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Assembly of the Cutin Polyester: From Cells to Extracellular Cell Walls. PLANTS 2017; 6:plants6040057. [PMID: 29156572 PMCID: PMC5750633 DOI: 10.3390/plants6040057] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 01/10/2023]
Abstract
Cuticular matrices covering aerial plant organs or delimiting compartments in these organs are composed of an insoluble hydrophobic polymer of high molecular mass, i.e., cutin, that encompass some cell wall polysaccharides and is filled by waxes. Cutin is a polyester of hydroxy and-or epoxy fatty acids including a low amount of glycerol. Screening of Arabidopsis and more recently of tomato (Solanum lycopersicum) mutants allowed the delineation of the metabolic pathway involved in the formation of cutin monomers, as well as their translocation in the apoplast. Furthermore, these studies identified an extracellular enzyme involved in the polymerization of these monomers, i.e., cutin synthase 1 (CUS1), an acyl transferase of the GDSL lipase protein family. By comparing the structure of tomato fruit cutins from wild type and down-regulated CUS1 mutants, as well as with the CUS1-catalyzed formation of oligomers in vitro, hypothetical models can be elaborated on the polymerization of cutins. The polymorphism of the GDSL-lipase family raises a number of questions concerning the function of the different isoforms in relation with the formation of a composite material, the cuticle, containing entangled hydrophilic and hydrophobic polymers, i.e., polysaccharides and cutin, and plasticizers, i.e., waxes.
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202
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Arkhipova IR, Yushenova IA, Rodriguez F. Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres. Mol Biol Evol 2017; 34:2245-2257. [PMID: 28575409 PMCID: PMC5850863 DOI: 10.1093/molbev/msx159] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3′-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple cooriented ORFs, including DEDDy 3′-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of interfamily variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer.
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Affiliation(s)
- Irina R Arkhipova
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA
| | - Irina A Yushenova
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA
| | - Fernando Rodriguez
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA
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203
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Gao M, Yin X, Yang W, Lam SM, Tong X, Liu J, Wang X, Li Q, Shui G, He Z. GDSL lipases modulate immunity through lipid homeostasis in rice. PLoS Pathog 2017; 13:e1006724. [PMID: 29131851 PMCID: PMC5703576 DOI: 10.1371/journal.ppat.1006724] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 11/27/2017] [Accepted: 10/31/2017] [Indexed: 12/04/2022] Open
Abstract
Lipids and lipid metabolites play important roles in plant-microbe interactions. Despite the extensive studies of lipases in lipid homeostasis and seed oil biosynthesis, the involvement of lipases in plant immunity remains largely unknown. In particular, GDSL esterases/lipases, characterized by the conserved GDSL motif, are a subfamily of lipolytic enzymes with broad substrate specificity. Here, we functionally identified two GDSL lipases, OsGLIP1 and OsGLIP2, in rice immune responses. Expression of OsGLIP1 and OsGLIP2 was suppressed by pathogen infection and salicylic acid (SA) treatment. OsGLIP1 was mainly expressed in leaf and leaf sheath, while OsGLIP2 showed high expression in elongating internodes. Biochemical assay demonstrated that OsGLIP1 and OsGLIP2 are functional lipases that could hydrolyze lipid substrates. Simultaneous down-regulation of OsGLIP1 and OsGLIP2 increased plant resistance to both bacterial and fungal pathogens, whereas disease resistance in OsGLIP1 and OsGLIP2 overexpression plants was significantly compromised, suggesting that both genes act as negative regulators of disease resistance. OsGLIP1 and OsGLIP2 proteins mainly localize to lipid droplets and the endoplasmic reticulum (ER) membrane. The proper cellular localization of OsGLIP proteins is indispensable for their functions in immunity. Comprehensive lipid profiling analysis indicated that the alteration of OsGLIP gene expression was associated with substantial changes of the levels of lipid species including monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). We show that MGDG and DGDG feeding could attenuate disease resistance. Taken together, our study indicates that OsGLIP1 and OsGLIP2 negatively regulate rice defense by modulating lipid metabolism, thus providing new insights into the function of lipids in plant immunity. Lipases are a large family of enzymes conferring lipid metabolism. Lipids and their metabolites play diverse roles in plant growth as well as response to environmental stimuli. Accumulating evidence implicates lipids as signaling molecules mediating plant immunity. Therefore, lipases are presumed to be actively involved in plant defense responses. Based on gene expression profiling, we have identified two functional GDSL lipases, encoded by OsGLIP1 and OsGLIP2, whose expression was suppressed by pathogen infection in the model cereal rice. Both OsGLIP1 and OsGLIP2 proteins localize to lipid droplets and the endoplasmic reticulum (ER) membrane, and they likely coordinate lipid metabolism with differential but complementary expression patterns in tissues and developmental stages. Consequently, alteration of OsGLIP gene expression was associated with substantial changes of lipid abundance and plant disease resistance. Our work identifies and characterizes two lipases that function as negative regulators of plant immune responses, strengthening the understanding of lipid metabolism in plant-microbe interactions.
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Affiliation(s)
- Mingjun Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Yin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Tong
- China National Rice Research Institute, Hangzhou, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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204
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Li C, Chen G, Mishina K, Yamaji N, Ma JF, Yukuhiro F, Tagiri A, Liu C, Pourkheirandish M, Anwar N, Ohta M, Zhao P, Lundqvist U, Li X, Komatsuda T. A GDSL-motif esterase/acyltransferase/lipase is responsible for leaf water retention in barley. PLANT DIRECT 2017; 1:e00025. [PMID: 31245672 PMCID: PMC6508521 DOI: 10.1002/pld3.25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/21/2017] [Accepted: 10/06/2017] [Indexed: 05/19/2023]
Abstract
The hydrophobic cuticle covers the surface of the most aerial organs of land plants. The barley mutant eceriferum-zv (cer-zv), which is hypersensitive to drought, is unable to accumulate a sufficient quantity of cutin in its leaf cuticle. The mutated locus has been mapped to a 0.02 cM segment in the pericentromeric region of chromosome 4H. As a map-based cloning approach to isolate the gene was therefore considered unlikely to be feasible, a comparison was instead made between the transcriptomes of the mutant and the wild type. In conjunction with extant genomic information, on the basis of predicted functionality, only two genes were considered likely to encode a product associated with cutin formation. When eight independent cer-zv mutant alleles were resequenced with respect to the two candidate genes, it was confirmed that the gene underlying the mutation in each allele encodes a Gly-Asp-Ser-Leu (GDSL)-motif esterase/acyltransferase/lipase. The gene was transcribed in the epidermis, and its product was exclusively deposited in cell wall at the boundary of the cuticle in the leaf elongation zone, coinciding with the major site of cutin deposition. CER-ZV is speculated to function in the deposition of cutin polymer. Its homologs were found in green algae, moss, and euphyllophytes, indicating that it is highly conserved in plant kingdom.
