Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds

Tawara, Mika; Sakatoku, Akihiro; Tiodjio, Rosine E.; Tanaka, Daisuke; Nakamura, Shōgo

doi:10.1007/s12010-015-1765-1

Cited by 17 publications

(7 citation statements)

References 38 publications

(39 reference statements)

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“…One way for bacteria to influence algal growth is through the production of agarases and carrageenases that degrade galactose-based algal polymers and, in the case of agarases, can cause disease and die-off of red seaweed ( Schroeder et al, 2003 ). We found that leaf microbiomes included a high proportion (average 3.3% leaf and 1.8% root) of organisms belonging to the Gammaproteobacteria genus Simiduia , which is associated with agarose hydrolysis ( Park et al, 2014 ; Tawara et al, 2015 ). We also found expression of beta-agarase genes and several galactosidases were assigned to Gammaproteobacteria in the Z. japonica leaf microbiome ( Figure 5 ).…”

Section: Discussionmentioning

confidence: 96%

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

et al. 2018

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Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.

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Section: Discussionmentioning

confidence: 96%

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

et al. 2018

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“…A few studies have been conducted using different macroalgae species as the substrate for agarase. The agarase AgaTM2 acted on seaweeds and degraded them into NA4 and NA6 (Tawara et al 2015). In the study conducted by Hou et al (2015), where Gracilaria lemaneiformis was used as the substrate for the recombinant agarase AgaP4383 exhibited a V max of 21 U/ mg and a K M of 32.41 mg/ml where it produced NA4 and NA6 as the products.…”

Section: Kinetic Properties Of the Recombinant Agarases And Their Degmentioning

confidence: 99%

“…The recombinant β-agarases belong to the glycoside hydrolase (GH) family such as GH16, GH39, GH50, GH86, and GH118. Predominantly, the recombinant β-agarases were from marine microbes and their genera include Agarivorans (Liu et al 2014a, b;Lee et al 2012;Lin et al 2012), Alteromonas (Seo et al 2014;Chi et al 2014), Aquimarina (Lin et al 2017), Catenovulum (An et al 2018;Cui et al 2014;Xie et al 2013), Cellulophaga (Ramos et al 2018), Flammeovirga (Dong et al 2016;Hou et al 2015;Yang et al 2011;Chen et al 2016;Di et al 2018), Gayadomonas (Lee et al 2018;Jung et al 2017a, b), Microbulbifer (Su et al 2017), Micrococcaceae (Xu et al 2018), Pseudoalteromonas (Chi et al 2015a, b;Oh et al 2010a, b), Pseudomonas (Hsu et al 2015), Saccharophagus (Kim et al 2010(Kim et al , 2017(Kim et al , 2018Lee et al 2013), Simiduia (Tawara et al 2015), Thalassomonas (Liang et al 2014), and Vibrio (Liao et al 2011) whereas few were from soil bacteria Streptomyces (Temuujin et al 2011(Temuujin et al , 2012, Cohnella (Li et al 2015) and one exclusive source was the activated sludges of sewage plant from which Cellvibrio (Osamu et al 2012) had been identified with agarolytic property.…”

Section: Introductionmentioning

confidence: 99%

Recombinant β-agarases: insights into molecular, biochemical, and physiochemical characteristics

