Genomic, Transcriptomic and Enzymatic Insight Into Lignocellulolytic System of a Plant Pathogen Dickeya Sp
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Enzymes Handling/Processing
Enzymes Handling/Processing 1 Identification of Petitioned Substance 2 3 This Technical Report addresses enzymes used in used in food processing (handling), which are 4 traditionally derived from various biological sources that include microorganisms (i.e., fungi and 5 bacteria), plants, and animals. Approximately 19 enzyme types are used in organic food processing, from 6 at least 72 different sources (e.g., strains of bacteria) (ETA, 2004). In this Technical Report, information is 7 provided about animal, microbial, and plant-derived enzymes generally, and more detailed information 8 is presented for at least one model enzyme in each group. 9 10 Enzymes Derived from Animal Sources: 11 Commonly used animal-derived enzymes include animal lipase, bovine liver catalase, egg white 12 lysozyme, pancreatin, pepsin, rennet, and trypsin. The model enzyme is rennet. Additional details are 13 also provided for egg white lysozyme. 14 15 Chemical Name: Trade Name: 16 Rennet (animal-derived) Rennet 17 18 Other Names: CAS Number: 19 Bovine rennet 9001-98-3 20 Rennin 25 21 Chymosin 26 Other Codes: 22 Prorennin 27 Enzyme Commission number: 3.4.23.4 23 Rennase 28 24 29 30 31 Chemical Name: CAS Number: 32 Peptidoglycan N-acetylmuramoylhydrolase 9001-63-2 33 34 Other Name: Other Codes: 35 Muramidase Enzyme Commission number: 3.2.1.17 36 37 Trade Name: 38 Egg white lysozyme 39 40 Enzymes Derived from Plant Sources: 41 Commonly used plant-derived enzymes include bromelain, papain, chinitase, plant-derived phytases, and 42 ficin. The model enzyme is bromelain. -
Comparison of Strand-Specific Transcriptomes Of
Landstorfer et al. BMC Genomics 2014, 15:353 http://www.biomedcentral.com/1471-2164/15/353 RESEARCH ARTICLE Open Access Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces Richard Landstorfer1, Svenja Simon2, Steffen Schober3, Daniel Keim2, Siegfried Scherer1 and Klaus Neuhaus1* Abstract Background: Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 (EHEC) are known, including animal products, fruit and vegetables. The ecology of this pathogen outside its human host is largely unknown and one third of its annotated genes are still hypothetical. To identify genetic determinants expressed under a variety of environmental factors, we applied strand-specific RNA-sequencing, comparing the SOLiD and Illumina systems. Results: Transcriptomes of EHEC were sequenced under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes in strain EDL933 (genome and plasmid), a surprising minority of only 144 had null sequencing reads under all conditions. We therefore developed a statistical method to distinguish weakly transcribed genes from background transcription. We find that 96% of all genes and 91.5% of the hypothetical genes exhibit a significant transcriptional signal under at least one condition. Comparing SOLiD and Illumina systems, we find a high correlation between both approaches for fold-changes of the induced or repressed genes. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. -
Generated by SRI International Pathway Tools Version 25.0, Authors S
An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility. -
Use of Plackett-Burman Design for Rapid Screening of Diverse Raw Pectin Sources for Cold-Active Polygalacturonase and Amylase Production by Geotrichum Sp
Int.J.Curr.Microbiol.App.Sci (2015) 4(6): 821-827 ISSN: 2319-7706 Volume 4 Number 6 (2015) pp. 821-827 http://www.ijcmas.com Original Research Article Use of Plackett-Burman Design for rapid Screening of Diverse Raw Pectin Sources for Cold-Active Polygalacturonase and Amylase Production by Geotrichum sp K. Divya and P. Naga Padma* Bhavan s Vivekananda College of Science, Humanities and Commerce, Secunderabad 94, India *Corresponding author A B S T R A C T Cold active polygalacturonases and amylases play significant role in extraction and clarification of fruit juices at industrial level. An optimized production medium with low cost substrates would be very useful for commercial production of these enzymes. The present study was done to screen low cost pectin and starch K e y w o r d s substrates for cold active enzymes production. The different pectin and starch sources screened were fruit and vegetables peels like citrus, pineapple, apple, Amylase, banana, mango, guava, carrot, beetroot, bottle gourd, ridge gourd and potato. For Cold-active efficient screening of the best sources a statistical design like Plackett-Burman was enzyme, used as in this design n variables can be studied in just n-1 experiments only. A Geotrichum sps, twelve experimental design Plackett-Burman was used as the best sources can be Poly shortlisted in consideration with their interactive effects. The pectinolytic and galacturonase, amylolytic yeast isolate was identified as Geotrichum sps and was used for the Plackett- present study. Cold-active pectinase and amylase enzyme activity was assayed by Burman, dinitrosalicylic acid (DNS) method. -
