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Taxonomic group: bacteria / Cyanobacteria (Phylum: Cyanobacteria)

The structure was elucidated in this paper
NCBI PubMed ID: 35793792
Publication DOI: 10.1021/acs.jnatprod.2c00162
Journal NLM ID: 7906882
Publisher: American Society of Pharmacognosy
Correspondence: P.N. Leão <pleao

ciimar.up.pt>
Institutions: Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal, Department of Biology, Faculty of Sciences, University of Porto Rua do Campo Alegre, Porto, Portugal, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany

Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixation. Here, we report the discovery of two new lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The desmamides are decapeptides featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate incubation experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis.

structure, NMR spectroscopy, mass spectrometry, cyanobacteria, marine, lipoglycopeptides, Desmonostoc muscorum

Structure type: cyclic polymer repeating unit ; 1388.7577 [M+H]+
C₆₆H₁₀₅N₁₁O₂₁
Location inside paper: p. 1705, table 1, desmamides A, structure 1
Trivial name: desmamides A
Compound class: lipoglycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_150900

Methods: 13C NMR, 1H NMR, NMR-2D, FTIR, HPLC, extraction, optical rotation measurement, bioinformatic analysis, antibacterial assay, cell viability assay, flash chromatography, genome sequencing, Marfey’s method, HRESIMS, LC-HRESIMS
Comments, role: the D-configuration of Xylp residue was proposed; NMR temperature was not specified

Related record ID(s): 20935
NCBI Taxonomy refs (TaxIDs): 1179
Show glycosyltransferases

NMR conditions: in DMSO-d6 [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
3,2,2,2,2,2,2,2,2,2	xDGln	171.7	53.1	27.7	31.7	171.7
3,2,2,2,2,2,2,2,2	xXGly	167.1	41.3
3,2,2,2,2,2,2,2	xLPro	172.4	59.2	28.9	24.4	46.6
3,2,2,2,2,2,2	xLVal	170.4	59.8	29.5	18.6	18.7
3,2,2,2,2,2,7	aDXylp	97.6	71.6	73.2	69.7	62.5
3,2,2,2,2,2	xDTyr	171.5	54.1	36.6	131.2	129.9	116.5	155.4	116.5	129.9
3,2,2,2,2	xLSer	169.8	56.5	61.5
3,2,2,2	xDLeu	172.1	48.8	40.3	24.0	23.2	23.2
3,2,2	xLThr	169.5	58.3	66.8	19.4
3,2	xDLeu	170.6	48.8	41.1	24.0	21.4	21.4
3	xLPro	171.4	59.0	28.5	24.7	45.9
	Subst	172.5	43.7	72.9	38.4	66.3	37.7	24.8	24.8	22.1	14.0	13.6


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9	H10	H11
3,2,2,2,2,2,2,2,2,2	xDGln	-	4.15	1.74-1.86	1.88-2.12	-
3,2,2,2,2,2,2,2,2	xXGly	-	3.80-3.96
3,2,2,2,2,2,2,2	xLPro	-	4.38	2.00	1.97	3.51-3.75
3,2,2,2,2,2,2	xLVal	-	3.76	1.72	0.46	0.66
3,2,2,2,2,2,7	aDXylp	5.31	3.36	3.55	3.34	3.33-3.45
3,2,2,2,2,2	xDTyr	-	4.53	2.64-3.13	-	7.13	6.91	-	6.91	7.13
3,2,2,2,2	xLSer	-	4.16	3.65-3.75
3,2,2,2	xDLeu	-	4.32	1.42-1.50	1.64	0.87	0.87
3,2,2	xLThr	-	4.19	3.91	1.00
3,2	xDLeu	-	4.65	1.48	1.64	0.83	0.83
3	xLPro	-	4.27	2.13	1.85	3.46
	Subst	-	2.55	5.06	1.46	3.33	1.28	1.28	1.28	1.25	0.86	0.98


