBM-fusions in: (a)modification of fi- Carbohydrate-binding activity bers, (b) production, purification and immobilization of recombinant proteins, (c) functionalization of Cellulose biomaterials and (d) development of microarrays and probes. CBM applications © 2015 Elsevier Inc. All rights reserved. Contents 1. Introduction.............................................................. 358 1.1. CBMnomenclature....................................................... 359 1.2. CBM classification........................................................ 359 1.3. Foldfamilies.......................................................... 359 1.4. TypesofCBMs......................................................... 359 1.5. RoleofCBMsinCAZymes.................................................... 359 1.6. GeneralapplicationsofCBMs................................................... 360 2. ApplicationsofrecombinantCBMs.................................................... 361 2.1. Modification of fibers...................................................... 361 2.2. Recombinant protein production and purification.......................................... 363 2.2.1. Affinity purificationtools................................................. 363 2.2.2. Productionofpeptidesandenzymes........................................... 364 2.3. Immobilizationofrecombinantproteins.............................................. 364 Functionalizationofbiomaterials.................................................... 365 2.4. Microarraysandprobes..................................................... 366 3. Perspectives.............................................................. 366 Acknowledgements............................................................. 367 References................................................................. 367 1. Introduction ⁎ Corresponding author at: CEB — Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal. Tel.: +351 253 604 400; The molecular recognition of carbohydrates by proteins, namely gly- fax: +351 253 604 429. coside hydrolases, is essential in several biological processes, including E-mail addresses: [email protected] (C. Oliveira), – [email protected] (V. Carvalho), [email protected] (L. Domingues), cell cell recognition, cellular adhesion, and host-pathogen interactions. [email protected] (F.M. Gama). Therefore, understanding the structural basis of the ligand specificity of http://dx.doi.org/10.1016/j.biotechadv.2015.02.006 0734-9750/© 2015 Elsevier Inc. All rights reserved. C. Oliveira et al. / Biotechnology Advances 33 (2015) 358–369 359 carbohydrate‐binding proteins is critical (Simpson et al., 2000). Many characterized by two β-sheets, each consisting of three to six antiparal- carbohydrate-active enzymes (CAZymes) are modular and constituted lel β-strands (Fig. 1-A, B, C). All of the β-sandwich CBMs have at least by a catalytic module and one or more non-catalytic carbohydrate- one bound metal atom (with the exception of CBM2a from Cellulomonas binding modules (CBMs) (Boraston et al., 2002, 2004; Hashimoto, fimi xylanase 10A). 2006). Originally, the CBMs were classified as cellulose-binding do- The β-trefoil is the second most frequent fold. It comprises twelve mains (CBDs), because the first examples of these classes of protein do- strands of β-sheet, establishing six hairpin turns. A β-barrel structure mains bound to crystalline cellulose (Gilkes et al., 1988; Tomme et al., is formed by six of the strands, associated with three hairpin turns. 1988). However, the more broad term CBM was proposed to depict The remainder three hairpin turns form a triangular cap on one end of the diverse ligand specificity of these sugar-binding modules derived the β-barrel named ‘hairpin triplet’ (Fig. 1-E). The trefoil domain, de- from glycoside hydrolases. The Carbohydrate-Active enZYmes Database fined by Boraston et al. (2004), is a contiguous amino acid sequence (CAZy) (Lombard et al., 2014)(www.cazy.org) describes the families of with four β-strands and two hairpin structures having a trefoil shape. structurally related catalytic domains and CBMs (or functional do- Each trefoil domain provides one hairpin (two β-strands) to the β- mains) of enzymes that degrade, modify, or create glycosidic bonds barrel and one hairpin to the hairpin triplet. such as glycoside hydrolases, glycosyltransferases, carbohydrate ester- The majority of the CBMs belonging to the fold family of OB (oligo- ases and polysaccharide lyases. nucleotide/oligosaccharide-binding) have planar carbohydrate- binding sites containing aromatic residues (Fig. 1-H). Hevein domains 1.1. CBM nomenclature are relatively small CBMs (~40 amino acids) and were originally identi- fied as chitin-binding proteins in plants. The fold is mainly coil, however The nomenclature system for CBMs is based on the systematic no- it has two small β-sheets and a tiny region of helix (Fig. 1-G). menclature adopted for glycoside hydrolases (Henrissat et al., 1998). Briefly, a CBM is named by its family number, e.g. the family 10 CBM 1.4. Types of CBMs from Cellvibrio japonicus Xyn10A would be called CBM10, however to improve clarity, it could also be included the organism and even the en- The protein fold allowed CBMs to be grouped into fold families, how- zyme from which it is derived. So, for this example, the CBM could be ever this is not predictive of function. The topology of CBM-ligand bind- defined as CjCBM10 or as Cj Xyn10ACBM10. If the glycoside hydrolase ing sites was also used by Boraston et al. (2004) to categorize CBMs into contains tandem CBMs of the same family, a number matching to the different “types” (Fig. 1), replicating the macromolecular structure of position of the CBM in the enzyme relative to the N-terminus is the target ligand. This organization was based on the structural and included. functional similarities of the CBMs, and three types of CBMs were de- scribed: type A (‘surface-binding’ CBMs), type B (‘glycan-chain-binding’ 1.2. CBM classification CBMs), and type C (‘small-sugar-binding’ CBMs). Type A CBMs or surface-binding CBMs (Fig. 1-A, D, F, H) have a flat In the CAZy database, a CBM is defined as a contiguous amino acid hydrophobic binding surface comprised of aromatic residues. The pla- sequence within a carbohydrate-active enzyme with a discrete fold hav- nar architecture of the binding sites is consistent with the flat surfaces ing carbohydrate-binding activity (Shoseyov et al., 2006). Numerous of crystalline polysaccharides like cellulose and chitin (Boraston et al., CBMs have been identified experimentally, and based on amino acid 2004). The interaction of type A CBMs with crystalline cellulose is relat- similarity many putative CBMs can be further identified. Currently, ed with positive entropy, indicating that the thermodynamic forces that 48756 CBMs have been divided into 71 different families based on drive the binding of CBMs to crystalline ligands are relatively unique amino acid sequence, binding specificity, and structure (extensive among CBMs. Another feature of type A CBMs is their little or no affinity data and classification can be found in the CAZy database www.cazy. for soluble polysaccharides (Bolam et al., 1998; Shoseyov et al., 2006). org). The information on the CAZy database is constantly reviewed Type B CBMs (Fig. 1-B) binding site architecture displays a cleft or and reanalyzed in order to keep the information updated in such way groove arrangement and comprise several subsites able to accommo- that new families are frequently added (Lombard et al., 2014). date the individual sugar units of the polysaccharide. The binding profi- ciency of the type B CBMs is assessed by the degree of polymerization of 1.3. Fold families the carbohydrate ligand: several studies revealed high affinity toward