Transcriptomic Analysis of Staphylococcus Xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind
microorganisms Article Transcriptomic Analysis of Staphylococcus xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind 1, 2 1, 3, 4 Sabine Leroy *, Sergine Even , Pierre Micheau y, Anne de La Foye y, Valérie Laroute , Yves Le Loir 2 and Régine Talon 1 1 Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France; [email protected] (P.M.); [email protected] (R.T.) 2 INRAE, Agrocampus Ouest, STLO, Rennes, France; [email protected] (S.E.); [email protected] (Y.L.L.) 3 INRAE, UMRH, Saint-Genès-Champanelle, France; [email protected] 4 TBI, Université de Toulouse, CNRS, INRAE, Toulouse, France; [email protected] * Correspondence: [email protected] Current address: Université Clermont Auvergne, INRAE, UNH, Clermont-Ferrand, France. y Received: 26 October 2020; Accepted: 14 November 2020; Published: 17 November 2020 Abstract: Staphylococcus xylosus is found in the microbiota of traditional cheeses, particularly in the rind of soft smeared cheeses. Despite its frequency, the molecular mechanisms allowing the growth and adaptation of S. xylosus in dairy products are still poorly understood. A transcriptomic approach was used to determine how the gene expression profile is modified during the fermentation step in a solid dairy matrix. S. xylosus developed an aerobic metabolism perfectly suited to the cheese rind. It overexpressed genes involved in the aerobic catabolism of two carbon sources in the dairy matrix, lactose and citrate. Interestingly, S. xylosus must cope with nutritional shortage such as amino acids, peptides, and nucleotides, consequently, an extensive up-regulation of genes involved in their biosynthesis was observed. -
Supplementary Materials
Supplementary Materials Figure S1. Differentially abundant spots between the mid-log phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 3. Figure S2. Differentially abundant spots between the stationary phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 4. S2 Table S1. Summary of the non-polysaccharide degrading proteins identified in the B. proteoclasticus cytosol by 2DE/MALDI-TOF. Protein Locus Location Score pI kDa Pep. Cov. Amino Acid Biosynthesis Acetylornithine aminotransferase, ArgD Bpr_I1809 C 1.7 × 10−4 5.1 43.9 11 34% Aspartate/tyrosine/aromatic aminotransferase Bpr_I2631 C 3.0 × 10−14 4.7 43.8 15 46% Aspartate-semialdehyde dehydrogenase, Asd Bpr_I1664 C 7.6 × 10−18 5.5 40.1 17 50% Branched-chain amino acid aminotransferase, IlvE Bpr_I1650 C 2.4 × 10−12 5.2 39.2 13 32% Cysteine synthase, CysK Bpr_I1089 C 1.9 × 10−13 5.0 32.3 18 72% Diaminopimelate dehydrogenase Bpr_I0298 C 9.6 × 10−16 5.6 35.8 16 49% Dihydrodipicolinate reductase, DapB Bpr_I2453 C 2.7 × 10−6 4.9 27.0 9 46% Glu/Leu/Phe/Val dehydrogenase Bpr_I2129 C 1.2 × 10−30 5.4 48.6 31 64% Imidazole glycerol phosphate synthase Bpr_I1240 C 8.0 × 10−3 4.7 22.5 8 44% glutamine amidotransferase subunit Ketol-acid reductoisomerase, IlvC Bpr_I1657 C 3.8 × 10−16 -
Pectinase: a Useful Tool in Fruit Processing Industries
Mini Review Nutri Food Sci Int J - Volume 5 Issue 5 March 2018 Copyright © All rights are reserved by Jyoti Singh Jadaun DOI: 10.19080/NFSIJ.2018.05.555673 Pectinase: A Useful Tool in Fruit Processing Industries Heena Verma1, Lokesh K Narnoliya2 and Jyoti Singh Jadaun3* 1Department of Microbiology, Panjab university, India 2Department of Biotechnology (DBT), Center of Innovative and Applied Bioprocessing (CIAB), India 3Dyanand Girls Post Graduate College, India Submission: February 03, 2018; Published: March 07, 2018 *Corresponding author: Jyoti Singh Jadaun, Dyanand Girls Post Graduate College, 13/394, Parwati Bagla Rd, Kanpur, Uttar Pradesh 208001, India, Email: Abstract Owing to increase in the demand of fruit juices and fruit products, it became an indispensable need for the fruit processing industries to improve the quality of the fruit juices in a cost effective manner. Enzymes, being the highly efficient biocatalysts, are used at different steps in ofthe juice. process Visual of juiceacceptance production. of the Pectinases juice by the are consumers used for theneed clarification better clarity of the and juice improved by breaking colour thethat polysaccharide remain stable evenpectin during structure cold presentstorage inof the cellproduct. wall of plants into galacturonic acid monomers. Pectin structure breakage facilitates the filtration process and it increases the total yield Keywords: Abbreviations: Biocatalyst; PG: Polygalcturonase; Pectinase; Amylase; PE: Pectin Cellulase; Esterase; Pectin; PL: Starch;Pectin Lyase; Galacturonic -
