Crystal structure of exo‐rhamnogalacturonan lyase from <i>Penicillium chrysogenum</i> as a member of polysaccharide lyase family 26

Kunishige, Yuika; Iwai, Mineko; Nakazawa, Masami; Ueda, Mitsuhiro; Tada, Toshiji; Nishimura, Shigenori; Sakamoto, Tatsuji

doi:10.1002/1873-3468.13034

Cited by 19 publications

(5 citation statements)

References 35 publications

(52 reference statements)

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“…In the RG‐I chains, 20%–80% of Rha residues are connected with Ara and Gal in branched chains. Hence, Ara/Gal ratio represented the loss of Ara and Gal in RG‐I branched chains, and (Gal + Ara)/Rha ratio represented the degradation degree of RG‐I backbone and branched chains (Kunishige et al ., 2018; Li et al ., 2018). As shown in Table 2, the Ara/Gal ratio significantly ( P < 0.05) decreased in three pectins of all samples after fermentation, demonstrating the loss of Ara in branched chains of RG I.…”

Section: Resultsmentioning

confidence: 99%

Changes in texture qualities and pectin characteristics of fermented minced pepper during natural and inoculated fermentation process

Chen

Ding

et al. 2021

Int J of Food Sci Tech

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Summary Texture qualities and pectin characteristics in fermented minced pepper (FMP) prepared by natural fermentation (NF) and inoculated fermentation (IF) were analysed during fermentation. The results showed variation in texture qualities and pectin characteristics was similar during NF and IF process. The hardness, cell wall material, sodium carbonate‐soluble pectin (SSP) and chelate‐soluble pectin (CSP) content, and CSP esterification degree decreased, while water‐soluble pectin (WSP) content significantly (P < 0.05) increased after fermentation. The rhamnose (Rha) molar ratio in three pectins increased, but arabinose (Ara) and galactose (Gal) molar ratios in most pectins decreased after fermentation. Changes in Ara/Gal and (Gal + Ara)/Rha ratios represented the backbone and branched chains of rhamnogalacturonan‐I in three pectins depolymerised during fermentation. The decrease of molecular weight (Mw) in CSP was more obvious than that in WSP and SSP, and it was extensively depolymerised into low‐Mw pectin after fermentation. Pearson's correlation analysis showed FMP hardness was extremely (P < 0.01) positively correlated with CSP content and significantly (P < 0.05) positively correlated with SSP content and CSP Mw. Hence, CSP was the main pectin to affect texture compared with WSP and SSP, and its characteristics played a crucial role for regulating FMP texture during NF and IF process.

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Section: Resultsmentioning

confidence: 99%

Changes in texture qualities and pectin characteristics of fermented minced pepper during natural and inoculated fermentation process

Chen

Ding

et al. 2021

Int J of Food Sci Tech

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“…Rhamnogalacturonan lyase [-L-rhamnopyranosyl-(1 → 4)-alpha-D-galactopyranosyluronate endolyase (EC 4.2.2.23)] cleaves the α-1,4 linkages of RG-I resulting in a double bond in the on-reducing GalA residue ( 130 ). Rhamnogalacturonan lyase and hydrolase ( Table 4 ) have been reported in Caldicellulosiruptor bescii ( 81 ), Bacteroides thetaiotaomicron ( 82 ), Bacteroides ovatus ( 83 ), Bacillus subtilis ( 92 ), Bacillus licheniformis ( 93 ), Cellvibrio japonicus ( 94 ), Clostridium cellulolyticum ( 95 ), Bacillus licheniformis DSM13 ( 93 ), Pseudomonas cellulose ( 94 ), Penicillium chrysogenum ( 96 ), and Monoglobus pectinilyticus ( 41 ).…”

Section: Microbial Degradation Of Rsm Cell Wall Carbohydratesmentioning

confidence: 99%

Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review

Cheng

Venema

2022

Front. Nutr.