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8	C9/H9	C10/H10	C11/H11
3,2,2,2,2,2,2,2,2,2	xDGln		53.1/4.15	27.7/1.74-1.86	31.7/1.88-2.12	
3,2,2,2,2,2,2,2,2	xXGly		41.3/3.80-3.96
3,2,2,2,2,2,2,2	xLPro		59.2/4.38	28.9/2.00	24.4/1.97	46.6/3.51-3.75
3,2,2,2,2,2,2	xLVal		59.8/3.76	29.5/1.72	18.6/0.46	18.7/0.66
3,2,2,2,2,2,7	aDXylp	97.6/5.31	71.6/3.36	73.2/3.55	69.7/3.34	62.5/3.33-3.45
3,2,2,2,2,2	xDTyr		54.1/4.53	36.6/2.64-3.13		129.9/7.13	116.5/6.91		116.5/6.91	129.9/7.13
3,2,2,2,2	xLSer		56.5/4.16	61.5/3.65-3.75
3,2,2,2	xDLeu		48.8/4.32	40.3/1.42-1.50	24.0/1.64	23.2/0.87	23.2/0.87
3,2,2	xLThr		58.3/4.19	66.8/3.91	19.4/1.00
3,2	xDLeu		48.8/4.65	41.1/1.48	24.0/1.64	21.4/0.83	21.4/0.83
3	xLPro		59.0/4.27	28.5/2.13	24.7/1.85	45.9/3.46
	Subst		43.7/2.55	72.9/5.06	38.4/1.46	66.3/3.33	37.7/1.28	24.8/1.28	24.8/1.28	22.1/1.25	14.0/0.86	13.6/0.98

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9	H10	H11
3,2,2,2,2,2,2,2,2,2	xDGln		4.15	1.74 1.86	1.88 2.12
3,2,2,2,2,2,2,2,2	xXGly		3.80 3.96
3,2,2,2,2,2,2,2	xLPro		4.38	2.00	1.97	3.51 3.75
3,2,2,2,2,2,2	xLVal		3.76	1.72	0.46	0.66
3,2,2,2,2,2,7	aDXylp	5.31	3.36	3.55	3.34	3.33 3.45
3,2,2,2,2,2	xDTyr		4.53	2.64 3.13		7.13	6.91		6.91	7.13
3,2,2,2,2	xLSer		4.16	3.65 3.75
3,2,2,2	xDLeu		4.32	1.42 1.50	1.64	0.87	0.87
3,2,2	xLThr		4.19	3.91	1.00
3,2	xDLeu		4.65	1.48	1.64	0.83	0.83
3	xLPro		4.27	2.13	1.85	3.46
	Subst		2.55	5.06	1.46	3.33	1.28	1.28	1.28	1.25	0.86	0.98

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
3,2,2,2,2,2,2,2,2,2	xDGln	171.7	53.1	27.7	31.7	171.7
3,2,2,2,2,2,2,2,2	xXGly	167.1	41.3
3,2,2,2,2,2,2,2	xLPro	172.4	59.2	28.9	24.4	46.6
3,2,2,2,2,2,2	xLVal	170.4	59.8	29.5	18.6	18.7
3,2,2,2,2,2,7	aDXylp	97.6	71.6	73.2	69.7	62.5
3,2,2,2,2,2	xDTyr	171.5	54.1	36.6	131.2	129.9	116.5	155.4	116.5	129.9
3,2,2,2,2	xLSer	169.8	56.5	61.5
3,2,2,2	xDLeu	172.1	48.8	40.3	24.0	23.2	23.2
3,2,2	xLThr	169.5	58.3	66.8	19.4
3,2	xDLeu	170.6	48.8	41.1	24.0	21.4	21.4
3	xLPro	171.4	59.0	28.5	24.7	45.9
	Subst	172.5	43.7	72.9	38.4	66.3	37.7	24.8	24.8	22.1	14.0	13.6

There is only one chemically distinct structure:

[*]N[C@H](CCC(N)=O)C(=O)NCC(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@H](Cc1ccc(O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)cc1)C(=O)N[C@@H](CO)C(=O)N[C@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@H](CC(C)C)C(=O)N1CCC[C@H]1C(=O)OC(CC(O)CCCCC)C(C)C([*])=O)[C@@H](C)O)C(C)C

