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Suzuki K, Okawa K, Ohkura M, Kanaizumi T, Kobayashi T, Takahashi K, Takei H, Otsuka M, Tabata E, Bauer PO, Oyama F. Evolutionary insights into sequence modifications governing chitin recognition and chitinase inactivity in YKL-40 (HC-gp39, CHI3L1). J Biol Chem 2024; 300:107365. [PMID: 38750795 PMCID: PMC11190707 DOI: 10.1016/j.jbc.2024.107365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 06/07/2024] Open
Abstract
YKL-40, also known as human cartilage glycoprotein-39 (HC-gp39) or CHI3L1, shares structural similarities with chitotriosidase (CHIT1), an active chitinase, but lacks chitinase activity. Despite being a biomarker for inflammatory disorders and cancer, the reasons for YKL-40's inert chitinase function have remained elusive. This study reveals that the loss of chitinase activity in YKL-40 has risen from multiple sequence modifications influencing its chitin affinity. Contrary to the common belief associating the lack of chitinase activity with amino acid substitutions in the catalytic motif, attempts to activate YKL-40 by creating two amino acid mutations in the catalytic motif (MT-YKL-40) proved ineffective. Subsequent exploration that included creating chimeras of MT-YKL-40 and CHIT1 catalytic domains (CatDs) identified key exons responsible for YKL-40 inactivation. Introducing YKL-40 exons 3, 6, or 8 into CHIT1 CatD resulted in chitinase inactivation. Conversely, incorporating CHIT1 exons 3, 6, and 8 into MT-YKL-40 led to its activation. Our recombinant proteins exhibited properly formed disulfide bonds, affirming a defined structure in active molecules. Biochemical and evolutionary analysis indicated that the reduced chitinase activity of MT-YKL-40 correlates with specific amino acids in exon 3. M61I and T69W substitutions in CHIT1 CatD diminished chitinase activity and increased chitin binding. Conversely, substituting I61 with M and W69 with T in MT-YKL-40 triggered chitinase activity while reducing the chitin-binding activity. Thus, W69 plays a crucial role in a unique subsite within YKL-40. These findings emphasize that YKL-40, though retaining the structural framework of a mammalian chitinase, has evolved to recognize chitin while surrendering chitinase activity.
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Affiliation(s)
- Keita Suzuki
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Kazuaki Okawa
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Masashi Ohkura
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Tomoki Kanaizumi
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Takaki Kobayashi
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Koro Takahashi
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Hiromu Takei
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Momo Otsuka
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan
| | - Eri Tabata
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan; Research Fellow of Japan Society for the Promotion of Science (PD), Chiyoda-ku, Tokyo, Japan
| | | | - Fumitaka Oyama
- Department of Chemistry and Life Science, Kogakuin University, Hachioji, Tokyo, Japan.
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Skvortsova L, Abdikerim S, Yergali K, Mit N, Perfilyeva A, Omarbayeva N, Zhunussova A, Kachiyeva Z, Sadykova T, Bekmanov B, Kaidarova D, Djansugurova L, Zhunussova G. Association of Genetic Markers with the Risk of Early-Onset Breast Cancer in Kazakh Women. Genes (Basel) 2024; 15:108. [PMID: 38254997 PMCID: PMC10815330 DOI: 10.3390/genes15010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due to mutations in the BRCA1/BRCA2 genes, and 90% have a more complex genetic background. This poses a significant challenge to timely cancer detection in young women and highlights the need for research and awareness. Therefore, identifying genetic risk factors for eBC is essential to solving these problems. This study represents an association analysis of 144 eBC cases and 163 control participants to identify genetic markers associated with eBC risks in Kazakh women. We performed a two-stage approach in association analysis to assess genetic predisposition to eBC. First-stage genome-wide association analysis revealed two risk intronic loci in the CHI3L2 gene (p = 5.2 × 10-6) and MGAT5 gene (p = 8.4 × 10-6). Second-stage exonic polymorphisms haplotype analysis showed significant risks for seven haplotypes (p < 9.4 × 10-4). These results point to the importance of studying medium- and low-penetrant genetic markers in their haplotype combinations for a detailed understanding of the role of detected genetic markers in eBC development and prediction.
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Affiliation(s)
- Liliya Skvortsova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kanagat Yergali
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Natalya Mit
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Nazgul Omarbayeva
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Aigul Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Zulfiya Kachiyeva
- Research Institute of Applied and Fundamental Medicine, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan;
| | - Tolkyn Sadykova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Bakhytzhan Bekmanov
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Dilyara Kaidarova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
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3
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Okawa K, Tabata E, Kida Y, Uno K, Suzuki H, Kamaya M, Bauer PO, Oyama F. Irreversible evolutionary loss of chitin-degrading ability in the chitinase-like protein Ym1 under positive selection in rodents. Protein Sci 2023; 32:e4620. [PMID: 36883357 PMCID: PMC10031810 DOI: 10.1002/pro.4620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Ym1 (chitinase-like 3, Chil3) expressed in mice is a nonenzymatic chitinase-like protein, which shows 67% identity with mouse acidic chitinase (Chia). Similar to Chia, Ym1 is overexpressed in asthma and parasitic infections in mouse lungs. Due to the lack of chitin-degrading activity, the biomedical role of Ym1 under these pathophysiological conditions remains to be determined. In this study, we investigated what region and amino acid changes in Ym1 resulted in the loss of enzymatic activity. Replacing two amino acids at the catalytic motif to obtain a Chia-like sequence (N136D and Q140E; MT-Ym1) did not activate the protein. We conducted a comparative study of Ym1 and Chia. We found that three protein segments-(i) the catalytic motif residues, (ii) exons 6 and 7, and (iii) exon 10-are responsible for chitinase activity loss in Ym1. We show that replacing each of these three segments in Chia that are also involved in substrate recognition and binding by the Ym1 sequence can fully abolish the enzymatic activity. In addition, we show that there have been extensive gene duplication events at the Ym1 locus specific to the rodent lineages. Consistent with this result, Ym1 orthologs from the rodent genome were under positive selection when analyzed through the CODEML program. These data suggest that numerous amino acid substitutions in the regions involved in the chitin recognition, binding, and degradation ability of the ancestor Ym1 molecule lead to the irreversible inactivation of the protein.
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Affiliation(s)
- Kazuaki Okawa
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Eri Tabata
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
- Japan Society for the Promotion of Science (PD)TokyoJapan
| | - Yuta Kida
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Kyohei Uno
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Hidetoshi Suzuki
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
| | - Minori Kamaya
- Department of Applied ChemistryKogakuin UniversityTokyoJapan
| | | | - Fumitaka Oyama
- Department of Chemistry and Life ScienceKogakuin UniversityTokyoJapan
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Sustar AE, Strand LG, Zimmerman SG, Berg CA. Imaginal disk growth factors are Drosophila chitinase-like proteins with roles in morphogenesis and CO2 response. Genetics 2023; 223:iyac185. [PMID: 36576887 PMCID: PMC9910413 DOI: 10.1093/genetics/iyac185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 07/18/2022] [Accepted: 11/16/2022] [Indexed: 12/29/2022] Open
Abstract
Chitinase-like proteins (CLPs) are members of the family 18 glycosyl hydrolases, which include chitinases and the enzymatically inactive CLPs. A mutation in the enzyme's catalytic site, conserved in vertebrates and invertebrates, allowed CLPs to evolve independently with functions that do not require chitinase activity. CLPs normally function during inflammatory responses, wound healing, and host defense, but when they persist at excessive levels at sites of chronic inflammation and in tissue-remodeling disorders, they correlate positively with disease progression and poor prognosis. Little is known, however, about their physiological function. Drosophila melanogaster has 6 CLPs, termed Imaginal disk growth factors (Idgfs), encoded by Idgf1, Idgf2, Idgf3, Idgf4, Idgf5, and Idgf6. In this study, we developed tools to facilitate characterization of the physiological roles of the Idgfs by deleting each of the Idgf genes using the CRISPR/Cas9 system and assessing loss-of-function phenotypes. Using null lines, we showed that loss of function for all 6 Idgf proteins significantly lowers viability and fertility. We also showed that Idgfs play roles in epithelial morphogenesis, maintaining proper epithelial architecture and cell shape, regulating E-cadherin and cortical actin, and remarkably, protecting these tissues against CO2 exposure. Defining the normal molecular mechanisms of CLPs is a key to understanding how deviations tip the balance from a physiological to a pathological state.
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Affiliation(s)
- Anne E Sustar
- Department of Genome Sciences, University of Washington, Foege Bldg. S-250, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
| | - Liesl G Strand
- Department of Genome Sciences, University of Washington, Foege Bldg. S-250, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
| | - Sandra G Zimmerman
- Department of Genome Sciences, University of Washington, Foege Bldg. S-250, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
| | - Celeste A Berg
- Department of Genome Sciences, University of Washington, Foege Bldg. S-250, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
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Hong DE, Yu JE, Lee JW, Son DJ, Lee HP, Kim Y, Chang JY, Lee DW, Lee WK, Yun J, Han SB, Hwang BY, Hong JT. A Natural CHI3L1-Targeting Compound, Ebractenoid F, Inhibits Lung Cancer Cell Growth and Migration and Induces Apoptosis by Blocking CHI3L1/AKT Signals. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010329. [PMID: 36615523 PMCID: PMC9822003 DOI: 10.3390/molecules28010329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/24/2022] [Accepted: 12/26/2022] [Indexed: 01/04/2023]
Abstract
Our previous big data analyses reported a strong association between CHI3L1 expression and lung tumor development. In this present study, we investigated whether a CHI3L1-inhibiting natural compound, ebractenoid F, inhibits lung cancer cell growth and migration and induces apoptosis. Ebractenoid F concentration-dependently (0, 17, 35, 70 µM) and significantly inhibited the proliferation and migration of A549 and H460 lung cancer cells and induced apoptosis. In the mechanism study, we found that ebractenoid F bound to CHI3L1 and suppressed CHI3L1-associated AKT signaling. Combined treatment with an AKT inhibitor, LY294002, and ebractenoid F synergistically decreased the expression of CHI3L1. Moreover, the combination treatment further inhibited the growth and migration of lung cancer cells and further induced apoptosis, as well as the expression levels of apoptosis-related proteins. Thus, our data demonstrate that ebractenoid F may serve as a potential anti-lung cancer compound targeting CHI3L1-associated AKT signaling.
