NodS

From Proteopedia

NodS is a bacterial methyltransferase involved in the pathway leading to the biosynthesis of Nod factor, an important signaling molecule released by rhizobial bacteria in the course of endosymbiotic interaction with legumes. NodS from Bradyrhizobium japonicum WM9 is the first S-adenosyl-L-methionine-dependent methyltransferase specific for chitooligosaccharide substrates, the structure of which has been solved. The structures with (3ofk) and without (3ofj) S-adenosyl-L-homocysteine ligand, which is chemically very similar to the methyl donor used by NodS, S-adenosyl-L-methionine, are available.^[1]^[2]

1 Biological significance
2 Structure and function of NodS
3 3D structures of NodS
4 Reference

Biological significance

Methylation reaction catalyzed by NodS

Rhizobia-legumes symbiosis

The endosymbiotic relationship between nitrogen-fixing rhizobial bacteria and certain plants (legumes) is of the utmost importance for the nitrogen cycle in the biosphere and hence an object of intense study by specialists from various areas of biology. What is more, although the use of artificial nitrogen-containing fertilizers made it possible to bypass the strict dependence on this process, its understanding is still crucial for the efficient agriculture. Biological nitrogen fixation requires nitrogenase, an enzyme present in, among others, rhizobial bacteria but absent in plants. The rhizobia are a diverse range of soil bacteria. It is thought that after the symbiotic capabilities were first acquired by some of them, they spread by means of horizontal transfer of a plasmid or genomic island containing genes important for the process. The symbiotic relationship between the two symbionts depends on the formation of invasion structures (nodules) by the host, allowing bacteria to enter the plant root, colonize a specific type of cells and be transformed into bacteroids which perform nitrogen fixation. As complementarity between various signals and their cognate receptors is required for the efficient symbiosis, its emergence most likely required coevolution of plants and bacteria.^[3]^[4] One of the bacterial nodulating symbionts is Bradyrhizobium japonicum WM9, which is involved in a partnership with lupine and serradella legumes.^[5]

Chemical signals

The very first stage of this process is an exchange of chemical signals between the symbionts. On sensing a flavonoid compound released by the plant, the bacteria produce a signalling molecule known as Nod factor, which is a lipochitooligosaccharide derivative. This molecule in turn induces nodule formation by the plant.^[6]^[7]^[8] Many types of flavonoids and Nod factors are known and which ones are present influences the specificity of the interaction. It must be mentioned that while these two molecules are important signals and specificity determinants, there are numerous others.^[9]^[10]

Nod factor synthesis

Nod factor synthesis involves the coordinated action of several rhizobial enzymes encoded by the nodulation-specific genes. NodC, NodB and NodA, found in nearly all rhizobial strains, synthesize the main part of Nod factor's structure, while several others, including NodS, NodU, NolO, NodL, and NolL, introduce species- and strain-specific modifications, such as N-methylation, carbamoylation, acetylation, fucosylation etc.^[11]^[12]

Structure and function of NodS

Structure of NodS 3ofj

Drag the structure with the mouse to rotate

Fold

NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase that methylates the deacetylated nitrogen atom at the nonreducing end of the chitooligosaccharide substrate, converting at the same time the S-adenosyl-L-methionine methyl donor into S-adenosyl-L-homocysteine, which is then released as a by-product (see figure above).^[13] S-adenosyl-L-methionine-dependent methyltransferases, many of which have been reported to date, methylate a wide variety of substrates and are involved in diverse processes ranging from biosynthetic pathways to gene silencing. Those of them which have been structurally analyzed have been divided into five structural families known as classes I–V, class I, to which NodS belongs, being the most numerous.^[14] Its consists of a (the strands are named 1-7 beginning from the N-terminus) with a (residues 182-189) at the C-terminal end of the sheet, between strands β6 and β7. The sheet, which is characterized by a curvature due to the presence of three β-bulges, is surrounded on both sides by (named A-G beginning from the N-terminus), forming an folding pattern. In the apo form shown here, only 6 out of 7 helices are visible. In addition to conventional helices, there are also three short, 3₁₀ helices (not represented as helices), each one-turn-long (residues 19-21, 63-65, 117-119), in the apo structure. The fact that results in a divergence from a classic Rossmann fold^[15], to which the structure is otherwise classifiable.

Ligand binding

During the NodS-catalyzed reaction, the chitooligosaccharide substrate is methylated while the methyl donor, S-adenosyl-L-methionine, is transformed into S-adenosyl-L-homocysteine. The latter product is, however, chemically still highly similar to S-adenosyl-L-methionine and hence gives reliable representation of the binding mode of both S-adenosyl-L-homocysteine and, by inference, S-adenosyl-L-methionine to the enzyme. Notice the position of the (the most N-terminal), which was not visible in the apo form, but got structured upon ligand binding; this helix, unlike others, is positioned on top of the β-sheet structure, not on its side, and is . There are many other small changes in the structure of ligand-bound NodS when compared to the apo form, mainly around the binding cavity, but the deviations do not exceed 0.9 Å. The -binding cavity is predominately hydrophobic, but numerous polar interactions are likely to play a role in positioning the ligand in its specific orientation. There are between NodS residues and S-adenosyl-L-methionine ligand and around 5-7 additional ones between the water molecules present in the binding pocket and the ligand. The by the main-chain carbonyl groups of Gly 52 and Ala 114 from loop β1–αC and strand β4, respectively. The with the side chains of the basic amino acid residues Arg 31 and His 32 in helix αB. The a pair of forked hydrogen bonds with both oxygen atoms of the carboxylic group of Asp 73 and a single hydrogen bond with main-chain nitrogen of Ala 54, Asp 73 being located at the tip of the β2 strand and Ala 54 in loop β1–αC. Finally, with the main-chain nitrogen of Ile 99 and by the side chain of Asp 98, both from the β3–β4 loop. This adenine ring is also capable of making CH-π interactions with aliphatic side chains of valines 74 and 116. can potentially be formed between the sulfonium group of the ligand and the π system of Trp 20 when the methyl donor, S-adenosyl-L-methionine is bound instead of the homocysteine derivative. This interaction is likely to contribute to the larger affinity of NodS towards the methyl donor (a substrate) comparing to the homocysteine derivative (a products). The overall positioning of the methyl donor inside the protein is such that it is , but the fragment of it where the methyl group of S-adenosyl-L-methionine is located to the putative substrate-binding canyon. The canyon is roughly 22 Å long, 10.5 Å wide and 10.5 Å deep. It is located near the N-terminal end of helix αB and the C-terminal end of strand β4. No structure of NodS with the substrate bound is available, but computational docking suggests that this canyon is indeed an energetically favourable binding site, mainly due to a number of possible polar interactions.^[16]

