1
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McGee R, Dean GH, Wu D, Zhang Y, Mansfield SD, Haughn GW. Pectin Modification in Seed Coat Mucilage by In Vivo Expression of Rhamnogalacturonan-I- and Homogalacturonan-Degrading Enzymes. PLANT & CELL PHYSIOLOGY 2021; 62:1912-1926. [PMID: 34059917 DOI: 10.1093/pcp/pcab077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 05/31/2021] [Indexed: 05/27/2023]
Abstract
The cell wall is essential for plant survival. Determining the relationship between cell wall structure and function using mutant analysis or overexpressing cell wall-modifying enzymes has been challenging due to the complexity of the cell wall and the appearance of secondary, compensatory effects when individual polymers are modified. In addition, viability of the plants can be severely impacted by wall modification. A useful model system for studying structure-function relationships among extracellular matrix components is the seed coat epidermal cells of Arabidopsis thaliana. These cells synthesize relatively simple, easily accessible, pectin-rich mucilage that is not essential for plant viability. In this study, we expressed enzymes predicted to modify polysaccharide components of mucilage in the apoplast of seed coat epidermal cells and explored their impacts on mucilage. The seed coat epidermal-specific promoter TESTA ABUNDANT2 (TBA2) was used to drive expression of these enzymes to avoid adverse effects in other parts of the plant. Mature transgenic seeds expressing Rhamnogalacturonate lyase A (RglA) or Rhamnogalacturonate lyase B (RglB) that degrade the pectin rhamnogalacturonan-I (RG-I), a major component of mucilage, had greatly reduced mucilage capsules surrounding the seeds and concomitant decreases in the monosaccharides that comprise the RG-I backbone. Degradation of the minor mucilage component homogalacturonan (HG) using the HG-degrading enzymes Pectin lyase A (PLA) or ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE2 (ADPG2) resulted in developing seed coat epidermal cells with disrupted cell-cell adhesion and signs of early cell death. These results demonstrate the feasibility of manipulating the seed coat epidermal cell extracellular matrix using a targeted genetic engineering approach.
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Affiliation(s)
- Robert McGee
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
- L'Institut National de la Recherche Scientifique Centre Armand-Frappier Santé Biotechnologie (INRS-CAFSB), 531 des Prairies Blvd. Laval, QC, H7V 1B7, Canada
| | - Gillian H Dean
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Di Wu
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
- Faculty of Land and Food Systems, University of British Columbia, 248-2357 Main Mall Vancouver, BC V6T 1Z4, Canada
| | - Yuelin Zhang
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, 2900-2424 Main Mall Vancouver, BC V6T 1Z4, Canada
| | - George W Haughn
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
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2
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Kunishige Y, Iwai M, Nakazawa M, Ueda M, Tada T, Nishimura S, Sakamoto T. Crystal structure of exo‐rhamnogalacturonan lyase fromPenicillium chrysogenumas a member of polysaccharide lyase family 26. FEBS Lett 2018; 592:1378-1388. [DOI: 10.1002/1873-3468.13034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Yuika Kunishige
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Marin Iwai
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Masami Nakazawa
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Mitsuhiro Ueda
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Toshiji Tada
- Department of Biological Science Graduate School of Science Osaka Prefecture University Sakai Japan
| | - Shigenori Nishimura
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
| | - Tatsuji Sakamoto
- Division of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University Sakai Japan
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3
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Lara-Márquez A, Oyama K, Zavala-Páramo MG, Villa-Rivera MG, Conejo-Saucedo U, Cano-Camacho H. Evolutionary Analysis of Pectin Lyases of the Genus Colletotrichum. J Mol Evol 2017; 85:120-136. [PMID: 29071357 DOI: 10.1007/s00239-017-9812-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022]
Abstract
Pectin lyases (PNLs) are important enzymes that are involved in plant cell wall degradation during the infection process. Colletotrichum is a diverse genus of fungi, which allows the study of the evolution of PNLs and their possible role in pathogen-host interactions and lifestyle adaptations. The phylogenetic reconstruction of PNLs from Colletotrichum and analysis of selection pressures showed the formation of protein lineages by groups of species with different selection pressures and specific patterns. The analysis of positive selection at individual sites using different methods allowed for the identification of three codons with evidence of positive selection in the oligosaccharide-binding region and two codons on the antiparallel sheet, which may influence the interaction with the substrate. Seven codons on the surface of the protein, mainly in the peripheral helices of the PNLs, could have an important function in evasion of plant defenses, as has been proposed in other enzymes. According to our results, it is possible that events of genetic duplication occurred in ancestral lines, followed by episodes of genetic diversification and gene loss, probably influenced by differences in the composition of the host cell wall. Additionally, different patterns of evolution in Colletotrichum appear to be molded by a strong purifying selection and positive selection episodes that forged the observed evolutionary patterns, possibly influenced by host interaction or substrate specificity. This work represents a starting point for the study of sites that may be important for evasion of plant defenses and biotechnological purposes.
