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Pourhassan N Z, Smits SHJ, Ahn JH, Schmitt L. Biotechnological applications of type 1 secretion systems. Biotechnol Adv 2021; 53:107864. [PMID: 34767962 DOI: 10.1016/j.biotechadv.2021.107864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 02/06/2023]
Abstract
Bacteria have evolved a diverse range of secretion systems to export different substrates across their cell envelope. Although secretion of proteins into the extracellular space could offer advantages for recombinant protein production, the low secretion titers of the secretion systems for some heterologous proteins remain a clear drawback of their utility at commercial scales. Therefore, a potential use of most of secretion systems as production platforms at large scales are still limited. To overcome this limitation, remarkable efforts have been made toward improving the secretion efficiency of different bacterial secretion systems in recent years. Here, we review the progress with respect to biotechnological applications of type I secretion system (T1SS) of Gram-negative bacteria. We will also focus on the applicability of T1SS for the secretion of heterologous proteins as well as vaccine development. Last but not least, we explore the employed engineering strategies that have enhanced the secretion efficiencies of T1SS. Attention is also paid to directed evolution approaches that may offer a more versatile approach to optimize secretion efficiency of T1SS.
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Affiliation(s)
- Zohreh Pourhassan N
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Jung Hoon Ahn
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, South Korea
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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2
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Motlova L, Klimova N, Fiser R, Sebo P, Bumba L. Continuous Assembly of β-Roll Structures Is Implicated in the Type I-Dependent Secretion of Large Repeat-in-Toxins (RTX) Proteins. J Mol Biol 2020; 432:5696-5710. [PMID: 32860773 DOI: 10.1016/j.jmb.2020.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 01/10/2023]
Abstract
Repeats-in-Toxin (RTX) proteins of Gram-negative bacteria are excreted through the type I secretion system (T1SS) that recognizes non-cleavable C-terminal secretion signals. These are preceded by arrays of glycine and aspartate-rich nonapeptide repeats grouped by four to eight β strands into blocks that fold into calcium-binding parallel β-roll structures. The β-rolls are interspersed by linkers of variable length and sequence and the organization of multiple RTX repeat blocks within large RTX domains remains unknown. Here we examined the structure and function of the RTX domain of Bordetella pertussis adenylate cyclase toxin (CyaA) that is composed of five β-roll RTX blocks. We show that the non-folded RTX repeats maintain the stability of the CyaA polypeptide in the Ca2+-depleted bacterial cytosol and thereby enable its efficient translocation through the T1SS apparatus. The efficacy of secretion of truncated CyaA constructs was dictated by the number of retained RTX repeat blocks and depended on the presence of extracellular Ca2+ ions. We further describe the crystal structure of the RTX blocks IV-V of CyaA (CyaA1372-1681) that consists of a contiguous assembly of two β-rolls that differs substantially from the arrangement of the RTX blocks observed in RTX lipases or other RTX proteins. These results provide a novel structural insight into the architecture of the RTX domains of large RTX proteins and support the "push-ratchet" mechanism of the T1SS-mediated secretion of very large RTX proteins.
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Affiliation(s)
- Lucia Motlova
- Faculty of Sciences, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic
| | - Nela Klimova
- Faculty of Sciences, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic.; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Radovan Fiser
- Faculty of Sciences, Charles University, Vinicna 5, 128 44 Prague 2, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic..
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3
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Murata D, Okano H, Angkawidjaja C, Akutsu M, Tanaka SI, Kitahara K, Yoshizawa T, Matsumura H, Kado Y, Mizohata E, Inoue T, Sano S, Koga Y, Kanaya S, Takano K. Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain. Biochemistry 2017; 56:6281-6291. [PMID: 29094929 DOI: 10.1021/acs.biochem.7b00985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Serratia marcescens secretes a lipase, LipA, through a type I secretion system (T1SS). The T1SS for LipA, the Lip system, is composed of an inner membrane ABC transporter with its nucleotide-binding domains (NBD), LipB, a membrane fusion protein, LipC, and an outer membrane channel protein, LipD. Passenger protein secreted by this system has been functionally and structurally characterized well, but relatively little information about the transporter complex is available. Here, we report the crystallographic studies of LipC without the membrane anchor region, LipC-, and the NBD of LipB (LipB-NBD). LipC- crystallographic analysis has led to the determination of the structure of the long α-helical and lipoyl domains, but not the area where it interacts with LipB, suggesting that the region is flexible without LipB. The long α-helical domain has three α-helices, which interacts with LipD in the periplasm. LipB-NBD has the common overall architecture and ATP hydrolysis activity of ABC transporter NBDs. Using the predicted models of full-length LipB and LipD, the overall structural insight into the Lip system is discussed.