3D structures of NodS

3ofj – BrNodS – Bradyrhibozium
3ofk – BrNodS + adenosyl homocysteine
2ocx, 2hhc, 2hlh – BrNodZ
1fh1 – NodF – Rhibozium leguminosarum

Reference

↑ Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M. Cloning, expression, purification, crystallization and preliminary X-ray analysis of NodS N-methyltransferase from Bradyrhizobium japonicum WM9. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Dec 1;64(Pt, 12):1149-52. Epub 2008 Nov 28. PMID:19052372 doi:10.1107/S174430910803604X
↑ Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M. Crystal Structures of NodS N-Methyltransferase from Bradyrhizobium japonicum in Ligand-Free Form and as SAH Complex. J Mol Biol. 2010 Oct 21. PMID:20970431 doi:10.1016/j.jmb.2010.10.016
↑ Martinez-Romero E. Coevolution in Rhizobium-legume symbiosis? DNA Cell Biol. 2009 Aug;28(8):361-70. PMID:19485766 doi:10.1089/dna.2009.0863
↑ Debelle F, Moulin L, Mangin B, Denarie J, Boivin C. Nod genes and Nod signals and the evolution of the Rhizobium legume symbiosis. Acta Biochim Pol. 2001;48(2):359-65. PMID:11732607
↑ Stepkowski T, Swiderska A, Miedzinska K, Czaplinska M, Swiderski M, Biesiadka J, Legocki AB. Low sequence similarity and gene content of symbiotic clusters of Bradyrhizobium sp. WM9 (Lupinus) indicate early divergence of "lupin" lineage in the genus Bradyrhizobium. Antonie Van Leeuwenhoek. 2003;84(2):115-24. PMID:14533715
↑ Oldroyd GE, Downie JA. Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol. 2008;59:519-46. PMID:18444906 doi:10.1146/annurev.arplant.59.032607.092839
↑ Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC. How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model. Nat Rev Microbiol. 2007 Aug;5(8):619-33. PMID:17632573 doi:10.1038/nrmicro1705
↑ Denarie J, Debelle F, Rosenberg C. Signaling and host range variation in nodulation. Annu Rev Microbiol. 1992;46:497-531. PMID:1444265 doi:http://dx.doi.org/10.1146/annurev.mi.46.100192.002433
↑ Downie JA. The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiol Rev. 2010 Mar;34(2):150-70. Epub 2009 Dec 15. PMID:20070373 doi:10.1111/j.1574-6976.2009.00205.x
↑ Fauvart M, Michiels J. Rhizobial secreted proteins as determinants of host specificity in the rhizobium-legume symbiosis. FEMS Microbiol Lett. 2008 Aug;285(1):1-9. PMID:18616593 doi:10.1111/j.1574-6968.2008.01254.x
↑ D'Haeze W, Holsters M. Nod factor structures, responses, and perception during initiation of nodule development. Glycobiology. 2002 Jun;12(6):79R-105R. PMID:12107077
↑ Riely BK, Ane JM, Penmetsa RV, Cook DR. Genetic and genomic analysis in model legumes bring Nod-factor signaling to center stage. Curr Opin Plant Biol. 2004 Aug;7(4):408-13. PMID:15231263 doi:10.1016/j.pbi.2004.04.005
↑ Geelen D, Leyman B, Mergaert P, Klarskov K, Van Montagu M, Geremia R, Holsters M. NodS is an S-adenosyl-L-methionine-dependent methyltransferase that methylates chitooligosaccharides deacetylated at the non-reducing end. Mol Microbiol. 1995 Jul;17(2):387-97. PMID:7494487
↑ Schubert HL, Blumenthal RM, Cheng X. Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci. 2003 Jun;28(6):329-35. PMID:12826405
↑ Rao ST, Rossmann MG. Comparison of super-secondary structures in proteins. J Mol Biol. 1973 May 15;76(2):241-56. PMID:4737475
↑ Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M. Crystal Structures of NodS N-Methyltransferase from Bradyrhizobium japonicum in Ligand-Free Form and as SAH Complex. J Mol Biol. 2010 Oct 21. PMID:20970431 doi:10.1016/j.jmb.2010.10.016

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Marcin Jozef Suskiewicz, Alexander Berchansky, David Canner, Michal Harel

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NodS

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Contents

Biological significance

Rhizobia-legumes symbiosis

Chemical signals

Nod factor synthesis

Structure and function of NodS

Fold

Ligand binding

3D structures of NodS

Reference

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