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Affiliation(s)
- Alicia Lara-Márquez
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, México
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, México
| | - María G Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Maria G Villa-Rivera
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Ulises Conejo-Saucedo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.
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4
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Zhou C, Xue Y, Ma Y. Characterization and overproduction of a thermo-alkaline pectate lyase from alkaliphilic Bacillus licheniformis with potential in ramie degumming. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Hadj Sassi A, Trigui-Lahiani H, Abdeljalil S, Gargouri A. Enhancement of solubility, purification and inclusion-bodies-refolding of an active pectin lyase from Penicillium occitanis expressed in Escherichia coli. Int J Biol Macromol 2016; 95:256-262. [PMID: 27845226 DOI: 10.1016/j.ijbiomac.2016.11.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/12/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
Pectin lyase (pnl) is the only pectinase able to hydrolyze directly the highly methylated pectin without liberating the toxic methanol and without disturbing ester content responsible for specific aroma of juices. The cDNA of Penicillium occitanis pnl (mature form) was cloned into pET-21a as expression vector and over-expressed into Esherichia coli. Most of recombinant pnl was expressed as inclusion bodies. Pnl activity was confirmed by colorimetric assay. To enhance the solubility yield of the expressed pnl, the effects of induction temperature, host strain and expression level were optimized. Maximal production of functional pnl was obtained after induction by 0.4mM IPTG at 30°C and 150rpm for 16h. Interestingly, the use of Origami host strain, having an oxidized cytoplasm favoring disulfide bonds formation required for the active conformation of the enzyme, has significantly improved the yield of the soluble active form of recombinant pnl. This pnl was successfully purified through a single step purification using His-Trap affinity column chromatography. This work is the first to report pnl expression into Origami strain. Alternatively, the inclusion bodies were isolated, denatured by high concentration of urea and gradually refolded by successive dialysis, leading to their transformation into soluble and active form.
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Affiliation(s)
- Azza Hadj Sassi
- Laboratoire de Biotechnologie Moléculaire des Eucaryotes, Centre de Biotechnologie de Sfax, PB1177, University of Sfax, Tunisia
| | - Hèla Trigui-Lahiani
- Laboratoire de Biotechnologie Moléculaire des Eucaryotes, Centre de Biotechnologie de Sfax, PB1177, University of Sfax, Tunisia
| | - Salma Abdeljalil
- Laboratoire de Biotechnologie Moléculaire des Eucaryotes, Centre de Biotechnologie de Sfax, PB1177, University of Sfax, Tunisia
| | - Ali Gargouri
- Laboratoire de Biotechnologie Moléculaire des Eucaryotes, Centre de Biotechnologie de Sfax, PB1177, University of Sfax, Tunisia.
