arabinan Search Results


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  • 93
    Millipore arabinan
    An araP mutant exhibits a significant growth defect on <t>arabinan.</t> (A) Growth of three B. thetaiotaomicron strains, one harboring a polar transposon insertion in the BT0356 gene ( BT0356 :pSAM, NS423), one deleted for the araP gene (NS401), and the isogenic wild-type strain (WT, GT23), in minimal medium containing 0.5% arabinose. (B) Growth of isogenic araP strain (NS401) and wild-type B. thetaiotaomicron in minimal medium containing 0.5% arabinan. (C) Growth of isogenic araP strain (NS401) and wild-type B. thetaiotaomicron in minimal medium containing 0.5% arabinobiose. Graphed are the mean and standard error of the mean from at least five independent replicates grown in the same plate.
    Arabinan, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Megazyme arabinan
    Primary and secondary transporters involved in the uptake of arabinooligosaccharides in B. subtilis and the role of MsmX in their transport. <t>Arabinan,</t> a homopolymer of arabinose, is extracellularly degraded by two endo-α-1,5-arabinanases, AbnA
    Arabinan, supplied by Megazyme, used in various techniques. Bioz Stars score: 89/100, based on 122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Megazyme debranched arabinan
    The exo-acting mechanism of the ruminal single-domain ABN (ARN3). A, catalytic interface of ARN3 ( white ) showing the residues that form the −2 subsite of the exo-enzyme ARN3 ( green ) and the endo-enzyme AbnB ( magenta ), the modeled oligosaccharide in the ARN3 structure ( yellow ball and sticks ), and the Arg 203 –Ala 230 loop ( green surface representation). B , topographical adaptations of the SRGEEP-ARN3 active site. The shortened loop is represented as a transparent magenta surface and the substrate from the AbnB complex structure is in magenta ball and sticks . For comparison, the original loop of ARN3 is shown as a green line. C, kinetic analysis of ARN3 and SRGEEP-ARN3 using <t>debranched</t> <t>arabinan</t> as substrate. Capillary zone electrophoresis analysis of cleavage products of linear arabinan and arabinoheptaose by SRGEEP-ARN3 ( D and F , respectively) and ARN3 ( E and G , respectively).
    Debranched Arabinan, supplied by Megazyme, used in various techniques. Bioz Stars score: 91/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Megazyme sugar beet arabinan
    Analysis of linear <t>arabinan</t> and debranched arabinan hydrolyzed by Tth Abn endo-arabinanase. The products of the reaction were examined with TLC. M: arabinose, arabinobiose and arabinotriose. a . Lane 1, 2, 3, 4: linear arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h. respectively. b . Lane 1, 2, 3, 4: debranched arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively. c . Lane 1, 2, 3, 4: sugar beet arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively.
    Sugar Beet Arabinan, supplied by Megazyme, used in various techniques. Bioz Stars score: 89/100, based on 125 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Megazyme 1 5 α l arabinan
    Analysis of linear <t>arabinan</t> and debranched arabinan hydrolyzed by Tth Abn endo-arabinanase. The products of the reaction were examined with TLC. M: arabinose, arabinobiose and arabinotriose. a . Lane 1, 2, 3, 4: linear arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h. respectively. b . Lane 1, 2, 3, 4: debranched arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively. c . Lane 1, 2, 3, 4: sugar beet arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively.
    1 5 α L Arabinan, supplied by Megazyme, used in various techniques. Bioz Stars score: 88/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Millipore cellstain double staining kit
    Analysis of linear <t>arabinan</t> and debranched arabinan hydrolyzed by Tth Abn endo-arabinanase. The products of the reaction were examined with TLC. M: arabinose, arabinobiose and arabinotriose. a . Lane 1, 2, 3, 4: linear arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h. respectively. b . Lane 1, 2, 3, 4: debranched arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively. c . Lane 1, 2, 3, 4: sugar beet arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively.
    Cellstain Double Staining Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 99 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Bio-Synthesis Inc cell wall arabinan biosynthesis
    Arabinosyltransferases involved in the biosynthesis of the <t>arabinan</t> domains of lipoarabinomannan (left panel) and arabinogalactan (right panel) in M. tuberculosis .
    Cell Wall Arabinan Biosynthesis, supplied by Bio-Synthesis Inc, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Megazyme sugar beet arabinan sba
    Arabinosyltransferases involved in the biosynthesis of the <t>arabinan</t> domains of lipoarabinomannan (left panel) and arabinogalactan (right panel) in M. tuberculosis .
    Sugar Beet Arabinan Sba, supplied by Megazyme, used in various techniques. Bioz Stars score: 86/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Epitope Biotech arabinans
    Arabinosyltransferases involved in the biosynthesis of the <t>arabinan</t> domains of lipoarabinomannan (left panel) and arabinogalactan (right panel) in M. tuberculosis .
    Arabinans, supplied by Epitope Biotech, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Megazyme linear arabinans
    Arabinosyltransferases involved in the biosynthesis of the <t>arabinan</t> domains of lipoarabinomannan (left panel) and arabinogalactan (right panel) in M. tuberculosis .
    Linear Arabinans, supplied by Megazyme, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    An araP mutant exhibits a significant growth defect on arabinan. (A) Growth of three B. thetaiotaomicron strains, one harboring a polar transposon insertion in the BT0356 gene ( BT0356 :pSAM, NS423), one deleted for the araP gene (NS401), and the isogenic wild-type strain (WT, GT23), in minimal medium containing 0.5% arabinose. (B) Growth of isogenic araP strain (NS401) and wild-type B. thetaiotaomicron in minimal medium containing 0.5% arabinan. (C) Growth of isogenic araP strain (NS401) and wild-type B. thetaiotaomicron in minimal medium containing 0.5% arabinobiose. Graphed are the mean and standard error of the mean from at least five independent replicates grown in the same plate.