Molecular Analysis of the Α-Amylase Gene, Astaag1, from Shoyu Koji Mold
Food Sci. Technol. Res., 19 (2), 255–261, 2013 Molecular Analysis of the α-Amylase Gene, AstaaG1, from Shoyu Koji Mold, Aspergillus sojae KBN1340 1* 1 1 2 1 Shoko YoShino-YaSuda , Emi Fujino , Junko MaTSui , Masashi kaTo and Noriyuki kiTaMoTo 1 Food Research Center, Aichi Center for Industry and Science Technology, 2-1-1 Shimpukuji-cho, Nishi-ku, Nagoya, Aichi 451-0083, Japan 2 Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi 468-8502, Japan Received October 1, 2012; Accepted November 28, 2012 Aspergillus sojae generally has only one ortholog of the Aspergillus oryzae taa (α-amylase) gene. The AstaaG1 gene from a shoyu koji mold, A. sojae KBN1340, comprised 2,063 bp with eight introns. AsTaaG1 consisted of 498 amino acid residues possessing high identity to other Aspergilli α-amylase sequences. Dis- ruption of the AstaaG1 gene resulted in no detectable α-amylase production in starch medium. Promoter activity of the AstaaG1 gene, monitored by xylanase activity, was upregulated with replacement of the CCAAT-like sequence. Site-directed mutation of the CCAAT-like sequence increased xylanase production approximately four times higher than that of the wild type. These results clearly demonstrate that the de- creased copy number of the taa gene and the low affinity binding sequence to the Hap complex lead to the lower amylolytic activity of A. sojae compared to that of A. oryzae. Keywords: amylase gene, Aspergillus sojae, CCAAT Introduction as Taka-amylase A (TAA) and has been studied extensively. The filamentous fungi Aspergillus sojae and Aspergil- A. -
Jejunal Mucosa Proteomics Unravel Metabolic Adaptive Processes to Mild Chronic Heat Stress in Dairy Cows Franziska Koch1, Dirk Albrecht2, Solvig Görs1 & Björn Kuhla1*
www.nature.com/scientificreports OPEN Jejunal mucosa proteomics unravel metabolic adaptive processes to mild chronic heat stress in dairy cows Franziska Koch1, Dirk Albrecht2, Solvig Görs1 & Björn Kuhla1* Climate change afects the duration and intensity of heat waves during summer months and jeopardizes animal health and welfare. High ambient temperatures cause heat stress in dairy cows resulting in a reduction of milk yield, feed intake, and alterations in gut barrier function. The objectives of this study were to investigate the mucosal amino acid, glucose and lactate metabolism, as well as the proteomic response of the small intestine in heat stressed (HS) Holstein dairy cows. Cows of the HS group (n = 5) were exposed for 4 days to 28 °C (THI = 76) in a climate chamber. Percentage decrease in daily ad libitum intake of HS cows was calculated to provide isocaloric energy intake to pair-fed control cows kept at 15 °C (THI = 60) for 4 days. The metabolite, mRNA and proteomic analyses revealed that HS induced incorrect protein folding, cellular destabilization, increased proteolytic degradation and protein kinase inhibitor activity, reduced glycolysis, and activation of NF-κB signaling, uronate cycling, pentose phosphate pathway, fatty acid and amino acid catabolism, mitochondrial respiration, ATPase activity and the antioxidative defence system. Our results highlight adaptive metabolic and immune mechanisms attempting to maintain the biological function in the small intestine of heat-stressed dairy cows. By the end of the twenty-frst century, mean ambient temperatures are predicted to increase resulting in a greater climate warming in the Northern hemisphere1. Consequently, both humans and animals are exposed to heat waves during summer months at a higher frequency, intensity and duration afecting behavior, health and welfare2,3. -
Lawrence Berkeley National Laboratory Recent Work