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Affiliation(s)
- Chao Li
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Shanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghaiChina
- Shanghai Chenshan Plant Science Research CenterChinese Academy of SciencesShanghaiChina
| | - Guoxiong Chen
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid RegionsGansu ProvinceChina
- Northwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Shapotou Desert Research and Experimental StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Kohei Mishina
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Institute of Crop ScienceNAROKannondaiTsukubaIbarakiJapan
| | - Naoki Yamaji
- Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan
| | - Jian Feng Ma
- Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan
| | - Fumiko Yukuhiro
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
| | - Akemi Tagiri
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
| | - Cheng Liu
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Crop Research InstituteShandong Academy of Agricultural SciencesJi'nanChina
| | - Mohammad Pourkheirandish
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Faculty of Agriculture and EnvironmentPlant Breeding InstituteThe University of SydneyCobbittyNSWAustralia
| | - Nadia Anwar
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
| | - Masaru Ohta
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Institute of Crop ScienceNAROKannondaiTsukubaIbarakiJapan
| | - Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid RegionsGansu ProvinceChina
- Northwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Shapotou Desert Research and Experimental StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | | | - Xinrong Li
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid RegionsGansu ProvinceChina
- Northwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Shapotou Desert Research and Experimental StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Takao Komatsuda
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Institute of Crop ScienceNAROKannondaiTsukubaIbarakiJapan
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205
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Syal P, Verma VV, Gupta R. Targeted mutations and MD simulations of a methanol-stable lipase YLIP9 from Yarrowia lipolytica MSR80 to develop a biodiesel enzyme. Int J Biol Macromol 2017; 104:78-88. [DOI: 10.1016/j.ijbiomac.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 11/17/2022]
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206
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Sychantha D, Little DJ, Chapman RN, Boons GJ, Robinson H, Howell PL, Clarke AJ. PatB1 is an O-acetyltransferase that decorates secondary cell wall polysaccharides. Nat Chem Biol 2017; 14:79-85. [DOI: 10.1038/nchembio.2509] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/29/2017] [Indexed: 11/09/2022]
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207
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In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA). PLoS Pathog 2017; 13:e1006667. [PMID: 29077761 PMCID: PMC5697884 DOI: 10.1371/journal.ppat.1006667] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/21/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022] Open
Abstract
The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens, including species of Staphylococcus, Streptococcus and Enterococcus. This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and, as such, is recognized as a virulence factor. The key enzyme involved, peptidoglycan O-acetyltransferase A (OatA) represents a particular challenge to biochemical study since it is a membrane associated protein whose substrate is the insoluble peptidoglycan cell wall polymer. OatA is predicted to be bimodular, being comprised of an N-terminal integral membrane domain linked to a C-terminal extracytoplasmic domain. We present herein the first biochemical and kinetic characterization of the C-terminal catalytic domain of OatA from two important human pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Using both pseudosubstrates and novel biosynthetically-prepared peptidoglycan polymers, we characterized distinct substrate specificities for the two enzymes. In addition, the high resolution crystal structure of the C-terminal domain reveals an SGNH/GDSL-like hydrolase fold with a catalytic triad of amino acids but with a non-canonical oxyanion hole structure. Site-specific replacements confirmed the identity of the catalytic and oxyanion hole residues. A model is presented for the O-acetylation of peptidoglycan whereby the translocation of acetyl groups from a cytoplasmic source across the cytoplasmic membrane is catalyzed by the N-terminal domain of OatA for their transfer to peptidoglycan by its C-terminal domain. This study on the structure-function relationship of OatA provides a molecular and mechanistic understanding of this bacterial resistance mechanism opening the prospect for novel chemotherapeutic exploration to enhance innate immunity protection against Gram-positive pathogens. Multi-drug resistance amongst important human pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE) and drug-resistant Streptococcus pneumoniae (DRSP), continues to challenge clinicians and threaten the lives of infected patients. Of the several approaches being taken to address this serious issue is the development of antagonists that render the bacterial infection more susceptible to the defensive enzymes and proteins of our innate immunity systems. One such target is the enzyme O-acetyltransferase A (OatA). This extracellular enzyme modifies the essential bacterial cell wall component peptidoglycan and thereby makes it resistant to the lytic action of lysozyme, our first line of defense against invading pathogens. In this study, we present the first biochemical and structural characterization of OatA. Using both the S. aureus and S. pneumoniae enzymes as model systems, we demonstrate that OatA has unique substrate specificities. We also show that the catalytic domain of OatA is a structural homolog of a well-studied superfamily of hydrolases. It uses a catalytic triad of Ser-His-Asp to transfer acetyl groups specifically to the C-6 hydroxyl group of muramoyl residues within peptidoglycan. This information on the structure and function relationship of OatA is important for the future development of effective inhibitors which may serve as antivirulence agents.
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208
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Uttam GA, Praveen M, Rao YV, Tonapi VA, Madhusudhana R. Molecular mapping and candidate gene analysis of a new epicuticular wax locus in sorghum (Sorghum bicolor L. Moench). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2109-2125. [PMID: 28702690 DOI: 10.1007/s00122-017-2945-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/25/2017] [Indexed: 05/12/2023]
Abstract
A new epicuticular wax (bloom) locus has been identified and fine mapped to the 207.89 kb genomic region on chromosome 1. A putative candidate gene, Sobic.001G269200, annotated as GDSL-like lipase/acylhydrolase, is proposed as the most probable candidate gene involved in bloom synthesis/deposition. Deposition of epicuticular wax on plant aerial surface is one strategy that plants adapt to reduce non-transpiration water loss. Epicuticular wax (bloom)-less mutants in sorghum with their glossy phenotypes exhibit changes in the accumulation of epicuticular wax on leaf and culm surfaces. We report molecular mapping of a new sorghum locus, bloomless mutant (bm39), involved in epicuticular wax biosynthesis in sorghum. Inheritance studies involving a profusely bloom parent (BTx623) and a spontaneous bloomless mutant (RS647) indicated that the parents differed in a single gene for bloom synthesis. Bloomless was recessive to bloom deposition. Genetic mapping involving F2 and F7 mapping populations in diverse genetic backgrounds (BTx623 × RS647; 296A × RS647 and 27A × RS647) identified and validated the map location of bm39 to a region of 207.89 kb on chromosome 1. SSR markers, Sblm13 and Sblm16, flanked the bm39 locus to a map interval of 0.3 cM on either side. Nine candidate genes were identified, of which Sobic.001G269200 annotated for GDSL-like lipase/acylhydrolase is the most likely gene associated with epicuticular wax deposition. Gene expression analysis in parents, isogenic lines and sets of near isogenic lines also confirmed the reduced expression of the putative candidate gene. The study opens possibilities for a detailed molecular analysis of the gene, its role in epicuticular wax synthesis and deposition, and may help to understand its function in moisture stress tolerance and insect and pathogen resistance in sorghum.
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Affiliation(s)
- G Anurag Uttam
- Marker-Assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad, 500 030, India
| | - M Praveen
- Marker-Assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad, 500 030, India
| | - Y Venkateswara Rao
- Department of Botany, Andhra University, Visakhapatnam, Andhra Pradesh, India
| | - Vilas A Tonapi
- Marker-Assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad, 500 030, India
| | - R Madhusudhana
- Marker-Assisted Selection Laboratory, ICAR-Indian Institute of Millet Research (IIMR), Rajendranagar, Hyderabad, 500 030, India.
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209
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210
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Lai CP, Huang LM, Chen LFO, Chan MT, Shaw JF. Genome-wide analysis of GDSL-type esterases/lipases in Arabidopsis. PLANT MOLECULAR BIOLOGY 2017; 95:181-197. [PMID: 28840447 DOI: 10.1007/s11103-017-0648-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 08/03/2017] [Indexed: 05/19/2023]
Abstract
In this present study, we introduce a fundamental framework and provide information regarding the possible roles of GDSL-type esterase/lipase gene family in Arabidopsis. GDSL-type esterases/lipases are hydrolytic enzymes with multifunctional properties such as broad substrate specificity, regiospecificity, and stereoselectivity. In this study, we identified 105 GDSL-type esterase/lipase genes in Arabidopsis thaliana by conducting a comprehensive computational analysis. Expression studies indicated that GDSL-type lipase proteins showed varied expression patterns. Phylogenetic tree analysis indicated that AtGELP (Arabidopsis thaliana GDSL-type esterase/lipase protein) gene family was divided into four clades. The phylogenetic analysis, combined with protein motif architectures, and expression profiling were used to predict the roles AtGELP genes. To investigate the physical roles of the AtGELP gene family, we successfully screened 88 AtGELP T-DNA knockout lines for 54 AtGELP genes from 199 putative SALK T-DNA mutants. Transgenic plants of AtGELP genes were used to elucidate the phenotypic characteristics in various developmental stages or stress conditions. Our results suggest that the AtGELP genes have diverse physical functions such as affecting the germination rate and early growth of seedlings subjected to high concentrations of glucose, or being involved in biotic stress responses.
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Affiliation(s)
- Chia-Ping Lai
- Department of Food and Beverage Management, Far East University, Tainan, Taiwan, Republic of China
| | - Li-Min Huang
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, Republic of China
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan, Republic of China
| | - Long-Fang O Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, Republic of China
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ming-Tsair Chan
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, Republic of China
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan, Republic of China
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan, Republic of China
| | - Jei-Fu Shaw
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, Republic of China.
- Department of Biological Science and Technology, I-Shou University, Kaohsiung, Taiwan, Republic of China.
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan, Republic of China.
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, Republic of China.
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211
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Yadav VK, Yadav VK, Pant P, Singh SP, Maurya R, Sable A, Sawant SV. GhMYB1 regulates SCW stage-specific expression of the GhGDSL promoter in the fibres of Gossypium hirsutum L. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1163-1174. [PMID: 28182326 PMCID: PMC5552479 DOI: 10.1111/pbi.12706] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 05/19/2023]
Abstract
Secondary cell wall (SCW) biosynthesis is an important stage of the cotton fibre development, and its transcriptional regulation is poorly understood. We selected the Gossypium hirsutum GDSL (GhGDSL) lipase/hydrolase gene (CotAD_74480), which is expressed during SCW biosynthesis (19 through to 25 days postanthesis; DPA), for study. T1 -transgenic cotton lines expressing the β-glucuronidase (gus) reporter under the control of a 1026-bp promoter fragment of GhGDSL (PGhGDSL ) showed 19 DPA stage-specific increase in GUS expression. 5' deletion indicated that the 194-bp fragment between -788 and -594 relative to the transcription start site was essential for this stage-specific expression. Site-directed mutagenesis of eight transcription factor binding sites within PGhGDSL demonstrated that the MYB1AT motif (AAACCA) at -603/-598 was critical for the 19 DPA-specific reporter gene expressions. Yeast one-hybrid (Y1H) analysis identified nine proteins, including GhMYB1 (CotAD_64719) that bound to the PGhGDSL promoter. Further, Y1H experiments using the 5' promoter deletions and individually mutated promoter motifs indicated that GhMYB1 interacted with PGhGDSL at MYB1AT sequence. GhMYB1 was expressed specifically in fibre from 19 DPA, overlapping with the sharp rise in GhGDSL expression, indicating that it could regulate GhGDSL during fibre development. Analysis of genes co-expressed with GhMYB1 showed that it potentially regulates a number of other 19-25 DPA-specific genes in networks including those functioning in the cell wall and precursor synthesis, but not the major polysaccharide and protein components of the fibre SCW. GhGDSL and its promoter are therefore potential tools for the improvement of cotton fibre quality traits.