SVG MW SMILES 3D mol Ionize

structure, NMR spectroscopy, mass spectrometry, cyanobacteria, marine, lipoglycopeptides, Desmonostoc muscorum

Structure type: cyclic polymer repeating unit ; 1430.7666 [M+H]+
C₆₈H₁₀₈N₁₁O₂₂
Location inside paper: p. 1705, table S3, desmamides B, structure 2
Trivial name: desmamides B
Compound class: lipoglycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_150900

Methods: 13C NMR, 1H NMR, NMR-2D, FTIR, HPLC, extraction, optical rotation measurement, bioinformatic analysis, antibacterial assay, cell viability assay, flash chromatography, genome sequencing, Marfey’s method, HRESIMS, LC-HRESIMS
Comments, role: the D-configuration of Xylp residue was proposed; NMR temperature was not specified

Related record ID(s): 8455
NCBI Taxonomy refs (TaxIDs): 1179
Show glycosyltransferases

NMR conditions: in DMSO-d6 [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
3,2,2,2,2,2,2,2,2,2	xDGln	173.7	53.2	27.7	31.7	171.7
3,2,2,2,2,2,2,2,2	xXGly	167.1	41.3
3,2,2,2,2,2,2,2	xLPro	172.3	59.2	28.9	24.4	46.6
3,2,2,2,2,2,2	xLVal	170.4	59.7	29.5	18.6	18.7
3,2,2,2,2,2,7,4	Ac	170.0	21.2
3,2,2,2,2,2,7	aDXylp	97.3	71.5	69.9	71.4	58.8
3,2,2,2,2,2	xDTyr	171.5	54.2	36.7	131.5	130.0-130.2	116.5	155.4	116.5	130.0-130.2
3,2,2,2,2	xLSer	169.8	56.6	61.4
3,2,2,2	xDLeu	172.2	48.9	40.0	24.0	23.2	23.2
3,2,2	xLThr	169.5	58.3	66.8	19.6
3,2	xDLeu	170.6	48.9	41.0	24.0	21.7	21.7
3	xLPro	171.4	59.0	28.5	24.4	45.9
	Subst	172.5	43.7	72.9	38.4	65.9	37.8	31.4	24.8	22.1	14.0	13.6


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9	H10	H11
3,2,2,2,2,2,2,2,2,2	xDGln	-	4.14	1.75-1.88	1.89-2.12	-
3,2,2,2,2,2,2,2,2	xXGly	-	3.80-3.96
3,2,2,2,2,2,2,2	xLPro	-	4.38	2.00	1.98	3.51-3.76
3,2,2,2,2,2,2	xLVal	-	3.75	1.72	0.46	0.66
3,2,2,2,2,2,7,4	Ac	-	2.02
3,2,2,2,2,2,7	aDXylp	5.40	3.48	3.78	4.62	3.37-3.58
3,2,2,2,2,2	xDTyr	-	4.53	2.65-3.13	-	7.15	6.93	-	6.93	7.15
3,2,2,2,2	xLSer	-	4.16	3.57-3.64
3,2,2,2	xDLeu	-	4.32	1.50-1.55	1.65	0.87	0.87
3,2,2	xLThr	-	4.19	3.91	1.00
3,2	xDLeu	-	4.65	1.40-1.50	1.65	0.83	0.83
3	xLPro	-	4.27	2.13	1.87	3.46
	Subst	-	2.55	5.06	1.46	3.33	1.28	1.24	1.29	1.26	0.85	0.97