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Affiliation(s)
- Da Eun Hong
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Ji Eun Yu
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Jin Woo Lee
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Dong Ju Son
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Hee Pom Lee
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Yuri Kim
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Ju Young Chang
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Dong Won Lee
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Won Kyu Lee
- Department of New Drug Development Center, Osong Medical Innovation Foundation (KBio Health), Cheongju 28644, Republic of Korea
| | - Jaesuk Yun
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Sang Bae Han
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Bang Yeon Hwang
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
| | - Jin Tae Hong
- Medical Research Center, College of Pharmacy, Chungbuk National University, Osongsaengmyeong 1-ro, 194-21, Osong-eup, Heungduk-gu, Cheongju 28160, Republic of Korea
- Correspondence: ; Tel.: +82-43-261-2813; Fax: +82-43-268-2732
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Xue L, Chu W, Wan F, Wu P, Zhao X, Ma L, She Y, Li C, Li Y. YKL-39 is an independent prognostic factor in gastric adenocarcinoma and is associated with tumor-associated macrophage infiltration and angiogenesis. World J Surg Oncol 2022; 20:362. [DOI: 10.1186/s12957-022-02830-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 11/04/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Gastric cancer has a high incidence and mortality rate. Angiogenesis is necessary for tumor infiltration and metastasis and affects patient prognosis. YKL-39 has monocyte chemotactic activity and pro-angiogenic activity in some tumors. In this study, we investigated the relationship between YKL-39 and tumor-associated macrophages and microangiogenesis in gastric cancer to determine its potential as a prognostic biomarker.
Materials and methods
A total of 119 patients with gastric cancer who had undergone gastrectomy at the 940th Hospital of the Joint Security Force between 2014 and 2018 were included in this study. We assayed the protein expression of YKL-39, CD68, and CD34 by immunohistochemistry in tissues of 119 patients with gastric cancer, as well as the intracellular expression of YKL-39 and CD68 by immunofluorescence. Data were analyzed with SPSS Statistics 25.0 to explore the impact of expression of YKL-39, CD68, and CD34 in gastric cancer patients and the relationship among them.
Results
Our results show that YKL-39 was expressed in both the nucleus and cytoplasm of gastric cancer cells and tumor mesenchyme. YKL-39 protein expression was associated with the depth of tumor infiltration, lymph node metastasis, and TNM stage; CD68 protein expression was associated with lymph node metastasis and TNM stage; CD34 protein expression was not associated with clinicopathological characteristics. Expression of YKL-39 was positively correlated with CD68 and CD34 (p < 0.001), and high expression of YKL-39 was associated with poor prognosis (p < 0.05).
Conclusion
In gastric cancer, YKL-39 expression is positively correlated with the degree of tumor-associated macrophage infiltration and angiogenesis, and is a potential prognostic marker for gastric cancer.
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Ogunkolade BW, Adaikalakoteswari A, Cardoso SR, Lowe R, Patel N, Rakyan V, Finer S, Wabitsch M, Saravanan P, Tripathi G, Bochukova E, Hitman GA. An integrative epi-transcriptomic approach identifies the human cartilage chitinase 3-like protein 2 ( CHI3L2) as a potential mediator of B12 deficiency in adipocytes. Epigenetics 2021; 17:1219-1233. [PMID: 34818986 PMCID: PMC9542961 DOI: 10.1080/15592294.2021.2003043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Vitamin B12 has multiple biochemical functions including in the one-carbon cycle generating a methyl group for DNA methylation, and metabolism of fatty acids and amino acids to generate energy via the citric acid cycle. The aim of our study was to use a combined epigenomic and transcriptomic approach to identify novel genes mediating the effect of B12 on adipogenesis.Human pre-adipocytes (CHUB-S7) were treated with a range of B12 (0-500 nM) concentrations from the day of cell seeding until harvesting in discovery and validation experiments prior to genome-wide methylation analysis using the Illumina HumanMethylation 450Beadchip. For transcriptomic analysis, RNA-seq libraries were run on the Illumina HiSeq 2500. To further investigate the expression of any genes on human adipogenesis, a second human preadipocyte strain was studied (SGBS) by real-time quantitative PCR (qRT-PCR).A combined epigenetic and transcriptomic approach in differentiated human pre-adipocyte cell line, CHUB-S7, identified that the Human cartilage chitinase 3-like protein 2 (CHI3L2) gene was hypo-methylated and had increased expression in low B12 conditions. Furthermore, there was an approximately 1000-fold increase in CHI3L2 expression in the early days of adipocyte differentiation, which paralleled an increase of lipid droplets in differentiated SGBS cells and an increased expression level of markers of mature adipocytes.In summary, we have identified a potential role of the human cartilage chitinase 3-like protein 2 (CHI3L2) in adipocyte function in the presence of low B12 levels.
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Affiliation(s)
- B William Ogunkolade
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Antonysunil Adaikalakoteswari
- Populations, Evidence, and Technologies, Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK.,Department of Bioscience, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Shirleny Romualdo Cardoso
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Rob Lowe
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nisha Patel
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vardhman Rakyan
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sarah Finer
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Martin Wabitsch
- Division of Paediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany
| | - Ponnusamy Saravanan
- Populations, Evidence, and Technologies, Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Gyanendra Tripathi
- Populations, Evidence, and Technologies, Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK.,Human Sciences Research Centre, University of Derby, Derby, UK
| | - Elena Bochukova
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Graham A Hitman
- Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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8
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Novikova IV, Zhou M, Evans JE, Du C, Parra M, Kim DN, VanAernum ZL, Shaw JB, Hellmann H, Wysocki VH. Tunable Heteroassembly of a Plant Pseudoenzyme-Enzyme Complex. ACS Chem Biol 2021; 16:2315-2325. [PMID: 34520180 PMCID: PMC9979268 DOI: 10.1021/acschembio.1c00475] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme-enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B6 production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme-enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2-PDX1.3 pseudoenzyme-enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2-PDX1.3 interactions. Our results provide a new model of pseudoenzyme-enzyme interactions and their native heterogeneity.
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Affiliation(s)
- Irina V. Novikova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - James E. Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States; School of Biological Sciences, Washington State University, Pullman, Washington 99164, United States
| | - Chen Du
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States; Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Marcelina Parra
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, United States
| | - Doo Nam Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States; Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, United States
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States; Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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Lee YS, Yu JE, Kim KC, Lee DH, Son DJ, Lee HP, Jung JK, Kim ND, Ham YW, Yun J, Han SB, Hong JT. A small molecule targeting CHI3L1 inhibits lung metastasis by blocking IL-13Rα2-mediated JNK-AP-1 signals. Mol Oncol 2021; 16:508-526. [PMID: 34758182 PMCID: PMC8763653 DOI: 10.1002/1878-0261.13138] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 09/07/2021] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Abstract
Our previous big data analyses showed a high level of association between chitinase 3 like1 (CHI3L1) expression and lung tumor development. In the present study, we investigated whether a CHI3L1‐inhibiting chemical, 2‐({3‐[2‐(1‐cyclohexen‐1‐yl)ethyl]‐6,7‐dimethoxy‐4‐oxo‐3,4‐dihydro‐2‐quinazolinyl}sulfanyl)‐N‐(4‐ethylphenyl)butanamide (K284), could inhibit lung metastasis and studied its mechanism of action. We investigated the antitumor effect of K284 both in vitro and in vivo. K284 (0.5 mg·kg−1 body weight) significantly inhibited lung metastasis in in vivo models after injection of murine melanoma cells (B16F10) or adenocarcinomic human alveolar basal epithelial cells (A549). K284 significantly and concentration‐dependently also inhibited cancer cell proliferation and migration in the A549 and H460 lung cancer cell lines. We found that the binding of K284 to the chitin‐binding domain (CBD) of CHI3L1 prevented the binding of CHI3L1 to its receptor, interleukin‐13 receptor subunit alpha‐2 (IL‐13Rα2), thereby suppressing the CHI3L1 signal. This blocking of the CHI3L1‐IL‐13Rα2 signal caused the inhibition of c‐Jun N‐terminal kinase (JNK)‐activator protein 1 (AP‐1) signals, resulting in the prevention of lung metastasis and cancer cell growth. Our data demonstrate that K284 may serve as a potential candidate anticancer compound targeting CHI3L1.
