1
|
Cheng X, Garcés-Carrera S, Whitworth RJ, Fellers JP, Park Y, Chen MS. A Horizontal Gene Transfer Led to the Acquisition of a Fructan Metabolic Pathway in a Gall Midge. ACTA ACUST UNITED AC 2020; 4:e1900275. [PMID: 32293157 DOI: 10.1002/adbi.201900275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/30/2020] [Indexed: 01/19/2023]
Abstract
Animals are thought to use only glucose polymers (glycogen) as energy reserve, whereas both glucose (starch) and fructose polymers (fructans) are used by microbes and plants. Here, it is reported that the gall midge Mayetiola destructor, and likely other herbivorous animal species, gained the ability to utilize dietary fructans directly as storage polysaccharides by a single horizontal gene transfer (HGT) of bacterial levanase/inulinase gene followed by gene expansion and differentiation. Multiple genes encoding levanases/inulinases have their origin in a single HGT event from a bacterium and they show high expression levels and enzymatic activities in different tissues of the gall midge, including nondigestive fat bodies and eggs, both of which contained significant amounts of fructans. This study provides evidence that animals can also use fructans as energy reserve by incorporating bacterial genes in their genomes.
Collapse
Affiliation(s)
- Xiaoyan Cheng
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | | | - Robert Jeff Whitworth
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | - John P Fellers
- Hard Winter Wheat Genetics Research Unit, Center for Grain and Animal Health Research Center, USDA-ARS, 4008 Throckmorton, Manhattan, KS, 66506, USA
| | - Yoonseong Park
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
| | - Ming-Shun Chen
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA
- Hard Winter Wheat Genetics Research Unit, Center for Grain and Animal Health Research Center, USDA-ARS, 4008 Throckmorton, Manhattan, KS, 66506, USA
| |
Collapse
|
2
|
Rawi MH, Zaman SA, Pa'ee KF, Leong SS, Sarbini SR. Prebiotics metabolism by gut-isolated probiotics. Journal of Food Science and Technology 2020; 57:2786-2799. [PMID: 32624588 DOI: 10.1007/s13197-020-04244-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/22/2019] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
There are numerous species of bacteria resides in the lumen of human colon. The word 'colon', resembles colony or the colonization of microbiota of which plays an important role in the fermentation of prebiotics. The standpoint of prebiotic nowadays is well reported for attenuating gut dysbiosis in many clinical studies tested on animals and human. However, because of the huge amount of gut microbiome, the attempt to connect the dots between bacterial population and the host are not plainly discernible. Thus, a need to analyse recent research on the pathways of prebiotic metabolism adopted by commonly studied probiotics i.e. Bifidobacteria and Lactobacillus. Several different substrate-dependent gene expressions are induced to break down oligosaccharide molecules shown by those probiotics. The hydrolysis can occur either by membrane bound (extracellular) or cytoplasmic (intracellular) enzyme of the enteric bacteria. Therefore, this review narrates several prebiotic metabolisms occur during gut fermentation, and metabolite production i.e. organic acids conversion.
Collapse
Affiliation(s)
- Muhamad Hanif Rawi
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| | - Siti Aisyah Zaman
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| | - Khairul Faizal Pa'ee
- Food Technology Section, Universiti Kuala Lumpur Branch Campus Malaysian Institute of Chemical and Bio-Engineering Technology (UniKL-MICET), Bandar Vendor, Taboh Naning, 78000 Alor Gajah, Melaka Malaysia
| | - Sui Sien Leong
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| | - Shahrul Razid Sarbini
- Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Jalan Nyabau, 97008 Bintulu, Sarawak Malaysia
| |
Collapse
|
3
|
Slugina MA, Shchennikova AV, Kochieva EZ. TAI vacuolar invertase orthologs: the interspecific variability in tomato plants (Solanum section Lycopersicon). Mol Genet Genomics 2017. [PMID: 28634826 DOI: 10.1007/s00438-017-1336-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Understanding the genetic mechanisms underlying carbohydrate metabolism can promote the development of biotechnological advances in fruit plants. The flesh tomato fruit represents an ideal system for examining the role of sucrose cleavage enzymes in fruit development, and wild tomato species differing in storage sugars serve as an excellent research material for this purpose. Plant vacuolar invertase is a key enzyme of sucrose metabolism in the sink organs. In the present study, we identified complete gene sequences encoding the TAI vacuolar invertase in 11 wild and one cultivated tomato accessions of the Solanum section Lycopersicon. The average level of interspecific polymorphism in TAI genes was 8.58%; however, in the green-fruited tomatoes, the TAI genes contained 100 times more SNPs than those in the red-fruited accessions. The TAI proteins demonstrated 8% variability, whereas the red-fruited species had none. A TAI-based phylogenetic tree revealed two main clusters containing self-compatible and self-incompatible species, which concurs with the previous crossability-based division and demonstrates that the TAI genes reflect the evolutionary relationships between the red- and green-fruited tomatoes. Furthermore, we detected differential expression patterns of the TAI genes in the fruits of wild and cultivated tomatoes, which corresponded to sugar composition. The polymorphism analysis of the TAI acid invertases of Solanum section Lycopersicon species will contribute to the understanding of the genetic potential of TAI genes to impact tomato breeding through genetic engineering of the carbohydrate composition in the fruit.
Collapse
Affiliation(s)
- M A Slugina
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russia. .,Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russia.
| | - A V Shchennikova
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russia
| | - E Z Kochieva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russia.,Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russia
| |
Collapse
|
4
|
Li R, Li J, Liao X, Wang Y. Purification and characterisation of soluble acid invertase from mango fruits. Int J Food Sci Technol 2017. [DOI: 10.1111/ijfs.13354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Renjie Li
- College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
- Beijing Key Laboratory for Food Nonthermal Processing; Beijing 100083 China
- Chinese National Engineering Research Center for Fruit and Vegetable Processing; Beijing 100083 China
- Key Lab of Fruit and Vegetable Processing; Ministry of Agriculture; Beijing 100083 China
| | - Jingyu Li
- College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
- Beijing Key Laboratory for Food Nonthermal Processing; Beijing 100083 China
- Chinese National Engineering Research Center for Fruit and Vegetable Processing; Beijing 100083 China
- Key Lab of Fruit and Vegetable Processing; Ministry of Agriculture; Beijing 100083 China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
- Beijing Key Laboratory for Food Nonthermal Processing; Beijing 100083 China
- Chinese National Engineering Research Center for Fruit and Vegetable Processing; Beijing 100083 China
- Key Lab of Fruit and Vegetable Processing; Ministry of Agriculture; Beijing 100083 China
| | - Yongtao Wang
- College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
- Beijing Key Laboratory for Food Nonthermal Processing; Beijing 100083 China
- Chinese National Engineering Research Center for Fruit and Vegetable Processing; Beijing 100083 China
- Key Lab of Fruit and Vegetable Processing; Ministry of Agriculture; Beijing 100083 China
| |
Collapse
|
5
|
Buntin N, Hongpattarakere T, Ritari J, Douillard FP, Paulin L, Boeren S, Shetty SA, de Vos WM. An Inducible Operon Is Involved in Inulin Utilization in Lactobacillus plantarum Strains, as Revealed by Comparative Proteogenomics and Metabolic Profiling. Appl Environ Microbiol 2017; 83:e02402-16. [PMID: 27815279 PMCID: PMC5203619 DOI: 10.1128/aem.02402-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022] Open
Abstract
The draft genomes of Lactobacillus plantarum strains isolated from Asian fermented foods, infant feces, and shrimp intestines were sequenced and compared to those of well-studied strains. Among 28 strains of L. plantarum, variations in the genomic features involved in ecological adaptation were elucidated. The genome sizes ranged from approximately 3.1 to 3.5 Mb, of which about 2,932 to 3,345 protein-coding sequences (CDS) were predicted. The food-derived isolates contained a higher number of carbohydrate metabolism-associated genes than those from infant feces. This observation correlated to their phenotypic carbohydrate metabolic profile, indicating their ability to metabolize the largest range of sugars. Surprisingly, two strains (P14 and P76) isolated from fermented fish utilized inulin. β-Fructosidase, the inulin-degrading enzyme, was detected in the supernatants and cell wall extracts of both strains. No activity was observed in the cytoplasmic fraction, indicating that this key enzyme was either membrane-bound or extracellularly secreted. From genomic mining analysis, a predicted inulin operon of fosRABCDXE, which encodes β-fructosidase and many fructose transporting proteins, was found within the genomes of strains P14 and P76. Moreover, pts1BCA genes, encoding sucrose-specific IIBCA components involved in sucrose transport, were also identified. The proteomic analysis revealed the mechanism and functional characteristic of the fosRABCDXE operon involved in the inulin utilization of L. plantarum The expression levels of the fos operon and pst genes were upregulated at mid-log phase. FosE and the LPXTG-motif cell wall anchored β-fructosidase were induced to a high abundance when inulin was present as a carbon source. IMPORTANCE Inulin is a long-chain carbohydrate that may act as a prebiotic, which provides many health benefits to the host by selectively stimulating the growth and activity of beneficial bacteria in the colon. While certain lactobacilli can catabolize inulin, this has not yet been described for Lactobacillus plantarum, and an associated putative inulin operon has not been reported in this species. By using comparative and functional genomics, we showed that two L. plantarum strains utilized inulin and identified functional inulin operons in their genomes. The proteogenomic data revealed that inulin degradation and uptake routes, which related to the fosRABCDXE operon and pstBCA genes, were widely expressed among L. plantarum strains. The present work provides a novel understanding of gene regulation and mechanisms of inulin utilization in probiotic L. plantarum generating opportunities for synbiotic product development.
