Molecular cloning and sequence analysis of an endoinulinase gene from Penicillium sp. strain TN-88

In Silico evaluation and identification of fungi capable of producing endo-inulinase enzyme

The enzyme endo-inulinase hydrolyzes inulin to short chain fructooligosaccharides (FOS) that are potential prebiotics with many health promoting benefits. Although the raw materials for inulin production are inexpensive and readily available, commercial production of FOS from inulin is limited due to inadequate availability of the enzyme source. This study aimed to identify the fungi capable of producing endo-inulinase based on the in silico analysis of proteins retrieved from non-redundant protein sequence database. The endo-inulinase of Aspergillus ficuum was used as reference sequence. The amino acid sequences with >90% sequence coverage, belonging to different fungi were retrieved from the database and used for constructing three-dimensional (3D) protein models using SWISS-MODEL and Bagheerath H. The 3D models of comparable quality as that of the reference endo-inulinase were selected based on QMEAN Z score. The selected models were evaluated and validated for different structural and functional qualities using Pro-Q, ProSA, PSN-QA, VERIFY-3D, PROCHECK, PROTSAV metaserver, STRAP, molecular docking, and molecular dynamic simulation analyses. A total of 230 proteins belonging to 53 fungal species exhibited sequence coverage >90%. Sixty one protein sequences with >60% sequence identity were modeled as endo-inulinase with higher QMEAN Z Score. The evaluations and validations of these 61 selected models for different structural and functional qualities revealed that 60 models belonging to 22 fungal species exhibited native like structure and unique motifs and residues as that of the reference endo-inulinase. Further, these models also exhibited similar kind of interaction between the active site around the conserved glutamate residue and substrate as that of the reference endo-inulinase. In conclusion, based on the current study, 22 fungal species could be identified as endo-inulinase producer. Nevertheless, further biological assessment of their capability for producing endo-inulinase is imminent if they are to be used for commercial endo-inulinase production for application in FOS industry.

Prebiotic Oligosaccharides: Special Focus on Fructooligosaccharides, Its Biosynthesis and Bioactivity

The bacterial groups in the gut ecosystem play key role in the maintenance of host's metabolic and structural functionality. The gut microbiota enhances digestion processing, helps in digestion of complex substances, synthesizes beneficial bioactive compounds, enhances bioavailability of minerals, impedes growth of pathogenic microbes, and prevents various diseases. It is, therefore, desirable to have an adequate intake of prebiotic biomolecules, which promote favorable modulation of intestinal microflora. Prebiotics are non-digestible and chemically stable structures that significantly enhance growth and functionality of gut microflora. The non-digestible carbohydrate, mainly oligosaccharides, covers a major part of total available prebiotics as dietary additives. The review describes the types of prebiotic low molecular weight carbohydrates, i.e., oligosaccharides, their structure, biosynthesis, functionality, and applications, with a special focus given to fructooligosaccharides (FOSs). The review provides an update on enzymes executing hydrolytic and fructosyltransferase activities producing prebiotic FOS biomolecules, and future perspectives.

Molecular characterization and expression of microbial inulinase genes

Many genes encoding exo- and endo-inulinases from bacteria, yeasts and filamentous fungi have been cloned and characterized. All the inulinases have several conserved motifs, such as WMND(E)PNGL, RDP, EC(V)P, SVEVF, Q and FS(T), which play an important role in inulinase catalysis and substrate binding. However, the exo-inulinases produced by yeasts has no conserved motif SVEVF and the yeasts do not produce any endo-inulinase. Exo- and endo-inulinases found in different microorganisms cluster separately at distant positions from each other. Most of the cloned inulinase genes have been expressed in Yarrowia lipolytica, Saccharomyces cerevisiae, Pichia pastoris, Klyuveromyces lactis and Escherichia coli, respectively. The recombinant inulinases produced and the engineered hosts using the cloned inulinase genes have many potential applications. Expression of most of the inulinase genes is repressed by glucose and fructose and induced by inulin and sucrose. However, the detailed mechanisms of the repression and induction are still unknown.