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Affiliation(s)
- Yong Sun Lee
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Ji Eun Yu
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Ki Cheon Kim
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Dong Hun Lee
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Dong Ju Son
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Hee Pom Lee
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Jae-Kyung Jung
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | | | - Young Wan Ham
- Department of Chemistry, Utah Valley University, Orem, UT, USA
| | - Jaesuk Yun
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Sang-Bae Han
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Jin Tae Hong
- College of Pharmacy & Medical Research Center, Chungbuk National University, Cheongju, Korea
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10
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Jeon SH, Lee YS, Yeo IJ, Lee HP, Yoon J, Son DJ, Han SB, Hong JT. Inhibition of Chitinase-3-like-1 by K284-6111 Reduces Atopic Skin Inflammation via Repressing Lactoferrin. Immune Netw 2021; 21:e22. [PMID: 34277112 PMCID: PMC8263211 DOI: 10.4110/in.2021.21.e22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Chitinase-3-like-1 (CHI3L1) is known to induce inflammation in the progression of allergic diseases. Previous our studies revealed that 2-({3-[2-(1-cyclohexen-1-yl)ethyl]-6,7-dimethoxy-4-oxo-3,4-dihydro-2-quinazolinyl}sulfanyl)-N-(4-ethylphenyl)butanamide (K284-6111; K284), the CHI3L1 inhibiting compound, has the anti-inflammatory effect on neuroinflammation. In this study, we investigated that K284 treatment could inhibit the development of atopic dermatitis (AD). To identify the effect of K284, we used phthalic anhydride (5% PA)-induced AD animal model and in vitro reconstructed human skin model. We analyzed the expression of AD-related cytokine mediators and NF-κB signaling by Western blotting, ELISA and quantitative real-time PCR. Histological analysis showed that K284 treatment suppressed PA-induced epidermal thickening and infiltration of mast cells. K284 treatment also reduced PA-induced release of inflammatory cytokines. In addition, K284 treatment inhibited the expression of NF-κB activity in PA-treated skin tissues and TNF-α and IFN-γ-treated HaCaT cells. Protein-association network analysis indicated that CHI3L1 is associated with lactoferrin (LTF). LTF was elevated in PA-treated skin tissues and TNF-α and IFN-γ-induced HaCaT cells. However, this expression was reduced by K284 treatment. Knockdown of LTF decreased the expression of inflammatory cytokines in TNF-α and IFN-γ-induced HaCaT cells. Moreover, anti-LTF antibody treatment alleviated AD development in PA-induced AD model. Our data demonstrate that CHI3L1 targeting K284 reduces AD-like skin inflammation and K284 could be a promising therapeutic agent for AD by inhibition of LTF expression.
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Affiliation(s)
- Seong Hee Jeon
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Yong Sun Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - In Jun Yeo
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Hee Pom Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Jaesuk Yoon
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Dong Ju Son
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Sang-Bae Han
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
| | - Jin Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju, Korea
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11
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Ojha A, Zhang W. Characterization of gustatory receptor 7 in the brown planthopper reveals functional versatility. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 132:103567. [PMID: 33741431 DOI: 10.1016/j.ibmb.2021.103567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Insect pests consume tastants as their necessary energy and nutrient sources. Gustatory receptors play important roles in insect life and can form within an extremely complicated regulatory network. However, there are still many gustatory genes that have a significant impact on insect physiology, but their functional mechanism is still unknown. Here, we purified and characterized a gustatory receptor (protein) coding gene, NlGr7, from the brown planthopper (BPH) Nilaparvata lugens, which is an important insect pest of rice. Our results revealed that NlGr7 has an active association with various ligands, such as lectins, lipids (phospho- and sphingolipid) and copper. The mass-spectrometry result showed that NlGr7 is a sugar receptor, and NlGr7 is validated by different types of insoluble polysaccharides and a varied range of tastants. Further, we observed that NlGr7-bound ATP hydrolysed on the ATPase activity assay, which indicated that NlGr7 may be associated with important biological functions in the BPH. Furthermore, an injection of NlGr7 (protein), into newly emerged female adults of BPH, showed the reduced vitellogenin in ovary. The important NlGr7 for chemoreception has now been characterized in the BPH. We showed that NlGr7 in the BPH is required for various protein-ligands, as well as protein-sugars interactions, and for regulation of fecundity marker to play crucial roles in this pest. This study will provide valuable information for further functional studies of chemoreception mechanisms in this important agricultural pest.
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Affiliation(s)
- Abhishek Ojha
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
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12
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Mackel JJ, Garth JM, Jones M, Ellis DA, Blackburn JP, Yu Z, Matalon S, Curtiss M, Lund FE, Hastie AT, Meyers DA, Steele C. Chitinase 3-like-1 protects airway function despite promoting type 2 inflammation during fungal-associated allergic airway inflammation. Am J Physiol Lung Cell Mol Physiol 2021; 320:L615-L626. [PMID: 33533316 DOI: 10.1152/ajplung.00528.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Joseph J Mackel
- Department of Medicine, University of Alabama Birmingham, Birmingham, Alabama
| | - Jaleesa M Garth
- Department of Medicine, University of Alabama Birmingham, Birmingham, Alabama
| | - MaryJane Jones
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana
| | - Diandra A Ellis
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana
| | | | - Zhihong Yu
- Department of Medicine, University of Alabama Birmingham, Birmingham, Alabama
| | - Sadis Matalon
- Department of Medicine, University of Alabama Birmingham, Birmingham, Alabama
| | - Miranda Curtiss
- Department of Medicine, University of Alabama Birmingham, Birmingham, Alabama.,Department of Microbiology, University of Alabama Birmingham, Birmingham, Alabama
| | - Frances E Lund
- Department of Microbiology, University of Alabama Birmingham, Birmingham, Alabama
| | - Annette T Hastie
- Department of Medicine, Wake Forest University, Winston-Salem, North Carolina
| | | | - Chad Steele
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana
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13
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Raposo CD, Canelas AB, Barros MT. Human Lectins, Their Carbohydrate Affinities and Where to Find Them. Biomolecules 2021; 11:188. [PMID: 33572889 PMCID: PMC7911577 DOI: 10.3390/biom11020188] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/02/2021] [Accepted: 01/26/2021] [Indexed: 12/20/2022] Open
Abstract
Lectins are a class of proteins responsible for several biological roles such as cell-cell interactions, signaling pathways, and several innate immune responses against pathogens. Since lectins are able to bind to carbohydrates, they can be a viable target for targeted drug delivery systems. In fact, several lectins were approved by Food and Drug Administration for that purpose. Information about specific carbohydrate recognition by lectin receptors was gathered herein, plus the specific organs where those lectins can be found within the human body.
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Affiliation(s)
- Cláudia D. Raposo
- LAQV-Requimte, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
| | - André B. Canelas
- Glanbia-AgriChemWhey, Lisheen Mine, Killoran, Moyne, E41 R622 Tipperary, Ireland;
| | - M. Teresa Barros
- LAQV-Requimte, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
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14
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Warkentin R, Kwan DH. Resources and Methods for Engineering "Designer" Glycan-Binding Proteins. Molecules 2021; 26:E380. [PMID: 33450899 PMCID: PMC7828330 DOI: 10.3390/molecules26020380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/04/2021] [Accepted: 01/10/2021] [Indexed: 12/11/2022] Open
Abstract
This review provides information on available methods for engineering glycan-binding proteins (GBP). Glycans are involved in a variety of physiological functions and are found in all domains of life and viruses. Due to their wide range of functions, GBPs have been developed with diagnostic, therapeutic, and biotechnological applications. The development of GBPs has traditionally been hindered by a lack of available glycan targets and sensitive and selective protein scaffolds; however, recent advances in glycobiology have largely overcome these challenges. Here we provide information on how to approach the design of novel "designer" GBPs, starting from the protein scaffold to the mutagenesis methods, selection, and characterization of the GBPs.
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Affiliation(s)
- Ruben Warkentin
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - David H. Kwan
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
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15
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Glycoside hydrolase family 18 chitinases: The known and the unknown. Biotechnol Adv 2020; 43:107553. [DOI: 10.1016/j.biotechadv.2020.107553] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/09/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
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16
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Kzhyshkowska J, Larionova I, Liu T. YKL-39 as a Potential New Target for Anti-Angiogenic Therapy in Cancer. Front Immunol 2020; 10:2930. [PMID: 32038607 PMCID: PMC6988383 DOI: 10.3389/fimmu.2019.02930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
YKL-39 belongs to the evolutionarily conserved family of Glyco_18-containing proteins composed of chitinases and chitinase-like proteins. Chitinase-like proteins (CLPs) are secreted lectins that lack hydrolytic activity due to the amino acid substitutions in their catalytic domain and combine the functions of cytokines and growth factors. One of the major cellular sources that produce CLPs in various pathologies, including cancer, are macrophages. Monocytes recruited to the tumor site and programmed by tumor cells differentiate into tumor-associated macrophages (TAMs), which are the primary source of pro-angiogenic factors. Tumor angiogenesis is a crucial process for supplying rapidly growing tumors with essential nutrients and oxygen. We recently determined that YKL-39 is produced by tumor-associated macrophages in breast cancer. YKL-39 acts as a strong chemotactic factor for monocytes and stimulates angiogenesis. Chemotherapy is a common strategy to reduce tumor size and aggressiveness before surgical intervention, but chemoresistance, resulting in the relapse of tumors, is a common clinical problem that is critical for survival in cancer patients. Accumulating evidence indicates that TAMs are essential regulators of chemoresistance. We have recently found that elevated levels of YKL-39 expression are indicative of the efficiency of the metastatic process in patients who undergo neoadjuvant chemotherapy. We suggest YKL-39 as a new target for anti-angiogenic therapy that can be combined with neoadjuvant chemotherapy to reduce chemoresistance and inhibit metastasis in breast cancer patients.
