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Biotransformation of bisphenol F by white-rot fungus Phanerochaete sordida YK-624 under non-ligninolytic condition. Appl Microbiol Biotechnol 2022; 106:6277-6287. [DOI: 10.1007/s00253-022-12133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 11/02/2022]
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2
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OUP accepted manuscript. Glycobiology 2022; 32:556-579. [DOI: 10.1093/glycob/cwac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/22/2022] [Accepted: 03/09/2022] [Indexed: 11/12/2022] Open
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3
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Norvienyeku J, Lin L, Waheed A, Chen X, Bao J, Aliyu SR, Lin L, Shabbir A, Batool W, Zhong Z, Zhou J, Lu G, Wang Z. Bayogenin 3-O-cellobioside confers non-cultivar-specific defence against the rice blast fungus Pyricularia oryzae. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:589-601. [PMID: 33043566 PMCID: PMC7955875 DOI: 10.1111/pbi.13488] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 09/27/2020] [Indexed: 05/06/2023]
Abstract
Rice cultivars from japonica and indica lineage possess differential resistance against blast fungus as a result of genetic divergence. Whether different rice cultivars also show distinct metabolomic changes in response to P. oryzae, and their role in host resistance, are poorly understood. Here, we examine the responses of six different rice cultivars from japonica and indica lineage challenged with P. oryzae. Both susceptible and resistant rice cultivars expressed several metabolites exclusively during P. oryzae infection, including the saponin Bayogenin 3-O-cellobioside. Bayogenin 3-O-cellobioside level in infected rice directly correlated with their resistant attributes. These findings reveal, for the first time to our knowledge that besides oat, other grass plants including rice produces protective saponins. Our study provides insight into the role of pathogen-mediated metabolomics reprogramming in host immunity. The correlation between Bayogenin 3-O-Cellobioside levels and blast resistance suggests that engineering saponin expression in cereal crops represents attractive and sustainable disease management.
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Affiliation(s)
- Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Abdul Waheed
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaomin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiandong Bao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Sami Rukaiya Aliyu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ammarah Shabbir
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wajjiha Batool
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jie Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Ministry of Education Key Laboratory of Biopesticides and Chemical BiologyCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- Institute of OceanographyMinjiang UniversityFuzhouChina
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4
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West CM, Malzl D, Hykollari A, Wilson IBH. Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective. Mol Cell Proteomics 2021; 20:100024. [PMID: 32994314 PMCID: PMC8724618 DOI: 10.1074/mcp.r120.002263] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022] Open
Abstract
Glycosylation is a highly diverse set of co- and posttranslational modifications of proteins. For mammalian glycoproteins, glycosylation is often site-, tissue-, and species-specific and diversified by microheterogeneity. Multitudinous biochemical, cellular, physiological, and organismic effects of their glycans have been revealed, either intrinsic to the carrier proteins or mediated by endogenous reader proteins with carbohydrate recognition domains. Furthermore, glycans frequently form the first line of access by or defense from foreign invaders, and new roles for nucleocytoplasmic glycosylation are blossoming. We now know enough to conclude that the same general principles apply in invertebrate animals and unicellular eukaryotes-different branches of which spawned the plants or fungi and animals. The two major driving forces for exploring the glycomes of invertebrates and protists are (i) to understand the biochemical basis of glycan-driven biology in these organisms, especially of pathogens, and (ii) to uncover the evolutionary relationships between glycans, their biosynthetic enzyme genes, and biological functions for new glycobiological insights. With an emphasis on emerging areas of protist glycobiology, here we offer an overview of glycan diversity and evolution, to promote future access to this treasure trove of glycobiological processes.
