Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies

Abstract

The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.

Keywords: biosynthesis; genomics; natural products; proteobacteria.

Figure 1

Overview of the relationship between marine proteobacteria and other major phyla of Eubacteria. The sub-phyla of proteobacteria and genera of marine proteobacteria discussed in this review are shown on the right, with non-marine proteobacterial genera used as hosts in heterologous expression experiments shown in brackets.

Figure 2

Alphaproteobacterial secondary metabolites with predicted and known biosynthetic origins.

Scheme 1

Proposed assembly-line biosynthesis of didemnin. Biosynthetic domains are denoted as: C = condensation, A = adenylation, T = Thiolation, KR = ketoreductase, MT = methyltransferase, E = epimerization, KS = ketosynthase, TE = thioesterase. The amino acid selectivity of each adenylation domain is written above the domain.

Scheme 2

Proposed biosynthesis of thalassospiramides by Thalassospira sp. CNJ-328. Biosynthetic domains are denoted as: C = condensation, A = adenylation, T = Thiolation, KR = ketoreductase, MT = methyltransferase, KS = ketosynthase, TE = thioesterase. The amino acid selectivity of each adenylation domain is written above the domain.

Scheme 3

(a) Proposed biosynthesis of tropodiethietic Acid (TDA); (b) The structure of the tropodithietic acid biosynthetic gene cluster, the genes tdaA–E are ~12 kb distant from tdaF and paaZ2.

Figure 3

Natural products from marine gammaproteobacteria with characterized biosynthetic pathways.

Scheme 4

(a) Proposed biosynthesis of thiomarinol from holothin and marinolic acid residues catalyzed by TmlU and HolE. Cy = cyclization, A = adenylation, T = thiolation; (b) the structure of the thiomarinol biosynthetic gene cluster. Genes for the synthesis of marinolic acid are shown in red, genes for the synthesis of holothin are shown in blue.

Scheme 5

Proposed biosynthesis of the alterochromides. A = Adenylation domain, C = Condensation domain, T = Thiolation domain, E = Epimerization domain, TE = Thioesterase domain.

Scheme 6

Pentabromopseudilin biosynthesis showing the synthesis of the bromopyrrole from proline, and the bromophenol from chorismate. A = adenyltransferase, ACP = Acyl carrier protein, DH = flavin-dependent dehydrogenase, Hal = flavin-dependent halogenase, TE = Thioesterase domain.

Figure 4

Residues in the putative pyrrole-binding active site of halogenase Bmp2. Residues in structurally equivalent positions in Mpy16 and in mutant Bmp2 are named in parentheses. Active site figure based upon crystal structures reported in [94].

Scheme 7

Biosynthetic route for violacein proposed by Shinoda et al. [113].

Figure 5

Marine gammaproteobacterial siderophores with characterized biosynthetic gene clusters.

Scheme 8

(a) General outline of the biosynthesis of NSD-derived siderophores avaroferrin, bisucaberin, and putrebactin; (b) the mbs gene cluster from metagenomic DNA that encodes the synthesis all three molecules.

Scheme 9

Biosynthesis of vibriobactin by Vibrio cholerae. C = condensation, Cy = cyclization, A = adenylation, ArCP = aryl carrier protein, PCP = peptidyl carrier protein, IL = isochorismate lyase.

Scheme 10

Anguibactin biosynthesis. C = condensation, A = adenylation, ArCP = aryl carrier protein, PCP = peptidyl carrier protein, IL = isochorismate lyase, Cy = cyclization. Non-functional domains are marked with an X.

Figure 6

Natural products produced by marine deltaproteobacteria with known gene clusters.

Scheme 11

(a) Haliangicin biosynthesis. Polyketide synthase modules are shown as circles. Inset in this scheme are the enzymes of the methyl branching cassette and methoxymalonyl-ACP cassette. AT = acyl transferase, ACP = acyl carrier protein. KS = keto synthase, DH = dehydratase. ER = enoyl reductase, KR = ketoreductase, HCS = HMG-CoA Synthase, ACAD = acyl-CoA dehydrogenase, 3HCDH = 3-hydroxyacyl-CoA dehydrogenase, O-MT = O-methyl transferase. Non-functional domains are indicated by an X. (b) The hli gene cluster from H. ochraceum.

Scheme 12

Proposed biosynthesis of haliamide. C = condensation, A = adenylation, ACP = acyl carrier protein, KS = ketosynthase, DH = dehydratase, KR = ketoreductase, AT = acyl transferase, ST = sulfotransferase.