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Affiliation(s)
- Julia Kzhyshkowska
- Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, University of Heidelberg, Mannheim, Germany
- German Red Cross Blood Service Baden-Württemberg—Hessen, Mannheim, Germany
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russia
| | - Irina Larionova
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russia
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Tengfei Liu
- Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, University of Heidelberg, Mannheim, Germany
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17
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Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA. Emerging concepts in pseudoenzyme classification, evolution, and signaling. Sci Signal 2019; 12:eaat9797. [PMID: 31409758 DOI: 10.1126/scisignal.aat9797] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 21st century is witnessing an explosive surge in our understanding of pseudoenzyme-driven regulatory mechanisms in biology. Pseudoenzymes are proteins that have sequence homology with enzyme families but that are proven or predicted to lack enzyme activity due to mutations in otherwise conserved catalytic amino acids. The best-studied pseudoenzymes are pseudokinases, although examples from other families are emerging at a rapid rate as experimental approaches catch up with an avalanche of freely available informatics data. Kingdom-wide analysis in prokaryotes, archaea and eukaryotes reveals that between 5 and 10% of proteins that make up enzyme families are pseudoenzymes, with notable expansions and contractions seemingly associated with specific signaling niches. Pseudoenzymes can allosterically activate canonical enzymes, act as scaffolds to control assembly of signaling complexes and their localization, serve as molecular switches, or regulate signaling networks through substrate or enzyme sequestration. Molecular analysis of pseudoenzymes is rapidly advancing knowledge of how they perform noncatalytic functions and is enabling the discovery of unexpected, and previously unappreciated, functions of their intensively studied enzyme counterparts. Notably, upon further examination, some pseudoenzymes have previously unknown enzymatic activities that could not have been predicted a priori. Pseudoenzymes can be targeted and manipulated by small molecules and therefore represent new therapeutic targets (or anti-targets, where intervention should be avoided) in various diseases. In this review, which brings together broad bioinformatics and cell signaling approaches in the field, we highlight a selection of findings relevant to a contemporary understanding of pseudoenzyme-based biology.
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Affiliation(s)
- António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sayoni Das
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Natalie Dawson
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Rossana Zaru
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Christine Orengo
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, Molecular and Cellular Biology, Faculty of Biological Sciences, Astbury Building, Room 8.109, University of Leeds, Leeds LS2 9JT, UK
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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18
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Yeo IJ, Lee CK, Han SB, Yun J, Hong JT. Roles of chitinase 3-like 1 in the development of cancer, neurodegenerative diseases, and inflammatory diseases. Pharmacol Ther 2019; 203:107394. [PMID: 31356910 DOI: 10.1016/j.pharmthera.2019.107394] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2019] [Indexed: 02/07/2023]
Abstract
Chitinase 3-like 1 (CHI3L1) is a secreted glycoprotein that mediates inflammation, macrophage polarization, apoptosis, and carcinogenesis. The expression of CHI3L1 is strongly increased by various inflammatory and immunological conditions, including rheumatoid arthritis, multiple sclerosis, Alzheimer's disease, and several cancers. However, its physiological and pathophysiological roles in the development of cancer and neurodegenerative and inflammatory diseases remain unclear. Several studies have reported that CHI3L1 promotes cancer proliferation, inflammatory cytokine production, and microglial activation, and that multiple receptors, such as advanced glycation end product, syndecan-1/αVβ3, and IL-13Rα2, are involved. In addition, the pro-inflammatory action of CHI3L1 may be mediated via the protein kinase B and phosphoinositide-3 signaling pathways and responses to various pro-inflammatory cytokines, including tumor necrosis factor-α, interleukin-1β, interleukin-6, and interferon-γ. Therefore, CHI3L1 could contribute to a vast array of inflammatory diseases. In this article, we review recent findings regarding the roles of CHI3L1 and suggest therapeutic approaches targeting CHI3L1 in the development of cancers, neurodegenerative diseases, and inflammatory diseases.
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Affiliation(s)
- In Jun Yeo
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Chong-Kil Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Sang-Bae Han
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Jaesuk Yun
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si, Chungbuk 28160, Republic of Korea.
| | - Jin Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si, Chungbuk 28160, Republic of Korea.
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19
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Singh S, Choudhary S, Anand V, Jaswal S, Verma AK, Kumar S, Kaushik JK, Mohanty AK. New insights into the catalytic inactivity of mammary gland protein-40, a chitinase-like protein expressed during mammary gland involution. Mol Biol Rep 2019; 46:2243-2257. [DOI: 10.1007/s11033-019-04679-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
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Kumar A, Zhang KYJ. Human Chitinases: Structure, Function, and Inhibitor Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:221-251. [PMID: 31102249 DOI: 10.1007/978-981-13-7318-3_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chitinases are glycosyl hydrolases that hydrolyze the β-(1-4)-linkage of N-acetyl-D-glucosamine units present in chitin polymers. Chitinases are widely distributed enzymes and are present in a wide range of organisms including insects, plants, bacteria, fungi, and mammals. These enzymes play key roles in immunity, nutrition, pathogenicity, and arthropod molting. Humans express two chitinases, chitotriosidase 1 (CHIT1) and acid mammalian chitinase (AMCase) along with several chitinase-like proteins (CLPs). Human chitinases are reported to play a protective role against chitin-containing pathogens through their capability to degrade chitin present in the cell wall of pathogens. Now, human chitinases are gaining attention as the key players in innate immune response. Although the exact mechanism of their role in immune response is not known, studies in recent years begin to relate chitin recognition and degradation with the activation of signaling pathways involved in inflammation. The roles of both CHIT1 and AMCase in the development of various diseases have been revealed and several classes of inhibitors have been developed. However, a clear understanding could not be established due to complexities in the design of the right experiment for studying the role of human chitinase in various diseases. In this chapter, we will first outline the structural features of CHIT1 and AMcase. We will then review the progress in understanding the role of human chitinases in the development of various diseases. Finally, we will summarize the inhibitor discovery efforts targeting both CHIT1 and AMCase.
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Affiliation(s)
- Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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Choi JY, Yeo IJ, Kim KC, Choi WR, Jung JK, Han SB, Hong JT. K284-6111 prevents the amyloid beta-induced neuroinflammation and impairment of recognition memory through inhibition of NF-κB-mediated CHI3L1 expression. J Neuroinflammation 2018; 15:224. [PMID: 30098604 PMCID: PMC6087013 DOI: 10.1186/s12974-018-1269-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Alzheimer's disease, which is pathologically characterized by an excessive accumulation of amyloid beta (Aβ) fibrils, is a degenerative brain disease and the most common cause of dementia. In a previous study, it was reported that an increased level of CHI3L1 in plasma was found in AD patients. We investigated the inhibitory effect of 2-({3-[2-(1-cyclohexen-1-yl)ethyl]-6,7-dimethoxy-4-oxo-3,4-dihydro-2-quinazolinyl}sulfanyl)-N-(4-ethylphenyl)butanamide (K284-6111), an inhibitor of chitinase 3 like 1 (CHI3L1), on memory impairment in Aβ1-42-infused mice, and microglial BV-2 cells and astrocytes. METHODS We examined whether K284-6111 (3 mg/kg given orally for 4 weeks) prevents amyloidogenesis and memory loss in Aβ1-42-induced AD mice model. After intracerebroventrical (ICV) infusion of Aβ1-42 for 14 days, the cognitive function was assessed by the Morris water maze test and passive avoidance test. K284-6111 treatment was found to reduce Aβ1-42-induced memory loss. RESULTS A memory recovery effect was found to be associated with the reduction of Aβ1-42-induced expression of inflammatory proteins (iNOS, COX-2, GFAP, and Iba-1) and the suppression of CHI3L1 expression in the brain. Additionally, K284-6111 reduced Aβ1-42-induced β-secretase activity and Aβ generation. Lipopolysaccharide (LPS)-induced (1 μg/mL) expression of inflammatory (COX-2, iNOS, GFAP, Iba-1) and amyloidogenic proteins (APP, BACE1) were decreased in microglial BV-2 cells and cultured astrocytes by the K284-6111 treatment (0.5, 1, and 2 μM). Moreover, K284-6111 treatment suppressed p50 and p65 translocation into the nucleus, and phosphorylation of IκB in vivo and in vitro. CONCLUSION These results suggest that CHI3L1 inhibitor could be an applicable intervention drug in amyloidogenesis and neuroinflammation, thereby preventing memory dysfunction via inhibition of NF-κB.
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Affiliation(s)
- Ji Yeon Choi
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju, Chungbuk 28160 Republic of Korea
| | - In Jun Yeo
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju, Chungbuk 28160 Republic of Korea
| | - Ki Cheon Kim
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju, Chungbuk 28160 Republic of Korea
| | - Won Rack Choi
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju, Chungbuk 28160 Republic of Korea
| | - Jae-Kyung Jung
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju, Chungbuk 28160 Republic of Korea
| | - Sang-Bae Han
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju, Chungbuk 28160 Republic of Korea
| | - Jin Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Osong-eup, Heungdeok-gu, Cheongju, Chungbuk 28160 Republic of Korea
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22
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Steven J. VD, Richard M. L. Chitins and chitinase activity in airway diseases. J Allergy Clin Immunol 2018; 142:364-369. [PMID: 29959948 PMCID: PMC6078791 DOI: 10.1016/j.jaci.2018.06.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/19/2018] [Accepted: 06/22/2018] [Indexed: 01/04/2023]
Abstract
Chitin, one of the most abundant biopolymers on Earth, is bound and degraded by chitinases, specialized enzymes that are similarly widespread in nature. Chitin catabolism affects global carbon and nitrogen cycles through a host of diverse biological processes, but recent work has focused attention on systems of chitin recognition and degradation conserved in mammals, connecting an ancient pathway of polysaccharide processing to human diseases influenced by persistent immune triggering. Here we review current advances in our understanding of how chitin-chitinase interactions affect mucosal immune feedback mechanisms essential to maintaining homeostasis and organ health.