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Affiliation(s)
- Christopher M West
- Department of Biochemistry & Molecular Biology, Center for Tropical and Emerging Global Diseases, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
| | - Daniel Malzl
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
| | - Alba Hykollari
- Department für Chemie, Universität für Bodenkultur, Wien, Austria; VetCore Facility for Research/Proteomics Unit, Veterinärmedizinische Universität, Vienna, Austria
| | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur, Wien, Austria
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5
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Kulinich A, Wang Q, Duan XC, Lyu YM, Zhang XY, Awad FN, Liu L, Voglmeir J. Biochemical characterization of the endo-α-N-acetylgalactosaminidase pool of the human gut symbiont Tyzzerella nexilis. Carbohydr Res 2020; 490:107962. [PMID: 32169671 DOI: 10.1016/j.carres.2020.107962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/18/2020] [Accepted: 02/22/2020] [Indexed: 02/07/2023]
Abstract
Three large (2084-, 984-, and 2104-amino acids) endo-α-N-acetylgalactosaminidase candidate genes from the commensal human gut bacterium Tyzzerella nexilis were successfully cloned and subsequently expressed in Escherichia coli. Activity tests of the purified proteins revealed that two of the candidate genes (Tn0153 and Tn2105) were able to hydrolyze the disaccharide unit from Galβ1-3GalNAc-α-pNP. The biochemical characterization revealed optimum pH conditions of 4.0 for both enzymes and temperature optima of 50 °C. The addition of 2-mercaptoethanol, Triton X-100 and urea had only minor effects on the activity of the enzymes, and the addition of imidazole and sodium dodecyl sulfate led to a significant reduction of the enzymes' activities. A mutational study identified and confirmed the role of the catalytically significant amino acids. The present study describes the first functional characterization of members of the GH101 family from this human gut symbiont.
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Affiliation(s)
- Anna Kulinich
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Qian Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Xu-Chu Duan
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Yong-Mei Lyu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Xiao-Yang Zhang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Faisal Nureldin Awad
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
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Ujor VC, Adukwu EC, Okonkwo CC. Fungal wars: The underlying molecular repertoires of combating mycelia. Fungal Biol 2018; 122:191-202. [PMID: 29551193 DOI: 10.1016/j.funbio.2018.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/05/2018] [Accepted: 01/06/2018] [Indexed: 10/18/2022]
Abstract
Non-self contact between fungi elicits strong morphological and biochemical reactions in the mycelia of interacting species. Although these reactions appear to be species- and interaction-specific, some responses such as pigmentation, increased secretion of phenol-oxidases, barrage formation and sealing of the mycelia front are common responses in most interactions. Hence, some species recruit similar molecular machineries in response to non-self. Increasing number of fully sequenced and annotated fungal genomes and advances in genome-wide and global proteome analytical tools now allow researchers to use techniques such as RNA sequencing, micro and macroarray analysis, 2-dimensional protein gel profiling, and differential display of mRNA to probe the underlying molecular mechanisms of combative mycelial interactions. This review provides an overview of the genes and proteins found to be differentially expressed in conflicting fungal mycelia by the use of 'omics' tools. Connections between observed gene and protein repertoires of competing mycelia and the attendant morphological and biochemical changes are presented.
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Affiliation(s)
- Victor C Ujor
- Bioenergy and Biological Waste Management Program, Agricultural Technical Institute, The Ohio State University, 1328 Dover Road, Wooster, OH, USA.
| | - Emmanuel C Adukwu
- Department of Applied Sciences, University of the West of England, Frenchay Campus, Cold Harbour Lane, Bristol, BS16 1QY, United Kingdom
| | - Christopher C Okonkwo
- Department of Animal Sciences, The Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Avenue, Wooster, OH, 44691, USA
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Crisà A, Ferrè F, Chillemi G, Moioli B. RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk. BMC Vet Res 2016; 12:264. [PMID: 27884183 PMCID: PMC5123407 DOI: 10.1186/s12917-016-0881-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/07/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism. RESULTS A total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference. A significant sequence similarity match was found for 40,353 transcripts (90%) against the NCBI NT and for 35,701 (80%) against the NR databases. 68% and 69% of the de novo assembled transcripts, in colostrum and 120 days of lactation samples respectively, have a significant match with the merged transcriptome obtained using Cufflinks/Cuffmerge. CSN2, PAEP, CSN1S2, CSN3, LALBA, TPT1, FTH1, M-SAA3, SPP1, GLYCAM1, EEF1A1, CTSD, FASN, RPS29, CSN1S1, KRT19 and CHEK1 were found between the top fifteen highly expressed genes. 418 loci were differentially expressed between lactation stages, among which 207 and 122 were significantly up- and down-regulated in colostrum, respectively. Functional annotation and pathway enrichment analysis showed that in goat colostrum somatic cells predominate biological processes involved in glycolysis, carbohydrate metabolism, defense response, cytokine activity, regulation of cell proliferation and cell death, vasculature development, while in mature milk, biological process associated with positive regulation of lymphocyte activation and anatomical structure morphogenesis are enriched. The analysis of 144 different oligosaccharide metabolism-related genes showed that most of these (64%) were more expressed in colostrum than in mature milk, with eight expressed at very high levels (SLCA3, GMSD, NME2, SLC2A1, B4GALT1, B3GNT2, NANS, HEXB). CONCLUSIONS To our knowledge, this is the first study comparing goat transcriptome of two lactation stages: colostrum and 120 days. Our findings suggest putative differences of expression between stages and can be envisioned as a base for further research in the topic. Moreover because a higher expression of genes involved in immune defense response, carbohydrate metabolism and related to oligosaccharide metabolism was identified in colostrum we here corroborate the potential of goat milk as a natural source of lactose-derived oligosaccharides and for the development of functional foods.