Collapse
Affiliation(s)
- Nirunya Buntin
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Tipparat Hongpattarakere
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jarmo Ritari
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Sudarshan A Shetty
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Program Unit Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
6
|
Holyavka M, Artyukhov V, Kovaleva T. Structural and functional properties of inulinases: A review. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1196486] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
7
|
Yang F, Liu ZC, Wang X, Li LL, Yang L, Tang WZ, Yu ZM, Li X. Invertase Suc2-mediated inulin catabolism is regulated at the transcript level in Saccharomyces cerevisiae. Microb Cell Fact 2015; 14:59. [PMID: 25890240 PMCID: PMC4404613 DOI: 10.1186/s12934-015-0243-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 04/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background Invertase Suc2 was recently identified as a key hydrolase for inulin catabolism in Saccharomyces cerevisiae, whereas the Suc2 activity degrading inulin varies greatly in different S. cerevisiae strains. The molecular mechanism causing such variation remained obscure. The aim of this study is to investigate how Suc2 activity is regulated in S. cerevisiae. Results The effect of SUC2 expression level on inulin hydrolysis was investigated by introducing different SUC2 genes or their corresponding promoters in S. cerevisiae strain BY4741 that can only weakly catabolize inulin. Both inulinase and invertase activities were increased with the rising SUC2 expression level. Variation in the promoter sequence has an obvious effect on the transcript level of the SUC2 gene. It was also found that the high expression level of SUC2 was beneficial to inulin degradation and ethanol yield. Conclusions Suc2-mediated inulin catabolism is regulated at transcript level in S. cerevisiae. Our work should be valuable for engineering advanced yeast strains in application of inulin for ethanol production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0243-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Zhi-Cheng Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Xue Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Li-Li Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Lan Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Wen-Zhu Tang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Zhi-Min Yu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, PR China.
| |
Collapse
|
8
|
Zhao C, Doucet D, Mittapalli O. Characterization of horizontally transferred β-fructofuranosidase (ScrB) genes in Agrilus planipennis. INSECT MOLECULAR BIOLOGY 2014; 23:821-832. [PMID: 25224649 DOI: 10.1111/imb.12127] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The emerald ash borer (Agrilus planipennis) is an important invasive insect pest of Fraxinus spp. that feeds on host tissues containing high levels of sucrose. However, little is known about how it digests sucrose. Here, using larval midgut transcriptome data and preliminary genome sequence efforts, two β-fructofuranosidase-encoding ScrB genes, AplaScrB-1 and AplaScrB-2, were identified, and proved to reside within the A. planipennis genome. Homology and phylogenetic analysis revealed that they were acquired by A. planipennis via horizontal gene transfer (HGT) from bacteria, possibly an event independent from that reported in bark beetles (eg ScrB genes). Microsynteny between A. planipennis DNA scaffold #2042940, which hosts AplaScrB-1, and a region in the Tribolium castaneum chromosome LG4 suggested that A. planipennis gained this gene after the separation of Buprestidae and Tenebrionidae. Although both of the putative AplaScrB proteins have conserved β-fructofuranosidase motifs, only AplaScrB-2 was predicted to be a secretory protein. Expression of AplaScrB-1 seemed constitutive during development and in all tissues examined, whereas AplaScrB-2 showed a peak expression in adults and in the midgut. We propose that acquisition of these genes by A. planipennis from bacteria is adaptive, and specifically AplaScrB-2 is involved in breaking down dietary sucrose to obtain energy for development.
Collapse
Affiliation(s)
- C Zhao
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA
| | | | | |
Collapse
|
9
|
Invertase SUC2 Is the key hydrolase for inulin degradation in Saccharomyces cerevisiae. Appl Environ Microbiol 2012; 79:403-6. [PMID: 23104410 DOI: 10.1128/aem.02658-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Specific Saccharomyces cerevisiae strains were recently found to be capable of efficiently utilizing inulin, but genetic mechanisms of inulin hydrolysis in yeast remain unknown. Here we report functional characteristics of invertase SUC2 from strain JZ1C and demonstrate that SUC2 is the key enzyme responsible for inulin metabolism in S. cerevisiae.
Collapse
|
10
|
Castrillón-Arbeláez PA, Martínez-Gallardo N, Arnaut HA, Tiessen A, Délano-Frier JP. Metabolic and enzymatic changes associated with carbon mobilization, utilization and replenishment triggered in grain amaranth (Amaranthus cruentus) in response to partial defoliation by mechanical injury or insect herbivory. BMC PLANT BIOLOGY 2012; 12:163. [PMID: 22966837 PMCID: PMC3515461 DOI: 10.1186/1471-2229-12-163] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/03/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Amaranthus cruentus and A. hypochondriacus are crop plants grown for grain production in subtropical countries. Recently, the generation of large-scale transcriptomic data opened the possibility to study representative genes of primary metabolism to gain a better understanding of the biochemical mechanisms underlying tolerance to defoliation in these species. A multi-level approach was followed involving gene expression analysis, enzyme activity and metabolite measurements. RESULTS Defoliation by insect herbivory (HD) or mechanical damage (MD) led to a rapid and transient reduction of non-structural carbohydrates (NSC) in all tissues examined. This correlated with a short-term induction of foliar sucrolytic activity, differential gene expression of a vacuolar invertase and its inhibitor, and induction of a sucrose transporter gene. Leaf starch in defoliated plants correlated negatively with amylolytic activity and expression of a β-amylase-1 gene and positively with a soluble starch synthase gene. Fatty-acid accumulation in roots coincided with a high expression of a phosphoenolpyruvate/phosphate transporter gene. In all tissues there was a long-term replenishment of most metabolite pools, which allowed damaged plants to maintain unaltered growth and grain yield. Promoter analysis of ADP-glucose pyrophosphorylase and vacuolar invertase genes indicated the presence of cis-regulatory elements that supported their responsiveness to defoliation. HD and MD had differential effects on transcripts, enzyme activities and metabolites. However, the correlation between transcript abundance and enzymatic activities was very limited. A better correlation was found between enzymes, metabolite levels and growth and reproductive parameters. CONCLUSIONS It is concluded that a rapid reduction of NSC reserves in leaves, stems and roots followed by their long-term recovery underlies tolerance to defoliation in grain amaranth. This requires the coordinate action of genes/enzymes that are differentially affected by the way leaf damage is performed. Defoliation tolerance in grain is a complex process that can't be fully explained at the transcriptomic level only.