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Approximately 35% of rapeseed meal (RSM) dry matter (DM) are carbohydrates, half of which are water-soluble carbohydrates. The cell wall of rapeseed meal contains arabinan, galactomannan, homogalacturonan, rhamnogalacturonan I, type II arabinogalactan, glucuronoxylan, XXGG-type and XXXG-type xyloglucan, and cellulose. Glycoside hydrolases including in the degradation of RSM carbohydrates are α-L-Arabinofuranosidases (EC 3.2.1.55), endo-α-1,5-L-arabinanases (EC 3.2.1.99), Endo-1,4-β-mannanase (EC 3.2.1.78), β-mannosidase (EC 3.2.1.25), α-galactosidase (EC 3.2.1.22), reducing-end-disaccharide-lyase (pectate disaccharide-lyase) (EC 4.2.2.9), (1 → 4)-6-O-methyl-α-D-galacturonan lyase (pectin lyase) (EC 4.2.2.10), (1 → 4)-α-D-galacturonan reducing-end-trisaccharide-lyase (pectate trisaccharide-lyase) (EC 4.2.2.22), α-1,4-D-galacturonan lyase (pectate lyase) (EC 4.2.2.2), (1 → 4)-α-D-galacturonan glycanohydrolase (endo-polygalacturonase) (EC 3.2.1.15), Rhamnogalacturonan hydrolase, Rhamnogalacturonan lyase (EC 4.2.2.23), Exo-β-1,3-galactanase (EC 3.2.1.145), endo-β-1,6-galactanase (EC 3.2.1.164), Endo-β-1,4-glucanase (EC 3.2.1.4), α-xylosidase (EC 3.2.1.177), β-glucosidase (EC 3.2.1.21) endo-β-1,4-glucanase (EC 3.2.1.4), exo-β-1,4-glucanase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21). In conclusion, this review summarizes the chemical and nutritional compositions of RSM, and the microbial degradation of RSM cell wall carbohydrates which are important to allow to develop strategies to improve recalcitrant RSM carbohydrate degradation by the gut microbiota, and eventually to improve animal feed digestibility, feed efficiency, and animal performance.

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“…RG-II contains HG as a backbone, with complex side chains composed of a variety of sugars. Although studies on HG degradation have progressed 28 – 30 , bacterial decomposition of RG-I and RG-II has been reported in a limited number of papers so far 31 – 33 .…”

Section: Introductionmentioning

confidence: 99%

Bacterial inducible expression of plant cell wall-binding protein YesO through conflict between Glycine max and saprophytic Bacillus subtilis

Sugiura

Oiki

Mikami

et al. 2020

Sci Rep

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Saprophytic bacteria and plants compete for limited nutrient sources. Bacillus subtilis grows well on steamed soybeans Glycine max to produce the fermented food, natto. Here we focus on bacterial responses in conflict between B. subtilis and G. max. B. subtilis cells maintained high growth rates specifically on non-germinating, dead soybean seeds. On the other hand, viable soybean seeds with germinating capability attenuated the initial growth of B. subtilis. Thus, B. subtilis cells may trigger saprophytic growth in response to the physiological status of G. max. Scanning electron microscope observation indicated that B. subtilis cells on steamed soybeans undergo morphological changes to form apertures, demonstrating cell remodeling during saprophytic growth. Further, transcriptomic analysis of B. subtilis revealed upregulation of the gene cluster, yesOPQR, in colonies growing on steamed soybeans. Recombinant YesO protein, a putative, solute-binding protein for the ATP-binding cassette transporter system, exhibited an affinity for pectin-derived oligosaccharide from plant cell wall. The crystal structure of YesO, in complex with the pectin oligosaccharide, was determined at 1.58 Å resolution. This study expands our knowledge of defensive and offensive strategies in interspecies competition, which may be promising targets for crop protection and fermented food production.

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Crystal structure of exo‐rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26

Cited by 19 publications

References 35 publications

Changes in texture qualities and pectin characteristics of fermented minced pepper during natural and inoculated fermentation process

Changes in texture qualities and pectin characteristics of fermented minced pepper during natural and inoculated fermentation process

Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review

Bacterial inducible expression of plant cell wall-binding protein YesO through conflict between Glycine max and saprophytic Bacillus subtilis

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