Gene cloning and enzyme structure modeling of the Aspergillus oryzae N74 fructosyltransferase

The fructooligosaccharides (FOS) represent an important source of prebiotic compounds that are widely used as an ingredient in functional foods. Recently, the strain Aspergillus oryzae N74 was reported as a potential microorganism for the industrial production of FOS, due to its high yields of FOS production. In this work, we used a PCR-cloning strategy to clone the A. oryzae N74 ftase gene as a previous step for recombinant enzyme production. Ftase showed a 1630 bp size with a 99% similarity with other A. oryzae strains and between 1 to 68% identities with other Aspergillus strains. This gene encodes for a 525 amino acids protein with 99% similarity with other A. oryzae strains and between 11 to 69% similarities with other Aspergillus strains. Finally, an A. oryzae N74 FTase tertiary structure model was predicted base on its similarity with other glycoside hydrolase 32 family members. The active site was located inside the β-propeller domain and was formed for non-charged polar and charged amino acids. In summary, these results shows the high level of sequence conservation between A. oryzae strains and represent a first step towards the development of a FOS production industrial process using recombinant microorganism carrying the ftase gene from A. oryzae N74.

Functional characterization and evolutionary implication of the internal 157-amino-acid sequence of an exoinulinase from Penicillium sp. strain TN-88

An extracellular exoinulinase from the filamentous fungus Penicillium sp. strain TN-88 has a 14-fold higher specific activity of 743 U/mg toward inulin than its equivalent from the Aspergillus niger strain 12 and possesses an internal 157-amino-acid sequence whose corresponding region is absent in the A. niger enzyme. On the basis of sequence alignment, the internal region D' encoding the 157-amino-acid sequence in the Penicillium exoinulinase gene inuD cDNA was inserted into the site between the nucleotides 897 and 898 of the A. niger exoinulinase gene inuE cDNA. The resultant inuE::D' fusion was expressed in the methylotrophic yeast Pichia pastoris. The K(m) value of the secreted hybrid enzyme InuE::D' for inulin hydrolysis was about 1/15 that of the A. niger InuE, whereas its k(cat) value did not differ greatly from that of the InuE. These observations indicate that the Penicillium exoinulinase has evolved by the horizontal transfer and integration of a relevant DNA segment and that the internal sequence D' functions as an additional noncatalytic inulin-affinity region.

Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger

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.

Quantitative expression analysis of inulinase gene cluster of Penicillium sp. strain TN-88

The filamentous fungus Penicillium sp. strain TN-88 carries the endoinulinase gene inuC and the exoinulinase gene inuD that are linked head-to-head on the genome and divergently transcribed from an 859-bp intergenic region [Moriyama et al., Biosci. Biotechnol. Biochem., 66, 1887-1896 (2002)]. Quantitative real-time PCR amplification revealed that the transcription levels of the inuC and inuD genes increased 42- and 3260-fold in inulin-grown mycelia, respectively. Sucrose as well as fructose did not induce the expression of the inuC or inuD gene at all. The levels of inuC and inuD transcripts in mycelia grown on the glucose/inulin mixture were both below their basal levels in glucose-grown mycelia. Thus, glucose exerts a strong carbon catabolite repression on the expression of the two genes.

Purification and properties of a family-10 xylanase from Aureobasidium pullulans ATCC 20524 and characterization of the encoding gene