    Journal: mBio

    Article Title: Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

    doi: 10.1128/mBio.01342-16

    Figure Lengend Snippet: An araP mutant exhibits a significant growth defect on arabinan. (A) Growth of three B. thetaiotaomicron strains, one harboring a polar transposon insertion in the BT0356 gene ( BT0356 :pSAM, NS423), one deleted for the araP gene (NS401), and the isogenic wild-type strain (WT, GT23), in minimal medium containing 0.5% arabinose. (B) Growth of isogenic araP strain (NS401) and wild-type B. thetaiotaomicron in minimal medium containing 0.5% arabinan. (C) Growth of isogenic araP strain (NS401) and wild-type B. thetaiotaomicron in minimal medium containing 0.5% arabinobiose. Graphed are the mean and standard error of the mean from at least five independent replicates grown in the same plate.

    Article Snippet: All chemicals were purchased from Sigma except arabinan (sugar beet, P-ARAB), arabinobiose (O-ABI), pectic galactan (P-PGAPT), and rhamnogalacturonan I (P-RHAM1), which were purchased from Megazyme, and beta-d -(−)-fructose (MP Biomedicals).

    Techniques: Mutagenesis

    Arabinan promotes transcription of arabinan PUL genes and arabinose utilization genes in a BT0366- dependent manner. (A) mRNA levels of the BT0364 , BT0367 , and BT0366 genes in isogenic BT0366 (GT44) and wild-type (WT, GT23) B. thetaiotaomicron prior to the switch (−5) and after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan. (B) Western blot of crude extracts from a strain specifying an HA-tagged BT0366 protein (NS204) collected from cultures grown to mid-log phase in minimal medium containing 0.5% glucose (−5) or 30, 60, and 120 min after switching to medium containing 0.1% arabinan. Data are representative of three independent experiments, which produced similar results. (C) mRNA levels of the araM gene in isogenic BT0366 mutant (GT44) and wild-type (GT23) B. thetaiotaomicron prior to the switch (−5) and after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan. Graphed are the mean and standard error of the mean from at least three independent experiments. Asterisks indicate significant differences from the wild-type strain for BT0364 and BT0367 expression and significant difference from the −5 sample for BT0366 expression (*, P ≤ 0.05; **, P ≤ 0.01 by two-tailed Student’s t test). Note log scale of y axis in panels A and C.

    Journal: mBio

    Article Title: Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

    doi: 10.1128/mBio.01342-16

    Figure Lengend Snippet: Arabinan promotes transcription of arabinan PUL genes and arabinose utilization genes in a BT0366- dependent manner. (A) mRNA levels of the BT0364 , BT0367 , and BT0366 genes in isogenic BT0366 (GT44) and wild-type (WT, GT23) B. thetaiotaomicron prior to the switch (−5) and after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan. (B) Western blot of crude extracts from a strain specifying an HA-tagged BT0366 protein (NS204) collected from cultures grown to mid-log phase in minimal medium containing 0.5% glucose (−5) or 30, 60, and 120 min after switching to medium containing 0.1% arabinan. Data are representative of three independent experiments, which produced similar results. (C) mRNA levels of the araM gene in isogenic BT0366 mutant (GT44) and wild-type (GT23) B. thetaiotaomicron prior to the switch (−5) and after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan. Graphed are the mean and standard error of the mean from at least three independent experiments. Asterisks indicate significant differences from the wild-type strain for BT0364 and BT0367 expression and significant difference from the −5 sample for BT0366 expression (*, P ≤ 0.05; **, P ≤ 0.01 by two-tailed Student’s t test). Note log scale of y axis in panels A and C.

