Cloning, sequencing and expression of the amylase isozyme gene from Pseudomonas sp. KFCC 10818

Kim, Eun-Seon; Na, Hye-Kyung; Jhon, Deok-Young; Yoo, Ook Joon; Chun, Soon-Bae; Wui, In-Sun

doi:10.1007/bf00128674

Cited by 8 publications

(5 citation statements)

References 10 publications

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“…It is worth mentioning that in the subfamily GH13_32, it is present only as a lysine and only in a few bacterial cases: Halomonas meridiana ([ 60 ]; CAB92963.1), Pseudoalteromonas haloplanktis ([ 31 ]; CAA41481.1), Pseudomonas sp. KFCC10818 ([ 61 ]; AAA86835.1), Thermobifida fusca ([ 62 ]; ABF13430.1) and Thermomonospora curvata ([ 63 ]; CAA41881.1), because none of GH13_32 α-amylase of fungal origin possesses it ( Figure S1 ). Finally, in remaining α-amylase subfamilies from this analysis—GH13_1, GH13_5 and GH13_42—neither arginine, nor lysine is found in the position corresponding with this arginine from the CSR-VII.…”

Section: Resultsmentioning

confidence: 99%

“…The GH13_32 bacterial α-amylases—outside actinobacteria—clustering with the chloride-activated GH13_15 and GH13_24 α-amylases from animals—come from Halomonas meridiana ([ 60 ]; CAB92963.1), Pseudoalteromonas haloplanktis ([ 31 ]; CAA41481.1), Pseudomonas sp. KFCC10818 ([ 61 ]; AAA86835.1) and Aeromonas hydrophila ([ 94 ]; AAA21016.1).…”

Section: Resultsmentioning

confidence: 99%

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In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites

Janíčková

Janeček

2021

Molecules

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This study brings a detailed bioinformatics analysis of fungal and chloride-dependent α-amylases from the family GH13. Overall, 268 α-amylase sequences were retrieved from subfamilies GH13_1 (39 sequences), GH13_5 (35 sequences), GH13_15 (28 sequences), GH13_24 (23 sequences), GH13_32 (140 sequences) and GH13_42 (3 sequences). Eight conserved sequence regions (CSRs) characteristic for the family GH13 were identified in all sequences and respective sequence logos were analysed in an effort to identify unique sequence features of each subfamily. The main emphasis was given on the subfamily GH13_32 since it contains both fungal α-amylases and their bacterial chloride-activated counterparts. In addition to in silico analysis focused on eventual ability to bind the chloride anion, the property typical mainly for animal α-amylases from subfamilies GH13_15 and GH13_24, attention has been paid also to the potential presence of the so-called secondary surface-binding sites (SBSs) identified in complexed crystal structures of some particular α-amylases from the studied subfamilies. As template enzymes with already experimentally determined SBSs, the α-amylases from Aspergillus niger (GH13_1), Bacillus halmapalus, Bacillus paralicheniformis and Halothermothrix orenii (all from GH13_5) and Homo sapiens (saliva; GH13_24) were used. Evolutionary relationships between GH13 fungal and chloride-dependent α-amylases were demonstrated by two evolutionary trees—one based on the alignment of the segment of sequences spanning almost the entire catalytic TIM-barrel domain and the other one based on the alignment of eight extracted CSRs. Although both trees demonstrated similar results in terms of a closer evolutionary relatedness of subfamilies GH13_1 with GH13_42 including in a wider sense also the subfamily GH13_5 as well as for subfamilies GH13_32, GH13_15 and GH13_24, some subtle differences in clustering of particular α-amylases may nevertheless be observed.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites

Janíčková

Janeček

2021

Molecules

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“…To date, more than ten novel species of alkaliphilic Bacillus species have been identified (Nielsen et al, 1995 ;Fritze, 1996 ;Yumoto et al, 1998). Although there are several reports on alkaliphilic Pseudomonas strains, these strains have not been identified at the species level (Jones et al, 1998 ;Kim et al, 1996 ;Na et al, 1996). Alkaliphilic strains belonging to genera other than Bacillus and Pseudomonas have also been reported (Horikoshi, 1991 ;Ikeda et al, 1994).…”

Section: Introductionmentioning

confidence: 99%

Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater.

Yumoto¹,

Yamazaki²,

Hishinuma³

et al. 2001

International Journal of Systematic and Evolutionary Microbiology

135

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Facultatively psychrophilic alkaliphilic strains were isolated from seawater obtained off the coast of Rumoi, Hokkaido, Japan. They were Gram-negative, aerobic straight rods with polar flagella. The isolates were catalase-and oxidase-positive and able to grow at 4 SC, but not at 40 SC. They produced acid from D-glucose under aerobic conditions. The isolates reduced nitrate to nitrite and hydrolysed casein and gelatin, but not starch or DNA. NaCl was required for growth at pH 10 but was not required at neutral pH. The major isoprenoid quinone was ubiquinone-9 (Q-9) and the DNA GMC content was 623-632 mol %.

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“…Even though chloride-activated amylases are specific to all animals, some bacterial amylases in the subfamily GH13_32, such as Pseudoalteromonas haloplanktis, have already been confirmed to have a dependence on chloride anion [32,33]. Based on the sequence logo, there are only five bacterial GH13_32 subfamilies, Halomonas meridiana, Pseudomonas sp., T. fusca, Thermomonospora_curvata and Pseudoalteromonas_haloplanktis, that contain three residues involved in chloride binding: Arg (strand β4), Asn (strand β7) and Lys (strand β8), located in the CSR-II, CSR-IV and CSR-VII, respectively [14,[34][35][36][37][38]. In HL11Amy, this lysine is replaced by a glutamine corresponding to the residue organization found in chloride-independent bacterial α-amylases, such as those from Bacillus amyloliquefaciens and B. licheniformis [39].…”

Section: Discussionmentioning

confidence: 99%

Functional Characterization of Recombinant Raw Starch Degrading α-Amylase from Roseateles terrae HL11 and Its Application on Cassava Pulp Saccharification

et al. 2022

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Exploring new raw starch-hydrolyzing -amylases and understanding their biochemical characteristics are important for the utilization of starch-rich materials in bio-industry. In this work, the biochemical characteristics of a novel raw starch-degrading -amylase (HL11 Amy) from Roseateles terrae HL11 was firstly reported. Evolutionary analysis revealed that HL11Amy was classified into glycoside hydrolase family 13 subfamily 32 (GH13_32). It contains four protein domains consisting of domain A, domain B, domain C and carbohydrate-binding module 20 (CMB20). The enzyme optimally worked at 50 °C, pH 4.0 with a specific activity of 6270 U/mg protein and 1030 raw starch-degrading (RSD) U/mg protein against soluble starch. Remarkably, HL11Amy exhibited activity toward both raw and gelatinized forms of various substrates, with the highest catalytic efficiency (kcat/Km) on starch from rice, followed by potato and cassava, respectively. HL11Amy effectively hydrolyzed cassava pulp (CP) hydrolysis, with a reducing sugar yield of 736 and 183 mg/g starch from gelatinized and raw CP, equivalent to 72% and 18% conversion based on starch content in the substrate, respectively. These demonstrated that HL11Amy represents a promising raw starch-degrading enzyme with potential applications in starch modification and cassava pulp saccharification.

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Cloning, sequencing and expression of the amylase isozyme gene from Pseudomonas sp. KFCC 10818

Cited by 8 publications

References 10 publications

In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites

In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites

Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater.

Functional Characterization of Recombinant Raw Starch Degrading α-Amylase from Roseateles terrae HL11 and Its Application on Cassava Pulp Saccharification

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