Fucoidans make life complicated for microbes. They are cell wall polysaccharides that comprise 23% of dry brown algae's weight and resist microbial degradation longer than other algal polymers. Their sheer grab-bag variety is to blame: they all vary in monosaccharide building blocks, some are branched and jazzed up with more monosaccharides, and most are festooned with hydroxy groups and sulfate moieties. To further bamboozle the hapless microbe, these structural variations differ between species of brown algae and even between seasons. So, to break down fucoidans and get at the carbon locked within, a microbe must possess an extensive toolbox of specialized enzymes: ones to clip off the heteroatom baubles, ones to debranch, others yet to break off more monomers. Enzymes aplenty.
Most microbes, understandably, pass up on fucoidans – no need to shunt precious energy into such a difficult proteome-demanding meal when simpler sources of carbon can be found. But a recent study by Sichert et al. discovered a bacterium that possesses the ability to enzymatically degrade fucoidans from start to finish. Enter 'Lentimonas' spp., brandishing hundreds of enzymes.
Maybe unsurprisingly, they are members of the Verrucomicrobia phylum. The blog has previously covered some of the oddities and wonders of these members of the notorious Planctomycetes-Verrucomicrobia-Chlamydiae superphylum, from the wart-like outer membrane protrusions to a microtubule system with an inkling of eukaryotic flavor. The latest chapter of the Verrucomicrobial saga now features the ability to degrade fucoidans. Verrucomicrobia already have built up a reputation for their polysaccharide-degrading knack, from starches to hemicellulose to polyacrylamide, but their ability to take apart a Gordian Knot of organic polymers is unseen in other bacteria.
The researchers, through laborious rounds of sampling seawater, culturing, plating, and waiting for weeks for tiny colonies to emerge, isolated microbes that were able to grow on fucoidan minimal media. They identified these as seven strains of 'Lentimonas', all of which possess a single chromosome and a single megaplasmid. While the chromosome is home primarily to genes for general metabolic functions, the plasmid is responsible for the bulk of the fucoidan-degrading pathway. This fucoidanase enzyme arsenal is stacked with 100 exo- and endo-acting glycoside hydrolases, 113 sulfatases, and 17 carbohydrate esterases, plus 54 extra enzymes from the chromosome, for a whopping grand total of 284 fucoidanases targeted to the stubborn polysaccharide.
For all its formidable polymer-degrading capacity, it turns out that this enzyme bunch is very fussy about its target. The researchers found that 'Lentimonas' was only able to grow on fucoidans and carrageenan from brown and red algae, ignoring other commonly metabolized marine polysaccharides. A picky eater, 'Lentimonas' occupies a very particular metabolic niche.
But how do these bacteria do it? To answer this question in molecular detail, the researchers selected one strain of 'Lentimonas,' CC4, and exposed it to five different fucoidans. Ever the stubborn polymer, the fucoidans ranged in level of degradation, some more resistant than others. Of the monosaccharides that resulted in this mix, only fucose was consistently taken up by the bacteria. Picky eaters indeed.
When they ran the culture supernatant through an anion-exchange chromatography system, they found a lack of mid-sized pieces of fucoidan, suggesting that the bacteria's first step is not to break fucoidans into smaller intermediates but instead to use extracellular exo-acting enzymes to snip fucose monomers off of the ends. Once fucose has been cut free, the pathway that breaks it down further into the toxic intermediate lactaldehyde is carried out inside the shielded safety of a highly expressed bacterial metabolic compartment. An organelle within a bacterium that has eukaryote-like tubulin proteins – a coincidence?
Proteomics and transcriptomics analyses supported the earlier predictions for the hundreds of enzymes, differentially upregulated in the presence of fucoidans. Enzymes that selectively degrade fucoidans of specific algal species are grouped together into substrate-specific operons to maximize efficiency. Indeed, efficiency must be a top priority for these 'Lentimonas' to survive when they are surrounded by fast-growing competitors chowing down on much simpler polysaccharides. Each type of fucoidan demands about a hundred 'Lentimonas' enzymes working en masse.
Taking a genomic peek into the enzymatic repertoire of other Verrucomicrobia, the researchers found that other species also contained high numbers of members belonging to single enzyme families. Examples included the enzyme family specialized in degrading mucin, a structural polysaccharide of human gut mucus; hemicellulose, abundant in plant cell walls; or porphyran, a major polysaccharide from Porphyra red algae. Verrucomicrobia boast some of the niche specialists of the microscopic world, from gut-dwellers to beachcombers.
This story is yet another fascinating bacterial equivalent of "one person's trash is another person's treasure." Life finds a way, and microbes will play the cards they've been dealt. Especially Verrucomicrobia.