Lawrence Berkeley National Laboratory Recent Work Title What we can deduce about metabolism in the moderate halophile chromohalobacter salexigens from its genomic sequence Permalink https://escholarship.org/uc/item/1df4q5m5 Authors Csonka, Laszlo N. O'Connor, Kathleen Larimer, Frank et al. Publication Date 2005 eScholarship.org Powered by the California Digital Library University of California 1 Biodata of Laszlo N. Csonka, author of “What We Can Deduce about Metabolism in the Moderate Halophile Chromohalobacter salexigens from its Genomic Sequence” Dr. Laszlo Csonka is a professor in the Department of Biological Sciences at Purdue University. He received his Ph. D. in 1975 at Harvard Medical School in the laboratory of Dr. Dan Fraenkel, studying the pathways of NADPH formation in Escherichia coli. His main research interests are the analysis of the response to osmotic stress in bacteria and plants, the connection between osmotic adaptation and thermotolerance, and carbon- source metabolism in bacteria. E-mail: [email protected] 2 3 WHAT WE CAN DEDUCE ABOUT METABOLISM IN THE MODERATE HALOPHILE CHROMOHALOBACTER SALEXIGENS FROM ITS GENOMIC SEQUENCE LASZLO N. CSONKA1, KATHLEEN O’CONNOR1, FRANK LARIMER2, PAUL RICHARDSON3, ALLA LAPIDUS3, ADAM D. EWING4, BRADLEY W. GOODNER4 and AHARON OREN5 1Department of Biological Sciences, Purdue University, West Lafayette IN 47907-1392, USA; 2Genome Analysis and Systems Modeling, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA; 3DOE Joint Genome Institute, Walnut Creek CA 94598, USA; 4Department of Biology, Hiram College, Hiram OH 44234, USA; 5The Institute of Life Science, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, 91904, Israel 1. -
Enzymatic Synthesis of L-Fucose from L-Fuculose Using a Fucose Isomerase
Kim et al. Biotechnol Biofuels (2019) 12:282 https://doi.org/10.1186/s13068-019-1619-0 Biotechnology for Biofuels RESEARCH Open Access Enzymatic synthesis of L-fucose from L-fuculose using a fucose isomerase from Raoultella sp. and the biochemical and structural analyses of the enzyme In Jung Kim1†, Do Hyoung Kim1†, Ki Hyun Nam1,2 and Kyoung Heon Kim1* Abstract Background: L-Fucose is a rare sugar with potential uses in the pharmaceutical, cosmetic, and food industries. The enzymatic approach using L-fucose isomerase, which interconverts L-fucose and L-fuculose, can be an efcient way of producing L-fucose for industrial applications. Here, we performed biochemical and structural analyses of L-fucose isomerase identifed from a novel species of Raoultella (RdFucI). Results: RdFucI exhibited higher enzymatic activity for L-fuculose than for L-fucose, and the rate for the reverse reaction of converting L-fuculose to L-fucose was higher than that for the forward reaction of converting L-fucose to L-fuculose. In the equilibrium mixture, a much higher proportion of L-fucose (~ ninefold) was achieved at 30 °C and pH 7, indicating that the enzyme-catalyzed reaction favors the formation of L-fucose from L-fuculose. When biochemical analysis was conducted using L-fuculose as the substrate, the optimal conditions for RdFucI activity were determined to be 40 °C and pH 10. However, the equilibrium composition was not afected by reaction temperature in the range 2 of 30 to 50 °C. Furthermore, RdFucI was found to be a metalloenzyme requiring Mn + as a cofactor. The comparative crystal structural analysis of RdFucI revealed the distinct conformation of α7–α8 loop of RdFucI. -
Exoproteome Analysis of Clostridium Cellulovorans in Natural Soft
Esaka et al. AMB Express (2015) 5:2 DOI 10.1186/s13568-014-0089-9 ORIGINAL ARTICLE Open Access Exoproteome analysis of Clostridium cellulovorans in natural soft-biomass degradation Kohei Esaka1, Shunsuke Aburaya1, Hironobu Morisaka1,2, Kouichi Kuroda1 and Mitsuyoshi Ueda1,2* Abstract Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading various types of soft biomass. Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates. In this study, we performed a quantitative proteome analysis to determine changes in the extracellular proteins produced by C. cellulovorans for degradation of several types of natural soft biomass. C. cellulovorans was cultured in media containing bagasse, corn germ, rice straw (natural soft biomass), or cellobiose (control). Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant. Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins. Statistical analysis showed that 18 of the proteins were specifically produced during degradation of types of natural soft biomass. Interestingly, the protein Clocel_3197 was found and commonly involved in the degradation of every natural soft biomass studied. This protein may perform functions, in addition to its