Simiduia agarivorans gen. nov., sp. nov., a marine, agarolytic bacterium isolated from shallow coastal water from Keelung, Taiwan

Shieh, Wung Yang; Liu, Tung Yen; Lin, Silk Yu; Jean, Wen Dar; Chen, Jwo-Sheng

doi:10.1099/ijs.0.65371-0

Cited by 41 publications

(21 citation statements)

References 18 publications

(11 reference statements)

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“…S1 in the Supplementary Section shows the sequence alignment between MIM-1, MIM-2 and well-known MBLs from each subgroup). Little is known about these microorganisms, but both are Gramnegative bacteria found in marine environments [35,36]. N. pentaromativorans is a poly-cyclic aromatic hydrocarbon-degrading bacterium, while S. agarivorans is a heterotrophic bacterium; neither of these organisms is pathogenic [35,36].…”

Section: Introductionmentioning

confidence: 99%

“…Little is known about these microorganisms, but both are Gramnegative bacteria found in marine environments [35,36]. N. pentaromativorans is a poly-cyclic aromatic hydrocarbon-degrading bacterium, while S. agarivorans is a heterotrophic bacterium; neither of these organisms is pathogenic [35,36]. Here, we demonstrate the propensity of these enzymes to act as efficient MBLs, but we also show how different metal ion compositions may affect the substrate preference of these enzymes, and thus potentially also their biological function(s).…”

Section: Introductionmentioning

confidence: 99%

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β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health

et al. 2015

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Metallo-β-lactamases (MBLs) are a family of Zn(II)-dependent enzymes that inactivate most of the commonly used β-lactam antibiotics. They have emerged as a major threat to global healthcare. Recently, we identified two novel MBL-like proteins, Maynooth IMipenemase-1 (MIM-1) and Maynooth IMipenemase-2 (MIM-2), in the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans, respectively. Here, we demonstrate that MIM-1 and MIM-2 have catalytic activities comparable to those of known MBLs, but from the pH dependence of their catalytic parameters it is evident that both enzymes differ with respect to their mechanisms, with MIM-1 preferring alkaline and MIM-2 acidic conditions. Both enzymes require Zn(II) but activity can also be reconstituted with other metal ions including Co(II), Mn(II), Cu(II) and Ca(II). Importantly, the substrate preference of MIM-1 and MIM-2 appears to be influenced by their metal ion composition. Since neither N. pentaromativorans nor S. agarivorans are human pathogens, the precise biological role(s) of MIM-1 and MIM-2 remains to be established. However, due to the similarity of at least some of their in vitro functional properties to those of known MBLs, MIM-1 and MIM-2 may provide essential structural insight that may guide the design of as of yet elusive clinically useful MBL inhibitors.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health

et al. 2015

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“…A mixture of methanol and isopropyl alcohol (7 : 3, v/v) was used as the mobile phase, and quinones were detected at 270 nm. Cells harvested from cultures grown on marine agar 2216 (MA; Difco) at 30 C for 5 days under aerobic conditions were used for analyses of cellular fatty acids and DNA base composition according to the methods described by Shieh et al (2008). Fatty acids in whole cells were extracted, saponified and esterified, followed by GC analysis of the fatty acid methyl esters (FAMEs) according to procedures required by the MIDI system (Sasser, 2001).…”

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confidence: 99%

Spongiibacter taiwanensis sp. nov., a marine bacterium isolated from aged seawater