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Affiliation(s)
- Daichi Murata
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hiroyuki Okano
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Clement Angkawidjaja
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt , Max-von-Laue-Straße, 60438 Frankfurt am Main, Germany
| | - Shun-Ichi Tanaka
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Kenyu Kitahara
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Takuya Yoshizawa
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Hiroyoshi Matsumura
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Yuji Kado
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Eiichi Mizohata
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Tsuyoshi Inoue
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Satoshi Sano
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Yuichi Koga
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Shigenori Kanaya
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
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Type I Protein Secretion-Deceptively Simple yet with a Wide Range of Mechanistic Variability across the Family. EcoSal Plus 2017; 7. [PMID: 28084193 DOI: 10.1128/ecosalplus.esp-0019-2015] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A very large type I polypeptide begins to reel out from a ribosome; minutes later, the still unidentifiable polypeptide, largely lacking secondary structure, is now in some cases a thousand or more residues longer. Synthesis of the final hundred C-terminal residues commences. This includes the identity code, the secretion signal within the last 50 amino acids, designed to dock with a waiting ATP binding cassette (ABC) transporter. What happens next is the subject of this review, with the main, but not the only focus on hemolysin HlyA, an RTX protein toxin secreted by the type I system. Transport substrates range from small peptides to giant proteins produced by many pathogens. These molecules, without detectable cellular chaperones, overcome enormous barriers, crossing two membranes before final folding on the cell surface, involving a unique autocatalytic process.Unfolded HlyA is extruded posttranslationally, C-terminal first. The transenvelope "tunnel" is formed by HlyB (ABC transporter), HlyD (membrane fusion protein) straddling the inner membrane and periplasm and TolC (outer membrane). We present a new evaluation of the C-terminal secretion code, and the structure function of HlyD and HlyB at the heart of this nanomachine. Surprisingly, key details of the secretion mechanism are remarkably variable in the many type I secretion system subtypes. These include alternative folding processes, an apparently distinctive secretion code for each type I subfamily, and alternative forms of the ABC transporter; most remarkably, the ABC protein probably transports peptides or polypeptides by quite different mechanisms. Finally, we suggest a putative structure for the Hly-translocon, HlyB, the multijointed HlyD, and the TolC exit.
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Mohammadi M, Sepehrizadeh Z, Ebrahim-Habibi A, Reza Shahverdi A, Ali Faramarzi M, Setayesh N. Bacterial expression and characterization of an active recombinant lipase A from Serratia marcescens with truncated C-terminal region. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Disorder-to-order transition in the CyaA toxin RTX domain: implications for toxin secretion. Toxins (Basel) 2014; 7:1-20. [PMID: 25559101 PMCID: PMC4303809 DOI: 10.3390/toxins7010001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/24/2014] [Indexed: 11/23/2022] Open
Abstract
The past decade has seen a fundamental reappraisal of the protein structure-to-function paradigm because it became evident that a significant fraction of polypeptides are lacking ordered structures under physiological conditions. Ligand-induced disorder-to-order transition plays a key role in the biological functions of many proteins that contain intrinsically disordered regions. This trait is exhibited by RTX (Repeat in ToXin) motifs found in more than 250 virulence factors secreted by Gram-negative pathogenic bacteria. We have investigated several RTX-containing polypeptides of different lengths, all derived from the Bordetella pertussis adenylate cyclase toxin, CyaA. Using a combination of experimental approaches, we showed that the RTX proteins exhibit the hallmarks of intrinsically disordered proteins in the absence of calcium. This intrinsic disorder mainly results from internal electrostatic repulsions between negatively charged residues of the RTX motifs. Calcium binding triggers a strong reduction of the mean net charge, dehydration and compaction, folding and stabilization of secondary and tertiary structures of the RTX proteins. We propose that the intrinsically disordered character of the RTX proteins may facilitate the uptake and secretion of virulence factors through the bacterial secretion machinery. These results support the hypothesis that the folding reaction is achieved upon protein secretion and, in the case of proteins containing RTX motifs, could be finely regulated by the calcium gradient across bacterial cell wall.