    Article Snippet: All chemicals were purchased from Sigma except arabinan (sugar beet, P-ARAB), arabinobiose (O-ABI), pectic galactan (P-PGAPT), and rhamnogalacturonan I (P-RHAM1), which were purchased from Megazyme, and beta-d -(−)-fructose (MP Biomedicals).

    Techniques: Western Blot, Produced, Mutagenesis, Expressing, Two Tailed Test

    The regulatory gene BT4338 is essential for arabinan utilization. (A) mRNA levels of the araM gene in isogenic wild-type (GT23), BT4338 (NS364), araR (NS367), araR BT4338 (NS404), and araR BT0366 BT4338 (NS408) strains prior to the switch (−5) and after 1- and 2-h exposure to minimal medium containing 0.1% arabinan. (B) Growth of isogenic BT4338 (NS364) and wild-type (GT23) strains in minimal medium containing 0.5% arabinose. (C) mRNA levels of the BT0364 gene in isogenic wild-type (GT23), BT4338 (NS364), araR (NS367), araR BT4338 (NS404), and araR BT0366 BT4338 (NS408) strains prior to the switch (−5) and after 1- and 2-h exposure to minimal medium containing 0.1% arabinan. (D) Growth of isogenic BT4338 (NS364) and wild-type (GT23) strains in minimal medium containing 0.5% arabinan. For transcription experiments, the mean and standard error of the mean from at least three independent experiments are graphed. Asterisks indicate significant difference from the background strain containing BT4338 (*, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001 by two-tailed Student’s t test). For growth experiments, graphed are the mean and standard error of the mean from at least five independent replicates grown in the same plate. Note log scale of y axis in panels A and C.

    Journal: mBio

    Article Title: Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

    doi: 10.1128/mBio.01342-16

    Figure Lengend Snippet: The regulatory gene BT4338 is essential for arabinan utilization. (A) mRNA levels of the araM gene in isogenic wild-type (GT23), BT4338 (NS364), araR (NS367), araR BT4338 (NS404), and araR BT0366 BT4338 (NS408) strains prior to the switch (−5) and after 1- and 2-h exposure to minimal medium containing 0.1% arabinan. (B) Growth of isogenic BT4338 (NS364) and wild-type (GT23) strains in minimal medium containing 0.5% arabinose. (C) mRNA levels of the BT0364 gene in isogenic wild-type (GT23), BT4338 (NS364), araR (NS367), araR BT4338 (NS404), and araR BT0366 BT4338 (NS408) strains prior to the switch (−5) and after 1- and 2-h exposure to minimal medium containing 0.1% arabinan. (D) Growth of isogenic BT4338 (NS364) and wild-type (GT23) strains in minimal medium containing 0.5% arabinan. For transcription experiments, the mean and standard error of the mean from at least three independent experiments are graphed. Asterisks indicate significant difference from the background strain containing BT4338 (*, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001 by two-tailed Student’s t test). For growth experiments, graphed are the mean and standard error of the mean from at least five independent replicates grown in the same plate. Note log scale of y axis in panels A and C.

    Article Snippet: All chemicals were purchased from Sigma except arabinan (sugar beet, P-ARAB), arabinobiose (O-ABI), pectic galactan (P-PGAPT), and rhamnogalacturonan I (P-RHAM1), which were purchased from Megazyme, and beta-d -(−)-fructose (MP Biomedicals).

    Techniques: Two Tailed Test

    AraR is a repressor of arabinose and arabinan utilization genes. (A) mRNA levels of the araM , BT0364 , and BT0367 genes in isogenic araR (NS367) and wild-type (WT, GT23) B. thetaiotaomicron strains following growth in minimal medium containing 0.5% of either arabinose or glucose. (B) mRNA levels of the arabinan PUL genes BT0364 and BT0367 in isogenic araR (NS367) and wild-type (GT23) B. thetaiotaomicron strains prior to the switch (−5) and after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan. (C) mRNA levels of the arabinose utilization gene araM in isogenic araR (NS367) and wild-type (GT23) B. thetaiotaomicron strains after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan and prior to the switch (−5) to medium containing arabinan. (D) Growth of isogenic araR (NS367) and wild-type B. thetaiotaomicron (GT23) strains after switching from minimal medium containing 0.5% glucose to minimal medium containing 0.1% arabinan. Graphed are the mean and standard error of the mean from at least three independent experiments. Asterisks indicate significant difference from the wild-type strain (*, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001 by two-tailed Student’s t test). Note log scale of y axis in panels A, B, and C.

