Using a periplasmic binding protein as a biosensor for thiamine

By Sophie Rugg

Twitter: @sophiejrugg

Thiamine, also known as vitamin B1, is an essential micronutrient with an important role in metabolism for all life forms. Thiamine can’t be synthesised by animals, and so has to be obtained from their diet. Until recently, detecting thiamine was limited to either the use of expensive high-performance liquid chromatography (HPLC), or a slow assay involving microbial growth. This is because there is no antibody available that is specific for thiamine, making commonly used high throughput detection techniques such as enzyme-linked immunosorbent assay (ELISA) impossible.

Periplasmic binding proteins are components of the ABC transporters of Gram-negative bacteria, and bind their substrates with high affinity and specificity to enable them to be transported into the bacterial cell. These properties of high affinity binding and specificity make periplasmic binding proteins ideal for use as the recognition element in a biosensor. As bacterial ABC transporters are used for the import of nutrients, including a transporter for thiamine, many of these binding proteins have evolved to recognise small molecules which it may be difficult to raise an antibody against.

Edwards et al., (2016) developed a biosensor for thiamine based on the periplasmic binding protein for thiamine from Escherichia coli. This binding protein was incorporated into dye-encapsulating liposomes in order to amplify the signal. Immobilised to the surface of a streptavidin coated plate is biotin conjugated thiamine analogue. The thiamine analogue is connected to the biotin via a long polyethylene glycol (PEG)linker, so that the thiamine analogue doesn’t get in the way of the biotin binding the streptavidin coating. The immobilised thiamine analogue binds to the periplasmic binding protein with lower affinity than thiamine. After the thiamine containing sample has been added, any material not bound to the surface is removed. Any liposomes still stuck to the surface of the plate are lysed and the resulting dye concentration is inversely proportional to the thiamine concentration.

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Overview of assay for thiamine detection taken from Edwards et al., (2016). Competitive assay with biotin conjugated thiamine analogue immobilized via streptavidin in microtiter plates and detected via periplasmic binding protein for thiamine conjugated to the lipid bilayer of dye encapsulating liposomes (left). After competition with sample thiamine, unbound materials are removed (middle) and liposomes remaining bound are lysed to release dye yielding a signal inversely proportional to thiamine concentration (right).

This work shows that periplasmic binding proteins can be used effectively in biosensors , particularly where there is no antibody available. With the wide range of periplasmic binding proteins evolved by bacteria to be able to transport nutrients into their cells, this technique is open to use across a wide range of applications provided that a suitable analogue of the substrate can be immobilised to the surface of a plate.

Source: Edwards et al., 2016. High-Throughput Detection of Thiamine Using Periplasmic Binding Protein-Based Biorecognition. Analytical  Chemisty88 (16), pp 8248–8256. DOI: 10.1021/acs.analchem.6b02092

ABC system for dietary oligosaccharides: a weapon of Bifidobacterium sp. in the ‘metabolic’ war of the gut

By: Constantinos Drousiotis

Twitter: @Ecolinnit

The human gut microbiota (HGM) is the community of microbes that thrive in the gastrointestinal tract. Lately, it has become evident that HGM has a profound impact on human health which has now attracted a great interest from the scientific community. Current research is aiming to understand the complicated metabolic interactions that exist in the microbiota which can reveal the type of imbalances in diet that could potentially lead to disease.

A rich diet in legumes and seeds leads to an increased population of Bifidobacteria in the HGM. This is ought to the fact that the latter can metabolise raffinose family oligosaccharides (RFO) as opposed to the human gut cells which are unable to. The specialised transport machinery enabling these bacteria to transport and utilise RFOs hasn’t been characterised previously.

The study carried out by Morten et al. aimed to characterise the substrate binding protein (SBP) of the ABC transport system that was expressed in response to growth on RFOs, ie. BlG16BP. The group solved the structure of the BlG16BP and showed that the binding pocket of the protein accommodates oligosaccharides with a glucosyl or galactosyl C4-OH at position 1(non-reducing glycosyl unit) and an α-glycosidic bond to a glucosyl moiety at position 2. Additionally, they showed that the fructosyl or glucosyl groups are tolerated well at position 3 because of the lack of direct polar contacts of the protein with the sugar at this position and additionally, the cleft’s open architecture. These are all features of the sugar structures of raffinose and panose.

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Crystal structure of BlG16BP in complex with panose (A) and raffinose (B). The SBPs consist of an N-terminal domain (Domain 1, brown) and a larger C-terminal domain (Domain 2, green). The two domains are linked by hinge regions shown in light blue. Shown on right-hand side, is a close-up of the binding sites of BlG16BP in complex with panose (D) and raffinose (E). The non-reducing end glycosyl unit of both ligands (galactosyl in raffinose and glucosyl in panose) stacks onto Phe-392 (defined as position 1) and makes polar contacts to Asp-394, Asn-109, and His-395. Asp-394 is able to form hydrogen bonds to both the equatorial C4-OH of the non-reducing end glucosyl in panose and the axial C4-OH of the galactosyl in raffinose. The glucosyl moiety of raffinose and panose at position 2 stacks onto Tyr-291 and makes polar contacts to Lys-58, Glu-60, and Asp-326. The position 3 is tolerated well, as the glucosyl moiety of panose stacks onto Trp-216 with almost parallel planes of the sugar rings as opposed to the fructosyl group of raffinose which sits orthogonal against Trp216 due to a smaller area of Van der Walls contacts. As a point of reference, the oligosaccharide structures are provided on the bottom of the figure.