Collapse
Affiliation(s)
- Paula Andrea Castrillón-Arbeláez
- Unidad de Biotecnología e Ingeniería Genética de Plantas (Cinvestav-Irapuato), Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto, México
| | - Norma Martínez-Gallardo
- Unidad de Biotecnología e Ingeniería Genética de Plantas (Cinvestav-Irapuato), Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto, México
| | - Hamlet Avilés Arnaut
- Unidad de Biotecnología e Ingeniería Genética de Plantas (Cinvestav-Irapuato), Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto, México
- Present address: Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Av. Pedro de Alba y Manuel L. Barragán s/n, Ciudad Universitaria, C.P. 66450, San Nicolás de los Garza, Nuevo León, México
| | - Axel Tiessen
- Unidad de Biotecnología e Ingeniería Genética de Plantas (Cinvestav-Irapuato), Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto, México
| | - John Paul Délano-Frier
- Unidad de Biotecnología e Ingeniería Genética de Plantas (Cinvestav-Irapuato), Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto, México
| |
Collapse
|
11
|
Purification and characterization of a novel extracellular inulinase from a new yeast species Candida kutaonensis sp. nov. KRF1T. Appl Microbiol Biotechnol 2012; 96:1517-26. [DOI: 10.1007/s00253-012-4108-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/09/2012] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
|
12
|
Kuzuwa S, Yokoi KJ, Kondo M, Kimoto H, Yamakawa A, Taketo A, Kodaira KI. Properties of the inulinase gene levH1 of Lactobacillus casei IAM 1045; cloning, mutational and biochemical characterization. Gene 2012; 495:154-62. [DOI: 10.1016/j.gene.2011.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/17/2011] [Accepted: 12/02/2011] [Indexed: 11/26/2022]
|
13
|
Naumoff DG. Hierarchical classification of glycoside hydrolases. BIOCHEMISTRY (MOSCOW) 2011; 76:622-35. [PMID: 21639842 DOI: 10.1134/s0006297911060022] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review deals with structural and functional features of glycoside hydrolases, a widespread group of enzymes present in almost all living organisms. Their catalytic domains are grouped into 120 amino acid sequence-based families in the international classification of the carbohydrate-active enzymes (CAZy database). At a higher hierarchical level some of these families are combined in 14 clans. Enzymes of the same clan have common evolutionary origin of their genes and share the most important functional characteristics such as composition of the active center, anomeric configuration of cleaved glycosidic bonds, and molecular mechanism of the catalyzed reaction (either inverting, or retaining). There are now extensive data in the literature concerning the relationship between glycoside hydrolase families belonging to different clans and/or included in none of them, as well as information on phylogenetic protein relationship within particular families. Summarizing these data allows us to propose a multilevel hierarchical classification of glycoside hydrolases and their homologs. It is shown that almost the whole variety of the enzyme catalytic domains can be brought into six main folds, large groups of proteins having the same three-dimensional structure and the supposed common evolutionary origin.
Collapse
Affiliation(s)
- D G Naumoff
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, 117312, Russia.
| |
Collapse
|
14
|
Molecular cloning and sequence analysis of an inulinase gene from an Aspergillus sp. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0683-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
15
|
|
16
|
Goosen C, Van Der Maarel MJEC, Dijkhuizen L. Exo-inulinase ofAspergillus nigerN402: A hydrolytic enzyme with significant transfructosylating activity. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701806686] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
17
|
Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses. BMC Evol Biol 2009; 9:148. [PMID: 19566942 PMCID: PMC2728104 DOI: 10.1186/1471-2148-9-148] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 06/30/2009] [Indexed: 01/30/2023] Open
Abstract
Background Many fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi. Results We detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0–12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota. Conclusion We found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability to access plant-synthesized sucrose. Endophytic fungi are more similar to plant pathogens in their possession of GH32 genes, whereas most genomes of mycorrhizal taxa lack GH32 genes. Reliance on plant GH32 enzyme activity for C acquisition in these symbionts supports earlier predictions of possible plant control over C allocation in the mycorrhizal symbiosis.
Collapse
|
18
|
Bocock PN, Morse AM, Dervinis C, Davis JM. Evolution and diversity of invertase genes in Populus trichocarpa. PLANTA 2008; 227:565-76. [PMID: 17938954 DOI: 10.1007/s00425-007-0639-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 09/27/2007] [Indexed: 05/21/2023]
Abstract
Invertase (EC 3.2.1.26) plays a key role in carbon utilization as it catalyzes the irreversible hydrolysis of sucrose into glucose and fructose. The invertase family in plants is composed of two sub-families thought to have distinct evolutionary origins and can be distinguished by their pH optima for activity: acid invertases and neutral/alkaline invertases. The acid invertases apparently originated in eubacteria and are targeted to the cell wall and vacuole, while neutral/alkaline invertases apparently originated in cyanobacteria and function in the cytosol. The recently sequenced genome of Populus trichocharpa (Torr. and Gray) allowed us to identify the genes encoding invertase in this woody perennial. Here we describe the identification of eight acid invertase genes; three of which belong to the vacuolar targeted group (PtVIN1-3), and five of which belong to the cell wall targeted group (PtCIN1-5). Similarly, we report the identification of 16 neutral/alkaline invertase genes (PtNIN1-16). Expression analyses using whole genome microarrays and RT-PCR reveal evidence for expression of all invertase family members. An examination of the micro-syntenic regions surrounding the poplar invertase genes reveals extensive colinearity with Arabidopsis invertases. We also find evidence for expression of a novel intronless vacuolar invertase (PtVIN1), which apparently arose from a processed PtVIN2 transcript that re-inserted into the genome. To our knowledge, this is the first intronless invertase found in plants. This work increases the understanding of the role this family plays in carbon allocation and partitioning in forest trees as well as its evolutionary development.
Collapse
Affiliation(s)
- Philip N Bocock
- Plant Molecular and Cellular Biology Program, University of Florida, PO Box 110690, Gainesville, FL 32611, USA
| | | | | | | |
Collapse
|
19
|
Abstract
We characterized two sucrose-metabolizing systems -sus and scr- and describe their roles in the physiology and virulence of Streptococcus pneumoniae in murine models of carriage and pneumonia. The sus and scr systems are regulated by LacI family repressors SusR and ScrR respectively. SusR regulates an adjacent ABC transporter (susT1/susT2/susX) and sucrose-6-phosphate (S-6-P) hydrolase (susH). ScrR controls an adjacent PTS transporter (scrT), fructokinase (scrK) and second S-6-P hydrolase (scrH). sus and scr play niche-specific roles in virulence. The susH and sus locus mutants are attenuated in the lung, but dispensable in nasopharyngeal carriage. Conversely, the scrH and scr locus mutants, while dispensable in the lung, are attenuated for nasopharyngeal colonization. The scrH/susH double mutant is more attenuated than scrH in the nasopharynx, indicating SusH can substitute in this niche. Both systems are sucrose-inducible, with ScrH being the major in vitro hydrolase. The scrH/susH mutant does not grow on sucrose indicating that sus and scr are the only sucrose-metabolizing systems in S. pneumoniae. We propose a model describing hierarchical regulation of the scr and sus systems by the putative inducer, S-6-P. The transport and metabolism of sucrose or a related disaccharide thus contributes to S. pneumoniae colonization and disease.