    Journal: mBio

    Article Title: Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

    doi: 10.1128/mBio.01342-16

    Figure Lengend Snippet: AraR is a repressor of arabinose and arabinan utilization genes. (A) mRNA levels of the araM , BT0364 , and BT0367 genes in isogenic araR (NS367) and wild-type (WT, GT23) B. thetaiotaomicron strains following growth in minimal medium containing 0.5% of either arabinose or glucose. (B) mRNA levels of the arabinan PUL genes BT0364 and BT0367 in isogenic araR (NS367) and wild-type (GT23) B. thetaiotaomicron strains prior to the switch (−5) and after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan. (C) mRNA levels of the arabinose utilization gene araM in isogenic araR (NS367) and wild-type (GT23) B. thetaiotaomicron strains after 1 and 2 h of exposure to minimal medium containing 0.1% arabinan and prior to the switch (−5) to medium containing arabinan. (D) Growth of isogenic araR (NS367) and wild-type B. thetaiotaomicron (GT23) strains after switching from minimal medium containing 0.5% glucose to minimal medium containing 0.1% arabinan. Graphed are the mean and standard error of the mean from at least three independent experiments. Asterisks indicate significant difference from the wild-type strain (*, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001 by two-tailed Student’s t test). Note log scale of y axis in panels A, B, and C.

    Article Snippet: All chemicals were purchased from Sigma except arabinan (sugar beet, P-ARAB), arabinobiose (O-ABI), pectic galactan (P-PGAPT), and rhamnogalacturonan I (P-RHAM1), which were purchased from Megazyme, and beta-d -(−)-fructose (MP Biomedicals).

    Techniques: Two Tailed Test

    BT0366 controls expression of arabinose utilization genes but does not bind to the corresponding promoter regions. (A) Electrophoretic mobility shift assay (EMSA) of a fragment of the BT0366 hybrid two-component system harboring the response regulator and DNA-binding domains with DNA fragments located upstream of the BT0365 coding region, intragenic to BT0366-BT0367 , and upstream of the araM coding region. (B) mRNA levels of the araM gene in isogenic araP (NS401) and wild-type B. thetaiotaomicron (GT23) strains prior to the switch (−5) and after 1-h exposure to minimal medium containing 0.1% arabinose or 0.1% arabinan. (C) mRNA levels of the araM gene in isogenic araR (NS367) and araR BT0366 (NS422) strains prior to the switch (−5) and after 1- and 2-h exposure to minimal medium containing 0.1% arabinan. (D) mRNA levels of the araM and BT0364 genes in isogenic araR (NS367) and wild-type (GT23) strains after 1- and 2-h exposure to minimal medium lacking a carbohydrate. Graphed are the mean and standard error of the mean from at least three independent experiments. Asterisks indicate significant differences from the wild-type strain in panels B and C and significant difference from the −5 sample in panel D (*, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001 by two-tailed Student’s t test). Note log scale of y axis in panels B, C, and D.

    Journal: mBio

    Article Title: Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

    doi: 10.1128/mBio.01342-16

    Figure Lengend Snippet: BT0366 controls expression of arabinose utilization genes but does not bind to the corresponding promoter regions. (A) Electrophoretic mobility shift assay (EMSA) of a fragment of the BT0366 hybrid two-component system harboring the response regulator and DNA-binding domains with DNA fragments located upstream of the BT0365 coding region, intragenic to BT0366-BT0367 , and upstream of the araM coding region. (B) mRNA levels of the araM gene in isogenic araP (NS401) and wild-type B. thetaiotaomicron (GT23) strains prior to the switch (−5) and after 1-h exposure to minimal medium containing 0.1% arabinose or 0.1% arabinan. (C) mRNA levels of the araM gene in isogenic araR (NS367) and araR BT0366 (NS422) strains prior to the switch (−5) and after 1- and 2-h exposure to minimal medium containing 0.1% arabinan. (D) mRNA levels of the araM and BT0364 genes in isogenic araR (NS367) and wild-type (GT23) strains after 1- and 2-h exposure to minimal medium lacking a carbohydrate. Graphed are the mean and standard error of the mean from at least three independent experiments. Asterisks indicate significant differences from the wild-type strain in panels B and C and significant difference from the −5 sample in panel D (*, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001 by two-tailed Student’s t test). Note log scale of y axis in panels B, C, and D.