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Cheng M, Angkawidjaja C, Koga Y, Kanaya S. Requirement of lid2 for interfacial activation of a family I.3 lipase with unique two lid structures. FEBS J 2012; 279:3727-3737. [DOI: 10.1111/j.1742-4658.2012.08734.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 06/28/2012] [Accepted: 07/30/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Maria Cheng
- Department of Material and Life Science; Graduate School of Engineering; Osaka University Japan
| | - Clement Angkawidjaja
- Department of Material and Life Science; Graduate School of Engineering; Osaka University Japan
- International College; Osaka University; Japan
| | - Yuichi Koga
- Department of Material and Life Science; Graduate School of Engineering; Osaka University Japan
| | - Shigenori Kanaya
- Department of Material and Life Science; Graduate School of Engineering; Osaka University Japan
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Park Y, Moon Y, Ryoo J, Kim N, Cho H, Ahn JH. Identification of the minimal region in lipase ABC transporter recognition domain of Pseudomonas fluorescens for secretion and fluorescence of green fluorescent protein. Microb Cell Fact 2012; 11:60. [PMID: 22578275 PMCID: PMC3430570 DOI: 10.1186/1475-2859-11-60] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 04/11/2012] [Indexed: 11/22/2022] Open
Abstract
Background TliA is a thermostable lipase secreted by the type 1 secretion system (T1SS) of Pseudomonas fluorescens. The secretion is promoted by its secretion/chaperone domain located near the C-terminus, which is composed mainly of four Repeat-in-Toxin (RTX) repeats. In order to identify the minimal region of TliA responsible for its secretion, five different copies of the secretion/chaperone domain, each involving truncated N-terminal residues and a common C-terminus, were acquired and named as lipase ABC transporter recognition domains (LARDs). Each LARD was fused to epidermal growth factor (EGF) or green fluorescent protein (GFP), and the secretion of EGF-LARD or GFP-LARD fusion proteins was assessed in Escherichia coli with ABC transporter. Results Among the fusion proteins, GFP or EGF with 105-residue LARD3 was most efficiently secreted. In addition, GFP-LARD3 emitted wild type GFP fluorescence. Structurally, LARD3 had the 4 RTX repeats exposed at the N-terminus, while other LARDs had additional residues prior to them or missed some of the RTX repeats. LARD3 was both necessary and sufficient for efficient secretion and maintenance of GFP fluorescence in E. coli, which was also confirmed in P. fluorescens and P. fluorescens ▵tliA, a knock-out mutant of tliA. Conclusion LARD3 was a potent secretion signal in T1SS for its fusion flanking RTX motif, which enhanced secretion and preserved the fluorescence of GFP. LARD3-mediated secretion in E. coli or P. fluorescens will enable the development of enhanced protein manufacturing factory and recombinant microbe secreting protein of interest in situ.
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Affiliation(s)
- Yeonwoo Park
- Korea Science Academy of KAIST, 899 Tanggam 3-Dong, Busanjin-Gu, Busan, 614-822, Korea
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Angkawidjaja C, Matsumura H, Koga Y, Takano K, Kanaya S. X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids. J Mol Biol 2010; 400:82-95. [DOI: 10.1016/j.jmb.2010.04.051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/08/2010] [Accepted: 04/26/2010] [Indexed: 11/16/2022]
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Szilvay GR, Blenner MA, Shur O, Cropek DM, Banta S. A FRET-based method for probing the conformational behavior of an intrinsically disordered repeat domain from Bordetella pertussis adenylate cyclase. Biochemistry 2009; 48:11273-82. [PMID: 19860484 DOI: 10.1021/bi901447j] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A better understanding of the conformational changes exhibited by intrinsically disordered proteins is necessary as we continue to unravel their myriad biological functions. In repeats in toxin (RTX) domains, calcium binding triggers the natively unstructured domain to adopt a beta roll structure. Here we present an in vitro Forster resonance energy transfer (FRET)-based method for the investigation of the conformational behavior of an RTX domain from the Bordetella pertussis adenylate cyclase consisting of nine repeat units. Equilibrium and stopped-flow FRET between fluorescent proteins, attached to the termini of the domain, were measured in an analysis of the end-to-end distance changes in the RTX domain. The method was complemented with circular dichroism spectroscopy, tryptophan fluorescence, and bis-ANS dye binding. High ionic strength was observed to decrease the calcium affinity of the RTX domain. A truncation and single amino acid mutations yielded insights into the structural determinants of beta roll formation. Mutating the conserved Asp residue in one of the nine repeats significantly reduced the affinity of the domains for calcium ions. Removal of the sequences flanking the repeat domain prevented folding, but replacing them with fluorescent proteins restored the conformational behavior, suggesting an entropic stabilization. The FRET-based method is a useful technique that complements other low-resolution techniques for investigating the dynamic conformational behavior of the RTX domain and other intrinsically disordered protein domains.
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Affiliation(s)
- Géza R Szilvay
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, USA
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11
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Chung CW, You J, Kim K, Moon Y, Kim H, Ahn JH. Export of recombinant proteins in Escherichia coli using ABC transporter with an attached lipase ABC transporter recognition domain (LARD). Microb Cell Fact 2009; 8:11. [PMID: 19178697 PMCID: PMC2642768 DOI: 10.1186/1475-2859-8-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 01/29/2009] [Indexed: 11/21/2022] Open
Abstract
Background ATP binding cassette (ABC) transporter secretes the protein through inner and outer membranes simultaneously in gram negative bacteria. Thermostable lipase (TliA) of Pseudomonas fluorescens SIK W1 is secreted through the ABC transporter. TliA has four glycine-rich repeats (GGXGXD) in its C-terminus, which appear in many ABC transporter-secreted proteins. From a homology model of TliA derived from the structure of P. aeruginosa alkaline protease (AprA), lipase ABC transporter domains (LARDs) were designed for the secretion of fusion proteins. Results The LARDs included four glycine-rich repeats comprising a β-roll structure, and were added to the C-terminus of test proteins. Either Pro-Gly linker or Factor Xa site was added between fusion proteins and LARDs. We attached different length of LARDs such as LARD0, LARD1 or whole TliA (the longest LARD) to three types of proteins; green fluorescent protein (GFP), epidermal growth factor (EGF) and cytoplasmic transduction peptide (CTP). These fusion proteins were expressed in Escherichia coli together with ABC transporter of either P. fluorescens or Erwinia chrysanthemi. Export of fusion proteins with the whole TliA through the ABC transporter was evident on the basis of lipase enzymatic activity. Upon supplementation of E. coli with ABC transporter, GFP-LARDs and EGF-LARDs were excreted into the culture supernatant. Conclusion The LARDs or whole TliA were attached to C-termini of model proteins and enabled the export of the model proteins such as GFP and EGF in E. coli supplemented with ABC transporter. These results open the possibility for the extracellular production of recombinant proteins in Pseudomonas using LARDs or TliA as a C-terminal signal sequence.
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Affiliation(s)
- Chan Woo Chung
- Korea Science Academy, #899, Tanggam 3-Dong, Busanjin-Gu, Busan, 614-822, Korea.
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Mala JGS, Takeuchi S. Understanding structural features of microbial lipases--an overview. ANALYTICAL CHEMISTRY INSIGHTS 2008; 3:9-19. [PMID: 19609386 PMCID: PMC2701168 DOI: 10.4137/aci.s551] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for 'lipase structure' in the RCSB Protein Data Bank (http://www.rcsb.org/pdb/) returns only 93 hits (as of September 2007) and, the NCBI database (http://www.ncbi.nlm.nih.gov) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL) has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.
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Affiliation(s)
- John Geraldine Sandana Mala
- SANDANA FLORALS, Module-7, Golden Jubilee Biotech Park for Women Society, In SIPCOT-IT Park, Old Mahabalipuram Road, Siruseri, Navalur P.O., Kanchipuram District-603103, Tamilnadu, India
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13
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Meier R, Drepper T, Svensson V, Jaeger KE, Baumann U. A Calcium-gated Lid and a Large β-Roll Sandwich Are Revealed by the Crystal Structure of Extracellular Lipase from Serratia marcescens. J Biol Chem 2007; 282:31477-83. [PMID: 17728256 DOI: 10.1074/jbc.m704942200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipase LipA from Serratia marcescens is a 613-amino acid enzyme belonging to family I.3 of lipolytic enzymes that has an important biotechnological application in the production of a chiral precursor for the coronary vasodilator diltiazem. Like other family I.3 lipases, LipA is secreted by Gram-negative bacteria via a type I secretion system and possesses 13 copies of a calcium binding tandem repeat motif, GGXGXDXUX (U, hydrophobic amino acids), in the C-terminal part of the polypeptide chain. The 1.8-A crystal structure of LipA reveals a close relation to eukaryotic lipases, whereas family I.1 and I.2 enzymes appear to be more distantly related. Interestingly, the structure shows for the N-terminal lipase domain a variation on the canonical alpha/beta hydrolase fold in an open conformation, where the putative lid helix is anchored by a Ca(2+) ion essential for activity. Another novel feature observed in this lipase structure is the presence of a helical hairpin additional to the putative lid helix that exposes a hydrophobic surface to the aqueous medium and might function as an additional lid. The tandem repeats form two separated parallel beta-roll domains that pack tightly against each other. Variations of the consensus sequence of the tandem repeats within the second beta-roll result in an asymmetric Ca(2+) binding on only one side of the roll. The analysis of the properties of the beta-roll domains suggests an intramolecular chaperone function.
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Affiliation(s)
- Reto Meier
- Department of Chemistry and Biochemistry, University Bern Freiestrasse 3, CH-3012 Bern, Switzerland
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Scotter AJ, Guo M, Tomczak MM, Daley ME, Campbell RL, Oko RJ, Bateman DA, Chakrabartty A, Sykes BD, Davies PL. Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides. BMC STRUCTURAL BIOLOGY 2007; 7:63. [PMID: 17908326 PMCID: PMC2174480 DOI: 10.1186/1472-6807-7-63] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 10/01/2007] [Indexed: 12/28/2022]
Abstract
BACKGROUND A right-handed, calcium-dependent beta-roll structure found in secreted proteases and repeat-in-toxin proteins was used as a template for the design of minimal, soluble, monomeric polypeptides that would fold in the presence of Ca2+. Two polypeptides were synthesised to contain two and four metal-binding sites, respectively, and exploit stacked tryptophan pairs to stabilise the fold and report on the conformational state of the polypeptide. RESULTS Initial analysis of the two polypeptides in the presence of calcium suggested the polypeptides were disordered. The addition of lanthanum to these peptides caused aggregation. Upon further study by right angle light scattering and electron microscopy, the aggregates were identified as ordered protein filaments that required lanthanum to polymerize. These filaments could be disassembled by the addition of a chelating agent. A simple head-to-tail model is proposed for filament formation that explains the metal ion-dependency. The model is supported by the capping of one of the polypeptides with biotin, which disrupts filament formation and provides the ability to control the average length of the filaments. CONCLUSION Metal ion-dependent, reversible protein filament formation is demonstrated for two designed polypeptides. The polypeptides form filaments that are approximately 3 nm in diameter and several hundred nm in length. They are not amyloid-like in nature as demonstrated by their behaviour in the presence of congo red and thioflavin T. A capping strategy allows for the control of filament length and for potential applications including the "decoration" of a protein filament with various functional moieties.