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8	C9/H9	C10/H10	C11/H11
3,2,2,2,2,2,2,2,2,2	xDGln		53.2/4.14	27.7/1.75-1.88	31.7/1.89-2.12	
3,2,2,2,2,2,2,2,2	xXGly		41.3/3.80-3.96
3,2,2,2,2,2,2,2	xLPro		59.2/4.38	28.9/2.00	24.4/1.98	46.6/3.51-3.76
3,2,2,2,2,2,2	xLVal		59.7/3.75	29.5/1.72	18.6/0.46	18.7/0.66
3,2,2,2,2,2,7,4	Ac		21.2/2.02
3,2,2,2,2,2,7	aDXylp	97.3/5.40	71.5/3.48	69.9/3.78	71.4/4.62	58.8/3.37-3.58
3,2,2,2,2,2	xDTyr		54.2/4.53	36.7/2.65-3.13		130.0-130.2/7.15	116.5/6.93		116.5/6.93	130.0-130.2/7.15
3,2,2,2,2	xLSer		56.6/4.16	61.4/3.57-3.64
3,2,2,2	xDLeu		48.9/4.32	40.0/1.50-1.55	24.0/1.65	23.2/0.87	23.2/0.87
3,2,2	xLThr		58.3/4.19	66.8/3.91	19.6/1.00
3,2	xDLeu		48.9/4.65	41.0/1.40-1.50	24.0/1.65	21.7/0.83	21.7/0.83
3	xLPro		59.0/4.27	28.5/2.13	24.4/1.87	45.9/3.46
	Subst		43.7/2.55	72.9/5.06	38.4/1.46	65.9/3.33	37.8/1.28	31.4/1.24	24.8/1.29	22.1/1.26	14.0/0.85	13.6/0.97

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9	H10	H11
3,2,2,2,2,2,2,2,2,2	xDGln		4.14	1.75 1.88	1.89 2.12
3,2,2,2,2,2,2,2,2	xXGly		3.80 3.96
3,2,2,2,2,2,2,2	xLPro		4.38	2.00	1.98	3.51 3.76
3,2,2,2,2,2,2	xLVal		3.75	1.72	0.46	0.66
3,2,2,2,2,2,7,4	Ac		2.02
3,2,2,2,2,2,7	aDXylp	5.40	3.48	3.78	4.62	3.37 3.58
3,2,2,2,2,2	xDTyr		4.53	2.65 3.13		7.15	6.93		6.93	7.15
3,2,2,2,2	xLSer		4.16	3.57 3.64
3,2,2,2	xDLeu		4.32	1.50 1.55	1.65	0.87	0.87
3,2,2	xLThr		4.19	3.91	1.00
3,2	xDLeu		4.65	1.40 1.50	1.65	0.83	0.83
3	xLPro		4.27	2.13	1.87	3.46
	Subst		2.55	5.06	1.46	3.33	1.28	1.24	1.29	1.26	0.85	0.97

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8	C9	C10	C11
3,2,2,2,2,2,2,2,2,2	xDGln	173.7	53.2	27.7	31.7	171.7
3,2,2,2,2,2,2,2,2	xXGly	167.1	41.3
3,2,2,2,2,2,2,2	xLPro	172.3	59.2	28.9	24.4	46.6
3,2,2,2,2,2,2	xLVal	170.4	59.7	29.5	18.6	18.7
3,2,2,2,2,2,7,4	Ac	170.0	21.2
3,2,2,2,2,2,7	aDXylp	97.3	71.5	69.9	71.4	58.8
3,2,2,2,2,2	xDTyr	171.5	54.2	36.7	131.5	130.0 130.2	116.5	155.4	116.5	130.0 130.2
3,2,2,2,2	xLSer	169.8	56.6	61.4
3,2,2,2	xDLeu	172.2	48.9	40.0	24.0	23.2	23.2
3,2,2	xLThr	169.5	58.3	66.8	19.6
3,2	xDLeu	170.6	48.9	41.0	24.0	21.7	21.7
3	xLPro	171.4	59.0	28.5	24.4	45.9
	Subst	172.5	43.7	72.9	38.4	65.9	37.8	31.4	24.8	22.1	14.0	13.6

There is only one chemically distinct structure:

[*]N[C@H](CCC(N)=O)C(=O)NCC(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@H](Cc1ccc(O[C@H]2OC[C@@H](OC(C)=O)[C@H](O)[C@H]2O)cc1)C(=O)N[C@@H](CO)C(=O)N[C@H](CC(C)C)C(=O)N[C@H](C(=O)N[C@H](CC(C)C)C(=O)N1CCC[C@H]1C(=O)OC(CC(O)CCCCC)C(C)C([*])=O)[C@@H](C)O)C(C)C

SVG MW SMILES 3D mol Ionize