    Article Snippet: All chemicals were purchased from Sigma except arabinan (sugar beet, P-ARAB), arabinobiose (O-ABI), pectic galactan (P-PGAPT), and rhamnogalacturonan I (P-RHAM1), which were purchased from Megazyme, and beta-d -(−)-fructose (MP Biomedicals).

    Techniques: Expressing, Electrophoretic Mobility Shift Assay, Binding Assay, Two Tailed Test

    Schematic of the regulation of arabinan and arabinose utilization genes in B. thetaiotaomicron . Arabinan is extracellularly bound by two SusD-like proteins and imported into the periplasm by two SusC-like transporters. Large arabinan polymers are broken down into polymers of six to eight subunits in chain length (oligoarabinose) and eventually smaller arabino-oligosaccharides, such as arabinobiose, which are transported into the cytoplasm by AraP. These oligosaccharides are broken down to arabinose in the cytoplasm by an unknown glycoside hydrolase. Oligoarabinose binds to and activates the transcriptional regulator BT0366, which, in turn, promotes transcription of the arabinan utilization genes BT0365 to - 60 , BT0366 , and BT0367 to - 69 . l -Arabinose is transported into the cell by an unknown mechanism. Cytoplasmic arabinose prevents binding of the transcriptional repressor AraR to the promoters of the arabinan utilization gene BT0365 and the arabinose utilization gene BT0356 ( araM ). The transcriptional regulator BT4338 is necessary for full activation of arabinan and arabinose utilization genes. The signal controlling the activity of BT4338 is at present unknown. OM, outer membrane; IM, inner membrane.

    Journal: mBio

    Article Title: Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

    doi: 10.1128/mBio.01342-16

    Figure Lengend Snippet: Schematic of the regulation of arabinan and arabinose utilization genes in B. thetaiotaomicron . Arabinan is extracellularly bound by two SusD-like proteins and imported into the periplasm by two SusC-like transporters. Large arabinan polymers are broken down into polymers of six to eight subunits in chain length (oligoarabinose) and eventually smaller arabino-oligosaccharides, such as arabinobiose, which are transported into the cytoplasm by AraP. These oligosaccharides are broken down to arabinose in the cytoplasm by an unknown glycoside hydrolase. Oligoarabinose binds to and activates the transcriptional regulator BT0366, which, in turn, promotes transcription of the arabinan utilization genes BT0365 to - 60 , BT0366 , and BT0367 to - 69 . l -Arabinose is transported into the cell by an unknown mechanism. Cytoplasmic arabinose prevents binding of the transcriptional repressor AraR to the promoters of the arabinan utilization gene BT0365 and the arabinose utilization gene BT0356 ( araM ). The transcriptional regulator BT4338 is necessary for full activation of arabinan and arabinose utilization genes. The signal controlling the activity of BT4338 is at present unknown. OM, outer membrane; IM, inner membrane.

    Article Snippet: All chemicals were purchased from Sigma except arabinan (sugar beet, P-ARAB), arabinobiose (O-ABI), pectic galactan (P-PGAPT), and rhamnogalacturonan I (P-RHAM1), which were purchased from Megazyme, and beta-d -(−)-fructose (MP Biomedicals).

    Techniques: Binding Assay, Activation Assay, Activity Assay

    Catalytic activity of Bt3069 and Cj Abf43A. The enzymes at 50 n m were incubated with sugar beet arabinan, and the reaction products generated were analyzed by HPAEC.

    Journal: The Journal of Biological Chemistry

    Article Title: The Structure and Function of an Arabinan-specific ?-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases *

    doi: 10.1074/jbc.M110.215962

    Figure Lengend Snippet: Catalytic activity of Bt3069 and Cj Abf43A. The enzymes at 50 n m were incubated with sugar beet arabinan, and the reaction products generated were analyzed by HPAEC.

    Article Snippet: The substrates 4-nitrophenyl-α- l -arabinofuranoside (4NPA) and sugar beet arabinan were purchased from Sigma and Megazyme, respectively.