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Affiliation(s)
- Vrijesh Kumar Yadav
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
| | - Vikash Kumar Yadav
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
| | - Poonam Pant
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
| | - Surendra Pratap Singh
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
| | - Rashmi Maurya
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
| | - Anshulika Sable
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
| | - Samir V. Sawant
- Plant Molecular Biology LaboratoryCSIR‐National Botanical Research InstituteLucknowIndia
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐National Botanical Research InstituteLucknowIndia
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212
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Liu NY, Wang JQ, Zhang ZB, Huang JM, Zhu JY. Unraveling the venom components of an encyrtid endoparasitoid wasp Diversinervus elegans. Toxicon 2017; 136:15-26. [DOI: 10.1016/j.toxicon.2017.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/13/2017] [Accepted: 06/20/2017] [Indexed: 11/24/2022]
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213
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Jang KK, Lee ZW, Kim B, Jung YH, Han HJ, Kim MH, Kim BS, Choi SH. Identification and characterization of Vibrio vulnificus plpA encoding a phospholipase A 2 essential for pathogenesis. J Biol Chem 2017; 292:17129-17143. [PMID: 28855258 DOI: 10.1074/jbc.m117.791657] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/28/2017] [Indexed: 12/23/2022] Open
Abstract
The marine bacterium Vibrio vulnificus causes food-borne diseases, which may lead to life-threatening septicemia in some individuals. Therefore, identifying virulence factors in V. vulnificus is of high priority. We performed a transcriptome analysis on V. vulnificus after infection of human intestinal HT29-methotrexate cells and found induction of plpA, encoding a putative phospholipase, VvPlpA. Bioinformatics, biochemical, and genetic analyses demonstrated that VvPlpA is a phospholipase A2 secreted in a type II secretion system-dependent manner. Compared with the wild type, the plpA mutant exhibited reduced mortality, systemic infection, and inflammation in mice as well as low cytotoxicity toward the human epithelial INT-407 cells. Moreover, plpA mutation attenuated the release of actin and cytosolic cyclophilin A from INT-407 cells, indicating that VvPlpA is a virulence factor essential for causing lysis and necrotic death of the epithelial cells. plpA transcription was growth phase-dependent, reaching maximum levels during the early stationary phase. Also, transcription factor HlyU and cAMP receptor protein (CRP) mediate additive activation and host-dependent induction of plpA Molecular biological analyses revealed that plpA expression is controlled via the promoter, P plpA , and that HlyU and CRP directly bind to P plpA upstream sequences. Taken together, this study demonstrated that VvPlpA is a type II secretion system-dependent secretory phospholipase A2 regulated by HlyU and CRP and is essential for the pathogenicity of V. vulnificus.
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Affiliation(s)
- Kyung Ku Jang
- From the National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, and
| | - Zee-Won Lee
- From the National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, and
| | - Bityeoul Kim
- From the National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, and
| | - Young Hyun Jung
- the Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Medicine, BK21 PLUS Creative Veterinary Research Center, Seoul National University, Seoul 08826, South Korea and
| | - Ho Jae Han
- the Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Medicine, BK21 PLUS Creative Veterinary Research Center, Seoul National University, Seoul 08826, South Korea and
| | - Myung Hee Kim
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Byoung Sik Kim
- the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Sang Ho Choi
- From the National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, and
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Chen F, Cui G, Wang S, Nair MKM, He L, Qi X, Han X, Zhang H, Zhang JR, Su J. Outer membrane vesicle-associated lipase FtlA enhances cellular invasion and virulence in Francisella tularensis LVS. Emerg Microbes Infect 2017; 6:e66. [PMID: 28745311 PMCID: PMC5567169 DOI: 10.1038/emi.2017.53] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 01/10/2023]
Abstract
Francisella tularensis is a highly infectious intracellular pathogen that infects a wide range of host species and causes fatal pneumonic tularemia in humans. ftlA was identified as a potential virulence determinant of the F. tularensis live vaccine strain (LVS) in our previous transposon screen, but its function remained undefined. Here, we show that an unmarked deletion mutant of ftlA was avirulent in a pneumonia mouse model with a severely impaired capacity to infect host cells. Consistent with its sequence homology with GDSL lipase/esterase family proteins, the FtlA protein displayed lipolytic activity in both E. coli and F. tularensis with a preference for relatively short carbon-chain substrates. FtlA thus represents the first F. tularensis lipase to promote bacterial infection of host cells and in vivo fitness. As a cytoplasmic protein, we found that FtlA was secreted into the extracellular environment as a component of outer membrane vesicles (OMVs). Further confocal microscopy analysis revealed that the FtlA-containing OMVs isolated from F. tularensis LVS attached to the host cell membrane. Finally, the OMV-associated FtlA protein complemented the genetic deficiency of the ΔftlA mutant in terms of host cell infection when OMVs purified from the parent strain were co-incubated with the mutant bacteria. These lines of evidence strongly suggest that the FtlA lipase promotes F. tularensis adhesion and internalization by modifying bacterial and/or host molecule(s) when it is secreted as a component of OMVs.
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Affiliation(s)
- Fei Chen
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Guolin Cui
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shuxia Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | | | - Lihong He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinyi Qi
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiangmin Han
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hanqi Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jingliang Su
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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215
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Leščić Ašler I, Štefanić Z, Maršavelski A, Vianello R, Kojić-Prodić B. Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth Insight into Structural Parameters Tuning the Catalytic Process of Extracellular Lipase from Streptomyces rimosus. ACS Chem Biol 2017; 12:1928-1936. [PMID: 28558229 DOI: 10.1021/acschembio.6b01140] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SrLip is an extracellular enzyme from Streptomyces rimosus (Q93MW7) exhibiting lipase, phospholipase, esterase, thioesterase, and tweenase activities. The structure of SrLip is one of a very few lipases, among the 3D-structures of the SGNH superfamily of hydrolases, structurally characterized by synchrotron diffraction data at 1.75 Å resolution (PDB: 5MAL ). Its crystal structure was determined by molecular replacement using a homology model based on the crystal structure of phospholipase A1 from Streptomyces albidoflavus (PDB: 4HYQ ). The structure reveals the Rossmann-like 3-layer αβα sandwich fold typical of the SGNH superfamily stabilized by three disulfide bonds. The active site shows a catalytic dyad involving Ser10 and His216 with Ser10-OγH···NεHis216, His216-NδH···O═C-Ser214, and Gly54-NH···Oγ-Ser10 hydrogen bonds essential for the catalysis; the carbonyl oxygen of the Ser214 main chain acts as a hydrogen bond acceptor ensuring the orientation of the His216 imidazole ring suitable for a proton transfer. Molecular dynamics simulations of the apoenzyme and its complex with p-nitrophenyl caprylate were used to probe the positioning of the substrate ester group within the active site and its aliphatic chain within the binding site. Quantum-mechanical calculations at the DFT level revealed the precise molecular mechanism of the SrLip catalytic activity, demonstrating that the overall hydrolysis is a two-step process with acylation as the rate-limiting step associated with the activation free energy of ΔG⧧ENZ = 17.9 kcal mol-1, being in reasonable agreement with the experimental value of 14.5 kcal mol-1, thus providing strong support in favor of the proposed catalytic mechanism based on a dyad.