Collapse
Affiliation(s)
- Ramkumar Iyer
- Howard Hughes Medical Institute, 136 Harrison Avenue, Tufts University, Boston, MA 02110, USA
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Tufts University, Boston, MA 02110, USA
- For correspondence. ; Tel. (+1) 617 636 6933; Fax (+1) 617 636 2175
| |
Collapse
|
20
|
Adindla S, Inampudi KK, Guruprasad L. Cell surface proteins in archaeal and bacterial genomes comprising "LVIVD", "RIVW" and "LGxL" tandem sequence repeats are predicted to fold as beta-propeller. Int J Biol Macromol 2007; 41:454-68. [PMID: 17681373 DOI: 10.1016/j.ijbiomac.2007.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 06/13/2007] [Accepted: 06/13/2007] [Indexed: 11/23/2022]
Abstract
Proteins that share even low sequence homologies are known to adopt similar folds. The beta-propeller structural motif is one such example. Identifying sequences that adopt a beta-propeller fold is useful to annotate protein structure and function. Often, tandem sequence repeats provide the necessary signal for identifying beta-propellers in proteins. In our recent analysis to identify cell surface proteins in archaeal and bacterial genomes, we identified some proteins that contain novel tandem repeats "LVIVD", "RIVW" and "LGxL". In this work, based on protein fold predictions and three-dimensional comparative modeling methods, we predicted that these repeat types fold as beta-propeller. Further, the evolutionary trace analysis of all proteins constituting amino acid sequence repeats in beta-propellers suggest that the novel repeats have diverged from a common ancestor.
Collapse
Affiliation(s)
- Swathi Adindla
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | | | | |
Collapse
|
21
|
Yuan XL, Goosen C, Kools H, van der Maarel MJEC, van den Hondel CAMJJ, Dijkhuizen L, Ram AFJ. Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger. MICROBIOLOGY-SGM 2007; 152:3061-3073. [PMID: 17005986 DOI: 10.1099/mic.0.29051-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As a soil fungus, Aspergillus niger can metabolize a wide variety of carbon sources, employing sets of enzymes able to degrade plant-derived polysaccharides. In this study the genome sequence of A. niger strain CBS 513.88 was surveyed, to analyse the gene/enzyme network involved in utilization of the plant storage polymer inulin, and of sucrose, the substrate for inulin synthesis in plants. In addition to three known activities, encoded by the genes suc1 (invertase activity; designated sucA), inuE (exo-inulinase activity) and inuA/inuB (endo-inulinase activity), two new putative invertase-like proteins were identified. These two putative proteins lack N-terminal signal sequences and therefore are expected to be intracellular enzymes. One of these two genes, designated sucB, is expressed at a low level, and its expression is up-regulated when A. niger is grown on sucrose- or inulin-containing media. Transcriptional analysis of the genes encoding the sucrose- (sucA) and inulin-hydrolysing enzymes (inuA and inuE) indicated that they are similarly regulated and all strongly induced on sucrose and inulin. Analysis of a DeltacreA mutant strain of A. niger revealed that expression of the extracellular inulinolytic enzymes is under control of the catabolite repressor CreA. Expression of the inulinolytic enzymes was not induced by fructose, not even in the DeltacreA background, indicating that fructose did not act as an inducer. Evidence is provided that sucrose, or a sucrose-derived intermediate, but not fructose, acts as an inducer for the expression of inulinolytic genes in A. niger.
Collapse
MESH Headings
- Aspergillus niger/enzymology
- Aspergillus niger/genetics
- Aspergillus niger/metabolism
- Blotting, Northern
- Computational Biology
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- Fructose
- Gene Expression Regulation, Fungal
- Genome, Fungal
- Inulin/metabolism
- Molecular Sequence Data
- Phylogeny
- Protein Sorting Signals/genetics
- RNA, Fungal/analysis
- RNA, Fungal/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Sequence Homology, Amino Acid
- Sucrose/metabolism
- Transcription, Genetic
- beta-Fructofuranosidase/genetics
Collapse
Affiliation(s)
- Xiao-Lian Yuan
- Institute of Biology Leiden, Leiden University, Fungal Genetics Research Group, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Coenie Goosen
- Centre for Carbohydrate Bioprocessing TNO-University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Harrie Kools
- Microbiology, Fungal Genomics Group, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | - Marc J E C van der Maarel
- TNO Quality of Life, Business Unit Innovative Ingredients and Products, Rouaanstraat 27, 9723 CC Groningen, The Netherlands
- Centre for Carbohydrate Bioprocessing TNO-University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Cees A M J J van den Hondel
- Institute of Biology Leiden, Leiden University, Fungal Genetics Research Group, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Lubbert Dijkhuizen
- Centre for Carbohydrate Bioprocessing TNO-University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Arthur F J Ram
- TNO Quality of Life, Business Unit Microbiology, Utrechtseweg 48, 3500 AJ Zeist, The Netherlands
- Institute of Biology Leiden, Leiden University, Fungal Genetics Research Group, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| |
Collapse
|
22
|
Goh YJ, Zhang C, Benson AK, Schlegel V, Lee JH, Hutkins RW. Identification of a putative operon involved in fructooligosaccharide utilization by Lactobacillus paracasei. Appl Environ Microbiol 2006; 72:7518-30. [PMID: 17028235 PMCID: PMC1694223 DOI: 10.1128/aem.00877-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growth and activity of some Lactobacillus and Bifidobacterium strains are stimulated by the presence of nondigestible fructooligosaccharides (FOS), which are selectively fermented by specific intestinal bacteria. Consumption of FOS, therefore, enriches for those bacteria that possess metabolic pathways necessary for FOS metabolism. In this study, a DNA microarray consisting of 7,680 random genomic library fragments of Lactobacillus paracasei 1195 was used to examine genes involved in the utilization of FOS in this organism. Differential expression profiles between cells grown on FOS and those grown on glucose provided a basis for identifying genes specifically induced by FOS. Several of the FOS-induced genes shared sequence identity with genes encoding beta-fructosidases and components of phosphoenolpyruvate-dependent phosphotransferase systems (PTS). These genes were organized in a putative operon, designated the fos operon, that may play an essential role in FOS utilization. The complete 7,631-bp nucleotide sequence of the putative fos operon was determined and consists of fosABCDXE genes, which encode a putative fructose/mannose PTS (FosABCDX) and a beta-fructosidase precursor (FosE). The latter contains an N-terminal signal peptide sequence and cell wall sorting signals at the C-terminal region, suggesting its localization at the cell wall. Inactivation of the fosE gene led to impaired growth on FOS and other beta-fructose-linked carbohydrates. Transcriptional analysis by reverse transcriptase PCR suggested that fosABCDXE was cotranscribed as a single mRNA during growth on FOS. Expression array analysis revealed that when glucose was added to FOS-grown cells, transcription of the FOS-induced genes was repressed, indicating that FOS metabolism is subject to catabolite regulation.