    Techniques: Activity Assay, Incubation, Generated

    Heteronuclear single quantum coherence one-bond 13 C- 1 H correlation spectroscopy. Reactions were performed in 5 m m sodium phosphate buffer, pH 7.0. Cj Abf43A (10 μ m ) was incubated with acid-hydrolyzed sugar beet arabinan for 1 h. Chemical shifts

    Journal: The Journal of Biological Chemistry

    Article Title: The Structure and Function of an Arabinan-specific ?-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases *

    doi: 10.1074/jbc.M110.215962

    Figure Lengend Snippet: Heteronuclear single quantum coherence one-bond 13 C- 1 H correlation spectroscopy. Reactions were performed in 5 m m sodium phosphate buffer, pH 7.0. Cj Abf43A (10 μ m ) was incubated with acid-hydrolyzed sugar beet arabinan for 1 h. Chemical shifts

    Article Snippet: The substrates 4-nitrophenyl-α- l -arabinofuranoside (4NPA) and sugar beet arabinan were purchased from Sigma and Megazyme, respectively.

    Techniques: Spectroscopy, Incubation

    AICAR treatment increased detection of p-AMPK and decreased CDX2 by Western blot. Top panel shows Western blots, Control (01, 02, 03) and AICAR-treated (A1, A2, A3) embryos. β-actin shows equal protein loading, not significantly different between control and AICAR-treated embryos. ( A ) p-AMPK after 48 h culture of 2-cell embryos. There was n = 3 independent sample pools (30 embryos per pool). Control (01, 02, 03) and AICAR-treated (A1, A2, A3) embryos were significantly different, * P

    Journal: Molecular Human Reproduction

    Article Title: Treatment with AICAR inhibits blastocyst development, trophectoderm differentiation and tight junction formation and function in mice

    doi: 10.1093/molehr/gax050

    Figure Lengend Snippet: AICAR treatment increased detection of p-AMPK and decreased CDX2 by Western blot. Top panel shows Western blots, Control (01, 02, 03) and AICAR-treated (A1, A2, A3) embryos. β-actin shows equal protein loading, not significantly different between control and AICAR-treated embryos. ( A ) p-AMPK after 48 h culture of 2-cell embryos. There was n = 3 independent sample pools (30 embryos per pool). Control (01, 02, 03) and AICAR-treated (A1, A2, A3) embryos were significantly different, * P

    Article Snippet: Embryos were then incubated overnight at 4°C in the following primary antibodies at the indicated dilutions: rabbit anti-CDX2 (ab76541, 1:100, Abcam, Cambridge, MA, USA), rabbit anti-phospho-AMPK (07–681, 1:75, Millipore, Temecula, CA), rat anti-ZO1 (MABT11, 1:100, Millipore, Temecula, CA), rat anti-AQP9 (AQP91-A, 1:100, Alpha Diagnostic International, San Antonio, TX), mouse anti-CDH1 ( , 1:100, BD Transduction Laboratories, San Jose CA).

    Techniques: Western Blot

    AICAR treatment increased detection of p-AMPK and decreased ZO1 (TJP1) localization to the cell membrane. ( A ) phospho-AMPK after 48 h culture of 2-cell embryos. Green panel shows p-AMPK fluorescence. Red is rhodamine-phalloidin staining of F-actin. Blue is DAPI-stained DNA. Merged figure shows color overlap. Arrowheads show evidence of loss of cell-to-cell contacts. Arrows show examples of condensed nuclei. Scale bar demonstrates 50 μM. Inset shows negative control with no primary antibody. ( B ) ZO1 (TJP1) after 48 h culture of 2-cell embryos. Green panel shows ZO1 fluorescence. Red is rhodamine-phalloidin staining of F-actin. Blue is DAPI-stained DNA. Yellow demonstrates overlap of ZO-1 and actin in the merged figure of the control embryos, which is missing in the AICAR-treated embryos. Scale bar demonstrates 50 μM. Inset shows negative control with no primary antibody.

    Journal: Molecular Human Reproduction

    Article Title: Treatment with AICAR inhibits blastocyst development, trophectoderm differentiation and tight junction formation and function in mice

    doi: 10.1093/molehr/gax050

    Figure Lengend Snippet: AICAR treatment increased detection of p-AMPK and decreased ZO1 (TJP1) localization to the cell membrane. ( A ) phospho-AMPK after 48 h culture of 2-cell embryos. Green panel shows p-AMPK fluorescence. Red is rhodamine-phalloidin staining of F-actin. Blue is DAPI-stained DNA. Merged figure shows color overlap. Arrowheads show evidence of loss of cell-to-cell contacts. Arrows show examples of condensed nuclei. Scale bar demonstrates 50 μM. Inset shows negative control with no primary antibody. ( B ) ZO1 (TJP1) after 48 h culture of 2-cell embryos. Green panel shows ZO1 fluorescence. Red is rhodamine-phalloidin staining of F-actin. Blue is DAPI-stained DNA. Yellow demonstrates overlap of ZO-1 and actin in the merged figure of the control embryos, which is missing in the AICAR-treated embryos. Scale bar demonstrates 50 μM. Inset shows negative control with no primary antibody.