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Affiliation(s)
- Van Dyken Steven J.
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO USA.
| | - Locksley Richard M.
- Howard Hughes Medical Institute, Departments of Medicine and Microbiology / Immuology, University of California San Francisco, San Francisco, CA, USA.
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23
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Soysa HSM, Schulte A, Suginta W. Functional analysis of an unusual porin-like channel that imports chitin for alternative carbon metabolism in Escherichia coli. J Biol Chem 2017; 292:19328-19337. [PMID: 28972167 DOI: 10.1074/jbc.m117.812321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/22/2017] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli have the genetic potential to use chitin as a carbon source in the absence of glucose, importing it via the chitin-uptake channel EcChiP for processing by the glucosamine catabolic pathway. The chip gene is usually not expressed when E. coli are grown on glucose-enriched nutrients, providing a general regulatory mechanism for the pathway. EcChiP is unusual in that it is homologous to porins and monomeric instead of trimeric, the typical form of sugar-specific channels, making it unclear how this channel operates. We recently reported that EcChiP could form a stable channel in lipid membranes and that the channel is specific for chitooligosaccharides. This report describes the biophysical nature of sugar-channel interactions and the kinetics of sugar association and dissociation. Titrating EcChiP with chitohexaose resulted in protein fluorescence enhancement in a concentration-dependent manner, yielding a binding constant of 2.9 × 105 m-1, consistent with the value of 2.5 × 105 m-1 obtained from isothermal titration microcalorimetry. Analysis of the integrated heat change suggested that the binding process was endothermic and driven by entropy. Single-channel recordings confirmed the voltage dependence of the penetration of chitohexaose molecules into and their release from EcChiP. Once inside the pore, the sugar release rate (koff) from the affinity site increased with elevated voltage, regardless of the side of sugar addition. Our findings revealed distinct thermodynamic and kinetic features of the activity of sugar-specific EcChiP and advance our knowledge of the physiological possibility of chitin utilization by non-chitinolytic bacteria.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and
| | - Albert Schulte
- the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and .,the Center of Excellence in Advanced Functional Materials, Suranaree University of Technology Nakhon Ratchasima 30000, Thailand and
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24
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Murphy JM, Mace PD, Eyers PA. Live and let die: insights into pseudoenzyme mechanisms from structure. Curr Opin Struct Biol 2017; 47:95-104. [PMID: 28787627 DOI: 10.1016/j.sbi.2017.07.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/30/2017] [Accepted: 07/20/2017] [Indexed: 12/22/2022]
Abstract
Pseudoenzymes were first described more than 50 years ago, when it was recognised that a subset of proteins that are structurally homologous to active enzymes lack amino acids necessary for catalytic activity. Recently, interest in pseudoenzymes has surged as it has become apparent that they constitute ∼10% of proteomes and perform essential metabolic and signalling functions that can be experimentally distinguished from catalytic outputs of enzymes. Here, we highlight recent structural studies of pseudoenzymes, which have revealed the molecular basis for roles as allosteric regulators of conventional enzymes, as molecular switches and integrators, as hubs for assembling protein complexes, and as competitors of substrate availability and holoenzyme assembly. As structural studies continue to illuminate pseudoenzyme molecular mechanisms, we anticipate that our knowledge of the breadth of their biological functions will expand in parallel.
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Affiliation(s)
- James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia.
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
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25
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Hamilton G, Rath B. Circulating tumor cell interactions with macrophages: implications for biology and treatment. Transl Lung Cancer Res 2017; 6:418-430. [PMID: 28904886 DOI: 10.21037/tlcr.2017.07.04] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer and metastasis are closely associated with inflammation. Macrophages are important effector cells in enhancing tumor proliferation, invasion and providing protection against the immune system. Despite advanced knowledge of tumor-macrophage interactions, the role of macrophages in emergence and invasion of circulating tumor cells (CTCs) is not known. A series of six CTC cell lines have been derived from blood of patients with extensive disease small cell lung cancer (ED-SCLC) in our lab, most likely representing a homogenous cell population of the actual metastasis-initiating cells (MIC) of CTCs. SCLC has an unfavorable prognosis due to rapid dissemination and early chemoresistant relapses. SCLC CTCs recruit macrophages and elicit secretion of various cytokines and the six CTC lines express chitinase-3-like-1 (CHI3L1), vascular endothelial growth factor (VEGF) and matrix metalloproteinase-9 (MMP9) in abundance. CHI3L1 is cytokine/growth factor expressed in inflammation and cancer and found to be correlated to metastasis and a dismal prognosis. In conclusion, SCLC CTCs have acquired the essential means for aggressiveness and invasion in a tumor microenvironment specifically shaped by macrophages and inflammation.
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Affiliation(s)
- Gerhard Hamilton
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Barbara Rath
- Department of Surgery, Medical University of Vienna, Vienna, Austria
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26
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Komi DEA, Kazemi T, Bussink AP. New Insights Into the Relationship Between Chitinase-3-Like-1 and Asthma. Curr Allergy Asthma Rep 2017; 16:57. [PMID: 27438466 DOI: 10.1007/s11882-016-0637-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW CHI3L1 (also known as YKL-40), a member of "mammalian chitinase-like proteins," is a serum protein lacking enzymatic activity. Although the protein is highly conserved in mammals, a consensus regarding its role in human pathologies is currently lacking. In an attempt to shed light on the many physiological functions of the protein, specifically with regard to asthma, a comprehensive overview of recent studies is provided. RECENT FINDINGS In asthma, CHI3L1 is secreted from macrophages and airway epithelial cells through an IL-13 related mechanism. Th2-associated inflammatory responses due to allergen exposure, resulting in airway hyper-responsiveness and smooth muscle contraction, play a role in tissue remodeling. The importance of CHI3L1 in initiation and development of asthma is not limited to its involvement in highly orchestrated events of inflammatory cytokines but further research is needed for further elucidation. Levels of the protein are associated with severity for numerous pathologies, including asthma, suggesting limited specificity as a biomarker.
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Affiliation(s)
- Daniel Elieh Ali Komi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, International Branch of Aras, Tabriz University of Medical Sciences, Tabriz, Iran.,Student's Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tohid Kazemi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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27
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Van Dyken SJ, Liang HE, Naikawadi RP, Woodruff PG, Wolters PJ, Erle DJ, Locksley RM. Spontaneous Chitin Accumulation in Airways and Age-Related Fibrotic Lung Disease. Cell 2017; 169:497-509.e13. [PMID: 28431248 DOI: 10.1016/j.cell.2017.03.044] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 02/22/2017] [Accepted: 03/28/2017] [Indexed: 01/21/2023]
Abstract
The environmentally widespread polysaccharide chitin is degraded and recycled by ubiquitous bacterial and fungal chitinases. Although vertebrates express active chitinases from evolutionarily conserved loci, their role in mammalian physiology is unclear. We show that distinct lung epithelial cells secrete acidic mammalian chitinase (AMCase), which is required for airway chitinase activity. AMCase-deficient mice exhibit premature morbidity and mortality, concomitant with accumulation of environmentally derived chitin polymers in the airways and expression of pro-fibrotic cytokines. Over time, these mice develop spontaneous pulmonary fibrosis, which is ameliorated by restoration of lung chitinase activity by genetic or therapeutic approaches. AMCase-deficient epithelial cells express fibrosis-associated gene sets linked with cell stress pathways. Mice with lung fibrosis due to telomere dysfunction and humans with interstitial lung disease also accumulate excess chitin polymers in their airways. These data suggest that altered chitin clearance could exacerbate fibrogenic pathways in the setting of lung diseases characterized by epithelial cell dysfunction.
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Affiliation(s)
- Steven J Van Dyken
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hong-Erh Liang
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ram P Naikawadi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Prescott G Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Paul J Wolters
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David J Erle
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Richard M Locksley
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
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28
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Murphy JM, Farhan H, Eyers PA. Bio-Zombie: the rise of pseudoenzymes in biology. Biochem Soc Trans 2017; 45:537-544. [PMID: 28408493 DOI: 10.1042/bst20160400] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/19/2017] [Accepted: 02/21/2017] [Indexed: 11/17/2022]
Abstract
Pseudoenzymes are catalytically dead counterparts of enzymes. Despite their first description some 50 years ago, the importance and functional diversity of these 'fit-for-purpose' polypeptides is only now being appreciated. Pseudoenzymes have been identified throughout all the kingdoms of life and, owing to predicted deficits in enzyme activity due to the absence of catalytic residues, have been variously referred to as pseudoenzymes, non-enzymes, dead enzymes, prozymes or 'zombie' proteins. An important goal of the recent Biochemical Society Pseudoenzymes-focused meeting was to explore the functional and evolutionary diversity of pseudoenzymes and to begin to evaluate their functions in biology, including cell signalling and metabolism. Here, we summarise the impressive breadth of enzyme classes that are known to have pseudoenzyme counterparts and present examples of known cellular functions. We predict that the next decades will represent golden years for the analysis of pseudoenzymes.