Collapse
Affiliation(s)
- Yong Jun Goh
- Department of Food Science and Technology, University of Nebraska, 338 FIC, Lincoln, NE 68583-0919, USA
| | | | | | | | | | | |
Collapse
|
23
|
Alberto F, Jordi E, Henrissat B, Czjzek M. Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose. Biochem J 2006; 395:457-62. [PMID: 16411890 PMCID: PMC1462702 DOI: 10.1042/bj20051936] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 01/11/2006] [Accepted: 01/16/2006] [Indexed: 11/17/2022]
Abstract
Thermotoga maritima invertase (beta-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases beta-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy sources for prokaryotes and eukaryotes. The invertase cleaves beta-fructopyranosidic linkages by a double-displacement mechanism, which involves a nucleophilic aspartate and a catalytic glutamic acid acting as a general acid/base. The three-dimensional structure of invertase shows a bimodular enzyme with a five bladed beta-propeller catalytic domain linked to a beta-sandwich of unknown function. In the present study we report the crystal structure of the inactivated invertase in interaction with the natural substrate molecule alpha-D-galactopyranosyl-(1,6)-alpha-D-glucopyranosyl-beta-D-fructofuranoside (raffinose) at 1.87 A (1 A=0.1 nm) resolution. The structural analysis of the complex reveals the presence of three binding-subsites, which explains why T. maritima invertase exhibits a higher affinity for raffinose than sucrose, but a lower catalytic efficiency with raffinose as substrate than with sucrose.
Collapse
Affiliation(s)
- François Alberto
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Emmanuelle Jordi
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Mirjam Czjzek
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| |
Collapse
|
24
|
Martínez-Fleites C, Ortíz-Lombardía M, Pons T, Tarbouriech N, Taylor EJ, Arrieta JG, Hernández L, Davies GJ. Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus. Biochem J 2005; 390:19-27. [PMID: 15869470 PMCID: PMC1188265 DOI: 10.1042/bj20050324] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The endophytic Gram-negative bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA, EC 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. The enzyme is included in GH (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. The three-dimensional structure of LsdA has been determined by X-ray crystallography at a resolution of 2.5 A (1 A=0.1 nm). The structure was solved by molecular replacement using the homologous Bacillus subtilis (Bs) levansucrase (Protein Data Bank accession code 1OYG) as a search model. LsdA displays a five-bladed beta-propeller architecture, where the catalytic residues that are responsible for sucrose hydrolysis are perfectly superimposable with the equivalent residues of the Bs homologue. The comparison of both structures, the mutagenesis data and the analysis of GH68 family multiple sequences alignment show a strong conservation of the sucrose hydrolytic machinery among levansucrases and also a structural equivalence of the Bs levansucrase Ca2+-binding site to the LsdA Cys339-Cys395 disulphide bridge, suggesting similar fold-stabilizing roles. Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction.
Collapse
|
25
|
Moriyama S, Tanaka H, Uwataki M, Muguruma M, Ohta K. Molecular cloning and characterization of an exoinulinase gene from Aspergillus niger strain 12 and its expression in Pichia pastoris. J Biosci Bioeng 2005; 96:324-31. [PMID: 16233531 DOI: 10.1016/s1389-1723(03)90131-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Accepted: 06/17/2003] [Indexed: 11/25/2022]
Abstract
A genomic DNA segment and cDNAs encoding an extracellular exoinulinase from Aspergillus niger strain 12 were cloned and sequenced. Southern blot analysis indicated that the exoinulinase gene (inuE) was present as a single copy in the genome. An open reading frame of 1611 by was interrupted by a single intron of 60 bp, and encoded a 19-amino acid signal peptide and a 518-amino acid mature protein. The mature protein contained a single Cys residue and nine potential N-linked glycosylation sites. Three distinct transcription start points were observed at positions -41 (A), -35 (A), and -31 (A) from the start codon. The 5'-noncoding region had a putative TATA at position -75 (TATAAA). Transcription of the inuE gene was induced by inulin or sucrose and repressed by fructose or glucose. The inuE cDNA was functionally expressed under the control of the alcohol oxidase gene promoter in the methylotrophic yeast Pichia pastoris. The deduced amino acid sequence of the inuE gene product was 91% identical to that of an exoinulinase from Aspergillus awamori. A neighbor-joining tree showed that exo- and endoinulinases found in Aspergillus and Penicillium spp. have independently evolved the respective hydrolytic activities toward terminal and internal beta-2,1-fructofuranosidic linkages in inulin.
Collapse
Affiliation(s)
- Satoshi Moriyama
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, Miyazaki University, 1-1 Gakuen Kibanadai Nishi, Miyazaki 889-2192, Japan
| | | | | | | | | |
Collapse
|
26
|
Chalmers J, Lidgett A, Cummings N, Cao Y, Forster J, Spangenberg G. Molecular genetics of fructan metabolism in perennial ryegrass. PLANT BIOTECHNOLOGY JOURNAL 2005; 3:459-74. [PMID: 17173633 DOI: 10.1111/j.1467-7652.2005.00148.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fructans are the main storage carbohydrates of temperate grasses, sustaining regrowth immediately after defoliation, as well as contributing to the nutritive value of feed. Fructan metabolism is based on the substrate sucrose and involves fructosyltransferases (FTs) for biosynthesis and fructan exohydrolases (FEHs) for degradation. Sucrose is also utilized by invertases (INVs), which hydrolyse it into its constituent monosaccharides for use in metabolism. The isolation, molecular characterization, functional analysis, and phylogenetic relationships of genes encoding FTs, FEHs, and INVs from temperate grasses are reviewed, with an emphasis on perennial ryegrass (Lolium perenne L.). The roles these enzymes play in fructan accumulation and remobilization, and future biotechnological applications in molecular plant breeding are discussed.
Collapse
Affiliation(s)
- Jaye Chalmers
- Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries and Molecular Plant Breeding CRC, La Trobe University, Victoria 3086, Australia
| | | | | | | | | | | |
Collapse
|
27
|
Ji X, Van den Ende W, Van Laere A, Cheng S, Bennett J. Structure, evolution, and expression of the two invertase gene families of rice. J Mol Evol 2005; 60:615-34. [PMID: 15983871 DOI: 10.1007/s00239-004-0242-1] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2004] [Accepted: 12/07/2004] [Indexed: 01/08/2023]
Abstract
Invertases catalyze the irreversible hydrolysis of sucrose to glucose and fructose. Plants contain two unrelated families of these enzymes: acid forms that derive from periplasmic invertases of eubacteria and are found in cell wall and vacuole, and neutral/alkaline forms evolved from the cytosolic invertases of cyanobacteria. Genomes of rice (Oryza sativa) and thale cress (Arabidopsis thaliana) contain multiple genes encoding these two families. Here for rice we identify the member genes of a cell-wall group (designated OsCIN1-9), a vacuolar group (OsVIN1-2), and two ancient neutral/alkaline groups: alpha (OsNIN1-4) and beta (OsNIN5-8). In Arabidopsis these groups contain six, two, four and five members, respectively. It is believed that the vacuolar group evolved from the cell-wall group. We provide evidence that the N-terminal signal peptide that directs cell-wall invertases co-translationally into the endoplasmic reticulum for secretion was replaced in the vacuolar group by a sequence similar to the complex N-terminal motif that targets alkaline phosphatase post-translationally to the vacuolar membrane of yeast. Since the last common ancestor of Arabidopsis and rice, the two invertase families evolved equally rapidly via gene duplication and gene loss, but the acid invertase family underwent approximately 10 events of intron loss compared with a single event of intron gain in the neutral/alkaline invertase family. Transcripts were detected for all rice invertase genes except OsCIN9. The acid invertase genes showed greater spatial and temporal diversity of expression than the neutral/alkaline genes.