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Affiliation(s)
- Ivana Leščić Ašler
- Division
of Physical Chemistry, Rudjer Bošković Institute, Bijenička
cesta 54, 10002 Zagreb, Croatia
| | - Zoran Štefanić
- Division
of Physical Chemistry, Rudjer Bošković Institute, Bijenička
cesta 54, 10002 Zagreb, Croatia
| | - Aleksandra Maršavelski
- Division
of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Robert Vianello
- Division
of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Biserka Kojić-Prodić
- Division
of Physical Chemistry, Rudjer Bošković Institute, Bijenička
cesta 54, 10002 Zagreb, Croatia
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216
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Cai X, Wang W, Lin L, He D, Huang G, Shen Y, Wei W, Wei D. Autotransporter domain-dependent enzymatic analysis of a novel extremely thermostable carboxylesterase with high biodegradability towards pyrethroid pesticides. Sci Rep 2017; 7:3461. [PMID: 28615636 PMCID: PMC5471204 DOI: 10.1038/s41598-017-03561-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 05/02/2017] [Indexed: 11/24/2022] Open
Abstract
The EstPS1 gene, which encodes a novel carboxylesterase of Pseudomonas synxantha PS1 isolated from oil well-produced water, was cloned and sequenced. EstPS1 has an open reading frame of 1923 bp and encodes the 640-amino acid carboxylesterase (EstPS1), which contains an autotransporter (AT) domain (357–640 amino acids). Homology analysis revealed that EstPS1 shared the highest identity (88%) with EstA from Pseudomonas fluorescens A506 (NCBI database) and belonged to the carboxylesterase family (EC 3.1.1.1). The optimum pH and temperature of recombinant EstPS1 were found to be 8.0 and 60 °C, respectively. EstPS1 showed high thermostability, and the half-lives (T1/2 thermal inactivation) at 60, 70, 80, 90, and 100 °C were 14 h, 2 h, 31 min, 10 min, and 1 min, respectively. To understand the role of the AT domain in carboxylesterase, AT domain-truncated carboxylesterase (EstPS1ΔAT) was generated. EstPS1ΔAT showed a clearly decreased secretion rate, owing to the AT domain strongly improved secretory expression in the heterogeneous system. EstPS1 degraded various pyrethroid pesticides, and hydrolysis efficiencies were dependent on the pyrethroid molecular structure. EstPS1 degraded all the tested pyrethroid pesticides and hydrolysed the p-nitrophenyl esters of medium-short-chain fatty acids, indicating that EstPS1 is an esterase with broad specificity.
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Affiliation(s)
- Xianghai Cai
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Lin Lin
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai, 200241, People's Republic of China.,Shanghai University of Medicine and Health Sciences, Shanghai, 200093, People's Republic of China
| | - Dannong He
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai, 200241, People's Republic of China.,Shanghai University of Medicine and Health Sciences, Shanghai, 200093, People's Republic of China
| | - Gang Huang
- Shanghai University of Medicine and Health Sciences, Shanghai, 200093, People's Republic of China
| | - Yaling Shen
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
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217
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Philippe F, Pelloux J, Rayon C. Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis. BMC Genomics 2017; 18:456. [PMID: 28595570 PMCID: PMC5465549 DOI: 10.1186/s12864-017-3833-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background Pectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning of pectin acetylation on cell wall properties has not yet been elucidated. Results In the present study, a bioinformatic approach was used on 72 plant PAEs from 16 species among 611 plant PAEs available in plant genomic databases. An overview of plant PAE proteins, particularly Arabidopsis thaliana PAEs, based on phylogeny analysis, protein motif identification and modeled 3D structure is presented. A phylogenetic tree analysis using protein sequences clustered the plant PAEs into five clades. AtPAEs clustered in four clades in the plant kingdom PAE tree while they formed three clades when a phylogenetic tree was performed only on Arabidopsis proteins, due to isoform AtPAE9. Primitive plants that display a smaller number of PAEs clustered into two clades, while in higher plants, the presence of multiple members of PAE genes indicated a diversification of AtPAEs. 3D homology modeling of AtPAE8 from clade 2 with a human Notum protein showed an α/β hydrolase structure with the hallmark Ser-His-Asp of the active site. A 3D model of AtPAE4 from clade 1 and AtPAE10 from clade 3 showed a similar shape suggesting that the diversification of AtPAEs is unlikely to arise from the shape of the protein. Primary structure prediction analysis of AtPAEs showed a specific motif characteristic of each clade and identified one major group of AtPAEs with a signal peptide and one group without a signal peptide. A multiple sequence alignment of the putative plant PAEs revealed consensus sequences with important putative catalytic residues: Ser, Asp, His and a pectin binding site. Data mining of gene expression profiles of AtPAE revealed that genes from clade 2 including AtPAE7, AtPAE8 and AtPAE11, which are duplicated genes, are highly expressed during plant growth and development while AtPAEs without a signal peptide, including AtPAE2 and AtPAE4, are more regulated in response to plant environmental conditions. Conclusion Bioinformatic analysis of plant, and particularly Arabidopsis, AtPAEs provides novel insights, including new motifs that could play a role in pectin binding and catalytic sites. The diversification of AtPAEs is likely to be related to neofunctionalization of some AtPAE genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3833-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian Philippe
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France
| | - Jérôme Pelloux
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France
| | - Catherine Rayon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France.
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218
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Maruthamuthu M, van Elsas JD. Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:142. [PMID: 28588643 PMCID: PMC5457731 DOI: 10.1186/s13068-017-0808-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance. RESULTS Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli. Four of the eight enzymes had significant activities on either pNP-β-d-galactopyranoside, pNP-β-d-xylopyranoside, pNP-α-l-arabinopyranoside or pNP-α-d-glucopyranoside. These proteins, denoted as proteins 1, 2, 5 and 6, were his-tag purified and their nature and activities further characterized using molecular and activity screens with the pNP-labeled substrates. Proteins 1 and 2 showed high homologies with (1) a β-galactosidase (74%) and (2) a β-xylosidase (84%), whereas the remaining two (5 and 6) were homologous with proteins reported as a diguanylate cyclase and an aquaporin, respectively. The β-galactosidase- and β-xylosidase-like proteins 1 and 2 were confirmed as being responsible for previously found thermo-alkaliphilic glycosidase activities of extracts of E. coli carrying the respective source fosmids. Remarkably, the β-xylosidase-like protein 2 showed activities with both pNP-Xyl and pNP-Ara in the temperature range 40-50 °C and pH range 8.0-10.0. Moreover, proteins 5 and 6 showed thermotolerant α-glucosidase activity at pH 10.0. In silico structure prediction of protein 5 revealed the presence of a potential "GGDEF" catalytic site, encoding α-glucosidase activity, whereas that of protein 6 showed a "GDSL" site, encoding a 'new family' α-glucosidase activity. CONCLUSION Using a rational screening approach, we identified and characterized four thermo-alkaliphilic glycosyl hydrolases that have the potential to serve as constituents of enzyme cocktails that produce sugars from lignocellulosic plant remains.
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Affiliation(s)
- Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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219
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Zhang H, Zhou KX, Wang WQ, Liu SJ, Song SQ. Proteome analysis reveals an energy-dependent central process for Populus×canadensis seed germination. JOURNAL OF PLANT PHYSIOLOGY 2017; 213:134-147. [PMID: 28384531 DOI: 10.1016/j.jplph.2017.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 06/07/2023]
Abstract
Poplar (Populus×canadensis) seeds rapidly germinated in darkness at 10, 15, and 20°C and reached 50% seed germination after about 22, 4.5, and 3.5h, respectively. Germination of poplar seeds was markedly inhibited by abscisic acid (ABA) at 50μM and cycloheximide (CHX) at 100μM, and these inhibitive roles were temperature-dependent. In the present study, mature poplar seeds were used to investigate the differentially changed proteome of seeds germinating in water, ABA, and CHX. A total of 130 protein spots showed a significant change (1.5-fold increase/decrease, P<0.05) in abundance, and 101 protein spots were successfully identified. Most of the proteins were associated with cell defense and rescue (21%), storage proteins (21%), protein synthesis and destination (20%), metabolism (16%), and energy (14%). The germination of poplar seeds is closely related with the increase in those proteins involved in amino acid and lipid metabolism, the tricarboxylic acid cycle and pentose phosphate pathway, protein synthesis and destination, cell defense and rescue, and degradation of storage proteins. ABA and CHX inhibit the germination of poplar seeds by decreasing the protein abundance associated with protein proteolysis, protein folding, and storage proteins. We conclude that poplar seed germination is an energy-dependent active process, and is accompanied by increasing amino acid activation, protein synthesis and destination, as well as cell defense and rescue, and degradation of storage proteins.
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Affiliation(s)
- Hong Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ke-Xin Zhou
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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220
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Mining lipolytic enzymes in community DNA from high Andean soils using a targeted approach. Antonie van Leeuwenhoek 2017; 110:1035-1051. [DOI: 10.1007/s10482-017-0877-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 04/18/2017] [Indexed: 12/23/2022]
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221
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SGNH hydrolase-type esterase domain containing Cbes-AcXE2: a novel and thermostable acetyl xylan esterase from Caldicellulosiruptor bescii. Extremophiles 2017; 21:687-697. [DOI: 10.1007/s00792-017-0934-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/17/2017] [Indexed: 12/18/2022]
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222
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Rodriguez F, Kenefick AW, Arkhipova IR. LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types. Viruses 2017; 9:v9040078. [PMID: 28398238 PMCID: PMC5408684 DOI: 10.3390/v9040078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/16/2022] Open
Abstract
Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highlydiversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotiferspecific and encode a dUTPase domain. However only one lineage contains a canonical envlike fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3'-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements.
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Affiliation(s)
- Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
| | - Aubrey W Kenefick
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
- Present address: UC Davis Genome Center-GBSF, University of California, Davis, CA 95616, USA.