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Affiliation(s)
- James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Hesso Farhan
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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29
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The Effects of Ferulic Acid Against Oxidative Stress and Inflammation in Formaldehyde-Induced Hepatotoxicity. Inflammation 2017; 39:1377-86. [PMID: 27235018 DOI: 10.1007/s10753-016-0369-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This study was designed to elucidate the protective effects of ferulic acid (FA) on formaldehyde-induced hepatotoxicity by measuring some routine biochemical parameters, cytokine levels, and oxidative stress-related parameters in addition to YKL-40 in male Wistar albino rats. Tissue superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px) activities, and tissue malondialdehyde (MDA) levels were measured. Also, serum YKL-40, TNF-α, IL-6, IL-1β, IL-8, total protein, albumin, total bilirubin concentrations, and AST, ALT, ALP, and LDH activities were measured. Histological specimens were examined in light microscopy. Formaldehyde significantly increased tissue MDA, and serum cytokine levels and also decreased activities of antioxidant enzymes. FA treatment decreased MDA and cytokine levels and increased activities of antioxidant enzymes. FA also alleviated degeneration due to formaldehyde toxicity. We suggested that FA can be used as a promising hepatoprotective agent against formaldehyde toxicity because of the obvious beneficial effects on oxidative stress parameters.
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30
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Abd El-Fattah AA, Sadik NAH, Shaker OG, Kamal AM. Are SMAD7 rs4939827 and CHI3L1 rs4950928 polymorphisms associated with colorectal cancer in Egyptian patients? Tumour Biol 2016; 37:9387-97. [PMID: 26779637 DOI: 10.1007/s13277-016-4813-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/06/2016] [Indexed: 02/07/2023] Open
Abstract
A wide variety of genes have been associated with colorectal cancer (CRC) development and progression. The SMAD7 gene encodes an intracellular protein, which inhibits the transforming growth factor beta (TGF-β) signaling pathway, thereby having a key role in the control of neoplastic processes in various organs. The CHI3L1 gene encodes glycoprotein YKL-40, which plays a role in cell proliferation, anti-apoptosis, and angiogenesis. The present study aimed to evaluate the association of single nucleotide polymorphisms (SNPs) SMAD7 rs4939827 and CHI3L1 rs4950928, as well as circulating TGFβ-1 and YKL-40 levels with CRC in an Egyptian population of 77 CRC patients and 36 healthy controls. Polymorphisms in the SMAD7 rs4939827 and the CHI3L1 rs4950928 genes were determined using the real-time polymerase chain reaction (RT-PCR). Both the SMAD7 rs4939827 TT genotype and the CHI3L1 rs4950928 C allele were associated with the rectal but not the colon cancer. In addition, the C allele of both SMAD7 rs4939827 and CHI3L1 rs4950928 was associated with increased serum levels of TGF-β1 and YKL-40, respectively. In conclusion, our data suggest that SMAD7 rs4939827 and CHI3L1 rs4950928 SNPs have no significant association with CRC. A significant association of SNP in SMAD7 rs4939827 and CHI3L1 rs4950928 was revealed between the rectal cancer and colon cancer patients.
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Affiliation(s)
- Amal Ahmed Abd El-Fattah
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Eini Street, Cairo, 11562, Egypt
| | - Nermin Abdel Hamid Sadik
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Eini Street, Cairo, 11562, Egypt
| | - Olfat Gamil Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Kasr El-Eini Street, Cairo, Egypt
| | - Amal Mohamed Kamal
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Eini Street, Cairo, 11562, Egypt.
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31
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Di Rosa M, Distefano G, Zorena K, Malaguarnera L. Chitinases and immunity: Ancestral molecules with new functions. Immunobiology 2015; 221:399-411. [PMID: 26686909 DOI: 10.1016/j.imbio.2015.11.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/30/2015] [Indexed: 02/07/2023]
Abstract
Chitinases belonging to 18 glycosyl hydrolase family is an ancient gene family that is widely expressed from prokaryotes to eukaryotes. In humans, despite the absence of endogenous chitin, a number of Chitinases and Chitinase-like Proteins (C/CLPs) have been identified. Chitinases with enzymatic activity have a chitin binding domain containing six cysteine residues responsible for their binding to chitin. In contrast, CLPs do not contain such typical chitin-binding domains, but still can bind to chitin with high affinity. Molecular phylogenetic analyses suggest that active Chitinases result from an early gene duplication event. Further duplication events, followed by mutations leading to loss of chitinase activity, allowed evolution of the chi-lectins. For the majority of the mammalian chitinases the last decades have witnessed the appearance of a substantial number of studies describing their expression differentially regulated during more specific immunologic activities. It is becoming increasingly clear that their function is not exclusive to catalyse the hydrolysis of chitin producing pathogens, but include crucial role in bacterial infections and inflammatory diseases. Here we provide an overview of all family members to shed light on the mechanisms and molecular interactions of Chitinases and CLPs in relation to immune response regulation, in order to delineate their future utilization as diagnostic and prognostic markers for numerous diseases.
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Affiliation(s)
- Michelino Di Rosa
- Department of Biomedical and Biotechnology Sciences, University of Catania, Italy
| | - Gisella Distefano
- Department of Biomedical and Biotechnology Sciences, University of Catania, Italy
| | - Katarzyna Zorena
- Department of Immunobiology and Environment Microbiology Medical University of Gdańsk, Poland
| | - Lucia Malaguarnera
- Department of Biomedical and Biotechnology Sciences, University of Catania, Italy.
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32
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Hamilton G, Rath B, Ulsperger E. How to target small cell lung cancer. Oncoscience 2015; 2:684-92. [PMID: 26425658 PMCID: PMC4580060 DOI: 10.18632/oncoscience.212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/15/2015] [Indexed: 12/27/2022] Open
Abstract
Small cell lung cancer (SCLC) is a highly malignant disease with dismal prognosis. Although great progress has been made in investigating genetic aberrations and putative drivers of this tumor entity, the mechanisms of rapid dissemination and acquisition of drug resistance are not clear. The majority of SCLC cases are characterized by inactivation of the tumor suppressors p53 and retinoblastoma (Rb) and, therefore, interchangeable drivers will be difficult to target successfully. Access to pure cultures of SCLC circulating tumor cells (CTCs) and study of their tumor biology has revealed a number of new potential targets. Most important, expression of chitinase-3-like-1/YKL-40 (CHI3L1) which controls expression of vascular epithelial growth factor (VEGF) and matrix metalloproteinase-9 (MMP9) was newly described in these cells. The process switching CHI3L1-negative SCLC cells to CHI3L1-positive CTCs seems to be associated with cytokines released by inflammatory immune cells. Furthermore, these CTCs were found to promote monocyte-macrophage differentiation, most likely of the M2 tumor-promoting type, recently described to express PD-1 immune checkpoint antigen in SCLC. In conclusion, dissemination of SCLC seems to be linked to conversion of regular tumor cells to highly invasive CHI3L1-positive CTCs, which are protected by immune system suppression. Besides the classical targets VEGF, MMP-9 and PD-1, CHI3L1 constitutes a new possibly drugable molecule to retard down dissemination of SCLC cells, which may be similarly relevant for glioblastoma and other tumor entities.
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Affiliation(s)
- Gerhard Hamilton
- Ludwig Boltzmann Cluster of Translational Oncology, A-1090 Vienna, Austria
| | - Barbara Rath
- Ludwig Boltzmann Cluster of Translational Oncology, A-1090 Vienna, Austria
| | - Ernst Ulsperger
- Ludwig Boltzmann Cluster of Translational Oncology, A-1090 Vienna, Austria
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33
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Hamilton G, Rath B, Burghuber O. Chitinase-3-like-1/YKL-40 as marker of circulating tumor cells. Transl Lung Cancer Res 2015. [PMID: 26207216 DOI: 10.3978/j.issn.2218-6751.2015.04.04] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ex vivo expansion of circulating tumor cells (CTCs) of small cell lung cancer (SCLC) patients enabled systematic screening of secreted cytokines. Permanent CTC cultures of different patients shared secretion of chitinase-3-like-1 (CHI3L1)/YKL-40, known to be upregulated in a range of tumor entities and to be associated with increased metastasis and decreased survival. This protein lacks enzymatic activity and its mechanism of promoting tumor dissemination has not been resolved. Results from SCLC CTC cultures suggest CHI3L1 as marker and important effector of tumor cell dissemination in the peripheral blood. Furthermore, this protein may link chronic inflammation of the lung, chronic obstructive pulmonary disease (COPD) and lung cancer.
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Affiliation(s)
- Gerhard Hamilton
- 1 Ludwig Boltzmann Cluster of Translational Oncology, A-1090 Vienna, Austria ; 2 Ludwig Boltzmann Institute for COPD and Respiratory Epidemiology, 1140 Vienna, Austria
| | - Barbara Rath
- 1 Ludwig Boltzmann Cluster of Translational Oncology, A-1090 Vienna, Austria ; 2 Ludwig Boltzmann Institute for COPD and Respiratory Epidemiology, 1140 Vienna, Austria
| | - Otto Burghuber
- 1 Ludwig Boltzmann Cluster of Translational Oncology, A-1090 Vienna, Austria ; 2 Ludwig Boltzmann Institute for COPD and Respiratory Epidemiology, 1140 Vienna, Austria
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34
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Kesari P, Patil DN, Kumar P, Tomar S, Sharma AK, Kumar P. Structural and functional evolution of chitinase-like proteins from plants. Proteomics 2015; 15:1693-705. [PMID: 25728311 DOI: 10.1002/pmic.201400421] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 02/06/2023]
Abstract
The plant genome contains a large number of sequences that encode catalytically inactive chitinases referred to as chitinase-like proteins (CLPs). Although CLPs share high sequence and structural homology with chitinases of glycosyl hydrolase 18 (TIM barrel domain) and 19 families, they may lack the binding/catalytic activity. Molecular genetic analysis revealed that gene duplication events followed by mutation in the existing chitinase gene have resulted in the loss of activity. The evidences show that adaptive functional diversification of the CLPs has been achieved through alterations in the flexible regions than in the rigid structural elements. The CLPs plays an important role in the defense response against pathogenic attack, biotic and abiotic stress. They are also involved in the growth and developmental processes of plants. Since the physiological roles of CLPs are similar to chitinase, such mutations have led to plurifunctional enzymes. The biochemical and structural characterization of the CLPs is essential for understanding their roles and to develop potential utility in biotechnological industries. This review sheds light on the structure-function evolution of CLPs from chitinases.