Veerakumar

Manian

2018

3 Biotech

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Agarases (agarose 4-glycanohydrolase; EC 3.2.1.81) are class of enzymes that belong to glycoside hydrolase (GH) family capable of hydrolyzing agar. Their classification depends on hydrolysis pattern and product formation. Among all the agarases, β-agarases and the oligosaccharides formed by its action have fascinated quite a lot of industries. Ample of β-agarase genes have been endowed from marine sources such as algae, sea water, and marine sediments, and the expression of these genes into suitable host gives rise to recombinant β-agarases. These recombinant β-agarases have wide range of industrial applications due to its improved catalytic efficiency and stability in tough environments with ease of production on large scale. In this review, we have perused different types of recombinant β-agarases in consort with their molecular, physiochemical, and kinetic properties in detail and the significant features of those agarases are spotlighted. From the literature reviewed after 2010, we have found that the recombinant β-agarases belonged to the families GH16, GH39, GH50, GH86, and GH118. Among that, GH39, GH50, and GH86 belonged to clan GH-A, while the GH16 family belonged to clan GH-B. It was observed that GH16 is the largest polyspecific glycoside hydrolase family with ample number of β-agarases and the families GH50 and GH118 were found to be monospecific with only β-agarase activity. And, out of 84 non-catalytic carbohydrate-binding modules (CBMs), only CBM6 and CBM13 were professed in β-agarases. We witnessed a larger heterogeneity in molecular, physiochemical, and catalytic characteristics of the recombinant β-agarases including molecular mass: 32-132 kDa, optimum pH: 4.5-9, optimum temperature 16-60 °C, K M : 0.68-59.8 mg/ml, and V max : 0.781-11,400 U/ mg. Owing to this extensive range of heterogeneity, they have lion's share in the multibillion dollar enzyme market. This review provides a holistic insight to a few aspects of recombinant β-agarases which can be referred by the upcoming explorers to this area.

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“…Compared with α -agarases, a large number of β-agarases have been found in many different genera, including Agarivorans [12], Cytophaga [13], Pseudomonas [14], Vibrio [15][16][17], Flammeovirga [18], and Agarivorans [19,20]. Based on amino acid sequence similarity, β-agarases have been classified into four distinct glycoside hydrolase (GH) families: GH16, GH50, GH86, and GH118 [21], which are recorded in the Carbohydrate-Active enZYmes Database (http://www.cazy.org). β-agarases from the GH16, GH50, GH86 families contain two major conserved modules: one a catalytic glycoside hydrolase module which is responsible for hydrolyzing of glycoside linkage and the other a non-catalytic carbohydrate binding module (CBM), which helps enzymes bind substrates by forming a substrate-binding groove [22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Isolation and Characterization of an Eosinophilic GH 16 ��-Agarase (AgaDL6) from an Agar-Degrading Marine Bacterium Flammeovirga sp. HQM9

Liu¹,

Tian²,

Peng³

et al. 2019

Journal of Microbiology and Biotechnology

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A special eosinophilic agarase exo-type β-agarase gene, AgaDL6, was cloned from a marine agar-degrading bacterium, Flammeovirga sp. HQM9. The gene comprised 1,383-bp nucleotides encoding a putative agarase AgaDL6 of 461 amino acids with a calculated molecular mass of 52.8 kDa. Sequence analysis revealed a β-agarase domain that belongs to the glycoside hydrolase family (GH) 16 and a carbohydrate-binding module (CBM_4_9) unique to agarases. AgaDL6 was heterologously expressed in Escherichia coli BL21 (DE3). Enzyme activity analysis of the purified protein showed that the optimal temperature and pH of AgaDL6 were 50°C and 3.0, respectively. AgaDL6 showed thermal stability by retaining more than 98% of activity after incubation for 2 h at 50°C, a feature quite different from other agarases. AgaDL6 also exhibited outstanding acid stability, retaining 100% of activity after incubation for 24 h at pH 2.0 to 5.0, a property distinct from other agarases. This is the first agarase characterized to have such high acid stability. In addition, we observed no obvious stimulation or inhibition of AgaDL6 in the presence of various metal ions and denaturants. AgaDL6 is an exo-type β-1,4 agarase that cleaved agarose into neoagarotetraose and neoagarohexaose as the final products. These characteristics make AgaDL6 a potentially valuable enzyme in the cosmetic, food, and pharmaceutical industries.

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Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds

Cited by 17 publications

References 38 publications

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Recombinant β-agarases: insights into molecular, biochemical, and physiochemical characteristics

Isolation and Characterization of an Eosinophilic GH 16 ��-Agarase (AgaDL6) from an Agar-Degrading Marine Bacterium Flammeovirga sp. HQM9

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