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6
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Rational Substitution of Surface Acidic Residues for Enhancing the Thermostability of Thermolysin. Appl Biochem Biotechnol 2015; 178:725-38. [DOI: 10.1007/s12010-015-1905-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022]
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7
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Heterologous expression of a Penicillium purpurogenum pectin lyase in Pichia pastoris and its characterization. Fungal Biol 2014; 118:507-15. [DOI: 10.1016/j.funbio.2014.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/11/2014] [Accepted: 04/02/2014] [Indexed: 11/20/2022]
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8
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Hung JE, Fogle EJ, Garg N, Chekan JR, Nair SK, van der Donk WA. Chemical rescue and inhibition studies to determine the role of Arg301 in phosphite dehydrogenase. PLoS One 2014; 9:e87134. [PMID: 24498026 PMCID: PMC3909101 DOI: 10.1371/journal.pone.0087134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/19/2013] [Indexed: 12/11/2022] Open
Abstract
Phosphite dehydrogenase (PTDH) catalyzes the NAD(+)-dependent oxidation of phosphite to phosphate. This reaction requires the deprotonation of a water nucleophile for attack on phosphite. A crystal structure was recently solved that identified Arg301 as a potential base given its proximity and orientation to the substrates and a water molecule within the active site. Mutants of this residue showed its importance for efficient catalysis, with about a 100-fold loss in k cat and substantially increased K m,phosphite for the Ala mutant (R301A). The 2.35 Å resolution crystal structure of the R301A mutant with NAD(+) bound shows that removal of the guanidine group renders the active site solvent exposed, suggesting the possibility of chemical rescue of activity. We show that the catalytic activity of this mutant is restored to near wild-type levels by the addition of exogenous guanidinium analogues; Brønsted analysis of the rates of chemical rescue suggests that protonation of the rescue reagent is complete in the transition state of the rate-limiting step. Kinetic isotope effects on the reaction in the presence of rescue agents show that hydride transfer remains at least partially rate-limiting, and inhibition experiments show that K i of sulfite with R301A is ∼400-fold increased compared to the parent enzyme, similar to the increase in K m for phosphite in this mutant. The results of our experiments indicate that Arg301 plays an important role in phosphite binding as well as catalysis, but that it is not likely to act as an active site base.
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Affiliation(s)
- John E. Hung
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Emily J. Fogle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Neha Garg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jonathan R. Chekan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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9
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Damak N, Abdeljalil S, Koubaa A, Trigui S, Ayadi M, Trigui-Lahiani H, Kallel E, Turki N, Djemal L, Belghith H, Taieb NH, Gargouri A. Cloning and heterologous expression of a thermostable pectate lyase from Penicillium occitanis in Escherichia coli. Int J Biol Macromol 2013; 62:549-56. [PMID: 24141072 DOI: 10.1016/j.ijbiomac.2013.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 10/26/2022]
Abstract
The entire pectate lyase cDNA (Pel1) of Penicillium occitanis was cloned from a cDNA bank and sequenced. The ORF exhibited a great homology to Penicillium marneffei and conservation of all features of fungal pectate lyases such as the barrel structure with "eight right-handed parallel β-helix" architecture. The structure modeling also showed the interesting resemblance with thermostable pectate lyases since several specific residues were also shared by Pel1 and these thermostable enzymes. Having shown that the enzyme retains its activity after endoH-mediated deglycosylation, we investigated its expression in Escherichia coli BL21 using the pET28-a vector. This expression was shown to be optimum when cells were induced at room temperature in 2YT medium rather than at 37 °C and LB medium. In such conditions, the recombinant protein was apparently produced more in soluble form than as inclusion bodies. The effect of NaCl concentration was investigated during the binding and elution steps of recombinant His-tagged enzyme on MagneHis Ni-particles. The purified enzyme was shown to retain its thermo-activity as well as a great tolerance to high concentration of NaCl and imidazole.
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Affiliation(s)
- Naourez Damak
- Laboratoire de Valorisation de la Biomasse et Production des Protéines chez les Eucaryotes, Centre de Biotechnologie de Sfax, Route Sidi Mansour Km 6, PO Box 1177, 3018 Sfax, Tunisia; University of Sfax, Tunisia
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10
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Andersen MR, Giese M, de Vries RP, Nielsen J. Mapping the polysaccharide degradation potential of Aspergillus niger. BMC Genomics 2012; 13:313. [PMID: 22799883 PMCID: PMC3542576 DOI: 10.1186/1471-2164-13-313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
Background The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation. Results Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from Aspergillus niger, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan. Conclusions The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in A. niger.