Collapse
Affiliation(s)
- Xuemei Ji
- Plant Breeding, Genetics and Biochemistry Division, International Rice Research Institute, Metro Manila, Philippines
| | | | | | | | | |
Collapse
|
28
|
Kim KY, Rhee S, Kim SI. Role of the N-Terminal Domain of Endoinulinase from Arthrobacter sp. S37 in Regulation of Enzyme Catalysis. ACTA ACUST UNITED AC 2005; 138:27-33. [PMID: 16046445 DOI: 10.1093/jb/mvi093] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Endoinulinase from Arthrobacter sp. S37 (EnIA), a member of the glycoside hydrolase family 32, is unique in that, unlike other members of the family, it contains a 250-residue N-terminal domain including a "laminin-G like jelly-roll" fold. This unique N-terminal domain is here suggested to be involved in dimerization and catalysis. The essentially inactive nature of enzymes produced by N-terminal truncation (Delta15, Delta45, Delta70, and Delta250) supported the pivotal role of this unique domain in catalysis and the need for its structural integrity. Significant reductions in the enzyme efficiency (kcat/Km) were observed when mutations were introduced at highly conserved tryptophan residues (Trp75 and Trp141) in the laminin-G like jelly-roll fold, implying their involvement in catalysis. Results from size-exclusion chromatography of the native and chimeric enzymes in the presence and absence of the domain suggested that the N-terminal domain could mediate dimerization.
Collapse
Affiliation(s)
- Kyoung-Yun Kim
- School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-742, Korea
| | | | | |
Collapse
|
29
|
Kang HK, Seo MY, Seo ES, Kim D, Chung SY, Kimura A, Day DF, Robyt JF. Cloning and expression of levansucrase from Leuconostoc mesenteroides B-512 FMC in Escherichia coli. ACTA ACUST UNITED AC 2005; 1727:5-15. [PMID: 15652153 DOI: 10.1016/j.bbaexp.2004.10.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Revised: 10/17/2004] [Accepted: 10/29/2004] [Indexed: 11/23/2022]
Abstract
Leuconostoc mesenteroides B-512 FMC produces dextran and levan using sucrose. Because of the industrial importance of dextrans and oligosaccharides synthesized by dextransucrase (one of glycansucrases from L. mesenteroides), much is known about the dextransucrase, including expression and regulation of gene. However, no detailed report about levansucrase, another industrially important glycansucrase from L. mesenteroides, and its gene was available. In this paper, we report the first-time isolation and molecular characterization of a L. mesenteroides levansucrase gene (m1ft). The gene m1ft is composed of 1272-bp nucleotides and codes for a protein of 424 amino acid residues with calculated molecular mass of 47.1 kDa. The purified protein was estimated to be about 51.7 kDa including a His-tag based on SDS-PAGE. It showed an activity band at 103 kDa on a non-denaturing SDS-PAGE, indicating a dimeric form of the active M1FT. M1FT levan structure was confirmed by NMR and dot blot analysis with an anti-levan-antibody. M1FT converted 150 mM sucrose to levan (18%), 1-kestose (17%), nystose (11%) and 1,1,1-kestopentaose (7%) with the liberation of glucose. The M1FT enzyme produced erlose [O-alpha-D-glucopyranosyl-(1-->4)-O-alpha-D-glucopyranosyl-(1-->2)-beta-D-fructofuranoside] as an acceptor product with maltose. The optimum temperature and pH of this enzyme for levan formation were 30 degrees C and pH 6.2, respectively. M1FT levansucrase activity was completely abolished by 1 mM Hg2+ or Ag2+. The Km and Vmax values for levansucrase were calculated to be 26.6 mM and 126.6 micromol min-1 mg-1.
Collapse
Affiliation(s)
- Hee Kyoung Kang
- Engineering Research Institute, Chonnam National University, Gwang-Ju, 500-757, South Korea
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Altenbach D, Nüesch E, Meyer AD, Boller T, Wiemken A. The large subunit determines catalytic specificity of barley sucrose:fructan 6-fructosyltransferase and fescue sucrose:sucrose 1-fructosyltransferase. FEBS Lett 2004; 567:214-8. [PMID: 15178325 DOI: 10.1016/j.febslet.2004.04.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Revised: 03/17/2004] [Accepted: 04/23/2004] [Indexed: 11/20/2022]
Abstract
Plant fructosyltransferases are highly homologous in primary sequence and typically consist of two subunits but catalyze widely different reactions. Using functional expression in the yeast Pichia pastoris, we show that the substrate specificity of festuca sucrose:sucrose 1--beta-D-fructosyltransferase (1-SST) and barley sucrose:fructan 6--beta-D-fructosyltransferase (6-SFT) is entirely determined by the large subunit. Chimeric enzymes with the large subunit of festuca 1-SST (LSuB) and the small subunit of barley 6-SFT have the same catalytic specificity as the native festuca 1-SST and vice versa. If the LSuB is expressed alone, it does not yield a functionally active enzyme, indicating that the small subunit is nevertheless essential.
Collapse
Affiliation(s)
- Denise Altenbach
- Zurich Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland
| | | | | | | | | |
Collapse
|
31
|
Alberto F, Bignon C, Sulzenbacher G, Henrissat B, Czjzek M. The Three-dimensional Structure of Invertase (β-Fructosidase) from Thermotoga maritima Reveals a Bimodular Arrangement and an Evolutionary Relationship between Retaining and Inverting Glycosidases. J Biol Chem 2004; 279:18903-10. [PMID: 14973124 DOI: 10.1074/jbc.m313911200] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thermotoga maritima invertase (beta-fructosidase) hydrolyzes sucrose to release fructose and glucose, which are major carbon and energy sources for both prokaryotes and eukaryotes. The name "invertase" was given to this enzyme over a century ago, because the 1:1 mixture of glucose and fructose that it produces was named "invert sugar." Despite its name, the enzyme operates with a mechanism leading to the retention of the anomeric configuration at the site of cleavage. The enzyme belongs to family GH32 of the sequence-based classification of glycosidases. The crystal structure, determined at 2-A resolution, reveals two modules, namely a five-bladed beta-propeller with structural similarity to the beta-propeller structures of glycosidase from families GH43 and GH68 connected to a beta-sandwich module. Three carboxylates at the bottom of a deep, negatively charged funnel-shaped depression of the beta-propeller are essential for catalysis and function as nucleophile, general acid, and transition state stabilizer, respectively. The catalytic machinery of invertase is perfectly superimposable to that of the enzymes of families GH43 and GH68. The variation in the position of the furanose ring at the site of cleavage explains the different mechanisms evident in families GH32 and GH68 (retaining) and GH43 (inverting) furanosidases.