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Affiliation(s)
- Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy.
| | - Fabrizio Ferrè
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 6, 40126, Bologna, Italy
| | - Giovanni Chillemi
- Applications and Innovation Department, CINECA, SCAI SuperComputing, Via dei Tizii 6, 00185, Rome, Italy
| | - Bianca Moioli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy
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8
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Chia J, Goh G, Bard F. Short O-GalNAc glycans: regulation and role in tumor development and clinical perspectives. Biochim Biophys Acta Gen Subj 2016; 1860:1623-39. [PMID: 26968459 DOI: 10.1016/j.bbagen.2016.03.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/03/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND While the underlying causes of cancer are genetic modifications, changes in cellular states mediate cancer development. Tumor cells display markedly changed glycosylation states, of which the O-GalNAc glycans called the Tn and TF antigens are particularly common. How these antigens get over-expressed is not clear. The expression levels of glycosylation enzymes fail to explain it. SCOPE OF REVIEW We describe the regulation of O-GalNAc glycosylation initiation and extension with emphasis on the initiating enzymes ppGalNAcTs (GALNTs), and introduce the GALA pathway--a change in GALNTs compartmentation within the secretory pathway that regulates Tn levels. We discuss the roles of O-GalNAc glycans and GALNTs in tumorigenic processes and finally consider diagnostic and therapeutic perspectives. MAJOR CONCLUSIONS Contrary to a common hypothesis, short O-glycans in tumors are not the result of an incomplete glycosylation process but rather reveal the activation of regulatory pathways. Surprisingly, high Tn levels reveal a major shift in the O-glycoproteome rather than a shortening of O-glycans. These changes are driven by membrane trafficking events. GENERAL SIGNIFICANCE Many attempts to use O-glycans for biomarker, antibody and therapeutic vaccine development have been made, but suffer limitations including poor sensitivity and/or specificity that may in part derive from lack of a mechanistic understanding. Deciphering how short O-GalNAc glycans are regulated would open new perspectives to exploit this biology for therapeutic usage. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Joanne Chia
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Germaine Goh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Frederic Bard
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, 138673, Singapore; Department of Biochemistry, National University of Singapore, 21 Lower Kent Ridge, Road, 119077, Singapore.
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9
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Tomono T, Kojima H, Fukuchi S, Tohsato Y, Ito M. Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling. Biophys Physicobiol 2015; 12:57-68. [PMID: 27493855 PMCID: PMC4736839 DOI: 10.2142/biophysico.12.0_57] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/12/2015] [Indexed: 02/06/2023] Open
Abstract
Glycans play important roles in such cell-cell interactions as signaling and adhesion, including processes involved in pathogenic infections, cancers, and neurological diseases. Glycans are biosynthesized by multiple glycosyltransferases (GTs), which function sequentially. Excluding mucin-type O-glycosylation, the non-reducing terminus of glycans is biosynthesized in the Golgi apparatus after the reducing terminus is biosynthesized in the ER. In the present study, we performed genome-wide analyses of human GTs by investigating the degree of conservation of homologues in other organisms, as well as by elucidating the phylogenetic relationship between cephalochordates and urochordates, which has long been controversial in deuterostome phylogeny. We analyzed 173 human GTs and functionally linked glycan synthesis enzymes by phylogenetic profiling and clustering, compiled orthologous genes from the genomes of other organisms, and converted them into a binary sequence based on the presence (1) or absence (0) of orthologous genes in the genomes. Our results suggest that the non-reducing terminus of glycans is biosynthesized by newly evolved GTs. According to our analysis, the phylogenetic profiles of GTs resemble the phylogenetic tree of life, where deuterostomes, metazoans, and eukaryotes are resolved into separate branches. Lineage-specific GTs appear to play essential roles in the divergence of these particular lineages. We suggest that urochordates lose several genes that are conserved among metazoans, such as those expressing sialyltransferases, and that the Golgi apparatus acquires the ability to synthesize glycans after the ER acquires this function.