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Affiliation(s)
- Pooja Kesari
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Dipak Narhari Patil
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pramod Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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35
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Gudmundsdottir S, Lieder R, Sigurjonsson OE, Petersen PH. Chitosan leads to downregulation of YKL-40 and inflammasome activation in human macrophages. J Biomed Mater Res A 2015; 103:2778-85. [PMID: 25684555 DOI: 10.1002/jbm.a.35417] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/18/2014] [Accepted: 02/05/2015] [Indexed: 11/07/2022]
Abstract
Chitosan, the deacetylated derivative of chitin, is used as biomaterial in diverse settings. It is also found on pathogens and can be proinflammatory. Shorter derivatives of chitosan can be generated chemically or enzymatically, chitosan oligosaccharides (ChOS). There is variation in the chemical composition of ChOS, including size distribution, but in general, they have been described as inert or anti-inflammatory. Active human chitinases can cleave chitin and chitosan, while inactive chitinases bind both but do not cleave. Both active and inactive chitinases have important roles in the immune response. The inactive chitinase YKL-40 is expressed highly during inflammation and has been proposed as a marker of poor prognosis. YKL-40 acts as a negative regulator of the inflammasome and as a positive regulator of angiogenesis. Levels of YKL-40 can therefore regulate levels of inflammation, the extent of angiogenesis, and the process of inflammation resolution. This study shows that chitosan leads to reduced secretion of YKL-40 by primary human macrophages and that this is concomitant with inflammasome activation. This was most pronounced with a highly deacetylated ChOS. No effect on the secretion of the active chitinase Chit-1 was detected. Smaller and more acetylated ChOS did not affect YKL-40 levels nor inflammasome activation. We conclude that this effect on the levels of YKL-40 is a part of the proinflammatory mechanisms of chitosan and its derivatives.
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Affiliation(s)
- Steinunn Gudmundsdottir
- Faculty of Medicine, School of Health Sciences, Department of Anatomy, Biomedical Center, University of Iceland, Reykjavik, 101, Iceland
| | - Ramona Lieder
- The Blood Bank, Landspitali University Hospital, Snorrabraut 60, Reykjavik, 105, Iceland.,School of Science and Engineering, Reykjavik University, Menntavegur 1, Reykjavik, 101, Iceland
| | - Olafur E Sigurjonsson
- The Blood Bank, Landspitali University Hospital, Snorrabraut 60, Reykjavik, 105, Iceland.,School of Science and Engineering, Reykjavik University, Menntavegur 1, Reykjavik, 101, Iceland.,Biomedical Center, University of Iceland, Reykjavik, 101, Iceland
| | - Petur H Petersen
- Faculty of Medicine, School of Health Sciences, Department of Anatomy, Biomedical Center, University of Iceland, Reykjavik, 101, Iceland.,Biomedical Center, University of Iceland, Reykjavik, 101, Iceland
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36
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Chaocharoen W, Ranok A, Suginta W, Schulte A. A microfluidic capacitive immunosensor system for human cartilage chitinase-3-like protein 2 (hYKL-39) quantification as an osteoarthritis marker in synovial joint fluid. RSC Adv 2015. [DOI: 10.1039/c5ra11379b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Flow-based electrochemical osteoarthritis biomarker quantification in joint synovial fluid has been established as first alternative to optical ELISA assays.
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Affiliation(s)
- W. Chaocharoen
- School of Biochemistry
- Institute of Science
- Suranaree University of Technology
- Nakhon Ratchasima 30000
- Thailand
| | - A. Ranok
- School of Biochemistry
- Institute of Science
- Suranaree University of Technology
- Nakhon Ratchasima 30000
- Thailand
| | - W. Suginta
- School of Biochemistry
- Institute of Science
- Suranaree University of Technology
- Nakhon Ratchasima 30000
- Thailand
| | - A. Schulte
- School of Chemistry
- Institute of Science
- Suranaree University of Technology
- Nakhon Ratchasima 30000
- Thailand
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37
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Djordjevic MA, Bezos A, Susanti, Marmuse L, Driguez H, Samain E, Vauzeilles B, Beau JM, Kordbacheh F, Rolfe BG, Schwörer R, Daines AM, Gresshoff PM, Parish CR. Lipo-chitin oligosaccharides, plant symbiosis signalling molecules that modulate mammalian angiogenesis in vitro. PLoS One 2014; 9:e112635. [PMID: 25536397 PMCID: PMC4275186 DOI: 10.1371/journal.pone.0112635] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 10/09/2014] [Indexed: 01/13/2023] Open
Abstract
Lipochitin oligosaccharides (LCOs) are signaling molecules required by ecologically and agronomically important bacteria and fungi to establish symbioses with diverse land plants. In plants, oligo-chitins and LCOs can differentially interact with different lysin motif (LysM) receptors and affect innate immunity responses or symbiosis-related pathways. In animals, oligo-chitins also induce innate immunity and other physiological responses but LCO recognition has not been demonstrated. Here LCO and LCO-like compounds are shown to be biologically active in mammals in a structure dependent way through the modulation of angiogenesis, a tightly-regulated process involving the induction and growth of new blood vessels from existing vessels. The testing of 24 LCO, LCO-like or oligo-chitin compounds resulted in structure-dependent effects on angiogenesis in vitro leading to promotion, or inhibition or nil effects. Like plants, the mammalian LCO biological activity depended upon the presence and type of terminal substitutions. Un-substituted oligo-chitins of similar chain lengths were unable to modulate angiogenesis indicating that mammalian cells, like plant cells, can distinguish between LCOs and un-substituted oligo-chitins. The cellular mode-of-action of the biologically active LCOs in mammals was determined. The stimulation or inhibition of endothelial cell adhesion to vitronectin or fibronectin correlated with their pro- or anti-angiogenic activity. Importantly, novel and more easily synthesised LCO-like disaccharide molecules were also biologically active and de-acetylated chitobiose was shown to be the primary structural basis of recognition. Given this, simpler chitin disaccharides derivatives based on the structure of biologically active LCOs were synthesised and purified and these showed biological activity in mammalian cells. Since important chronic disease states are linked to either insufficient or excessive angiogenesis, LCO and LCO-like molecules may have the potential to be a new, carbohydrate-based class of therapeutics for modulating angiogenesis.
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Affiliation(s)
- Michael A. Djordjevic
- Research School of Biology, Plant Science Division, College of Medicine, Biology and the Environment, Australian National University, Canberra, ACT, Australia
| | - Anna Bezos
- John Curtin School of Medical Research, College of Medicine, Biology and the Environment, Australian National University, Canberra, ACT, Australia
| | - Susanti
- John Curtin School of Medical Research, College of Medicine, Biology and the Environment, Australian National University, Canberra, ACT, Australia
| | - Laurence Marmuse
- University Grenoble Alpes, CERMAV, Grenoble, France CNRS, CERMAV, Grenoble, France
| | - Hugues Driguez
- University Grenoble Alpes, CERMAV, Grenoble, France CNRS, CERMAV, Grenoble, France
| | - Eric Samain
- University Grenoble Alpes, CERMAV, Grenoble, France CNRS, CERMAV, Grenoble, France
| | - Boris Vauzeilles
- University Paris Sud, Institut de Chimie Moléculaire et des Matériaux d’Orsay, Orsay, France, and Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, Gif-sur-Yvette, France
| | - Jean-Marie Beau
- University Paris Sud, Institut de Chimie Moléculaire et des Matériaux d’Orsay, Orsay, France, and Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, Gif-sur-Yvette, France
| | - Farzaneh Kordbacheh
- Research School of Biology, Plant Science Division, College of Medicine, Biology and the Environment, Australian National University, Canberra, ACT, Australia
| | - Barry G. Rolfe
- Research School of Biology, Plant Science Division, College of Medicine, Biology and the Environment, Australian National University, Canberra, ACT, Australia
| | - Ralf Schwörer
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt Wellington, New Zealand
| | - Alison M. Daines
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt Wellington, New Zealand
| | - Peter M. Gresshoff
- The Centre for Integrative Legume Research, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
| | - Christopher R. Parish
- John Curtin School of Medical Research, College of Medicine, Biology and the Environment, Australian National University, Canberra, ACT, Australia
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38
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Ranok A, Wongsantichon J, Robinson RC, Suginta W. Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39). J Biol Chem 2014; 290:2617-29. [PMID: 25477513 DOI: 10.1074/jbc.m114.588905] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy.