Collapse
Affiliation(s)
- François Alberto
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Université Aix-Marseille I & II, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
| | | | | | | | | |
Collapse
|
32
|
Pons T, Naumoff DG, Martínez-Fleites C, Hernández L. Three acidic residues are at the active site of a beta-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68. Proteins 2004; 54:424-32. [PMID: 14747991 DOI: 10.1002/prot.10604] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Multiple-sequence alignment of glycoside hydrolase (GH) families 32, 43, 62, and 68 revealed three conserved blocks, each containing an acidic residue at an equivalent position in all the enzymes. A detailed analysis of the site-directed mutations so far performed on invertases (GH32), arabinanases (GH43), and bacterial fructosyltransferases (GH68) indicated a direct implication of the conserved residues Asp/Glu (block I), Asp (block II), and Glu (block III) in substrate binding and hydrolysis. These residues are close in space in the 5-bladed beta-propeller fold determined for Cellvibrio japonicus alpha-L-arabinanase Arb43A [Nurizzo et al., Nat Struct Biol 2002;9:665-668] and Bacillus subtilis endo-1,5-alpha-L-arabinanase. A sequence-structure compatibility search using 3D-PSSM, mGenTHREADER, INBGU, and SAM-T02 programs predicted indistinctly the 5-bladed beta-propeller fold of Arb43A and the 6-bladed beta-propeller fold of sialidase/neuraminidase (GH33, GH34, and GH83) as the most reliable topologies for GH families 32, 62, and 68. We conclude that the identified acidic residues are located at the active site of a beta-propeller architecture in GH32, GH43, GH62, and GH68, operating with a canonical reaction mechanism of either inversion (GH43 and likely GH62) or retention (GH32 and GH68) of the anomeric configuration. Also, we propose that the beta-propeller architecture accommodates distinct binding sites for the acceptor saccharide in glycosyl transfer reaction.
Collapse
Affiliation(s)
- Tirso Pons
- Centro de Ingeniería Genética y Biotecnología, Habana, Cuba.
| | | | | | | |
Collapse
|
33
|
Ohta K, Akimoto H, Moriyama S. Fungal Inulinases: Enzymology, Molecular Biology and Biotechnology. J Appl Glycosci (1999) 2004. [DOI: 10.5458/jag.51.247] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
34
|
Juan D, Graña O, Pazos F, Fariselli P, Casadio R, Valencia A. A neural network approach to evaluate fold recognition results. Proteins 2003; 50:600-8. [PMID: 12577266 DOI: 10.1002/prot.10322] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fold recognition techniques assist the exploration of protein structures, and web-based servers are part of the standard set of tools used in the analysis of biochemical problems. Despite their success, current methods are only able to predict the correct fold in a relatively small number of cases. We propose an approach that improves the selection of correct folds from among the results of two methods implemented as web servers (SAMT99 and 3DPSSM). Our approach is based on the training of a system of neural networks with models generated by the servers and a set of associated characteristics such as the quality of the sequence-structure alignment, distribution of sequence features (sequence-conserved positions and apolar residues), and compactness of the resulting models. Our results show that it is possible to detect adequate folds to model 80% of the sequences with a high level of confidence. The improvements achieved by taking into account sequence characteristics open the door to future improvements by directly including such factors in the step of model generation. This approach has been implemented as an automatic system LIBELLULA, available as a public web server at http://www.pdg.cnb.uam.es/servers/libellula.html.
Collapse
Affiliation(s)
- D Juan
- Protein Design Group, National Center for Biotechnology, CNB-CSIC, Campus Universidad Autónoma, Cantoblanco, Madrid, M-28049, Spain
| | | | | | | | | | | |
Collapse
|
35
|
Saito K, Oda Y, Tomita F, Yokota A. Molecular cloning of the gene for 2,6-beta-D-fructan 6-levanbiohydrolase from Streptomyces exfoliatus F3-2. FEMS Microbiol Lett 2003; 218:265-70. [PMID: 12586402 DOI: 10.1111/j.1574-6968.2003.tb11527.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The gene encoding a 2,6-beta-D-fructan 6-levanbiohydrolase (LF2ase) (EC 3.2.1.64) that converts levan into levanbiose was cloned from the genomic DNA of Streptomyces exfoliatus F3-2. The gene encoded a signal peptide of 37 amino acids and a mature protein of 482 amino acids with a total length of 1560 bp and was successfully expressed in Escherichia coli. The similarities of primary structure were observed with levanases from Clostridium acetobutylicum, Bacillus subtilis, B. stearothermophilus (51.0-54.3%) and with LF2ase from Microbacterium levaniformans (53.9%). The enzyme from S. exfoliatus F3-2 shared the conserved six domains and the completely conserved five amino acid residues with family 32 glycosyl hydrolases, which include levanase, inulinase, and invertase. These observations led to the conclusion that the enzyme belongs to family 32 glycosyl hydrolases.
Collapse
Affiliation(s)
- Katsuichi Saito
- Department of Upland Agriculture Research, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro, Kasai, 082-0071, Hokkaido, Japan.
| | | | | | | |
Collapse
|
36
|
MORIYAMA SATOSHI, TANAKA HIDENORI, UWATAKI MASATO, MUGURUMA MICHIO, OHTA KAZUYOSHI. Molecular Cloning and Characterization of an Exoinulinase Gene from Aspergillus niger Strain 12 and Its Expression in Pichia pastoris. J Biosci Bioeng 2003. [DOI: 10.1263/jbb.96.324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
37
|
Abstract
Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.
Collapse
Affiliation(s)
- Zahra Jawad
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QW, Cambridge, United Kingdom
| | | |
Collapse
|
38
|
Thompson J, Robrish SA, Immel S, Lichtenthaler FW, Hall BG, Pikis A. Metabolism of sucrose and its five linkage-isomeric alpha-D-glucosyl-D-fructoses by Klebsiella pneumoniae. Participation and properties of sucrose-6-phosphate hydrolase and phospho-alpha-glucosidase. J Biol Chem 2001; 276:37415-25. [PMID: 11473129 DOI: 10.1074/jbc.m106504200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Klebsiella pneumoniae is presently unique among bacterial species in its ability to metabolize not only sucrose but also its five linkage-isomeric alpha-d-glucosyl-d-fructoses: trehalulose, turanose, maltulose, leucrose, and palatinose. Growth on the isomeric compounds induced a protein of molecular mass approximately 50 kDa that was not present in sucrose-grown cells and which we have identified as an NAD(+) and metal ion-dependent 6-phospho-alpha-glucosidase (AglB). The aglB gene has been cloned and sequenced, and AglB (M(r) = 49,256) has been purified from a high expression system using the chromogenic p-nitrophenyl alpha-glucopyranoside 6-phosphate as substrate. Phospho-alpha-glucosidase catalyzed the hydrolysis of a wide variety of 6-phospho-alpha-glucosides including maltose-6'-phosphate, maltitol-6-phosphate, isomaltose-6'-phosphate, and all five 6'-phosphorylated isomers of sucrose (K(m) approximately 1-5 mm) yet did not hydrolyze sucrose-6-phosphate. By contrast, purified sucrose-6-phosphate hydrolase (M(r) approximately 53,000) hydrolyzed only sucrose-6-phosphate (K(m) approximately 80 microm). Differences in molecular shape and lipophilicity potential between sucrose and its isomers may be important determinants for substrate discrimination by the two phosphoglucosyl hydrolases. Phospho-alpha-glucosidase and sucrose-6-phosphate hydrolase exhibit no significant homology, and by sequence-based alignment, the two enzymes are assigned to Families 4 and 32, respectively, of the glycosyl hydrolase superfamily. The phospho-alpha-glucosidase gene (aglB) lies adjacent to a second gene (aglA), which encodes an EII(CB) component of the phosphoenolpyruvate-dependent sugar:phosphotransferase system. We suggest that the products of the two genes facilitate the phosphorylative translocation and subsequent hydrolysis of the five alpha-d-glucosyl-d-fructoses by K. pneumoniae.
