Agar degradation by microorganisms and agar-degrading enzymes

Chi, Won-Jae; Chang, YongKeun; Hong, Soon-Kwang

doi:10.1007/s00253-012-4023-2

Cited by 224 publications

(150 citation statements)

References 93 publications

(107 reference statements)

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“…Interestingly, there is one bacterial species, Saccharophagus degradans, that has been reported to possess nnrS as its only gene under the control of a dedicated NO-responsive transcription factor (19). This species of bacteria is found in a habitat in which its only carbon source is agar, which is another sugar polymer (44). Thus, the phylogenetic distribution of NnrS, as well as the data in this study, support the conclusion that NnrS is important in resisting nitrosative stress, particularly in environments with low carbon diversity, abundant iron, or low oxygen, in order to protect the cell against inhibition of iron-containing proteins by NO.…”

Section: Discussionmentioning

confidence: 99%

A Novel Protein Protects Bacterial Iron-Dependent Metabolism from Nitric Oxide

et al. 2013

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Reactive nitrogen species (RNS), in particular nitric oxide (NO), are toxic to bacteria, and bacteria have mechanisms to allow growth despite this stress. Understanding how bacteria interact with NO is essential to understanding bacterial physiology in many habitats, including pathogenesis; however, many targets of NO and enzymes involved in NO resistance remain uncharacterized. We performed for the first time a metabolomic screen on NO-treated and -untreated bacteria to define broadly the effects of NO on bacterial physiology, as well as to identify the function of NnrS, a previously uncharacterized enzyme involved in defense against NO. We found many known and novel targets of NO. We also found that iron-sulfur cluster enzymes were preferentially inhibited in a strain lacking NnrS due to the formation of iron-NO complexes. We then demonstrated that NnrS is particularly important for resistance to nitrosative stress under anaerobic conditions. Our data thus reveal the breadth of the toxic effects of NO on metabolism and identify the function of an important enzyme in alleviating this stress. Vibrio cholerae causes cholera, a severe watery diarrhea responsible for millions of cases and thousands of deaths each year (Centers for Disease Control and Prevention [http://www.cdc .gov]). It is not, however, a member of the Enterobacteriaceae-its natural habitat is aquatic. It is thought that during most of its life cycle, when not infecting humans, V. cholerae resides in association with zooplankton, forming biofilms on the chitinous surfaces of crustaceans (1, 2). Thus, V. cholerae must display metabolic flexibility in order to thrive in these two different environments and respond to the different metabolic challenges therein.A commonly encountered metabolic stress for pathogenic and nonpathogenic bacteria is the presence of reactive nitrogen species (RNS), in particular the well-studied molecule nitric oxide (NO). NO is formed as a by-product of nitrogen metabolism for many bacteria as an intermediate in denitrification (3), as well as from dedicated nitric oxide synthases (NOSs) in both bacteria and eukaryotes (4, 5), and is present in micromolar concentrations in some bacterial biofilms (6). NO can also be formed by chemical decomposition of nitrite in acid environments, such as the human stomach (7). NO is also a prominent component of the mammalian innate immune system, part of a battery of reactive oxygen species (ROS) and RNS produced by phagocytes when they encounter bacteria (7).The mechanisms whereby NO inhibits bacterial growth are diverse, but one of the most important properties of NO is its ability to bind iron and form dinitrosyl iron complexes (DNICs) bound to iron-sulfur cluster proteins, inhibiting their function (8, 9). DNICs have also been shown to mediate the formation of nitrosothiols, another form of nitrosative stress that inhibits thiolcontaining proteins (10). Through this mechanism and others, NO has been shown to inhibit a few enzymes in vitro, including such central metabolic enzymes as ...

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Section: Discussionmentioning

confidence: 99%

A Novel Protein Protects Bacterial Iron-Dependent Metabolism from Nitric Oxide

et al. 2013

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“…3.2.1.158), which cleave α-1,3 linkages to produce agarooligosaccharides 3,6-anhydro-L-galactose (Anr) residues at their reducing ends; or by β-agarases (E.C. 3.2.1.81), which cleave β-1,4 linkage to produce neoagarooligosaccharides with D-galactose residues at their reducing ends (Fu and Kim, 2010;Chi et al, 2012). Agarases may display either endo-or exo-activity, or both actitivities .…”

Section: Agarasesmentioning

confidence: 99%

“…and Vibrio sp. (Hu et al, 2009;Fu and Kim, 2010;Chi et al, 2012;Vijayaraghavan and Rajendran, 2012) β-Agarases can be classified into four GH families, GH16, GH50, GH86, and GH118, based on the similarity of amino acid (www.cazy.org, assessed on June 30, 2014). Typically, β-agarases are divided into types I and II, depending on substrate specificity and product profile.…”

Section: Agarasesmentioning

confidence: 99%

Marine enzymes and food industry: insight on existing and potential interactions

Fernandes

2014

Front. Mar. Sci.