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Affiliation(s)
- Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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11
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Hung JE, Fogle EJ, Christman HD, Johannes TW, Zhao H, Metcalf WW, van der Donk WA. Investigation of the role of Arg301 identified in the X-ray structure of phosphite dehydrogenase. Biochemistry 2012; 51:4254-62. [PMID: 22564138 PMCID: PMC3361975 DOI: 10.1021/bi201691w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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Phosphite dehydrogenase (PTDH) from Pseudomonas
stutzeri catalyzes the nicotinamide adenine dinucleotide-dependent
oxidation
of phosphite to phosphate. The enzyme belongs to the family of d-hydroxy acid dehydrogenases (DHDHs). A search of the protein
databases uncovered many additional putative phosphite dehydrogenases.
The genes encoding four diverse candidates were cloned and expressed,
and the enzymes were purified and characterized. All oxidized phosphite
to phosphate and had similar kinetic parameters despite a low level
of pairwise sequence identity (39–72%). A recent crystal structure
identified Arg301 as a residue in the active site that has not been
investigated previously. Arg301 is fully conserved in the enzymes
shown here to be PTDHs, but the residue is not conserved in other
DHDHs. Kinetic analysis of site-directed mutants of this residue shows
that it is important for efficient catalysis, with an ∼100-fold
decrease in kcat and an almost 700-fold
increase in Km,phosphite for the R301A
mutant. Interestingly, the R301K mutant displayed a slightly higher kcat than the parent PTDH, and a more modest
increase in Km for phosphite (nearly 40-fold).
Given these results, Arg301 may be involved in the binding and orientation
of the phosphite substrate and/or play a catalytic role via electrostatic
interactions. Three other residues in the active site region that
are conserved in the PTDH orthologs but not DHDHs were identified
(Trp134, Tyr139, and Ser295). The importance of these residues was
also investigated by site-directed mutagenesis. All of the mutants
had kcat values similar to that of the
wild-type enzyme, indicating these residues are not important for
catalysis.
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Affiliation(s)
- John E Hung
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA
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12
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Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL, Larsen S, Leggio LL. Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus aculeatus. J Mol Biol 2010; 404:100-11. [DOI: 10.1016/j.jmb.2010.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/02/2010] [Accepted: 09/06/2010] [Indexed: 11/24/2022]
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13
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Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family. Appl Environ Microbiol 2008; 75:101-7. [PMID: 18978091 DOI: 10.1128/aem.01749-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The filamentous fungus Trichoderma reesei produces glucuronan lyase (TrGL) when it is grown on beta-(1-->4)-polyglucuronate (cellouronate) as a sole carbon source. The cDNA encoding TrGL was cloned, and the recombinant enzyme was heterologously expressed in Pichia pastoris. The cDNA of TrGL includes a 777-bp open reading frame encoding a 20-amino-acid signal peptide and the 238-amino-acid mature protein. The amino acid sequence showed no similarity to the amino acid sequences of previously described functional proteins, indicating that the enzyme should be classified in a novel polysaccharide lyase (PL) family. Recombinant TrGL catalyzed depolymerization of cellouronate endolytically by beta-elimination and was highly specific for cellouronate. The enzyme was most active at pH 6.5 and 50 degrees C, and its activity and thermostability increased in the presence of Ca2+, suggesting that its calcium dependence is similar to that of other PLs, such as pectate lyases.