    Article Snippet: Embryos were then incubated overnight at 4°C in the following primary antibodies at the indicated dilutions: rabbit anti-CDX2 (ab76541, 1:100, Abcam, Cambridge, MA, USA), rabbit anti-phospho-AMPK (07–681, 1:75, Millipore, Temecula, CA), rat anti-ZO1 (MABT11, 1:100, Millipore, Temecula, CA), rat anti-AQP9 (AQP91-A, 1:100, Alpha Diagnostic International, San Antonio, TX), mouse anti-CDH1 ( , 1:100, BD Transduction Laboratories, San Jose CA).

    Techniques: Fluorescence, Staining, Negative Control

    Primary and secondary transporters involved in the uptake of arabinooligosaccharides in B. subtilis and the role of MsmX in their transport. Arabinan, a homopolymer of arabinose, is extracellularly degraded by two endo-α-1,5-arabinanases, AbnA

    Journal: Journal of Bacteriology

    Article Title: A Multitask ATPase Serving Different ABC-Type Sugar Importers in Bacillus subtilis ▿

    doi: 10.1128/JB.00832-10

    Figure Lengend Snippet: Primary and secondary transporters involved in the uptake of arabinooligosaccharides in B. subtilis and the role of MsmX in their transport. Arabinan, a homopolymer of arabinose, is extracellularly degraded by two endo-α-1,5-arabinanases, AbnA

    Article Snippet: α-1,5-Linked arabinooligosaccharides (arabinobiose, arabinotriose, and arabinotetraose), arabinan, and debranched arabinan (sugar beet, purity 95%) were purchased from Megazyme International Ireland Ltd.; arabinose, maltotriose, maltotetraose, and maltopentaose were from Sigma-Aldrich Co.; and glucose was from BDH.

    Techniques:

    The exo-acting mechanism of the ruminal single-domain ABN (ARN3). A, catalytic interface of ARN3 ( white ) showing the residues that form the −2 subsite of the exo-enzyme ARN3 ( green ) and the endo-enzyme AbnB ( magenta ), the modeled oligosaccharide in the ARN3 structure ( yellow ball and sticks ), and the Arg 203 –Ala 230 loop ( green surface representation). B , topographical adaptations of the SRGEEP-ARN3 active site. The shortened loop is represented as a transparent magenta surface and the substrate from the AbnB complex structure is in magenta ball and sticks . For comparison, the original loop of ARN3 is shown as a green line. C, kinetic analysis of ARN3 and SRGEEP-ARN3 using debranched arabinan as substrate. Capillary zone electrophoresis analysis of cleavage products of linear arabinan and arabinoheptaose by SRGEEP-ARN3 ( D and F , respectively) and ARN3 ( E and G , respectively).

    Journal: The Journal of Biological Chemistry

    Article Title: Mechanistic Strategies for Catalysis Adopted by Evolutionary Distinct Family 43 Arabinanases *

    doi: 10.1074/jbc.M113.537167

    Figure Lengend Snippet: The exo-acting mechanism of the ruminal single-domain ABN (ARN3). A, catalytic interface of ARN3 ( white ) showing the residues that form the −2 subsite of the exo-enzyme ARN3 ( green ) and the endo-enzyme AbnB ( magenta ), the modeled oligosaccharide in the ARN3 structure ( yellow ball and sticks ), and the Arg 203 –Ala 230 loop ( green surface representation). B , topographical adaptations of the SRGEEP-ARN3 active site. The shortened loop is represented as a transparent magenta surface and the substrate from the AbnB complex structure is in magenta ball and sticks . For comparison, the original loop of ARN3 is shown as a green line. C, kinetic analysis of ARN3 and SRGEEP-ARN3 using debranched arabinan as substrate. Capillary zone electrophoresis analysis of cleavage products of linear arabinan and arabinoheptaose by SRGEEP-ARN3 ( D and F , respectively) and ARN3 ( E and G , respectively).

    Article Snippet: WT and mutant versions of ARN3 (SRGEEP-ARN3, ARN3/F237A, ARN3/D37W, ARN3/S329P, ARN3/D37W/S329P) were incubated with 0.25% (w/v) linear arabinan (Megazyme) for 15 min at 20 °C.