Collapse
Affiliation(s)
- J Thompson
- Microbial Biochemistry and Genetics Unit, Oral Infection and Immunity Branch, NIDCR, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | | | | | | | | | | |
Collapse
|
39
|
Van den Ende W, Michiels A, Van Wonterghem D, Clerens SP, De Roover J, Van Laere AJ. Defoliation induces fructan 1-exohydrolase II in Witloof chicory roots. Cloning and purification of two isoforms, fructan 1-exohydrolase IIa and fructan 1-exohydrolase IIb. Mass fingerprint of the fructan 1-exohydrolase II enzymes. PLANT PHYSIOLOGY 2001; 126:1186-95. [PMID: 11457968 PMCID: PMC116474 DOI: 10.1104/pp.126.3.1186] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2001] [Accepted: 02/22/2001] [Indexed: 05/17/2023]
Abstract
The cloning of two highly homologous chicory (Cichorium intybus var. foliosum cv Flash) fructan 1-exohydrolase cDNAs (1-FEH IIa and 1-FEH IIb) is described. Both isoenzymes could be purified from forced chicory roots as well as from the etiolated "Belgian endive" leaves where the 1-FEH IIa isoform is present in higher concentrations. Full-length cDNAs were obtained by a combination of reverse transcriptase-polymerase chain reaction (PCR), PCR and 5'- and 3'-rapid amplification of cDNA ends using primers based on N-terminal and conserved amino acid sequences. 1-FEH IIa and 1-FEH IIb cDNA-derived amino acid sequences are most homologous to a new group of plant glycosyl hydrolases harboring cell wall-type enzymes with acid isoelectric points. Unlike the observed expression profiles of chicory 1-FEH I, northern analysis revealed that 1-FEH II is expressed when young chicory plants are defoliated, suggesting that this enzyme can be induced at any developmental stage when large energy supplies are necessary (regrowth after defoliation).
Collapse
Affiliation(s)
- W Van den Ende
- Department of Biology, Laboratory for Developmental Biology, Botany Institute, K.U. Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium.
| | | | | | | | | | | |
Collapse
|
40
|
García B, Castellanos A, Menéndez J, Pons T. Molecular cloning of an alpha-glucosidase-like gene from Penicillium minioluteum and structure prediction of its gene product. Biochem Biophys Res Commun 2001; 281:151-8. [PMID: 11178973 DOI: 10.1006/bbrc.2001.4316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The dexC cDNA, which is expressed in dextran-containing medium by the filamentous fungus Penicillium minioluteum, was cloned and sequence characterized. The cDNA sequence comprises 1859 bp plus a poly (A) tail, coding for a predicted protein of 597 amino acids. The genomic counterpart was isolated by PCR, finding three introns in its sequence. The dexC gene was located by Southern blot in the same 9-kb fragment that the previously isolated dextranase-encoding gene (dexA). Sequence analysis revealed that the deduced DexC protein belongs to glycosyl hydrolase family 13, showing a high sequence identity (58%) with Aspergillus parasiticus alpha-1,6-glucosidase. In addition, the high sequence identity (51%) between DexC protein and oligo-1,6-glucosidase of Bacillus cereus, with three-dimensional (3D) structure determined, leads us to proposed a 3D model for the structural core of DexC protein.
Collapse
Affiliation(s)
- B García
- Centro de Ingeniería Genética y Biotecnología (CIGB), Havana, Cuba
| | | | | | | |
Collapse
|
41
|
Smyth E, Syme CD, Blanch EW, Hecht L, Vasák M, Barron LD. Solution structure of native proteins with irregular folds from Raman optical activity. Biopolymers 2001; 58:138-51. [PMID: 11093113 DOI: 10.1002/1097-0282(200102)58:2<138::aid-bip30>3.0.co;2-w] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Raman optical activity (ROA) spectra have been measured for the proteins hen phosvitin, yeast invertase, bovine alpha-casein, soybean Bowman-Birk protease inhibitor, and rabbit Cd(7)-metallothionein, all of which have irregular folds in the native state. The results show that ROA is able to distinguish between two types of disorder. Specifically, invertase, alpha-casein, the Bowman-Birk inhibitor, and metallothionein appear to possess a "static" type of disorder similar to that in disordered states of poly(L-lysine) and poly(L-glutamic acid); whereas phosvitin appears to possess a more "dynamic" type of disorder similar to that in reduced (unfolded) lysozyme and ribonuclease A and also in molten globule protein states. In the delimiting cases, static disorder corresponds to that found in loops and turns within native proteins with well-defined tertiary folds that contain sequences of residues with fixed but nonrepetitive phi,psi angles; and dynamic disorder corresponds to that envisaged for the model random coil in which there is a distribution of Ramachandran phi,psi angles for each amino acid residue, giving rise to an ensemble of interconverting conformers. In both cases there is a propensity for the phi,psi angles to correspond to the alpha, beta and poly(L-proline) II (PPII) regions of the Ramachandran surface, as in native proteins with well-defined tertiary folds. Our results suggest that, with the exception of invertase and metallothionein, an important conformational element present in the polypeptide and protein states supporting the static type of disorder is that of the PPII helix. Long sequences of relatively unconstrained PPII helix, as in alpha-casein, may impart a plastic (rheomorphic) character to the structure.
Collapse
Affiliation(s)
- E Smyth
- Chemistry Department, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Comparison of the amino acid sequences of four families of glycosyl hydrolases reveals that they are homologous and have several common conserved regions. Two of these families contain beta-fructosidases (glycosyl hydrolase families GH32 and GH68) and the other two include alpha-L-arabinases and beta-xylosidases (families GH43 and GH62). The latter two families are proposed to be grouped together with the former two into the beta-fructosidase (furanosidase) superfamily. Several ORFs can be considered as a fifth family of the superfamily on the basis of sequence similarity. It is shown for the first time that a glycosyl hydrolase superfamily can include enzymes with both inversion and retention mechanism of action. Composition of the active center for enzymes of the superfamily is discussed.
Collapse
Affiliation(s)
- D G Naumoff
- State Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia.
| |
Collapse
|
43
|
Pons T, Hernández L, Batista FR, Chinea G. Prediction of a common beta-propeller catalytic domain for fructosyltransferases of different origin and substrate specificity. Protein Sci 2000; 9:2285-91. [PMID: 11305239 PMCID: PMC2144480 DOI: 10.1110/ps.9.11.2285] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The three-dimensional (3D) structure of fructan biosynthetic enzymes is still unknown. Here, we have explored folding similarities between reported microbial and plant enzymes that catalyze transfructosylation reactions. A sequence-structure compatibility search using TOPITS, SDP, 3D-PSSM, and SAM-T98 programs identified a beta-propeller fold with scores above the confidence threshold that indicate a structurally conserved catalytic domain in fructosyltransferases (FTFs) of diverse origin and substrate specificity. The predicted fold appeared related to that of neuraminidase and sialidase, of glycoside hydrolase families 33 and 34, respectively. The most reliable structural model was obtained using the crystal structure of neuraminidase (Protein Data Bank file: 5nn9) as template, and it is consistent with the location of previously identified functional residues of bacterial levansucrases (Batista et al., 1999; Song & Jacques, 1999). The sequence-sequence analysis presented here reinforces the recent inclusion of fungal and plant FTFs into glycoside hydrolase family 32, and suggests a modified sequence pattern H-x (2)-[PTV]-x (4)-[LIVMA]-[NSCAYG]-[DE]-P-[NDSC][GA]3 for this family.
Collapse
Affiliation(s)
- T Pons
- Centro de Ingeniería Genética y Biotecnología (CIGB), Havana, Cuba.
| | | | | | | |
Collapse
|
44
|
Abstract
Recently solved structures and proposed models have helped to reveal the structural characteristics of the beta-propeller fold, as well as the features that contribute to its high rigidity and stability. Possible strategies for identifying beta-propeller proteins in newly characterised sequences are helping to overcome the problems of predicting the beta-propeller fold from amino acid sequences.
Collapse
Affiliation(s)
- V Fülöp
- Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | | |
Collapse
|