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Evidence that support the marine environment as source of useful biocatalysts for application in several areas of industry pile up, both as scientific reports or patent applications. Marine microorganisms have to endure habitats characterized by extreme conditions of salinity, temperature or pressure. Their enzymes present concomitant features, viz. thermostability or halostability, which are appealing for practical applications. The food sector is a field where enzymes are used, given their specificity, compliance with strict regulations, relatively mild operational conditions required and environmental friendly nature. The specific features presented by marine enzymes can be advantageously used both for process improvement or to develop new processes and products. In the present review the role of relevant types of enzymes for the food sector is described and recent findings on those enzymes from marine are put into context. The information provided is illustrative that in spite of the relative novelty concerning the use of marine enzymes within the scope of the food sector, some processes have reached commercial status and promising results are being obtained with several others. Moreover, there is still a vast field of resources for enzyme activity to be explored, namely since the screening process that has been considerably improved with the contribution of metagenomic libraries. It can thus be considered that future and exciting developments can be expected concerning the use of marine enzymes in the food and feed areas.

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“…It is also one of the gelling materials commonly used in preparation of solid medium for cultivation of microorganisms. On the other hand, degradation products of agar formed by the hydrolysing enzyme agarase are simple sugars that can be used as substrates for biofuel production (Chi et al, 2012). During a sample collection and bacterial biodiversity study to isolate novel bacteria in Asan Bay, Korea, one novel strain, designated strain hydD622 T ,with agardegrading activity was recovered.…”

mentioning

confidence: 99%

Agarivorans aestuarii sp. nov., an agar-degrading bacterium isolated from a tidal flat

Kim

Pheng

Lee

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A Gram-reaction-negative, aerobic, non-spore forming, rod-shaped bacterium motile with a single polar flagellum, designated strain hydD622 T , was isolated from the sediment of a tidal flat at Asan Bay, Korea. Strain hydD622 T exhibited an agarolytic activity. Comparison of 16S rRNA gene sequences revealed that strain hydD622 T was closely related to Agarivorans litoreus KCTC 42116 T , Agarivorans albus KCTC 22256 T and Agarivorans gilvus KCTC 32555 T with similarities of 98.4, 98.0 and 96.5 %, respectively. Strain hydD622 T was clustered distantly from the other genera in the family Alteromonadaceae but formed a unique clade within the genus Agarivorans based on the 16S rRNA gene sequence. The DNA-DNA relatedness with Agarivorans litoreus KCTC 42116 T and Agarivorans. albus KCTC 22256 T was 39.0 and 37.8 %, respectively. The major fatty acids (>10 %) were C 16 : 0 ,C 16 : 1 !6c/C 16 : 1 !7c and C 18 : 1 !6c/C 18 : 1 !7c. The respiratory quinone was ubiquinone-8, and the polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified lipid. The DNA G+C content was 44 mol%. On the basis of physiological, chemotaxonomic and phylogenetic analyses, strain hydD622 T represents a novel species within the genus Agarivorans, for which the name Agarivorans aestuarii sp. nov. is proposed. The type strain of Agarivorans aestuarii sp. nov. is hydD622 T (=KCTC 32543 T =CGMCC 1.12692 T ).The genus Agarivorans was first proposed by Kurahasi & Yokota (2004), who isolated bacterial strains from the marine mollusk Omphalius pfeifferi in the Kanto area, Japan. The major characteristic of the genus Agarivorans is its agarolytic activity, and members have isolated from marine environments including marine animals, seawater, and seaweeds (Kurahasi & Yokota, 2004;Du et al., 2011;Park et al., 2014). Agar is a complex polysaccharide and can be obtained from red algae. Agar has been used as a food additive in many Asian countries. It is also one of the gelling materials commonly used in preparation of solid medium for cultivation of microorganisms. On the other hand, degradation products of agar formed by the hydrolysing enzyme agarase are simple sugars that can be used as substrates for biofuel production (Chi et al., 2012). During a sample collection and bacterial biodiversity study to isolate novel bacteria in Asan Bay, Korea, one novel strain, designated strain hydD622 T ,with agardegrading activity was recovered. Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate is affiliated within the genus Agarivorans by having similarity with Agarivorans litoreus GJSW-6 T (98.4 %), Agarivorans albus MKT 106 T (98.0 %) and Agarivorans gilvus WH0801 T (96.5 %), respectively. Through phenotypic and phylogenetic analyses, we report that strain hydD622 T represents a novel species in the genus Agarivorans for which the name Agarivorans aestuarii sp. nov is proposed.To isolate strain hydD622 T , a serially diluted seawater suspension of tidal flat sediment from Asan...

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Agar degradation by microorganisms and agar-degrading enzymes

Cited by 224 publications

References 93 publications

A Novel Protein Protects Bacterial Iron-Dependent Metabolism from Nitric Oxide

A Novel Protein Protects Bacterial Iron-Dependent Metabolism from Nitric Oxide

Marine enzymes and food industry: insight on existing and potential interactions

Agarivorans aestuarii sp. nov., an agar-degrading bacterium isolated from a tidal flat

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