An extracellular endo-1,4-beta-xylanase was purified from the culture supernatant of the ascomycete Aureobasidium pullulans ATCC 20524 grown on xylan. The purified enzyme was homogeneous as judged by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and isoelectric focusing, which showed an apparent M (r) of 39 kDa and a pI of 8.9, respectively. Xylanase activity was optimal at pH 6.0 and 70 degrees C. The genomic DNA and cDNAs encoding this protein were cloned and sequenced. The xylanase gene (xynII) encoded a 26 amino acid signal peptide and a 335 amino acid mature protein. DNA regions encoding the signal sequence and the mature protein were interrupted by introns of 56 and 73 bp, respectively. The xynII 5'-noncoding region had two consensus binding sites (5'-GCCARG-3') for the transcription factor PacC mediating pH regulation. Quantitative real-time polymerase chain reaction analysis revealed that the transcription levels at pH 6.0 and 8.0 were 8-fold and 22-fold higher than that at pH 2.7, respectively. A cloned xynII cDNA was expressed and secreted in the yeast Pichia pastoris. Sequence alignment and phylogenetic analysis suggested that the XynII belongs to glycosyl hydrolase family 10 and that it is evolutionarily distant from two clusters formed by other family-10 xylanases.

Purification and properties of an extracellular endo-1,4-β-xylanase from Penicillium citrinum and characterization of the encoding gene

An extracellular endo-1,4-beta-xylanase was purified from the culture filtrate of a filamentous fungus Penicillium citrinum FERM P-15944 grown on birch-wood xylan. The purified enzyme showed a single band on SDS-PAGE with an apparent M(r) of 20,000 and had an isoelectric point below 3.5. Xylanase activity was optimal at pH 5.0 and 55 degrees C. The genomic DNA and cDNAs encoding this protein were cloned and sequenced. Southern blot analysis indicated that the xylanase gene (xynA) was present as a single copy in the genome. An open reading frame of 657 bp was interrupted by two introns of 65 and 55 bp, and encoded a presumed prepropeptide of 27 amino acids and a mature protein of 190 amino acids. Three distinct transcription start points were observed at positions -20 (A), -31 (A), and -36 (A) from the start codon. The 5'-noncoding region had a putative TATA box at nt -66 (TATAAA). The xynA cDNA was functionally expressed under the control of the alcohol oxidase I gene promoter in the methylotrophic yeast Pichia pastoris. A neighbor-joining tree showed that the P. citrinum enzyme is closely related to several other fungal xylanases belonging to the glycoside hydrolase family 11: Trichoderma reesei XYN2, Aspergillus niger xynNB, Penicillium funiculosum xynC, Penicillium sp. strain 40 xynA, Chaetomium gracile cgxB, and Aspergillus nidulans xlnA and xlnB.

Molecular cloning and characterization of an exoinulinase gene from Aspergillus niger strain 12 and its expression in Pichia pastoris

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.

Purification and Characterization of an Acidophilic Xylanase from Aureobasidium pullulans var. melanigenum and Sequence Analysis of the Encoding Gene

An extracellular endo-1,4-beta-xylanase was purified from the culture supernatant of Aureobasidium pullulans var. melanigenum (ATCC 20524) grown on oat-spelt xylan. The purified enzyme showed a single band on SDS-polyacrylamide gel electrophoresis with an apparent M(r) of 24 kDa and had an isoelectric point of 6.7. Xylanase activity was optimal at pH 2.0 and 50 degrees C. The genomic DNA and cDNAs encoding this protein were cloned and sequenced. Southern blot analysis indicated that the xylanase gene (xynI) was present as a single copy in the genome. An open reading frame, consisting of 663 bp, encoded a presumed prepropeptide of 34 amino acids and a mature protein of 187 amino acid. The DNA region encoding the prepeptide was interrupted by a 59-bp intron. A single transcription start point was observed at position -46 (A) from the start codon. The 5'-noncoding region had a putative TATA box at -91 (TATATAA) and two possible CCAAT boxes at -247 (CAAT) and -283 (CCAAT). A cloned xynI cDNA was expressed in Saccharomyces cerevisiae. The deduced amino acid sequence showed 94% identity with that of a previously reported equivalent gene (xynA) encoding a xylanase with an optimal pH of 4.8 from a color variant strain, NRRL Y-2311-1, of A. pullulans. A neighbor-joining tree showed that the Aureobasidium enzymes are closely related to several other family-11 xylanases from black aspergilli and Penicillium purpurogenum.