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Affiliation(s)
- Takayoshi Tomono
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Hisao Kojima
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Satoshi Fukuchi
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, Gunma 371-0816, Japan
| | - Yukako Tohsato
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
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Abstract
This chapter describes the KEGG GLYCAN database of the KEGG resource, including descriptions of links to the other databases in KEGG. In particular, KEGG GLYCAN consists of glycan structures, with links to glycogenes, orthologs, reactions, pathways, drugs, diseases, and others, all within the KEGG resources. A number of analytical tools are also available, including the composite structure map (CSM), KegDraw, KCam, and GECS. These databases and tools will be described along with simple examples of their usage.
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11
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Liang DM, Liu JH, Wu H, Wang BB, Zhu HJ, Qiao JJ. Glycosyltransferases: mechanisms and applications in natural product development. Chem Soc Rev 2015; 44:8350-74. [DOI: 10.1039/c5cs00600g] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation reactions mainly catalyzed by glycosyltransferases (Gts) occur almost everywhere in the biosphere, and always play crucial roles in vital processes.
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Affiliation(s)
- Dong-Mei Liang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jia-Heng Liu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hao Wu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Bin-Bin Wang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hong-Ji Zhu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jian-Jun Qiao
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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Petit D, Teppa E, Mir AM, Vicogne D, Thisse C, Thisse B, Filloux C, Harduin-Lepers A. Integrative view of α2,3-sialyltransferases (ST3Gal) molecular and functional evolution in deuterostomes: significance of lineage-specific losses. Mol Biol Evol 2014; 32:906-27. [PMID: 25534026 PMCID: PMC4379398 DOI: 10.1093/molbev/msu395] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Sialyltransferases are responsible for the synthesis of a diverse range of sialoglycoconjugates predicted to be pivotal to deuterostomes’ evolution. In this work, we reconstructed the evolutionary history of the metazoan α2,3-sialyltransferases family (ST3Gal), a subset of sialyltransferases encompassing six subfamilies (ST3Gal I–ST3Gal VI) functionally characterized in mammals. Exploration of genomic and expressed sequence tag databases and search of conserved sialylmotifs led to the identification of a large data set of st3gal-related gene sequences. Molecular phylogeny and large scale sequence similarity network analysis identified four new vertebrate subfamilies called ST3Gal III-r, ST3Gal VII, ST3Gal VIII, and ST3Gal IX. To address the issue of the origin and evolutionary relationships of the st3gal-related genes, we performed comparative syntenic mapping of st3gal gene loci combined to ancestral genome reconstruction. The ten vertebrate ST3Gal subfamilies originated from genome duplication events at the base of vertebrates and are organized in three distinct and ancient groups of genes predating the early deuterostomes. Inferring st3gal gene family history identified also several lineage-specific gene losses, the significance of which was explored in a functional context. Toward this aim, spatiotemporal distribution of st3gal genes was analyzed in zebrafish and bovine tissues. In addition, molecular evolutionary analyses using specificity determining position and coevolved amino acid predictions led to the identification of amino acid residues with potential implication in functional divergence of vertebrate ST3Gal. We propose a detailed scenario of the evolutionary relationships of st3gal genes coupled to a conceptual framework of the evolution of ST3Gal functions.