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
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223
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Gutiérrez-Ortega A, Rivera I, Cruz-Franco S, Gutiérrez-Mora A, Alpuche-Solís ÁG, Sánchez-Hernández C, Horchani H, Sandoval G. Identification, cloning and expression of a new GDSL lipase from Carica papaya. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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224
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Zhang B, Zhang L, Li F, Zhang D, Liu X, Wang H, Xu Z, Chu C, Zhou Y. Control of secondary cell wall patterning involves xylan deacetylation by a GDSL esterase. NATURE PLANTS 2017; 3:17017. [PMID: 28260782 DOI: 10.1038/nplants.2017.17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/27/2017] [Indexed: 05/17/2023]
Abstract
O-acetylation, a ubiquitous modification of cell wall polymers, has striking impacts on plant growth and biomass utilization and needs to be tightly controlled. However, the mechanisms that underpin the control of cell wall acetylation remain elusive. Here, we show a rice brittle leaf sheath1 (bs1) mutant, which contains a lesion in a Golgi-localized GDSL esterase that deacetylates the prominent hemicellulose xylan. Cell wall composition, detailed xylan structure characterization and enzyme kinetics and activity assays on acetylated sugars and xylooligosaccharides demonstrate that BS1 is an esterase that cleaves acetyl moieties from the xylan backbone at O-2 and O-3 positions of xylopyranosyl residues. BS1 thus plays an important role in the maintenance of proper acetylation level on the xylan backbone, which is crucial for secondary wall formation and patterning. Our findings outline a mechanism for how plants modulate wall acetylation and endow a plethora of uncharacterized GDSL esterases with surmisable activities.
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Affiliation(s)
- Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongmei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangling Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hang Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuopeng Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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225
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Sánchez-Carbente MDR, Batista-García RA, Sánchez-Reyes A, Escudero-Garcia A, Morales-Herrera C, Cuervo-Soto LI, French-Pacheco L, Fernández-Silva A, Amero C, Castillo E, Folch-Mallol JL. The first description of a hormone-sensitive lipase from a basidiomycete: Structural insights and biochemical characterization revealed Bjerkandera adusta BaEstB as a novel esterase. Microbiologyopen 2017; 6. [PMID: 28251842 PMCID: PMC5552909 DOI: 10.1002/mbo3.463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/25/2017] [Accepted: 02/02/2017] [Indexed: 11/06/2022] Open
Abstract
The heterologous expression and characterization of a Hormone-Sensitive Lipases (HSL) esterase (BaEstB) from the Basidiomycete fungus Bjerkandera adusta is reported for the first time. According to structural analysis, amino acid similarities and conservation of particular motifs, it was established that this enzyme belongs to the (HSL) family. The cDNA sequence consisted of 969 nucleotides, while the gene comprised 1133, including three introns of 57, 50, and 57 nucleotides. Through three-dimensional modeling and phylogenetic analysis, we conclude that BaEstB is an ortholog of the previously described RmEstB-HSL from the phylogenetically distant fungus Rhizomucor miehei. The purified BaEstB was characterized in terms of its specificity for the hydrolysis of different acyl substrates confirming its low lipolytic activity and a noticeable esterase activity. The biochemical characterization of BaEstB, the DLS analysis and the kinetic parameters determination revealed this enzyme as a true esterase, preferentially found in a dimeric state, displaying activity under alkaline conditions and relative low temperature (pH = 10, 20°C). Our data suggest that BaEstB is more active on substrates with short acyl chains and bulky aromatic moieties. Phylogenetic data allow us to suggest that a number of fungal hypothetical proteins could belong to the HSL family.
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Affiliation(s)
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Ayixón Sánchez-Reyes
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Angela Escudero-Garcia
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Catalina Morales-Herrera
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Laura I Cuervo-Soto
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Departamento de Biología, Facultad de Ciencias, Universidad Antonio Nariño, Bogota, Colombia
| | - Leidys French-Pacheco
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Arline Fernández-Silva
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Carlos Amero
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Edmundo Castillo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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226
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Memarpoor-Yazdi M, Karbalaei-Heidari HR, Khajeh K. Production of the renewable extremophile lipase: Valuable biocatalyst with potential usage in food industry. FOOD AND BIOPRODUCTS PROCESSING 2017. [DOI: 10.1016/j.fbp.2016.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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227
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Ramnath L, Sithole B, Govinden R. Classification of lipolytic enzymes and their biotechnological applications in the pulping industry. Can J Microbiol 2017; 63:179-192. [DOI: 10.1139/cjm-2016-0447] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the pulp and paper industry, during the manufacturing process, the agglomeration of pitch particles (composed of triglycerides, fatty acids, and esters) leads to the formation of black pitch deposits in the pulp and on machinery, which impacts on the process and pulp quality. Traditional methods of pitch prevention and treatment are no longer feasible due to environmental impact and cost. Consequently, there is a need for more efficient and environmentally friendly approaches. The application of lipolytic enzymes, such as lipases and esterases, could be the sustainable solution to this problem. Therefore, an understanding of their structure, mechanism, and sources are essential. In this report, we review the microbial sources for the different groups of lipolytic enzymes, the differences between lipases and esterases, and their potential applications in the pulping industry.
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Affiliation(s)
- L. Ramnath
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, P/Bag X54001, Durban 4000, South Africa
| | - B. Sithole
- Forestry and Forest Products Research Centre, Council for Scientific and Industrial Research, Durban 4000, South Africa
- Discipline of Chemical Engineering, University of KwaZulu-Natal, Durban 4000, South Africa
| | - R. Govinden
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, P/Bag X54001, Durban 4000, South Africa
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228
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Kang LJ, Meng ZT, Hu C, Zhang Y, Guo HL, Li Q, Li M. Screening, purification, and characterization of a novel organic solvent-tolerant esterase, Lip2, from Monascus purpureus strain M7. Extremophiles 2017; 21:345-355. [DOI: 10.1007/s00792-016-0907-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/19/2016] [Indexed: 12/01/2022]
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229
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Smith PJ, Wang HT, York WS, Peña MJ, Urbanowicz BR. Designer biomass for next-generation biorefineries: leveraging recent insights into xylan structure and biosynthesis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:286. [PMID: 29213325 PMCID: PMC5708106 DOI: 10.1186/s13068-017-0973-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/20/2017] [Indexed: 05/02/2023]
Abstract
Xylans are the most abundant noncellulosic polysaccharides in lignified secondary cell walls of woody dicots and in both primary and secondary cell walls of grasses. These polysaccharides, which comprise 20-35% of terrestrial biomass, present major challenges for the efficient microbial bioconversion of lignocellulosic feedstocks to fuels and other value-added products. Xylans play a significant role in the recalcitrance of biomass to degradation, and their bioconversion requires metabolic pathways that are distinct from those used to metabolize cellulose. In this review, we discuss the key differences in the structural features of xylans across diverse plant species, how these features affect their interactions with cellulose and lignin, and recent developments in understanding their biosynthesis. In particular, we focus on how the combined structural and biosynthetic knowledge can be used as a basis for biomass engineering aimed at developing crops that are better suited as feedstocks for the bioconversion industry.
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Affiliation(s)
- Peter J. Smith
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Hsin-Tzu Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - William S. York
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Maria J. Peña
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Breeanna R. Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
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230
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Zhang S, Shi Q, Albrecht U, Shatters RG, Stange R, McCollum G, Zhang S, Fan C, Stover E. Comparative transcriptome analysis during early fruit development between three seedy citrus genotypes and their seedless mutants. HORTICULTURE RESEARCH 2017; 4:17041. [PMID: 28904803 PMCID: PMC5596110 DOI: 10.1038/hortres.2017.41] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 05/03/2023]
Abstract
Identification of genes with differential transcript abundance (GDTA) in seedless mutants may enhance understanding of seedless citrus development. Transcriptome analysis was conducted at three time points during early fruit development (Phase 1) of three seedy citrus genotypes: Fallglo (Bower citrus hybrid (Citrus reticulata×C. reticulata×C. paradisi)×Temple (C. reticulata×C. sinensis)), grapefruit (C. paradisi), Pineapple sweet orange (C. sinensis), and their seedless mutants. Seed abortion in seedless mutants was observed at 26 days post anthesis (Time point 2). Affymetrix transcriptomic analysis revealed 359 to 1077 probe sets with differential transcript abundance in the comparison of seedless versus seedy fruits for each citrus genotypes and time points. The GDTA identified by 18 microarray probe sets were validated by qPCR. Hierarchical clustering analysis revealed a range of GDTA associated with development, hormone and protein metabolism, all of which may reflect genes associated with seedless fruit development. There were 14, 9 and 12 genes found exhibiting similar abundance ratios in all three seedless versus seedy genotype comparisons at time point 1, 2 and 3, respectively. Among those genes were genes coding for an aspartic protease and a cysteine protease, which may play important roles in seedless fruit development. New insights into seedless citrus fruit development may contribute to biotech approaches to create seedless cultivars.