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15
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Frankel BA, Tong Y, Bentley ML, Fitzgerald MC, McCafferty DG. Mutational analysis of active site residues in the Staphylococcus aureus transpeptidase SrtA. Biochemistry 2007; 46:7269-78. [PMID: 17518446 DOI: 10.1021/bi700448e] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Staphylococcus aureus, virulence and colonization-associated surface proteins are covalently anchored to the cell wall by the transpeptidase Sortase A (SrtA). In order to better understand the contribution of specific active site residues to substrate recognition and catalysis, we performed mutational analysis of several key residues in the SrtA active site. Analysis of protein stability, kinetic parameters, solvent isotope effects, and pH-rate profiles for key SrtA variants are consistent with a reverse protonated Cys184-His120 catalytic dyad, and implicate a role for Arg197 in formation of an oxyanion hole to stabilize the transition state. In contrast, mutation of Asp185 and Asp186 produced negligible effects on catalysis, and no evidence was found to support the existence of a functional catalytic triad. Mutation of Thr180, Leu181, and Ile182 to alanine produced modest decreases in SrtA activity and led to substrate inhibition. Thermodynamic stability measurements by SUPREX (stability of unpurified proteins from rates of H/D exchange) revealed decreases in conformational stability that correlate with the observed substrate inhibition for each variant, signifying a potential role for the conserved 180TLITC184 motif in defining the active-site architecture of SrtA. In contrast, mutation of Thr183 to alanine led to a significant 1200-fold decrease in kcat, which appears to be unrelated to conformational stability. Potential explanations for these results are discussed, and a revised model for SrtA catalysis is presented.
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Affiliation(s)
- Brenda A Frankel
- Department of Biochemistry and Biophysics and the Johnson Research Foundation, The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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16
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Trigui-Lahiani H, Gargouri A. Cloning, genomic organisation and mRNA expression of a pectin lyase gene from a mutant strain of Penicillium occitanis. Gene 2007; 388:54-60. [PMID: 17107764 DOI: 10.1016/j.gene.2006.09.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/06/2006] [Accepted: 09/22/2006] [Indexed: 11/30/2022]
Abstract
The regulatory cis elements of fungal pectinases are well studied in Aspergillus genera but little is known in other fungal species. A genomic bank from Penicillium occitanis fungus is constructed and screened by previously isolated cDNA probe of a pectin lyase. From several isolated clones, the nucleotide sequence of the pectin lyase gene was completed and led to the identification of introns and promoter-terminator regions. A streaking future was found in pnl gene of P. occitanis: it exhibits the highest nucleotide homology with the pnlA of Aspergillus niger but the positions of its 4 introns is completely identical to that of A. niger pnlB gene. In addition to the determination of transcription start site, the promoter sequence from the pnl gene was analysed. It showed the conservation of known consensus sequences -CreA, Hap2-3-4, PacC ...-, and the existence of a particular sequence -CCTGA- which is similar to that already found to be specific of pectinolytic gene in Aspergillus, CCCTGA. This result suggests that the corresponding regulatory trans-acting factor should be the same as in Aspergillus.
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MESH Headings
- 3' Flanking Region
- 5' Flanking Region
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Cloning, Molecular
- Codon
- DNA, Fungal/analysis
- DNA, Fungal/genetics
- Exons
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Fungal
- Genomic Library
- Introns
- Molecular Sequence Data
- Mutation
- Penicillium/enzymology
- Penicillium/genetics
- Phylogeny
- Polysaccharide-Lyases/genetics
- Polysaccharide-Lyases/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transcription Initiation Site
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Affiliation(s)
- Hèla Trigui-Lahiani
- Laboratoire de Génétique Moléculaire des Eucaryotes, Centre de Biotechnologie de Sfax, BP K 3038-Sfax, Tunisia
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17
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Affiliation(s)
- James P McEvoy
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
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18
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Guillén Schlippe YV, Hedstrom L. A twisted base? The role of arginine in enzyme-catalyzed proton abstractions. Arch Biochem Biophys 2005; 433:266-78. [PMID: 15581582 DOI: 10.1016/j.abb.2004.09.018] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Revised: 09/13/2004] [Indexed: 10/26/2022]
Abstract
Arginine residues are generally considered poor candidates for the role of general bases because they are predominantly protonated at physiological pH. Nonetheless, Arg residues have recently emerged as general bases in several enzymes: IMP dehydrogenase, pectate/pectin lyases, fumarate reductase, and l-aspartate oxidase. The experimental evidence suggesting this mechanistic function is reviewed. Although these enzymes have several different folds and distinct evolutionary origins, a common structural motif is found where the critical Arg residue is solvent accessible and adjacent to carboxylate groups. The chemistry of the guanidine group suggests unique strategies to lower the pK(a) of Arg. Lastly, the presumption that general bases must be predominantly deprotonated is revisited.
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