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Affiliation(s)
- Araya Ranok
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Jantana Wongsantichon
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and
| | - Robert C Robinson
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and the Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand,
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39
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Periplasmic de-acylase helps bacteria don their biofilm coat. Proc Natl Acad Sci U S A 2014; 111:10904-5. [PMID: 25006258 DOI: 10.1073/pnas.1410789111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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40
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Ranok A, Khunkaewla P, Suginta W. Human cartilage chitinase 3-like protein 2: cloning, expression, and production of polyclonal and monoclonal antibodies for osteoarthritis detection and identification of potential binding partners. Monoclon Antib Immunodiagn Immunother 2014; 32:317-25. [PMID: 24111862 DOI: 10.1089/mab.2013.0016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39) is a member of family-18 glycosyl hydrolases that lacks chitinase activity. YKL-39 is known as a potential marker for the activation of chondrocytes and the progression of osteoarthritis. In this study, we cloned and expressed a functional form of human YKL-39 in the bacterial system. The Escherichia coli expressed YKL-30 was used as immugen for production of anti YKL-39 polyclonal and monoclonal antibodies. Both antibody types were highly selective, reacting only with YKL-39. Isotype mapping identified two hybridoma clones (so called clones 6H11 and 8H3) to be IgM isotype. Dot blot assay showed that the monoclonal antibody was strongly active with the synovial fluid of an osteoarthritis patient, human monocyte, and T lymphocyte cell lines. Database search for protein binding partners gave high hits with several glycoproteins that play particular roles in cartilage tissue scaffolding, connective tissue formation, and cell-cell interactions. In conclusion, anti YKL-39 polyclonal and monoclonal antibodies were raised and tested to be suitable for immunological applications, such as the investigation of the YKL-39 regulating pathway and the development of an immunosensing tool for sensitive detection of cartilage tissue destruction.
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Affiliation(s)
- Araya Ranok
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology , Nakhon Ratchasima, Thailand
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41
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Nagae M, Yamaguchi Y. Three-dimensional structural aspects of protein-polysaccharide interactions. Int J Mol Sci 2014; 15:3768-83. [PMID: 24595239 PMCID: PMC3975366 DOI: 10.3390/ijms15033768] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 12/18/2022] Open
Abstract
Linear polysaccharides are typically composed of repeating mono- or disaccharide units and are ubiquitous among living organisms. Polysaccharide diversity arises from chain-length variation, branching, and additional modifications. Structural diversity is associated with various physiological functions, which are often regulated by cognate polysaccharide-binding proteins. Proteins that interact with linear polysaccharides have been identified or developed, such as galectins and polysaccharide-specific antibodies, respectively. Currently, data is accumulating on the three-dimensional structure of polysaccharide-binding proteins. These proteins are classified into two types: exo-type and endo-type. The former group specifically interacts with the terminal units of polysaccharides, whereas the latter with internal units. In this review, we describe the structural aspects of exo-type and endo-type protein-polysaccharide interactions. Further, we discuss the structural basis for affinity and specificity enhancement in the face of inherently weak binding interactions.
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Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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42
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Larsen T, Yoshimura Y, Voldborg BGR, Cazzamali G, Bovin NV, Westerlind U, Palcic MM, Leisner JJ. Human chitotriosidase CHIT1 cross reacts with mammalian-like substrates. FEBS Lett 2014; 588:746-51. [PMID: 24462685 DOI: 10.1016/j.febslet.2013.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/27/2013] [Accepted: 12/27/2013] [Indexed: 10/25/2022]
Abstract
Humans do not synthesize chitin, yet they produce a number of active and inactive chitinases. One of the active enzymes is chitotriosidase whose serum levels are elevated in a number of diseases such as Gaucher's disease and upon fungal infection. Since the biological role of chitotriosidase in disease pathogenesis is not understood we screened a panel of mammalian GlcNAc-containing glycoconjugates as alternate substrates. LacNAc and LacdiNAc-terminating substrates are hydrolyzed, the latter with a turnover comparable to that of pNP-chitotriose. Glycolipids or glycoproteins with LacNAc and LacdiNAc represent potential chitinase substrates and the subsequent alteration of glycosylation pattern could be a factor in disease pathogenesis.
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Affiliation(s)
- Tanja Larsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C, Denmark
| | - Yayoi Yoshimura
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark
| | - Bjørn G R Voldborg
- Novo Nordisk Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark
| | - Giuseppe Cazzamali
- Novo Nordisk Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark
| | - Nicolai V Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Ulrika Westerlind
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V., ISAS - Leibniz Institute for Analytical Sciences, Otto-Hahn-Str. 6b, D-44227 Dortmund, Germany
| | - Monica M Palcic
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark
| | - Jørgen J Leisner
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C, Denmark.
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43
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The significance of YKL-40 protein in liver fibrosis. Inflamm Res 2014; 63:249-54. [DOI: 10.1007/s00011-013-0698-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/30/2013] [Accepted: 12/04/2013] [Indexed: 12/15/2022] Open
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44
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Diverse pathological implications of YKL-40: Answers may lie in ‘outside-in’ signaling. Cell Signal 2013; 25:1567-73. [DOI: 10.1016/j.cellsig.2013.03.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 03/28/2013] [Indexed: 12/24/2022]
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45
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Sakuda S, Inoue H, Nagasawa H. Novel biological activities of allosamidins. Molecules 2013; 18:6952-68. [PMID: 23765233 PMCID: PMC6269690 DOI: 10.3390/molecules18066952] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 06/07/2013] [Indexed: 11/23/2022] Open
Abstract
Allosamidins, which are secondary metabolites of the Streptomyces species, have chitin-mimic pseudotrisaccharide structures. They bind to catalytic centers of all family 18 chitinases and inhibit their enzymatic activity. Allosamidins have been used as chitinase inhibitors to investigate the physiological roles of chitinases in a variety of organisms. Two prominent biological activities of allosamidins were discovered, where one has anti-asthmatic activity in mammals, while the other has the chitinase-production- promoting activity in allosamidin-producing Streptomyces. In this article, recent studies on the novel biological activities of allosamidins are reviewed.
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Affiliation(s)
- Shohei Sakuda
- Department of Applied Biological Chemistry, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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46
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Structural investigation of a novel N-acetyl glucosamine binding chi-lectin which reveals evolutionary relationship with class III chitinases. PLoS One 2013; 8:e63779. [PMID: 23717482 PMCID: PMC3662789 DOI: 10.1371/journal.pone.0063779] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 04/06/2013] [Indexed: 01/03/2023] Open
Abstract
The glycosyl hydrolase 18 (GH18) family consists of active chitinases as well as chitinase like lectins/proteins (CLPs). The CLPs share significant sequence and structural similarities with active chitinases, however, do not display chitinase activity. Some of these proteins are reported to have specific functions and carbohydrate binding property. In the present study, we report a novel chitinase like lectin (TCLL) from Tamarindus indica. The crystal structures of native TCLL and its complex with N-acetyl glucosamine were determined. Similar to the other CLPs of the GH18 members, TCLL lacks chitinase activity due to mutations of key active site residues. Comparison of TCLL with chitinases and other chitin binding CLPs shows that TCLL has substitution of some chitin binding site residues and more open binding cleft due to major differences in the loop region. Interestingly, the biochemical studies suggest that TCLL is an N-acetyl glucosamine specific chi-lectin, which is further confirmed by the complex structure of TCLL with N-acetyl glucosamine complex. TCLL has two distinct N-acetyl glucosamine binding sites S1 and S2 that contain similar polar residues, although interaction pattern with N-acetyl glucosamine varies extensively among them. Moreover, TCLL structure depicts that how plants utilize existing structural scaffolds ingenuously to attain new functions. To date, this is the first structural investigation of a chi-lectin from plants that explore novel carbohydrate binding sites other than chitin binding groove observed in GH18 family members. Consequently, TCLL structure confers evidence for evolutionary link of lectins with chitinases.
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47
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Einarsson JM, Bahrke S, Sigurdsson BT, Ng CH, Petersen PH, Sigurjonsson OE, Jonsson H, Gislason J, Thormodsson FR, Peter MG. Partially acetylated chitooligosaccharides bind to YKL-40 and stimulate growth of human osteoarthritic chondrocytes. Biochem Biophys Res Commun 2013; 434:298-304. [PMID: 23541584 DOI: 10.1016/j.bbrc.2013.02.122] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 02/26/2013] [Indexed: 11/17/2022]
Abstract
Recent evidences indicating that cellular kinase signaling cascades are triggered by oligomers of N-acetylglucosamine (ChOS) and that condrocytes of human osteoarthritic cartilage secrete the inflammation associated chitolectin YKL-40, prompted us to study the binding affinity of partially acetylated ChOS to YKL-40 and their effect on primary chondrocytes in culture. Extensive chitinase digestion and filtration of partially deacetylated chitin yielded a mixture of ChOS (Oligomin™) and further ultrafiltration produced T-ChOS™, with substantially smaller fraction of the smallest sugars. YKL-40 binding affinity was determined for the different sized homologues, revealing micromolar affinities of the larger homologues to YKL-40. The response of osteoarthritic chondrocytes to Oligomin™ and T-ChOS™ was determined, revealing 2- to 3-fold increases in cell number. About 500 μg/ml was needed for Oligomin™ and around five times lower concentration for T-ChOS™, higher concentrations abolished this effect for both products. Addition of chitotriose inhibited cellular responses mediated by larger oligosaccharides. These results, and the fact that the partially acetylated T-ChOS™ homologues should resist hydrolysis, point towards a new therapeutic concept for treating inflammatory joint diseases.
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Affiliation(s)
- Jon M Einarsson
- Genis hf, KÍM Medical Park, Vatnagarðar 18, IS-104 Reykjavik, Iceland.
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48
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Rosa MD, Tibullo D, Malaguarnera M, Tuttobene M, Malaguarnera L. Comparison of YKL-39 and CHIT-1 expression during macrophages differentiation and polarization. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/mri.2013.24011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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