Jean

Yeh

Huang

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A Gram-reaction-negative, heterotrophic, marine bacterium, designated strain SPT1 T , was isolated from an aged seawater sample which was collected from the shallow coastal region of Nanya, Keelung, Taiwan and stored at room temperature for more than 7 years. Strain SPT1 T was a motile rod which exhibited monotrichous flagellation. It required NaCl for growth and exhibited optimal growth at 30-35 C, 1-3 % NaCl and pH 7-8. The strain was a strictly aerobic bacterium, incapable of anaerobic growth by nitrate reduction or denitrification, or by fermenting glucose or other carbohydrates. Cellular fatty acids were dominated by C 16 : 1 !7c and/or C 16 : 1 !6c (23.4 %), C 17 : 1 !8c (18.1 %), C 16 : 0 (8.5 %), C 18 : 1 !7c (8.4 %) and C 10 : 0 3-OH (6.3 %). The predominant isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and phosphatidic acid. The DNA G+C content was 57.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain SPT1 A 250 ml seawater sample collected from the shallow coastal region of Nanya, Keelung, Taiwan was sealed in a 500 ml serum bottle and stored at room temperature for more than seven years. A novel bacterium, designated strain SPT1 T , was isolated from this aged seawater sample which measured pH 8.3 and 3.5 % salinity at the time of bacterial isolation. Data from the present taxonomy study conducted using a polyphasic approach support the establishment of a novel species of the genus Spongiibacter, for which the name Spongiibacter taiwanensis is proposed with SPT1T as the type strain.The aged seawater sample was decimally diluted to the order of 10 -2 with sterile NaCl-Tris buffer (30 g NaCl and 0.24 g Tris base in 1 l deionized water, pH 8.0). Aliquots (0.1 ml) of 1Â to 10 -2 Â diluted samples were spread onto polypeptone-yeast extract (PY) agar plates (Shieh et al., 2000) in duplicates. The plates were incubated at 30 C in the dark for Abbreviation: FAME, fatty acid methyl ester.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SPT1 T is KT966463.One supplementary figure and One supplementary table are available with the online Supplementary Material.

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“…Strain TM-2 had flagella and was motile (Fig. 2), while strain SA-1 was non-motile [32]. In the API ZYM system, TM-2 was weakly positive for α-chymotrypsin and negative for α-glucosidase (Table 1), and, in the API 20NE system, TM-2 showed differences in the indole production and in the hydrolysis of gelatin and p-nitro-phenyl-β-D-galactopyranoside compared with Simiduia areninigrae M2-5 (Table 1) [26].…”

Section: Identification and Characterization Of Strain Tm-2mentioning

confidence: 99%

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

Tawara

Sakatoku

Tiodjio

et al. 2015

Appl Biochem Biotechnol

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A new bacterial strain capable of reducing thalli of various seaweeds (red, green, and brown algae) was isolated from marine sediments of Uozu in Toyama Prefecture, Japan. We designated the strain Simiduia sp. TM-2 based on analyses of the 16S rRNA gene and gyrB gene sequences and its biochemical and morphological characteristics. Zymography methods revealed numerous active bands of alginate lyases, cellulases, and agarases in the cells and culture supernatants of TM-2, showing that the strain possessed multiple polysaccharide lyases. A novel agarase gene (agaTM2) was cloned from TM-2 and expressed in Escherichia coli. The resulting DNA sequence contained an open reading frame of 1764 bp that encoded a protein of 587 amino acids with an estimated molecular mass of 64 kDa and pI of 4.62. The deduced amino acid sequence, AgaTM2, had a typical signal peptide followed by a glycoside hydrolase family 16 catalytic domain and two carbohydrate-binding modules 6. A BLAST search indicated that AgaTM2 shared 75.5 % amino acid sequence identity with agarase from Simiduia agarivorans SA1. The cloned and purified AgaTM2 protein showed optimal activity at 35 °C and pH 8.0, and its thermostability increased in the presence of calcium ions. AgaTM2 degraded agarose to tetraose and hexaose.

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Simiduia agarivorans gen. nov., sp. nov., a marine, agarolytic bacterium isolated from shallow coastal water from Keelung, Taiwan

Cited by 41 publications

References 18 publications

β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health

β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health

Spongiibacter taiwanensis sp. nov., a marine bacterium isolated from aged seawater

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

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