NMR data for RG-I isolated from Arabidopsis thaliana siliques
Data files
Sep 01, 2025 version files 248.98 MB
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deposition.zip
248.97 MB
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README.md
2.67 KB
Abstract
Pectin is generally divided into four distinct structural categories, namely homogalacturonan, xylogalacturonan, rhamnogalacturonan I (RG-I), and rhamnogalacturonan II. While much of the structural diversity of homogalacturonan, xylogalacturonan, and rhamnogalacturonan II has been elucidated, the structural features of RG-I are less well understood. In this work, we employed multiple complementary analytical techniques to present a detailed structural analysis of RG-I in the model system Arabidopsis thaliana. Starting with highly purified RG-I from different Arabidopsis tissues, we employed comparative linkage and NMR analysis along with mass spectrometry analysis of enzymatically digested RG-I oligosaccharides. Besides the presence of the canonical 5-arabinan, 4-galactan, 6-galactan, and arabino-galactan RG-I side chains of varying lengths, we show that a large portion of the 6-galactan is terminated by either 4-O-methyl β-GlcA residues or, to a smaller degree, β-GlcA that lacks the Me-ether group. Importantly, O-acetylation of RG-I GalA residues is a minor modification, while 10% of the backbone Rha residues are 3-O-acetylated, and most of the acetylated Rha additionally branches with β-Gal side chain. Taken together, the combined results of these different analytical techniques present the most comprehensive structural overview of Arabidopsis thaliana RG-I to date.
https://doi.org/10.5061/dryad.8gtht7707
Description of the data and file structure
This dataset contains NMR data acquired for rhamnogalacturonan I (RG-I) isolated from A. thaliana silique tissues. It contains raw and processed NMR data in the Bruker format that were acquired on rhamnogalacturonan I (RG-I) isolated from Arabidopsis thaliana silique tissue.
Files and variables
File: deposition.zip
Description:
The NMR data for the sample were collected at two different pD values: 4.7 and 1.7, and are saved in the respective directories "At_silique_RG-I_pD4.7" and "At_silique_RG-I_pD1.7".
The NMR data are in the standard Bruker format, and the directories contain the raw as well as the processed data for each spectrum as they were used for the analysis.
Each of the two data directories contains a notes.txt file that lists the NMR experiments included in the directory.
The directory "At_silique_RGI_OR_PME_ccp" is the project directory for CCPN Analysis (2.4.2) used to analyze the data.
The file "At silique RG-I assignments.xlsx" contains the RG-I chemical shift assignments made with the NMR data. Notes associated with several cells contain details about a particular assignment or a list of linkage NOE contacts.
Directories
At_silique_RG-I_pD4.7
- Sample details
- At silique RG1 BE, treated with PME+EPG, S75 f. 1+2
- 50 mg/ml, lyoph. 2x, D2O (99.99), 40 nmol DSS-d6, 300.8 K
- (pD ~4.7)
Sub-directories with experiments
#1421 1H
#1422 hsqc
#1423 1H
#1424 cosygpppqf
#1425 mlevphpp 70m
#1426 mlevphpp 150m
#1427 noesygpphpp 60m
#1428 noesygpphpp 10m
#1429 hsqcdietgpsisp.2 60m
#1430 1H
#1431 hsqc
#1432 hmbcetgpl3nd: ns 120, ni 160, nus 50%
#1433 roesyadjsph 150m
#1434 hsqcdietgpsisp.2 120m
#1435 1H
At_silique_RG-I_pD4.7
- Sample details
- At silique RG1 BE, treated with PME+EPG, S75 f. 1+2
- 50 mg/ml, lyoph. 2x, D2O (99.99), 40 nmol DSS-d6, 300.8 K
- pD adjusted to ~1.7
Sub-directories with experiments
#1436 1H
#1437 hsqc
#1438 cosygpppqf
#1439 mlevphpp 70m
#1440 noesygpphpp 60m
#1441 roesyadjsph 150m
#1442 hsqcdietgpsisp.2 60m
#1443 1H
#1444 hmbcetgpl3nd
#1445 hsqc
#1446 1H
#1447 hsqcetgpsisp2.3
At_silique_RGI_OR_PME_ccp
This is the project directory for the CCPN Analysis (version 2.4.2) software that was used to analyze the data.
Code/software
Software that can be used to analyze the data:
CCPN Analysis 2.4.2
Bruker Topspin