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Affiliation(s)
- Shujian Zhang
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
| | - Qingchun Shi
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
| | - Ute Albrecht
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
| | - Robert G Shatters
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
| | - Ric Stange
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
| | - Greg McCollum
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
| | - Shuo Zhang
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
| | - Chengming Fan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ed Stover
- U.S. Horticultural Research Laboratory, USDA-ARS, Ft. Pierce, FL 34945, USA
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231
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Kim Y, Ryu BH, Kim J, Yoo W, An DR, Kim BY, Kwon S, Lee S, Wang Y, Kim KK, Kim TD. Characterization of a novel SGNH-type esterase from Lactobacillus plantarum. Int J Biol Macromol 2016; 96:560-568. [PMID: 28040493 DOI: 10.1016/j.ijbiomac.2016.12.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 12/27/2022]
Abstract
Lactic acid bacteria (LAB) are sources of a large variety of microbial ester hydrolases because they can produce a wide range of short-chain esters, phenolic alcohols, and fatty acids. Here, a novel SGNH-type esterase (LpSGNH1) from Lactobacillus plantarum WCFS1 was identified, functionally characterized, and immobilized for biotechnological applications. Homologs of LpSGNH1 are also found in many lactic acid bacteria (LAB) species. Biochemical features of LpSGNH1 were investigated using mass spectrometry, gel filtration chromatography, enzyme kinetics, fluorescence, and circular dichroism (CD) spectroscopy. LpSGNH1 were retained its activity under conditions that would be encountered during fermentations. Interestingly, LpSGNH1 exhibited the ability to act on a broad range of substrates including ketoprofen acetate, cefotaxime (CTX), and 7-aminocephalosporanic acid (7-ACA) as well as glucose pentaacetate, acetylxylan, and acetylalginate, which make LpSGNH1 a great candidate for extensive industrial applications. Furthermore, cross-linked enzyme aggregates of LpSGNH1 (CLEA-LpSGNH1) displayed recycling ability and thermal stability compared to free LpSGNH1, which could be useful for industrial applications. This work highlights the importance of LpSGNH1 in the preparation of commercial compounds, and LpSGNH1 can be used as a model system of SGNH esterases in lactic acid bacteria.
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Affiliation(s)
- Yonggyu Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Jimin Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Deu Rae An
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Boo-Young Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Sena Kwon
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Sojeong Lee
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Ying Wang
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - T Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea.
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232
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Nunes-Costa D, Maranha A, Costa M, Alarico S, Empadinhas N. Glucosylglycerate metabolism, bioversatility and mycobacterial survival. Glycobiology 2016; 27:213-227. [DOI: 10.1093/glycob/cww132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
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233
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Luan ZJ, Yu HL, Ma BD, Qi YK, Chen Q, Xu JH. Dramatically Improved Performance of an Esterase for Cilastatin Synthesis by Cap Domain Engineering. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b02440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zheng-Jiao Luan
- State
Key Laboratory of Bioreactor Engineering and Shanghai Collaborative
Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Hui-Lei Yu
- State
Key Laboratory of Bioreactor Engineering and Shanghai Collaborative
Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Bao-Di Ma
- School
of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai 201418, China
| | - Yi-Ke Qi
- State
Key Laboratory of Bioreactor Engineering and Shanghai Collaborative
Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Qi Chen
- State
Key Laboratory of Bioreactor Engineering and Shanghai Collaborative
Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Jian-He Xu
- State
Key Laboratory of Bioreactor Engineering and Shanghai Collaborative
Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
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234
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Adesioye FA, Makhalanyane TP, Biely P, Cowan DA. Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases. Enzyme Microb Technol 2016; 93-94:79-91. [DOI: 10.1016/j.enzmictec.2016.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/18/2016] [Accepted: 07/01/2016] [Indexed: 02/06/2023]
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235
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Deng D, Zhang Y, Sun A, Hu Y. Enantio-selective preparation of (S)-1-phenylethanol by a novel marine GDSL lipase MT6 with reverse stereo-selectivity. CHINESE JOURNAL OF CATALYSIS 2016. [DOI: 10.1016/s1872-2067(16)62505-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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236
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Ben Bacha A, Al-Assaf A, Moubayed NMS, Abid I. Evaluation of a novel thermo-alkaline Staphylococcus aureus lipase for application in detergent formulations. Saudi J Biol Sci 2016; 25:409-417. [PMID: 29686504 PMCID: PMC5910647 DOI: 10.1016/j.sjbs.2016.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/24/2016] [Accepted: 10/03/2016] [Indexed: 11/26/2022] Open
Abstract
An extracellular lipase of a newly isolated S. aureus strain ALA1 (SAL4) was purified from the optimized culture medium. The SAL4 specific activity determined at 60 °C and pH 12 by using olive oil emulsion or TC4, reached 7215 U/mg and 2484 U/mg, respectively. The 38 NH2-terminal amino acid sequence of the purified enzyme starting with two extra amino acid residues (LK) was similar to known staphylococcal lipase sequences. This novel lipase maintained almost 100% and 75% of its full activity in a pH range of 4.0-12 after a 24 h incubation or after 0.5 h treatment at 70 °C, respectively. Interestingly, SAL4 displayed appreciable stability toward oxidizing agents, anionic and non-ionic surfactants in addition to its compatibility with several commercial detergents. Overall, these interesting characteristics make this new lipase promising for its application in detergent industry.
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Key Words
- Characterization
- Detergent-stable
- HPLC, high-performance liquid chromatography
- NaDC, sodium deoxycholic acid
- NaTDC, sodium taurodeoxy cholic acid
- OD, optical density
- PCR, polymerase chain reaction
- Purification
- S. aureus, Staphylococcus aureus
- SAL, Staphylococcus aureus lipase
- SDS, sodium dodecyl sulfate
- SEL, Staphylococcus epidermidis lipase
- SHyL, Staphylococcus hyicus lipase
- SL1, Staphylococcus sp. lipase
- SSL, Staphylococcus simulans lipase
- SXL, Staphylococcus xylosus lipase
- Staphylococcus aureus lipase
- TC18, triolein
- TC3, tripropionin
- TC4, tributryin
- TC8, trioctanoin
- TFA, tri fluoroacetic acid
- Thermo-alkaline
- rDNA, ribosomal deoxy ribo nucleic acid
- rpm, revolutions per minute
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Affiliation(s)
- Abir Ben Bacha
- Biochemistry Department, Science College, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia.,Laboratory of Plant Biotechnology Applied to Crop Improvement, Faculty of Science of Sfax, University of Sfax, Sfax 3038, Tunisia
| | - Alaa Al-Assaf
- Biochemistry Department, Science College, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Nadine M S Moubayed
- Botany and Microbiology Department, Science College, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Islem Abid
- Botany and Microbiology Department, Science College, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
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237
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Tiwari GJ, Chiang MY, De Silva JR, Song BK, Lau YL, Rahman S. Lipase genes expressed in rice bran: LOC_Os11g43510 encodes a novel rice lipase. J Cereal Sci 2016. [DOI: 10.1016/j.jcs.2016.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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238
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Heng W, Wang Z, Jiang X, Jia B, Liu P, Liu L, Ye Z, Zhu L. The role of polyamines during exocarp formation in a russet mutant of 'Dangshansuli' pear (Pyrus bretschneideri Rehd.). PLANT CELL REPORTS 2016; 35:1841-52. [PMID: 27255339 DOI: 10.1007/s00299-016-1998-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/12/2016] [Indexed: 05/26/2023]
Abstract
Differential genes of suberin, polyamine and transcription factors in transcriptome sequences and the contents of H 2 O 2 , spermidine, spermine, and putrescine changed significantly after treating with MGBG. Russeting is a commercially important process that restores the control of water loss through the skin via the formation of a waterproofing periderm just beneath the microcracked skin of pear primary fruit. A spontaneous russet skin mutant, the yellow-green 'Dangshansuli' pear, has been identified. To understand the role of polyamines in the formation of the russet skin of the mutant-type (MT) pear, it was treated with methylglyoxal-bis-(guanylhydrazone) (MGBG) for 4 weeks after full bloom. One week later, differentially expressed genes among the wild-type (WT), MT, and MGBG-treated MT pears were screened, hydrogen peroxide (H2O2) was localized using CeCl3, and the contents of H2O2 and polyamine were measured. A total of 57,086,772, 61,240,014, and 67,919,420 successful reads were generated from the transcriptomes of WT, MT, and MGBG-treated MT, with average unigene lengths of 701, 720, and 735 bp, respectively. Differentially expressed genes involved in polyamine metabolism and suberin synthesis were screened in 'Dangshansuli' and in the mutant libraries, and their relative expression was found to be significantly altered after treatment with MGBG, which was confirmed by real-time PCR. The expression patterns of differentially expressed transcription factors were identified and were found to be similar to those of the polyamine- and suberin-related genes. The results indicated that the H2O2 generated during polyamine metabolism might contribute to russet formation on the exocarp of the mutant pear. Furthermore, the contents of H2O2, spermidine, spermine, and putrescine and H2O2 localization provided a comprehensive transcriptomic view of russet formation in the mutant pear.
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Affiliation(s)
- Wei Heng
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China
| | - Ziteng Wang
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China
| | - Xianghong Jiang
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China
| | - Bing Jia
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China
| | - Pu Liu
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China
| | - Li Liu
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China
| | - Zhenfeng Ye
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China
| | - Liwu Zhu
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, People's Republic of China.