    Techniques: Electrophoresis

    The exo-acting mechanism of the ruminal single-domain ABN (ARN3). A, catalytic interface of ARN3 ( white ) showing the residues that form the −2 subsite of the exo-enzyme ARN3 ( green ) and the endo-enzyme AbnB ( magenta ), the modeled oligosaccharide in the ARN3 structure ( yellow ball and sticks ), and the Arg 203 –Ala 230 loop ( green surface representation). B , topographical adaptations of the SRGEEP-ARN3 active site. The shortened loop is represented as a transparent magenta surface and the substrate from the AbnB complex structure is in magenta ball and sticks . For comparison, the original loop of ARN3 is shown as a green line. C, kinetic analysis of ARN3 and SRGEEP-ARN3 using debranched arabinan as substrate. Capillary zone electrophoresis analysis of cleavage products of linear arabinan and arabinoheptaose by SRGEEP-ARN3 ( D and F , respectively) and ARN3 ( E and G , respectively).

    Journal: The Journal of Biological Chemistry

    Article Title: Mechanistic Strategies for Catalysis Adopted by Evolutionary Distinct Family 43 Arabinanases *

    doi: 10.1074/jbc.M113.537167

    Figure Lengend Snippet: The exo-acting mechanism of the ruminal single-domain ABN (ARN3). A, catalytic interface of ARN3 ( white ) showing the residues that form the −2 subsite of the exo-enzyme ARN3 ( green ) and the endo-enzyme AbnB ( magenta ), the modeled oligosaccharide in the ARN3 structure ( yellow ball and sticks ), and the Arg 203 –Ala 230 loop ( green surface representation). B , topographical adaptations of the SRGEEP-ARN3 active site. The shortened loop is represented as a transparent magenta surface and the substrate from the AbnB complex structure is in magenta ball and sticks . For comparison, the original loop of ARN3 is shown as a green line. C, kinetic analysis of ARN3 and SRGEEP-ARN3 using debranched arabinan as substrate. Capillary zone electrophoresis analysis of cleavage products of linear arabinan and arabinoheptaose by SRGEEP-ARN3 ( D and F , respectively) and ARN3 ( E and G , respectively).

    Article Snippet: Debranched arabinan was used as substrate in a concentration range from 0.8 to 25.0 mg/ml.

    Techniques: Electrophoresis

    Analysis of linear arabinan and debranched arabinan hydrolyzed by Tth Abn endo-arabinanase. The products of the reaction were examined with TLC. M: arabinose, arabinobiose and arabinotriose. a . Lane 1, 2, 3, 4: linear arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h. respectively. b . Lane 1, 2, 3, 4: debranched arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively. c . Lane 1, 2, 3, 4: sugar beet arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively.

    Journal: BMC Biotechnology

    Article Title: Expression and characterization of a GH43 endo-arabinanase from Thermotoga thermarum

    doi: 10.1186/1472-6750-14-35

    Figure Lengend Snippet: Analysis of linear arabinan and debranched arabinan hydrolyzed by Tth Abn endo-arabinanase. The products of the reaction were examined with TLC. M: arabinose, arabinobiose and arabinotriose. a . Lane 1, 2, 3, 4: linear arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h. respectively. b . Lane 1, 2, 3, 4: debranched arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively. c . Lane 1, 2, 3, 4: sugar beet arabinan samples (2%, wt/vol) incubated with 1 μg Tth Abn endo-arabinanase for 0.5 h, 1 h, 2 h and 3 h, respectively.

    Article Snippet: Substrates Linear arabinan, debranched arabinan, sugar beet arabinan, 1,4-β-D-mannan and galactan were purchased from Megazyme (Wicklow, Ireland). p NPX and p NPAF were purchased from Sigma Chemical Co., Ltd. (St. louis, USA).

    Techniques: Thin Layer Chromatography, Incubation

    Arabinosyltransferases involved in the biosynthesis of the arabinan domains of lipoarabinomannan (left panel) and arabinogalactan (right panel) in M. tuberculosis .

    Journal: Methods in molecular biology (Clifton, N.J.)

    Article Title: Characterization of arabinosyl transfer reactions in the biosynthesis of mycobacterial cell envelope (lipo)polysaccharides

    doi: 10.1007/978-1-4939-9154-9_14

    Figure Lengend Snippet: Arabinosyltransferases involved in the biosynthesis of the arabinan domains of lipoarabinomannan (left panel) and arabinogalactan (right panel) in M. tuberculosis .

    Article Snippet: Seidel M, Alderwick LJ, Birch, et al. (2007) Identification of a novel arabinofuranosyltransferase AftB involved in a terminal step of cell wall arabinan biosynthesis in Corynebacterianeae, such as Corynebacterium glutamicum and Mycobacterium tuberculosis , J Biol Chem 282 , 14729–14740.

    Techniques: