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Qu Y, Feng J, Deng S, Cao L, Zhang Q, Zhao R, Zhang Z, Jiang Y, Zink EM, Baker SE, Lipton MS, Paša-Tolić L, Hu JZ, Wu S. Structural analysis of N- and O-glycans using ZIC-HILIC/dialysis coupled to NMR detection. Fungal Genet Biol 2014; 72:207-215. [PMID: 25117693 PMCID: PMC5175459 DOI: 10.1016/j.fgb.2014.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/15/2014] [Accepted: 08/02/2014] [Indexed: 11/21/2022]
Abstract
Protein glycosylation, an important and complex post-translational modification (PTM), is involved in various biological processes, including the receptor-ligand and cell-cell interaction, and plays a crucial role in many biological functions. However, little is known about the glycan structures of important biological complex samples, and the conventional glycan enrichment strategy (i.e., size-exclusion column [SEC] separation) prior to nuclear magnetic resonance (NMR) detection is time-consuming and tedious. In this study, we developed a glycan enrichment strategy that couples Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) with dialysis to enrich the glycans from the pronase E digests of RNase B, followed by NMR analysis of the glycoconjugate. Our results suggest that the ZIC-HILIC enrichment coupled with dialysis is a simple, fast, and efficient sample preparation approach. The approach was thus applied to analysis of a biological complex sample, the pronase E digest of the secreted proteins from the fungus Aspergillus niger. The NMR spectra revealed that the secreted proteins from A. niger contain both N-linked glycans with a high-mannose core similar to the structure of the glycan from RNase B, and O-linked glycans bearing mannose and glucose with 1→3 and 1→6 linkages. In all, our study provides compelling evidence that ZIC-HILIC separation coupled with dialysis is very effective and accessible in preparing glycans for the downstream NMR analysis, which could greatly facilitate the future NMR-based glycoproteomics research.
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Affiliation(s)
- Yi Qu
- Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Ju Feng
- Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Shuang Deng
- Energy and Environment Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Li Cao
- Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Qibin Zhang
- Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Zhaorui Zhang
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Yuxuan Jiang
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Erika M Zink
- Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Mary S Lipton
- Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Jian Zhi Hu
- Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA.
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Abstract
Plant ribosome-inactivating proteins (RIPs) are a group of toxic proteins that can irreversibly inactivate ribosomes by specifically removing the conserved adenine base from the "Sarcin/Ricin domain" of the 28S RNA in ribosome. Cinnamomin is a novel type II RIP isolated in our laboratory from the mature seeds of camphor tree. Besides site-specific deadenylation of the A4324 in the Sarcin/Ricin domain of rat ribosome, this protein could also release the adenine base from DNA molecules at multiple sites and from AMP, ADP, dAMP and adenosine. Furthermore, cinnamomin displays cytotoxicity to carcinoma cells and insect larvae by modifying their ribosomal RNA. These functions possessed by cinnamomin shed a new light on the possible application of cinnamomin in the field of immunotoxin design and transgenic reagents. In this review, we introduce the major recent results on cinnamomin obtained in our laboratory, including purification of this protein, characterization of its enzymatic mechanism, structure and function, gene pattern, physiological role and its biological implications in cytotoxicity.
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Affiliation(s)
- Wen-Jun He
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
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Liu RS, Wei GQ, Yang Q, He WJ, Liu WY. Cinnamomin, a type II ribosome-inactivating protein, is a storage protein in the seed of the camphor tree (Cinnamomum camphora). Biochem J 2002; 362:659-63. [PMID: 11879193 PMCID: PMC1222430 DOI: 10.1042/0264-6021:3620659] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cinnamomin is a novel type II ribosome-inactivating protein (RIP) isolated in our laboratory from the seed of the camphor tree (Cinnamomum camphora). In this paper the physiological role it plays in the plant cell was studied. Northern and Western blotting revealed that cinnamomin was expressed specifically in cotyledons. It accumulated in large amounts simultaneously with other proteins at the post-stages of seed development. Cinnamomin degraded rapidly during the early stages of seed germination. Endopeptidase was proved to play an important role in the degradation of cinnamomin. Western blotting of total proteins from the protein body with antibodies against cinnamomin demonstrated that it only existed in this specific cellular organelle as a storage protein. The similar properties of cinnamomin and other seed storage proteins of dicotyledons were compared. We conclude that cinnamomin is a special storage protein in the seed of C. camphora.