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239
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Enzymatic modification of polysaccharides: Mechanisms, properties, and potential applications: A review. Enzyme Microb Technol 2016; 90:1-18. [DOI: 10.1016/j.enzmictec.2016.04.004] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 11/24/2022]
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240
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Yousuf PY, Ganie AH, Khan I, Qureshi MI, Ibrahim MM, Sarwat M, Iqbal M, Ahmad A. Nitrogen-Efficient and Nitrogen-Inefficient Indian Mustard Showed Differential Expression Pattern of Proteins in Response to Elevated CO2 and Low Nitrogen. FRONTIERS IN PLANT SCIENCE 2016; 7:1074. [PMID: 27524987 PMCID: PMC4965474 DOI: 10.3389/fpls.2016.01074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 07/07/2016] [Indexed: 06/06/2023]
Abstract
Carbon (C) and nitrogen (N) are two essential elements that influence plant growth and development. The C and N metabolic pathways influence each other to affect gene expression, but little is known about which genes are regulated by interaction between C and N or the mechanisms by which the pathways interact. In the present investigation, proteome analysis of N-efficient and N-inefficient Indian mustard, grown under varied combinations of low-N, sufficient-N, ambient [CO2], and elevated [CO2] was carried out to identify proteins and the encoding genes of the interactions between C and N. Two-dimensional gel electrophoresis (2-DE) revealed 158 candidate protein spots. Among these, 72 spots were identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins are related to various molecular processes including photosynthesis, energy metabolism, protein synthesis, transport and degradation, signal transduction, nitrogen metabolism and defense to oxidative, water and heat stresses. Identification of proteins like PII-like protein, cyclophilin, elongation factor-TU, oxygen-evolving enhancer protein and rubisco activase offers a peculiar overview of changes elicited by elevated [CO2], providing clues about how N-efficient cultivar of Indian mustard adapt to low N supply under elevated [CO2] conditions. This study provides new insights and novel information for a better understanding of adaptive responses to elevated [CO2] under N deficiency in Indian mustard.
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Affiliation(s)
| | - Arshid H. Ganie
- Department of Botany, Faculty of ScienceJamia Hamdard, New Delhi, India
| | - Ishrat Khan
- Department of Botany, Faculty of ScienceJamia Hamdard, New Delhi, India
| | - Mohammad I. Qureshi
- Proteomics and Bioinformatics Laboratory, Department of Biotechnology, Faculty of Natural SciencesJamia Millia Islamia, New Delhi, India
| | - Mohamed M. Ibrahim
- Department of Botany and Microbiology, Science College, King Saud UniversityRiyadh, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Alexandria UniversityAlexandria, Egypt
| | - Maryam Sarwat
- Pharmaceutic Biotechnology, Amity Institute of Pharmacy, Amity UniversityNoida, India
| | - Muhammad Iqbal
- Department of Botany, Faculty of ScienceJamia Hamdard, New Delhi, India
| | - Altaf Ahmad
- Proteomics and Nanobiotechnology Laboratory, Department of Botany, Faculty of Life Sciences, Aligarh Muslim UniversityAligarh, India
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241
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Identification of Novel Abiotic Stress Proteins in Triticum aestivum Through Functional Annotation of Hypothetical Proteins. Interdiscip Sci 2016; 10:205-220. [PMID: 27421996 DOI: 10.1007/s12539-016-0178-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 06/15/2016] [Accepted: 07/07/2016] [Indexed: 01/14/2023]
Abstract
Cereal grain bread wheat (T. aestivum) is an important source of food and belongs to Poaceae family. Hypothetical proteins (HPs), i.e., proteins with unknown functions, share a substantial portion of wheat proteomes and play important roles in growth and physiology of plant system. Several functional annotations studies utilizing the protein sequences for characterization of role of individual protein in physiology of plant systems were being reported in recent past. In this study, an integrated pipeline of software/servers has been used for the identification and functional annotation of 124 unique HPs of T. aestivum considering available data in NCBI till date. All HPs were broadly annotated, out of which functions of 77 HPs were successfully assigned with high confidence level. Precisely functional annotation of remaining 47 HPs is also characterized with low confidence. Several latest versions of protein family databases, pathways information, genomics context methods and in silico tools were utilized to identify and assign function for individual HPs. Annotation result of several HPs mainly belongs to cellular protein, metabolic enzymes, binding proteins, transmembrane proteins, transcription factors and photosystem regulator proteins. Subsequently, functional analysis has revealed the role of few HPs in abiotic stress, which were further verified by phylogenetic analysis. The functionally associated proteins with each of above-mentioned abiotic stress-related proteins were identified through protein-protein interaction network analysis. The outcome of this study may be helpful for formulating general set pipeline/protocols for a better understanding of the role of HPs in physiological development of various plant systems.
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242
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Miller CN, Harper AL, Trick M, Werner P, Waldron K, Bancroft I. Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics. BMC Genomics 2016; 17:500. [PMID: 27423334 PMCID: PMC4947262 DOI: 10.1186/s12864-016-2775-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/25/2016] [Indexed: 01/16/2023] Open
Abstract
Background The current approach to reducing the tendency for wheat grown under high fertilizer conditions to collapse (lodge) under the weight of its grain is based on reducing stem height via the introduction of Rht genes. However, these reduce the yield of straw (itself an important commodity) and introduce other undesirable characteristics. Identification of alternative height-control loci is therefore of key interest. In addition, the improvement of stem mechanical strength provides a further way through which lodging can be reduced. Results To investigate the prospects for genetic alternatives to Rht, we assessed variation for plant height and stem strength properties in a training genetic diversity panel of 100 wheat accessions fixed for Rht. Using mRNAseq data derived from RNA purified from leaves, functional genotypes were developed for the panel comprising 42,066 Single Nucleotide Polymorphism (SNP) markers and 94,060 Gene Expression Markers (GEMs). In the first application in wheat of the recently-developed method of Associative Transcriptomics, we identified associations between trait variation and both SNPs and GEMs. Analysis of marker-trait associations revealed candidates for the causative genes underlying the trait variation, implicating xylan acetylation and the COP9 signalosome as contributing to stem strength and auxin in the control of the observed variation for plant height. Predictive capabilities of key markers for stem strength were validated using a test genetic diversity panel of 30 further wheat accessions. Conclusions This work illustrates the power of Associative Transcriptomics for the exploration of complex traits of high agronomic importance in wheat. The careful selection of genotypes included in the analysis, allowed for high resolution mapping of novel trait-controlling loci in this staple crop. The use of Gene Expression markers coupled with the more traditional sequence-based markers, provides the power required to understand the biological context of the marker-trait associations observed. This not only adds to the wealth of knowledge that we strive to accumulate regarding gene function and plant adaptation, but also provides breeders with the information required to make more informed decisions regarding the potential consequences of incorporating the use of particular markers into future breeding programmes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2775-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Andrea L Harper
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Department of Biology, University of York, York, YO10 5DD, UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Peter Werner
- KWS UK Ltd, 56 Church Street, Thriplow, Hertfordshire, SG8 7RE, UK
| | - Keith Waldron
- Institute of Food Research, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,Department of Biology, University of York, York, YO10 5DD, UK.
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243
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Crost EH, Tailford LE, Monestier M, Swarbreck D, Henrissat B, Crossman LC, Juge N. The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases. Gut Microbes 2016; 7:302-312. [PMID: 27223845 PMCID: PMC4988440 DOI: 10.1080/19490976.2016.1186334] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 02/07/2023] Open
Abstract
We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit.
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Affiliation(s)
- Emmanuelle H. Crost
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Louise E. Tailford
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Marie Monestier
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - David Swarbreck
- The Genome Analysis Center, Norwich Research Park, Norwich, United Kingdom
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université Aix-Marseille, CNRS UMR 7257, France
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lisa C. Crossman
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- SequenceAnalysis.co.uk, NRP Innovation Center, Norwich, United Kingdom
| | - Nathalie Juge
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
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244
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Abstract
Bacterial sphingomyelinases and phospholipases are a heterogeneous group of esterases which are usually surface associated or secreted by a wide variety of Gram-positive and Gram-negative bacteria. These enzymes hydrolyze sphingomyelin and glycerophospholipids, respectively, generating products identical to the ones produced by eukaryotic enzymes which play crucial roles in distinct physiological processes, including membrane dynamics, cellular signaling, migration, growth, and death. Several bacterial sphingomyelinases and phospholipases are essential for virulence of extracellular, facultative, or obligate intracellular pathogens, as these enzymes contribute to phagosomal escape or phagosomal maturation avoidance, favoring tissue colonization, infection establishment and progression, or immune response evasion. This work presents a classification proposal for bacterial sphingomyelinases and phospholipases that considers not only their enzymatic activities but also their structural aspects. An overview of the main physiopathological activities is provided for each enzyme type, as are examples in which inactivation of a sphingomyelinase- or a phospholipase-encoding gene impairs the virulence of a pathogen. The identification of sphingomyelinases and phospholipases important for bacterial pathogenesis and the development of inhibitors for these enzymes could generate candidate vaccines and therapeutic agents, which will diminish the impacts of the associated human and animal diseases.
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245
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Vorapreeda T, Thammarongtham C, Laoteng K. Integrative computational approach for genome-based study of microbial lipid-degrading enzymes. World J Microbiol Biotechnol 2016; 32:122. [DOI: 10.1007/s11274-016-2067-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/05/2016] [Indexed: 01/19/2023]
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246
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Kelly AA, Feussner I. Oil is on the agenda: Lipid turnover in higher plants. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1253-1268. [PMID: 27155216 DOI: 10.1016/j.bbalip.2016.04.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/23/2016] [Accepted: 04/25/2016] [Indexed: 12/13/2022]
Abstract
Lipases hydrolyze ester bonds within lipids. This process is called lipolysis. They are key players in lipid turnover and involved in numerous metabolic pathways, many of which are shared between organisms like the mobilization of neutral or storage lipids or lipase-mediated membrane lipid homeostasis. Some reactions though are predominantly present in certain organisms, such as the production of signaling molecules (endocannabinoids) by diacylglycerol (DAG) and monoacylglycerol (MAG) lipases in mammals and plants or the jasmonate production in flowering plants. This review aims at giving an overview of the different functional classes of lipases and respective well-known activities, with a focus on the most recent findings in plant biology for selected classes. Here we will put an emphasis on the physiological role and contribution of lipases to the turnover of neutral lipids found in seed oil and other vegetative tissue as candidates for increasing the economical values of crop plants. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Amélie A Kelly
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Ivo Feussner
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany; Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig Weg 11, 37077 Göttingen, Germany; Georg-August-University, International Center for Advanced Studies of Energy Conversion (ICASEC), Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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247
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Barbaglia AM, Tamot B, Greve V, Hoffmann-Benning S. Phloem Proteomics Reveals New Lipid-Binding Proteins with a Putative Role in Lipid-Mediated Signaling. FRONTIERS IN PLANT SCIENCE 2016; 7:563. [PMID: 27200036 PMCID: PMC4849433 DOI: 10.3389/fpls.2016.00563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/11/2016] [Indexed: 05/13/2023]
Abstract
Global climate changes inversely affect our ability to grow the food required for an increasing world population. To combat future crop loss due to abiotic stress, we need to understand the signals responsible for changes in plant development and the resulting adaptations, especially the signaling molecules traveling long-distance through the plant phloem. Using a proteomics approach, we had identified several putative lipid-binding proteins in the phloem exudates. Simultaneously, we identified several complex lipids as well as jasmonates. These findings prompted us to propose that phloem (phospho-) lipids could act as long-distance developmental signals in response to abiotic stress, and that they are released, sensed, and moved by phloem lipid-binding proteins (Benning et al., 2012). Indeed, the proteins we identified include lipases that could release a signaling lipid into the phloem, putative receptor components, and proteins that could mediate lipid-movement. To test this possible protein-based lipid-signaling pathway, three of the proteins, which could potentially act in a relay, are characterized here: (I) a putative GDSL-motif lipase (II) a PIG-P-like protein, with a possible receptor-like function; (III) and PLAFP (phloem lipid-associated family protein), a predicted lipid-binding protein of unknown function. Here we show that all three proteins bind lipids, in particular phosphatidic acid (PtdOH), which is known to participate in intracellular stress signaling. Genes encoding these proteins are expressed in the vasculature, a prerequisite for phloem transport. Cellular localization studies show that the proteins are not retained in the endoplasmic reticulum but surround the cell in a spotted pattern that has been previously observed with receptors and plasmodesmatal proteins. Abiotic signals that induce the production of PtdOH also regulate the expression of GDSL-lipase and PLAFP, albeit in opposite patterns. Our findings suggest that while all three proteins are indeed lipid-binding and act in the vasculature possibly in a function related to long-distance signaling, the three proteins do not act in the same but rather in distinct pathways. It also points toward PLAFP as a prime candidate to investigate long-distance lipid signaling in the plant drought response.
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Affiliation(s)
| | | | | | - Susanne Hoffmann-Benning
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
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248
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Chap H. Forty five years with membrane phospholipids, phospholipases and lipid mediators: A historical perspective. Biochimie 2016; 125:234-49. [PMID: 27059515 DOI: 10.1016/j.biochi.2016.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/01/2016] [Indexed: 01/02/2023]
Abstract
Phospholipases play a key role in the metabolism of phospholipids and in cell signaling. They are also a very useful tool to explore phospholipid structure and metabolism as well as membrane organization. They are at the center of this review, covering a period starting in 1971 and focused on a number of subjects in which my colleagues and I have been involved. Those include determination of phospholipid asymmetry in the blood platelet membrane, biosynthesis of lysophosphatidic acid, biochemistry of platelet-activating factor, first attempts to define the role of phosphoinositides in cell signaling, and identification of novel digestive (phospho)lipases such as pancreatic lipase-related protein 2 (PLRP2) or phospholipase B. Besides recalling some of our contributions to those various fields, this review makes an appraisal of the impressive and often unexpected evolution of those various aspects of membrane phospholipids and lipid mediators. It is also the occasion to propose some new working hypotheses.
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Affiliation(s)
- Hugues Chap
- Centre de Physiopathologie de Toulouse Purpan, Institut National de la Santé et de la Recherche Médicale, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Université de Toulouse, Université Paul Sabatier, Toulouse F-31300, France. hugues.chap.@univ-tlse3.fr
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249
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Oh C, Ryu BH, An DR, Nguyen DD, Yoo W, Kim T, Ngo TD, Kim HS, Kim KK, Kim TD. Structural and Biochemical Characterization of an Octameric Carbohydrate Acetylesterase from Sinorhizobium meliloti. FEBS Lett 2016; 590:1242-52. [PMID: 26991446 DOI: 10.1002/1873-3468.12135] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 11/06/2022]
Abstract
Carbohydrate acetylesterases, which have a highly specific role among plant-interacting bacterial species, remove the acetyl groups from plant carbohydrates. Here, we determined the crystal structure of Est24, an octameric carbohydrate acetylesterase from Sinorhizobium meliloti, at 1.45 Å resolution and investigated its biochemical properties. The structure of Est24 consisted of five parallel β strands flanked by α helices, which formed an octameric assembly with two distinct interfaces. The deacetylation activity of Est24 and its mutants around the substrate-binding pocket was investigated using several substrates, including glucose pentaacetate and acetyl alginate. Elucidation of the structure-function relationships of Est24 could provide valuable opportunities for biotechnological explorations.
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Affiliation(s)
- Changsuk Oh
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Bum Han Ryu
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea.,Department of Chemistry, College of Natural Sciences, Sookmyung Woman's University, Seoul, Korea
| | - Deu Rae An
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea.,Department of Chemistry, College of Natural Sciences, Sookmyung Woman's University, Seoul, Korea
| | - Duy Duc Nguyen
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Wanki Yoo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea.,Department of Chemistry, College of Natural Sciences, Sookmyung Woman's University, Seoul, Korea
| | - Truc Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hee Sook Kim
- Department of Food Science and Biotechnology, Kyungsung University, Busan, Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - T Doohun Kim
- Department of Chemistry, College of Natural Sciences, Sookmyung Woman's University, Seoul, Korea
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250
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A novel cold-adapted and highly salt-tolerant esterase from Alkalibacterium sp. SL3 from the sediment of a soda lake. Sci Rep 2016; 6:19494. [PMID: 26915906 PMCID: PMC4768246 DOI: 10.1038/srep19494] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/14/2015] [Indexed: 01/26/2023] Open
Abstract
A novel esterase gene (estSL3) was cloned from the Alkalibacterium sp. SL3, which was isolated from the sediment of soda lake Dabusu. The 636-bp full-length gene encodes a polypeptide of 211 amino acid residues that is closely related with putative GDSL family lipases from Alkalibacterium and Enterococcus. The gene was successfully expressed in E. coli, and the recombinant protein (rEstSL3) was purified to electrophoretic homogeneity and characterized. rEstSL3 exhibited the highest activity towards pNP-acetate and had no activity towards pNP-esters with acyl chains longer than C8. The enzyme was highly cold-adapted, showing an apparent temperature optimum of 30 °C and remaining approximately 70% of the activity at 0 °C. It was active and stable over the pH range from 7 to 10, and highly salt-tolerant up to 5 M NaCl. Moreover, rEstSL3 was strongly resistant to most tested metal ions, chemical reagents, detergents and organic solvents. Amino acid composition analysis indicated that EstSL3 had fewer proline residues, hydrogen bonds and salt bridges than mesophilic and thermophilic counterparts, but more acidic amino acids and less hydrophobic amino acids when compared with other salt-tolerant esterases. The cold active, salt-tolerant and chemical-resistant properties make it a promising enzyme for basic research and industrial applications.
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