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Affiliation(s)
- Daniel Petit
- INRA, UMR 1061, Unité Génétique Moléculaire Animale, F-87060 Limoges Cedex, France Université de Limoges, UMR 1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, F-87060 Limoges Cedex, France
| | - Elin Teppa
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Anne-Marie Mir
- Laboratoire de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Université Lille Nord de France, Lille1, Villeneuve d'Ascq, France
| | - Dorothée Vicogne
- Laboratoire de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Université Lille Nord de France, Lille1, Villeneuve d'Ascq, France
| | - Christine Thisse
- Department of Cell Biology, School of Medicine, University of Virginia
| | - Bernard Thisse
- Department of Cell Biology, School of Medicine, University of Virginia
| | - Cyril Filloux
- INRA, UMR 1061, Unité Génétique Moléculaire Animale, F-87060 Limoges Cedex, France Université de Limoges, UMR 1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, F-87060 Limoges Cedex, France
| | - Anne Harduin-Lepers
- Laboratoire de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Université Lille Nord de France, Lille1, Villeneuve d'Ascq, France
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13
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Hsieh YC, Chiu HH, Huang YC, Fun HK, Lu CY, Li YK, Chen CJ. Purification, crystallization and preliminary X-ray crystallographic analysis of glycosyltransferase-1 from Bacillus cereus. Acta Crystallogr F Struct Biol Commun 2014; 70:1228-31. [PMID: 25195897 PMCID: PMC4157424 DOI: 10.1107/s2053230x14014629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/20/2014] [Indexed: 11/10/2022] Open
Abstract
Glycosyltransferases (GTs), which are distributed widely in various organisms, including bacteria, fungi, plants and animals, play a role in synthesizing biological compounds. Glycosyltransferase-1 from Bacillus cereus (BcGT-1), which is capable of transferring glucose to small molecules such as kaempferol and quercetin, has been identified as a member of the family 1 glycosyltransferases which utilize uridine diphosphate glucose (UDP-glucose) as the sugar donor. BcGT-1 (molecular mass 45.5 kDa) has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction of BcGT-1 crystals to 2.10 Å resolution, the crystal belonged to space group P1, with unit-cell parameters a = 54.56, b = 84.81, c = 100.12 Å, α = 78.36, β = 84.66, γ = 84.84°. Preliminary analysis indicates the presence of four BcGT-1 molecules in the asymmetric unit with a solvent content of 50.27%.
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Affiliation(s)
- Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hsi-Ho Chiu
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yen-Chieh Huang
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hoong-Kun Fun
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Malaysia
| | - Chia-Yu Lu
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yaw-Kuen Li
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Biotechnology and the Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan City 701, Taiwan
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14
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Mickum ML, Prasanphanich NS, Heimburg-Molinaro J, Leon KE, Cummings RD. Deciphering the glycogenome of schistosomes. Front Genet 2014; 5:262. [PMID: 25147556 PMCID: PMC4122909 DOI: 10.3389/fgene.2014.00262] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/15/2014] [Indexed: 11/16/2022] Open
Abstract
Schistosoma mansoni and other Schistosoma sp. are multicellular parasitic helminths (worms) that infect humans and mammals worldwide. Infection by these parasites, which results in developmental maturation and sexual differentiation of the worms over a period of 5–6 weeks, induces antibodies to glycan antigens expressed in surface and secreted glycoproteins and glycolipids. There is growing interest in defining these unusual parasite-synthesized glycan antigens and using them to understand immune responses, their roles in immunomodulation, and in using glycan antigens as potential vaccine targets. A key problem in this area, however, has been the lack of information about the enzymes involved in elaborating the complex repertoire of glycans represented by the schistosome glycome. Recent availability of the nuclear genome sequences for Schistosoma sp. has created the opportunity to define the glycogenome, which represents the specific genes and cognate enzymes that generate the glycome. Here we describe the current state of information in regard to the schistosome glycogenome and glycome and highlight the important classes of glycans and glycogenes that may be important in their generation.
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Affiliation(s)
- Megan L Mickum
- Department of Biochemistry, Emory University School of Medicine Atlanta, GA, USA
| | - Nina S Prasanphanich
- Department of Biochemistry, Emory University School of Medicine Atlanta, GA, USA
| | | | - Kristoffer E Leon
- Department of Biochemistry, Emory University School of Medicine Atlanta, GA, USA
| | - Richard D Cummings
- Department of Biochemistry, Emory University School of Medicine Atlanta, GA, USA
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15
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Malik V, Zhang M, Dover LG, Northen JS, Flinn A, Perry JJ, Black GW. Sterol 3β-glucosyltransferase biocatalysts with a range of selectivities, including selectivity for testosterone. MOLECULAR BIOSYSTEMS 2014; 9:2816-22. [PMID: 24056940 DOI: 10.1039/c3mb70303g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The main objectives of this work were to characterise a range of purified recombinant sterol 3β-glucosyltransferases and show that rational sampling of the diversity that exists within sterol 3β-glucosyltransferase sequence space can result in a range of enzyme selectivities. In our study the catalytically active domain of the Saccharomyces cerevisiae 3β-glucosyltransferase was used to mine putative sterol 3β-glucosyltransferases from the databases. Selected diverse sequences were expressed in and purified from Escherichia coli and shown to have different selectivities for the 3β-hydroxysteroids ergosterol and cholesterol. Surprisingly, three enzymes were also selective for testosterone, a 17β-hydroxysteroid. This study therefore reports for the first time sterol 3β-glucosyltransferases with selectivity for both 3β- and 17β-hydroxysteroids and is also the first report of recombinant 3β-glucosyltransferases with selectivity for steroids with a hydroxyl group at positions other than C-3. These enzymes could therefore find utility in the pharmaceutical industry for the green synthesis of a range of glycosylated compounds of medicinal interest.