 

Growth assays with a mixture of RFOs as the carbon source revealed that raffinose and melibiose were utilised first in order throughout the course of growth assays of B. animalis subsp. lactis Bl-04, indicating that are preferentially recognised over tetra- and pentasaccharides. The group suggests that the preferential binding by this transporter could potentially reflect the levels of the respective sugars in the gut or reveal the ability of bifidobacteria to further process the tetra- and pentasaccharides extracellularly. Nonetheless, BlG16BP SBP has a lower affinity to the only two previously characterised oligosaccharide binding proteins from bifidobacteria; the lower affinity could indicate that RFOs are found in higher concentrations than the ligands of the other two oligosaccharide binding proteins.  Also, it could point out to the low level of competition for RFOs which would be agreeable with the fact that this ABC system is not phylogenetically diverse.

Notably, phylogenetic analysis showed, that as far as Lactobacillus species are concerned, this α-galactoside transporter is only found in the human-gut adapted clade of thereof. The lack of this system in Lactobacillus which thrive in other ecological niches suggests that the transporter was acquired by horizontal gene transfer as a survival strategy in response to the fierce microbial competition in the gut. This is in accordance with previous studies which point towards horizontal gene transfer viewed as an adaptation strategy to gut niche.

The study reports the first biochemical and structural insight into an ABC-associated glycoside transport protein and provides evidence that ABC-mediated uptake may confer a competitive edge in the fierce competition for metabolic resources in the human gut niche. Altogether, the findings improved our understanding of the impact of oligosaccharide uptake in preferential glycan utilization.

 

Source: Morten et. al., (2016) , An ATP Binding Cassette Transporter Mediates the Uptake of α-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates. The Journal of Biological Chemistry, 291(38), 20220-231.

Eating the Poison

By Bryony Ackroyd

Twitter: @BryonyAckroyd

The oligopeptide permease system (Opp) is an ABC transporter that commonly transports peptides into Gram-positive and Gram-negative bacterial cells. However, it has been demonstrated that Opp can also transport the antibiotic GE81112. This means the bacteria are effectively “eating the poison” that will eventually kill them.

GE81112 belongs to a structurally novel class of antibiotics and is key in the fight against antibiotic resistance and “super-bugs”. The tetrapeptide antibiotic GE81112 binds the 30S ribosomal subunit and interferes with the binding of initiator fMet-tRNA to the 30S subunit therefore inhibiting protein synthesis.

When Maio et al., began testing the microbiological activity of GE81112 on a series of microorganisms they obtained a number of unusual results. For example, the same bacteria (S. aureus, B. subtilis and E. coli) that in complete media are insensitive to GE81112 were sensitive to GE81112 in minimal or chemically defined rich media. One explanation for these results could be that GE81112, once in the cytoplasm, was disrupting 30S subunit with a different efficiency, however in vitro studies disproved this theory.

It was then hypothesised that a possible inhibitory or inactivating molecule was present in the rich media, causing the discrepancies in antibiotic sensitivity between rich media and minimal media. It was also noted that in chemically defined complete medium the activity of GE81112 is only slightly reduced compared to minimal media, indicating that the ineffectiveness of GE81112 in complete medium is not due to the concentration of nutrients.

To test the above hypothesis a series of experiments were conducted. The activity of GE81112 was measured by the change in the minimum inhibitory concentration in different growth medias. Whereas addition of individual amino acids to the growth media did not have any influence on GE81112 activity, the addition of casamino acids resulted in an increase in the minimum inhibitory concentration of GE81112. The difference between these two results was put down to the presence of di-, tri- and oligopeptides in casamino acids that may compete with GE81112 for an import system.

Due to GE81112 being a tetrapeptide the dipeptide and tripeptide transport systems were ruled out and instead the oligopeptide transport system, Opp, was investigated. An E. coli opp- mutant and wild-type were grown on minimal medium agar plates with the addition of the GE81112 antibiotic. The opp- mutants were not inhibited by GE81112, whereas the wild-type cells produced a large halo of inhibition indicating that Opp is the means of import for GE81112. Further experiments were carried out showing that presence of the whole Opp transporter was necessary for transport and sensitivity to GE81112.

Although the antimicrobial activity of GE81112 is not very efficient on bacteria growing in rich media, due to the competition for the Opp transport systems by other oligopeptides, it is important for antimicrobial resistance as it has been shown to be effective against methicillin resistant bacteria. Evidence suggests that mutations altering the cytoplasmic antibiotic target of GE81112 are few and far between, indicating that bacterial resistance to GE81112 could be slowed if entry into the bacterial cell is not blocked by oligopeptides. Could it then be possible to modify GE81112 to enter the bacterial cell without the aid of Opp to improve GE81112 efficiency and reduce resistance?

 

Source: Gualerzi et al., (2016). The Oligopeptide Permease Opp Mediates Illicit Transport of the Bacterial P-site Decoding Inhibitor GE81112. Antibiotics, 5(2): 17.