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Affiliation(s)
- Andrew J Scotter
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Meng Guo
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Medical Biophysics, University of Toronto, ON, M5G 2M9, Canada
- Ontario Cancer Institute, University of Toronto, ON, M5G 2M9, Canada
| | - Melanie M Tomczak
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Margaret E Daley
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, 6G 2H7, Canada
| | - Robert L Campbell
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Richard J Oko
- Department of Anatomy and Cell Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - David A Bateman
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Medical Biophysics, University of Toronto, ON, M5G 2M9, Canada
- Ontario Cancer Institute, University of Toronto, ON, M5G 2M9, Canada
| | - Avijit Chakrabartty
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Medical Biophysics, University of Toronto, ON, M5G 2M9, Canada
- Ontario Cancer Institute, University of Toronto, ON, M5G 2M9, Canada
| | - Brian D Sykes
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, 6G 2H7, Canada
| | - Peter L Davies
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
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Angkawidjaja C, You DJ, Matsumura H, Kuwahara K, Koga Y, Takano K, Kanaya S. Crystal structure of a family I.3 lipase fromPseudomonassp. MIS38 in a closed conformation. FEBS Lett 2007; 581:5060-4. [DOI: 10.1016/j.febslet.2007.09.048] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2007] [Revised: 09/20/2007] [Accepted: 09/21/2007] [Indexed: 10/22/2022]
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Aachmann FL, Svanem BIG, Güntert P, Petersen SB, Valla S, Wimmer R. NMR Structure of the R-module. J Biol Chem 2006; 281:7350-6. [PMID: 16407237 DOI: 10.1074/jbc.m510069200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the bacterium Azotobacter vinelandii, a family of seven secreted and calcium-dependent mannuronan C-5 epimerases (AlgE1-7) has been identified. These epimerases are responsible for the epimerization of beta-d-mannuronic acid to alpha-l-guluronic acid in alginate polymers. The epimerases consist of two types of structural modules, designated A (one or two copies) and R (one to seven copies). The structure of the catalytically active A-module from the smallest epimerase AlgE4 (consisting of AR) has been solved recently. This paper describes the NMR structure of the R-module from AlgE4 and its titration with a substrate analogue and paramagnetic thulium ions. The R-module folds into a right-handed parallel beta-roll. The overall shape of the R-module is an elongated molecule with a positively charged patch that interacts with the substrate. Titration of the R-module with thulium indicated possible calcium binding sites in the loops formed by the nonarepeat sequences in the N-terminal part of the molecule and the importance of calcium binding for the stability of the R-module. Structure calculations showed that calcium ions can be incorporated in these loops without structural violations and changes. Based on the structure and the electrostatic surface potential of both the A- and R-module from AlgE4, a model for the appearance of the whole protein is proposed.
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Affiliation(s)
- Finn L Aachmann
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Angkawidjaja C, Paul A, Koga Y, Takano K, Kanaya S. Importance of a repetitive nine-residue sequence motif for intracellular stability and functional structure of a family I.3 lipase. FEBS Lett 2005; 579:4707-12. [PMID: 16098975 DOI: 10.1016/j.febslet.2005.07.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 07/06/2005] [Accepted: 07/19/2005] [Indexed: 10/25/2022]
Abstract
PML5 is a functional derivative of a family I.3 lipase from Pseudomonas sp. MIS38 and contains five repeats of a nine-residue sequence motif. Two aspartate residues within the second and third repetitive sequences of PML5 were replaced by Ala. The secretion level, intracellular accumulation level, and stability of the resultant mutant protein were greatly reduced as compared to those of PML5. In addition, this mutant protein was inactive and did not bind Ca2+ ion. We propose that the repetitive sequences of PML5 form a beta-roll structure in the cells and thereby contribute to the intracellular stability and secretion efficiency of the protein.
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Affiliation(s)
- Clement Angkawidjaja
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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