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Affiliation(s)
- Vatsala Malik
- Industrial Biotechnology Research Group, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
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16
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Kotera M, Goto S, Kanehisa M. Predictive genomic and metabolomic analysis for the standardization of enzyme data. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2014.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Malik V, Black GW. Structural, functional, and mutagenesis studies of UDP-glycosyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 87:87-115. [PMID: 22607753 DOI: 10.1016/b978-0-12-398312-1.00004-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
The biosynthesis of the complex carbohydrates that govern many cellular functions requires the action of a diverse range of selective glycosyltransferases (GTs). Uridine diphosphate sugar-utilizing GTs (UGTs) account for the majority of characterized GTs. GTs have been classified into families (currently 92) based on amino-acid sequence similarity. However, as amino-acid sequence similarity cannot reliable predict catalytic mechanism, GTs have also been grouped into four clans based on catalytic mechanism and structural fold. GTs catalyze glycosidic bond formation with two possible stereochemical outcomes: inversion or retention of anomeric configuration. All UGTs also belong to one of two distinct structural folds, GT-A and GT-B. UGTs have conserved residues that are associated with nucleotide diphosphate sugar recognition and acceptor recognition. UGT diversification has been performed using in vitro DNA recombination, domain swapping, and random mutagenesis.
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Affiliation(s)
- Vatsala Malik
- School of Life Sciences, Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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18
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Yang Z, Drew DP, Jørgensen B, Mandel U, Bach SS, Ulvskov P, Levery SB, Bennett EP, Clausen H, Petersen BL. Engineering mammalian mucin-type O-glycosylation in plants. J Biol Chem 2012; 287:11911-23. [PMID: 22334671 PMCID: PMC3320939 DOI: 10.1074/jbc.m111.312918] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/16/2012] [Indexed: 11/06/2022] Open
Abstract
Mucin-type O-glycosylation is an important post-translational modification that confers a variety of biological properties and functions to proteins. This post-translational modification has a particularly complex and differentially regulated biosynthesis rendering prediction and control of where O-glycans are attached to proteins, and which structures are formed, difficult. Because plants are devoid of GalNAc-type O-glycosylation, we have assessed requirements for establishing human GalNAc O-glycosylation de novo in plants with the aim of developing cell systems with custom-designed O-glycosylation capacity. Transient expression of a Pseudomonas aeruginosa Glc(NAc) C4-epimerase and a human polypeptide GalNAc-transferase in leaves of Nicotiana benthamiana resulted in GalNAc O-glycosylation of co-expressed human O-glycoprotein substrates. A chimeric YFP construct containing a 3.5 tandem repeat sequence of MUC1 was glycosylated with up to three and five GalNAc residues when co-expressed with GalNAc-T2 and a combination of GalNAc-T2 and GalNAc-T4, respectively, as determined by mass spectrometry. O-Glycosylation was furthermore demonstrated on a tandem repeat of MUC16 and interferon α2b. In plants, prolines in certain classes of proteins are hydroxylated and further substituted with plant-specific O-glycosylation; unsubstituted hydroxyprolines were identified in our MUC1 construct. In summary, this study demonstrates that mammalian type O-glycosylation can be established in plants and that plants may serve as a host cell for production of recombinant O-glycoproteins with custom-designed O-glycosylation. The observed hydroxyproline modifications, however, call for additional future engineering efforts.
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Affiliation(s)
- Zhang Yang
- From the Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | | | - Bodil Jørgensen
- Department of Agriculture and Ecology, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark, and
| | - Ulla Mandel
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Søren S. Bach
- the Department of Plant Biology and Biotechnology and
| | - Peter Ulvskov
- the Department of Plant Biology and Biotechnology and
| | - Steven B. Levery
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Eric P. Bennett
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Henrik Clausen
- the Center for Glycomics, Departments of Cellular and Molecular Medicine, and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
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Ujor V, Peiris D, Monti M, Kang A, Clements M, Hedger J. Quantitative proteomic analysis of the response of the wood-rot fungus, Schizophyllum commune, to the biocontrol fungus, Trichoderma viride. Lett Appl Microbiol 2012; 54:336-43. [DOI: 10.1111/j.1472-765x.2012.03215.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Clark MC, Baum LG. T cells modulate glycans on CD43 and CD45 during development and activation, signal regulation, and survival. Ann N Y Acad Sci 2012; 1253:58-67. [PMID: 22288421 DOI: 10.1111/j.1749-6632.2011.06304.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Glycosylation affects many essential T cell processes and is intrinsically controlled throughout the lifetime of a T cell. CD43 and CD45 are the two most abundant glycoproteins on the T cell surface and are decorated with O- and N-glycans. Global T cell glycosylation and specific glycosylation of CD43 and CD45 are modulated during thymocyte development and T cell activation; T cells control the type and abundance of glycans decorating CD43 and CD45 by regulating expression of glycosyltransferases and glycosidases. Additionally, T cells regulate glycosylation of CD45 by expressing alternatively spliced isoforms of CD45 that have different glycan attachment sites. The glycophenotype of CD43 and CD45 on T cells influences how T cells interact with the extracellular environment, including how T cells interact with endogenous lectins. This review focuses on changes in glycosylation of CD43 and CD45 occurring throughout T cell development and activation and the role that glycosylation plays in regulating T cell processes, such as migration, T cell receptor signaling, and apoptosis.
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Affiliation(s)
- Mary C Clark
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, University of California, Los Angeles, USA
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21
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Merrill AH. Sphingolipid and glycosphingolipid metabolic pathways in the era of sphingolipidomics. Chem Rev 2011; 111:6387-422. [PMID: 21942574 PMCID: PMC3191729 DOI: 10.1021/cr2002917] [Citation(s) in RCA: 527] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Indexed: 12/15/2022]
Affiliation(s)
- Alfred H Merrill
- School of Biology, and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0230, USA.
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22
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Saito S, Onuma Y, Ito Y, Tateno H, Toyoda M, Hidenori A, Nishino K, Chikazawa E, Fukawatase Y, Miyagawa Y, Okita H, Kiyokawa N, Shimma Y, Umezawa A, Hirabayashi J, Horimoto K, Asashima M. Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells. BMC SYSTEMS BIOLOGY 2011; 5 Suppl 1:S17. [PMID: 21689476 PMCID: PMC3121117 DOI: 10.1186/1752-0509-5-s1-s17] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Background Human iPS cells (hiPSCs) have attracted considerable attention for applications to drug screening and analyses of disease mechanisms, and even as next generation materials for regenerative medicine. Genetic reprogramming of human somatic cells to a pluripotent state was first achieved by the ectopic expression of four factors (Sox2, Oct4, Klf4 and c-Myc), using a retrovirus. Subsequently, this method was applied to various human cells, using different combinations of defined factors. However, the transcription factor-induced acquisition of replication competence and pluripotency raises the question as to how exogenous factors induce changes in the inner and outer cellular states. Results We analyzed both the RNA profile, to reveal changes in gene expression, and the glycan profile, to identify changes in glycan structures, between 51 cell samples of four parental somatic cell (SC) lines from amniotic mesodermal, placental artery endothelial, and uterine endometrium sources, fetal lung fibroblast (MRC-5) cells, and nine hiPSC lines that were originally established. The analysis of this information by standard statistical techniques combined with a network approach, named network screening, detected significant expression differences between the iPSCs and the SCs. Subsequent network analysis of the gene expression and glycan signatures revealed that the glycan transfer network is associated with known epitopes for differentiation, e.g., the SSEA epitope family in the glycan biosynthesis pathway, based on the characteristic changes in the cellular surface states of the hiPSCs. Conclusions The present study is the first to reveal the relationships between gene expression patterns and cell surface changes in hiPSCs, and reinforces the importance of the cell surface to identify established iPSCs from SCs. In addition, given the variability of iPSCs, which is related to the characteristics of the parental SCs, a glycosyltransferase expression assay might be established to define hiPSCs more precisely and thus facilitate their standardization, which are important steps towards the eventual therapeutic applications of hiPSCs.
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Affiliation(s)
- Shigeru Saito
- Computational Biology Research Center, National Institute of Advanced Industrial Science Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan
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Gill DJ, Clausen H, Bard F. Location, location, location: new insights into O-GalNAc protein glycosylation. Trends Cell Biol 2011; 21:149-58. [PMID: 21145746 DOI: 10.1016/j.tcb.2010.11.004] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/10/2010] [Accepted: 11/11/2010] [Indexed: 01/04/2023]
Abstract
O-GalNAc glycosylation of proteins confers essential structural, protective and signaling roles in eumetazoans. Addition of O-glycans onto proteins is an extremely complex process that regulates both sites of attachment and the types of oligosaccharides added. Twenty distinct polypeptide GalNAc-transferases (GalNAc-Ts) initiate O-glycosylation and fine-tuning their expression provides a mechanism for regulating this action. Recently, a new mode of regulation has emerged where activation of Src kinase selectively redistributes Golgi-localized GalNAc-Ts to the ER. This relocalization results in a strong increase in the density of O-glycan decoration. In this review, we discuss how different mechanisms can regulate the number and the types of O-glycans decorating proteins. In addition, we speculate how Src-dependent relocation of GalNAc-Ts could play an important role in cancerous cellular transformation.
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Affiliation(s)
- David J Gill
- Institute of Molecular and Cell Biology (IMCB), Proteos, 61 Biopolis Drive, Singapore, 138673
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Akune Y, Hosoda M, Kaiya S, Shinmachi D, Aoki-Kinoshita KF. The RINGS Resource for Glycome Informatics Analysis and Data Mining on the Web. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:475-86. [DOI: 10.1089/omi.2009.0129] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yukie Akune
- Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Masae Hosoda
- Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Sakiko Kaiya
- Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Daisuke Shinmachi
- Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Kiyoko F. Aoki-Kinoshita
- Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
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Popper ZA, Tuohy MG. Beyond the green: understanding the evolutionary puzzle of plant and algal cell walls. PLANT PHYSIOLOGY 2010; 153:373-83. [PMID: 20421458 PMCID: PMC2879814 DOI: 10.1104/pp.110.158055] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 04/26/2010] [Indexed: 05/18/2023]
Affiliation(s)
- Zoë A Popper
- Botany and Plant Science , School of Natural Sciences, National University of Ireland, Galway, Ireland.
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26
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Hashimoto K, Madej T, Bryant SH, Panchenko AR. Functional states of homooligomers: insights from the evolution of glycosyltransferases. J Mol Biol 2010; 399:196-206. [PMID: 20381499 DOI: 10.1016/j.jmb.2010.03.059] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 03/29/2010] [Accepted: 03/29/2010] [Indexed: 02/02/2023]
Abstract
Glycosylation is an important aspect of epigenetic regulation. Glycosyltransferase is a key enzyme in the biosynthesis of glycans, which glycosylates more than half of all proteins in eukaryotes and is involved in a wide range of biological processes. It has been suggested previously that homooligomerization in glycosyltransferases and other proteins might be crucial for their function. In this study, we explore functional homooligomeric states of glycosyltransferases in various organisms, trace their evolution, and perform comparative analyses to find structural features that can mediate or disrupt the formation of different homooligomers. First, we make a structure-based classification of the diverse superfamily of glycosyltransferases and confirm that the majority of the structures are indeed clustered into the GT-A or GT-B folds. We find that homooligomeric glycosyltransferases appear to be as ancient as monomeric glycosyltransferases and go back in evolution to the last universal common ancestor (LUCA). Moreover, we show that interface residues have significant bias to be gapped out or unaligned in the monomers, implying that they might represent features crucial for oligomer formation. Structural analysis of these features reveals that the majority of them represent loops, terminal regions, and helices, indicating that these secondary-structure elements mediate the formation of glycosyltransferases' homooligomers and directly contribute to the specific binding. We also observe relatively short protein regions that disrupt the homodimer interactions, although such cases are rare. These results suggest that relatively small structural changes in the nonconserved regions may contribute to the formation of different functional oligomeric states and might be important in regulation of enzyme activity through homooligomerization.
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Affiliation(s)
- Kosuke Hashimoto
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A 8S814, Bethesda, MD 20894, USA
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Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2009; 38:D355-60. [PMID: 19880382 PMCID: PMC2808910 DOI: 10.1093/nar/gkp896] [Citation(s) in RCA: 1623] [Impact Index Per Article: 108.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Most human diseases are complex multi-factorial diseases resulting from the combination of various genetic and environmental factors. In the KEGG database resource (http://www.genome.jp/kegg/), diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. Disease information is computerized in two forms: pathway maps and gene/molecule lists. The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. This database also captures knowledge about two types of molecular networks: the interaction network with target molecules, metabolizing enzymes, other drugs, etc. and the chemical structure transformation network in the history of drug development. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.
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Affiliation(s)
- Minoru Kanehisa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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