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Affiliation(s)
- Ren-shui Liu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, People's Republic of China
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Yang Q, Liu RS, Gong ZZ, Liu WY. Studies of three genes encoding Cinnamomin (a type II RIP) isolated from the seeds of camphor tree and their expression patterns. Gene 2002; 284:215-23. [PMID: 11891062 DOI: 10.1016/s0378-1119(01)00890-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cinnamomin, which has three isoforms, is a type II ribosome-inactivating protein (RIP) purified from the mature seeds of camphor tree (Cinnamomum camphora). In a previous study, an incomplete cDNA that encoded the A- and B-chain of Cinnamomin but lacked signal peptide sequence was cloned. In the present paper, its full-length cDNA was obtained by 5' rapid amplification of cDNA ends (5'RACE). Subsequently, polymerase chain reaction (PCR) amplification of its genomic DNA was performed. Unexpectedly, sequence analysis of the PCR products revealed three cinnamomin genes with >98.0% sequence identity. One of them corresponded to the published cDNA and was designated as cinnamomin I, whereas the other two genes were named as cinnamomin II and cinnamomin III, respectively. RT-PCR amplification of the cDNAs of cinnamomin II and III manifested that these two genes were functional. The three genes have no intron. Three Cinnamomin precursors that were inferred from the cDNA sequence of three cinnamomin genes exhibited relatively high sequence homology with other type II RIPs. Northern blot analysis demonstrated that the cinnamomin genes only expressed in cotyledons of C. camphora seeds and the acmes of expression emerged at 75-90 DAF when seeds were close to maturity. It is proposed that the three cinnamomin genes may encode three isoforms of Cinnamomin. The physiological function of Cinnamomin in C. camphora seeds is briefly discussed.
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Affiliation(s)
- Qiang Yang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. 320 Yue-Yang Road, Shanghai 200031, China
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Xie L, Wang BZ, Hu RG, Ji HB, Zhang L, Liu WY. Structural and functional studies of cinnamomin, a new type II ribosome-inactivating protein isolated from the seeds of the camphor tree. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5723-33. [PMID: 11722556 DOI: 10.1046/j.0014-2956.2001.02515.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cinnamomin is a new type II ribosome-inactivating protein (RIP). Its A-chain exhibits RNA N-glycosidase activity to inactivate the ribosome and thus inhibit protein synthesis, whereas the glycosylated B-chain is a lectin. The primary structure of cinnamomin, which exhibits approximately 55% identity with those of ricin and abrin, was deduced from the nucleotide sequences of cDNAs of cinnamomin A- and B-chains. It is composed of a total of 549 amino-acid residues: 271 residues in the A-chain, a 14-residue linker and 264 residues in the B-chain. To explore its biological function, the cinnamomin A-chain was expressed in Escherichia coli with a yield of 100 mg per L of culture, and purified through two-step column chromatography. After renaturation, the recovery of the enzyme activity of the expressed A-chain was 80% of that of native A-chain. Based on the modeling of the three-dimensional structure of the A-chain, the functional roles of five amino acids and the only cysteine residues were investigated by site-directed mutagenesis or chemical modification. The conserved single mutation of the five amino-acid residues led to 8-50-fold losses of enzymatic activity, suggesting that these residues were crucial for maintaining the RNA N-glycosidase activity of the A-chain. Most interestingly, the strong electric charge introduced at the position of the single cysteine in A-chain seemed to play a role in enzyme/substrate binding.
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Affiliation(s)
- L Xie
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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